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Sample records for asv integrase proteins

  1. Inhibition of HIV-1 Integrase gene expression by 10-23 DNAzyme

    Indian Academy of Sciences (India)

    We have designed three novel DNAzymes, DIN54, DIN116, and DIN152, against HIV-1 Integrase gene using Mfold software and evaluated them for target site cleavage activity on the in vitro transcribed mRNA. All DNAzymes were tested for its inhibition of expression of HIV Integrase protein in the transiently transfected cell ...

  2. Comparison of Newly Assembled Full Length HIV-1 Integrase With Prototype Foamy Virus Integrase: Structure-Function Prospective.

    Science.gov (United States)

    Dayer, Mohammad Reza

    2016-05-01

    Drug design against human immunodeficiency virus type 1 (HIV-1) integrase through its mechanistic study is of great interest in the area in biological research. The main obstacle in this area is the absence of the full-length crystal structure for HIV-1 integrase to be used as a model. A complete structure, similar to HIV-1 of a prototype foamy virus integrase in complex with DNA, including all conservative residues, is available and has been extensively used in recent investigations. The aim of this study was to determine whether the above model is precisely representative of HIV-1 integrase. This would critically determine the success of any designed drug using the model in deactivation of integrase and AIDS treatment. Primarily, a new structure for HIV-1 was constructed, using a crystal structure of prototype foamy virus as the starting structure. The constructed structure of HIV-1 integrase was simultaneously simulated with a prototype foamy virus integrase on a separate occasion. Our results indicate that the HIV-1 system behaves differently from the prototype foamy virus in terms of folding, hydration, hydrophobicity of binding site and stability. Based on our findings, we can conclude that HIV-1 integrase is vastly different from the prototype foamy virus integrase and does not resemble it, and the modeling output of the prototype foamy virus simulations could not be simply generalized to HIV-1 integrase. Therefore, our HIV-1 model seems to be more representative and more useful for future research.

  3. Architecture and Assembly of HIV Integrase Multimers in the Absence of DNA Substrates*

    Science.gov (United States)

    Bojja, Ravi Shankar; Andrake, Mark D.; Merkel, George; Weigand, Steven; Dunbrack, Roland L.; Skalka, Anna Marie

    2013-01-01

    We have applied small angle x-ray scattering and protein cross-linking coupled with mass spectrometry to determine the architectures of full-length HIV integrase (IN) dimers in solution. By blocking interactions that stabilize either a core-core domain interface or N-terminal domain intermolecular contacts, we show that full-length HIV IN can form two dimer types. One is an expected dimer, characterized by interactions between two catalytic core domains. The other dimer is stabilized by interactions of the N-terminal domain of one monomer with the C-terminal domain and catalytic core domain of the second monomer as well as direct interactions between the two C-terminal domains. This organization is similar to the “reaching dimer” previously described for wild type ASV apoIN and resembles the inner, substrate binding dimer in the crystal structure of the PFV intasome. Results from our small angle x-ray scattering and modeling studies indicate that in the absence of its DNA substrate, the HIV IN tetramer assembles as two stacked reaching dimers that are stabilized by core-core interactions. These models of full-length HIV IN provide new insight into multimer assembly and suggest additional approaches for enzyme inhibition. PMID:23322775

  4. Developing a Dynamic Pharmacophore Model for HIV-1 Integrase

    International Nuclear Information System (INIS)

    Carlson, Heather A.; Masukawa, Keven M.; Rubins, Kathleen; Bushman, Frederic; Jorgensen, William L.; Lins, Roberto; Briggs, James; Mccammon, Andy

    2000-01-01

    We present the first receptor-based pharmacophore model for HIV-1 integrase. The development of ''dynamic'' pharmacophore models is a new method that accounts for the inherent flexibility of the active site and aims to reduce the entropic penalties associated with binding a ligand. Furthermore, this new drug discovery method overcomes the limitation of an incomplete crystal structure of the target protein. A molecular dynamics (MD) simulation describes the flexibility of the uncomplexed protein. Many conformational models of the protein are saved from the MD simulations and used in a series of multi-unit search for interacting conformers (MUSIC) simulations. MUSIC is a multiple-copy minimization method, available in the BOSS program; it is used to determine binding regions for probe molecules containing functional groups that complement the active site. All protein conformations from the MD are overlaid, and conserved binding regions for the probe molecules are identified. Those conserved binding regions define the dynamic pharmacophore model. Here, the dynamic model is compared to known inhibitors of the integrase as well as a three-point, ligand-based pharmacophore model from the literature. Also, a ''static'' pharmacophore model was determined in the standard fashion, using a single crystal structure. Inhibitors thought to bind in the active site of HIV-1 integrase fit the dynamic model but not the static model. Finally, we have identified a set of compounds from the Available Chemicals Directory that fit the dynamic pharmacophore model, and experimental testing of the compounds has confirmed several new inhibitors

  5. Discovery of small-molecule HIV-1 fusion and integrase inhibitors oleuropein and hydroxytyrosol: Part II. Integrase inhibition

    International Nuclear Information System (INIS)

    Lee-Huang, Sylvia; Huang, Philip Lin; Zhang Dawei; Lee, Jae Wook; Bao Ju; Sun Yongtao; Chang, Young-Tae; Zhang, John; Huang, Paul Lee

    2007-01-01

    We report molecular modeling and functional confirmation of Ole and HT binding to HIV-1 integrase. Docking simulations identified two binding regions for Ole within the integrase active site. Region I encompasses the conserved D64-D116-E152 motif, while region II involves the flexible loop region formed by amino acid residues 140-149. HT, on the other hand, binds to region II. Both Ole and HT exhibit favorable interactions with important amino acid residues through strong H-bonding and van der Waals contacts, predicting integrase inhibition. To test and confirm modeling predictions, we examined the effect of Ole and HT on HIV-1 integrase activities including 3'-processing, strand transfer, and disintegration. Ole and HT exhibit dose-dependent inhibition on all three activities, with EC 50 s in the nanomolar range. These studies demonstrate that molecular modeling of target-ligand interaction coupled with structural-activity analysis should facilitate the design and identification of innovative integrase inhibitors and other therapeutics

  6. Intellivent-ASV

    African Journals Online (AJOL)

    mode of ventilation, ASV, for 2 hours, followed by a change to SIMV mode for a ... patient condition, based on tidal volume of 6 - 10 mL/kg, respiratory rate of 10 ... To reach a statistical power of 90%, we therefore needed only seven subjects. A.

  7. Characterization of natural polymorphic sites of the HIV-1 integrase before the introduction of HIV-1 integrase inhibitors in Germany

    Science.gov (United States)

    Meixenberger, Karolin; Pouran Yousef, Kaveh; Somogyi, Sybille; Fiedler, Stefan; Bartmeyer, Barbara; von Kleist, Max; Kücherer, Claudia

    2014-01-01

    Introduction The aim of our study was to analyze the occurrence and evolution of HIV-1 integrase polymorphisms during the HIV-1 epidemic in Germany prior to the introduction of the first integrase inhibitor raltegravir in 2007. Materials and Methods Plasma samples from drug-naïve HIV-1 infected individuals newly diagnosed between 1986 and 2006 were used to determine PCR-based population sequences of the HIV-1 integrase (amino acids 1–278). The HIV-1 subtype was determined using the REGA HIV-1 subtyping tool. We calculated the frequency of amino acids at each position of the HIV-1 integrase in 337 subtype B strains for the time periods 1986–1989, 1991–1994, 1995–1998, 1999–2002, and 2003–2006. Positions were defined as polymorphic if amino acid variation was >1% in any period. Logistic regression was used to identify trends in amino acid variation over time. Resistance-associated mutations were identified according to the IAS 2013 list and the HIVdb, ANRS and GRADE algorithms. Results Overall, 56.8% (158/278) amino acid positions were polymorphic and 15.8% (25/158) of these positions exhibited a significant trend in amino acid variation over time. Proportionately, most polymorphic positions (63.3%, 31/49) were detected in the N-terminal zinc finger domain of the HIV-1 integrase. Motifs and residues essential for HIV-1 integrase activity were little polymorphic, but within the minimal non-specific DNA binding region I220-D270 up to 18.1% amino acid variation was noticed, including four positions with significant amino acid variation over time (S230, D232, D256, A265). No major resistance mutations were identified, and minor resistance mutations were rarely observed without trend over time. E157Q considered by HIVdb, ANRS, and GRADE algorithms was the most frequent resistance-associated polymorphism with an overall prevalence of 2.4%. Conclusions Detailed knowledge of the evolutionary variation of HIV-1 integrase polymorphisms is important to understand

  8. Development of a novel in vitro assay for the evaluation of integron DNA integrase activity

    Directory of Open Access Journals (Sweden)

    Fatemeh Tohidi

    2016-05-01

    Full Text Available Integrons play an important role in multidrug resistance. The integron platform codes for integrase (intI that is required for gene cassette integration through site-specific recombination. The recombination crossover occurs between the G and TT nucleotides in non-palindromic attI and palindromic attC sites. The aim of this study was to establish an efficient in vitro assay for integrase purification and activity detection. To this end, the intI gene was cloned into the pET-22b plasmid. Then, the resulting recombinant plasmid was transformed into Escherichia coli Origami™ strain. The recombinant protein expression was confirmed by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE and western blot assays. The recombinant intI protein was purified by nickel–nitrilotriacetic acid (Ni–NTA affinity chromatography, and its activity was measured by a newly introduced assay. Briefly, specific primers for each side of attI and attC were used, thereby, a polymerase chain reaction would be performed, if a fused plasmid containing both attI and attC sites was created upon recombination. SDS-PAGE and western blotting confirmed the presence of a 38-kDa recombinant protein. Optimum conditions were established for the measurement of the integrase activity and a new model assay was conducted to analyse the recombination activity in vitro. Although the electrophoretic mobility shift assay is an efficient and reliable method, the newly introduced assay provided new or enhanced capability to determine the integrase activity, suggesting that there is no need for expensive and advanced equipment.

  9. The allosteric HIV-1 integrase inhibitor BI-D affects virion maturation but does not influence packaging of a functional RNA genome

    NARCIS (Netherlands)

    van Bel, Nikki; van der Velden, Yme; Bonnard, Damien; Le Rouzic, Erwann; Das, Atze T.; Benarous, Richard; Berkhout, Ben

    2014-01-01

    The viral integrase (IN) is an essential protein for HIV-1 replication. IN inserts the viral dsDNA into the host chromosome, thereby aided by the cellular co-factor LEDGF/p75. Recently a new class of integrase inhibitors was described: allosteric IN inhibitors (ALLINIs). Although designed to

  10. Iron-complexed adsorptive membrane for As(V) species in water

    International Nuclear Information System (INIS)

    Shinde, Rakesh N.; Das, Sadananda; Acharya, R.; Rajurkar, N.S.; Pandey, Ashok K.

    2012-01-01

    Highlights: ► Functionalized membrane was prepared by graft polymerization in host membrane. ► Fe 3+ ions fixed in membrane made it selective for As(V) ions. ► As(V) preconcentrated selectively in membrane samples was quantified by INAA. ► As(V) in ground water sample was easily quantified in 2–3 ppb using membrane. ► Total inorganic arsenic could be quantified by oxidation of As(III) to As(V). - Abstract: Selective preconcentration of a target analyte in the solid phase is an effective route not only to enhance detection limit of the conventional analytical method but also for elimination of interfering matrix. An adsorptive membrane was developed for selective preconcentration and quantification of ultra-trace (ppb) amounts of As(V) present in a variety of aqueous samples. The precursor membrane was prepared by UV-initiator induced graft polymerization of sulphate and phosphate bearing monomers (1:1 mol proportion) in pores of the host microporous poly(propylene) membrane. Fe 3+ ions were loaded in the precursor membrane to make it selective for As(V) ions. The presence of phosphate functional groups prevent leaching of Fe 3+ ions from the membrane when it comes in contact with solution like seawater having high ionic strength. The optimized membrane was characterized in terms of its physical structure, chemical structure and experimental conditions affecting As(V) uptake in the membrane. The possibility of quantifying total preconcentration of As content was also explored by converting As(III) to As(V). To quantify As(V), the membrane samples were subjected to instrumental neutron activation analysis (INAA). The studies carried in the present work showed that quantification of inorganic arsenic species in natural water samples is easily possible in 2–3 ppb concentration range.

  11. Primary resistance to integrase strand-transfer inhibitors in Europe.

    NARCIS (Netherlands)

    M. Casadellá; P.M. van Ham (Petra); M. Noguera-Julian; A. van Kessel; C. Pou; L.M. Hofstra (Marije); G.A. Metcalf (Ginger A.); F. Garcia; D. Struck (Daniel); I. Alexiev (Ivailo); A.M. Bakken Kran; A.I.M. Hoepelman; L.G. Kostrikis (Leondios); S. Somogyi; K. Liitsola (Kirsi); M. Linka (Marek); C. Nielsen; D. Otelea (Dan); D. Paraskevis (Dimitrios); M. Poljak (Mario); E. Puchhammer-Stöckl (Elisabeth); D. Stanekova (Danica); M. Stanojevic (Maja); K. Van Laethem (Kristel); S. Zidovec Lepej (Snjezana); B. Clotet; C.A.B. Boucher (Charles); R. Paredes (Roger); A.M.J. Wensing (Annemarie)

    2015-01-01

    markdownabstractThe objective of this study was to define the natural genotypic variation of the HIV-1 integrase gene across Europe for epidemiological surveillance of integrase strand-transfer inhibitor (InSTI) resistance. This was a multicentre, cross-sectional study within the European SPREAD

  12. Primary resistance to integrase strand-transfer inhibitors in Europe

    NARCIS (Netherlands)

    Casadella, M.; van Ham, P. M.; Noguera-Julian, M.; van Kessel, A.; Pou, C.; Hofstra, L. M.; Santos, J. R.; Garcia, F.; Struck, D.; Alexiev, I.; Kran, A. M. Bakken; Hoepelman, A. I.; Kostrikis, L. G.; Somogyi, S.; Liitsola, K.; Linka, M.; Nielsen, C.; Otelea, D.; Paraskevis, D.; Poljak, M.; Puchhammer-Stoeckl, E.; Stanekova, D.; Stanojevic, M.; Van Laethem, K.; Lepej, S. Zidovec; Clotet, B.; Boucher, C. A. B.; Paredes, R.; Wensing, A. M. J.; Schuurman, R

    2015-01-01

    Objectives: The objective of this study was to define the natural genotypic variation of the HIV-1 integrase gene across Europe for epidemiological surveillance of integrase strand-transfer inhibitor (InSTI) resistance. Methods: This was a multicentre, cross-sectional study within the European

  13. Thalassiolins A-C: new marine-derived inhibitors of HIV cDNA integrase.

    Science.gov (United States)

    Rowley, David C; Hansen, Mark S T; Rhodes, Denise; Sotriffer, Christoph A; Ni, Haihong; McCammon, J Andrew; Bushman, Frederic D; Fenical, William

    2002-11-01

    Human immunodeficiency virus (HIV) replication requires integration of viral cDNA into the host genome, a process mediated by the viral enzyme integrase. We describe a new series of HIV integrase inhibitors, thalassiolins A-C (1-3), isolated from the Caribbean sea grass Thalassia testudinum. The thalassiolins are distinguished from other flavones previously studied by the substitution of a sulfated beta-D-glucose at the 7-position, a substituent that imparts increased potency against integrase in biochemical assays. The most active of these molecules, thalassiolin A (1), displays in vitro inhibition of the integrase catalyzed strand transfer reaction (IC50=0.4 microM) and an antiviral IC50 of 30 microM. Molecular modeling studies indicate a favorable binding mode is probable at the catalytic core domain of HIV-1 integrase.

  14. Tight regulation of the intS gene of the KplE1 prophage: a new paradigm for integrase gene regulation.

    Directory of Open Access Journals (Sweden)

    Gaël Panis

    2010-10-01

    Full Text Available Temperate phages have the ability to maintain their genome in their host, a process called lysogeny. For most, passive replication of the phage genome relies on integration into the host's chromosome and becoming a prophage. Prophages remain silent in the absence of stress and replicate passively within their host genome. However, when stressful conditions occur, a prophage excises itself and resumes the viral cycle. Integration and excision of phage genomes are mediated by regulated site-specific recombination catalyzed by tyrosine and serine recombinases. In the KplE1 prophage, site-specific recombination is mediated by the IntS integrase and the TorI recombination directionality factor (RDF. We previously described a sub-family of temperate phages that is characterized by an unusual organization of the recombination module. Consequently, the attL recombination region overlaps with the integrase promoter, and the integrase and RDF genes do not share a common activated promoter upon lytic induction as in the lambda prophage. In this study, we show that the intS gene is tightly regulated by its own product as well as by the TorI RDF protein. In silico analysis revealed that overlap of the attL region with the integrase promoter is widely encountered in prophages present in prokaryotic genomes, suggesting a general occurrence of negatively autoregulated integrase genes. The prediction that these integrase genes are negatively autoregulated was biologically assessed by studying the regulation of several integrase genes from two different Escherichia coli strains. Our results suggest that the majority of tRNA-associated integrase genes in prokaryotic genomes could be autoregulated and that this might be correlated with the recombination efficiency as in KplE1. The consequences of this unprecedented regulation for excessive recombination are discussed.

  15. Novel Bifunctional Quinolonyl Diketo Acid Derivatives as HIV-1 Integrase Inhibitors: Design, Synthesis, Biological Activities and Mechanism of Action

    Science.gov (United States)

    Di Santo, Roberto; Costi, Roberta; Roux, Alessandra; Artico, Marino; Lavecchia, Antonio; Marinelli, Luciana; Novellino, Ettore; Palmisano, Lucia; Andreotti, Mauro; Amici, Roberta; Galluzzo, Clementina Maria; Nencioni, Lucia; Palamara, Anna Teresa; Pommier, Yves; Marchand, Christophe

    2008-01-01

    The virally encoded integrase protein is an essential enzyme in the life cycle of the HIV-1 virus and represents an attractive and validated target in the development of therapeutics against HIV infection. Drugs that selectively inhibit this enzyme, when used in combination with inhibitors of reverse transcriptase and protease, are believed to be highly effective in suppressing the viral replication. Among the HIV-1 integrase inhibitors, the β-diketo acids (DKAs) represent a major lead for anti-HIV-1drug development. In this study, novel bifunctional quinolonyl diketo acid derivatives were designed, synthesized and tested for their inhibitory ability against HIV-1 integrase. The compounds are potent inhibitors of integrase activity. Particularly, derivative 8 is a potent IN inhibitor for both steps of the reaction (3′-processing and strand transfer) and exhibits both high antiviral activity against HIV-1 infected cells and low cytotoxicity. Molecular modeling studies provide a plausible mechanism of action, which is consistent with ligand SARs and enzyme photo-crosslinking experiments. PMID:16539381

  16. Bovine Lactoferrampin, Human Lactoferricin, and Lactoferrin 1-11 Inhibit Nuclear Translocation of HIV Integrase.

    Science.gov (United States)

    Wang, Winston Yan; Wong, Jack Ho; Ip, Denis Tsz Ming; Wan, David Chi Cheong; Cheung, Randy Chifai; Ng, Tzi Bun

    2016-08-01

    This study aimed to investigate fragments derived from human and bovine lactoferrins for ability to inhibit nuclear translocation of HIV-1 integrase. It was shown that human lactoferricin, human lactoferrin 1-11, and bovine lactoferrampin reduced nuclear distribution of HIV-1 integrase. Bovine lactoferrampin could inhibit both the activity and nuclear translocation of HIV-1 integrase. Human lactoferrampin, bovine lactoferricin, and bovine lactoferrin 1-11 had no effect on HIV-1 integrase nuclear translocation. Human lactoferrampin which inhibited the activity of integrase did not prevent its nuclear translocation. Human lactoferricin and lactoferrin 1-11 did not inhibit HIV-1 integrase nuclear translocation despite their ability to attenuate the enzyme activity. The discrepancy between the findings on reduction of HIV-1 activity and inhibition of nuclear translocation of HIV-1 integrase was due to the different mechanisms involved. A similar reasoning can also be applied to the different inhibitory potencies of the milk peptides on different HIV enzymes, i.e., nuclear translocation.

  17. Serine integrase chimeras with activity in E. coli and HeLa cells

    Directory of Open Access Journals (Sweden)

    Alfonso P. Farruggio

    2014-09-01

    Full Text Available In recent years, application of serine integrases for genomic engineering has increased in popularity. The factor-independence and unidirectionality of these large serine recombinases makes them well suited for reactions such as site-directed vector integration and cassette exchange in a wide variety of organisms. In order to generate information that might be useful for altering the specificity of serine integrases and to improve their efficiency, we tested a hybridization strategy that has been successful with several small serine recombinases. We created chimeras derived from three characterized members of the serine integrase family, phiC31, phiBT1, and TG1 integrases, by joining their amino- and carboxy-terminal portions. We found that several phiBT1-phiC31 (BC and phiC31-TG1 (CT hybrid integrases are active in E. coli. BC chimeras function on native att-sites and on att-sites that are hybrids between those of the two donor enzymes, while CT chimeras only act on the latter att-sites. A BC hybrid, BC{−1}, was also active in human HeLa cells. Our work is the first to demonstrate chimeric serine integrase activity. This analysis sheds light on integrase structure and function, and establishes a potentially tractable means to probe the specificity of the thousands of putative large serine recombinases that have been revealed by bioinformatics studies.

  18. Comparison of Different Dosing Protocols of Anti-Snake Venom (ASV) in Snake Bite Cases.

    Science.gov (United States)

    Daswani, B R; Chandanwale, A S; Kadam, D B; Ghongane, B B; Ghorpade, V S; Manu, H C

    2017-09-01

    Considering the cost of Anti-Snake Venom (ASV) and irregularity in its supply, there is often a need to curtail doses of ASV, despite guidelines for management of snake bite. During June 2013 to September 2013, when ASV was in short supply, our institutional committee reviewed the overall hospital statistics of snake bite cases as well as scientific literature and formulated a working modified protocol that used low dose of ASV in snake bite cases. To retrospectively analyse and compare the modified ASV protocol versus conventional ASV protocol with respect to outcome, number of ASV vials required, duration of stay in the hospital/ ICU, and additional supportive interventions needed. This was a retrospective study conducted at a tertiary care teaching hospital, Maharashtra, India. Hospital records of inpatients admitted for snake bite during June 2013 to September 2013 (since introduction of the modified protocol) as well as during June 2012 to September 2012, (when patients received conventional protocol-historical controls) were retrospectively analysed to assess the number of ASV vials received by the patients during the stay, need for supportive therapy, duration of stay and outcome of the patients. There was a significant reduction in average number of ASV vials per patient, required vide the modified protocol compared to their historical controls (10.74±0.95 vs 28.17±2.75 pcost of management of each patient reduced by approximately 11974.41 INR per treated patient, based on the requirement of ASV. The modified ASV protocol used in this study is more cost effective as compared to the conventional protocol, deserves prospective evaluation and may be followed at least during prime time of scarcity of ASV.

  19. Efficient site-specific integration in Plasmodium falciparum chromosomes mediated by mycobacteriophage Bxb1 integrase.

    Science.gov (United States)

    Nkrumah, Louis J; Muhle, Rebecca A; Moura, Pedro A; Ghosh, Pallavi; Hatfull, Graham F; Jacobs, William R; Fidock, David A

    2006-08-01

    Here we report an efficient, site-specific system of genetic integration into Plasmodium falciparum malaria parasite chromosomes. This is mediated by mycobacteriophage Bxb1 integrase, which catalyzes recombination between an incoming attP and a chromosomal attB site. We developed P. falciparum lines with the attB site integrated into the glutaredoxin-like cg6 gene. Transfection of these attB(+) lines with a dual-plasmid system, expressing a transgene on an attP-containing plasmid together with a drug resistance gene and the integrase on a separate plasmid, produced recombinant parasites within 2 to 4 weeks that were genetically uniform for single-copy plasmid integration. Integrase-mediated recombination resulted in proper targeting of parasite proteins to intra-erythrocytic compartments, including the apicoplast, a plastid-like organelle. Recombinant attB x attP parasites were genetically stable in the absence of drug and were phenotypically homogeneous. This system can be exploited for rapid genetic integration and complementation analyses at any stage of the P. falciparum life cycle, and it illustrates the utility of Bxb1-based integrative recombination for genetic studies of intracellular eukaryotic organisms.

  20. Preparation and certification of arsenate [As(V)] reference material, NMIJ CRM 7912-a.

    Science.gov (United States)

    Narukawa, Tomohiro; Kuroiwa, Takayoshi; Narushima, Izumi; Jimbo, Yasujiro; Suzuki, Toshihiro; Chiba, Koichi

    2010-05-01

    Arsenate [As(V)] solution reference material, National Metrology Institute of Japan (NMIJ) certified reference material (CRM) 7912-a, for speciation of arsenic species was developed and certified by NMIJ, the National Institute of Advanced Industrial Science and Technology. High-purity As(2)O(3) reagent powder was dissolved in 0.8 M HNO(3) solution and As(III) was oxidized to As(V) with HNO(3) to prepare 100 mg kg(-1) of As(V) candidate CRM solution. The solution was bottled in 400 bottles (50 mL each). The concentration of As(V) was determined by four independent analytical techniques-inductively coupled plasma mass spectrometry, inductively coupled plasma optical emission spectrometry, graphite furnace atomic absorption spectrometry, and liquid chromatography inductively coupled plasma mass spectrometry-according to As(V) calibration solutions, which were prepared from the arsenic standard of the Japan Calibration Service system and whose species was guaranteed to be As(V) by NMIJ. The uncertainties of all the measurements and preparation procedures were evaluated. The certified value of As(V) in the CRM is (99.53 +/- 1.67) mg kg(-1) (k = 2).

  1. Determination of As(III) and As(V) by Flow Injection-Hydride Generation-Atomic Absorption Spectrometry via On-line Reduction of As(V) by KI

    DEFF Research Database (Denmark)

    Nielsen, Steffen; Hansen, Elo Harald

    1997-01-01

    A volume-based flow injection (FI) procedure is described for the determination and speciation of trace inorganic arsenic, As(III) and As(V), via hydride generation-atomic absorption spectrometry (HG-AAS) of As(III). The determination of total arsenic is obtained by on-line reduction of As(V) to As...

  2. Adherence to Positive Airway Therapy After Switching From CPAP to ASV: A Big Data Analysis.

    Science.gov (United States)

    Pépin, Jean-Louis D; Woehrle, Holger; Liu, Dongquan; Shao, Shiyun; Armitstead, Jeff P; Cistulli, Peter A; Benjafield, Adam V; Malhotra, Atul

    2018-01-15

    There is a lack of data regarding adherence trajectories when switching from continuous positive airway pressure (CPAP) to adaptive servoventilation (ASV) in the context of persistent or treatment-emergent central sleep apnea (CSA). This study investigated 90-day adherence rates in patients with sleep apnea based on the type of positive airway pressure (PAP) device used and any switching of PAP modality over time. Telemonitoring data were obtained from a United States PAP database. Eligible patients were a 30% random sample who started PAP, plus all who started ASV, from January 1, 2015 to October 2, 2015. All received PAP and had at least one session with usage of 1 hour or more. Adherence and device usage were determined in three groups: started on CPAP and stayed on CPAP (CPAP only); started on ASV and stayed on ASV (ASV only); started on CPAP, switched to ASV (Switch). The United States Medicare definition of adherence was used. The study included 198,890 patients; 189,724 (CPAP only), 8,957 (ASV only) and 209 (Switch). In the Switch group, average apnea-hypopnea index decreased significantly on ASV versus CPAP. At 90 days, adherence rates were 73.8% and 73.2% in the CPAP only and ASV only groups. In the Switch group, CPAP adherence was 62.7%, improving to 76.6% after the switch to ASV. Mean device usage at 90 days was 5.27, 5.31, and 5.73 h/d in the CPAP only, ASV only, and Switch groups, respectively. Treatment-emergent or persistent CSA during CPAP reduced therapy adherence, but adherence improved early after switching from CPAP to ASV. © 2018 American Academy of Sleep Medicine

  3. Reduction of adsorbed As(V) on nano-TiO2 by sulfate-reducing bacteria.

    Science.gov (United States)

    Luo, Ting; Ye, Li; Ding, Cheng; Yan, Jinlong; Jing, Chuanyong

    2017-11-15

    Reduction of surface-bound arsenate [As(V)] and subsequent release into the aqueous phase contribute to elevated As in groundwater. However, this natural process is not fully understood, especially in the presence of sulfate-reducing bacteria (SRB). Gaining mechanistic insights into solid-As(V)-SRB interactions motivated our molecular level study on the fate of nano-TiO 2 bound As(V) in the presence of Desulfovibrio vulgaris DP4, a strain of SRB, using incubation and in situ ATR-FTIR experiments. The incubation results clearly revealed the reduction of As(V), either adsorbed on nano-TiO 2 or dissolved, in the presence of SRB. In contrast, this As(V) reduction was not observed in abiotic control experiments where sulfide was used as the reductant. Moreover, the reduction was faster for surface-bound As(V) than for dissolved As(V), as evidenced by the appearance of As(III) at 45h and 75h, respectively. ATR-FTIR results provided direct evidence that the surface-bound As(V) was reduced to As(III) on TiO 2 surfaces in the presence of SRB. In addition, the As(V) desorption from nano-TiO 2 was promoted by SRB relative to abiotic sulfide, due to the competition between As(V) and bacterial phosphate groups for TiO 2 surface sites. This competition was corroborated by the ATR-FTIR analysis, which showed inner-sphere surface complex formation by bacterial phosphate groups on TiO 2 surfaces. The results from this study highlight the importance of indirect bacteria-mediated As(V) reduction and release in geochemical systems. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. HIV-1 integrase inhibitor resistance among treatment naïve patients in the West of Scotland.

    Science.gov (United States)

    Bradley-Stewart, A; Urcia, C; MacLean, A; Aitken, C; Gunson, R

    2017-07-01

    Transmitted integrase inhibitor resistance is rare, with only a small number of cases reported world-wide to date. The aim of this study was to assess whether transmitted integrase inhibitor resistance has occurred in Scotland and if so, could there be a case for performing genotypic integrase resistance testing at baseline. The study population consisted of 106 treatment naïve, newly diagnosed, HIV positive patients. The patient samples were collected between October 2015 and March 2016 at the time of HIV diagnosis and prior to initiation of anti-retroviral therapy. The integrase region was amplified and sequenced. We detected integrase inhibitor resistance (T66I/T) at baseline in one patient sample. This is a non-polymorphic mutation seen in patients receiving elvitegravir which confers high-level resistance to elvitegravir and intermediate resistance to raltegravir. A further 10 patients had accessory mutations which have minimal or no effect on susceptibility to integrase inhibitors. Transmitted integrase inhibitor resistance remains rare. The results of the present study do not support performing integrase resistance testing at baseline. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

  5. Nucleic acid amplification of HIV-1 integrase sequence subtypes CRF01_AE and B for development of HIV anti-integrase drug resistance genotyping assay

    Science.gov (United States)

    Adlar, F. R.; Bela, B.

    2017-08-01

    To anticipate the potential use of anti-integrase drugs in Indonesia for treatment of HIV-1 infection, the development of a drug resistance genotyping assay for anti-integrase is crucial in identifying the genetic drug resistance profile of Indonesian HIV-1 strains. This experiment aimed to amplify a target region in the integrase gene of Indonesian HIV-1 subtypes CRF01_AE and B that contain genetic mutations known to confer resistance to anti-integrase drug. Eleven archived plasma samples from individuals living with HIV-1 were obtained from the Virology and Cancer Pathobiology Research Center for Health Service (VCPRC FKUI-RSCM) laboratory. One of the plasma samples contained HIV-1 subtype B, and the remaining plasma samples contained subtype CRF01_AE. The target regions for all samples were amplified through RT-PCR, with an annealing temperature of 55 °C, using the primer pair AE_POL 4086F and AE_POL 5232R that were designed by VCPRC FKUI-RSCM. The results of this experiment show that 18.2% (2/11) of the samples were successfully amplified using the one-step RT-PCR. While the primer pair was effective in amplifying the target region in the integrase gene sequence for subtype B (100%; 1/1), it had a low efficacy (10%, 1/10) for subtype CRF01_AE. In conclusion, the primer pair can be used to amplify the target region in Indonesian HIV-1 strain subtypes CRF01_AE and B. However, optimization of the PCR condition and an increased number of samples would help to determine an accurate representation of the efficacy of the primer pair.

  6. Factors influencing As(V) stabilization in the mine soils amended with iron-rich materials.

    Science.gov (United States)

    Kim, Mijin; Kim, Juhee; Kim, Minhee; Kim, Yong-Seong; Nam, Seung Mo; Moon, Deok Hyun; Hyun, Seunghun

    2017-09-04

    Chemical stability of As(V) in amended mine-impacted soils was assessed according to functions of incubation period (0, 1, 2, 4, and 6 months), amendment dose (2.5 and 5%), and application timing (0 and 3rd month). Six soils contaminated with 26-209 mg kg -1 of As(V) were collected from two abandoned mine sites and were treated with two alkaline iron-rich materials (mine discharge sludge (MS) and steel-making slag (SS)). Seventeen to 23% of As(V) in soils was labile. After each designated time, As(V) stability was assessed by the labile fractions determined with sequential extraction procedures (F1-F5). Over 6 months, a reduction (26.9-70.4%) of the two labile fractions (F1 and F2) and a quantitative increase (7.4-29.9%) of As(V) in F3 were observed (r 2  = 0.956). Two recalcitrant fractions (F4 and F5) remained unchanged. Temporal change of As(V) stability in a sample was well described by the two-domain model (k fast , k slow , and F fast ). The stabilization (%) correlated well with the fast-stabilizing domain (F fast ), clay content (%), and Fe oxide content (mg kg -1 ), but correlated poorly with kinetic rate constants (k fast and k slow ). Until the 3rd month, the 2.5%-MS amended sample resulted in lower As(V) stabilization (25-40%) compared to the 5% sample (50-60%). However, the second 2.5% MS addition on the 2.5% sample upon the lapse of the 3rd month led to a substantial reduction (up to 38%) of labile As(V) fraction in the following 4th and 6th months. As a result, an additional 15-25% of As(V) stability was obtained when splitting the amendment dose into 3-month intervals. In conclusion, the As(V) stabilization by Fe-rich amendment is time-dependent and its efficacy can be improved by optimizing the amendment dose and its timing.

  7. Lead Screening for HIV-1 Integrase (IN Inhibited by Traditional Chinese Medicine

    Directory of Open Access Journals (Sweden)

    Tzu-Chieh Hung

    2014-01-01

    Full Text Available Human immunodeficiency virus causes the acquired immunodeficiency syndrome (AIDS and becomes a serious world-wide problem because of this disease's rapid propagation and incurability. Integrase strand transfer inhibitors (INSTIs supports HIV have rapid drug resistance for antitreatment. Screening the traditional Chinese medicine (TCM database by simulating molecular docking and molecular dynamics may select molecular compounds to inhibit INSTIs against HIV drug resistance. (S-cathinone and (1S,2S-norpseudoephedrine are selected based on structure and ligand-based drugs are designed and then get higher bioactivity predicted score from SVM than Raltegravir and other TCM compounds. The molecular dynamics are helpful in the analysis and detection of protein-ligand interactions. According to the docking poses, hydrophobic interactions and hydrogen bond variations define the main regions of important amino acids in integrase. In addition to the detection of TCM compound efficacy, we suggest (1S,2S-norpseudoephedrine is better than the others based on the analysis of interaction and the effect on the structural variation.

  8. Integrase of Mason-Pfizer monkey virus

    Czech Academy of Sciences Publication Activity Database

    Snášel, Jan; Krejčík, Zdeněk; Jenčová, Věra; Rosenberg, Ivan; Ruml, Tomáš; Alexandratos, J.; Gustchina, A.; Pichová, Iva

    2005-01-01

    Roč. 272, č. 1 (2005), s. 203-216 ISSN 1742-464X R&D Projects: GA AV ČR(CZ) IAA4055304 Institutional research plan: CEZ:AV0Z4055905 Keywords : integrase * Mason-Pfizer monkey virus * HIV-1 Subject RIV: CE - Biochemistry

  9. A method for producing transgenic cells using a multi-integrase system on a human artificial chromosome vector.

    Directory of Open Access Journals (Sweden)

    Shigeyuki Yamaguchi

    Full Text Available The production of cells capable of expressing gene(s of interest is important for a variety of applications in biomedicine and biotechnology, including gene therapy and animal transgenesis. The ability to insert transgenes at a precise location in the genome, using site-specific recombinases such as Cre, FLP, and ΦC31, has major benefits for the efficiency of transgenesis. Recent work on integrases from ΦC31, R4, TP901-1 and Bxb1 phages demonstrated that these recombinases catalyze site-specific recombination in mammalian cells. In the present study, we examined the activities of integrases on site-specific recombination and gene expression in mammalian cells. We designed a human artificial chromosome (HAC vector containing five recombination sites (ΦC31 attP, R4 attP, TP901-1 attP, Bxb1 attP and FRT; multi-integrase HAC vector and de novo mammalian codon-optimized integrases. The multi-integrase HAC vector has several functions, including gene integration in a precise locus and avoiding genomic position effects; therefore, it was used as a platform to investigate integrase activities. Integrases carried out site-specific recombination at frequencies ranging from 39.3-96.8%. Additionally, we observed homogenous gene expression in 77.3-87.5% of colonies obtained using the multi-integrase HAC vector. This vector is also transferable to another cell line, and is capable of accepting genes of interest in this environment. These data suggest that integrases have high DNA recombination efficiencies in mammalian cells. The multi-integrase HAC vector enables us to produce transgene-expressing cells efficiently and create platform cell lines for gene expression.

  10. A novel function for spumaretrovirus integrase: an early requirement for integrase-mediated cleavage of 2 LTR circles

    Directory of Open Access Journals (Sweden)

    Mouscadet Jean-François

    2005-05-01

    Full Text Available Abstract Retroviral integration is central to viral persistence and pathogenesis, cancer as well as host genome evolution. However, it is unclear why integration appears essential for retrovirus production, especially given the abundance and transcriptional potential of non-integrated viral genomes. The involvement of retroviral endonuclease, also called integrase (IN, in replication steps apart from integration has been proposed, but is usually considered to be accessory. We observe here that integration of a retrovirus from the spumavirus family depends mainly on the quantity of viral DNA produced. Moreover, we found that IN directly participates to linear DNA production from 2-LTR circles by specifically cleaving the conserved palindromic sequence found at LTR-LTR junctions. These results challenge the prevailing view that integrase essential function is to catalyze retroviral DNA integration. Integrase activity upstream of this step, by controlling linear DNA production, is sufficient to explain the absolute requirement for this enzyme. The novel role of IN over 2-LTR circle junctions accounts for the pleiotropic effects observed in cells infected with IN mutants. It may explain why 1 2-LTR circles accumulate in vivo in mutants carrying a defective IN while their linear and integrated DNA pools decrease; 2 why both LTRs are processed in a concerted manner. It also resolves the original puzzle concerning the integration of spumaretroviruses. More generally, it suggests to reassess 2-LTR circles as functional intermediates in the retrovirus cycle and to reconsider the idea that formation of the integrated provirus is an essential step of retrovirus production.

  11. Synergistic toxic effect of nano-Al2O3 and As(V) on Ceriodaphnia dubia

    International Nuclear Information System (INIS)

    Wang Demin; Hu Ji; Forthaus, Brett E.; Wang Jianmin

    2011-01-01

    Engineered nanomaterials (ENMs) alone could negatively impact the environment and human health. However, their role in the presence of other toxic substances is not well understood. The toxicity of nano-Al 2 O 3 , inorganic As(V), and a combination of both was examined with C. dubia as the model organisms. Bare nano-Al 2 O 3 particles exhibited partial mortality at concentrations of greater than 200 mg/L. When As(V) was also present, a significant amount of As(V) was accumulated on the nano-Al 2 O 3 surface, and the calculated LC 50 of As(V) in the presence of nano-Al 2 O 3 was lower than that it was without the nano-Al 2 O 3 . The adsorption of As(V) on the nano-Al 2 O 3 surface and the uptake of nano-Al 2 O 3 by C. dubia were both verified. Therefore, the uptake of As(V)-loaded nano-Al 2 O 3 was a major reason for the enhanced toxic effect. - Highlights: → Nano-Al 2 O 3 particles alone do not have significant toxic effect on C. dubia. → However, nano-Al 2 O 3 particles significantly enhance the toxicity of As(V). → The uptake of As-loaded nano-Al 2 O 3 by C. dubia plays the major role on the toxicity. - Nano-Al 2 O 3 could accumulate background As(V) and enhance As(V) toxicity on C. dubia through the uptake of As(V)-loaded nano-Al 2 O 3 particles.

  12. Removal of arsenic from water using manganese (III) oxide: Adsorption of As(III) and As(V).

    Science.gov (United States)

    Babaeivelni, Kamel; Khodadoust, Amid P

    2016-01-01

    Removal of arsenic from water was evaluated with manganese (III) oxide (Mn2O3) as adsorbent. Adsorption of As(III) and As(V) onto Mn2O3 was favorable according to the Langmuir and Freundlich adsorption equilibrium equations, while chemisorption of arsenic occurred according to the Dubinin-Radushkevich equation. Adsorption parameters from the Langmuir, Freundlich, and Temkin equations showed a greater adsorption and removal of As(III) than As(V) by Mn2O3. Maximum removal of As(III) and As(V) occurred at pH 3-9 and at pH 2, respectively, while removal of As(V) in the pH range of 6-9 was 93% (pH 6) to 61% (pH 9) of the maximum removal. Zeta potential measurements for Mn2O3 in As(III) was likely converted to As(V) solutions indicated that As(III) was likely converted to As(V) on the Mn2O3 surface at pH 3-9. Overall, the effective Mn2O3 sorbent rapidly removed As(III) and As(V) from water in the pH range of 6-9 for natural waters.

  13. Reduction of As(V) to As(III) by commercial ZVI or As(0) with acid-treated ZVI

    International Nuclear Information System (INIS)

    Sun, Fenglong; Osseo-Asare, Kwadwo A.; Chen, Yongsheng; Dempsey, Brian A.

    2011-01-01

    Graphical abstract: Acid-treated ZVI (right) reduced As(V) to the less toxic As(0) while commercial ZVI reduced As(V) to As(III). There was no lag phase in either reaction when rigorously anoxic conditions were maintained. Highlights: ► Acid-treated ZVI reduced As(V) to the less toxic As(0). ► Commercial ZVI reduced As(V) to As(III), which was not released to solution. ► Magnetite/Fe(II) did not reduce As(V) even though the reaction is thermodynamically spontaneous. ► No lag phase was observed in any of the reactions, contrary to prior reports. ► Rigorously anoxic conditions seem necessary for observing these reactions. - Abstract: Zero-valent iron (ZVI) consists of an elemental iron core surrounded by a shell of corrosion products, especially magnetite. ZVI is used for in situ removal or immobilization of a variety of contaminants but the mechanisms for removal of arsenic remain controversial and the mobility of arsenic after reaction with ZVI is uncertain. These issues were addressed by separately studying reactions of As(V) with magnetite, commercial ZVI, and acid-treated ZVI. Strictly anoxic conditions were used. Adsorption of As(V) on magnetite was fast with pH dependence similar to previous reports using oxic conditions. As(V) was not reduced by magnetite and Fe(II) although the reaction is thermodynamically spontaneous. As(V) reactions with ZVI were also fast and no lag phase was observed which was contrary to previous reports. Commercial ZVI reduced As(V) to As(III) only when As(V) was adsorbed, i.e., for pH < 7. As(III) was not released to solution. Acid-treated ZVI reduced As(V) to As(0), shown using wet chemical analyses and XANES/EXAFS. Comparisons were drawn between reactivity of acid-treated ZVI and nano-ZVI; if true then acid-treated ZVI could provide similar reactive benefits at lower cost.

  14. Raltegravir: first in class HIV integrase inhibitor

    Directory of Open Access Journals (Sweden)

    Zelalem Temesgen

    2008-06-01

    Full Text Available Zelalem Temesgen1, Dawd S Siraj21Mayo Clinic, Rochester, MN, USA; 2East Carolina University Greenville, NC, USAAbstract: On October 16, 2007, the US Food and Drug Administration (FDA approved raltegravir for treatment of human immunodeficiency virus (HIV-1 infection in combination with other antiretroviral agents in treatment-experienced adult patients who have evidence of viral replication and HIV-1 strains resistant to multiple antiretroviral agents. Raltegravir is first in a novel class of antiretroviral drugs known as integrase inhibitors. It has demonstrated potent anti HIV activity in both antiretroviral treatment-naïve and experienced patients. The most common adverse events reported with raltegravir during phase 2 and 3 clinical trials were diarrhea, nausea, and headache. Laboratory abnormalities include mild elevations in liver transaminases and creatine phosphokinase.Keywords: raltegravir, HIV, antiretroviral agents, integrase inhibitors

  15. A historical sketch of the discovery and development of HIV-1 integrase inhibitors.

    Science.gov (United States)

    Savarino, Andrea

    2006-12-01

    The long process of HIV-1 integrase inhibitor discovery and development can be attributed to both the complexity of HIV-1 integration and poor 'integration' of these researches into mainstream investigations on antiretroviral therapy in the mid-1990s. Of note, some fungal extracts investigated during this period contain the beta-hydroxyketo group, later recognised to be a key structural requirement for keto-enol acids (also referred to as diketo acids) and other integrase inhibitors. This review reconstructs (in the general context of the history of AIDS research) the principal steps that led to the integrase inhibitors currently in clinical trials, and discusses possible future directions.

  16. Electrodialytic separation of Cu(II) and As(V) in acidic electrolytes; Separacion electrodialitica de Cu(II) y As(V) en electrolitos acidos

    Energy Technology Data Exchange (ETDEWEB)

    Ibanez, J. P.; Ipinza, J.; Cifuentes, L.

    2007-07-01

    The separation of copper and arsenic from acidic electrolytes by electrodialysis was investigated at room temperature. the effect of current density and pH was studied in a batch cell during 3 hours. The kinetic parameters showed that Cu(II) transport rate was 0.75 mol/m''2/h and the As(V) transport rate was 0.002 mol/m''2/h. An efficient separation between Cu(II) and As(V) was achieved; Generating a concentrated solution of copper with no arsenic, which was obtained independently of the electrolyte acidity and current density used. The effect of the arsenic speciation with pH is discussed as well. (Author) 23 refs.

  17. HIV-1 integrase resistance among antiretroviral treatment naive and experienced patients from Northwestern Poland

    Directory of Open Access Journals (Sweden)

    Parczewski Miłosz

    2012-12-01

    Full Text Available Abstract Background HIV integrase inhibitor use is limited by low genetic barrier to resistance and possible cross-resistance among representatives of this class of antiretrovirals. The aim of this study was to analyse integrase sequence variability among antiretroviral treatment naive and experienced patients with no prior integrase inhibitor (InI exposure and investigate development of the InI drug resistance mutations following the virologic failure of the raltegravir containing regimen. Methods Sequencing of HIV-1 integrase region from plasma samples of 80 integrase treatment naive patients and serial samples from 12 patients with observed virologic failure on raltegravir containing treatment whenever plasma vireamia exceeded >50 copies/ml was performed. Drug resistance mutations were called with Stanford DB database and grouped into major and minor variants. For subtyping bootstrapped phylogenetic analysis was used; Bayesian Monte Carlo Marcov Chain (MCMC model was implemented to infer on the phylogenetic relationships between the serial sequences from patients failing on raltegravir. Results Majority of the integrase region sequences were classified as subtype B; the remaining ones being subtype D, C, G, as well as CRF01_AE , CRF02_AG and CRF13_cpx recombinants. No major integrase drug resistance mutations have been observed in InI-treatment naive patients. In 30 (38.5% cases polymorphic variation with predominance of the E157Q mutation was observed. This mutation was more common among subtype B (26 cases, 54.2% than non-B sequences (5 cases, 16.7%, p=0.00099, OR: 5.91 (95% CI:1.77-22.63]. Other variants included L68V, L74IL, T97A, E138D, V151I, R263K. Among 12 (26.1% raltegravir treated patients treatment failure was observed; major InI drug resistance mutations (G140S, Q148H and N155H, V151I, E92EQ, V151I, G163R were noted in four of these cases (8.3% of the total InI-treated patients. Time to the development of drug resistance ranged

  18. The extraction behaviour of As(III) and As(V) in APDC-CCl4 system

    International Nuclear Information System (INIS)

    Yang Ruiying; Zhu Xuping

    1997-01-01

    The extraction and back-extraction behaviour of As(III) and As(V) in APDC-CCl 4 system have been studied by using 76 As trace technique. As(III) can be extracted quantitatively by APDC-CCl 4 system at pH = 1-3. As(V) can be extracted after being reduced to As(III) by Na 2 S 2 O 3 . Water with high pH value can be used for back-extraction. The method can be applied in the separation of inorganic As(III) and As(V) in water quality inspection

  19. Small molecule inhibitors of the LEDGF site of human immunodeficiency virus integrase identified by fragment screening and structure based design.

    Directory of Open Access Journals (Sweden)

    Thomas S Peat

    Full Text Available A fragment-based screen against human immunodeficiency virus type 1 (HIV integrase led to a number of compounds that bound to the lens epithelium derived growth factor (LEDGF binding site of the integrase catalytic core domain. We determined the crystallographic structures of complexes of the HIV integrase catalytic core domain for 10 of these compounds and quantitated the binding by surface plasmon resonance. We demonstrate that the compounds inhibit the interaction of LEDGF with HIV integrase in a proximity AlphaScreen assay, an assay for the LEDGF enhancement of HIV integrase strand transfer and in a cell based assay. The compounds identified represent a potential framework for the development of a new series of HIV integrase inhibitors that do not bind to the catalytic site of the enzyme.

  20. Investigation of As(V) removal from acid mine drainage by iron (hydr) oxide modified zeolite.

    Science.gov (United States)

    Nekhunguni, Pfano Mathews; Tavengwa, Nikita Tawanda; Tutu, Hlanganani

    2017-07-15

    In this work, the synthesis of iron (hydr) oxide modified zeolite was achieved through precipitation of iron on the zeolite. The structure and surface morphology of iron (hydr) oxide modified zeolite (IHOMZ) was studied by scanning electron microscopy (SEM), coupled with an energy-dispersive X-ray spectroscopy (EDX), and Fourier transform infrared (FT-IR) spectra. The efficiency of IHOMZ was then investigated through batch technique for the extraction of As(V) from mine waste water. The optimum parameters for maximum As(V) adsorption were: an initial As(V) concentration (10 mg L -1 ), adsorbent dosage (3.0 g), contact time (90 min) and temperature (53 °C). The initial pH of the solution had no compelling effect on As(V) adsorption by IHOMZ. However, adsorption capacity was significantly affected by the solution temperature with 53 °C registering the maximum removal efficiency. The thermodynamic parameters: Entropy (ΔS° = 0.00815 kJ (K mol) -1 ), variation of the Gibbs free energy (ΔG°) and enthalpy (ΔH° = 9.392 kJ mol -1 ) of As(V) adsorption onto IHOMZ system signified a non-spontaneous and endothermic process. It was noted that Freundlich isotherm model exhibited a better fit to the equilibrium experimental data, implying that the adsorption process occurred on a heterogeneous surface. The kinetic data from As(V) adsorption experiments was depicted by the pseudo-second-order kinetic model (R 2  > 0.999), suggesting a chemisorption adsorption process. The experimental batch equilibrium results indicated that IHOMZ could be used as an effective sorbent for As(V) ion extraction from acid mine drainage. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. Magnetite nanoparticles coated glass wool for As(V) removal from drinking water

    International Nuclear Information System (INIS)

    Kango, Sarita; Kumar, Rajesh

    2015-01-01

    Arsenic (As) removal from contaminated groundwater is a key environmental concern worldwide. In this study, glass wool was coated with magnetite nanoparticles under argon gas flow and magnetite coated glass wool have been investigated for application as an adsorbent for As(V) removal from water. The adsorbent was characterized by using Scanning Electron Microscopy (SEM) and arsenic contaminated water treated with adsorbent was analyzed by Inductively Coupled Plasma Mass Spectroscopy (ICP-MS). The ICP-MS results showed that 10 g/L of adsorbent removed 99.4% of As(V) within 5 hours at pH-7 and initial arsenic concentration of 360µg/L. Adsorption kinetics data fitted well in pseudo-first-order kinetics model with high correlation coefficient (R 2 = 0.995). As magnetite nanoparticles coated glass wool showed favorable adsorption behavior for As(V), it can be a promising tool for water purification

  2. Magnetite nanoparticles coated glass wool for As(V) removal from drinking water

    Energy Technology Data Exchange (ETDEWEB)

    Kango, Sarita; Kumar, Rajesh, E-mail: rajesh.kumar@juit.ac.in [Department of Physics and Materials Science, Jaypee University of Information Technology, Waknaghat, District Solan (H.P.)- 173 234 (India)

    2015-08-28

    Arsenic (As) removal from contaminated groundwater is a key environmental concern worldwide. In this study, glass wool was coated with magnetite nanoparticles under argon gas flow and magnetite coated glass wool have been investigated for application as an adsorbent for As(V) removal from water. The adsorbent was characterized by using Scanning Electron Microscopy (SEM) and arsenic contaminated water treated with adsorbent was analyzed by Inductively Coupled Plasma Mass Spectroscopy (ICP-MS). The ICP-MS results showed that 10 g/L of adsorbent removed 99.4% of As(V) within 5 hours at pH-7 and initial arsenic concentration of 360µg/L. Adsorption kinetics data fitted well in pseudo-first-order kinetics model with high correlation coefficient (R{sup 2} = 0.995). As magnetite nanoparticles coated glass wool showed favorable adsorption behavior for As(V), it can be a promising tool for water purification.

  3. Preparation and characterization of an organic/inorganic hybrid sorbent (PLE) to enhance selectivity for As(V).

    Science.gov (United States)

    An, Byungryul; Kim, Hakchan; Park, Chanhyuk; Lee, Sang-Hyup; Choi, Jae-Woo

    2015-05-30

    For the selective removal of arsenate (As(V)) a hybrid sorbent was prepared using a non-toxic natural organic material, chitosan, by loading a transition metal, nickel. The immobilization of nickel was achieved by coordination with a deprotonated amino group (NH2) in the chitosan polymer chain. The amount of nickel was directly correlated to the presence of the amino group and was calculated to be 62 mg/g. FTIR spectra showed a peak shift from 1656 to 1637 cm(-1) after Ni(2+) loading, indicating the complexation between the amino group and nickel, and a peak of As(V) was observed at 834 cm(-1). An increase of sulfate concentration from 100 mg/L to 200 mg/L did not significantly affect As(V) sorption, and an increase in the concentration of bicarbonate reduced the As(V) uptake by 33%. The optimal pH of the solution was determined at pH 10, which is in accordance with the fraction of HAsO4(2-) and AsO4(-3). According to a fixed column test, a break through behavior of As(V) revealed that selectivity for As(V) was over sulfate. Regeneration using 5% NaCl extended the use of sorbent to up to uses without big loss of sorption capacity. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Radiation induced emulsion graft polymerization of 4-vinylpyridine onto PE/PP nonwoven fabric for As(V) adsorption

    International Nuclear Information System (INIS)

    Akkaş Kavaklı, Pınar; Kavaklı, Cengiz; Seko, Noriaki; Tamada, Masao; Güven, Olgun

    2016-01-01

    A novel nonwoven fabric adsorbent having 4-vinylpyridine functional groups was prepared by using radiation-induced emulsion graft polymerization method and grafting 4-vinylpyridine monomer onto a polyethylene-coated polypropylene nonwoven fabric (NWF) in aqueous emulsion solution. The grafting conditions of the 4-vinylpyridine monomer onto the NWF were optimised and 150% D g VP-g-NWF was prepared using 30 kGy pre-irradiation dose, 5% VP monomer concentration and 0.5% (w/w) Tween 20 in aqueous emulsion. Grafted 4-vinylpyridine chains on the NWF were then quaternized for the preparation of QVP-g-NWF adsorbent. All fabric structures were characterized by using Fourier-transform infrared spectrometer, x-ray photoelectron spectrometer and scanning electron microscope. QVP-g-NWF adsorbent was used in batch adsorption experiments for As(V) ions by studying the pH, contact time, and initial As(V) ion concentration parameters. Results showed that QVP-g-NWF adsorbent has significant As(V) adsorption and experimental As(V) adsorption capacity was 98.04 mg As(V)/g polymer from 500 mg/L initial As(V) concentration at pH 7.00. - Highlights: • Radiation induced grafting of 4-vinylpyridine onto PE/PP nonwoven fabric in emulsion. • 4-vinylpyridine grafting was characterized by FTIR, SEM and XPS. • As(V) adsorption was studied by QVP-g- NWF. • As(V) adsorption capacity was found to be 98.04 mg As(V)/g polymer.

  5. Effect of fulvic acid on adsorptive removal of Cr(VI) and As(V) from groundwater by iron oxide-based adsorbents

    KAUST Repository

    Uwamariya, V.

    2015-05-15

    Abstract Natural contamination has become a challenging problem in drinking water production due to metal contamination of groundwater throughout the world, and arsenic and chromium are well-known toxic elements. In this study, iron oxide-coated sand (IOCS) and granular ferric hydroxide (GFH) were used to study the effects of fulvic acid (FA) on the adsorptive removal of Cr(VI) and As(V) from synthetic groundwater. IOCS and GFH were characterized by SEM/EDS, and experiments were performed at different pH levels (6, 7, and 8). The surface of IOCS and GFH showed a high content of Fe and O (75 and 60 % of the atomic composition, respectively), suggesting that they can highly effectively adsorb Cr(VI) and As(V). Adsorption tests with the simultaneous presence of As(V) and FA, on the one hand, and Cr(VI) with FA, on the other hand, revealed that the role of FA on chromate and arsenate adsorption was insignificant at almost all pH values investigated with both adsorbents. A small influence as a result of FA was only observed for the removal of As(V) by IOCS at pH 6 with a decrease of 13 and 23 % when 2 and 5 mg/l were added to the synthetic water, respectively. It was also found that organic matter (OM) was leached from the IOCS during batch adsorption experiments. The use of FEEM revealed that humic-like, fulvic-like, and protein-like organic matter fractions are present on the IOCS surface. © 2015 Springer International Publishing Switzerland.

  6. Ethyl malonate amides: a diketo acid offspring fragment for HIV integrase inhibition.

    Science.gov (United States)

    Serafin, Katarzyna; Mazur, Pawel; Bak, Andrzej; Laine, Elodie; Tchertanov, Luba; Mouscadet, Jean-François; Polanski, Jaroslaw

    2011-08-15

    While searching for new HIV integrase inhibitors we discovered that some ethyl malonate amides (EMA) are active against this enzyme. Surprisingly, the main function can only very rarely be found among the reported drug candidates. We synthesised a series of compounds in order to establish and analyse the structure-activity relationship. The similarity to the important classes of HIV integrase inhibitors as well as the synthetic availability of the different targets including this pharmacophore makes EMA compounds an interesting object of investigations. Copyright © 2011 Elsevier Ltd. All rights reserved.

  7. Lack of integrase inhibitors associated resistance mutations among HIV-1C isolates.

    Science.gov (United States)

    Mulu, Andargachew; Maier, Melanie; Liebert, Uwe Gerd

    2015-12-01

    Although biochemical analysis of HIV-1 integrase enzyme suggested the use of integrase inhibitors (INIs) against HIV-1C, different viral subtypes may favor different mutational pathways potentially leading to varying levels of drug resistance. Thus, the aim of this study was to search for the occurrence and natural evolution of integrase polymorphisms and/or resistance mutations in HIV-1C Ethiopian clinical isolates prior to the introduction of INIs. Plasma samples from chronically infected drug naïve patients (N = 45), of whom the PR and RT sequence was determined previously, were used to generate population based sequences of HIV-1 integrase. HIV-1 subtype was determined using the REGA HIV-1 subtyping tool. Resistance mutations were interpreted according to the Stanford HIV drug resistance database ( http://hivdb.stanford.edu ) and the updated International Antiviral Society (IAS)-USA mutation lists. Moreover, rates of polymorphisms in the current isolates were compared with South African and global HIV-1C isolates. All subjects were infected with HIV-1C concordant to the protease (PR) and reverse transcriptase (RT) regions. Neither major resistance-associated IN mutations (T66I/A/K, E92Q/G, T97A, Y143HCR, S147G, Q148H/R/K, and N155H) nor silent mutations known to change the genetic barrier were observed. Moreover, the DDE-catalytic motif (D64G/D116G/E152 K) and signature HHCC zinc-binding motifs at codon 12, 16, 40 and 43 were found to be highly conserved. However, compared to other South African subtype C isolates, the rate of polymorphism was variable at various positions. Although the sample size is small, the findings suggest that this drug class could be effective in Ethiopia and other southern African countries where HIV-1C is predominantly circulating. The data will contribute to define the importance of integrase polymorphism and to improve resistance interpretation algorithms in HIV-1C isolates.

  8. Radiation induced emulsion graft polymerization of 4-vinylpyridine onto PE/PP nonwoven fabric for As(V) adsorption

    Science.gov (United States)

    Akkaş Kavaklı, Pınar; Kavaklı, Cengiz; Seko, Noriaki; Tamada, Masao; Güven, Olgun

    2016-10-01

    A novel nonwoven fabric adsorbent having 4-vinylpyridine functional groups was prepared by using radiation-induced emulsion graft polymerization method and grafting 4-vinylpyridine monomer onto a polyethylene-coated polypropylene nonwoven fabric (NWF) in aqueous emulsion solution. The grafting conditions of the 4-vinylpyridine monomer onto the NWF were optimised and 150% Dg VP-g-NWF was prepared using 30 kGy pre-irradiation dose, 5% VP monomer concentration and 0.5% (w/w) Tween 20 in aqueous emulsion. Grafted 4-vinylpyridine chains on the NWF were then quaternized for the preparation of QVP-g-NWF adsorbent. All fabric structures were characterized by using Fourier-transform infrared spectrometer, x-ray photoelectron spectrometer and scanning electron microscope. QVP-g-NWF adsorbent was used in batch adsorption experiments for As(V) ions by studying the pH, contact time, and initial As(V) ion concentration parameters. Results showed that QVP-g-NWF adsorbent has significant As(V) adsorption and experimental As(V) adsorption capacity was 98.04 mg As(V)/g polymer from 500 mg/L initial As(V) concentration at pH 7.00.

  9. Treatment of As(V) and As(III) by electrocoagulation using Al and Fe electrode.

    Science.gov (United States)

    Kuan, W H; Hu, C Y; Chiang, M C

    2009-01-01

    A batch electrocoagulation (EC) process with bipolar electrode and potentiodynamic polarization tests with monopolar systems were investigated as methods to explore the effects of electrode materials and initial solution pH on the As(V) and As(III) removal. The results displayed that the system with Al electrode has higher reaction rate during the initial period from 0 to 25 minutes than that of Fe electrode for alkaline condition. The pH increased with the EC time because the As(V) and As(III) removal by either co-precipitation or adsorption resulted in that the OH positions in Al-hydroxide or Fe-hydroxide were substituted by As(V) and As(III). The pH in Fe electrode system elevate higher than that in Al electrode because the As(V) removal substitutes more OH position in Fe-hydroxide than that in Al-hydroxide. EC system with Fe electrode can successfully remove the As(III) but system with Al electrode cannot because As(III) can strongly bind to the surface of Fe-hydroxide with forming inner-sphere species but weakly adsorb to the Al-hydroxide surface with forming outer-sphere species. The acidic solution can destroy the deposited hydroxide passive film then allow the metallic ions liberate into the solution, therefore, the acidic initial solution can enhance the As(V) and As(III) removal. The over potential calculation and potentiodynamic polarization tests reveal that the Fe electrode systems possess higher over potential and pitting potential than that of Al electrode system due to the fast hydrolysis of and the occurrence of Fe-hydroxide passive film.

  10. A Mos1 transposase in vivo assay to screen new HIV-1 integrase inhibitors.

    Science.gov (United States)

    Cancian, Mariana; Loreto, Elgion L S

    2018-04-01

    The integrase and transposase enzymes of retrovirus and transposons, respectively, share the catalytic DDE domain. In vitro assays showed that inhibitors of HIV-1 integrase generally inhibit the mariner Mos1 transposase. Using a Drosophila strain in which the mobilisation of the mariner element can be quantified by mosaic eyes, we showed that flies maintained in medium containing 210 µM to 4 mM of raltegravir, or 1 or 2 mM of dolutegravir, which are HIV-1 integrase inhibitor used in AIDS treatment, have 23-33% less somatic mobilisation in mosaic eyes when treated with raltegravir and 28-32% when treated with dolutegravir. The gene expression of the mariner transposase gene, estimated by qPCR, is similar among treated and control flies. The results suggest that in vivo assays using Drosophila can be used as a primary screening of inhibitory drugs for transposase and retroviral integrase. The advantages of this assay are that it is easy, quick, cheap and is an in vivo test, meaning that the tested substance has to have been taken in by cells and has arrived at the target site, which is not the case when in vitro assays are applied.

  11. Sato's Baecklund transformations, additional symmetries and ASvM formula for the discrete KP hierarchy

    International Nuclear Information System (INIS)

    Liu Shaowei; Cheng Yi

    2010-01-01

    Two kinds of symmetries, Sato's Baecklund transformations and additional symmetries, for the discrete KP (dKP) hierarchy are introduced, and the ASvM formula which demonstrates the equivalence of these two kinds of symmetries is obtained. In this process the Fay identity and the difference Fay identity of the dKP hierarchy are introduced and the ASvM formula in the form of tau function is calculated.

  12. Adsorption Characteristics of Different Adsorbents and Iron(III Salt for Removing As(V from Water

    Directory of Open Access Journals (Sweden)

    Josip Ćurko

    2016-01-01

    Full Text Available The aim of this study is to determine the adsorption performance of three types of adsorbents for removal of As(V from water: Bayoxide® E33 (granular iron(III oxide, Titansorb® (granular titanium oxide and a suspension of precipitated iron(III hydroxide. Results of As(V adsorption stoichiometry of two commercial adsorbents and precipitated iron(III hydroxide in tap and demineralized water were fitted to Freundlich and Langmuir adsorption isotherm equations, from which adsorption constants and adsorption capacity were calculated. The separation factor RL for the three adsorbents ranged from 0.04 to 0.61, indicating effective adsorption. Precipitated iron(III hydroxide had the greatest, while Titansorb had the lowest capacity to adsorb As(V. Comparison of adsorption from tap or demineralized water showed that Bayoxide and precipitated iron(III hydroxide had higher adsorption capacity in demineralized water, whereas Titansorb showed a slightly higher capacity in tap water. These results provide mechanistic insights into how commonly used adsorbents remove As(V from water.

  13. Next-generation site-directed transgenesis in the malaria vector mosquito Anopheles gambiae: self-docking strains expressing germline-specific phiC31 integrase.

    Directory of Open Access Journals (Sweden)

    Janet M Meredith

    Full Text Available Diseases transmitted by mosquitoes have a devastating impact on global health and the situation is complicated due to difficulties with both existing control measures and the impact of climate change. Genetically modified mosquitoes that are refractory to disease transmission are seen as having great potential in the delivery of novel control strategies. The Streptomyces phage phiC31 integrase system has been successfully adapted for site-directed transgene integration in a range of insects, thus overcoming many limitations due to size constraints and random integration associated with transposon-mediated transformation. Using this technology, we previously published the first site-directed transformation of Anopheles gambiae, the principal vector of human malaria. Mosquitoes were initially engineered to incorporate the phiC31 docking site at a defined genomic location. A second phase of genetic modification then achieved site-directed integration of an anti-malarial effector gene. In the current publication we report improved efficiency and utility of the phiC31 integrase system following the generation of Anopheles gambiae self-docking strains. Four independent strains, with docking sites at known locations on three different chromosome arms, were engineered to express integrase under control of the regulatory regions of the nanos gene from Anopheles gambiae. The resulting protein accumulates in the posterior oocyte to provide integrase activity at the site of germline development. Two self-docking strains, exhibiting significantly different levels of integrase expression, were assessed for site-directed transgene integration and found to demonstrate greatly improved survival and efficiency of transformation. In the fight against malaria, it is imperative to establish a broad repertoire of both anti-malarial effector genes and tissue-specific promoters to regulate their expression, enabling those offering maximum effect with minimum fitness

  14. Structural and Functional Insights into Foamy Viral Integrase

    Directory of Open Access Journals (Sweden)

    Cha-Gyun Shin

    2013-07-01

    Full Text Available Successful integration of retroviral DNA into the host chromosome is an essential step for viral replication. The process is mediated by virally encoded integrase (IN and orchestrated by 3'-end processing and the strand transfer reaction. In vitro reaction conditions, such as substrate specificity, cofactor usage, and cellular binding partners for such reactions by the three distinct domains of prototype foamy viral integrase (PFV-IN have been described well in several reports. Recent studies on the three‑dimensional structure of the interacting complexes between PFV-IN and DNA, cofactors, binding partners, or inhibitors have explored the mechanistic details of such interactions and shown its utilization as an important target to develop anti-retroviral drugs. The presence of a potent, non-transferable nuclear localization signal in the PFV C-terminal domain extends its use as a model for investigating cellular trafficking of large molecular complexes through the nuclear pore complex and also to identify novel cellular targets for such trafficking. This review focuses on recent advancements in the structural analysis and in vitro functional aspects of PFV-IN.

  15. D77, one benzoic acid derivative, functions as a novel anti-HIV-1 inhibitor targeting the interaction between integrase and cellular LEDGF/p75

    International Nuclear Information System (INIS)

    Du Li; Zhao Yaxue; Chen, Jing; Yang Liumeng; Zheng Yongtang; Tang Yun; Shen Xu; Jiang Hualiang

    2008-01-01

    Integration of viral-DNA into host chromosome mediated by the viral protein HIV-1 integrase (IN) is an essential step in the HIV-1 life cycle. In this process, Lens epithelium-derived growth factor (LEDGF/p75) is discovered to function as a cellular co-factor for integration. Since LEDGF/p75 plays an important role in HIV integration, disruption of the LEDGF/p75 interaction with IN has provided a special interest for anti-HIV agent discovery. In this work, we reported that a benzoic acid derivative, 4-[(5-bromo-4-{[2,4-dioxo-3-(2-oxo-2-phenylethyl) -1,3-thiazolidin-5-ylidene]methyl}-2-ethoxyphenoxy)methyl]benzoic acid (D77) could potently inhibit the IN-LEDGF/p75 interaction and affect the HIV-1 IN nuclear distribution thus exhibiting antiretroviral activity. Molecular docking with site-directed mutagenesis analysis and surface plasmon resonance (SPR) binding assays has clarified possible binding mode of D77 against HIV-1 integrase. As the firstly discovered small molecular compound targeting HIV-1 integrase interaction with LEDGF/p75, D77 might supply useful structural information for further anti-HIV agent discovery

  16. The mechanisms of detoxification of As(III), dimethylarsinic acid (DMA) and As(V) in the microalga Chlorella vulgaris.

    Science.gov (United States)

    Pantoja Munoz, L; Purchase, D; Jones, H; Raab, A; Urgast, D; Feldmann, J; Garelick, H

    2016-06-01

    The response of Chlorella vulgaris when challenged by As(III), As(V) and dimethylarsinic acid (DMA) was assessed through experiments on adsorption, efflux and speciation of arsenic (reduction, oxidation, methylation and chelation with glutathione/phytochelatin [GSH/PC]). Our study indicates that at high concentrations of phosphate (1.62mM of HPO4(2-)), upon exposure to As(V), cells are able to shift towards methylation of As(V) rather than PC formation. Treatment with As(V) caused a moderate decrease in intracellular pH and a strong increase in the concentration of free thiols (GSH). Passive surface adsorption was found to be negligible for living cells exposed to DMA and As(V). However, adsorption of As(III) was observed to be an active process in C. vulgaris, because it did not show saturation at any of the exposure periods. Chelation of As(III) with GS/PC and to a lesser extent hGS/hPC is a major detoxification mechanism employed by C. vulgaris cells when exposed to As(III). The increase of bound As-GS/PC complexes was found to be strongly related to an increase in concentration of As(III) in media. C. vulgaris cells did not produce any As-GS/PC complex when exposed to As(V). This may indicate that a reduction step is needed for As(V) complexation with GSH/PC. C. vulgaris cells formed DMAS(V)-GS upon exposure to DMA independent of the exposure period. As(III) triggers the formation of arsenic complexes with PC and homophytochelatins (hPC) and their compartmentalisation to vacuoles. A conceptual model was devised to explain the mechanisms involving ABCC1/2 transport. The potential of C. vulgaris to bio-remediate arsenic from water appeared to be highly selective and effective without the potential hazard of reducing As(V) to As(III), which is more toxic to humans. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. Effect of calcium on adsorptive removal of As(III) and As(V) by iron oxide-based adsorbents

    KAUST Repository

    Uwamariya, V.; Petruševski, Branislav; Lens, Piet Nl L; Amy, Gary L.

    2014-01-01

    for filter columns with IOCS and GFH, respectively. The adsorption of As(III) and As(V) onto GFH follows a second-order reaction, with and without addition of calcium. The adsorption of As(III) and As(V) onto IOCS follows a first-order reaction without

  18. In vivo and in vitro characterization of site-specific recombination of a novel serine integrase from the temperate phage EFC-1

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Bohyun; Kim, Inki; Nam, Ja-Ae [Asan Institute for Life Sciences, Asan Medical Center, College of Medicine, University of Ulsan, 86 Asanbyeoungwon-gil, Songpa-gu, Seoul 138-736 (Korea, Republic of); Chang, Hyo-Ihl [College of Life Sciences & Biotechnology, Korea University, 5-1 Anam-dong, Seongbuk-gu, Seoul 136-701 (Korea, Republic of); Ha, Chang Hoon, E-mail: chhoonha@amc.seoul.kr [Asan Institute for Life Sciences, Asan Medical Center, College of Medicine, University of Ulsan, 86 Asanbyeoungwon-gil, Songpa-gu, Seoul 138-736 (Korea, Republic of)

    2016-04-22

    EFC-1 integrase is a site-specific recombinase that belongs to the large family of serine recombinase. In previously study, we isolated the temperate phage EFC-1, and characterized its genomic sequence. Within its genome, Orf28 was predicted encode a 464 amino acid of a putative integrase gene. In this study, EFC-1 integrase was characterized in vitro and in vivo. In vitro assay was performed using purified His-tag fusion integrase. Also, to identify which serine is involved in the catalytic domain, we used site-directed mutagenesis and analyzed by a recombination assay in vitro. In vivo assay involved PCR and confocal microscopy in HEK293 cells, and determined the minimal lengths of attP and attB sites. According to our results, the EFC-1 integrase-mediated recombination was site-specific and unidirectional system in vitro and in vivo. Serine 21 of EFC-1 integrase plays a major role in the catalytic domain, and minimal sizes of attB and attP was defined 48 and 54 bp. Our finding may help develop a useful tool for gene therapy and gene delivery system. - Highlights: • EFC-1 integrase-mediated recombination was site-specific and unidirectional system. • Serine 21 of EFC-1 integrase plays a major role in the catalytic domain. • The functional minimal sizes of attB and attP was defined 48 and 54 bp.

  19. In vivo and in vitro characterization of site-specific recombination of a novel serine integrase from the temperate phage EFC-1

    International Nuclear Information System (INIS)

    Yoon, Bohyun; Kim, Inki; Nam, Ja-Ae; Chang, Hyo-Ihl; Ha, Chang Hoon

    2016-01-01

    EFC-1 integrase is a site-specific recombinase that belongs to the large family of serine recombinase. In previously study, we isolated the temperate phage EFC-1, and characterized its genomic sequence. Within its genome, Orf28 was predicted encode a 464 amino acid of a putative integrase gene. In this study, EFC-1 integrase was characterized in vitro and in vivo. In vitro assay was performed using purified His-tag fusion integrase. Also, to identify which serine is involved in the catalytic domain, we used site-directed mutagenesis and analyzed by a recombination assay in vitro. In vivo assay involved PCR and confocal microscopy in HEK293 cells, and determined the minimal lengths of attP and attB sites. According to our results, the EFC-1 integrase-mediated recombination was site-specific and unidirectional system in vitro and in vivo. Serine 21 of EFC-1 integrase plays a major role in the catalytic domain, and minimal sizes of attB and attP was defined 48 and 54 bp. Our finding may help develop a useful tool for gene therapy and gene delivery system. - Highlights: • EFC-1 integrase-mediated recombination was site-specific and unidirectional system. • Serine 21 of EFC-1 integrase plays a major role in the catalytic domain. • The functional minimal sizes of attB and attP was defined 48 and 54 bp.

  20. Effect of calcium on adsorptive removal of As(III) and As(V) by iron oxide-based adsorbents

    KAUST Repository

    Uwamariya, V.

    2014-06-25

    The effects of calcium on the equilibrium adsorption capacity of As(III) and As(V) onto iron oxide-coated sand (IOCS) and granular ferric hydroxide (GFH) were investigated through batch experiments, rapid small-scale column tests (RSSCT) and kinetics modelling. Batch experiments showed that at calcium concentrations≤20 mg/L, high As(III) and As(V) removal efficiencies by IOCS and GFH are achieved at pH 6. An increase of the calcium concentration to 40 and 80 mg/L reversed this trend, giving higher removal efficiencies at higher pH (8). The adsorption capacities of IOCS and GFH at an equilibrium arsenic concentration of 10 g/L were found to be between 2.0 and 3.1 mg/g for synthetic water without calcium and between 2.8 and 5.3 mg/g when 80 mg/L of calcium was present at the studied pH values. After 10 hours of filter run in RSSCT, approximately 1000 empty bed volumes, the ratios of C/Co for As(V) were 26% and 18% for calcium-free model water; and only 1% and 0.2% after addition of 80 mg/L of Ca for filter columns with IOCS and GFH, respectively. The adsorption of As(III) and As(V) onto GFH follows a second-order reaction, with and without addition of calcium. The adsorption of As(III) and As(V) onto IOCS follows a first-order reaction without calcium addition, and moves to the second-reaction-order kinetics when calcium is added. Based on the intraparticle diffusion model, the main controlling mechanism for As(III) adsorption is intraparticle diffusion, while surface diffusion contributes greatly to the adsorption of As(V).

  1. Nanobody-based chimeric receptor gene integration in Jurkat cells mediated by PhiC31 integrase

    International Nuclear Information System (INIS)

    Iri-Sofla, Farnoush Jafari; Rahbarizadeh, Fatemeh; Ahmadvand, Davoud; Rasaee, Mohammad J.

    2011-01-01

    The crucial role of T lymphocytes in anti-tumor immunity has led to the development of novel strategies that can target and activate T cells against tumor cells. Recombinant DNA technology has been used to generate non-MHC-restricted chimeric antigen receptors (CARs). Here, we constructed a panel of recombinant CAR that harbors the anti-MUC1 nanobody and the signaling and co-signaling moieties (CD3ζ/CD28) with different spacer regions derived from human IgG3 with one or two repeats of the hinge sequence or the hinge region of FcγRII. The PhiC31 integrase system was employed to investigate if the recombination efficiency could be recruited for high and stable expression of T cell chimeric receptor genes. The effect of nuclear localization signal (NLS) and two different promoters (CMV and CAG) on efficacy of PhiC31 integrase in human T cell lines was evaluated. The presence of integrase in combination with NLS, mediated up to 7.6 and 8.5 fold increases in CAR expression in ZCHN-attB and ZCHHN-attB cassette integrated T cells, respectively. Our results showed that highly efficient and stable transduction of the Jurkat cell line by PhiC31 integrase is a feasible modality for generating anti-cancer chimeric T cells for use in cancer immunotherapy.

  2. Nanobody-based chimeric receptor gene integration in Jurkat cells mediated by PhiC31 integrase

    Energy Technology Data Exchange (ETDEWEB)

    Iri-Sofla, Farnoush Jafari [Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran (Iran, Islamic Republic of); Rahbarizadeh, Fatemeh, E-mail: rahbarif@modares.ac.ir [Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran (Iran, Islamic Republic of); Ahmadvand, Davoud [Center of Pharmaceutical Nanotechnology and Nanotoxicology, Department of Pharmaceutics and Analytical Chemistry, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen O (Denmark); Rasaee, Mohammad J. [Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran (Iran, Islamic Republic of)

    2011-11-01

    The crucial role of T lymphocytes in anti-tumor immunity has led to the development of novel strategies that can target and activate T cells against tumor cells. Recombinant DNA technology has been used to generate non-MHC-restricted chimeric antigen receptors (CARs). Here, we constructed a panel of recombinant CAR that harbors the anti-MUC1 nanobody and the signaling and co-signaling moieties (CD3{zeta}/CD28) with different spacer regions derived from human IgG3 with one or two repeats of the hinge sequence or the hinge region of Fc{gamma}RII. The PhiC31 integrase system was employed to investigate if the recombination efficiency could be recruited for high and stable expression of T cell chimeric receptor genes. The effect of nuclear localization signal (NLS) and two different promoters (CMV and CAG) on efficacy of PhiC31 integrase in human T cell lines was evaluated. The presence of integrase in combination with NLS, mediated up to 7.6 and 8.5 fold increases in CAR expression in ZCHN-attB and ZCHHN-attB cassette integrated T cells, respectively. Our results showed that highly efficient and stable transduction of the Jurkat cell line by PhiC31 integrase is a feasible modality for generating anti-cancer chimeric T cells for use in cancer immunotherapy.

  3. [Isolation, idetification and anti-HIV-1 integrase activity of culturable endophytic fungi from Tibetan medicinal plant Phlomis younghusbandii Mukerjee].

    Science.gov (United States)

    Zhang, Da-Wei; Zhao, Ming-Ming; Chen, Juan; Li, Chao; Guo, Shun-Xing

    2013-05-01

    A total of 52 endophytic fungi were isolated from roots and stems of Tibetan medicinal plant Phlomis younghusbandii Mukerjee. These fungal isolates were molecularly identified based on ITS sequnces and 28S sequences distributed to 12 genera, including Phoma, Chaetosphaeronema, Fusarium and Leptosphaeria, etc. Among them, the dominant genus was Phoma. Extracts of all strains were evaluated for anti-HIV-1 integrase activity by using soluable integrase expressed in E. coli BL21 (DE3). The results showed that seven samples from five fungal endophytes PHY-24, PHY-38, PHY-40, PHY-51, PHY-53, which belonged to genus Chaetosphaeronema, inhibited strand transfer reaction catalyzed by HIV-1 integrase with IC50 values, of 6.60, 5.20, 2.86, 7.86, 4.47, 4.56 and 3.23 microg x mL(-1) respectively. In conclusion, the endophytic fungi of Phlomis younghusbandii Mukerjee are valuable for further screening anti-HIV-1 integrase agents.

  4. Impact of hydrodynamic injection and phiC31 integrase on tumor latency in a mouse model of MYC-induced hepatocellular carcinoma.

    Directory of Open Access Journals (Sweden)

    Lauren E Woodard

    2010-06-01

    Full Text Available Hydrodynamic injection is an effective method for DNA delivery in mouse liver and is being translated to larger animals for possible clinical use. Similarly, phiC31 integrase has proven effective in mediating long-term gene therapy in mice when delivered by hydrodynamic injection and is being considered for clinical gene therapy applications. However, chromosomal aberrations have been associated with phiC31 integrase expression in tissue culture, leading to questions about safety.To study whether hydrodynamic delivery alone, or in conjunction with delivery of phiC31 integrase for long-term transgene expression, could facilitate tumor formation, we used a transgenic mouse model in which sustained induction of the human C-MYC oncogene in the liver was followed by hydrodynamic injection. Without injection, mice had a median tumor latency of 154 days. With hydrodynamic injection of saline alone, the median tumor latency was significantly reduced, to 105 days. The median tumor latency was similar, 106 days, when a luciferase donor plasmid and backbone plasmid without integrase were administered. In contrast, when active or inactive phiC31 integrase and donor plasmid were supplied to the mouse liver, the median tumor latency was 153 days, similar to mice receiving no injection.Our data suggest that phiC31 integrase does not facilitate tumor formation in this C-MYC transgenic mouse model. However, in groups lacking phiC31 integrase, hydrodynamic injection appeared to contribute to C-MYC-induced hepatocellular carcinoma in adult mice. Although it remains to be seen to what extent these findings may be extrapolated to catheter-mediated hydrodynamic delivery in larger species, they suggest that caution should be used during translation of hydrodynamic injection to clinical applications.

  5. Fragment Based Strategies for Discovery of Novel HIV-1 Reverse Transcriptase and Integrase Inhibitors.

    Science.gov (United States)

    Latham, Catherine F; La, Jennifer; Tinetti, Ricky N; Chalmers, David K; Tachedjian, Gilda

    2016-01-01

    Human immunodeficiency virus (HIV) remains a global health problem. While combined antiretroviral therapy has been successful in controlling the virus in patients, HIV can develop resistance to drugs used for treatment, rendering available drugs less effective and limiting treatment options. Initiatives to find novel drugs for HIV treatment are ongoing, although traditional drug design approaches often focus on known binding sites for inhibition of established drug targets like reverse transcriptase and integrase. These approaches tend towards generating more inhibitors in the same drug classes already used in the clinic. Lack of diversity in antiretroviral drug classes can result in limited treatment options, as cross-resistance can emerge to a whole drug class in patients treated with only one drug from that class. A fresh approach in the search for new HIV-1 drugs is fragment-based drug discovery (FBDD), a validated strategy for drug discovery based on using smaller libraries of low molecular weight molecules (FBDD is aimed at not only finding novel drug scaffolds, but also probing the target protein to find new, often allosteric, inhibitory binding sites. Several fragment-based strategies have been successful in identifying novel inhibitory sites or scaffolds for two proven drug targets for HIV-1, reverse transcriptase and integrase. While any FBDD-generated HIV-1 drugs have yet to enter the clinic, recent FBDD initiatives against these two well-characterised HIV-1 targets have reinvigorated antiretroviral drug discovery and the search for novel classes of HIV-1 drugs.

  6. Synthesis, characterization and adsorptive properties of carbon with iron nanoparticles and iron carbide for the removal of As(V) from water.

    Science.gov (United States)

    Gutierrez-Muñiz, O E; García-Rosales, G; Ordoñez-Regil, E; Olguin, M T; Cabral-Prieto, A

    2013-01-15

    This manuscript presents the synthesis of carbon modified with iron nanoparticles (CFe) and iron carbide (CarFe) from the pyrolyzed crown leaves of pineapple (Ananas comosus) treated with iron salts. The materials that were obtained were used for the removal of As(V) from aqueous media. The carbonaceous materials were characterized by Scanning Electron Microscopy (SEM), Transmission electron microscopy (TEM), X-ray diffraction (XRD), X-Ray Photoelectron Spectroscopy (XPS) and Mossbauer Spectroscopy. The specific area (BET), number site density and point of zero charge (pH(pzc)) were also determined. The kinetic parameters were obtained by fitting the experimental data to the pseudo-first-order and pseudo-second-order models. Different isotherm models were applied to describe the As(V) adsorption behavior. The kinetics of As(V) sorption by CFe and CarFe was well defined for the pseudo-second-order model (R(2) = 0.9994 and 0.999, respectively). The maximum As(V) uptake was 1.8 mg g(-1) for CFe and 1.4 mg g(-1) for CarFe. The results obtained indicated that both materials are equally useful for As(V) sorption. The As(V) experimental isotherm data were described by the Freundlich model for CFe and CarFe. Copyright © 2012 Elsevier Ltd. All rights reserved.

  7. Separación electrodialítica de Cu(II y As(V en electrolitos ácidos

    Directory of Open Access Journals (Sweden)

    Ibáñez, J. P.

    2007-02-01

    Full Text Available The separation of copper and arsenic from acidic electrolytes by electrodialysis was investigated at room temperature. The effect of current density and pH was studied in a batch cell during 3 hours. The kinetic parameters showed that Cu(II transport rate was 0.75 mol/m2/h and the As(V transport rate was 0.002 mol/m2/h. An efficient separation between Cu(II and As(V was achieved; generating a concentrated solution of copper with no arsenic, which was obtained independently of the electrolyte acidity and current density used. The effect of the arsenic speciation with pH is discussed as well.

    Se investigó el uso de la electrodiálisis para separar cobre y arsénico desde soluciones ácidas a temperatura ambiente. Se estudió el efecto de la densidad de corriente y grado de
    acidez del electrolito en la separación a través de experimentos en celda batch de 5 compartimientos durante 3 h. Los parámetros cinéticos indican que la velocidad de transporte de Cu(II fue de 0,75 mol/h/m2 y de As(V fue de 0,002 mol/h/m2 a una densidad de corriente de 225 A/m2. Se logró obtener una eficiente separación de Cu(II y As(V, con la generación de una solución concentrada de cobre sin presencia de arsénico, lo cual fue independiente del grado de acidez de la operación y de la densidad de corriente. El efecto de la distribución de las especies iónicas de As(V con el pH también se discute.

  8. Postexposure protection of macaques from vaginal SHIV infection by topical integrase inhibitors.

    Science.gov (United States)

    Dobard, Charles; Sharma, Sunita; Parikh, Urvi M; West, Rolieria; Taylor, Andrew; Martin, Amy; Pau, Chou-Pong; Hanson, Debra L; Lipscomb, Jonathan; Smith, James; Novembre, Francis; Hazuda, Daria; Garcia-Lerma, J Gerardo; Heneine, Walid

    2014-03-12

    Coitally delivered microbicide gels containing antiretroviral drugs are important for HIV prevention. However, to date, microbicides have contained entry or reverse transcriptase inhibitors that block early steps in virus infection and thus need to be given as a preexposure dose that interferes with sexual practices and may limit compliance. Integrase inhibitors block late steps after virus infection and therefore are more suitable for post-coital dosing. We first determined the kinetics of strand transfer in vitro and confirmed that integration begins about 6 hours after infection. We then used a repeat-challenge macaque model to assess efficacy of vaginal gels containing integrase strand transfer inhibitors when applied before or after simian/human immunodeficiency virus (SHIV) challenge. We showed that gel containing the strand transfer inhibitor L-870812 protected two of three macaques when applied 30 min before SHIV challenge. We next evaluated the efficacy of 1% raltegravir gel and demonstrated its ability to protect macaques when applied 3 hours after SHIV exposure (five of six protected; P infections showed no evidence of drug resistance in plasma or vaginal secretions despite continued gel dosing after infection. We documented rapid vaginal absorption reflecting a short pharmacological lag time and noted that vaginal, but not plasma, virus load was substantially reduced in the breakthrough infection after raltegravir gel treatment. We provide a proof of concept that topically applied integrase inhibitors protect against vaginal SHIV infection when administered shortly before or 3 hours after virus exposure.

  9. Adaptive servo-ventilation to treat central sleep apnea in heart failure with reduced ejection fraction: the Bad Oeynhausen prospective ASV registry.

    Science.gov (United States)

    Oldenburg, Olaf; Wellmann, Birgit; Bitter, Thomas; Fox, Henrik; Buchholz, Anika; Freiwald, Eric; Horstkotte, Dieter; Wegscheider, Karl

    2018-04-13

    Central sleep apnea (CSA) is highly prevalent in heart failure patients with reduced left ventricular ejection fraction (HF-REF). The Bad Oeynhausen Adaptive Servo-ventilation (ASV) registry (NCT01657188) was designed to investigate whether treatment of CSA with ASV improved survival in HF-REF patients; the effects of ASV on symptoms and cardiopulmonary performance were also investigated. From January 2004 to October 2013, the registry prospectively enrolled HF-REF patients [NYHA class ≥ II, left ventricular ejection fraction (LVEF) ≤ 45%] with moderate to severe predominant CSA [apnea-hypopnea index (AHI) ≥ 15/h]. ASV-treated patients were followed up at 3, 6, 12 and 24 months, including natriuretic peptide concentrations, blood gas analyses, echocardiography, 6-min walk distance (6MWD), and cardiopulmonary exercise (CPX) testing. 550 patients were included [age 67.7 ± 10 years, 90% male, 52% in NYHA class ≥ III, LVEF 29.9 ± 8%, AHI 35.4 ± 13.6/h, and time with nocturnal oxygen saturation concentration, and nocturnal hypoxemia were significant predictors of mortality. Patient reported NYHA functional class improved in the ASV group, but LVEF, CPX, 6MWD, natriuretic peptides and blood gases remained unchanged. Long-term ASV treatment of predominant CSA in HF-REF patients included in our registry had no statistically significant effect on survival. ASV improved HF symptoms, but had no significant effects on exercise capacity, LVEF, natriuretic peptide concentrations or blood gases during follow-up as compared to control patients.

  10. Sketching the historical development of pyrimidones as the inhibitors of the HIV integrase

    Czech Academy of Sciences Publication Activity Database

    Patel, Rahul V.; Keum, Y.S.; Park, S.W.

    2015-01-01

    Roč. 97, JUN 5 (2015), s. 649-663 ISSN 0223-5234 Institutional support: RVO:61389030 Keywords : Pyrimidones * Anti-HIV * Integrase inhibitors Subject RIV: CE - Biochemistry Impact factor: 3.902, year: 2015

  11. Comparison Between Several Integrase-defective Lentiviral Vectors Reveals Increased Integration of an HIV Vector Bearing a D167H Mutant

    Directory of Open Access Journals (Sweden)

    Muhammad Qamar Saeed

    2014-01-01

    Full Text Available HIV-1 derived vectors are among the most efficient for gene transduction in mammalian tissues. As the parent virus, they carry out vector genome insertion into the host cell chromatin. Consequently, their preferential integration in transcribed genes raises several conceptual and safety issues. To address part of these questions, HIV-derived vectors have been engineered to be nonintegrating. This was mainly achieved by mutating HIV-1 integrase at functional hotspots of the enzyme enabling the development of streamlined nuclear DNA circles functional for transgene expression. Few integrase mutant vectors have been successfully tested so far for gene transfer. They are cleared with time in mitotic cells, but stable within nondividing retina cells or neurons. Here, we compared six HIV vectors carrying different integrases, either wild type or with different mutations (D64V, D167H, Q168A, K186Q+Q214L+Q216L, and RRK262-264AAH shown to modify integrase enzymatic activity, oligomerization, or interaction with key cellular cofactor of HIV DNA integration as LEDGF/p75 or TNPO3. We show that these mutations differently affect the transduction efficiency as well as rates and patterns of integration of HIV-derived vectors suggesting their different processing in the nucleus. Surprisingly and most interestingly, we report that an integrase carrying the D167H substitution improves vector transduction efficiency and integration in both HEK-293T and primary CD34+ cells.

  12. Development, characterization and evaluation of iron-coated honeycomb briquette cinders for the removal of As(V from aqueous solutions

    Directory of Open Access Journals (Sweden)

    Tiantian Sheng

    2014-01-01

    Full Text Available The adsorptive removal of As(V from aqueous solutions using iron-coated honeycomb briquette cinder (Fe-HBC is presented. Low cost mechanical granulation process was integrated with surface amendment technology to prepare iron-oxide modified granular adsorbent for clean water production. Detailed characterizations were performed using FTIR, XRD, EDS and SEM techniques. Operating parameters including initial As(V concentration, pH, contact time, adsorbent dose, iron leaching and the effects of competing ions on As(V removal were evaluated. Results demonstrated that high amount of arsenate (961.5 μg g−1 was adsorbed at pH 7.5 in 14 h contact time. Langmuir, Freundlich and Temkin isotherm models were used to analyze the adsorption data, whereas Langmuir model was found to best represent the data with a correlation co-efficient (R2 = 0.999. Thus, As(V sorption on Fe-HBC surface suggested monolayer adsorption and indicated surface homogeneity. Moreover, the dimensionless parameter (RL value calculated to be about 0.118 that reiterated the process is favorable and spontaneous. The influences of competing ions on As(V removal decreased in the following order:PO43−>HCO3−>F−>Cl−. The profound inhibition effects ofPO43− revealed a high affinity toward iron(oxy hydroxide. Life-cycle assessment confirmed that spent HBC is non-hazardous and can be used as a promising sorbent for arsenic removal.

  13. Preconcentration determination of arsenic species by sorption of As(V) on Amberlite IRA-410 coupled with fluorescence quenching of L-cysteine capped CdS nanoparticles.

    Science.gov (United States)

    Hosseini, Mohammad Saeid; Nazemi, Sahar

    2013-10-07

    A simple and accurate method for arsenic speciation analysis in natural and drinking water samples is described in which preconcentration of arsenic as As(V) was coupled with spectrofluorometric determination. The extracted As(V) species with a column containing Amberlite IRA-410 were subjected to L-cysteine capped CdS quantum dots (QDs) and the fluorescence quenching of the QDs due to reduction of As(V) by L-cysteine was considered as a signal relevant to As(V) concentration. The As(III) species were also determined after oxidation of As(III) ions to As(V) with H2O2 and measurement of the total arsenic content. In treatment with 400 mL portions of water samples containing 30 μg L(-1) As(V), the relative standard deviation was 2.8%. The detection limit of arsenic was also found to be 0.75 μg L(-1) (1 × 10(-8) M). The reliability of proposed method was confirmed using certified reference materials. The trace amounts of arsenic species were then determined in different water samples, satisfactorily.

  14. Molecular features related to HIV integrase inhibition obtained from structure- and ligand-based approaches.

    Directory of Open Access Journals (Sweden)

    Luciana L de Carvalho

    Full Text Available Among several biological targets to treat AIDS, HIV integrase is a promising enzyme that can be employed to develop new anti-HIV agents. The aim of this work is to propose a mechanistic interpretation of HIV-1 integrase inhibition and to rationalize the molecular features related to the binding affinity of studied ligands. A set of 79 HIV-1 integrase inhibitors and its relationship with biological activity are investigated employing 2D and 3D QSAR models, docking analysis and DFT studies. Analyses of docking poses and frontier molecular orbitals revealed important features on the main ligand-receptor interactions. 2D and 3D models presenting good internal consistency, predictive power and stability were obtained in all cases. Significant correlation coefficients (r(2 = 0.908 and q(2= 0.643 for 2D model; r(2= 0.904 and q(2= 0.719 for 3D model were obtained, indicating the potential of these models for untested compounds. The generated holograms and contribution maps revealed important molecular requirements to HIV-1 IN inhibition and several evidences for molecular modifications. The final models along with information resulting from molecular orbitals, 2D contribution and 3D contour maps should be useful in the design of new inhibitors with increased potency and selectivity within the chemical diversity of the data.

  15. Microwave-assisted rapid synthesis of Fe{sub 2}O{sub 3}/ACF hybrid for high efficient As(V) removal

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Huiyun; Lv, Kangle; Du, Ying; Ye, Hengpeng; Du, Dongyun, E-mail: dydu666@mail.scuec.edu.cn

    2016-07-25

    In this paper, an efficient adsorbent, iron-modified activated carbon fiber (Fe{sub 2}O{sub 3}/ACF), was rapidly fabricated by microwave-assisted heating treatment strategy, which is used to remove As(V) from simulated wastewater. The adsorbent was characterized by scanning electron microscopy (SEM), TEM, N{sub 2} sorption, X-ray diffraction (XRD), and X-ray photoelectron spectroscopy (XPS). The characterization results showed that rod-like Fe{sub 2}O{sub 3} particles in sizes of about 20 nm × 50 nm were homogeneously anchored on the surface of ACF. The goal of high As(V) removal efficiency was achieved with maximum adsorption capacity of 20.33 mg g{sup −1}. The effects of temperature on thermodynamics and kinetics of As(V) adsorption were systematically studied. It was found that the adsorption of As(V) on the surface of Fe{sub 2}O{sub 3}/ACF is an endothermic process with a standard enthalpy change (ΔH{sup 0}) of 24.79 kJ mol{sup −1}. Batch experimental result showed that almost all of the As(V) with initial concentration of 3.0 mg L{sup −1} can be removed in the presence of Fe{sub 2}O{sub 3}/ACF, where the residual As(V) in filtrate was less than 0.01 mg L{sup −1}, below the tolerance level of drinking water suggested by World Health Organization (WHO). The presence of salt such as NaCl, Na{sub 2}SO{sub 4}, and MgSO{sub 4} showed little effects on the adsorption of As(V), indicating the promising application of Fe{sub 2}O{sub 3}/ACF in industrial wastewater. - Highlights: • Fe{sub 2}O{sub 3}/ACF hybrid was rapidly fabricated using a microwave-assisted heating strategy. • Fe{sub 2}O{sub 3} nanorods in sizes of 20 × 50 nm were homogeneously anchored on the surface of ACF. • The maximum adsorption capacity of 20.33 mg g{sup −1} As (V) on Fe{sub 2}O{sub 3}/ACF was achieved. • The adsorption of As (V) is an endothermic process (ΔH{sup 0} = 24.79 kJ mol{sup −1}). • The presence of salt shows little effect on the adsorption of As (V).

  16. Metaforu lietojums ziņu rakstos par 2016. gada ASV prezidenta vēlēšanām

    OpenAIRE

    Safronovs, Imants

    2017-01-01

    Bakalaura darbs ir veltīts metaforu lietojuma izmeklēšanai divu ASV laikrakstu (The Wall Street Journal un The New York Times) interneta vietnēs. Pētījums analizē konceptuālās metaforas lietojumu ziņu rakstos par 2016. ASV prezidenta vēlēšanām. Pētījuma mērķis ir izmeklēt konceptuālo metaforu nozīmi ASV prezidenta vēlēšanu konceptualizācijā. Pielietotā metode ir konceptuālo metaforu analīze. Apkopotie dati ļauj secināt, ka analizētajos rakstos koncetuālajām metaforām ir būtiska nozīme vēstīju...

  17. Removal and co-transport of Zn, As(V), and Cd during leachate seepage through downgradient mine soils: A batch sorption and column study

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Juhee [Division of Environmental Science and Ecological Engineering, Korea University, Seoul (Korea, Republic of); Nam, Seung Mo [Korea Testing and Research Institute, Gyeonggi-do (Korea, Republic of); Hyun, Seunghun, E-mail: soilhyun@korea.ac.kr [Division of Environmental Science and Ecological Engineering, Korea University, Seoul (Korea, Republic of)

    2016-05-01

    The removal of Zn, As(V), and Cd during the leachate seepage process was measured in single, binary, and ternary solute systems by batch sorption and 1-D column flow experiments, followed by a sequential extraction procedure (SEP). In single-solute systems, sorption (K{sub d}{sup ⁎}) occurred in the order of As(V) > Zn ≫ Cd, and this sequence did not change in the presence of other solutes. In multi-solute systems, the sorption of Zn (~ 20%) and Cd (~ 27%) was enhanced by As(V), while Zn and Cd suppressed the sorption of each other. In all cases, As(V) sorption was not affected by the cations, indicating that As(V) is prioritized by sorption sites to a much greater degree than Zn and Cd. Element retention by column soils was strongly correlated (r{sup 2} = 0.77) with K{sub d}{sup ⁎}. Across column segments, mass retention was in the order of inlet (36–54%) > middle (26–35%) > outlet (20–31%), except for Cd in the Zn–Cd binary system. The result of SEP revealed that most of the retained Cd (98–99%) and Zn (56–71%) was in the labile fraction (e.g., the sum of F1 and F2) while only 9–12% of As(V) was labile and most (> 55%) was specifically adsorbed to Fe/Al oxides. Plots of the labile fraction (f{sub labile}) and the fast sorption fraction (f{sub fast}) suggested that the kinetics of specific As(V) sorption occur rapidly (f{sub fast} > f{sub labile}), whereas labile Zn and Cd sorption occurs slowly (f{sub labile} > f{sub fast}), indicating the occurrence of kinetically limited labile sorption sites, probably due to Zn–Cd competition. In conclusion, the element leaching potential of mine leachate can be greatly attenuated during downgradient soil seepage. However, when assessing the soil attenuation process, the impact of sorption competitors and the lability of adsorbed elements should first be considered. - Highlights: • During soil seepage, element leaching potential is reduced as As(V) > Zn > Cd. • Element removal during leachate seepage

  18. Cancer-specific binary expression system activated in mice by bacteriophage HK022 Integrase

    DEFF Research Database (Denmark)

    Elias, Amer; Spector, Itay; Sogolovsky-Bard, Ilana

    2016-01-01

    Binary systems based on site-specific recombination have been used for tumor specific transcription targeting of suicide genes in animal models. In these binary systems a site specific recombinase or integrase that is expressed from a tumor specific promoter drives tumor specific expression of a ...

  19. Raltegravir, elvitegravir, and metoogravir: the birth of "me-too" HIV-1 integrase inhibitors

    Directory of Open Access Journals (Sweden)

    Neamati Nouri

    2009-03-01

    Full Text Available Abstract Merck's MK-0518, known as raltegravir, has recently become the first FDA-approved HIV-1 integrase (IN inhibitor and has since risen to blockbuster drug status. Much research has in turn been conducted over the last few years aimed at recreating but optimizing the compound's interactions with the protein. Resulting me-too drugs have shown favorable pharmacokinetic properties and appear drug-like but, as expected, most have a highly similar interaction with IN to that of raltegravir. We propose that, based upon conclusions drawn from our docking studies illustrated herein, most of these me-too MK-0518 analogues may experience a low success rate against raltegravir-resistant HIV strains. As HIV has a very high mutational competence, the development of drugs with new mechanisms of inhibitory action and/or new active substituents may be a more successful route to take in the development of second- and third-generation IN inhibitors.

  20. Plasmid integration in a wide range of bacteria mediated by the integrase of Lactobacillus delbrueckii bacteriophage mv4.

    Science.gov (United States)

    Auvray, F; Coddeville, M; Ritzenthaler, P; Dupont, L

    1997-01-01

    Bacteriophage mv4 is a temperate phage infecting Lactobacillus delbrueckii subsp. bulgaricus. During lysogenization, the phage integrates its genome into the host chromosome at the 3' end of a tRNA(Ser) gene through a site-specific recombination process (L. Dupont et al., J. Bacteriol., 177:586-595, 1995). A nonreplicative vector (pMC1) based on the mv4 integrative elements (attP site and integrase-coding int gene) is able to integrate into the chromosome of a wide range of bacterial hosts, including Lactobacillus plantarum, Lactobacillus casei (two strains), Lactococcus lactis subsp. cremoris, Enterococcus faecalis, and Streptococcus pneumoniae. Integrative recombination of pMC1 into the chromosomes of all of these species is dependent on the int gene product and occurs specifically at the pMC1 attP site. The isolation and sequencing of pMC1 integration sites from these bacteria showed that in lactobacilli, pMC1 integrated into the conserved tRNA(Ser) gene. In the other bacterial species where this tRNA gene is less or not conserved; secondary integration sites either in potential protein-coding regions or in intergenic DNA were used. A consensus sequence was deduced from the analysis of the different integration sites. The comparison of these sequences demonstrated the flexibility of the integrase for the bacterial integration site and suggested the importance of the trinucleotide CCT at the 5' end of the core in the strand exchange reaction. PMID:9068626

  1. Speciation of As(III), As(V), MMA and DMA in contaminated soil extracts by HPLC-ICP/MS

    Energy Technology Data Exchange (ETDEWEB)

    Bissen, M.; Frimmel, F.H. [Engler-Bunte-Institut, Univ. Karlsruhe (Germany)

    2000-05-01

    A method to separate and quantify two inorganic arsenic species As(III) and As(V) and two organic arsenic species, monomethylarsonic acid (MMA) and dimethylarsinic acid (DMA), by HPLC-ICP/MS has been developed. The separation of arsenic species was achieved on the anionic exchange column IonPac {sup trademark} AS11 (Dionex) with NaOH as mobile phase. The technique was successfully applied to analyze extracts of two contaminated soils, sampled at a former tannery site (soil 1) and a former paint production site (soil 2). The soils were extracted at pH values similar to the natural environment. Extractions were performed at different pH values with 0.3 M ammonium oxalate (pH = 3), milli-Q water (pH = 5.8), 0.3 M sodium carbonate (pH = 8) and 0.3 M sodium bicarbonate (pH = 11). No organically bound arsenic was found in the extracts. As(V) was the major component. Only up to 0.04% of the total arsenic contained in soil 1 were mobilized. The highest amount of extracted arsenic was found at the highest pH. In the milli-Q water extract of soil 1 As(III) and As(V) were found. High amounts of As(V) were found in the extracts of soil 2. Up to 20% of the total arsenic bound to soil 2 constituents were released. The results show that the mobilization of arsenic depended on the pH value of the extraction solution and the kind of extracted soil. Dramatic consequences have to be expected for pH changes in the environment especially in cases where soils contain high amounts of mobile arsenic. (orig.)

  2. As(III) oxidation by active chlorine and subsequent removal of As(V) by Al13 polymer coagulation using a novel dual function reagent.

    Science.gov (United States)

    Hu, Chengzhi; Liu, Huijuan; Chen, Guixia; Jefferson, William A; Qu, Jiuhui

    2012-06-19

    An electrochemically prepared water treatment reagent containing a high concentration of Al(13) polymer and active chlorine (PACC) showed promising potential for the removal of As(III) due to the combined function of oxidation and coagulation. The results indicated that PACC was effective for As(III) removal through oxidation by the active chlorine and subsequent removal of As(V) by coagulation with the Al(13) polymer. The As(III) was oxidized to As(V) by active chlorine in PACC, with a stoichiometric rate of 0.99 mg Cl(2)/mg As(III). The Al(13) polymer was the most active Al species responsible for As(V) removal in PACC. To meet As drinking water standards the stoichiometric weight ratio of Cl(2)/Al within PACC was 0.09 for the treatment of As(III). Considering the process of As(III) oxidation and As(V) coagulation together, the optimal pH conditions for the removal of As by PACC was within the neutral range, which facilitated the reaction of As(III) with active chlorine and favored the formation of Al hydroxide flocs. The presence of humic acid reduced the As(III) removal efficiency of PACC due to its negative influence on subsequent As(V) coagulation, and disinfection byproduct yields were very low in the presence of insufficient or stoichiometric active chlorine.

  3. Real-time monitoring of disintegration activity of catalytic core domain of HIV-1 integrase using molecular beacon.

    Science.gov (United States)

    Zhang, Da-wei; Zhao, Ming-ming; He, Hong-qiu; Guo, Shun-xing

    2013-09-15

    HIV-1 integrase, an essential enzyme for retroviral replication, is a validated target for anti-HIV therapy development. The catalytic core domain of integrase (IN-CCD) is capable of catalyzing disintegration reaction. In this work, a hairpin-shaped disintegration substrate was designed and validated by enzyme-linked immunosorbent assay; a molecular beacon-based assay was developed for disintegration reaction of IN-CCD. Results showed that the disintegration substrate could be recognized and catalyzed by IN-CCD, and the disintegration reaction can be monitored according to the increase of fluorescent signal. The assay can be applied to real-time detection of disintegration with advantages of simplicity, high sensitivity, and excellent specificity. Copyright © 2013 Elsevier Inc. All rights reserved.

  4. Adsorption of As(III), As(V) and Cu(II) on zirconium oxide immobilized alginate beads in aqueous phase.

    Science.gov (United States)

    Kwon, Oh-Hun; Kim, Jong-Oh; Cho, Dong-Wan; Kumar, Rahul; Baek, Seung Han; Kurade, Mayur B; Jeon, Byong-Hun

    2016-10-01

    A composite adsorbent to remove arsenite [As(III)], arsenate [As(V)], and copper [Cu(II)] from aqueous phase was synthesized by immobilizing zirconium oxide on alginate beads (ZOAB). The composition (wt%) of ZOAB (Zr-34.0; O-32.7; C-21.3; Ca-1.0) was confirmed by energy dispersive X-ray (EDX) analysis. Sorption studies were conducted on single and binary sorbate systems, and the effects of contact time, initial adsorbate concentration, and pH on the adsorption performance of ZOAB (pHPZC = 4.3) were monitored. The sorption process for As(III)/As(V) and Cu(II) reached an equilibrium state within 240 h and 24 h, respectively, with maximum sorption capacities of 32.3, 28.5, and 69.9 mg g(-1), respectively. The addition of Cu(II) was favorable for As(V) sorption in contrast to As(III). In the presence of 48.6 mg L(-1) Cu(II), the sorption capacity of As(V) increased from 1.5 to 3.8 mg g(-1) after 240 h. The sorption data for As(III)/As(V) and Cu(II) conformed the Freundlich and Langmuir isotherm models, respectively. The adsorption of As(III), As(V), and Cu(II) followed pseudo second order kinetics. The effect of arsenic species on Cu(II) sorption was insignificant. The results of present study demonstrated that the synthesized sorbent could be useful for the simultaneous removal of both anionic and cationic contaminants from wastewaters. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. Uric acid levels in plasma and urine in rats chronically exposed to inorganic As (III) and As(V).

    Science.gov (United States)

    Jauge, P; Del-Razo, L M

    1985-07-01

    The effect of inorganic arsenic (III) and arsenic (V) on renal excretion and plasma levels of uric acid was examined in rats. Oral administration of 1200 micrograms As/kg/day for 6 weeks diminished uric acid levels in plasma by 67.1% and 26.5% of control after the administration of As(III) and As(V), respectively. Renal excretion of uric acid was significantly reduced during the first 3 weeks following As (III) administration, with a subsequent increase to approach control values at the end of the treatment. When As(V) was administered, the diminution in renal excretion was significant at 6 weeks.

  6. Fabrication of magnetic biochar as a treatment medium for As(V) via pyrolysis of FeCl3-pretreated spent coffee ground

    International Nuclear Information System (INIS)

    Cho, Dong-Wan; Yoon, Kwangsuk; Kwon, Eilhann E.; Biswas, Jayanta Kumar; Song, Hocheol

    2017-01-01

    This study investigated the preparation of magnetic biochar from N 2 - and CO 2 -assisted pyrolysis of spent coffee ground (SCG) for use as an adsorption medium for As(V), and the effects of FeCl 3 pretreatment of SCG on the material properties and adsorption capability of the produced biochar. Pyrolysis of FeCl 3 -pretreated SCG in CO 2 atmosphere produced highly porous biochar with its surface area ∼70 times greater than that produced in N 2 condition. However, despite the small surface area, biochar produced in N 2 showed greater As(V) adsorption capability. X-ray diffraction and X-ray photoelectron spectrometer analyses identified Fe 3 C and Fe 3 O 4 as dominant mineral phases in N 2 and CO 2 conditions, with the former being much more adsorptive toward As(V). The overall results suggest functional biochar can be facilely fabricated by necessary pretreatment to expand the applicability of biochar for specific purposes. - Highlights: • Fabrication of biochar via pyrolysis of FeCl 3 pretreated spent coffee ground. • Mineral phases of Fe 3 O 4 in CO 2 environment and Fe 3 C in N 2 environment. • As(V) adsorption governed by Fe mineral phase rather than porosity.

  7. The allosteric HIV-1 integrase inhibitor BI-D affects virion maturation but does not influence packaging of a functional RNA genome.

    Directory of Open Access Journals (Sweden)

    Nikki van Bel

    Full Text Available The viral integrase (IN is an essential protein for HIV-1 replication. IN inserts the viral dsDNA into the host chromosome, thereby aided by the cellular co-factor LEDGF/p75. Recently a new class of integrase inhibitors was described: allosteric IN inhibitors (ALLINIs. Although designed to interfere with the IN-LEDGF/p75 interaction to block HIV DNA integration during the early phase of HIV-1 replication, the major impact was surprisingly found on the process of virus maturation during the late phase, causing a reverse transcription defect upon infection of target cells. Virus particles produced in the presence of an ALLINI are misformed with the ribonucleoprotein located outside the virus core. Virus assembly and maturation are highly orchestrated and regulated processes in which several viral proteins and RNA molecules closely interact. It is therefore of interest to study whether ALLINIs have unpredicted pleiotropic effects on these RNA-related processes. We confirm that the ALLINI BI-D inhibits virus replication and that the produced virus is non-infectious. Furthermore, we show that the wild-type level of HIV-1 genomic RNA is packaged in virions and these genomes are in a dimeric state. The tRNAlys3 primer for reverse transcription was properly placed on this genomic RNA and could be extended ex vivo. In addition, the packaged reverse transcriptase enzyme was fully active when extracted from virions. As the RNA and enzyme components for reverse transcription are properly present in virions produced in the presence of BI-D, the inhibition of reverse transcription is likely to reflect the mislocalization of the components in the aberrant virus particle.

  8. The allosteric HIV-1 integrase inhibitor BI-D affects virion maturation but does not influence packaging of a functional RNA genome.

    Science.gov (United States)

    van Bel, Nikki; van der Velden, Yme; Bonnard, Damien; Le Rouzic, Erwann; Das, Atze T; Benarous, Richard; Berkhout, Ben

    2014-01-01

    The viral integrase (IN) is an essential protein for HIV-1 replication. IN inserts the viral dsDNA into the host chromosome, thereby aided by the cellular co-factor LEDGF/p75. Recently a new class of integrase inhibitors was described: allosteric IN inhibitors (ALLINIs). Although designed to interfere with the IN-LEDGF/p75 interaction to block HIV DNA integration during the early phase of HIV-1 replication, the major impact was surprisingly found on the process of virus maturation during the late phase, causing a reverse transcription defect upon infection of target cells. Virus particles produced in the presence of an ALLINI are misformed with the ribonucleoprotein located outside the virus core. Virus assembly and maturation are highly orchestrated and regulated processes in which several viral proteins and RNA molecules closely interact. It is therefore of interest to study whether ALLINIs have unpredicted pleiotropic effects on these RNA-related processes. We confirm that the ALLINI BI-D inhibits virus replication and that the produced virus is non-infectious. Furthermore, we show that the wild-type level of HIV-1 genomic RNA is packaged in virions and these genomes are in a dimeric state. The tRNAlys3 primer for reverse transcription was properly placed on this genomic RNA and could be extended ex vivo. In addition, the packaged reverse transcriptase enzyme was fully active when extracted from virions. As the RNA and enzyme components for reverse transcription are properly present in virions produced in the presence of BI-D, the inhibition of reverse transcription is likely to reflect the mislocalization of the components in the aberrant virus particle.

  9. Cloning, purification and structure determination of the HIV integrase-binding domain of lens epithelium-derived growth factor.

    Science.gov (United States)

    Hannon, Clare; Cruz-Migoni, Abimael; Platonova, Olga; Owen, Robin L; Nettleship, Joanne E; Miller, Ami; Carr, Stephen B; Harris, Gemma; Rabbitts, Terence H; Phillips, Simon E V

    2018-03-01

    Lens epithelium-derived growth factor (LEDGF)/p75 is the dominant binding partner of HIV-1 integrase in human cells. The crystal structure of the HIV integrase-binding domain (IBD) of LEDGF has been determined in the absence of ligand. IBD was overexpressed in Escherichia coli, purified and crystallized by sitting-drop vapour diffusion. X-ray diffraction data were collected at Diamond Light Source to a resolution of 2.05 Å. The crystals belonged to space group P2 1 , with eight polypeptide chains in the asymmetric unit arranged as an unusual octamer composed of four domain-swapped IBD dimers. IBD exists as a mixture of monomers and dimers in concentrated solutions, but the dimers are unlikely to be biologically relevant.

  10. HIV-2 integrase polymorphisms and longitudinal genotypic analysis of HIV-2 infected patients failing a raltegravir-containing regimen.

    Science.gov (United States)

    Cavaco-Silva, Joana; Abecasis, Ana; Miranda, Ana Cláudia; Poças, José; Narciso, Jorge; Águas, Maria João; Maltez, Fernando; Almeida, Isabel; Germano, Isabel; Diniz, António; Gonçalves, Maria de Fátima; Gomes, Perpétua; Cunha, Celso; Camacho, Ricardo Jorge

    2014-01-01

    To characterize the HIV-2 integrase gene polymorphisms and the pathways to resistance of HIV-2 patients failing a raltegravir-containing regimen, we studied 63 integrase strand transfer inhibitors (INSTI)-naïve patients, and 10 heavily pretreated patients exhibiting virological failure while receiving a salvage raltegravir-containing regimen. All patients were infected by HIV-2 group A. 61.4% of the integrase residues were conserved, including the catalytic motif residues. No INSTI-major resistance mutations were detected in the virus population from naïve patients, but two amino acids that are secondary resistance mutations to INSTIs in HIV-1 were observed. The 10 raltegravir-experienced patients exhibited resistance mutations via three main genetic pathways: N155H, Q148R, and eventually E92Q - T97A. The 155 pathway was preferentially used (7/10 patients). Other mutations associated to raltegravir resistance in HIV-1 were also observed in our HIV-2 population (V151I and D232N), along with several novel mutations previously unreported. Data retrieved from this study should help build a more robust HIV-2-specific algorithm for the genotypic interpretation of raltegravir resistance, and contribute to improve the clinical monitoring of HIV-2-infected patients.

  11. Fabrication of magnetic biochar as a treatment medium for As(V) via pyrolysis of FeCl3-pretreated spent coffee ground.

    Science.gov (United States)

    Cho, Dong-Wan; Yoon, Kwangsuk; Kwon, Eilhann E; Biswas, Jayanta Kumar; Song, Hocheol

    2017-10-01

    This study investigated the preparation of magnetic biochar from N 2 - and CO 2 -assisted pyrolysis of spent coffee ground (SCG) for use as an adsorption medium for As(V), and the effects of FeCl 3 pretreatment of SCG on the material properties and adsorption capability of the produced biochar. Pyrolysis of FeCl 3 -pretreated SCG in CO 2 atmosphere produced highly porous biochar with its surface area ∼70 times greater than that produced in N 2 condition. However, despite the small surface area, biochar produced in N 2 showed greater As(V) adsorption capability. X-ray diffraction and X-ray photoelectron spectrometer analyses identified Fe 3 C and Fe 3 O 4 as dominant mineral phases in N 2 and CO 2 conditions, with the former being much more adsorptive toward As(V). The overall results suggest functional biochar can be facilely fabricated by necessary pretreatment to expand the applicability of biochar for specific purposes. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Construction and evaluation of As(V) selective electrodes based on iron oxyhydroxide embedded in silica gel membrane

    International Nuclear Information System (INIS)

    Rodriguez, J.A.; Barrado, E.; Vega, M.; Prieto, F.; Lima, J.L.F.C.

    2005-01-01

    Two As(V) selective electrodes (with and without inner reference solution) have been developed using selective membranes based on iron oxyhydroxide embedded on silica gel mixed with ultrapure graphite at a 2/98 (w/w) ratio. The active component of the membrane was synthesised by means of the sol-gel technique and characterized by X-ray and FTIR spectroscopy. This compound shows a great affinity towards As(V) ions adsorbing 408 mg g -1 . Using 1 mol l -1 phosphate buffer (at a 1/1, v/v ratio) to adjust the pH and the ionic strength to 7 and 0.5 mol l -1 , respectively, the calibration curve is linear from 1.0 x 10 -1 to 1.0 x 10 -6 mol l -1 As(V), with a practical detection limit of 4 x 10 -7 mol l -1 (0.03 mg l -1 ) and a slope close to 30 mV decade -1 . The effect of potentially interfering ions was investigated. The accuracy and precision of the procedure have been tested on arsenic-free drinking water samples spiked with known amounts of arsenic and on groundwater samples containing high levels of arsenic. Total arsenic in these samples was determined after oxidation of As(III) with iodine at pH 7. The results of total As were comparable to those generated by ET-AAS

  13. Raltegravir, elvitegravir, and metoogravir: the birth of "me-too" HIV-1 integrase inhibitors

    Directory of Open Access Journals (Sweden)

    Neamati Nouri

    2009-04-01

    Full Text Available Abstract Correction to Erik Serrao, Srinivas Odde, Kavya Ramkumar and Nouri Neamati: Raltegravir, elvitegravir, and metoogravir: the birth of "me-too" HIV-1 integrase inhibitors. Retrovirology 2009, 6:25. Since the recent publication of our article (Neamati, Retrovirology 2009, 6:25, we have noticed an error which we would like to correct and we would like to apologise to the readers for this mistake.

  14. ФC31 Integrase-Mediated Isolation and Characterization of Novel Safe Harbors for Transgene Expression in the Pig Genome

    Science.gov (United States)

    Bi, Yanzhen; Hua, Zaidong; Ren, Hongyan; Zhang, Liping; Xiao, Hongwei; Liu, Ximei; Hua, Wenjun; Mei, Shuqi; Molenaar, Adrian; Laible, Götz; Zheng, Xinmin

    2018-01-01

    Programmable nucleases have allowed the rapid development of gene editing and transgenics, but the technology still suffers from the lack of predefined genetic loci for reliable transgene expression and maintenance. To address this issue, we used ФC31 integrase to navigate the porcine genome and identify the pseudo attP sites suitable as safe harbors for sustained transgene expression. The combined ФC31 integrase mRNA and an enhanced green fluorescence protein (EGFP) reporter donor were microinjected into one-cell zygotes for transgene integration. Among the resulting seven EGFP-positive piglets, two had transgene integrations at pseudo attP sites, located in an intergenic region of chromosome 1 (chr1-attP) and the 6th intron of the TRABD2A gene on chromosome 3 (chr3-attP), respectively. The integration structure was determined by TAIL-PCR and Southern blotting. Primary fibroblast cells were isolated from the two piglets and examined using fluorescence-activated cell sorting (FACS) and enzyme-linked immunosorbent assay (ELISA), which demonstrated that the chr1-attP site was more potent than chr3-attP site in supporting the EGFP expression. Both piglets had green feet under the emission of UV light, and pelleted primary fibroblast cells were green-colored under natural light, corroborating that the two pseudo attP sites are beneficial to transgene expression. The discovery of these two novel safe harbors for robust and durable transgene expression will greatly facilitate the use of transgenic pigs for basic, biomedical and agricultural studies and applications. PMID:29300364

  15. Corynebacterium glutamicum MTCC 2745 immobilized on granular activated carbon/MnFe2O4 composite: A novel biosorbent for removal of As(III) and As(V) ions.

    Science.gov (United States)

    Podder, M S; Majumder, C B

    2016-11-05

    The optimization of biosorption/bioaccumulation process of both As(III) and As(V) has been investigated by using the biosorbent; biofilm of Corynebacterium glutamicum MTCC 2745 supported on granular activated carbon/MnFe2O4 composite (MGAC). The presence of functional groups on the cell wall surface of the biomass that may interact with the metal ions was proved by FT-IR. To determine the most appropriate correlation for the equilibrium curves employing the procedure of the non-linear regression for curve fitting analysis, isotherm studies were performed for As(III) and As(V) using 30 isotherm models. The pattern of biosorption/bioaccumulation fitted well with Vieth-Sladek isotherm model for As(III) and Brouers-Sotolongo and Fritz-Schlunder-V isotherm models for As(V). The maximum biosorption/bioaccumulation capacity estimated using Langmuir model were 2584.668mg/g for As(III) and 2651.675mg/g for As(V) at 30°C temperature and 220min contact time. The results showed that As(III) and As(V) removal was strongly pH-dependent with an optimum pH value of 7.0. D-R isotherm studies specified that ion exchange might play a prominent role. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. Contribution of HIV minority variants to drug resistance in an integrase strand transfer inhibitor-based therapy

    Czech Academy of Sciences Publication Activity Database

    Weber, Jan; Gibson, R. M.; Meyer, A. M.; Winner, D.; Robertson, D. L.; Miller, M. D.; Quinones-Mateu, M. E.

    2013-01-01

    Roč. 18, Suppl. 1 (2013), A66-A66 ISSN 1359-6535. [International Workshop on HIV & Hepatitis Virus Drug Resistance Curative Strategies. 04.06.2013-08.06.2013, Toronto] Institutional support: RVO:61388963 Keywords : HIV minority variants * integrase inhibitor * replicative fitness Subject RIV: CE - Biochemistry

  17. Study on competitive adsorption mechanism among oxyacid-type heavy metals in co-existing system: Removal of aqueous As(V), Cr(III) and As(III) using magnetic iron oxide nanoparticles (MIONPs) as adsorbents

    Science.gov (United States)

    Lin, Sen; Lian, Cheng; Xu, Meng; Zhang, Wei; Liu, Lili; Lin, Kuangfei

    2017-11-01

    The adsorption and co-adsorption of As(V), Cr(VI) and As(III) onto the magnetic iron oxide nanoparticles (MIONPs) surface were investigated comprehensively to clarify the competitive processes. The results reflected that the MIONPs had remarkable preferential adsorption to As(V) compared with Cr(VI) and As(III). And it was determined, relying on the analysis of heavy metals variations on the MIONPs surface at different co-adsorption stages using FTIR and XPS, that the inner-sphere complexation made vital contribution to the preferential adsorption for As(V), corresponding with the replacement experiments where As(V) could grab extensively active sites on the MIONPs pre-occupied by As(III) or Cr(V) uniaxially. The desorption processes displayed that the strongest affinity between the MIONPs and As(V) where As(III) and Cr(VI) were more inclined to wash out. It is wish to provide a helpful direction with this study for the wastewater treatment involving multiple oxyacid-type heavy metals using MIONPs as adsorbents.

  18. Discovery of small-molecule HIV-1 fusion and integrase inhibitors oleuropein and hydroxytyrosol: Part I. Integrase inhibition

    International Nuclear Information System (INIS)

    Lee-Huang, Sylvia; Huang, Philip Lin; Zhang Dawei; Lee, Jae Wook; Bao Ju; Sun Yongtao; Chang, Young-Tae; Zhang, John; Huang, Paul Lee

    2007-01-01

    We have identified oleuropein (Ole) and hydroxytyrosol (HT) as a unique class of HIV-1 inhibitors from olive leaf extracts effective against viral fusion and integration. We used molecular docking simulation to study the interactions of Ole and HT with viral targets. We find that Ole and HT bind to the conserved hydrophobic pocket on the surface of the HIV-gp41 fusion domain by hydrogen bonds with Q577 and hydrophobic interactions with I573, G572, and L568 on the gp41 N-terminal heptad repeat peptide N36, interfering with formation of the gp41 fusion-active core. To test and confirm modeling predications, we examined the effect of Ole and HT on HIV-1 fusion complex formation using native polyacrylamide gel electrophoresis and circular dichroism spectroscopy. Ole and HT exhibit dose-dependent inhibition on HIV-1 fusion core formation with EC 50 s of 66-58 nM, with no detectable toxicity. Our findings on effects of HIV-1 integrase are reported in the subsequent article

  19. As(III) and As(V) sorption on iron-modified non-pyrolyzed and pyrolyzed biomass from Petroselinum crispum (parsley).

    Science.gov (United States)

    Jiménez-Cedillo, M J; Olguín, M T; Fall, C; Colin-Cruz, A

    2013-03-15

    The sorption of As(III) and As(V) from aqueous solutions onto iron-modified Petroselinum crispum (PCFe) and iron-modified carbonaceous material from the pyrolysis of P. crispum (PCTTFe) was investigated. The modified sorbents were characterized with scanning electron microscopy. The sorbent elemental composition was determined with energy-dispersive X-ray spectroscopy (EDS). The principal functional groups from the sorbents were determined with FT-IR. The specific surfaces and points of zero charge (pzc) of the materials were also determined. As(III) and As(V) sorption onto the modified sorbents were performed in a batch system. After the sorption process, the As content in the liquid and solid phases was determined with atomic absorption and neutron activation analyses, respectively. After the arsenic sorption processes, the desorption of Fe from PCFe and PCTTFe was verified with atomic absorption spectrometry. The morphology of PC changed after iron modification. The specific area and pzc differed significantly between the iron-modified non-pyrolyzed and pyrolyzed P. crispum. The kinetics of the arsenite and arsenate sorption processes were described with a pseudo-second-order model. The Langmuir-Freundlich model provided the isotherms with the best fit. Less than 0.02% of the Fe was desorbed from the PCFe and PCTTFe after the As(III) and As(V) sorption processes. Copyright © 2013 Elsevier Ltd. All rights reserved.

  20. Adsorption of As(V) from water using Mg-Fe-based hydrotalcite (FeHT)

    Energy Technology Data Exchange (ETDEWEB)

    Tuerk, T. [Mineral Processing Division, Department of Mining Engineering, Karadeniz Technical University, 61080 Trabzon (Turkey); Alp, I., E-mail: ialp@ktu.edu.tr [Mineral Processing Division, Department of Mining Engineering, Karadeniz Technical University, 61080 Trabzon (Turkey); Deveci, H. [Mineral Processing Division, Department of Mining Engineering, Karadeniz Technical University, 61080 Trabzon (Turkey)

    2009-11-15

    This paper describes a study of the sorptive removal of arsenate (As(V)) from aqueous solutions by synthetically prepared Mg-Fe-based hydrotalcites (FeHT) as layered double hydroxide (LDH) adsorbents. The synthesis of Fe{sup 3+}-substituted hydrotalcites (FeHT) with the chemical formula [Mg(II){sub 6}Fe(III){sub 2}(OH){sub 16}]{sup 2+}[CO{sub 3} x yH{sub 2}O]{sup 2-} was achieved by a co-precipitation method. The reaction products were characterized by powder X-ray diffraction analysis. The influences of solution pH, initial arsenate (As(V)) concentration, and sorbent concentration were investigated in multiple kinetic runs. The adsorption rates and isotherms were investigated in batch experiments. The pseudo-first-order and second-order kinetic models were tested and the latter was found to fit better to the experimental data. Langmuir and Freundlich isotherms were used to describe the adsorption data from equilibrium experiments. The results have shown that FeHT has a high arsenate removal efficiency, with the ability to reduce the concentration of arsenate in the aqueous solution from an initial value of 330 {mu}g/l to <10 {mu}g/l (i.e. below the limit value specified by WHO).

  1. Advances in Shallow-Water, High-Resolution Seafloor Mapping: Integrating an Autonomous Surface Vessel (ASV) Into Nearshore Geophysical Studies

    Science.gov (United States)

    Denny, J. F.; O'Brien, T. F.; Bergeron, E.; Twichell, D.; Worley, C. R.; Danforth, W. W.; Andrews, B. A.; Irwin, B.

    2006-12-01

    The U.S. Geological Survey (USGS) has been heavily involved in geological mapping of the seafloor since the 1970s. Early mapping efforts such as GLORIA provided broad-scale imagery of deep waters (depths > 400 meters) within the Exclusive Economic Zone (EEZ). In the early 1990's, the USGS research emphasis shifted from deep- to shallow-water environments (inner continental shelf, nearshore, estuaries) to address pertinent coastal issues such as erosion, sediment availability, sediment transport, vulnerability of coastal areas to natural and anthropogenic hazards, and resource management. Geologic framework mapping in these shallow- water environments has provided valuable data used to 1) define modern sediment distribution and thickness, 2) determine underlying stratigraphic and structural controls on shoreline behavior, and 3) enable onshore-to- offshore geologic mapping within the coastal zone when coupled with subaerial techniques such as GPR and topographic LIDAR. Research in nearshore areas presents technological challenges due to the dynamics of the environment, high volume of data collected, and the geophysical limitations of operating in very shallow water. In 2004, the USGS, in collaboration with NOAA's Coastal Services Center, began a multi-year seafloor mapping effort to better define oyster habitats within Apalachicola Bay, Florida, a shallow water estuary along the northern Gulf of Mexico. The bay poses a technological challenge due to its shallow depths (turbidity that prohibits the use of bathymetric LIDAR. To address this extreme shallow water setting, the USGS incorporated an Autonomous Surface Vessel (ASV) into seafloor mapping operations, in June 2006. The ASV is configured with a chirp sub-bottom profiler (4 24 kHz), dual-frequency chirp sidescan-sonar (100/500 kHz), single-beam echosounder (235 kHz), and forward-looking digital camera, and will be used to delineate the distribution and thickness of surficial sediment, presence of oyster beds

  2. Th(As(III)4As(V)4O18): a mixed-valent oxoarsenic(III)/arsenic(V) actinide compound obtained under extreme conditions.

    Science.gov (United States)

    Yu, Na; Klepov, Vladislav V; Kegler, Philip; Bosbach, Dirk; Albrecht-Schmitt, Thomas E; Alekseev, Evgeny V

    2014-08-18

    A high-temperature/high-pressure method was employed to investigate phase formation in the Th(NO3)4·5H2O-As2O3-CsNO3 system. It was observed that an excess of arsenic(III) in starting system leads to the formation of Th(As(III)4As(V)4O18), which is representative of a rare class of mixed-valent arsenic(III)/arsenic(V) compounds. This compound was studied with X-ray diffraction, energy-dispersive X-ray, and Raman spectroscopy methods. Crystallographic data show that Th(As(III)4As(V)4O18) is built from (As(III)4As(V)4O18)(4-) layers connected through Th atoms. The arsenic layers are found to be isoreticular to those in previously reported As2O3 and As3O5(OH), and the geometric differences between them are discussed. Bands in the Raman spectrum are assigned with respect to the presence of AsO3 and AsO4 groups.

  3. Molecular dynamics simulation studies of the wild type and E92Q/N155H mutant of Elvitegravir-resistance HIV-1 integrase.

    Science.gov (United States)

    Chen, Qi; Cheng, Xiaolin; Wei, Dongqing; Xu, Qin

    2015-03-01

    Although Elvitegravir (EVG) is a newly developed antiretrovirals drug to treat the acquired immunodeficiency syndrome (AIDS), drug resistance has already been found in clinic, such as E92Q/N155H and Q148H/G140S. Several structural investigations have already been reported to reveal the molecular mechanism of the drug resistance. As full length crystal structure for HIV-1 integrase is still unsolved, we herein use the crystal structure of the full length prototype foamy virus (PFV) in complex with virus DNA and inhibitor Elvitegravir as a template to construct the wild type and E92Q/N155H mutant system of HIV-1 integrase. Molecular dynamic simulations was used to revel the binding mode and the drug resistance of the EVG ligand in E92Q/N155H. Several important interactions were discovered between the mutated residues and the residues in the active site of the E92Q/N155H double mutant pattern, and cross correlation and clustering methods were used for detailed analysis. The results from the MD simulation studies will be used to guide the experimental efforts of developing novel inhibitors against drug-resistant HIV integrase mutants.

  4. Anodic stripping voltammetry – ASV for determination of heavy metals

    International Nuclear Information System (INIS)

    Barón-Jaimez, J; Joya, M R; Barba-Ortega, J

    2013-01-01

    Although voltammetric methods presented a number of difficulties in its early stages, nowadays ''ASV'' anodic stripping voltammetry is considered one of the most sensitive electro-analytical and suitable for trace-level determination of many metals and compounds in environmental samples, clinical and industrial. Its sensitivity is attributed to the combination of a step of pre-concentration effective together with an electrochemical advanced measurement of accumulated analyte. This paper presents an overview of the voltammetry, which includes a group of electro-analytical methods, in them the information about analyte is obtained from measurements of the current flowing in an electrochemical cell when applied a potential difference to an suitable electrode system

  5. Titanium dioxide-based DGT for measuring dissolved As(V), V(V), Sb(V), Mo(VI) and W(VI) in water

    DEFF Research Database (Denmark)

    Panther, Jared G.; Stewart, Ryan R.; Teasdale, Peter R.

    2013-01-01

    A titanium dioxide-based DGT method (Metsorb-DGT) was evaluated for the measurement of As(V), V(V), Sb(V), Mo(VI), W(VI) and dissolved reactive phosphorus (DRP) in synthetic waters. Mass vs. time DGT deployments at pH 6.06 (0.01 mol L-1 NaNO3) demonstrated linear uptake of all analytes (R2...... for deployment times >4 h (CDGT=0.27-0.72). For ferrihydrite-DGT, CDGT/CSol values in the range 0.92-1.16 were obtained for As(V), V(V) and DRP, however, Mo(VI), Sb(V) and W(VI) could not be measured to within 15% of the solution concentration (C DGT/CSol 0.02-0.83)....

  6. X-ray crystal structure of the N-terminal region of Moloney murine leukemia virus integrase and its implications for viral DNA recognition: N-Terminal Region of M-MuLV Integrase

    Energy Technology Data Exchange (ETDEWEB)

    Guan, Rongjin [Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854; Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854; Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854; Aiyer, Sriram [Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854; Cote, Marie L. [Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ, Piscataway New Jersey 08854; Xiao, Rong [Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854; Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854; Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854; Jiang, Mei [Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854; Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854; Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854; Acton, Thomas B. [Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854; Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854; Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854; Roth, Monica J. [Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854; Montelione, Gaetano T. [Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854; Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854; Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854; Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ, Piscataway New Jersey 08854

    2017-02-03

    The retroviral integrase (IN) carries out the integration of a dsDNA copy of the viral genome into the host DNA, an essential step for viral replication. All IN proteins have three general domains, the N-terminal domain (NTD), the catalytic core domain, and the C-terminal domain. The NTD includes an HHCC zinc finger-like motif, which is conserved in all retroviral IN proteins. Two crystal structures of Moloney murine leukemia virus (M-MuLV) IN N-terminal region (NTR) constructs that both include an N-terminal extension domain (NED, residues 1–44) and an HHCC zinc-finger NTD (residues 45–105), in two crystal forms are reported. The structures of IN NTR constructs encoding residues 1–105 (NTR1–105) and 8–105 (NTR8–105) were determined at 2.7 and 2.15 Å resolution, respectively and belong to different space groups. While both crystal forms have similar protomer structures, NTR1–105 packs as a dimer and NTR8–105 packs as a tetramer in the asymmetric unit. The structure of the NED consists of three anti-parallel β-strands and an α-helix, similar to the NED of prototype foamy virus (PFV) IN. These three β-strands form an extended β-sheet with another β-strand in the HHCC Zn2+ binding domain, which is a unique structural feature for the M-MuLV IN. The HHCC Zn2+ binding domain structure is similar to that in HIV and PFV INs, with variations within the loop regions. Differences between the PFV and MLV IN NEDs localize at regions identified to interact with the PFV LTR and are compared with established biochemical and virological data for M-MuLV. Proteins 2017; 85:647–656.

  7. Integrase-independent HIV-1 infection is augmented under conditions of DNA damage and produces a viral reservoir

    International Nuclear Information System (INIS)

    Ebina, Hirotaka; Kanemura, Yuka; Suzuki, Yasutsugu; Urata, Kozue; Misawa, Naoko; Koyanagi, Yoshio

    2012-01-01

    HIV-1 possesses a viral protein, integrase (IN), which is necessary for its efficient integration in target cells. However, it has been reported that an IN-defective HIV strain is still capable of integration. Here, we assessed the ability of wild type (WT) HIV-1 to establish infection in the presence of IN inhibitors. We observed a low, yet clear infection of inhibitor-incubated cells infected with WT HIV which was identical to cells infected with IN-deficient HIV, D64A. Furthermore, the IN-independent integration could be enhanced by the pretreatment of cells with DNA-damaging agents suggesting that integration is mediated by a DNA repair system. Moreover, significantly faster viral replication kinetics with augmented viral DNA integration was observed after infection in irradiated cells treated with IN inhibitor compared to nonirradiated cells. Altogether, our results suggest that HIV DNA has integration potential in the presence of an IN inhibitor and may serve as a virus reservoir.

  8. Integrase-independent HIV-1 infection is augmented under conditions of DNA damage and produces a viral reservoir

    Energy Technology Data Exchange (ETDEWEB)

    Ebina, Hirotaka, E-mail: hebina@virus.kyoto-u.ac.jp; Kanemura, Yuka; Suzuki, Yasutsugu; Urata, Kozue; Misawa, Naoko; Koyanagi, Yoshio

    2012-05-25

    HIV-1 possesses a viral protein, integrase (IN), which is necessary for its efficient integration in target cells. However, it has been reported that an IN-defective HIV strain is still capable of integration. Here, we assessed the ability of wild type (WT) HIV-1 to establish infection in the presence of IN inhibitors. We observed a low, yet clear infection of inhibitor-incubated cells infected with WT HIV which was identical to cells infected with IN-deficient HIV, D64A. Furthermore, the IN-independent integration could be enhanced by the pretreatment of cells with DNA-damaging agents suggesting that integration is mediated by a DNA repair system. Moreover, significantly faster viral replication kinetics with augmented viral DNA integration was observed after infection in irradiated cells treated with IN inhibitor compared to nonirradiated cells. Altogether, our results suggest that HIV DNA has integration potential in the presence of an IN inhibitor and may serve as a virus reservoir.

  9. Docking studies on a new human immunodeficiency virus integrase-Mg-DNA complex: phenyl ring exploration and synthesis of 1H-benzylindole derivatives through fluorine substitutions.

    Science.gov (United States)

    Ferro, Stefania; De Luca, Laura; Barreca, Maria Letizia; Iraci, Nunzio; De Grazia, Sara; Christ, Frauke; Witvrouw, Myriam; Debyser, Zeger; Chimirri, Alba

    2009-01-22

    A new model of HIV-1 integrase-Mg-DNA complex that is useful for docking experiments has been built. It was used to study the binding mode of integrase strand transfer inhibitor 1 (CHI-1043) and other fluorine analogues. Molecular modeling results prompted us to synthesize the designed derivatives which showed potent enzymatic inhibition at nanomolar concentration, high antiviral activity, and low toxicity. Microwave assisted organic synthesis (MAOS) was employed in several steps of the synthetic pathway, thus reducing reaction times and improving yields.

  10. Molecular dynamics simulation studies of the wild type and E92Q/N155H mutant of Elvitegravir-resistance HIV-1 integrase

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Qi [Shanghai Jiao Tong Univ., Shanghai (China). State Key Lab. of Microbial Metabolism and College of Life Science and Biotechnology; Cheng, Xiaolin [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Center for Molecular Biophysics; Univ. of Tennessee, Knoxville, TN (United States). Dept. of Biochemistry and Cellular and Molecular Biology; Wei, Dongqing [Shanghai Jiao Tong Univ., Shanghai (China). State Key Lab. of Microbial Metabolism and College of Life Science and Biotechnology; Xu, Qin [Shanghai Jiao Tong Univ., Shanghai (China). State Key Lab. of Microbial Metabolism and College of Life Science and Biotechnology

    2014-11-06

    Although Elvitegravir (EVG) is a newly developed antiretrovirals drug to treat the acquired immunodeficiency syndrome (AIDS), drug resistance has already been found in clinic, such as E92Q/N155H and Q148H/G140S. Several structural investigations have already been reported to reveal the molecular mechanism of the drug resistance. As full length crystal structure for HIV-1 integrase is still unsolved, we use in this paper the crystal structure of the full length prototype foamy virus (PFV) in complex with virus DNA and inhibitor Elvitegravir as a template to construct the wild type and E92Q/N155H mutant system of HIV-1 integrase. Molecular dynamic simulations was used to revel the binding mode and the drug resistance of the EVG ligand in E92Q/N155H. Several important interactions were discovered between the mutated residues and the residues in the active site of the E92Q/N155H double mutant pattern, and cross correlation and clustering methods were used for detailed analysis. The results from the MD simulation studies will be used to guide the experimental efforts of developing novel inhibitors against drug-resistant HIV integrase mutants.

  11. Primary resistance to integrase strand transfer inhibitors in patients infected with diverse HIV-1 subtypes in sub-Saharan Africa

    NARCIS (Netherlands)

    Inzaule, Seth C.; Hamers, Raph L.; Noguera-Julian, Marc; Casadellà, Maria; Parera, Mariona; Rinke de Wit, Tobias F.; Paredes, Roger

    2018-01-01

    To investigate the prevalence and patterns of major and accessory resistance mutations associated with integrase strand transfer inhibitors (INSTIs), across diverse HIV-1 subtypes in sub-Saharan Africa. pol gene sequences were obtained using Illumina next-generation sequencing from 425 INSTI-naive

  12. BF integrase genes of HIV-1 circulating in São Paulo, Brazil, with a recurrent recombination region.

    Directory of Open Access Journals (Sweden)

    Atila Iamarino

    Full Text Available Although some studies have shown diversity in HIV integrase (IN genes, none has focused particularly on the gene evolving in epidemics in the context of recombination. The IN gene in 157 HIV-1 integrase inhibitor-naïve patients from the São Paulo State, Brazil, were sequenced tallying 128 of subtype B (23 of which were found in non-B genomes, 17 of subtype F (8 of which were found in recombinant genomes, 11 integrases were BF recombinants, and 1 from subtype C. Crucially, we found that 4 BF recombinant viruses shared a recurrent recombination breakpoint region between positions 4900 and 4924 (relative to the HXB2 that includes 2 gRNA loops, where the RT may stutter. Since these recombinants had independent phylogenetic origin, we argue that these results suggest a possible recombination hotspot not observed so far in BF CRF in particular, or in any other HIV-1 CRF in general. Additionally, 40% of the drug-naïve and 45% of the drug-treated patients had at least 1 raltegravir (RAL or elvitegravir (EVG resistance-associated amino acid change, but no major resistance mutations were found, in line with other studies. Importantly, V151I was the most common minor resistance mutation among B, F, and BF IN genes. Most codon sites of the IN genes had higher rates of synonymous substitutions (dS indicative of a strong negative selection. Nevertheless, several codon sites mainly in the subtype B were found under positive selection. Consequently, we observed a higher genetic diversity in the B portions of the mosaics, possibly due to the more recent introduction of subtype F on top of an ongoing subtype B epidemics and a fast spread of subtype F alleles among the B population.

  13. Discovery and optimization of 2-pyridinone aminal integrase strand transfer inhibitors for the treatment of HIV.

    Science.gov (United States)

    Schreier, John D; Embrey, Mark W; Raheem, Izzat T; Barbe, Guillaume; Campeau, Louis-Charles; Dubost, David; McCabe Dunn, Jamie; Grobler, Jay; Hartingh, Timothy J; Hazuda, Daria J; Klein, Daniel; Miller, Michael D; Moore, Keith P; Nguyen, Natalie; Pajkovic, Natasa; Powell, David A; Rada, Vanessa; Sanders, John M; Sisko, John; Steele, Thomas G; Wai, John; Walji, Abbas; Xu, Min; Coleman, Paul J

    2017-05-01

    HIV integrase strand transfer inhibitors (InSTIs) represent an important class of antiviral therapeutics with proven efficacy and excellent tolerability for the treatment of HIV infections. In 2007, Raltegravir became the first marketed strand transfer inhibitor pioneering the way to a first-line therapy for treatment-naïve patients. Challenges with this class of therapeutics remain, including frequency of the dosing regimen and the genetic barrier to resistance. To address these issues, research towards next-generation integrase inhibitors has focused on imparting potency against RAL-resistent mutants and improving pharmacokinetic profiles. Herein, we detail medicinal chemistry efforts on a novel class of 2-pyridinone aminal InSTIs, inpsired by MK-0536, which led to the discovery of important lead molecules for our program. Systematic optimization carried out at the amide and aminal positions on the periphery of the core provided the necessary balance of antiviral activity and physiochemical properties. These efforts led to a novel aminal lead compound with the desired virological profile and preclinical pharmacokinetic profile to support a once-daily human dose prediction. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. The effect of adaptive servo ventilation (ASV) on objective and subjective outcomes in Cheyne-Stokes respiration (CSR) with central sleep apnea (CSA) in heart failure (HF): A systematic review.

    Science.gov (United States)

    Yang, Hyunju; Sawyer, Amy M

    2016-01-01

    To summarize the current evidence for adaptive servo ventilation (ASV) in Cheyne-Stokes respiration (CSR) with central sleep apnea (CSA) in heart failure (HF) and advance a research agenda and clinical considerations for ASV-treated CSR-CSA in HF. CSR-CSA in HF is associated with higher overall mortality, worse outcomes and lower quality of life (QOL) than HF without CSR-CSA. Five databases were searched using key words (n = 234). Randomized controlled trials assessed objective sleep quality, cardiac, and self-reported outcomes in adults (≥18 years) with HF (n = 10). ASV has a beneficial effect on the reduction of central sleep apnea in adult patients with CSR-CSA in HF, but it is not be superior to CPAP, bilevel PPV, or supplemental oxygen in terms of sleep quality defined by polysomnography, cardiovascular outcomes, subjective daytime sleepiness, and quality of life. ASV is not recommended for CSR-CSA in HF. It is important to continue to refer HF patients for sleep evaluation to clearly discern OSA from CSR-CSA. Symptom management research, inclusive of objective and subjective outcomes, in CSR-CSA in HF adults is needed. Copyright © 2016 Elsevier Inc. All rights reserved.

  15. A resolvase-like protein is requered for the site-specific integration of the temperate lactococcal bacteriophage TP901-1

    DEFF Research Database (Denmark)

    Christiansen, Bettina; Brøndsted, Lone; Vogensen, Finn K.

    1996-01-01

    upstream of attP. The N-terminal 150 to 1180 amino acids of Orf1 showed 38 to 44% similarity to the resolvase group of site-specific integrases, while no similarity to know proteins was found in the C-terminal end. Bacteriophage 'TP901-1 therefore contains a unique integration system that does not resemble...... the Int class of site-specific integrases usually found in temperate bacteriophages. The constructed integration vector, pBC170, integrates into the chromosomal attachment site very efficiently and forms stable transformants with a frequency corresponding to 20% of the transformation efficiency....

  16. Adsorption of Pb(II), Cu(II), Cd(II), Zn(II), Ni(II), Fe(II), and As(V) on bacterially produced metal sulfides.

    Science.gov (United States)

    Jong, Tony; Parry, David L

    2004-07-01

    The adsorption of Pb(II), Cu(II), Cd(II), Zn(II), Ni(II), Fe(II) and As(V) onto bacterially produced metal sulfide (BPMS) material was investigated using a batch equilibrium method. It was found that the sulfide material had adsorptive properties comparable with those of other adsorbents with respect to the specific uptake of a range of metals and, the levels to which dissolved metal concentrations in solution can be reduced. The percentage of adsorption increased with increasing pH and adsorbent dose, but decreased with increasing initial dissolved metal concentration. The pH of the solution was the most important parameter controlling adsorption of Cd(II), Cu(II), Fe(II), Ni(II), Pb(II), Zn(II), and As(V) by BPMS. The adsorption data were successfully modeled using the Langmuir adsorption isotherm. Desorption experiments showed that the reversibility of adsorption was low, suggesting high-affinity adsorption governed by chemisorption. The mechanism of adsorption for the divalent metals was thought to be the formation of strong, inner-sphere complexes involving surface hydroxyl groups. However, the mechanism for the adsorption of As(V) by BPMS appears to be distinct from that of surface hydroxyl exchange. These results have important implications to the management of metal sulfide sludge produced by bacterial sulfate reduction.

  17. TISSUE DISTRIBUTION OF INORGANIC ARSENIC (AS) AND ITS METHYLATED METABOLITES IN MICE FOLLOWING ORAL ADMINISTRATION OF ARSENATE (ASV)

    Science.gov (United States)

    TISSUE DISTRIBUTION OF INORGANIC ARSENIC (iAs) AND ITS METHYLATED METABOLITES IN MICE FOLLOWING ORAL ADMINISTRATION OF ARSENATE (AsV). E M Kenyon1, L M Del Razo2, and M F Hughes1. 1NHEERL, ORD, US EPA, RTP, NC, USA; 2CINVESTAV-IPN, Mexico City, Mexico.The relationship o...

  18. Studies on voltammetric determination of cadmium in samples containing native and digested proteins

    Energy Technology Data Exchange (ETDEWEB)

    Drozd, Marcin; Pietrzak, Mariusz, E-mail: mariusz@ch.pw.edu.pl; Malinowska, Elżbieta

    2014-03-01

    Highlights: • Proteins exhibit diverse impact on the DPASV cadmium signals. • Proteins subjected to HNO{sub 3} introduce less interference, than the native ones. • Optimal amount of SDS depends on the kind of protein. • Presence of thiolated coating agents of QDs do not influence the analysis. - Abstract: This work focuses on determination of cadmium ions using anodic stripping voltammetry (ASV) on thin film mercury electrode in conditions corresponding to those obtained after digestion of cadmium-based quantum dots and their conjugates. It presents the impact of selected proteins, including potential receptors and surface blocking agents on the voltammetric determination of cadmium. Experiments regarding elimination of interferences related to proteins presence using sodium dodecyl sulfate (SDS) are also shown. Effect of SDS on selected analytical parameters and simplicity of analyses carried out was investigated in the framework of current studies. The significant differences of influence among tested proteins on ASV cadmium determination, as well as the variability in SDS effectiveness as the antifouling agent were observed and explained. This work is especially important for those, who design new bioassays and biosensors with a use of quantum dots as electrochemical labels, as it shows what problems may arise from presence of native and digested proteins in tested samples.

  19. Potential disruption of protein-protein interactions by graphene oxide

    International Nuclear Information System (INIS)

    Feng, Mei; Kang, Hongsuk; Luan, Binquan; Yang, Zaixing; Zhou, Ruhong

    2016-01-01

    Graphene oxide (GO) is a promising novel nanomaterial with a wide range of potential biomedical applications due to its many intriguing properties. However, very little research has been conducted to study its possible adverse effects on protein-protein interactions (and thus subsequent toxicity to human). Here, the potential cytotoxicity of GO is investigated at molecular level using large-scale, all-atom molecular dynamics simulations to explore the interaction mechanism between a protein dimer and a GO nanosheet oxidized at different levels. Our theoretical results reveal that GO nanosheet could intercalate between the two monomers of HIV-1 integrase dimer, disrupting the protein-protein interactions and eventually lead to dimer disassociation as graphene does [B. Luan et al., ACS Nano 9(1), 663 (2015)], albeit its insertion process is slower when compared with graphene due to the additional steric and attractive interactions. This study helps to better understand the toxicity of GO to cell functions which could shed light on how to improve its biocompatibility and biosafety for its wide potential biomedical applications.

  20. Potential disruption of protein-protein interactions by graphene oxide

    Energy Technology Data Exchange (ETDEWEB)

    Feng, Mei [Department of Physics, Institute of Quantitative Biology, Zhejiang University, Hangzhou 310027 (China); Kang, Hongsuk; Luan, Binquan [Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598 (United States); Yang, Zaixing [Institute of Quantitative Biology and Medicine, SRMP and RAD-X, and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123 (China); Zhou, Ruhong, E-mail: ruhong@us.ibm.com [Department of Physics, Institute of Quantitative Biology, Zhejiang University, Hangzhou 310027 (China); Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598 (United States); Department of Chemistry, Columbia University, New York, New York 10027 (United States)

    2016-06-14

    Graphene oxide (GO) is a promising novel nanomaterial with a wide range of potential biomedical applications due to its many intriguing properties. However, very little research has been conducted to study its possible adverse effects on protein-protein interactions (and thus subsequent toxicity to human). Here, the potential cytotoxicity of GO is investigated at molecular level using large-scale, all-atom molecular dynamics simulations to explore the interaction mechanism between a protein dimer and a GO nanosheet oxidized at different levels. Our theoretical results reveal that GO nanosheet could intercalate between the two monomers of HIV-1 integrase dimer, disrupting the protein-protein interactions and eventually lead to dimer disassociation as graphene does [B. Luan et al., ACS Nano 9(1), 663 (2015)], albeit its insertion process is slower when compared with graphene due to the additional steric and attractive interactions. This study helps to better understand the toxicity of GO to cell functions which could shed light on how to improve its biocompatibility and biosafety for its wide potential biomedical applications.

  1. Study of Structure-active Relationship for Inhibitors of HIV-1 Integrase LEDGF/p75 Interaction by Machine Learning Methods.

    Science.gov (United States)

    Li, Yang; Wu, Yanbin; Yan, Aixia

    2017-07-01

    HIV-1 integrase (IN) is a promising target for anti-AIDS therapy, and LEDGF/p75 is proved to enhance the HIV-1 integrase strand transfer activity in vitro. Blocking the interaction between IN and LEDGF/p75 is an effective way to inhibit HIV replication infection. In this work, 274 LEDGF/p75-IN inhibitors were collected as the dataset. Support Vector Machine (SVM), Decision Tree (DT), Function Tree (FT) and Random Forest (RF) were applied to build several computational models for predicting whether a compound is an active or weakly active LEDGF/p75-IN inhibitor. Each compound is represented by MACCS fingerprints and CORINA Symphony descriptors. The prediction accuracies for the test sets of all the models are over 70 %. The best model Model 3B built by FT obtained a prediction accuracy and a Matthews Correlation Coefficient (MCC) of 81.08 % and 0.62 on test set, respectively. We found that the hydrogen bond and hydrophobic interactions are important for the bioactivity of an inhibitor. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Molecular modeling study on the allosteric inhibition mechanism of HIV-1 integrase by LEDGF/p75 binding site inhibitors.

    Directory of Open Access Journals (Sweden)

    Weiwei Xue

    Full Text Available HIV-1 integrase (IN is essential for the integration of viral DNA into the host genome and an attractive therapeutic target for developing antiretroviral inhibitors. LEDGINs are a class of allosteric inhibitors targeting LEDGF/p75 binding site of HIV-1 IN. Yet, the detailed binding mode and allosteric inhibition mechanism of LEDGINs to HIV-1 IN is only partially understood, which hinders the structure-based design of more potent anti-HIV agents. A molecular modeling study combining molecular docking, molecular dynamics simulation, and binding free energy calculation were performed to investigate the interaction details of HIV-1 IN catalytic core domain (CCD with two recently discovered LEDGINs BI-1001 and CX14442, as well as the LEDGF/p75 protein. Simulation results demonstrated the hydrophobic domain of BI-1001 and CX14442 engages one subunit of HIV-1 IN CCD dimer through hydrophobic interactions, and the hydrophilic group forms hydrogen bonds with HIV-1 IN CCD residues from other subunit. CX14442 has a larger tert-butyl group than the methyl of BI-1001, and forms better interactions with the highly hydrophobic binding pocket of HIV-1 IN CCD dimer interface, which can explain the stronger affinity of CX14442 than BI-1001. Analysis of the binding mode of LEDGF/p75 with HIV-1 IN CCD reveals that the LEDGF/p75 integrase binding domain residues Ile365, Asp366, Phe406 and Val408 have significant contributions to the binding of the LEDGF/p75 to HIV1-IN. Remarkably, we found that binding of BI-1001 and CX14442 to HIV-1 IN CCD induced the structural rearrangements of the 140 s loop and oration displacements of the side chains of the three conserved catalytic residues Asp64, Asp116, and Glu152 located at the active site. These results we obtained will be valuable not only for understanding the allosteric inhibition mechanism of LEDGINs but also for the rational design of allosteric inhibitors of HIV-1 IN targeting LEDGF/p75 binding site.

  3. Targeted transgene insertion into the CHO cell genome using Cre recombinase-incorporating integrase-defective retroviral vectors.

    Science.gov (United States)

    Kawabe, Yoshinori; Shimomura, Takuya; Huang, Shuohao; Imanishi, Suguru; Ito, Akira; Kamihira, Masamichi

    2016-07-01

    Retroviral vectors have served as efficient gene delivery tools in various biotechnology fields. However, viral DNA is randomly inserted into the genome, which can cause problems, such as insertional mutagenesis and gene silencing. Previously, we reported a site-specific gene integration system, in which a transgene is integrated into a predetermined chromosomal locus of Chinese hamster ovary (CHO) cells using integrase-defective retroviral vectors (IDRVs) and Cre recombinase. In this system, a Cre expression plasmid is transfected into founder cells before retroviral transduction. In practical applications of site-specific gene modification such as for hard-to-transfect cells or for in vivo gene delivery, both the transgene and the Cre protein into retroviral virions should be encapsulate. Here, we generated novel hybrid IDRVs in which viral genome and enzymatically active Cre can be delivered (Cre-IDRVs). Cre-IDRVs encoding marker genes, neomycin resistance and enhanced green fluorescent protein (EGFP), flanked by wild-type and mutated loxP sites were produced using an expression plasmid for a chimeric protein of Cre and retroviral gag-pol. After analyzing the incorporation of the Cre protein into retroviral virions by Western blotting, the Cre-IDRV was infected into founder CHO cells, in which marker genes (hygromycin resistance and red fluorescent protein) flanked with corresponding loxP sites are introduced into the genome. G418-resistant colonies expressing GFP appeared and the site-specific integration of the transgene into the expected chromosomal site was confirmed by PCR and sequencing of amplicons. Moreover, when Cre-IDRV carried a gene expression unit for a recombinant antibody, the recombinant cells in which the antibody expression cassette was integrated in a site-specific manner were generated and the cells produced the recombinant antibody. This method may provide a promising tool to perform site-specific gene modification according to Cre

  4. Otimização das condições de pré-redução do As(V em extratos do método BCR para quantificação de arsênio por HG-AAS Optimization of pre-reduction conditions of as(V in BCR extracts to quantify arsenic by HG-AAS

    Directory of Open Access Journals (Sweden)

    Eduardo Vinícius Vieira Varejão

    2009-08-01

    Full Text Available A determinação de As por espectrometria de absorção atômica com geração de hidretos (HG-AAS constitui um método simples, sensível, preciso e de baixo custo. Entretanto, essa técnica requer a pré-redução das espécies de As(V, o que se obtém através do uso de agentes redutores como o KI. Em extratos contendo agentes oxidantes, a pré-redução do As é comprometida, como acontece em extratos obtidos pela aplicação do método BCR (acrônimo francês para Community Bureau of Reference para a extração sequencial de As em sedimentos. O objetivo deste trabalho foi avaliar as condições de redução do As(V a As(III, de modo a permitir o uso da HG-AAS para a quantificação do arsênio em extratos obtidos a partir do método BCR. Foram avaliadas condições reacionais utilizando KI, L-cisteína e ácido ascórbico. Para cada uma das etapas de extração do método BCR, diferentes condições de pré-redução possibilitaram a detecção quantitativa do As presente. O uso do método BCR para a extração de arsênio em amostras de sedimentos contaminadas e a aplicação das condições de pré-redução do As(V selecionadas, seguida pela detecção por HG-AAS, forneceram percentagens de recuperação entre 91 e 99 %.The determination of As by hydride generation atomic absorption spectroscopy (HG-AAS is a simple, sensitive, precise and low-cost method. However, this technique requires the pre-reduction of the existing As(V species, which is obtained by the use of reducing agents such as KI. In extracts containing oxidizing agents, the pre-reduction of As is impaired, as it occurs in extracts obtained by the BCR (French acronym for Community Bureau of Reference method for the sequential extraction of As in sediments. The objective of this study was to evaluate the conditions for the reduction of As(V to As(III in a way that allows the use of HG-AAS for the quantification of arsenic in extracts obtained using the BCR method. Reaction

  5. Removal of bacterial cells, antibiotic resistance genes and integrase genes by on-site hospital wastewater treatment plants: surveillance of treated hospital effluent quality

    KAUST Repository

    Timraz, Kenda Hussain Hassan; Xiong, Yanghui; Al Qarni, Hamed; Hong, Pei-Ying

    2016-01-01

    This study aims to evaluate the removal efficiency of microbial contaminants, including total cell counts, antibiotic-resistant bacteria (ARB), antibiotic resistance genes (ARGs, e.g. tetO, tetZ, sul1 and sul2) and integrase genes (e.g. intl1

  6. Insights into the subsurface transport of As(V) and Se(VI) in produced water from hydraulic fracturing using soil samples from Qingshankou Formation, Songliao Basin, China.

    Science.gov (United States)

    Chen, Season S; Sun, Yuqing; Tsang, Daniel C W; Graham, Nigel J D; Ok, Yong Sik; Feng, Yujie; Li, Xiang-Dong

    2017-04-01

    Produced water is a type of wastewater generated from hydraulic fracturing, which may pose a risk to the environment and humans due to its high ionic strength and the presence of elevated concentrations of metals/metalloids that exceed maximum contamination levels. The mobilization of As(V) and Se(VI) in produced water and selected soils from Qingshankou Formation in the Songliao Basin in China were investigated using column experiments and synthetic produced water whose quality was representative of waters arising at different times after well creation. Temporal effects of produced water on metal/metalloid transport and sorption/desorption were investigated by using HYDRUS-1D transport modelling. Rapid breakthrough and long tailings of As(V) and Se(VI) transport were observed in Day 1 and Day 14 solutions, but were reduced in Day 90 solution probably due to the elevated ionic strength. The influence of produced water on the hydrogeological conditions (i.e., change between equilibrium and non-equilibrium transport) was evidenced by the change of tracer breakthrough curves before and after the leaching of produced water. This possibly resulted from the sorption of polyacrylamide (PAM (-CH 2 CHCONH 2 -) n ) onto soil surfaces, through its use as a friction reducer in fracturing solutions. The sorption was found to be reversible in this study. Minimal amounts of sorbed As(V) were desorbed whereas the majority of sorbed Se(VI) was readily leached out, to an extent which varied with the composition of the produced water. These results showed that the mobilization of As(V) and Se(VI) in soil largely depended on the solution pH and ionic strength. Understanding the differences in metal/metalloid transport in produced water is important for proper risk management. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Design and Synthesis of Bis-amide and Hydrazide-containing Derivatives of Malonic Acid as Potential HIV-1 Integrase Inhibitors

    Directory of Open Access Journals (Sweden)

    Nouri Neamati

    2008-10-01

    Full Text Available HIV-1 integrase (IN is an attractive and validated target for the development of novel therapeutics against AIDS. In the search for new IN inhibitors, we designed and synthesized three series of bis-amide and hydrazide-containing derivatives of malonic acid. We performed a docking study to investigate the potential interactions of the title compounds with essential amino acids on the IN active site.

  8. 6-(1-Benzyl-1H-pyrrol-2-yl)-2,4-dioxo-5-hexenoic acids as dual inhibitors of recombinant HIV-1 integrase and ribonuclease H, synthesized by a parallel synthesis approach.

    Science.gov (United States)

    Costi, Roberta; Métifiot, Mathieu; Esposito, Francesca; Cuzzucoli Crucitti, Giuliana; Pescatori, Luca; Messore, Antonella; Scipione, Luigi; Tortorella, Silvano; Zinzula, Luca; Novellino, Ettore; Pommier, Yves; Tramontano, Enzo; Marchand, Christophe; Di Santo, Roberto

    2013-11-14

    The increasing efficiency of HAART has helped to transform HIV/AIDS into a chronic disease. Still, resistance and drug-drug interactions warrant the development of new anti-HIV agents. We previously discovered hit 6, active against HIV-1 replication and targeting RNase H in vitro. Because of its diketo-acid moiety, we speculated that this chemotype could serve to develop dual inhibitors of both RNase H and integrase. Here, we describe a new series of 1-benzyl-pyrrolyl diketohexenoic derivatives, 7a-y and 8a-y, synthesized following a parallel solution-phase approach. Those 50 analogues have been tested on recombinant enzymes (RNase H and integrase) and in cell-based assays. Approximately half (22) exibited inhibition of HIV replication. Compounds 7b, 7u, and 8g were the most active against the RNase H activity of reverse-transcriptase, with IC50 values of 3, 3, and 2.5 μM, respectively. Compound 8g was also the most potent integrase inhibitor with an IC50 value of 26 nM.

  9. Application of granular activated carbon/MnFe2O4 composite immobilized on C. glutamicum MTCC 2745 to remove As(III) and As(V): Kinetic, mechanistic and thermodynamic studies

    Science.gov (United States)

    Podder, M. S.; Majumder, C. B.

    2016-01-01

    The main objective of the present study was to investigate the efficiency of Corynebacterium glutamicum MTCC 2745 immobilized on granular activated carbon/MnFe2O4 (GAC/MnFe2O4) composite to treat high concentration of arsenic bearing wastewater. Non-linear regression analysis was done for determining the best-fit kinetic model on the basis of three correlation coefficients and three error functions and also for predicting the parameters involved in kinetic models. The results showed that Fractal-like mixed 1,2 order model for As(III) and Brouser-Weron-Sototlongo as well as Fractal-like pseudo second order models for As(V) were proficient to provide realistic description of biosorption/bioaccumulation kinetic. Applicability of mechanistic models in the current study exhibited that the rate governing step in biosorption/bioaccumulation of both As(III) and As(V) was film diffusion rather than intraparticle diffusion. The evaluated thermodynamic parameters ΔG0, ΔH0 and ΔS0 revealed that biosorption/bioaccumulation of both As(III) and As(V) was feasible, spontaneous and exothermic under studied conditions.

  10. Evidence for the horizontal transfer of an integrase gene from a fusellovirus to a pRN-like plasmid within a single strain of Sulfolobus and the implications for plasmid survival

    DEFF Research Database (Denmark)

    Peng, Xu

    2008-01-01

    of the integrase gene occurs in the viral attachment site (attP), which corresponds to the anticodon region of the targeted tRNA gene in the host chromosome. This point mutation confers on pXZ1 the ability to integrate into the tRNA(Glu)[CUC] gene, which differs from the integration site of SSV4, t......RNA(Glu)[UUC]. SSV4 and pXZ1 were also shown experimentally to integrate into separate sites on the host chromosome. This is believed to be the first report of a pRN plasmid sharing its natural host with a fusellovirus and carrying a highly similar integrase gene....

  11. Novel 3′-Processing Integrase Activity Assay by Real-Time PCR for Screening and Identification of HIV-1 Integrase Inhibitors

    Directory of Open Access Journals (Sweden)

    Supachai Sakkhachornphop

    2015-01-01

    Full Text Available The 3′-end processing (3′P of each viral long terminal repeat (LTR during human immunodeficiency virus type-1 (HIV-1 integration is a vital step in the HIV life cycle. Blocking the 3′P using 3′P inhibitor has recently become an attractive strategy for HIV-1 therapeutic intervention. Recently, we have developed a novel real-time PCR based assay for the detection of 3′P activity in vitro. The methodology usually involves biotinylated HIV-1 LTR, HIV-1 integrase (IN, and specific primers and probe. In this novel assay, we designed the HIV-1 LTR substrate based on a sequence with a homology to HIV-1 LTR labeled at its 3′ end with biotin on the sense strand. Two nucleotides at the 3′ end were subsequently removed by IN activity. Only two nucleotides labeled biotin were captured on an avidin-coated tube; therefore, inhibiting the binding of primers and probe results in late signals in the real-time PCR. This novel assay has successfully detected both the 3′P activity of HIV-1 IN and the anti-IN activity by Raltegravir and sodium azide agent. This real-time PCR assay has been shown to be effective and inexpensive for a high-throughput screening of novel IN inhibitors.

  12. Removal of As(V) and simultaneous production of copper powder from a Cu(II)-As(V)-H{sub 2}SO{sub 4} electrolyte by using reactive electrodialysis; Eliminacion de As (V) y produccion simultanea de polvo de cobre de un electrolito de Cu(II) - As(V) - H{sub 2}SO{sub 4} mediante electrodialisis reactiva

    Energy Technology Data Exchange (ETDEWEB)

    Ibanez, J. P.

    2012-11-01

    The removal of As(V) and the simultaneous generation of powder of copper from an electrolyte made of As(V) - Cu(II) - H{sub 2}SO{sub 4} was studied by using electro dialysis at several current densities, temperatures and aeration of the electrolyte. The removal of arsenic was proportional to the current density, temperature and aeration used. The removal of arsenic reached a value of 0.14 mmol/h at 500 A/m2, 25 degree centigrade and without aeration, this value increased to 0.31 mmol/h by increasing the aeration to 6.6 l/h. The Cu(II) was recovered in a 98 % as a fine arsenic free powder of metallic copper with oxides of copper. The arsenic was removed from the electrolyte by adsorption onto the anodic slimes generated from the lead anode oxidation. (Author) 24 refs.

  13. Determination of As(III and As(V in waters by chronopotentiometric stripping analysis

    Directory of Open Access Journals (Sweden)

    Švarc-Gajić Jaroslava V.

    2006-01-01

    Full Text Available Arsenic is a naturally occurring toxic and carcinogenic element. The degree of the toxicity depends on its chemical form and the concentration. Application of a sensitive, selective, simple and rapid method for detection and monitoring of different oxidation states of arsenic in waters is of great importance because main route of population exposure is through drinking water. In this work chronopotentiometric stripping analysis (CSA was used for the determination of As(III and As(V in tap, well, river and rain waters from Vojvodina (Serbia. Gold film electrode on the glassy carbon support was used as the working electrode. The experimental parameters of the technique were investigated and optimized. Detection limit of the method for the electrolysis time of 600 s was 2 μg/dm3 of As(III.

  14. Mutational analyses of the core domain of Avian Leukemia and Sarcoma Viruses integrase: critical residues for concerted integration and multimerization

    International Nuclear Information System (INIS)

    Moreau, Karen; Faure, Claudine; Violot, Sebastien; Gouet, Patrice; Verdier, Gerard; Ronfort, Corinne

    2004-01-01

    During replicative cycle of retroviruses, the reverse-transcribed viral DNA is integrated into the cell DNA by the viral integrase (IN) enzyme. The central core domain of IN contains the catalytic site of the enzyme and is involved in binding viral ends and cell DNA as well as dimerization. We previously performed single amino acid substitutions in the core domain of an Avian Leukemia and Sarcoma Virus (ALSV) IN [Arch. Virol. 147 (2002) 1761]. Here, we modeled the resulting IN mutants and analyzed the ability of these mutants to mediate concerted DNA integration in an in vitro assay, and to form dimers by protein-protein cross-linking and size exclusion chromatography. The N197C mutation resulted in the inability of the mutant to perform concerted integration that was concomitant with a loss of IN dimerization. Surprisingly, mutations Q102G and A106V at the dimer interface resulted in mutants with higher efficiencies than the wild-type IN in performing two-ended concerted integration of viral DNA ends. The G139D and A195V mutants had a trend to perform one-ended DNA integration of viral ends instead of two-ended integration. More drastically, the I88L and L135G mutants preferentially mediated nonconcerted DNA integration although the proteins form dimers. Therefore, these mutations may alter the formation of IN complexes of higher molecular size than a dimer that would be required for concerted integration. This study points to the important role of core domain residues in the concerted integration of viral DNA ends as well as in the oligomerization of the enzyme

  15. L-Chicoric acid inhibits human immunodeficiency virus type 1 integration in vivo and is a noncompetitive but reversible inhibitor of HIV-1 integrase in vitro

    International Nuclear Information System (INIS)

    Reinke, Ryan A.; Lee, Deborah J.; McDougall, Brenda R.; King, Peter J.; Victoria, Joseph; Mao Yingqun; Lei Xiangyang; Reinecke, Manfred G.; Robinson, W. Edward

    2004-01-01

    The human immunodeficiency virus (HIV) integrase (IN) must covalently join the viral cDNA into a host chromosome for productive HIV infection. L-Chicoric acid (L-CA) enters cells poorly but is a potent inhibitor of IN in vitro. Using quantitative real-time polymerase chain reaction (PCR), L-CA inhibits integration at concentrations from 500 nM to 10 μM but also inhibits entry at concentrations above 1 μM. Using recombinant HIV IN, steady-state kinetic analyses with L-CA were consistent with a noncompetitive or irreversible mechanism of inhibition. IN, in the presence or absence of L-CA, was successively washed. Inhibition of IN diminished, demonstrating that L-CA was reversibly bound to the protein. These data demonstrate that L-CA is a noncompetitive but reversible inhibitor of IN in vitro and of HIV integration in vivo. Thus, L-CA likely interacts with amino acids other than those which bind substrate

  16. Adeno-associated virus Rep-mediated targeting of integrase-defective retroviral vector DNA circles into human chromosome 19

    International Nuclear Information System (INIS)

    Huang, Shuohao; Kawabe, Yoshinori; Ito, Akira; Kamihira, Masamichi

    2012-01-01

    Highlights: ► Adeno-associated virus (AAV) is capable of targeted integration in human cells. ► Integrase-defective retroviral vector (IDRV) enables a circular DNA delivery. ► A targeted integration system of IDRV DNA using the AAV integration mechanism. ► Targeted IDRV integration ameliorates the safety concerns for retroviral vectors. -- Abstract: Retroviral vectors have been employed in clinical trials for gene therapy owing to their relative large packaging capacity, alterable cell tropism, and chromosomal integration for stable transgene expression. However, uncontrollable integrations of transgenes are likely to cause safety issues, such as insertional mutagenesis. A targeted transgene integration system for retroviral vectors, therefore, is a straightforward way to address the insertional mutagenesis issue. Adeno-associated virus (AAV) is the only known virus capable of targeted integration in human cells. In the presence of AAV Rep proteins, plasmids possessing the p5 integration efficiency element (p5IEE) can be integrated into the AAV integration site (AAVS1) in the human genome. In this report, we describe a system that can target the circular DNA derived from non-integrating retroviral vectors to the AAVS1 site by utilizing the Rep/p5IEE integration mechanism. Our results showed that after G418 selection 30% of collected clones had retroviral DNA targeted at the AAVS1 site.

  17. Mode of inhibition of HIV-1 Integrase by a C-terminal domain-specific monoclonal antibody*

    Directory of Open Access Journals (Sweden)

    Merkel George

    2006-06-01

    Full Text Available Abstract Background To further our understanding of the structure and function of HIV-1 integrase (IN we developed and characterized a library of monoclonal antibodies (mAbs directed against this protein. One of these antibodies, mAb33, which is specific for the C-terminal domain, was found to inhibit HIV-1 IN processing activity in vitro; a corresponding Fv fragment was able to inhibit HIV-1 integration in vivo. Our subsequent studies, using heteronuclear nuclear magnetic resonance spectroscopy, identified six solvent accessible residues on the surface of the C-terminal domain that were immobilized upon binding of the antibody, which were proposed to comprise the epitope. Here we test this hypothesis by measuring the affinity of mAb33 to HIV-1 proteins that contain Ala substitutions in each of these positions. To gain additional insight into the mode of inhibition we also measured the DNA binding capacity and enzymatic activities of the Ala substituted proteins. Results We found that Ala substitution of any one of five of the putative epitope residues, F223, R224, Y226, I267, and I268, caused a decrease in the affinity of the mAb33 for HIV-1 IN, confirming the prediction from NMR data. Although IN derivatives with Ala substitutions in or near the mAb33 epitope exhibited decreased enzymatic activity, none of the epitope substitutions compromised DNA binding to full length HIV-1 IN, as measured by surface plasmon resonance spectroscopy. Two of these derivatives, IN (I276A and IN (I267A/I268A, exhibited both increased DNA binding affinity and uncharacteristic dissociation kinetics; these proteins also exhibited non-specific nuclease activity. Results from these investigations are discussed in the context of current models for how the C-terminal domain interacts with substrate DNA. Conclusion It is unlikely that inhibition of HIV-1 IN activity by mAb33 is caused by direct interaction with residues that are essential for substrate binding. Rather

  18. The HIV-1 integrase-LEDGF allosteric inhibitor MUT-A: resistance profile, impairment of virus maturation and infectivity but without influence on RNA packaging or virus immunoreactivity

    NARCIS (Netherlands)

    Amadori, Céline; Ubeles van der Velden, Yme; Bonnard, Damien; Orlov, Igor; van Bel, Nikki; Le Rouzic, Erwann; Miralles, Laia; Brias, Julie; Chevreuil, Francis; Spehner, Daniele; Chasset, Sophie; Ledoussal, Benoit; Mayr, Luzia; Moreau, François; García, Felipe; Gatell, José; Zamborlini, Alessia; Emiliani, Stéphane; Ruff, Marc; Klaholz, Bruno P.; Moog, Christiane; Berkhout, Ben; Plana, Montserrat; Benarous, Richard

    2017-01-01

    HIV-1 Integrase (IN) interacts with the cellular co-factor LEDGF/p75 and tethers the HIV preintegration complex to the host genome enabling integration. Recently a new class of IN inhibitors was described, the IN-LEDGF allosteric inhibitors (INLAIs). Designed to interfere with the IN-LEDGF

  19. Four-tiered π interaction at the dimeric interface of HIV-1 integrase critical for DNA integration and viral infectivity

    International Nuclear Information System (INIS)

    Al-Mawsawi, Laith Q.; Hombrouck, Anneleen; Dayam, Raveendra; Debyser, Zeger; Neamati, Nouri

    2008-01-01

    HIV-1 integrase (IN) is an essential enzyme for viral infection. Here, we report an extensive π electron orbital interaction between four amino acids, W132, M178, F181 and F185, located at the dimeric interface of IN that is critical for the strand transfer activity alone. Catalysis of nine different mutant IN proteins at these positions were evaluated. Whereas the 3'-processing activity is predominantly strong, the strand transfer activity of each enzyme was completely dependent on an intact π electron orbital interaction at the dimeric interface. Four representative IN mutants were constructed in the context of the infectious NL4.3 HIV-1 viral clone. Whereas viruses with an intact π electron orbital interaction at the IN dimeric interface replicated comparable to wild type, viruses containing an abolished π interaction were non-infectious. Q-PCR analysis of viral DNA forms during viral replication revealed pleiotropic effects of most mutations. We hypothesize that the π interaction is a critical contact point for the assembly of functional IN multimeric complexes, and that IN multimerization is required for a functional pre-integration complex. The rational design of small molecule inhibitors targeting the disruption of this π-π interaction should lead to powerful anti-retroviral drugs

  20. COMPARATIVE TISSUE DISTRIBUTION AND URINARY EXCRETION OF INORGANIC ARSENIC (IAS) AND ITS METHYLATED METABOLITES IN MICE FOLLOWING ORAL ADMINISTRATION OF ARSENATE (ASV) AND ARSENITE (ASIII)

    Science.gov (United States)

    COMPARATIVE TISSUE DISTRIBUTION AND URINARY EXCRETION OF INORGANIC ARSENIC (iAs) AND ITS METHYLATED METABOLITES IN MICE FOLLOWING ORAL ADMINISTRATION OF ARSENATE (AsV) AND ARSENITE (AsIII). E M Kenyon, L M Del Razo and M F Hughes. U.S. EPA, ORD, NHEERL, ETD, PKB, RTP, NC, USA; ...

  1. Integrase-Deficient Lentiviral Vector as an All-in-One Platform for Highly Efficient CRISPR/Cas9-Mediated Gene Editing

    Directory of Open Access Journals (Sweden)

    Pavel I. Ortinski

    2017-06-01

    Full Text Available The CRISPR/Cas9 systems have revolutionized the field of genome editing by providing unprecedented control over gene sequences and gene expression in many species, including humans. Lentiviral vectors (LVs are one of the primary delivery platforms for the CRISPR/Cas9 system due to their ability to accommodate large DNA payloads and sustain robust expression in a wide range of dividing and non-dividing cells. However, long-term expression of LV-delivered Cas9/guide RNA may lead to undesirable off-target effects characterized by non-specific RNA-DNA interactions and off-target DNA cleavages. Integrase-deficient lentiviral vectors (IDLVs present an attractive means for delivery of CRISPR/Cas9 components because: (1 they are capable of transducing a broad range of cells and tissues, (2 have superior packaging capacity compared to other vectors (e.g., adeno-associated viral vectors, and (3 they are expressed transiently and demonstrate very weak integration capability. In this manuscript, we aimed to establish IDLVs as a means for safe and efficient delivery of CRISPR/Cas9. To this end, we developed an all-in-one vector cassette with increased production efficacy and demonstrated that CRISPR/Cas9 delivered by the improved IDLV vectors can mediate rapid and robust gene editing in human embryonic kidney (HEK293T cells and post-mitotic brain neurons in vivo, via transient expression and with higher gene-targeting specificity than the corresponding integrase-competent vectors.

  2. Speciation of the immediately mobilisable As(III), As(V), MMA and DMA in river sediments by high performance liquid chromatography-hydride generation-atomic fluorescence spectrometry following ultrasonic extraction

    International Nuclear Information System (INIS)

    Huerga, A.; Lavilla, I.; Bendicho, C.

    2005-01-01

    In this work, a fast method is developed for the speciation of As(III), As(V), MMA and DMA in the immediately mobilisable fraction of river sediments (i.e. water-soluble and phosphate-exchangeable) by high performance liquid chromatography-hydride generation-atomic fluorescence detection (HPLC-HG-AFD) after extraction using focused ultrasound. The influence of relevant parameters influencing an ion-pairing chromatographic separation following isocratic elution (i.e. amount of MeOH in the mobile phase, ion pair reagent concentration, pH, flow rate) was studied. Focused ultrasound transmitted from an ultrasonic probe provided the same extractable contents as conventional extraction with no changes in the species distribution. The effect of the drying step over extraction of As species was investigated. The following drying procedures were compared: freeze-, oven-, microwave- and air-drying. No influence of the drying operation on the water-extractable fraction was observed. However, freeze- and air-drying yielded significantly higher phosphate-extractable amounts of As(III) and As(V) as compared to oven and microwaves. Detection limits for the As species were in the range 1.3-4.1 ng/g for the water-soluble fraction and 1.6-4.8 ng/g for the phosphate buffer exchangeable fraction. The method was applied to the speciation of immediately mobilisable As(III), As(V), DMA and MMA in 11 sediment samples collected along the beds of the Louro River (southern Galicia, Spain)

  3. The phytopathogenic virulent effector protein RipI induces apoptosis in budding yeast Saccharomyces cerevisiae.

    Science.gov (United States)

    Deng, Meng-Ying; Sun, Yun-Hao; Li, Pai; Fu, Bei; Shen, Dong; Lu, Yong-Jun

    2016-10-01

    Virulent protein toxins secreted by the bacterial pathogens can cause cytotoxicity by various molecular mechanisms to combat host cell defense. On the other hand, these proteins can also be used as probes to investigate the defense pathway of host innate immunity. Ralstonia solanacearum, one of the most virulent bacterial phytopathogens, translocates more than 70 effector proteins via type III secretion system during infection. Here, we characterized the cytotoxicity of effector RipI in budding yeast Saccharomyce scerevisiae, an alternative host model. We found that over-expression of RipI resulted in severe growth defect and arginine (R) 117 within the predicted integrase motif was required for inhibition of yeast growth. The phenotype of death manifested the hallmarks of apoptosis. Our data also revealed that RipI-induced apoptosis was independent of Yca1 and mitochondria-mediated apoptotic pathways because Δyca1 and Δaif1 were both sensitive to RipI as compared with the wild type. We further demonstrated that RipI was localized in the yeast nucleus and the N-terminal 1-174aa was required for the localization. High-throughput RNA sequencing analysis showed that upon RipI over-expression, 101 unigenes of yeast ribosome presented lower expression level, and 42 GO classes related to the nucleus or recombination were enriched with differential expression levels. Taken together, our data showed that a nuclear-targeting effector RipI triggers yeast apoptosis, potentially dependent on its integrase function. Our results also provided an alternative strategy to dissect the signaling pathway of cytotoxicity induced by the protein toxins. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Speciation of As(III) and As(V) in water and sediment using reverse-phase ion-pair high-performance liquid chromatography-neutron activation analysis (HPLC-NAA).

    Science.gov (United States)

    Tulasi, Delali; Adotey, Dennis; Affum, Andrews; Carboo, Derick; Serfor-Armah, Yaw

    2013-10-01

    Total As content and the As species distribution in water and sediments from the Kwabrafo stream, a major water body draining the Obuasi gold mining community in southwestern Ghana, have been investigated. Total As content was determined by instrumental neutron activation analysis (INAA). Ion-pair reverse phase high-performance liquid chromatography-neutron activation analysis (HPLC-NAA) was used for speciation of As species. Solid phase extraction with phosphate buffer was used to extract soluble As species from lyophilized sediment. The mass balance after phosphate extraction of soluble As species in sediment varied from 89 to 96 %. Compositionally appropriate reference material International Atomic Energy Agency (IAEA)-Lake Sediment (SL)-1 was used to check the validity of INAA method for total As determination. The measured values are in good agreement with the IAEA recommended value and also within the 95 % confidence interval. The accuracy of the measurement in terms of relative deviation from the IAEA recommended value was ±0.83 %. "In-house" prepared As(III) and As(V) standards were used to validate the HPLC-INAA method used for the As species determination. Total As concentration in the water samples ranged from 1.15 to 9.20 mg/L. As(III) species in water varied from 0.13 to 0.7 mg/L, while As(V) species varied from 0.79 to 3.85 mg/L. Total As content in sediment ranged from 2,134 to 3,596 mg/kg dry mass. The levels of As(III) and As(V) species in the sediment ranges from 138 to 506 mg/kg dry mass and 156 to 385 mg/kg dry mass, respectively.

  5. Effects of changing pH, incubation time, and As(V) competition, on F- retention on soils, natural adsorbents, by-products, and waste materials

    Science.gov (United States)

    Quintáns-Fondo, Ana; Santás-Miguel, Vanesa; Nóvoa-Muñoz, Juan C.; Arias-Estévez, Manuel; Fernández-Sanjurjo, María J.; Álvarez-Rodríguez, Esperanza; Núñez-Delgado, Avelino

    2018-03-01

    The purpose of this work was to elucidate the repercussion of changing pH, incubation time and As(V) competition on fluoride (F-) sorption on forest and vineyard soil samples, pyritic and granitic materials, as well as on the by-products pine sawdust, oak wood ash, mussel shell ash, fine and coarse mussel shell, and slate processing waste fines. To reach this end, the methodological approach was based on batch-type experiments. The results indicate that, for most materials, F- sorption was very high at the start, but was clearly diminished when the pH value increased. However, oak wood ash and shell ash showed high F- sorption even at alkaline pH, and pine sawdust showed low F- sorption for any pH value. Specifically, F- sorption was close to 100% for both ashes at pH time on F- sorption, it was very low for both soils, pyritic material, granitic material and both kinds of ashes, as all of them showed very rapid F- sorption from the start, with differences being lesser than 10% between sorption at 30 min and 1 month of incubation. However, sawdust and slate fines sorbed 20% of added F- in 30 minutes, remaining constant up to twelve hours, and doubling after 30 days. And finally, mussel shell sorbed 20% at 30 minutes, increasing to close to 60% when incubation time was 30 days. This means that some of the materials showed a first sorption phase characterized by rapid F- sorption, and a slower sorption in a second phase. As regards the effect of the presence of As(V) on F- sorption, it was almost negligible, indicating the absence of competition for sorption sites. In view of that all, these results could aid to appropriately manage soils and by-products when focusing on F- removal, in circumstances where pH value changes, contact time vary from hours to days, and potential competition between F- and As(V) could take place.

  6. A novel co-crystal structure affords the design of gain-of-function lentiviral integrase mutants in the presence of modified PSIP1/LEDGF/p75.

    Directory of Open Access Journals (Sweden)

    Stephen Hare

    2009-01-01

    Full Text Available Lens epithelium derived growth factor (LEDGF, also known as PC4 and SFRS1 interacting protein 1 (PSIP1 and transcriptional co-activator p75, is the cellular binding partner of lentiviral integrase (IN proteins. LEDGF accounts for the characteristic propensity of Lentivirus to integrate within active transcription units and is required for efficient viral replication. We now present a crystal structure containing the N-terminal and catalytic core domains (NTD and CCD of HIV-2 IN in complex with the IN binding domain (IBD of LEDGF. The structure extends the known IN-LEDGF interface, elucidating primarily charge-charge interactions between the NTD of IN and the IBD. A constellation of acidic residues on the NTD is characteristic of lentiviral INs, and mutations of the positively charged residues on the IBD severely affect interaction with all lentiviral INs tested. We show that the novel NTD-IBD contacts are critical for stimulation of concerted lentiviral DNA integration by LEDGF in vitro and for its function during the early steps of HIV-1 replication. Furthermore, the new structural details enabled us to engineer a mutant of HIV-1 IN that primarily functions only when presented with a complementary LEDGF mutant. These findings provide structural basis for the high affinity lentiviral IN-LEDGF interaction and pave the way for development of LEDGF-based targeting technologies for gene therapy.

  7. Ultrasensitive liquid chromatography-tandem mass spectrometric methodologies for quantification of five HIV-1 integrase inhibitors in plasma for a microdose clinical trial.

    Science.gov (United States)

    Sun, Li; Li, Hankun; Willson, Kenneth; Breidinger, Sheila; Rizk, Matthew L; Wenning, Larissa; Woolf, Eric J

    2012-10-16

    HIV-1 integrase strand transfer inhibitors are an important class of compounds targeted for the treatment of HIV-1 infection. Microdosing has emerged as an attractive tool to assist in drug candidate screening for clinical development, but necessitates extremely sensitive bioanalytical assays, typically in the pg/mL concentration range. Currently, accelerator mass spectrometry is the predominant tool for microdosing support, which requires a specialized facility and synthesis of radiolabeled compounds. There have been few studies attempted to comprehensively assess a liquid chromatography-tandem mass spectrometry (LC-MS/MS) approach in the context of microdosing applications. Herein, we describe the development of automated LC-MS/MS methods to quantify five integrase inhibitors in plasma with the limits of quantification at 1 pg/mL for raltegravir and 2 pg/mL for four proprietary compounds. The assays involved double extractions followed by UPLC coupled with negative ion electrospray MS/MS analysis. All methods were fully validated to the rigor of regulated bioanalysis requirements, with intraday precision between 1.20 and 14.1% and accuracy between 93.8 and 107% at the standard curve concentration range. These methods were successfully applied to a human microdose study and demonstrated to be accurate, reproducible, and cost-effective. Results of the study indicate that raltegravir displayed linear pharmacokinetics between a microdose and a pharmacologically active dose.

  8. Anti-HIV-1 integrase activity of medicinal plants used as self medication by AIDS patients

    Directory of Open Access Journals (Sweden)

    Sopa Kummee

    2006-07-01

    Full Text Available The extracts of selected medicinal plants used as self medication by AIDS patients were investigated for their inhibitory activities against HIV-1 integrase (HIV-1 IN using the multiplate integration assay (MIA. Of these, the water extract of Eclipta prostrata (whole plant exhibited the most potent inhibitory activity with an IC50 value of 4.8 μg/ml, followed by the methanol extract of Eclipta prostrata (whole plant, IC50 = 21.1 μg/ ml, the water extract of Barleria lupulina (stem, IC50 = 26.4 μg/ml, the chloroform extract of Barleria lupulina (stem, IC50 = 33.0 μg/ml, the methanol extract of Barleria lupulina (stem, IC50 = 38.2 μg/ml and the chloroform extract of Piper betle (leaf, IC50 = 39.3 μg/ml, respectively.

  9. Present status of promotion of advanced safety vehicle in phase 2 (ASV2); Dai 2 ki senshin anzen jidosha (ASV) suishin keikaku ni okeru kenkyu jokyo

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1999-11-01

    For active safety enhancement, drivers will be provided with information and warning that will help them drive with safety. Studies are under way about functions to facilitate drivers' perception and to lighten the burdens imposed on them. As for accident avoidance techniques, onboard systems will perform controls involving vehicle maneuver for safety enhancement. This includes the improvement of vehicle maneuvering performance, in addition to brake control and steering control, for lightening drivers' burdens and for complementing their operating skill. Danger avoidance is based on the concept that the related system is to work in case warnings alone are not enough to avoid a collision. Full automation will be implemented by two ways, the autonomous way aided by the existing infrastructures such as GPS (Global Positioning System) or the way in which infrastructures to be newly built will be utilized. Passive safety technologies aim at minimizing damage upon collision, and involve structural improvement, air bags, etc. Disaster aggravation prevention means to prevent disaster from spreading after collision. Communication is one of safety-related elements on which studies will continue. Under the Phase 2 ASV program, research and development will be conducted for putting passenger cars to practical use, and the same will be conducted, in the case of large vehicles and motorcycles, for the construction of their prototypes. (NEDO)

  10. Virus evolution reveals an exclusive role for LEDGF/p75 in chromosomal tethering of HIV.

    Directory of Open Access Journals (Sweden)

    Anneleen Hombrouck

    2007-03-01

    Full Text Available Retroviruses by definition insert their viral genome into the host cell chromosome. Although the key player of retroviral integration is viral integrase, a role for cellular cofactors has been proposed. Lentiviral integrases use the cellular protein LEDGF/p75 to tether the preintegration complex to the chromosome, although the existence of alternative host proteins substituting for the function of LEDGF/p75 in integration has been proposed. Truncation mutants of LEDGF/p75 lacking the chromosome attachment site strongly inhibit HIV replication by competition for the interaction with integrase. In an attempt to select HIV strains that can overcome the inhibition, we now have used T-cell lines that stably express a C-terminal fragment of LEDGF/p75. Despite resistance development, the affinity of integrase for LEDGF/p75 is reduced and replication kinetics in human primary T cells is impaired. Detection of the integrase mutations A128T and E170G at key positions in the LEDGF/p75-integrase interface provides in vivo evidence for previously reported crystallographic data. Moreover, the complementary inhibition by LEDGF/p75 knockdown and mutagenesis at the integrase-LEDGF/p75 interface points to the incapability of HIV to circumvent LEDGF/p75 function during proviral integration. Altogether, the data provide a striking example of the power of viral molecular evolution. The results underline the importance of the LEDGF/p75 HIV-1 interplay as target for innovative antiviral therapy. Moreover, the role of LEDGF/p75 in targeting integration will stimulate research on strategies to direct gene therapy vectors into safe landing sites.

  11. Structural and Functional Annotation of Hypothetical Proteins of O139

    Directory of Open Access Journals (Sweden)

    Md. Saiful Islam

    2015-06-01

    Full Text Available In developing countries threat of cholera is a significant health concern whenever water purification and sewage disposal systems are inadequate. Vibrio cholerae is one of the responsible bacteria involved in cholera disease. The complete genome sequence of V. cholerae deciphers the presence of various genes and hypothetical proteins whose function are not yet understood. Hence analyzing and annotating the structure and function of hypothetical proteins is important for understanding the V. cholerae. V. cholerae O139 is the most common and pathogenic bacterial strain among various V. cholerae strains. In this study sequence of six hypothetical proteins of V. cholerae O139 has been annotated from NCBI. Various computational tools and databases have been used to determine domain family, protein-protein interaction, solubility of protein, ligand binding sites etc. The three dimensional structure of two proteins were modeled and their ligand binding sites were identified. We have found domains and families of only one protein. The analysis revealed that these proteins might have antibiotic resistance activity, DNA breaking-rejoining activity, integrase enzyme activity, restriction endonuclease, etc. Structural prediction of these proteins and detection of binding sites from this study would indicate a potential target aiding docking studies for therapeutic designing against cholera.

  12. Labeling of multiple HIV-1 proteins with the biarsenical-tetracysteine system.

    Directory of Open Access Journals (Sweden)

    Cândida F Pereira

    Full Text Available Due to its small size and versatility, the biarsenical-tetracysteine system is an attractive way to label viral proteins for live cell imaging. This study describes the genetic labeling of the human immunodeficiency virus type 1 (HIV-1 structural proteins (matrix, capsid and nucleocapsid, enzymes (protease, reverse transcriptase, RNAse H and integrase and envelope glycoprotein 120 with a tetracysteine tag in the context of a full-length virus. We measure the impact of these modifications on the natural virus infection and, most importantly, present the first infectious HIV-1 construct containing a fluorescently-labeled nucleocapsid protein. Furthermore, due to the high background levels normally associated with the labeling of tetracysteine-tagged proteins we have also optimized a metabolic labeling system that produces infectious virus containing the natural envelope glycoproteins and specifically labeled tetracysteine-tagged proteins that can easily be detected after virus infection of T-lymphocytes. This approach can be adapted to other viral systems for the visualization of the interplay between virus and host cell during infection.

  13. Structure-based virtual screening toward the discovery of novel inhibitors for impeding the protein-protein interaction between HIV-1 integrase and human lens epithelium-derived growth factor (LEDGF/p75).

    Science.gov (United States)

    Panwar, Umesh; Singh, Sanjeev Kumar

    2017-10-23

    HIV-1 integrase is a unique promising component of the viral replication cycle, catalyzing the integration of reverse transcribed viral cDNA into the host cell genome. Generally, IN activity requires both viral as well as a cellular co-factor in the processing replication cycle. Among them, the human lens epithelium-derived growth factor (LEDGF/p75) represented as promising cellular co-factor which supports the viral replication by tethering IN to the chromatin. Due to its major importance in the early steps of HIV replication, the interaction between IN and LEDGF/p75 has become a pleasing target for anti-HIV drug discovery. The present study involves the finding of novel inhibitor based on the information of dimeric CCD of IN in complex with known inhibitor, which were carried out by applying a structure-based virtual screening concept with molecular docking. Additionally, Free binding energy, ADME properties, PAINS analysis, Density Functional Theory, and Enrichment Calculations were performed on selected compounds for getting a best lead molecule. On the basis of these analyses, the current study proposes top 3 compounds: Enamine-Z742267384, Maybridge-HTS02400, and Specs-AE-848/37125099 with acceptable pharmacological properties and enhanced binding affinity to inhibit the interaction between IN and LEDGF/p75. Furthermore, Simulation studies were carried out on these molecules to expose their dynamics behavior and stability. We expect that the findings obtained here could be future therapeutic agents and may provide an outline for the experimental studies to stimulate the innovative strategy for research community.

  14. Combining short- and long-range fluorescence reporters with simulations to explore the intramolecular dynamics of an intrinsically disordered protein

    Science.gov (United States)

    Zosel, Franziska; Haenni, Dominik; Soranno, Andrea; Nettels, Daniel; Schuler, Benjamin

    2017-10-01

    Intrinsically disordered proteins (IDPs) are increasingly recognized as a class of molecules that can exert essential biological functions even in the absence of a well-defined three-dimensional structure. Understanding the conformational distributions and dynamics of these highly flexible proteins is thus essential for explaining the molecular mechanisms underlying their function. Single-molecule fluorescence spectroscopy in combination with Förster resonance energy transfer (FRET) is a powerful tool for probing intramolecular distances and the rapid long-range distance dynamics in IDPs. To complement the information from FRET, we combine it with photoinduced electron transfer (PET) quenching to monitor local loop-closure kinetics at the same time and in the same molecule. Here we employed this combination to investigate the intrinsically disordered N-terminal domain of HIV-1 integrase. The results show that both long-range dynamics and loop closure kinetics on the sub-microsecond time scale can be obtained reliably from a single set of measurements by the analysis with a comprehensive model of the underlying photon statistics including both FRET and PET. A more detailed molecular interpretation of the results is enabled by direct comparison with a recent extensive atomistic molecular dynamics simulation of integrase. The simulations are in good agreement with experiment and can explain the deviation from simple models of chain dynamics by the formation of persistent local secondary structure. The results illustrate the power of a close combination of single-molecule spectroscopy and simulations for advancing our understanding of the dynamics and detailed mechanisms in unfolded and intrinsically disordered proteins.

  15. Inorganic and organic fertilizers impact the abundance and proportion of antibiotic resistance and integron-integrase genes in agricultural grassland soil.

    Science.gov (United States)

    Nõlvak, Hiie; Truu, Marika; Kanger, Kärt; Tampere, Mailiis; Espenberg, Mikk; Loit, Evelin; Raave, Henn; Truu, Jaak

    2016-08-15

    Soil fertilization with animal manure or its digestate may facilitate an important antibiotic resistance dissemination route from anthropogenic sources to the environment. This study examines the effect of mineral fertilizer (NH4NO3), cattle slurry and cattle slurry digestate amendment on the abundance and proportion dynamics of five antibiotic resistance genes (ARGs) and two classes of integron-integrase genes (intI1 and intI2) in agricultural grassland soil. Fertilization was performed thrice throughout one vegetation period. The targeted ARGs (sul1, tetA, blaCTX-M, blaOXA2 and qnrS) encode resistance to several major antibiotic classes used in veterinary medicine such as sulfonamides, tetracycline, cephalosporins, penicillin and fluoroquinolones, respectively. The non-fertilized grassland soil contained a stable background of tetA, blaCTX-M and sul1 genes. The type of applied fertilizer significantly affected ARGs and integron-integrase genes abundances and proportions in the bacterial community (porganic fertilizer's application event, but this increase was followed by a stage of decrease, suggesting that microbes possessing these genes were predominantly entrained into soil via cattle slurry or its digestate application and had somewhat limited survival potential in a soil environment. However, the abundance of these three target genes did not decrease to a background level by the end of the study period. TetA was most abundant in mineral fertilizer treated soil and blaCTX-M in cattle slurry digestate amended soil. Despite significantly different abundances, the abundance dynamics of bacteria possessing these genes were similar (p<0.05 in all cases) in different treatments and resembled the dynamics of the whole bacterial community abundance in each soil treatment. Copyright © 2016. Published by Elsevier B.V.

  16. Incorporation of aptamers in the terminal loop of shRNAs yields an effective and novel combinatorial targeting strategy.

    Science.gov (United States)

    Pang, Ka Ming; Castanotto, Daniela; Li, Haitang; Scherer, Lisa; Rossi, John J

    2018-01-09

    Gene therapy by engineering patient's own blood cells to confer HIV resistance can potentially lead to a functional cure for AIDS. Toward this goal, we have previously developed an anti-HIV lentivirus vector that deploys a combination of shRNA, ribozyme and RNA decoy. To further improve this therapeutic vector against viral escape, we sought an additional reagent to target HIV integrase. Here, we report the development of a new strategy for selection and expression of aptamer for gene therapy. We developed a SELEX protocol (multi-tag SELEX) for selecting RNA aptamers against proteins with low solubility or stability, such as integrase. More importantly, we expressed these aptamers in vivo by incorporating them in the terminal loop of shRNAs. This novel strategy allowed efficient expression of the shRNA-aptamer fusions that targeted RNAs and proteins simultaneously. Expressed shRNA-aptamer fusions targeting HIV integrase or reverse transcriptase inhibited HIV replication in cell cultures. Viral inhibition was further enhanced by combining an anti-integrase aptamer with an anti-HIV Tat-Rev shRNA. This construct exhibited efficacy comparable to that of integrase inhibitor Raltegravir. Our strategy for the selection and expression of RNA aptamers can potentially extend to other gene therapy applications. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  17. Insights into the subsurface transport of As(V) and Se(VI) in produced water from hydraulic fracturing using soil samples from Qingshankou Formation, Songliao Basin, China.

    OpenAIRE

    Chen, SS; Sun, Y; Tsang, DC; Graham, NJ; Ok, YS; Feng, Y; Li, XD

    2017-01-01

    Produced water is a type of wastewater generated from hydraulic fracturing, which may pose a risk to the environment and humans due to its high ionic strength and the presence of elevated concentrations of metals/metalloids that exceed maximum contamination levels. The mobilization of As(V) and Se(VI) in produced water and selected soils from Qingshankou Formation in the Songliao Basin in China were investigated using column experiments and synthetic produced water whose quality was represent...

  18. Cellular and molecular mechanisms of HIV-1 integration targeting.

    Science.gov (United States)

    Engelman, Alan N; Singh, Parmit K

    2018-07-01

    Integration is central to HIV-1 replication and helps mold the reservoir of cells that persists in AIDS patients. HIV-1 interacts with specific cellular factors to target integration to interior regions of transcriptionally active genes within gene-dense regions of chromatin. The viral capsid interacts with several proteins that are additionally implicated in virus nuclear import, including cleavage and polyadenylation specificity factor 6, to suppress integration into heterochromatin. The viral integrase protein interacts with transcriptional co-activator lens epithelium-derived growth factor p75 to principally position integration within gene bodies. The integrase additionally senses target DNA distortion and nucleotide sequence to help fine-tune the specific phosphodiester bonds that are cleaved at integration sites. Research into virus-host interactions that underlie HIV-1 integration targeting has aided the development of a novel class of integrase inhibitors and may help to improve the safety of viral-based gene therapy vectors.

  19. Insights into the Functions of a Prophage Recombination Directionality Factor

    Directory of Open Access Journals (Sweden)

    Mireille Ansaldi

    2012-10-01

    Full Text Available Recombination directionality factors (RDFs, or excisionases, are essential players of prophage excisive recombination. Despite the essentially catalytic role of the integrase in both integrative and excisive recombination, RDFs are required to direct the reaction towards excision and to prevent re-integration of the prophage genome when entering a lytic cycle. KplE1, HK620 and numerous (prophages that integrate at the same site in enterobacteria genomes (such as the argW tRNA gene all share a highly conserved recombination module. This module comprises the attL and attR recombination sites and the RDF and integrase genes. The KplE1 RDF was named TorI after its initial identification as a negative regulator of the tor operon. However, it was characterized as an essential factor of excisive recombination. In this study, we designed an extensive random mutagenesis protocol of the torI gene and identified key residues involved in both functions of the TorI protein. We show that, in addition to TorI-TorR protein-protein interaction, TorI interacts in solution with the IntS integrase. Moreover, in vitro, TorR and IntS appear to compete for TorI binding. Finally, our mutagenesis results suggest that the C-terminal part of the TorI protein is dedicated to protein-protein interactions with both proteins TorR and IntS.

  20. Function and regulation of plant major intrinsic proteins

    DEFF Research Database (Denmark)

    Popovic, Milan

    ;1 in Arabidopsis. That led to the discovery that tip4;1 is gametophytic lethal- gene essential for normal seed set. ICP-MS analyses of the elemental composition of tip4;1 heterozygous T-DNA insert mutant plants and 35S::TIP4;1 over-expression plants indicate that AtTIP4;1 has a role in arsenic distribution...... inorganic forms of arsenic in the environment, can be taken up by plants and thus enter the food chain. Once inside the root cells, As(V) is reduced to As(III) which is then extruded to the soil solution or bound to phytochelatins (PCs) and transported to the vacuole in an effort to accomplish...... detoxification. Plant Noduline 26-like Intrinsic Proteins (NIPs) can channel As(III) and consequently influence the detoxification process. The role of the Tonoplast Intrinsic Proteins (TIPs) in As(III) detoxification remains to be clarified, yet TIPs could have an impact on As(III) accumulation in plant cell...

  1. An effective HIV-1 integrase inhibitor screening platform: Rationality validation of drug screening, conformational mobility and molecular recognition analysis for PFV integrase complex with viral DNA.

    Science.gov (United States)

    Du, Wenyi; Zuo, Ke; Sun, Xin; Liu, Wei; Yan, Xiao; Liang, Li; Wan, Hua; Chen, Fengzheng; Hu, Jianping

    2017-11-01

    As an important target for the development of novel anti-AIDS drugs, HIV-1 integrase (IN) has been widely concerned. However, the lack of a complete accurate crystal structure of HIV-1 IN greatly blocks the discovery of novel inhibitors. In this work, an effective HIV-1 IN inhibitor screening platform, namely PFV IN, was filtered from all species of INs. Next, the 40.8% similarity with HIV-1 IN, as well as the high efficiency of virtual screening and the good agreement between calculated binding free energies and experimental ones all proved PFV IN is a promising screening platform for HIV-1 IN inhibitors. Then, the molecular recognition mechanism of PFV IN by its substrate viral DNA and six naphthyridine derivatives (NRDs) inhibitors was investigated through molecular docking, molecular dynamics simulations and water-mediated interactions analyses. The functional partition of NRDs IN inhibitors could be divided into hydrophobic and hydrophilic ones, and the Mg 2+ ions, water molecules and conserved DDE motif residues all interacted with the hydrophilic partition, while the bases in viral DNA and residues like Tyr212, Pro214 interacted with the hydrophobic one. Finally, the free energy landscape (FEL) and cluster analyses were performed to explore the molecular motion of PFV IN-DNA system. It is found that the association with NRDs inhibitors would obviously decrease the motion amplitude of PFV IN-DNA, which may be one of the most potential mechanisms of IN inhibitors. This work will provide a theoretical basis for the inhibitor design based on the structure of HIV-1 IN. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Resistance Analyses of Integrase Strand Transfer Inhibitors within Phase 3 Clinical Trials of Treatment-Naive Patients

    Directory of Open Access Journals (Sweden)

    Kirsten L. White

    2014-07-01

    Full Text Available The integrase (IN strand transfer inhibitors (INSTIs, raltegravir (RAL, elvitegravir (EVG and dolutegravir (DTG, comprise the newest drug class approved for the treatment of HIV-1 infection, which joins the existing classes of reverse transcriptase, protease and binding/entry inhibitors. The efficacy of first-line regimens has attained remarkably high levels, reaching undetectable viral loads in 90% of patients by Week 48; however, there remain patients who require a change in regimen due to adverse events, virologic failure with emergent resistance or other issues of patient management. Large, randomized clinical trials conducted in antiretroviral treatment-naive individuals are required for drug approval in this population in the US, EU and other countries, with the primary endpoint for virologic success at Week 48. However, there are differences in the definition of virologic failure and the evaluation of drug resistance among the trials. This review focuses on the methodology and tabulation of resistance to INSTIs in phase 3 clinical trials of first-line regimens and discusses case studies of resistance.

  3. Speciation of As(III) and As(V) in water samples by graphite furnace atomic absorption spectrometry after solid phase extraction combined with dispersive liquid-liquid microextraction based on the solidification of floating organic drop.

    Science.gov (United States)

    Shamsipur, Mojtaba; Fattahi, Nazir; Assadi, Yaghoub; Sadeghi, Marzieh; Sharafi, Kiomars

    2014-12-01

    A solid phase extraction (SPE) coupled with dispersive liquid-liquid microextraction based on the solidification of floating organic drop (DLLME-SFO) method, using diethyldithiphosphate (DDTP) as a proper chelating agent, has been developed as an ultra preconcentration technique for the determination of inorganic arsenic in water samples prior to graphite furnace atomic absorption spectrometry (GFAAS). Variables affecting the performance of both steps were thoroughly investigated. Under optimized conditions, 100mL of As(ΙΙΙ) solution was first concentrated using a solid phase sorbent. The extract was collected in 2.0 mL of acetone and 60.0 µL of 1-undecanol was added into the collecting solvent. The mixture was then injected rapidly into 5.0 mL of pure water for further DLLME-SFO. Total inorganic As(III, V) was extracted similarly after reduction of As(V) to As(III) with potassium iodide and sodium thiosulfate and As(V) concentration was calculated by difference. A mixture of Pd(NO3)2 and Mg(NO3)2 was used as a chemical modifier in GFAAS. The analytical characteristics of the method were determined. The calibration graph was linear in the rage of 10-100 ng L(-1) with detection limit of 2.5 ng L(-1). Repeatability (intra-day) and reproducibility (inter-day) of method based on seven replicate measurements of 80 ng L(-1) of As(ΙΙΙ) were 6.8% and 7.5%, respectively. The method was successfully applied to speciation of As(III), As(V) and determination of the total amount of As in water samples and in a certified reference material (NIST RSM 1643e). Copyright © 2014 Elsevier B.V. All rights reserved.

  4. Removal of bacterial cells, antibiotic resistance genes and integrase genes by on-site hospital wastewater treatment plants: surveillance of treated hospital effluent quality

    KAUST Repository

    Timraz, Kenda Hussain Hassan

    2016-12-15

    This study aims to evaluate the removal efficiency of microbial contaminants, including total cell counts, antibiotic-resistant bacteria (ARB), antibiotic resistance genes (ARGs, e.g. tetO, tetZ, sul1 and sul2) and integrase genes (e.g. intl1 and intl2), by wastewater treatment plants (WWTPs) operated on-site of two hospitals (i.e., SH WWTP and IH WWTP). Both SH and IH WWTPs utilize the conventional activated sludge process but differences in the removal efficiencies were observed. Over the 2 week sampling period, IH WWTP outperformed SH WWTP, and achieved an approximate 0.388 to 2.49-log log removal values (LRVs) for total cell counts compared to the 0.010 to 0.162-log removal in SH WWTP. Although ARB were present in the hospital influent, the treatment process of both hospitals effectively removed ARB from most of the effluent samples. In instances where ARB were recovered in the effluent, none of the viable isolates were identified to be opportunistic pathogenic species based on 16S rRNA gene sequencing. However, sul1 and intl1 genes remained detectable at up to 105 copies per mL or 8 x 10(-1) copies per 16S rRNA gene in the treated effluent, with an LRV of less than 1.2. When the treated effluent is discharged from hospital WWTPs into the public sewer for further treatment as per requirement in many countries, the detected amount of ARGs and integrase genes in the hospital effluent can become a potential source of horizontal gene dissemination in the municipal WWTP. Proper on-site wastewater treatment and surveillance of the effluent quality for emerging contaminants are therefore highly recommended.

  5. Eiropas Savienības uzņēmējdarbības vide start-up uzņēmumu attīstīšanai (salīdzinošā analīze ar ASV)

    OpenAIRE

    Kapenieks, Kristaps

    2014-01-01

    Maģistra darbā „Eiropas Savienības uzņēmējdarbības vide start-up uzņēmumu attīstīšanai (salīdzinošā analīze ar ASV)” tiek pētīts, kā uzņēmējdarbības vide ietekmē start-up uzņēmējdarbības aktivitāti un kur uzņēmējdarbības vide ir piemērotāka start-up uzņēmējdarbībai – Eiropas Savienībā vai ASV. Lai iegūtu atbildi uz šiem jautājumiem, maģistra darbā tiek pētīts, kas ir start-up uzņēmums un kā to ietekmē ārējā uzņēmējdarbības vide, salīdzināti vides faktoru dati par četrām Eiropas Savienības da...

  6. Preadipocyte 11beta-hydroxysteroid dehydrogenase type 1 is a keto-reductase and contributes to diet-induced visceral obesity in vivo.

    Science.gov (United States)

    De Sousa Peixoto, R A; Turban, S; Battle, J H; Chapman, K E; Seckl, J R; Morton, N M

    2008-04-01

    Glucocorticoid excess promotes visceral obesity and cardiovascular disease. Similar features are found in the highly prevalent metabolic syndrome in the absence of high levels of systemic cortisol. Although elevated activity of the glucocorticoid-amplifying enzyme 11beta-hydroxysteroid dehydrogenase type 1 (11beta-HSD1) within adipocytes might explain this paradox, the potential role of 11beta-HSD1 in preadipocytes is less clear; human omental adipose stromal vascular (ASV) cells exhibit 11beta-dehydrogenase activity (inactivation of glucocorticoids) probably due to the absence of cofactor provision by hexose-6-phosphate dehydrogenase. To clarify the depot-specific impact of 11beta-HSD1, we assessed whether preadipocytes in ASV from mesenteric (as a representative of visceral adipose tissue) and sc tissue displayed 11beta-HSD1 activity in mice. 11beta-HSD1 was highly expressed in freshly isolated ASV cells, predominantly in preadipocytes. 11beta-HSD1 mRNA and protein levels were comparable between ASV and adipocyte fractions in both depots. 11beta-HSD1 was an 11beta-reductase, thus reactivating glucocorticoids in ASV cells, consistent with hexose-6-phosphate dehydrogenase mRNA expression. Unexpectedly, glucocorticoid reactivation was higher in intact mesenteric ASV cells despite a lower expression of 11beta-HSD1 mRNA and protein (homogenate activity) levels than sc ASV cells. This suggests a novel depot-specific control over 11beta-HSD1 enzyme activity. In vivo, high-fat diet-induced obesity was accompanied by increased visceral fat preadipocyte differentiation in wild-type but not 11beta-HSD1(-/-) mice. The results suggest that 11beta-HSD1 reductase activity is augmented in mouse mesenteric preadipocytes where it promotes preadipocyte differentiation and contributes to visceral fat accumulation in obesity.

  7. Retroviral DNA Integration

    Science.gov (United States)

    2016-01-01

    The integration of a DNA copy of the viral RNA genome into host chromatin is the defining step of retroviral replication. This enzymatic process is catalyzed by the virus-encoded integrase protein, which is conserved among retroviruses and LTR-retrotransposons. Retroviral integration proceeds via two integrase activities: 3′-processing of the viral DNA ends, followed by the strand transfer of the processed ends into host cell chromosomal DNA. Herein we review the molecular mechanism of retroviral DNA integration, with an emphasis on reaction chemistries and architectures of the nucleoprotein complexes involved. We additionally discuss the latest advances on anti-integrase drug development for the treatment of AIDS and the utility of integrating retroviral vectors in gene therapy applications. PMID:27198982

  8. Resistance to pyridine-based inhibitor KF116 reveals an unexpected role of integrase in HIV-1 Gag-Pol polyprotein proteolytic processing.

    Science.gov (United States)

    Hoyte, Ashley C; Jamin, Augusta V; Koneru, Pratibha C; Kobe, Matthew J; Larue, Ross C; Fuchs, James R; Engelman, Alan N; Kvaratskhelia, Mamuka

    2017-12-01

    The pyridine-based multimerization selective HIV-1 integrase (IN) inhibitors (MINIs) are a distinct subclass of allosteric IN inhibitors. MINIs potently inhibit HIV-1 replication during virion maturation by inducing hyper- or aberrant IN multimerization but are largely ineffective during the early steps of viral replication. Here, we investigated the mechanism for the evolution of a triple IN substitution (T124N/V165I/T174I) that emerges in cell culture with a representative MINI, KF116. We show that HIV-1 NL4-3(IN T124N/V165I/T174I) confers marked (>2000-fold) resistance to KF116. Two IN substitutions (T124N/T174I) directly weaken inhibitor binding at the dimer interface of the catalytic core domain but at the same time markedly impair HIV-1 replication capacity. Unexpectedly, T124N/T174I IN substitutions inhibited proteolytic processing of HIV-1 polyproteins Gag and Gag-Pol, resulting in immature virions. Strikingly, the addition of the third IN substitution (V165I) restored polyprotein processing, virus particle maturation, and significant levels of replication capacity. These results reveal an unanticipated role of IN for polyprotein proteolytic processing during virion morphogenesis. The complex evolutionary pathway for the emergence of resistant viruses, which includes the need for the compensatory V165I IN substitution, highlights a relatively high genetic barrier exerted by MINI KF116. Additionally, we have solved the X-ray structure of the drug-resistant catalytic core domain protein, which provides means for rational development of second-generation MINIs. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  9. 基于Copula-ASV-EVT-CoVaR模型的中小板与创业板风险溢出度量研究%Study on the risk spillover effect between the small and medium-sized board market and the second board market in China based on Copula-ASV-EVT-CoVaR model

    Institute of Scientific and Technical Information of China (English)

    周孝华; 陈九生

    2016-01-01

    本文以条件在险价值(CoVaR)法为基础,结合Copula-ASV-EVT模型分析了我国中小板与创业板市场之间的风险溢出效应.结果表明,中小板与创业板市场之间存在双向风险溢出效应,且中小板市场对创业板市场的风险溢出效应强于创业板市场对中小板市场的风险溢出效应.此外,文章还分析了波动冲击对中小板与创业板的影响.最后,本文为风险监管以及投资者在中小板与创业板之间进行资产配置提供了建议.%This paper analyzes the risk spillover effect between the small and medium-sized board market and the second board market in China based on CoVaR method combined with Copula-ASV-EVT model.The results show that there are bidirectional risk spillover effect between the small and medium-sized board market and the growth enterprise market in China,the degree of risk spillover effect from the small and medium-sized board market to the growth enterprise market is stronger than that of from the second board market to the small and medium-sized board market.In addition,this paper also analyzes the influence of volatility impulse on the small and medium-sized board market and the second board market in China.Finally,the paper provides some suggestions for investors and supervisory authorities.

  10. Targeting Virus-host Interactions of HIV Replication.

    Science.gov (United States)

    Weydert, Caroline; De Rijck, Jan; Christ, Frauke; Debyser, Zeger

    2016-01-01

    Cellular proteins that are hijacked by HIV in order to complete its replication cycle, form attractive new targets for antiretroviral therapy. In particular, the protein-protein interactions between these cellular proteins (cofactors) and viral proteins are of great interest to develop new therapies. Research efforts have led to the validation of different cofactors and some successes in therapeutic applications. Maraviroc, the first cofactor inhibitor approved for human medicinal use, provided a proof of concept. Furthermore, compounds developed as Integrase-LEDGF/p75 interaction inhibitors (LEDGINs) have advanced to early clinical trials. Other compounds targeting cofactors and cofactor-viral protein interactions are currently under development. Likewise, interactions between cellular restriction factors and their counteracting HIV protein might serve as interesting targets in order to impair HIV replication. In this respect, compounds targeting the Vif-APOBEC3G interaction have been described. In this review, we focus on compounds targeting the Integrase- LEDGF/p75 interaction, the Tat-P-TEFb interaction and the Vif-APOBEC3G interaction. Additionally we give an overview of currently discovered compounds presumably targeting cellular cofactor-HIV protein interactions.

  11. HIV-1 integrase inhibitors are substrates for the multidrug transporter MDR1-P-glycoprotein

    Directory of Open Access Journals (Sweden)

    Cara Andrea

    2007-03-01

    Full Text Available Abstract Background The discovery of diketoacid-containing derivatives as inhibitors of HIV-1 Integrase (IN (IN inhibitors, IINs has played a major role in validating this enzyme as an important target for antiretroviral therapy. Since the in vivo efficacy depends on access of these drugs to intracellular sites where HIV-1 replicates, we determined whether the IINs are recognized by the multidrug transporter MDR1-P-glycoprotein (P-gp thereby reducing their intracellular accumulation. To address the effect of IINs on drug transport, nine quinolonyl diketo acid (DKA derivatives active on the HIV-1 IN strand transfer (ST step and with EC50 ranging from 1.83 to >50 μm in cell-based assays were tested for their in vitro interaction with P-gp in the CEM-MDR cell system. IINs were investigated for the inhibition and induction of the P-gp function and expression as well as for multidrug resistance (MDR reversing ability. Results The HIV-1 IINs act as genuine P-gp substrates by inhibiting doxorubicin efflux and inducing P-gp functional conformation changes as evaluated by the modulation of UIC2 mAb epitope. Further, IINs chemosensitize MDR cells to vinblastine and induce P-gp expression in drug sensitive revertants of CEM-MDR cells. Conclusion To our knowledge, this is the first demonstration that HIV-1 IINs are P-gp substrates. This biological property may influence the absorption, distribution and elimination of these novels anti HIV-1 compounds.

  12. Integrase inhibitors in late pregnancy and rapid HIV viral load reduction.

    Science.gov (United States)

    Rahangdale, Lisa; Cates, Jordan; Potter, JoNell; Badell, Martina L; Seidman, Dominika; Miller, Emilly S; Coleman, Jenell S; Lazenby, Gweneth B; Levison, Judy; Short, William R; Yawetz, Sigal; Ciaranello, Andrea; Livingston, Elizabeth; Duthely, Lunthita; Rimawi, Bassam H; Anderson, Jean R; Stringer, Elizabeth M

    2016-03-01

    Minimizing time to HIV viral suppression is critical in pregnancy. Integrase strand transfer inhibitors (INSTIs), like raltegravir, are known to rapidly suppress plasma HIV RNA in nonpregnant adults. There are limited data in pregnant women. We describe time to clinically relevant reduction in HIV RNA in pregnant women using INSTI-containing and non-INSTI-containing antiretroviral therapy (ART) options. We conducted a retrospective cohort study of pregnant HIV-infected women in the United States from 2009 through 2015. We included women who initiated ART, intensified their regimen, or switched to a new regimen due to detectable viremia (HIV RNA >40 copies/mL) at ≥20 weeks gestation. Among women with a baseline HIV RNA permitting 1-log reduction, we estimated time to 1-log RNA reduction using the Kaplan-Meier estimator comparing women starting/adding an INSTI in their regimen vs other ART. To compare groups with similar follow-up time, we also conducted a subgroup analysis limited to women with ≤14 days between baseline and follow-up RNA data. This study describes 101 HIV-infected pregnant women from 11 US clinics. In all, 75% (76/101) of women were not taking ART at baseline; 24 were taking non-INSTI containing ART, and 1 received zidovudine monotherapy. In all, 39% (39/101) of women started an INSTI-containing regimen or added an INSTI to their ART regimen. Among 90 women with a baseline HIV RNA permitting 1-log reduction, the median time to 1-log RNA reduction was 8 days (interquartile range [IQR], 7-14) in the INSTI group vs 35 days (IQR, 20-53) in the non-INSTI ART group (P pregnancy. Inclusion of an INSTI may play a role in optimal reduction of HIV RNA for HIV-infected pregnant women presenting late to care or failing initial therapy. Larger studies are urgently needed to assess the safety and effectiveness of this approach. Copyright © 2016 Elsevier Inc. All rights reserved.

  13. Contribution of the C-terminal tri-lysine regions of human immunodeficiency virus type 1 integrase for efficient reverse transcription and viral DNA nuclear import

    Directory of Open Access Journals (Sweden)

    Fowke Keith R

    2005-10-01

    Full Text Available Abstract Background In addition to mediating the integration process, HIV-1 integrase (IN has also been implicated in different steps during viral life cycle including reverse transcription and viral DNA nuclear import. Although the karyophilic property of HIV-1 IN has been well demonstrated using a variety of experimental approaches, the definition of domain(s and/or motif(s within the protein that mediate viral DNA nuclear import and its mechanism are still disputed and controversial. In this study, we performed mutagenic analyses to investigate the contribution of different regions in the C-terminal domain of HIV-1 IN to protein nuclear localization as well as their effects on virus infection. Results Our analysis showed that replacing lysine residues in two highly conserved tri-lysine regions, which are located within previously described Region C (235WKGPAKLLWKGEGAVV and sequence Q (211KELQKQITK in the C-terminal domain of HIV-1 IN, impaired protein nuclear accumulation, while mutations for RK263,4 had no significant effect. Analysis of their effects on viral infection in a VSV-G pseudotyped RT/IN trans-complemented HIV-1 single cycle replication system revealed that all three C-terminal mutant viruses (KK215,9AA, KK240,4AE and RK263,4AA exhibited more severe defect of induction of β-Gal positive cells and luciferase activity than an IN class 1 mutant D64E in HeLa-CD4-CCR5-β-Gal cells, and in dividing as well as non-dividing C8166 T cells, suggesting that some viral defects are occurring prior to viral integration. Furthermore, by analyzing viral DNA synthesis and the nucleus-associated viral DNA level, the results clearly showed that, although all three C-terminal mutants inhibited viral reverse transcription to different extents, the KK240,4AE mutant exhibited most profound effect on this step, whereas KK215,9AA significantly impaired viral DNA nuclear import. In addition, our analysis could not detect viral DNA integration in each C

  14. A QSAR study of integrase strand transfer inhibitors based on a large set of pyrimidine, pyrimidone, and pyridopyrazine carboxamide derivatives

    Science.gov (United States)

    de Campos, Luana Janaína; de Melo, Eduardo Borges

    2017-08-01

    In the present study, 199 compounds derived from pyrimidine, pyrimidone and pyridopyrazine carboxamides with inhibitory activity against HIV-1 integrase were modeled. Subsequently, a multivariate QSAR study was conducted with 54 molecules employed by Ordered Predictors Selection (OPS) and Partial Least Squares (PLS) for the selection of variables and model construction, respectively. Topological, electrotopological, geometric, and molecular descriptors were used. The selected real model was robust and free from chance correlation; in addition, it demonstrated favorable internal and external statistical quality. Once statistically validated, the training model was used to predict the activity of a second data set (n = 145). The root mean square deviation (RMSD) between observed and predicted values was 0.698. Although it is a value outside of the standards, only 15 (10.34%) of the samples exhibited higher residual values than 1 log unit, a result considered acceptable. Results of Williams and Euclidean applicability domains relative to the prediction showed that the predictions did not occur by extrapolation and that the model is representative of the chemical space of test compounds.

  15. Contribution of the C-terminal region within the catalytic core domain of HIV-1 integrase to yeast lethality, chromatin binding and viral replication

    Directory of Open Access Journals (Sweden)

    Belhumeur Pierre

    2008-11-01

    Full Text Available Abstract Background HIV-1 integrase (IN is a key viral enzymatic molecule required for the integration of the viral cDNA into the genome. Additionally, HIV-1 IN has been shown to play important roles in several other steps during the viral life cycle, including reverse transcription, nuclear import and chromatin targeting. Interestingly, previous studies have demonstrated that the expression of HIV-1 IN induces the lethal phenotype in some strains of Saccharomyces cerevisiae. In this study, we performed mutagenic analyses of the C-terminal region of the catalytic core domain of HIV-1 IN in order to delineate the critical amino acid(s and/or motif(s required for the induction of the lethal phenotype in the yeast strain HP16, and to further elucidate the molecular mechanism which causes this phenotype. Results Our study identified three HIV-1 IN mutants, V165A, A179P and KR186,7AA, located in the C-terminal region of the catalytic core domain of IN that do not induce the lethal phenotype in yeast. Chromatin binding assays in yeast and mammalian cells demonstrated that these IN mutants were impaired for the ability to bind chromatin. Additionally, we determined that while these IN mutants failed to interact with LEDGF/p75, they retained the ability to bind Integrase interactor 1. Furthermore, we observed that VSV-G-pseudotyped HIV-1 containing these IN mutants was unable to replicate in the C8166 T cell line and this defect was partially rescued by complementation with the catalytically inactive D64E IN mutant. Conclusion Overall, this study demonstrates that three mutations located in the C-terminal region of the catalytic core domain of HIV-1 IN inhibit the IN-induced lethal phenotype in yeast by inhibiting the binding of IN to the host chromatin. These results demonstrate that the C-terminal region of the catalytic core domain of HIV-1 IN is important for binding to host chromatin and is crucial for both viral replication and the promotion of

  16. [Isolation and identification of the temperate bacteriophage from isolated strains of Streptococcus suis serotype 2].

    Science.gov (United States)

    Ma, Yuling; Lu, Chengping; Fan, Hongjie

    2008-04-01

    A PCR assay was developed to study the distributional characteristics of phage integrase gene in Streptococcus suis serotype 2 (SS2). A 323bp distinct DNA target can be amplified in 25 strains of virulent SS2, while can not be amplified in avirulent strain T15, 5 strains of other serotypes (SS1, SS7, SS9) and strains of group C Streptococcus strains from pigs, which suggested that the phage integrase gene may be related to the pathogenicity of SS2 and can be consider as a detection factor of the virulent gene of SS2. The sequencing and restriction endonuclease analysis of the PCR products were also done. Comparisons between the sequences of phage integrase gene with that of SS2 strain, showed a high homology with SS2 China strains 98HAH33, 05ZYH33 and North American strain 89-1591. Complete cell lysis was observed with SS2 virulent strains but not with avirulent strain T15 after the induction by mitomycin C. Electron microscopy analysis of the lysate from SS2 virulent strains HA9801 and ZY05719 revealed the presence of phage particles. The induced phage, named SS2-HA and SS2-ZY, both have a small isometric nucleocapsid approximately 50 nm in diameter and have no tail and is therefore a member of the Tectiviridae family. The phage integrase gene sequence of phage SS2-HA and SS2-ZY shared high homologue identities with virulent SS2 strains, which suggested that the phage integrase gene of SS2 has high specify. The temperate phage and phage integrase gene can only detected from SS2 virulent strains but not from avirulent strain, and the detection of phage integrase gene was related to the virulence-associate factors of SS2, such as the muramidase-released protein gene (mrp), which suggested that the temperate phage of SS2 may be related to the pathogenicity of SS2.

  17. Human immunodeficiency virus integrase inhibitors efficiently suppress feline immunodeficiency virus replication in vitro and provide a rationale to redesign antiretroviral treatment for feline AIDS

    Directory of Open Access Journals (Sweden)

    Ciervo Alessandra

    2007-10-01

    Full Text Available Abstract Background Treatment of feline immunodeficiency virus (FIV infection has been hampered by the absence of a specific combination antiretroviral treatment (ART. Integrase strand transfer inhibitors (INSTIs are emerging as a promising new drug class for HIV-1 treatment, and we evaluated the possibility of inhibiting FIV replication using INSTIs. Methods Phylogenetic analysis of lentiviral integrase (IN sequences was carried out using the PAUP* software. A theoretical three-dimensional structure of the FIV IN catalytic core domain (CCD was obtained by homology modeling based on a crystal structure of HIV-1 IN CCD. The interaction of the transferred strand of viral DNA with the catalytic cavity of FIV IN was deduced from a crystal structure of a structurally similar transposase complexed with transposable DNA. Molecular docking simulations were conducted using a genetic algorithm (GOLD. Antiviral activity was tested in feline lymphoblastoid MBM cells acutely infected with the FIV Petaluma strain. Circular and total proviral DNA was quantified by real-time PCR. Results The calculated INSTI-binding sites were found to be nearly identical in FIV and HIV-1 IN CCDs. The close similarity of primate and feline lentivirus IN CCDs was also supported by phylogenetic analysis. In line with these bioinformatic analyses, FIV replication was efficiently inhibited in acutely infected cell cultures by three investigational INSTIs, designed for HIV-1 and belonging to different classes. Of note, the naphthyridine carboxamide INSTI, L-870,810 displayed an EC50 in the low nanomolar range. Inhibition of FIV integration in situ was shown by real-time PCR experiments that revealed accumulation of circular forms of FIV DNA within cells treated with L-870,810. Conclusion We report a drug class (other than nucleosidic reverse transcriptase inhibitors that is capable of inhibiting FIV replication in vitro. The present study helped establish L-870,810, a compound

  18. Human immunodeficiency virus integrase inhibitors efficiently suppress feline immunodeficiency virus replication in vitro and provide a rationale to redesign antiretroviral treatment for feline AIDS

    Science.gov (United States)

    Savarino, Andrea; Pistello, Mauro; D'Ostilio, Daniela; Zabogli, Elisa; Taglia, Fabiana; Mancini, Fabiola; Ferro, Stefania; Matteucci, Donatella; De Luca, Laura; Barreca, Maria Letizia; Ciervo, Alessandra; Chimirri, Alba; Ciccozzi, Massimo; Bendinelli, Mauro

    2007-01-01

    Background Treatment of feline immunodeficiency virus (FIV) infection has been hampered by the absence of a specific combination antiretroviral treatment (ART). Integrase strand transfer inhibitors (INSTIs) are emerging as a promising new drug class for HIV-1 treatment, and we evaluated the possibility of inhibiting FIV replication using INSTIs. Methods Phylogenetic analysis of lentiviral integrase (IN) sequences was carried out using the PAUP* software. A theoretical three-dimensional structure of the FIV IN catalytic core domain (CCD) was obtained by homology modeling based on a crystal structure of HIV-1 IN CCD. The interaction of the transferred strand of viral DNA with the catalytic cavity of FIV IN was deduced from a crystal structure of a structurally similar transposase complexed with transposable DNA. Molecular docking simulations were conducted using a genetic algorithm (GOLD). Antiviral activity was tested in feline lymphoblastoid MBM cells acutely infected with the FIV Petaluma strain. Circular and total proviral DNA was quantified by real-time PCR. Results The calculated INSTI-binding sites were found to be nearly identical in FIV and HIV-1 IN CCDs. The close similarity of primate and feline lentivirus IN CCDs was also supported by phylogenetic analysis. In line with these bioinformatic analyses, FIV replication was efficiently inhibited in acutely infected cell cultures by three investigational INSTIs, designed for HIV-1 and belonging to different classes. Of note, the naphthyridine carboxamide INSTI, L-870,810 displayed an EC50 in the low nanomolar range. Inhibition of FIV integration in situ was shown by real-time PCR experiments that revealed accumulation of circular forms of FIV DNA within cells treated with L-870,810. Conclusion We report a drug class (other than nucleosidic reverse transcriptase inhibitors) that is capable of inhibiting FIV replication in vitro. The present study helped establish L-870,810, a compound successfully tested in

  19. Simultaneous speciation of arsenic (As(III), MMA, DMA, and As(V)) and selenium (Se(IV), Se(VI), and SeCN{sup -}) in petroleum refinery aqueous streams

    Energy Technology Data Exchange (ETDEWEB)

    Tonietto, Gisele B.; Godoy, Jose M.; Oliveira, Ana Cristina [Pontificia Universidade Catolica do Rio de Janeiro, Rio de Janeiro, RJ (Brazil); Souza, Marcia V. de [Petrobras/Cenpes, Research and Development Center, Rio de Janeiro (Brazil)

    2010-07-15

    High-performance liquid chromatography (HPLC) coupled to an ICP-MS with an octapole reaction system (ORS) has been used to carry out quantitative speciation of selenium (Se) and arsenic (As) in the stream waters of a refining process. The argon dimers interfering with the {sup 78}Se and {sup 80}Se isotopes were suppressed by pressurizing the octapole chamber with 3.1 mL min{sup -1} H{sub 2} and 0.5 mL min{sup -1} He. Four arsenic species arsenite - As(III), arsenate (As(V)), monomethylarsonic acid (MMA), and dimethylarsinic acid (DMA) - and three inorganic Se species - selenite Se(IV), selenate Se(VI), and selenocyanate (SeCN{sup -}) - were separated in a single run by ion chromatography (IC) using gradient elution with 100 mmol L{sup -1} NH{sub 4}NO{sub 3}, pH 8.5, adjusted by addition of NH{sub 3}, as eluent. Repeatabilities of peak position and of peak area evaluation were better than 1% and about 3%, respectively. Detection limits (as 3{sigma} of the baseline noise) were 81, 56, and 75 ng L{sup -1} for Se(IV), Se(VI), and SeCN{sup -}, respectively, and 22, 19, 25, and 16 ng L{sup -1} for As(III), As(V), MMA, and DMA, respectively. Calibration curve R {sup 2} values ranged between 0.996 and 0.999 for the arsenic and selenium species. Column recovery for ion chromatography was calculated to be 97 {+-} 6% for combined arsenic species and 98 {+-} 3% for combined selenium species. Because certified reference materials for As and Se speciation studies are still not commercially available, in order to check accuracy and precision the method was applied to certified reference materials, BCR 714, BCR 1714, and BCR 715 and to two different refinery samples - inlet and outlet wastewater. The method was successfully used to study the quantitative speciation of selenium and arsenic in petroleum refinery wastewaters. (orig.)

  20. Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein-ligand binding challenge

    Science.gov (United States)

    Perryman, Alexander L.; Santiago, Daniel N.; Forli, Stefano; Santos-Martins, Diogo; Olson, Arthur J.

    2014-04-01

    To rigorously assess the tools and protocols that can be used to understand and predict macromolecular recognition, and to gain more structural insight into three newly discovered allosteric binding sites on a critical drug target involved in the treatment of HIV infections, the Olson and Levy labs collaborated on the SAMPL4 challenge. This computational blind challenge involved predicting protein-ligand binding against the three allosteric sites of HIV integrase (IN), a viral enzyme for which two drugs (that target the active site) have been approved by the FDA. Positive control cross-docking experiments were utilized to select 13 receptor models out of an initial ensemble of 41 different crystal structures of HIV IN. These 13 models of the targets were selected using our new "Rank Difference Ratio" metric. The first stage of SAMPL4 involved using virtual screens to identify 62 active, allosteric IN inhibitors out of a set of 321 compounds. The second stage involved predicting the binding site(s) and crystallographic binding mode(s) for 57 of these inhibitors. Our team submitted four entries for the first stage that utilized: (1) AutoDock Vina (AD Vina) plus visual inspection; (2) a new common pharmacophore engine; (3) BEDAM replica exchange free energy simulations, and a Consensus approach that combined the predictions of all three strategies. Even with the SAMPL4's very challenging compound library that displayed a significantly lower amount of structural diversity than most libraries that are conventionally employed in prospective virtual screens, these approaches produced hit rates of 24, 25, 34, and 27 %, respectively, on a set with 19 % declared binders. Our only entry for the second stage challenge was based on the results of AD Vina plus visual inspection, and it ranked third place overall according to several different metrics provided by the SAMPL4 organizers. The successful results displayed by these approaches highlight the utility of the computational

  1. Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein-ligand binding challenge.

    Science.gov (United States)

    Perryman, Alexander L; Santiago, Daniel N; Forli, Stefano; Martins, Diogo Santos; Olson, Arthur J

    2014-04-01

    To rigorously assess the tools and protocols that can be used to understand and predict macromolecular recognition, and to gain more structural insight into three newly discovered allosteric binding sites on a critical drug target involved in the treatment of HIV infections, the Olson and Levy labs collaborated on the SAMPL4 challenge. This computational blind challenge involved predicting protein-ligand binding against the three allosteric sites of HIV integrase (IN), a viral enzyme for which two drugs (that target the active site) have been approved by the FDA. Positive control cross-docking experiments were utilized to select 13 receptor models out of an initial ensemble of 41 different crystal structures of HIV IN. These 13 models of the targets were selected using our new "Rank Difference Ratio" metric. The first stage of SAMPL4 involved using virtual screens to identify 62 active, allosteric IN inhibitors out of a set of 321 compounds. The second stage involved predicting the binding site(s) and crystallographic binding mode(s) for 57 of these inhibitors. Our team submitted four entries for the first stage that utilized: (1) AutoDock Vina (AD Vina) plus visual inspection; (2) a new common pharmacophore engine; (3) BEDAM replica exchange free energy simulations, and a Consensus approach that combined the predictions of all three strategies. Even with the SAMPL4's very challenging compound library that displayed a significantly lower amount of structural diversity than most libraries that are conventionally employed in prospective virtual screens, these approaches produced hit rates of 24, 25, 34, and 27 %, respectively, on a set with 19 % declared binders. Our only entry for the second stage challenge was based on the results of AD Vina plus visual inspection, and it ranked third place overall according to several different metrics provided by the SAMPL4 organizers. The successful results displayed by these approaches highlight the utility of the computational

  2. Mechanism of inhibition of HIV-1 integrase by G-tetrad-forming oligonucleotides in Vitro.

    Science.gov (United States)

    Jing, N; Marchand, C; Liu, J; Mitra, R; Hogan, M E; Pommier, Y

    2000-07-14

    The G-tetrad-forming oligonucleotides and have been identified as potent inhibitors of human immunodeficiency virus type 1 integrase (HIV-1 IN) activity (Rando, R. F., Ojwang, J., Elbaggari, A., Reyes, G. R., Tinder, R., McGrath, M. S., and Hogan, M. E. (1995) J. Biol. Chem. 270, 1754-1760; Mazumder, A., Neamati, N., Ojwang, J. O., Sunder, S., Rando, R. F., and Pommier, Y. (1996) Biochemistry 35, 13762-13771; Jing, N., and Hogan, M. E. (1998) J. Biol. Chem. 273, 34992-34999). To understand the inhibition of HIV-1 IN activity by the G-quartet inhibitors, we have designed the oligonucleotides and, composed of three and four G-quartets with stem lengths of 19 and 24 A, respectively. The fact that increasing the G-quartet stem length from 15 to 24 A kept inhibition of HIV-1 IN activity unchanged suggests that the binding interaction occurs between a GTGT loop domain of the G-quartet inhibitors and a catalytic site of HIV-1 IN, referred to as a face-to-face interaction. Docking the NMR structure of (Jing and Hogan (1998)) into the x-ray structure of the core domain of HIV-1 IN, HIV-1 IN-(51-209) (Maignan, S., Guilloteau, J.-P. , Qing, Z.-L., Clement-Mella, C., and Mikol, V. (1998) J. Mol. Biol. 282, 359-368), was performed using the GRAMM program. The statistical distributions of hydrogen bonding between HIV-1 IN and were obtained from the analyses of 1000 random docking structures. The docking results show a high probability of interaction between the GTGT loop residues of the G-quartet inhibitors and the catalytic site of HIV-1 IN, in agreement with the experimental observation.

  3. A new location to split Cre recombinase for protein fragment complementation.

    Science.gov (United States)

    Rajaee, Maryam; Ow, David W

    2017-11-01

    We have previously described a recombinase-mediated gene stacking system in which the Cre recombinase is used to remove lox-site flanked DNA no longer needed after each round of Bxb1 integrase-mediated site-specific integration. The Cre recombinase can be conveniently introduced by hybridization with a cre-expressing plant. However, maintaining an efficient cre-expressing line over many generations can be a problem, as high production of this DNA-binding protein might interfere with normal chromosome activities. To counter this selection against high Cre activity, we considered a split-cre approach, in which Cre activity is reconstituted after separate parts of Cre are brought into the same genome by hybridization. To insure that the recombinase-mediated gene stacking system retains its freedom to operate, we tested for new locations to split Cre into complementing fragments. In this study, we describe testing four new locations for splitting the Cre recombinase for protein fragment complementation and show that the two fragments of Cre split between Lys244 and Asn245 can reconstitute activity that is comparable to that of wild-type Cre. © 2017 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

  4. Synthesis and Characterization of β-Cyclodextrin Functionalized Ionic Liquid Polymer as a Macroporous Material for the Removal of Phenols and As(V

    Directory of Open Access Journals (Sweden)

    Muggundha Raoov

    2013-12-01

    Full Text Available β-Cyclodextrin-ionic liquid polymer (CD-ILP was first synthesized by functionalized β-cyclodextrin (CD with 1-benzylimidazole (BIM to form monofunctionalized CD (βCD-BIMOTs and was further polymerized using a toluene diisocyanate (TDI linker to form insoluble CD-ILP (βCD-BIMOTs-TDI. The βCD-BIMOTs-TDI polymer was characterized using various tools and the results obtained were compared with those derived from the native β-cyclodextrin polymer (βCD-TDI. The SEM result shows that the presence of ionic liquid (IL increases the pore size, while the thermo gravimetric analysis (TGA result shows that the presence of IL increases the stability of the polymer. Meanwhile, Brunauer-Emmett-Teller (BET results show that βCD-BIMOTs-TDI polymer has 1.254 m2/g surface areas and the Barret-Joyner-Halenda (BJH pore size distribution result reveals that the polymer exhibits macropores with a pore size of 77.66 nm. Preliminary sorption experiments were carried out and the βCD-BIMOTs-TDI polymer shows enhanced sorption capacity and high removal towards phenols and As(V.

  5. The S230R Integrase Substitution Associated with Viral Rebound during DTG Monotherapy Confers Low Levels INSTI Drug Resistance.

    Science.gov (United States)

    Pham, Hanh T; Labrie, Lydia; Wijting, Ingeborg E A; Hassounah, Said; Lok, Ka Yee; Portna, Inna; Goring, Mark; Han, Yingshan; Lungu, Cynthia; van der Ende, Marchina E; Brenner, Bluma G; Boucher, Charles A; Rijnders, Bart J A; van Kampen, Jeroen J A; Mesplède, Thibault; Wainberg, Mark A

    2018-03-29

    Dolutegravir (DTG) is an integrase strand-transfer inhibitor (INSTI) used for treatment of HIV-infected individuals. Due to its high genetic barrier to resistance, DTG has been clinically investigated as maintenance monotherapy to maintain viral suppression and to reduce complication and healthcare costs. Our study aims to explain the underlying mechanism related to the emergence of a S230R substitution in patients who experienced virological failure while using DTG monotherapy. We evaluated the effect of S230R substitution in regard to IN enzyme activity, viral infectivity, replicative capacity and susceptibility to different INSTIs by biochemical and cell-based assays. S230R substitution conferred 63% reduction in enzyme efficiency. The S230R virus was 1.29-fold less infectious than wildtype (WT), but could replicate in PM1 cells without significant delay. Resistance levels against DTG, CAB, RAL and EVG in tissue culture were 3.85-, 3.72-, 1.52-, and 1.21-fold, respectively. Our data indicate that the S230R substitution is comparable to the previously reported R263K in some respects. Virological failure under DTG monotherapy can occur through the development of such S230R or R263K mutations without the need for high levels DTG resistance.

  6. A long-acting integrase inhibitor protects female macaques from repeated high-dose intravaginal SHIV challenge.

    Science.gov (United States)

    Andrews, Chasity D; Yueh, Yun Lan; Spreen, William R; St Bernard, Leslie; Boente-Carrera, Mar; Rodriguez, Kristina; Gettie, Agegnehu; Russell-Lodrigue, Kasi; Blanchard, James; Ford, Susan; Mohri, Hiroshi; Cheng-Mayer, Cecilia; Hong, Zhi; Ho, David D; Markowitz, Martin

    2015-01-14

    Long-acting GSK1265744 (GSK744 LA) is a strand transfer inhibitor of the HIV/SIV (simian immunodeficiency virus) integrase and was shown to be an effective preexposure prophylaxis (PrEP) agent in a low-dose intrarectal SHIV (simian-human immunodeficiency virus) rhesus macaque challenge model. We examined the pharmacokinetics and efficacy of GSK744 LA as PrEP against repeat high-dose intravaginal SHIV challenge in female rhesus macaques treated with Depo-Provera (depot medroxyprogesterone acetate), which promotes viral transmission vaginally. When Depo-Provera-treated female rhesus macaques were dosed with GSK744 LA (50 mg/kg) monthly, systemic and tissue drug concentrations were lower than previously observed in male rhesus macaques. GSK744 concentrations were fivefold lower on average in cervical tissues than in rectal tissues. Eight female rhesus macaques were treated with GSK744 LA at week 0, and four female rhesus macaques served as controls. All animals received a high-dose challenge of SHIV162P3 at week 1. No infection was detected in GSK744 LA-treated rhesus macaques, whereas viremia was detected 1 to 2 weeks after SHIV challenge in all control animals. The GSK744 LA-treated rhesus macaques were given a second administration of drug at week 4 and further challenged at weeks 5 and 7. GSK744 LA treatment protected six of eight female rhesus macaques against three high-dose SHIV challenges, whereas all control animals became infected after the first challenge (P = 0.0003, log-rank test). These results support further clinical development of GSK744 LA for PrEP. Copyright © 2015, American Association for the Advancement of Science.

  7. Ulysses transposable element of Drosophila shows high structural similarities to functional domains of retroviruses.

    Science.gov (United States)

    Evgen'ev, M B; Corces, V G; Lankenau, D H

    1992-06-05

    We have determined the DNA structure of the Ulysses transposable element of Drosophila virilis and found that this transposon is 10,653 bp and is flanked by two unusually large direct repeats 2136 bp long. Ulysses shows the characteristic organization of LTR-containing retrotransposons, with matrix and capsid protein domains encoded in the first open reading frame. In addition, Ulysses contains protease, reverse transcriptase, RNase H and integrase domains encoded in the second open reading frame. Ulysses lacks a third open reading frame present in some retrotransposons that could encode an env-like protein. A dendrogram analysis based on multiple alignments of the protease, reverse transcriptase, RNase H, integrase and tRNA primer binding site of all known Drosophila LTR-containing retrotransposon sequences establishes a phylogenetic relationship of Ulysses to other retrotransposons and suggests that Ulysses belongs to a new family of this type of elements.

  8. Mediji un populisms: ASV mediju dienaskārtība un ziņu atspoguļojums kā veicinošs faktors Donalda Trampa priekšvēlēšanu kampaņas atbalstam. 2011. un 2015. gada ziņu raidījumu salīdzinošā analīze

    OpenAIRE

    Aleksejeva, Santa

    2017-01-01

    Maģistra darba tēmas ir “Mediji un populisms: ASV mediju dienaskārtība un ziņu atspoguļojums kā veicinošs faktors Donalda Trampa priekšvēlēšanu kampaņas atbalstam. 2011. un 2015. gada ziņu raidījumu salīdzinošā analīze”. Pētījuma mērķis ir izpētīt mediju un populisma saikni un apstiprināt hipotēzi, ka mediju veidotā dienaskārtība un ziņu atspoguļojums par brīvo tirdzniecību, Pieejmās Aprūpes likumu un imigrāciju ASV televīzijas kanālos CNN, MSNBC un FOX News 2015. gadā ir veicinājis sabiedrīb...

  9. Modulation of the functional association between the HIV-1 intasome and the nucleosome by histone amino-terminal tails.

    Science.gov (United States)

    Benleulmi, Mohamed S; Matysiak, Julien; Robert, Xavier; Miskey, Csaba; Mauro, Eric; Lapaillerie, Delphine; Lesbats, Paul; Chaignepain, Stéphane; Henriquez, Daniel R; Calmels, Christina; Oladosu, Oyindamola; Thierry, Eloïse; Leon, Oscar; Lavigne, Marc; Andreola, Marie-Line; Delelis, Olivier; Ivics, Zoltán; Ruff, Marc; Gouet, Patrice; Parissi, Vincent

    2017-11-28

    Stable insertion of the retroviral DNA genome into host chromatin requires the functional association between the intasome (integrase·viral DNA complex) and the nucleosome. The data from the literature suggest that direct protein-protein contacts between integrase and histones may be involved in anchoring the intasome to the nucleosome. Since histone tails are candidates for interactions with the incoming intasomes we have investigated whether they could participate in modulating the nucleosomal integration process. We show here that histone tails are required for an optimal association between HIV-1 integrase (IN) and the nucleosome for efficient integration. We also demonstrate direct interactions between IN and the amino-terminal tail of human histone H4 in vitro. Structure/function studies enabled us to identify amino acids in the carboxy-terminal domain of IN that are important for this interaction. Analysis of the nucleosome-binding properties of catalytically active mutated INs confirmed that their ability to engage the nucleosome for integration in vitro was affected. Pseudovirus particles bearing mutations that affect the IN/H4 association also showed impaired replication capacity due to altered integration and re-targeting of their insertion sites toward dynamic regions of the chromatin with lower nucleosome occupancy. Collectively, our data support a functional association between HIV-1 IN and histone tails that promotes anchoring of the intasome to nucleosomes and optimal integration into chromatin.

  10. Ce–Fe-modified zeolite-rich tuff to remove Ba{sup 2+}-like {sup 226}Ra{sup 2+} in presence of As(V) and F{sup −} from aqueous media as pollutants of drinking water

    Energy Technology Data Exchange (ETDEWEB)

    Olguín, María Teresa, E-mail: teresa.olguin@inin.gob.mx [Department of Chemical & Materials Engineering, New Mexico State University, P.O. Box 30001, MSC 3805, Las Cruces, NM 88003 (United States); Departamento de Química, Instituto Nacional de Investigaciones Nucleares, A.P. 18-1027, Col. Escandón, Delegación Miguel Hidalgo, C.P. 11801, México D.F. (Mexico); Deng, Shuguang [Department of Chemical & Materials Engineering, New Mexico State University, P.O. Box 30001, MSC 3805, Las Cruces, NM 88003 (United States)

    2016-01-25

    Graphical abstract: Ba{sup 2+}-like {sup 226}Ra{sup 2+}, As(V) and F{sup −} simultaneous removal from aqueous media by Ce–Fe-modified natural zeolites. - Highlights: • The metallic species which modified the zeolite change the textural properties. • The pH{sub pzc} is acid for ZUSCeFe and neutral for ZUSNa. • The Linear model describes the Ba{sup 2+}-like {sup 226}Ra{sup 2+} sorption by ZUSNa and ZUSCeFe. • K{sub d} is highest for Ba{sup 2+-} like {sup 226}Ra{sup 2+}-As(V)-F{sup -} solution in contact with ZUSCeFe. • The ZUSCeFe remove simultaneously Ba{sup 2+}-like {sup 226}Ra{sup 2+}, As(V) and F{sup −}. - Abstract: The sorption behavior of the Ba{sup 2+}-like {sup 226}Ra{sup 2+} in the presence of H{sub 2}AsO{sub 4}{sup −}/HAsO{sub 4}{sup 2−} and F{sup −} from aqueous media using Ce–Fe-modified zeolite-rich tuff was investigated in this work. The Na-modified zeolite-rich tuff was also considered for comparison purposes. The zeolite-rich tuff collected from Wyoming (US) was in contact with NaCl and CeCl{sub 3}–FeCl{sub 3} solutions to obtain the Na- and Ce–Fe-modified zeolite-rich tuffs (ZUSNa and ZUSCeFe). These zeolites were characterized by scanning electron microscopy and X-ray diffraction. The BET-specific surface and the points of zero charge were determined as well as the content of Na, Ce and Fe by neutron activation analysis. The textural characteristics and the point of zero charge were changed by the presence of Ce and Fe species in the zeolitic network. A linear model described the Ba{sup 2+}-like {sup 226}Ra{sup 2+} sorption isotherms and the distribution coefficients (K{sub d}) varied with respect to the metallic species present in the zeolitic material. The As(V) oxianionic chemical species and F{sup −} affected this parameter when the Ba{sup 2+}-like {sup 226}Ra{sup 2+}-As(V)-F{sup −} solutions were in contact with ZUSCeFe. The H{sub 2}AsO{sub 4}{sup −}/HAsO{sub 4}{sup 2−} and F{sup −} were adsorbed by ZUSCe

  11. Mutations in the catalytic core or the C-terminus of murine leukemia virus (MLV) integrase disrupt virion infectivity and exert diverse effects on reverse transcription

    International Nuclear Information System (INIS)

    Steinrigl, Adolf; Nosek, Dagmara; Ertl, Reinhard; Guenzburg, Walter H.; Salmons, Brian; Klein, Dieter

    2007-01-01

    Understanding of the structures and functions of the retroviral integrase (IN), a key enzyme in the viral replication cycle, is essential for developing antiretroviral treatments and facilitating the development of safer gene therapy vehicles. Thus, four MLV IN-mutants were constructed in the context of a retroviral vector system, harbouring either a substitution in the catalytic centre, deletions in the C-terminus, or combinations of both modifications. IN-mutants were tested for their performance in different stages of the viral replication cycle: RNA-packaging; RT-activity; transient and stable infection efficiency; dynamics of reverse transcription and nuclear entry. All mutant vectors packaged viral RNA with wild-type efficiencies and displayed only slight reductions in RT-activity. Deletion of either the IN C-terminus alone, or in addition to part of the catalytic domain exerted contrasting effects on intracellular viral DNA levels, implying that IN influences reverse transcription in more than one direction

  12. Metagenomic analysis of lysogeny in Tampa Bay: implications for prophage gene expression.

    Directory of Open Access Journals (Sweden)

    Lauren McDaniel

    Full Text Available Phage integrase genes often play a role in the establishment of lysogeny in temperate phage by catalyzing the integration of the phage into one of the host's replicons. To investigate temperate phage gene expression, an induced viral metagenome from Tampa Bay was sequenced by 454/Pyrosequencing. The sequencing yielded 294,068 reads with 6.6% identifiable. One hundred-three sequences had significant similarity to integrases by BLASTX analysis (e < or =0.001. Four sequences with strongest amino-acid level similarity to integrases were selected and real-time PCR primers and probes were designed. Initial testing with microbial fraction DNA from Tampa Bay revealed 1.9 x 10(7, and 1300 gene copies of Vibrio-like integrase and Oceanicola-like integrase L(-1 respectively. The other two integrases were not detected. The integrase assay was then tested on microbial fraction RNA extracted from 200 ml of Tampa Bay water sampled biweekly over a 12 month time series. Vibrio-like integrase gene expression was detected in three samples, with estimated copy numbers of 2.4-1280 L(-1. Clostridium-like integrase gene expression was detected in 6 samples, with estimated copy numbers of 37 to 265 L(-1. In all cases, detection of integrase gene expression corresponded to the occurrence of lysogeny as detected by prophage induction. Investigation of the environmental distribution of the two expressed integrases in the Global Ocean Survey Database found the Vibrio-like integrase was present in genome equivalents of 3.14% of microbial libraries and all four viral metagenomes. There were two similar genes in the library from British Columbia and one similar gene was detected in both the Gulf of Mexico and Sargasso Sea libraries. In contrast, in the Arctic library eleven similar genes were observed. The Clostridium-like integrase was less prevalent, being found in 0.58% of the microbial and none of the viral libraries. These results underscore the value of metagenomic data

  13. Sorption and redox reactions of As(III) and As(V) within secondary mineral coatings on aquifer sediment grains.

    Science.gov (United States)

    Singer, David M; Fox, Patricia M; Guo, Hua; Marcus, Matthew A; Davis, James A

    2013-10-15

    Important reactive phenomena that affect the transport and fate of many elements occur at the mineral-water interface (MWI), including sorption and redox reactions. Fundamental knowledge of these phenomena are often based on observations of ideal mineral-water systems, for example, studies of molecular scale reactions on single crystal faces or the surfaces of pure mineral powders. Much less is understood about MWI in natural environments, which typically have nanometer to micrometer scale secondary mineral coatings on the surfaces of primary mineral grains. We examined sediment grain coatings from a well-characterized field site to determine the causes of rate limitations for arsenic (As) sorption and redox processes within the coatings. Sediments were obtained from the USGS field research site on Cape Cod, MA, and exposed to synthetic contaminated groundwater solutions. Uptake of As(III) and As(V) into the coatings was studied with a combination of electron microscopy and synchrotron techniques to assess concentration gradients and reactive processes, including electron transfer reactions. Transmission electron microscopy (TEM) and X-ray microprobe (XMP) analyses indicated that As was primarily associated with micrometer- to submicrometer aggregates of Mn-bearing nanoparticulate goethite. As(III) oxidation by this phase was observed but limited by the extent of exposed surface area of the goethite grains to the exterior of the mineral coatings. Secondary mineral coatings are potentially both sinks and sources of contaminants depending on the history of a contaminated site, and may need to be included explicitly in reactive transport models.

  14. Isolation and characterization of Staphylococcus sp. strain NBRIEAG-8 from arsenic contaminated site of West Bengal

    Energy Technology Data Exchange (ETDEWEB)

    Srivastava, Shubhi; Singh, Namrata; Singh, Nandita [CSIR - National Botanical Research Institute, Lucknow, UP (India). Eco-auditing Lab.; Verma, Praveen C.; Singh, Ankit; Mishra, Manisha [CSIR - National Botanical Research Institute, Lucknow, UP (India). Plant Molecular Biology and Genetic Engineering; Sharma, Neeta [Lucknow Univ., UP (India). Plant Pathology Lab.

    2012-09-15

    Arsenic contaminated rhizospheric soils of West Bengal, India were sampled for arsenic resistant bacteria that could transform different arsenic forms. Staphylococcus sp. NBRIEAG-8 was identified by16S rDNA ribotyping, which was capable of growing at 30,000 mg l{sup -1} arsenate [As(V)] and 1,500 mg l{sup -1} arsenite [As(III)]. This bacterial strain was also characterized for arsenical resistance (ars) genes which may be associated with the high-level resistance in the ecosystems of As-contaminated areas. A comparative proteome analysis was conducted with this strain treated with 1,000 mg l{sup -1} As(V) to identify changes in their protein expression profiles. A 2D gel analysis showed a significant difference in the proteome of arsenic treated and untreated bacterial culture. The change in pH of cultivating growth medium, bacterial growth pattern (kinetics), and uptake of arsenic were also evaluated. After 72 h of incubation, the strain was capable of removing arsenic from the culture medium amended with arsenate and arsenite [12% from As(V) and 9% from As(III)]. The rate of biovolatilization of As(V) was 23% while As(III) was 26%, which was determined indirectly by estimating the sum of arsenic content in bacterial biomass and medium. This study demonstrates that the isolated strain, Staphylococcus sp., is capable for uptake and volatilization of arsenic by expressing ars genes and 8 new upregulated proteins which may have played an important role in reducing arsenic toxicity in bacterial cells and can be used in arsenic bioremediation. (orig.)

  15. Single and combined effects of cadmium and arsenate in Gammarus pulex (Crustacea, Amphipoda): Understanding the links between physiological and behavioural responses

    Energy Technology Data Exchange (ETDEWEB)

    Vellinger, Céline, E-mail: celine.vellinger@gmail.com [Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), CNRS UMR 7360, Université de Lorraine – Metz (France); Gismondi, Eric, E-mail: gismondi.eric@gmail.com [Laboratoire d’Ecologie animale et d’Ecotoxicologie, Institut de Chimie, Université de Liège, Allée du 6 Août 15, B-4000 Sart-Tilman, Liège (Belgium); Felten, Vincent, E-mail: vincent.felten@univ-lorraine.fr [Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), CNRS UMR 7360, Université de Lorraine – Metz (France); Rousselle, Philippe, E-mail: rousselle@univ-lorraine.fr [Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), CNRS UMR 7360, Université de Lorraine – Metz (France); Mehennaoui, Kahina, E-mail: meh_kahina@yahoo.fr [Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), CNRS UMR 7360, Université de Lorraine – Metz (France); Parant, Marc, E-mail: parant@univ-lorraine.fr [Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), CNRS UMR 7360, Université de Lorraine – Metz (France); Usseglio-Polatera, Philippe, E-mail: usseglio-polatera@univ-lorraine.fr [Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), CNRS UMR 7360, Université de Lorraine – Metz (France)

    2013-09-15

    Highlights: •Linking physiological to behavioural responses of G. pulex exposed to AsV and/or Cd. •AsV and/or Cd exposure exhibited similar biomarkers responses. •Contamination increases the mobilization of detoxification systems in gammarids. •Both changes in energy reserve use and allocation are involved in gammarid response. •Increased lipid peroxidation could be the cause of increasing gammarid mortality. -- Abstract: This study aimed at investigating the individual and interactive effects of cadmium (Cd) and arsenate (AsV) in Gammarus pulex (Crustacea, Amphipoda) through the use of several biomarkers. Individuals were exposed for 240 h to two concentrations of AsV or Cd alone, and all the possible binary mixtures of these concentrations of AsV and Cd in a complete factorial design. The pattern of the biomarkers’ responses to Cd and AsV alone or in mixture was similar in Gammarus pulex, even if the response intensity varied depending on the tested conditions. G. pulex responded to contamination with increased mobilization of the detoxification systems [i.e. γ-glutamyl-cystein ligase activity (GCL), reduced glutathione content (GSH) and metallothionein concentrations (MT)]. This response seems to imply changes in energy reserve utilization (total lipids and proteins are used prior to glycogen reserves), but also a possible energy reallocation from locomotion to detoxification processes. The observed increase in lipid peroxidation could be relied to the increasing gammarid mortality, despite the higher mobilization of detoxification systems. Even if the outcome of the complex interactions between AsV and Cd remains difficult to unravel, such studies are critically important for better assessing the effects of stressors on organisms, populations and communities in a multi-contamination context of ecosystems.

  16. Clinical Improvement by Switching to an Integrase Strand Transfer Inhibitor in Hemophiliac Patients with HIV: The Japan Cohort Study of HIV Patients Infected through Blood Products.

    Science.gov (United States)

    Kawado, Miyuki; Hashimoto, Shuji; Oka, Shin-Ichi; Fukutake, Katsuyuki; Higasa, Satoshi; Yatsuhashi, Hiroshi; Ogane, Miwa; Okamoto, Manabu; Shirasaka, Takuma

    2017-01-01

    This study aimed to determine improvement in HIV RNA levels and the CD4 cell count by switching to an antiretroviral regimen with an integrase strand transfer inhibitor (INSTI) in patients with HIV. This study was conducted on Japanese patients with HIV who were infected by blood products in the 1980s. Data were collected between 2007 and 2014. Data of 564 male hemophiliac patients with HIV from the Japan Cohort Study of HIV Patients Infected through Blood Products were available. Changes in antiretroviral regimen use, HIV RNA levels, and the CD4 cell count between 2007 and 2014 were examined. From 2007 to 2014, the proportion of use of a regimen with an INSTI increased from 0.0% to 41.0%. For patients with HIV who used a regimen, including an INSTI, the proportion of HIV RNA levels products. This suggests that performing this switch in clinical practice will lead to favorable effects.

  17. The Microbiota and Abundance of the Class 1 Integron-Integrase Gene in Tropical Sewage Treatment Plant Influent and Activated Sludge.

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    Magna C Paiva

    Full Text Available Bacteria are assumed to efficiently remove organic pollutants from sewage in sewage treatment plants, where antibiotic-resistance genes can move between species via mobile genetic elements known as integrons. Nevertheless, few studies have addressed bacterial diversity and class 1 integron abundance in tropical sewage. Here, we describe the extant microbiota, using V6 tag sequencing, and quantify the class 1 integron-integrase gene (intI1 in raw sewage (RS and activated sludge (AS. The analysis of 1,174,486 quality-filtered reads obtained from RS and AS samples revealed complex and distinct bacterial diversity in these samples. The RS sample, with 3,074 operational taxonomic units, exhibited the highest alpha-diversity indices. Among the 25 phyla, Proteobacteria, Bacteroidetes and Firmicutes represented 85% (AS and 92% (RS of all reads. Increased relative abundance of Micrococcales, Myxococcales, and Sphingobacteriales and reduced pathogen abundance were noted in AS. At the genus level, differences were observed for the dominant genera Simplicispira and Diaphorobacter (AS as well as for Enhydrobacter (RS. The activated sludge process decreased (55% the amount of bacteria harboring the intI1 gene in the RS sample. Altogether, our results emphasize the importance of biological treatment for diminishing pathogenic bacteria and those bearing the intI1 gene that arrive at a sewage treatment plant.

  18. Glutathione-supported arsenate reduction coupled to arsenolysis catalyzed by ornithine carbamoyl transferase

    International Nuclear Information System (INIS)

    Nemeti, Balazs; Gregus, Zoltan

    2009-01-01

    Three cytosolic phosphorolytic/arsenolytic enzymes, (purine nucleoside phosphorylase [PNP], glycogen phosphorylase, glyceraldehyde-3-phosphate dehydrogenase) have been shown to mediate reduction of arsenate (AsV) to the more toxic arsenite (AsIII) in a thiol-dependent manner. With unknown mechanism, hepatic mitochondria also reduce AsV. Mitochondria possess ornithine carbamoyl transferase (OCT), which catalyzes phosphorolytic or arsenolytic citrulline cleavage; therefore, we examined if mitochondrial OCT facilitated AsV reduction in presence of glutathione. Isolated rat liver mitochondria were incubated with AsV, and AsIII formed was quantified. Glutathione-supplemented permeabilized or solubilized mitochondria reduced AsV. Citrulline (substrate for OCT-catalyzed arsenolysis) increased AsV reduction. The citrulline-stimulated AsV reduction was abolished by ornithine (OCT substrate inhibiting citrulline cleavage), phosphate (OCT substrate competing with AsV), and the OCT inhibitor norvaline or PALO, indicating that AsV reduction is coupled to OCT-catalyzed arsenolysis of citrulline. Corroborating this conclusion, purified bacterial OCT mediated AsV reduction in presence of citrulline and glutathione with similar responsiveness to these agents. In contrast, AsIII formation by intact mitochondria was unaffected by PALO and slightly stimulated by citrulline, ornithine, and norvaline, suggesting minimal role for OCT in AsV reduction in intact mitochondria. In addition to OCT, mitochondrial PNP can also mediate AsIII formation; however, its role in AsV reduction appears severely limited by purine nucleoside supply. Collectively, mitochondrial and bacterial OCT promote glutathione-dependent AsV reduction with coupled arsenolysis of citrulline, supporting the hypothesis that AsV reduction is mediated by phosphorolytic/arsenolytic enzymes. Nevertheless, because citrulline cleavage is disfavored physiologically, OCT may have little role in AsV reduction in vivo.

  19. Arsenate reduction and mobilization in the presence of indigenous aerobic bacteria obtained from high arsenic aquifers of the Hetao basin, Inner Mongolia

    International Nuclear Information System (INIS)

    Guo, Huaming; Liu, Zeyun; Ding, Susu; Hao, Chunbo; Xiu, Wei; Hou, Weiguo

    2015-01-01

    Intact aquifer sediments were collected to obtain As-resistant bacteria from the Hetao basin. Two strains of aerobic As-resistant bacteria (Pseudomonas sp. M17-1 and Bacillus sp. M17-15) were isolated from the aquifer sediments. Those strains exhibited high resistances to both As(III) and As(V). Results showed that both strains had arr and ars genes, and led to reduction of dissolved As(V), goethite-adsorbed As(V), scorodite As(V) and sediment As(V), in the presence of organic carbon as the carbon source. After reduction of solid As(V), As release was observed from the solids to solutions. Strain M17-15 had a higher ability than strain M17-1 in reducing As(V) and promoting the release of As. These results suggested that the strains would mediate As(V) reduction to As(III), and thereafter release As(III), due to the higher mobility of As(III) in most aquifer systems. The processes would play an important role in genesis of high As groundwater. - Highlights: • Two strains of As-resistant bacteria were isolated from high As aquifer sediment. • The strains (M17–1 and M17-15) had an As tolerance under oxic conditions. • The strains had arr and ars genes, and reduced both dissolved As(V) and solid As(V). • Reduction of solid As(V) resulted in As release into solutions. • M17-15 had a higher ability in reducing As(V) and promoting As release than M17-1. - Indigenous aerobic bacteria from the high-As aquifer sediment had arr and ars genes and led to reduction of dissolved As(V), goethite-adsorbed As(V), scorodite As(V) and sedimentary As

  20. The ΦBT1 large serine recombinase catalyzes DNA integration at pseudo-attB sites in the genus Nocardia

    Directory of Open Access Journals (Sweden)

    Marion Herisse

    2018-05-01

    Full Text Available Plasmid vectors based on bacteriophage integrases are important tools in molecular microbiology for the introduction of foreign DNA, especially into bacterial species where other systems for genetic manipulation are limited. Site specific integrases catalyze recombination between phage and bacterial attachment sites (attP and attB, respectively and the best studied integrases in the actinomycetes are the serine integrases from the Streptomyces bacteriophages ΦC31 and ΦBT1. As this reaction is unidirectional and highly stable, vectors containing phage integrase systems have been used in a number of genetic engineering applications. Plasmids bearing the ΦBT1 integrase have been used to introduce DNA into Streptomyces and Amycolatopsis strains; however, they have not been widely studied in other actinobacterial genera. Here, we show that vectors based on ΦBT1 integrase can stably integrate into the chromosomes of a range of Nocardia species, and that this integration occurs despite the absence of canonical attB sites in these genomes. Furthermore, we show that a ΦBT1 integrase-based vector can insert at multiple pseudo-attB sites within a single strain and we determine the sequence of a pseudo-attB motif. These data suggest that ΦBT1 integrase-based vectors can be used to readily and semi-randomly introduce foreign DNA into the genomes of a range of Nocardia species. However, the precise site of insertion will likely require empirical determination in each species to avoid unexpected off-target effects.

  1. Adaptive servo ventilation improves Cheyne-Stokes respiration, cardiac function, and prognosis in chronic heart failure patients with cardiac resynchronization therapy.

    Science.gov (United States)

    Miyata, Makiko; Yoshihisa, Akiomi; Suzuki, Satoshi; Yamada, Shinya; Kamioka, Masashi; Kamiyama, Yoshiyuki; Yamaki, Takayoshi; Sugimoto, Koichi; Kunii, Hiroyuki; Nakazato, Kazuhiko; Suzuki, Hitoshi; Saitoh, Shu-ichi; Takeishi, Yasuchika

    2012-09-01

    Cheyne-Stokes respiration (CSR-CSA) is often observed in patients with chronic heart failure (CHF). Although cardiac resynchronization therapy (CRT) is effective for CHF patients with left ventricular dyssynchrony, it is still unclear whether adaptive servo ventilation (ASV) improves cardiac function and prognosis of CHF patients with CSR-CSA after CRT. Twenty two patients with CHF and CSR-CSA after CRT defibrillator (CRTD) implantation were enrolled in the present study and randomly assigned into two groups: 11 patients treated with ASV (ASV group) and 11 patients treated without ASV (non-ASV group). Measurement of plasma B-type natriuretic peptide (BNP) levels (before 3, and 6 months later) and echocardiography (before and 6 months) were performed in each group. Patients were followed up to register cardiac events (cardiac death and re-hospitalization) after discharge. In the ASV group, indices for apnea-hypopnea, central apnea, and oxyhemoglobin saturation were improved on ASV. BNP levels, cardiac systolic and diastolic function were improved with ASV treatment for 6 months. Importantly, the event-free rate was significantly higher in the ASV group than in the non-ASV group. ASV improves CSR-CSA, cardiac function, and prognosis in CHF patients with CRTD. Patients with CSR-CSA and post CRTD implantation would get benefits by treatment with ASV. Copyright © 2012 Japanese College of Cardiology. Published by Elsevier Ltd. All rights reserved.

  2. Dolutegravir versus placebo in subjects harbouring HIV-1 with integrase inhibitor resistance associated substitutions: 48-week results from VIKING-4, a randomized study.

    Science.gov (United States)

    Akil, Bisher; Blick, Gary; Hagins, Debbie P; Ramgopal, Moti N; Richmond, Gary J; Samuel, Rafik M; Givens, Naomi; Vavro, Cindy; Song, Ivy H; Wynne, Brian; Ait-Khaled, Mounir

    2015-01-01

    The Phase III VIKING-3 study demonstrated that dolutegravir (DTG) 50 mg twice daily was efficacious in antiretroviral therapy (ART)-experienced subjects harbouring raltegravir- and/or elvitegravir-resistant HIV-1. VIKING-4 (ING116529) included a placebo-controlled 7-day monotherapy phase to demonstrate that short-term antiviral activity was attributable to DTG. VIKING-4 is a Phase III randomized, double-blind study in therapy-experienced adults with integrase inhibitor (INI)-resistant virus randomized to DTG 50 mg twice daily or placebo while continuing their failing regimen (without raltegravir or elvitegravir) for 7 days (clinicaltrials.gov identifier NCT01568892). At day 8, all subjects switched to open-label DTG 50 mg twice daily and optimized background therapy including ≥1 fully active drug. The primary end point was change from baseline in plasma HIV-1 RNA at day 8. The study population (n=30) was highly ART-experienced with advanced HIV disease. Patients had extensive baseline resistance to all approved antiretroviral classes. Adjusted mean change in HIV-1 RNA at day 8 was 
-1.06 log10 copies/ml for the DTG arm and 0.10 log10 copies/ml for the placebo arm (treatment difference -1.16 log10 copies/ml [-1.52, -0.80]; PVIKING-3 study.

  3. Characterization of Magnaporthe oryzae chrysovirus 1 structural proteins and their expression in Saccharomyces cerevisiae.

    Science.gov (United States)

    Urayama, Syunichi; Ohta, Tomoko; Onozuka, Nobuya; Sakoda, Hirofumi; Fukuhara, Toshiyuki; Arie, Tsutomu; Teraoka, Tohru; Moriyama, Hiromitsu

    2012-08-01

    Magnaporthe oryzae chrysovirus 1 (MoCV1), which is associated with an impaired growth phenotype of its host fungus, harbors four major proteins: P130 (130 kDa), P70 (70 kDa), P65 (65 kDa), and P58 (58 kDa). N-terminal sequence analysis of each protein revealed that P130 was encoded by double-stranded RNA1 (dsRNA1) (open reading frame 1 [ORF1] 1,127 amino acids [aa]), P70 by dsRNA4 (ORF4; 812 aa), and P58 by dsRNA3 (ORF3; 799 aa), although the molecular masses of P58 and P70 were significantly smaller than those deduced for ORF3 and ORF4, respectively. P65 was a degraded form of P70. Full-size proteins of ORF3 (84 kDa) and ORF4 (85 kDa) were produced in Escherichia coli. Antisera against these recombinant proteins detected full-size proteins encoded by ORF3 and ORF4 in mycelia cultured for 9, 15, and 28 days, and the antisera also detected smaller degraded proteins, namely, P58, P70, and P65, in mycelia cultured for 28 days. These full-size proteins and P58 and P70 were also components of viral particles, indicating that MoCV1 particles might have at least two forms during vegetative growth of the host fungus. Expression of the ORF4 protein in Saccharomyces cerevisiae resulted in cytological changes, with a large central vacuole associated with these growth defects. MoCV1 has five dsRNA segments, as do two Fusarium graminearum viruses (FgV-ch9 and FgV2), and forms a separate clade with FgV-ch9, FgV2, Aspergillus mycovirus 1816 (AsV1816), and Agaricus bisporus virus 1 (AbV1) in the Chrysoviridae family on the basis of their RdRp protein sequences.

  4. Calcium-dependent protein kinase CPK31 interacts with arsenic transporter AtNIP1;1 and regulates arsenite uptake in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Ruijie Ji

    Full Text Available Although arsenite [As(III] is non-essential and toxic for plants, it is effectively absorbed through various transporters into the roots. Here we identified a calcium-dependent protein kinase (CPK31 response for As(III tolerance in Arabidopsis. We identified CPK31 as an interacting protein of a nodulin 26-like intrinsic protein (NIP1;1, an aquaporin involved in As(III uptake. Similarly to the nip1;1 mutants, the loss-of-function mutants of CPK31 improved the tolerance against As(III but not As(V, and accumulated less As(III in roots than that of the wild-type plants. The promoter-β-glucuronidase and quantitative Real-Time PCR analysis revealed that CPK31 displayed overlapping expression profiles with NIP1;1 in the roots, suggesting that they might function together in roots. Indeed, the cpk31 nip1;1 double mutants exhibited stronger As(III tolerance than cpk31 mutants, but similar to nip1;1 mutants, supporting the idea that CPK31 might serve as an upstream regulator of NIP1;1. Furthermore, transient CPK31 overexpression induced by dexamethasone caused the decrease in As(III tolerance of transgenic Arabidopsis lines. These findings reveal that CPK31 is a key factor in As(III response in plants.

  5. Genome Sequences of Four Subcluster L2 Mycobacterium Phages, Finemlucis, Miley16, Wilder, and Zakai

    OpenAIRE

    Herren, Christopher D.; Peister, Alexandra; Breton, Timothy S.; Hill, Maggie S.; Anderson, Marcy S.; Chang, Adeline W.; Klein, Sydney B.; Thornton, Mackenzie M.; Vars, Stacy J.; Wagner, Kasey E.; Wiebe, Paige L.; Williams, Thomas G.; Yanez, Coraima P.; Ackles, Jasanta M.; Artis, Darius

    2017-01-01

    ABSTRACT Four subcluster L2 mycobacteriophages, Finemlucis, Miley16, Wilder, and Zakai, that infect Mycobacterium smegmatis mc2155 were isolated. The four phages are closely related to each other and code for 12 to 14 tRNAs and 130 to 132 putative protein-coding genes, including tyrosine integrases, cro, immunity repressors, and excise genes involved in the establishment of lysogeny.

  6. Development of elvitegravir resistance and linkage of integrase inhibitor mutations with protease and reverse transcriptase resistance mutations.

    Directory of Open Access Journals (Sweden)

    Mark A Winters

    Full Text Available Failure of antiretroviral regimens containing elvitegravir (EVG and raltegravir (RAL can result in the appearance of integrase inhibitor (INI drug-resistance mutations (DRMs. While several INI DRMs have been identified, the evolution of EVG DRMs and the linkage of these DRMs with protease inhibitor (PI and reverse transcriptase inhibitor (RTI DRMs have not been studied at the clonal level. We examined the development of INI DRMs in 10 patients failing EVG-containing regimens over time, and the linkage of INI DRMs with PI and RTI DRMs in these patients plus 6 RAL-treated patients. A one-step RT-nested PCR protocol was used to generate a 2.7 kB amplicon that included the PR, RT, and IN coding region, and standard cloning and sequencing techniques were used to determine DRMs in 1,277 clones (mean 21 clones per time point. Results showed all patients had multiple PI, NRTI, and/or NNRTI DRMs at baseline, but no primary INI DRM. EVG-treated patients developed from 2 to 6 strains with different primary INI DRMs as early as 2 weeks after initiation of treatment, predominantly as single mutations. The prevalence of these strains fluctuated and new strains, and/or strains with new combinations of INI DRMs, developed over time. Final failure samples (weeks 14 to 48 typically showed a dominant strain with multiple mutations or N155H alone. Single N155H or multiple mutations were also observed in RAL-treated patients at virologic failure. All patient strains showed evidence of INI DRM co-located with single or multiple PI and/or RTI DRMs on the same viral strand. Our study shows that EVG treatment can select for a number of distinct INI-resistant strains whose prevalence fluctuates over time. Continued appearance of new INI DRMs after initial INI failure suggests a potent, highly dynamic selection of INI resistant strains that is unaffected by co-location with PI and RTI DRMs.

  7. Comparative analysis of prophages in Streptococcus mutans genomes

    Science.gov (United States)

    Fu, Tiwei; Fan, Xiangyu; Long, Quanxin; Deng, Wanyan; Song, Jinlin

    2017-01-01

    Prophages have been considered genetic units that have an intimate association with novel phenotypic properties of bacterial hosts, such as pathogenicity and genomic variation. Little is known about the genetic information of prophages in the genome of Streptococcus mutans, a major pathogen of human dental caries. In this study, we identified 35 prophage-like elements in S. mutans genomes and performed a comparative genomic analysis. Comparative genomic and phylogenetic analyses of prophage sequences revealed that the prophages could be classified into three main large clusters: Cluster A, Cluster B, and Cluster C. The S. mutans prophages in each cluster were compared. The genomic sequences of phismuN66-1, phismuNLML9-1, and phismu24-1 all shared similarities with the previously reported S. mutans phages M102, M102AD, and ϕAPCM01. The genomes were organized into seven major gene clusters according to the putative functions of the predicted open reading frames: packaging and structural modules, integrase, host lysis modules, DNA replication/recombination modules, transcriptional regulatory modules, other protein modules, and hypothetical protein modules. Moreover, an integrase gene was only identified in phismuNLML9-1 prophages. PMID:29158986

  8. Effect of temperature on the fate of genes encoding tetracycline resistance and the integrase of class 1 integrons within anaerobic and aerobic digesters treating municipal wastewater solids.

    Science.gov (United States)

    Diehl, David L; LaPara, Timothy M

    2010-12-01

    The objective of this research was to investigate the ability of anaerobic and aerobic digesters to reduce the quantity of antibiotic resistant bacteria in wastewater solids. Lab-scale digesters were operated at different temperatures (22 °C, 37 °C, 46 °C, and 55 °C) under both anaerobic and aerobic conditions and fed wastewater solids collected from a full-scale treatment facility. Quantitative PCR was used to track five genes encoding tetracycline resistance (tet(A), tet(L), tet(O), tet(W), and tet(X)) and the gene encoding the integrase (intI1) of class 1 integrons. Statistically significant reductions in the quantities of these genes occurred in the anaerobic reactors at 37 °C, 46 °C, and 55 °C, with the removal rates and removal efficiencies increasing as a function of temperature. The aerobic digesters, in contrast, were generally incapable of significantly decreasing gene quantities, although these digesters were operated at much shorter mean hydraulic residence times. This research suggests that high temperature anaerobic digestion of wastewater solids would be a suitable technology for eliminating various antibiotic resistance genes, an emerging pollutant of concern.

  9. A Single-Center Retrospective Cohort Analysis of Maternal and Infant Outcomes in HIV-Infected Mothers Treated with Integrase Inhibitors During Pregnancy.

    Science.gov (United States)

    Mounce, Monique L; Pontiggia, Laura; Adams, Jessica L

    2017-12-01

    Integrase strand transfer inhibitors (INSTI) are currently being investigated for the treatment of HIV in pregnancy. The purpose of this study is to evaluate the differences in maternal and infant outcomes in HIV-positive mothers treated with INSTI-containing antiretroviral therapy (ART) during pregnancy compared to protease inhibitor (PI)-containing ART. A retrospective, cohort study of INSTI- and PI-based ART used in pregnancy between 2007 and 2015 was performed. The primary objective was to evaluate the differences in viral load (VL) suppression prior to delivery. Secondary endpoints included time to and duration of VL suppression and safety parameters in both mothers and infants. For the primary analysis, the two arms were matched 1:2 INSTI to PI based on the presence or absence of viremia at the time of pregnancy determination. Additional analysis was performed on the entire matched and unmatched dataset. Twenty-one patients were matched (7 INSTI and 14 PI). There were no significant differences between groups with respect to the proportion of patients with VL suppression prior to delivery (71.4% INSTI vs. 92.9% PI, p = 0.247), and there were no significant differences in any of the secondary endpoints. Patients with documented adherence issues were statistically more likely to not be virologically suppressed prior to delivery (p = 0.002). No differences in efficacy or safety were found between patients treated with INSTIs compared to PIs. This study supports the further investigation of the use of INSTIs during pregnancy to reduce HIV transmission.

  10. Optimizing HIV-1 protease production in Escherichia coli as fusion protein

    Directory of Open Access Journals (Sweden)

    Piubelli Luciano

    2011-06-01

    Full Text Available Abstract Background Human immunodeficiency virus (HIV is the etiological agent in AIDS and related diseases. The aspartyl protease encoded by the 5' portion of the pol gene is responsible for proteolytic processing of the gag-pol polyprotein precursor to yield the mature capsid protein and the reverse transcriptase and integrase enzymes. The HIV protease (HIV-1Pr is considered an attractive target for designing inhibitors which could be used to tackle AIDS and therefore it is still the object of a number of investigations. Results A recombinant human immunodeficiency virus type 1 protease (HIV-1Pr was overexpressed in Escherichia coli cells as a fusion protein with bacterial periplasmic protein dithiol oxidase (DsbA or glutathione S-transferase (GST, also containing a six-histidine tag sequence. Protein expression was optimized by designing a suitable HIV-1Pr cDNA (for E. coli expression and to avoid autoproteolysis and by screening six different E. coli strains and five growth media. The best expression yields were achieved in E. coli BL21-Codon Plus(DE3-RIL host and in TB or M9 medium to which 1% (w/v glucose was added to minimize basal expression. Among the different parameters assayed, the presence of a buffer system (based on phosphate salts and a growth temperature of 37°C after adding IPTG played the main role in enhancing protease expression (up to 10 mg of chimeric DsbA:HIV-1Pr/L fermentation broth. GST:HIVPr was in part (50% produced as soluble protein while the overexpressed DsbA:HIV-1Pr chimeric protein largely accumulated in inclusion bodies as unprocessed fusion protein. A simple refolding procedure was developed on HiTrap Chelating column that yielded a refolded DsbA:HIV-1Pr with a > 80% recovery. Finally, enterokinase digestion of resolubilized DsbA:HIV-1Pr gave more than 2 mg of HIV-1Pr per liter of fermentation broth with a purity ≤ 80%, while PreScission protease cleavage of soluble GST:HIVPr yielded ~ 0.15 mg of pure HIV-1

  11. Exploring the Genome and Proteome of Desulfitobacterium hafniense DCB2 for its Protein Complexes Involved in Metal Reduction and Dechlorination

    Energy Technology Data Exchange (ETDEWEB)

    Sang-Hoon, Kim; Hardzman, Christina; Davis, John k.; Hutcheson, Rachel; Broderick, Joan B.; Marsh, Terence L.; Tiedje, James M.

    2012-09-27

    Desulfitobacteria are of interest to DOE mission because of their ability to reduce many electron acceptors including Fe(III), U(VI), Cr(VI), As(V), Mn(IV), Se(VI), NO3- and well as CO2, sulfite, fumarate and humates, their ability to colonize more stressful environments because they form spores, fix nitrogen and they have the more protective Gram positive cell walls. Furthermore at least some of them reductively dechlorinate aromatic and aliphatic pollutants. Importantly, most of the metals and the organochlorine reductions are coupled to ATP production and support growth providing for the organism's natural selection at DOE's contaminant sites. This work was undertaken to gain insight into the genetic and metabolic pathways involved in dissimilatory metal reduction and reductive dechlorination, (ii) to discern the commonalities among these electron-accepting processes, (iii) to identify multi-protein complexes catalyzing these functions and (iv) to elucidate the coordination in expression of these pathways and processes.

  12. Pathogenicity Island Cross Talk Mediated by Recombination Directionality Factors Facilitates Excision from the Chromosome.

    Science.gov (United States)

    Carpenter, Megan R; Rozovsky, Sharon; Boyd, E Fidelma

    2015-12-14

    Pathogenicity islands (PAIs) are mobile integrated genetic elements (MIGEs) that contain a diverse range of virulence factors and are essential in the evolution of pathogenic bacteria. PAIs are widespread among bacteria and integrate into the host genome, commonly at a tRNA locus, via integrase-mediated site-specific recombination. The excision of PAIs is the first step in the horizontal transfer of these elements and is not well understood. In this study, we examined the role of recombination directionality factors (RDFs) and their relationship with integrases in the excision of two PAIs essential for Vibrio cholerae host colonization: Vibrio pathogenicity island 1 (VPI-1) and VPI-2. VPI-1 does not contain an RDF, which allowed us to answer the question of whether RDFs are an absolute requirement for excision. We found that an RDF was required for efficient excision of VPI-2 but not VPI-1 and that RDFs can induce excision of both islands. Expression data revealed that the RDFs act as transcriptional repressors to both VPI-1- and VPI-2-encoded integrases. We demonstrated that the RDFs Vibrio excision factor A (VefA) and VefB bind at the attachment sites (overlapping the int promoter region) of VPI-1 and VPI-2, thus supporting this mode of integrase repression. In addition, V. cholerae RDFs are promiscuous due to their dual functions of promoting excision of both VPI-1 and VPI-2 and acting as negative transcriptional regulators of the integrases. This is the first demonstration of cross talk between PAIs mediated via RDFs which reveals the complex interactions that occur between separately acquired MIGEs. Deciphering the mechanisms of pathogenicity island excision is necessary for understanding the evolution and spread of these elements to their nonpathogenic counterparts. Such mechanistic insight would assist in predicting the mobility of uncharacterized genetic elements. This study identified extensive RDF-mediated cross talk between two nonhomologous VPIs and

  13. Computational modeling of Repeat1 region of INI1/hSNF5: An evolutionary link with ubiquitin

    Science.gov (United States)

    Bhutoria, Savita

    2016-01-01

    Abstract The structure of a protein can be very informative of its function. However, determining protein structures experimentally can often be very challenging. Computational methods have been used successfully in modeling structures with sufficient accuracy. Here we have used computational tools to predict the structure of an evolutionarily conserved and functionally significant domain of Integrase interactor (INI)1/hSNF5 protein. INI1 is a component of the chromatin remodeling SWI/SNF complex, a tumor suppressor and is involved in many protein‐protein interactions. It belongs to SNF5 family of proteins that contain two conserved repeat (Rpt) domains. Rpt1 domain of INI1 binds to HIV‐1 Integrase, and acts as a dominant negative mutant to inhibit viral replication. Rpt1 domain also interacts with oncogene c‐MYC and modulates its transcriptional activity. We carried out an ab initio modeling of a segment of INI1 protein containing the Rpt1 domain. The structural model suggested the presence of a compact and well defined ββαα topology as core structure in the Rpt1 domain of INI1. This topology in Rpt1 was similar to PFU domain of Phospholipase A2 Activating Protein, PLAA. Interestingly, PFU domain shares similarity with Ubiquitin and has ubiquitin binding activity. Because of the structural similarity between Rpt1 domain of INI1 and PFU domain of PLAA, we propose that Rpt1 domain of INI1 may participate in ubiquitin recognition or binding with ubiquitin or ubiquitin related proteins. This modeling study may shed light on the mode of interactions of Rpt1 domain of INI1 and is likely to facilitate future functional studies of INI1. PMID:27261671

  14. Multiple cellular proteins interact with LEDGF/p75 through a conserved unstructured consensus motif

    Czech Academy of Sciences Publication Activity Database

    Těšina, Petr; Čermáková, K.; Hořejší, Magdalena; Procházková, Kateřina; Fábry, Milan; Sharma, S.; Christ, F.; Demeulemeester, J.; Debyser, Z.; De Rijck, J.; Veverka, Václav; Řezáčová, Pavlína

    2015-01-01

    Roč. 6, Aug (2015), 7968/1-7968/14 ISSN 2041-1723 R&D Projects: GA MŠk(CZ) LK11205; GA MŠk(CZ) 7E08066; GA MŠk(CZ) LO1304; GA MŠk LO1302 EU Projects: European Commission(XE) 201032 - THINC Institutional support: RVO:61388963 ; RVO:68378050 Keywords : LEDGF/p75 * PogZ * JPO2 * PSIP1 * IWS1 * H3K36me3 * integrase Subject RIV: CE - Biochemistry Impact factor: 11.329, year: 2015

  15. Sorptive removal of arsenate using termite mound.

    Science.gov (United States)

    Fufa, Fekadu; Alemayehu, Esayas; Lennartz, Bernd

    2014-01-01

    Long-term consumption of arsenic results in severe and permanent health damages. The aim of the study was to investigate arsenate (As(V)) sorption capacity of termite mound (TM), containing mainly silicon, aluminum, iron and titanium oxides, under batch adsorption setup. The pattern of As(V) removal with varying contact time, solution pH, adsorbent dose, As(V) concentration and competing anions was investigated. Dissolution of the adsorbent was insignificant under the equilibrium conditions. Equilibrium was achieved within 40 min of agitation time. Kinetic data of As(V) adsorption followed well the pseudo-second order equation (R(2) > 0.99). High As(V) removal efficiency (∼ 99%) was observed over a pH range ∼ 3-∼ 10, which is of great importance in the practical application. The Freundlich and Dubinin-Radushkevich isotherms well described (R(2) > 0.99, χ(2) ∼ 0.05) the equilibrium As(V) adsorption, giving a coefficient of adsorption 1.48 mg(1-1/n)L(1/n)/g and a saturation capacity 13.50 mg/g respectively. The obtained value of mean sorption energy (EDR = 13.32 kJ/mol) suggested the chemisorption mechanism of As(V) adsorption on TM. The removal of As(V) was significantly decreased in the presence of phosphate ions. The As(V) loaded adsorbent was successfully regenerated using NaOH solution with insignificant loss of metals. Therefore, the results of the study demonstrated that TM could be considered as a promising adsorbent for the treatment of As(V) in drinking water. Copyright © 2013 Elsevier Ltd. All rights reserved.

  16. Adsorptive removal of arsenate from aqueous solutions by biochar supported zero-valent iron nanocomposite: Batch and continuous flow tests

    International Nuclear Information System (INIS)

    Wang, Shengsen; Gao, Bin; Li, Yuncong; Creamer, Anne Elise; He, Feng

    2017-01-01

    Highlights: • Biochar supported nZVI (nZVI/BC) was synthesized. • nZVI/BC showed excellent As(V) removal efficiency in batch and CMR experiments. • 100% removal efficiency was achieved in CMRs. • Surface adsorption was the dominant removal mechanism. - Abstract: Arsenate (As(V)) removal ability by nanoscale zero-valent iron (nZVI) is compromised by aggregation of nZVI particles. In this work, pine derived biochar (PB) was used as a supporting material to stabilize nZVI for As(V) removal. The biochar supported nZVI (nZVI/BC) was synthesized by precipitating the nanoparticles on carbon surfaces. Experiments using batch and continuous flow, completely mixed reactors (CMRs) were carried out to investigate the removal of As(V) by the nZVI/BC from aqueous solutions. Batch experiments showed that nZVI/BC had high As(V) removal capacity in a wide range of pH (3–8). Kinetic data revealed that equilibrium was reached within 1 h and the isotherm data showed that the Langmuir maximum adsorption capacity of the nZVI/BC for As(V) at pH 4.1 was 124.5 g kg −1 . As(V) (100 mg L −1 ) adsorption in anoxic condition was about 8% more than in oxic conditions, where As(V) reduction was observed in anoxic condition. The performance of the nZVI/BC in flowing condition was evaluated in CMRs at influent As(V) concentrations of 2.1 and 5.5 mg L −1 and the adsorbent removed 100% and 90% of the As(V), respectively. Furthermore, the nZVI/BC composite is magnetic which facilitates collection from aqueous solutions.

  17. Adsorptive removal of arsenate from aqueous solutions by biochar supported zero-valent iron nanocomposite: Batch and continuous flow tests

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Shengsen [Department of Agricultural and Biological Engineering, University of Florida, Gainesville, FL 32611 (United States); Gao, Bin, E-mail: bg55@ufl.edu [Department of Agricultural and Biological Engineering, University of Florida, Gainesville, FL 32611 (United States); Li, Yuncong [Tropical Research and Education Center, University of Florida, Homestead, FL 33031 (United States); Creamer, Anne Elise [Department of Agricultural and Biological Engineering, University of Florida, Gainesville, FL 32611 (United States); He, Feng [College of Biological and Environmental Engineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014 (China)

    2017-01-15

    Highlights: • Biochar supported nZVI (nZVI/BC) was synthesized. • nZVI/BC showed excellent As(V) removal efficiency in batch and CMR experiments. • 100% removal efficiency was achieved in CMRs. • Surface adsorption was the dominant removal mechanism. - Abstract: Arsenate (As(V)) removal ability by nanoscale zero-valent iron (nZVI) is compromised by aggregation of nZVI particles. In this work, pine derived biochar (PB) was used as a supporting material to stabilize nZVI for As(V) removal. The biochar supported nZVI (nZVI/BC) was synthesized by precipitating the nanoparticles on carbon surfaces. Experiments using batch and continuous flow, completely mixed reactors (CMRs) were carried out to investigate the removal of As(V) by the nZVI/BC from aqueous solutions. Batch experiments showed that nZVI/BC had high As(V) removal capacity in a wide range of pH (3–8). Kinetic data revealed that equilibrium was reached within 1 h and the isotherm data showed that the Langmuir maximum adsorption capacity of the nZVI/BC for As(V) at pH 4.1 was 124.5 g kg{sup −1}. As(V) (100 mg L{sup −1}) adsorption in anoxic condition was about 8% more than in oxic conditions, where As(V) reduction was observed in anoxic condition. The performance of the nZVI/BC in flowing condition was evaluated in CMRs at influent As(V) concentrations of 2.1 and 5.5 mg L{sup −1} and the adsorbent removed 100% and 90% of the As(V), respectively. Furthermore, the nZVI/BC composite is magnetic which facilitates collection from aqueous solutions.

  18. A modular open platform for systematic functional studies under physiological conditions

    Science.gov (United States)

    Mulholland, Christopher B.; Smets, Martha; Schmidtmann, Elisabeth; Leidescher, Susanne; Markaki, Yolanda; Hofweber, Mario; Qin, Weihua; Manzo, Massimiliano; Kremmer, Elisabeth; Thanisch, Katharina; Bauer, Christina; Rombaut, Pascaline; Herzog, Franz; Leonhardt, Heinrich; Bultmann, Sebastian

    2015-01-01

    Any profound comprehension of gene function requires detailed information about the subcellular localization, molecular interactions and spatio-temporal dynamics of gene products. We developed a multifunctional integrase (MIN) tag for rapid and versatile genome engineering that serves not only as a genetic entry site for the Bxb1 integrase but also as a novel epitope tag for standardized detection and precipitation. For the systematic study of epigenetic factors, including Dnmt1, Dnmt3a, Dnmt3b, Tet1, Tet2, Tet3 and Uhrf1, we generated MIN-tagged embryonic stem cell lines and created a toolbox of prefabricated modules that can be integrated via Bxb1-mediated recombination. We used these functional modules to study protein interactions and their spatio-temporal dynamics as well as gene expression and specific mutations during cellular differentiation and in response to external stimuli. Our genome engineering strategy provides a versatile open platform for efficient generation of multiple isogenic cell lines to study gene function under physiological conditions. PMID:26007658

  19. Uptake and biotransformation of arsenate in the lichen Hypogymnia physodes (L.) Nyl

    Energy Technology Data Exchange (ETDEWEB)

    Mrak, Tanja [Department of Environmental Sciences, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana (Slovenia); Slejkovec, Zdenka [Department of Environmental Sciences, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana (Slovenia)], E-mail: zdenka.slejkovec@ijs.si; Jeran, Zvonka; Jacimovic, Radojko [Department of Environmental Sciences, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana (Slovenia); Kastelec, Damijana [Agronomy Department, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana (Slovenia)

    2008-01-15

    The uptake and metabolism of arsenate, As(V), as a function of time and concentration were examined in the lichen Hypogymnia physodes (L.) Nyl. Lichen thalli were exposed to As(V) in the form of a solution. Exponential uptake of As(V) from 4 {mu}g mL{sup -1} As(V) solution was accompanied by constant arsenite, As(III), excretion back into the solution. Arsenate taken up into the lichens from 0, 0.1, 1, 10 {mu}g mL{sup -1} As(V) solutions was partially transformed into As(III), dimethylarsinic acid (DMA) and (mono)methylarsonic acid (MA). 48 h after exposure, the main arsenic compound in the lichens was DMA in 0.1, As(III) in 1 and As(V) in 10 {mu}g mL{sup -1} treatment. The proportion of methylated arsenic compounds decreased with increasing arsenate concentration in the exposure solution. These results suggest that at least two types of As(V) detoxification exist in lichens; arsenite excretion and methylation. - Lichens are able to metabolize the inorganic arsenic taken up.

  20. Uptake and biotransformation of arsenate in the lichen Hypogymnia physodes (L.) Nyl

    International Nuclear Information System (INIS)

    Mrak, Tanja; Slejkovec, Zdenka; Jeran, Zvonka; Jacimovic, Radojko; Kastelec, Damijana

    2008-01-01

    The uptake and metabolism of arsenate, As(V), as a function of time and concentration were examined in the lichen Hypogymnia physodes (L.) Nyl. Lichen thalli were exposed to As(V) in the form of a solution. Exponential uptake of As(V) from 4 μg mL -1 As(V) solution was accompanied by constant arsenite, As(III), excretion back into the solution. Arsenate taken up into the lichens from 0, 0.1, 1, 10 μg mL -1 As(V) solutions was partially transformed into As(III), dimethylarsinic acid (DMA) and (mono)methylarsonic acid (MA). 48 h after exposure, the main arsenic compound in the lichens was DMA in 0.1, As(III) in 1 and As(V) in 10 μg mL -1 treatment. The proportion of methylated arsenic compounds decreased with increasing arsenate concentration in the exposure solution. These results suggest that at least two types of As(V) detoxification exist in lichens; arsenite excretion and methylation. - Lichens are able to metabolize the inorganic arsenic taken up

  1. A quantitative structure–activity relationship study on HIV-1 integrase inhibitors using genetic algorithm, artificial neural networks and different statistical methods

    Directory of Open Access Journals (Sweden)

    Ghasem Ghasemi

    2016-09-01

    Full Text Available In this work, quantitative structure–activity relationship (QSAR study has been done on tricyclic phthalimide analogues acting as HIV-1 integrase inhibitors. Forty compounds were used in this study. Genetic algorithm (GA, artificial neural network (ANN and multiple linear regressions (MLR were utilized to construct the non-linear and linear QSAR models. It revealed that the GA–ANN model was much better than other models. For this purpose, ab initio geometry optimization performed at B3LYP level with a known basis set 6–31G (d. Hyperchem, ChemOffice and Gaussian 98W softwares were used for geometry optimization of the molecules and calculation of the quantum chemical descriptors. To include some of the correlation energy, the calculation was done with the density functional theory (DFT with the same basis set and Becke’s three parameter hybrid functional using the LYP correlation functional (B3LYP/6–31G (d. For the calculations in solution phase, the polarized continuum model (PCM was used and also included optimizations at gas-phase B3LYP/6–31G (d level for comparison. In the aqueous phase, the root–mean–square errors of the training set and the test set for GA–ANN model using jack–knife method, were 0.1409, 0.1804, respectively. In the gas phase, the root–mean–square errors of the training set and the test set for GA–ANN model were 0.1408, 0.3103, respectively. Also, the R2 values in the aqueous and the gas phase were obtained as 0.91, 0.82, respectively.

  2. Human Polycomb group EED protein negatively affects HIV-1 assembly and release

    Directory of Open Access Journals (Sweden)

    Darlix Jean-Luc

    2007-06-01

    Full Text Available Abstract Background The human EED protein, a member of the superfamily of Polycomb group (PcG proteins with WD-40 repeats, has been found to interact with three HIV-1 components, namely the structural Gag matrix protein (MA, the integrase enzyme (IN and the Nef protein. The aim of the present study was to analyze the possible biological role of EED in HIV-1 replication, using the HIV-1-based vector HIV-Luc and EED protein expressed by DNA transfection of 293T cells. Results During the early phase of HIV-1 infection, a slight negative effect on virus infectivity occurred in EED-expressing cells, which appeared to be dependent on EED-MA interaction. At late times post infection, EED caused an important reduction of virus production, from 20- to 25-fold as determined by CAp24 immunoassay, to 10- to 80-fold based on genomic RNA levels, and this decrease was not due to a reduction of Gag protein synthesis. Coexpression of WTNef, or the non-N-myristoylated mutant NefG2A, restored virus yields to levels obtained in the absence of exogenous EED protein. This effect was not observed with mutant NefΔ57 mimicking the Nef core, or with the lipid raft-retargeted fusion protein LAT-Nef. LATAA-Nef, a mutant defective in the lipid raft addressing function, had the same anti-EED effect as WTNef. Cell fractionation and confocal imaging showed that, in the absence of Nef, EED mainly localized in membrane domains different from the lipid rafts. Upon co-expression with WTNef, NefG2A or LATAA-Nef, but not with NefΔ57 or LAT-Nef, EED was found to relocate into an insoluble fraction along with Nef protein. Electron microscopy of HIV-Luc producer cells overexpressing EED showed significant less virus budding at the cell surface compared to control cells, and ectopic assembly and clustering of nuclear pore complexes within the cytoplasm. Conclusion Our data suggested that EED exerted an antiviral activity at the late stage of HIV-1 replication, which included genomic

  3. Multiple cellular proteins interact with LEDGF/p75 through a conserved unstructured consensus motif

    Czech Academy of Sciences Publication Activity Database

    Těšina, Petr; Čermáková, K.; Hořejší, M.; Procházková, K.; Fábry, Milan; Sharma, S.; Christ, F.; Demeulemeester, J.; Debyser, Z.; De Rijck, J.; Veverka, V.; Řezáčová, Pavlína

    2015-01-01

    Roč. 6, Aug (2015), 7968/1-7968/14 ISSN 2041-1723 R&D Projects: GA MŠk(CZ) LK11205; GA MŠk(CZ) 7E08066; GA MŠk(CZ) LO1304; GA MŠk LO1302 EU Projects: European Commission 201032 Institutional support: RVO:61388963 ; RVO:68378050 Keywords : LEDGF/p75 * PogZ * JPO2 * PSIP1 * IWS1 * H3K36me3 * integrase Subject RIV: EB - Genetics ; Molecular Biology; CE - Biochemistry (UOCHB-X) Impact factor: 11.329, year: 2015

  4. Cloud point extraction for trace inorganic arsenic speciation analysis in water samples by hydride generation atomic fluorescence spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Li, Shan, E-mail: ls_tuzi@163.com; Wang, Mei, E-mail: wmei02@163.com; Zhong, Yizhou, E-mail: yizhz@21cn.com; Zhang, Zehua, E-mail: kazuki.0101@aliyun.com; Yang, Bingyi, E-mail: e_yby@163.com

    2015-09-01

    A new cloud point extraction technique was established and used for the determination of trace inorganic arsenic species in water samples combined with hydride generation atomic fluorescence spectrometry (HGAFS). As(III) and As(V) were complexed with ammonium pyrrolidinedithiocarbamate and molybdate, respectively. The complexes were quantitatively extracted with the non-ionic surfactant (Triton X-114) by centrifugation. After addition of antifoam, the surfactant-rich phase containing As(III) was diluted with 5% HCl for HGAFS determination. For As(V) determination, 50% HCl was added to the surfactant-rich phase, and the mixture was placed in an ultrasonic bath at 70 °C for 30 min. As(V) was reduced to As(III) with thiourea–ascorbic acid solution, followed by HGAFS. Under the optimum conditions, limits of detection of 0.009 and 0.012 μg/L were obtained for As(III) and As(V), respectively. Concentration factors of 9.3 and 7.9, respectively, were obtained for a 50 mL sample. The precisions were 2.1% for As(III) and 2.3% for As(V). The proposed method was successfully used for the determination of trace As(III) and As(V) in water samples, with satisfactory recoveries. - Highlights: • Cloud point extraction was firstly established to determine trace inorganic arsenic(As) species combining with HGAFS. • Separate As(III) and As(V) determinations improve the accuracy. • Ultrasonic release of complexed As(V) enables complete As(V) reduction to As(III). • Direct HGAFS analysis can be performed.

  5. A novel system for simultaneous or sequential integration of multiple gene-loading vectors into a defined site of a human artificial chromosome.

    Science.gov (United States)

    Suzuki, Teruhiko; Kazuki, Yasuhiro; Oshimura, Mitsuo; Hara, Takahiko

    2014-01-01

    Human artificial chromosomes (HACs) are gene-delivery vectors suitable for introducing large DNA fragments into mammalian cells. Although a HAC theoretically incorporates multiple gene expression cassettes of unlimited DNA size, its application has been limited because the conventional gene-loading system accepts only one gene-loading vector (GLV) into a HAC. We report a novel method for the simultaneous or sequential integration of multiple GLVs into a HAC vector (designated as the SIM system) via combined usage of Cre, FLP, Bxb1, and φC31 recombinase/integrase. As a proof of principle, we first attempted simultaneous integration of three GLVs encoding EGFP, Venus, and TdTomato into a gene-loading site of a HAC in CHO cells. These cells successfully expressed all three fluorescent proteins. Furthermore, microcell-mediated transfer of HACs enabled the expression of those fluorescent proteins in recipient cells. We next demonstrated that GLVs could be introduced into a HAC one-by-one via reciprocal usage of recombinase/integrase. Lastly, we introduced a fourth GLV into a HAC after simultaneous integration of three GLVs by FLP-mediated DNA recombination. The SIM system expands the applicability of HAC vectors and is useful for various biomedical studies, including cell reprogramming.

  6. A novel system for simultaneous or sequential integration of multiple gene-loading vectors into a defined site of a human artificial chromosome.

    Directory of Open Access Journals (Sweden)

    Teruhiko Suzuki

    Full Text Available Human artificial chromosomes (HACs are gene-delivery vectors suitable for introducing large DNA fragments into mammalian cells. Although a HAC theoretically incorporates multiple gene expression cassettes of unlimited DNA size, its application has been limited because the conventional gene-loading system accepts only one gene-loading vector (GLV into a HAC. We report a novel method for the simultaneous or sequential integration of multiple GLVs into a HAC vector (designated as the SIM system via combined usage of Cre, FLP, Bxb1, and φC31 recombinase/integrase. As a proof of principle, we first attempted simultaneous integration of three GLVs encoding EGFP, Venus, and TdTomato into a gene-loading site of a HAC in CHO cells. These cells successfully expressed all three fluorescent proteins. Furthermore, microcell-mediated transfer of HACs enabled the expression of those fluorescent proteins in recipient cells. We next demonstrated that GLVs could be introduced into a HAC one-by-one via reciprocal usage of recombinase/integrase. Lastly, we introduced a fourth GLV into a HAC after simultaneous integration of three GLVs by FLP-mediated DNA recombination. The SIM system expands the applicability of HAC vectors and is useful for various biomedical studies, including cell reprogramming.

  7. Arsenate Impact on the Metabolite Profile, Production, and Arsenic Loading of Xylem Sap in Cucumbers (Cucumis sativus L.)

    Science.gov (United States)

    Uroic, M. Kalle; Salaün, Pascal; Raab, Andrea; Feldmann, Jörg

    2012-01-01

    Arsenic uptake and translocation studies on xylem sap focus generally on the concentration and speciation of arsenic in the xylem. Arsenic impact on the xylem sap metabolite profile and its production during short term exposure has not been reported in detail. To investigate this, cucumbers were grown hydroponically and arsenate (AsV) and DMA were used for plant treatment for 24 h. Total arsenic and arsenic speciation in xylem sap was analyzed including a metabolite profiling under AsV stress. Produced xylem sap was quantified and absolute arsenic transported was determined. AsV exposure had a significant impact on the metabolite profile of xylem sap. Four m/z values corresponding to four compounds were up-regulated, one compound down-regulated by AsV exposure. The compound down-regulated was identified to be isoleucine. Furthermore, AsV exposure had a significant influence on sap production, leading to a reduction of up to 96% sap production when plants were exposed to 1000 μg kg−1 AsV. No difference to control plants was observed when plants were exposed to 1000 μg kg−1 DMA. Absolute arsenic amount in xylem sap was the lowest at high AsV exposure. These results show that AsV has a significant impact on the production and metabolite profile of xylem sap. The physiological importance of isoleucine needs further attention. PMID:22536187

  8. Environmental Risks of Nano Zerovalent Iron for Arsenate Remediation: Impacts on Cytosolic Levels of Inorganic Phosphate and MgATP2- in Arabidopsis thaliana.

    Science.gov (United States)

    Zhang, Weilan; Lo, Irene M C; Hu, Liming; Voon, Chia Pao; Lim, Boon Leong; Versaw, Wayne K

    2018-04-03

    The use of nano zerovalent iron (nZVI) for arsenate (As(V)) remediation has proven effective, but full-scale injection of nZVI into the subsurface has aroused serious concerns for associated environmental risks. This study evaluated the efficacy of nZVI treatment for arsenate remediation and its potential hazards to plants using Arabidopsis thaliana grown in a hydroponic system. Biosensors for inorganic phosphate (Pi) and MgATP 2- were used to monitor in vivo Pi and MgATP 2- levels in plant cells. The results showed that nZVI could remove As(V) from growth media, decrease As uptake by plants, and mitigate As(V) toxicity to plants. However, excess nZVI could cause Pi starvation in plants leading to detrimental effects on plant growth. Due to the competitive adsorption of As(V) and Pi on nZVI, removing As(V) via nZVI treatment at an upstream site could relieve downstream plants from As(V) toxicity and Pi deprivation, in which case 100 mg/L of nZVI was the optimal dosage for remediation of As(V) at a concentration around 16.13 mg/L.

  9. Development of pharmacophore similarity-based quantitative activity hypothesis and its applicability domain: applied on a diverse data-set of HIV-1 integrase inhibitors.

    Science.gov (United States)

    Kumar, Sivakumar Prasanth; Jasrai, Yogesh T; Mehta, Vijay P; Pandya, Himanshu A

    2015-01-01

    Quantitative pharmacophore hypothesis combines the 3D spatial arrangement of pharmacophore features with biological activities of the ligand data-set and predicts the activities of geometrically and/or pharmacophoric similar ligands. Most pharmacophore discovery programs face difficulties in conformational flexibility, molecular alignment, pharmacophore features sampling, and feature selection to score models if the data-set constitutes diverse ligands. Towards this focus, we describe a ligand-based computational procedure to introduce flexibility in aligning the small molecules and generating a pharmacophore hypothesis without geometrical constraints to define pharmacophore space, enriched with chemical features necessary to elucidate common pharmacophore hypotheses (CPHs). Maximal common substructure (MCS)-based alignment method was adopted to guide the alignment of carbon molecules, deciphered the MCS atom connectivity to cluster molecules in bins and subsequently, calculated the pharmacophore similarity matrix with the bin-specific reference molecules. After alignment, the carbon molecules were enriched with original atoms in their respective positions and conventional pharmacophore features were perceived. Distance-based pharmacophoric descriptors were enumerated by computing the interdistance between perceived features and MCS-aligned 'centroid' position. The descriptor set and biological activities were used to develop support vector machine models to predict the activities of the external test set. Finally, fitness score was estimated based on pharmacophore similarity with its bin-specific reference molecules to recognize the best and poor alignments and, also with each reference molecule to predict outliers of the quantitative hypothesis model. We applied this procedure to a diverse data-set of 40 HIV-1 integrase inhibitors and discussed its effectiveness with the reported CPH model.

  10. Versatile P(acman) BAC Libraries for Transgenesis Studies in Drosophila melanogaster

    Energy Technology Data Exchange (ETDEWEB)

    Venken, Koen J.T.; Carlson, Joseph W.; Schulze, Karen L.; Pan, Hongling; He, Yuchun; Spokony, Rebecca; Wan, Kenneth H.; Koriabine, Maxim; de Jong, Pieter J.; White, Kevin P.; Bellen, Hugo J.; Hoskins, Roger A.

    2009-04-21

    We constructed Drosophila melanogaster BAC libraries with 21-kb and 83-kb inserts in the P(acman) system. Clones representing 12-fold coverage and encompassing more than 95percent of annotated genes were mapped onto the reference genome. These clones can be integrated into predetermined attP sites in the genome using Phi C31 integrase to rescue mutations. They can be modified through recombineering, for example to incorporate protein tags and assess expression patterns.

  11. Antiviral activity of dolutegravir in subjects with failure on an integrase inhibitor-based regimen: week 24 phase 3 results from VIKING-3

    Science.gov (United States)

    Nichols, G; Mills, A; Grossberg, R; Lazzarin, A; Maggiolo, F; Molina, J; Pialoux, G; Wright, D; Ait-Khaled, M; Huang, J; Vavro, C; Wynne, B; Yeo, J

    2012-01-01

    Background VIKING-3 aimed to examine efficacy and safety of dolutegravir (DTG) 50 mg twice daily in patients with resistance to multiple ARV classes, including integrase inhibitors (INI). Methods RAL and/or EVG-resistant (current or historical) adult subjects with screening plasma HIV-1 RNA ≥500 c/mL and resistance to ≥2 other ART classes received open-label DTG 50 mg BID while continuing their failing regimen (without RAL/EVG). At Day 8 the background regimen was optimised and DTG continued. Activity of the optimized background regimen (OBR) was determined by Monogram Net Assessment. Primary endpoints were antiviral efficacy at Day 8 and Week 24. Results 183 subjects enrolled, 124 with INI-resistance at screening and 59 with historical (but no screening) resistance. Population was advanced: at BL, median CD4 140, prior ART 13 yrs, 56% CDC Class C; 79% had >2 NRTI, 75% >1 NNRTI, and 70% >2 PI resistance-associated mutations, and 61% had non-R5 HIV detected. Of the 114 subjects who had the opportunity to complete 24 weeks on study before data cutoff, 72 (63%) had 1 log HIV RNA decline of 2, respectively. Discontinuations due to adverse events were uncommon (6/183, 3%); the most common drug-related AEs were diarrhoea, nausea and headache, each reported in only 5% of subjects. Conclusion A majority of the highly treatment-experienced subjects in VIKING-3 achieved suppression with DTG-based therapy. Responses were associated with Baseline IN genotype but not OSS, highlighting the importance and independence of DTG antiviral activity. DTG had a low rate of discontinuation due to adverse events at 50 mg BID in this advanced patient population.

  12. Speciation-dependent studies on removal of arsenic by iron-doped calcium alginate beads

    International Nuclear Information System (INIS)

    Banerjee, Anupam; Nayak, Dalia; Lahiri, Susanta

    2007-01-01

    This work aims to study the differential attitude of Fe-doped calcium alginate (Fe-CA) beads towards As(III) and As(V) compounds so that speciation-dependent environmentally sustainable methodologies can be developed for removal of arsenic from contaminated water. Throughout the experiment, 76 As has been used as precursor of stable arsenic. The affinity of As(V) towards the Fe-CA beads is greater than that of As(III). Removal efficiency of Fe-CA beads for As(V) increases with increasing number of beads and longer shaking times. At pH 3, 30 Fe-CA beads remove As(V) completely from a solution containing 20 mg kg -1 As(V). The technique has been successfully applied to the ground water collected from an arsenic-contaminated area

  13. [Usefulness of arterial calcium stimulation with hepatic venous sampling in the localization diagnosis of endogenous hyperinsulinism].

    Science.gov (United States)

    Moreno Moreno, Paloma; Gutiérrez Alcántara, Carmen; Muñoz-Villanueva, María Del Carmen; Ortega, Rafael Palomares; Corpas Jiménez, María del Sierra; Zurera Tendero, Luis; Benito López, Pedro

    2010-03-01

    The aim of this study was to assess the utility of arterial calcium stimulation with hepatic venous sampling (ASVS) in the localization of tumors in patients with endogenous hyperinsulinism not detected with other methods. We performed a retrospective study of 26 patients admitted to our hospital for hypoglycemia who underwent ASVS because the source of hyperinsulinism was not clearly identified by other imaging techniques. The histopathological result in patients who underwent a surgical procedure was considered the reference for statistical study of the accuracy of this technique. Statistical analysis was performed by comparing proportions with the chi-squared test with Yates' correction for contingency tables, and Cohen's kappa coefficient as a measure of interrater agreement between two observations. Surgery was performed in 17 patients, 13 with positive ASVS and the remaining four with negative results. An insulinoma was removed in 12 patients, and 10 of these were detected in the ASVS. A total of 76.9 % of positive ASVS tests corresponded to a histological diagnosis of insulinoma, and 83% of these insulinomas were positive in ASVS. This association was statistically significant (chi cuadrado=7.340; p=0.012). Two of three patients with nesidioblastosis had a positive response in the ASVS. A good and statistically significant agreement was obtained between histopathologic diagnosis and ASVS results (kappa=0.556, p = 0.007). ASVS is a useful procedure in the localization diagnosis of endogenous hyperinsulinism not detected by other imaging tests. This technique allows tumors in the pancreatic gland to be identified and may be useful in the choice of the surgical technique to be used. Copyright 2009 SEEN. Published by Elsevier Espana. All rights reserved.

  14. Potential benefit of dolutegravir once daily: efficacy and safety

    Directory of Open Access Journals (Sweden)

    Fantauzzi A

    2013-02-01

    Full Text Available Alessandra Fantauzzi,1 Ombretta Turriziani,2 Ivano Mezzaroma11Department of Clinical Medicine, 2Department of Molecular Medicine, Sapienza, University of Rome, Rome, ItalyAbstract: The viral integrase enzyme has recently emerged as a primary alternative target to block HIV-1 replication, and integrase inhibitors are considered a pivotal new class of antiretroviral drugs. Dolutegravir is an investigational next-generation integrase inhibitor showing some novel and intriguing characteristics, ie, it has a favorable pharmacokinetic profile with a prolonged intracellular half-life, rendering feasible once-daily dosing without the need for ritonavir boosting and without regard to meals. Moreover, dolutegravir is primarily metabolized via uridine diphosphate glucuronosyltranferase 1A1, with a minor component of the cytochrome P450 3A4 isoform, thereby limiting drug–drug interactions. Furthermore, its metabolic profile enables coadministration with most of the other available antiretroviral agents without dose adjustment. Recent findings also demonstrate that dolutegravir has significant activity against HIV-1 isolates with resistance mutations associated with raltegravir and/or elvitegravir. The attributes of once-daily administration and the potential to treat integrase inhibitor-resistant viruses make dolutegravir an interesting and promising investigational drug. In this review, the main concerns about the efficacy and safety of dolutegravir as well as its resistance profile are explored by analysis of currently available data from preclinical and clinical studies.Keywords: antiretroviral drugs, HIV-1 integrase, integrase inhibitors, dolutegravir, once daily

  15. One-pot synthesis of ternary zero-valent iron/phosphotungstic acid/g-C3N4 composite and its high performance for removal of arsenic(V) from water

    Science.gov (United States)

    Chen, Chunhua; Xu, Jia; Yang, Zhihua; Zhang, Li; Cao, Chunhua; Xu, Zhihua; Liu, Jiyan

    2017-12-01

    Ternary zero-valent iron/phos photungstic acid/g-C3N4 composite (Fe0@PTA/g-C3N4) was synthesized via photoreduction of iron (II) ions assisted by phosphotungstic acid (PTA) over g-C3N4 flakes. The as-prepared Fe0@PTA/g-C3N4 was investigated for removal of As(III) and As(V) species from water. The result showed that Fe0@PTA/g-C3N4 exhibited a better performance for As(V) removal than As(III) species from water, and the maximum adsorption capacity for As(V) was 70.3 mg/g, much higher than most of the reported adsorbents. As(V) removal by the Fe0@PTA/g-C3N4 adsorbent is mainly via a chemical process, synergistically occurring of reduction of As(V) and oxidation of Fe0. Moreover, the Fe0@PTA/g-C3N4 adsorbent showed effective As(V) removal from the simulated industrial wastewater and underground water. This study demonstrates that Fe0@PTA/g-C3N4 can be a potential adsorbent for As(V) removal due to its high performance, and simple one-pot synthesis process.

  16. Clinical impact of adaptive servoventilation compared to other ventilatory modes in patients with treatment-emergent sleep apnea, central sleep apnea and Cheyne–Stokes respiration

    Directory of Open Access Journals (Sweden)

    Sílvia Correia

    2015-05-01

    Full Text Available Introduction: Adaptive servoventilation is a recent ventilatory mode initially designed to treat Cheyne–Stokes respiration (CSR. Recently, the efficacy of ASV has been discussed for the treatment of central sleep apnea (CSA and treatment-emergent central sleep apnea (treatment-emergent CSA where other forms of traditional positive airway pressure (PAP may be insufficient. Objectives: To compare the clinical impact of ASV with other forms of PAP in treating patients with treatment-emergent CSA, CSA and CSR. Methods: Medical data of all the patients who underwent polysomnography (PSG with ASV titration were evaluated. The patients were divided into two groups according to the mode of ventilation reimbursed: ASV and PAP (AutoCPAP/CPAP/BIPAP. All patients had a minimal follow-up of 6 months. Both groups were compared in terms of symptoms, apnea hypopnea index, compliance, cardiac function and cardiovascular events. Results: ASV titration was performed in 33 patients (30M/3F with a mean age of 69 ± 8 years. The majority (58% present a treatment-emergent SA and 42% a CSA and or CSR. The median initial diagnostic AHI was 46 ± 22 events/h.After the initial diagnosis, 28 patients were treated with PAP and 5 with servoventilation. All of the patients treated with PAP were posteriorly submitted to PSG and ASV titration because of suboptimal response to PAP. Despite a clear indication for ASV, due to differences in reimbursement, 15 patients continued treatment with PAP (12 with AutoCPAP, 1 with BIPAP and 2 with CPAP and 16 changed to ASV. Two patients were lost in follow-up.In both groups, most of patients present a treatment-emergent SA (53% in ASV group vs. 67% in PAP group or a CSA/CSR (29.4% in ASV group vs. 20% in PAP. After ASV titration, the mean follow-up was 25 ± 14 months. Both groups (ASV vs. PAP were similar in terms of compliance (77 ± 23% vs.88 ± 14% and in terms of Epworth sleepiness scale

  17. Synthesis of green nano iron particles (GnIP) and their application in adsorptive removal of As(III) and As(V) from aqueous solution

    Energy Technology Data Exchange (ETDEWEB)

    Prasad, Kumar Suranjit, E-mail: suranjit@gmail.com [Department of Environmental Studies, Faculty of Science, The M. S. University of Baroda, Vadodara, 390002, Gujarat (India); Gandhi, Pooja, E-mail: poojagandhi.3090@gmail.com [Department of Environmental Sciences, Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences (ARIBAS), New Vallabh Vidyanagar, Anand, Gujarat, 388121 (India); Selvaraj, Kaliaperumal, E-mail: k.selvaraj@ncl.res.in [Nano and Computational Materials Lab, Catalysis Division, National Chemical Laboratory, Council of Scientific and Industrial Research, Pune, 411008 (India)

    2014-10-30

    Graphical abstract: - Highlights: • Colloidal GnIP synthesised using extract of Mint leaves were entrapped in chitosan beads. • GnIP loaded beads were employed for removal of As ions, showed excellent removal efficiency. • Iron and chitosan are cost effective materials hence can be a good adsorbent for removal of arsenic. - Abstract: The present study reports a new approach to synthesise nano iron particles using leaf extract of Mint (Mentha spicata L.) plant. The synthesised GnIPs were subjected to detailed adsorption studies for removal of arsenite and arsenate from aqueous solution of defined concentration. Iron nanoparticles synthesised using leaf extract showed UV–vis absorption peaks at 360 and 430 nm. TEM result showed the formation of polydispersed nanoparticles of size ranging from 20 to 45 nm. Nanoparticles were found to have core–shell structure. The planer reflection of selected area electron diffraction (SAED) and XRD analysis suggested that iron particles were crystalline and belonged to fcc (face centred cubic) type. Energy-dispersive X-ray analysis (EDAX) shows that Fe was an integral component of synthesised nanoparticles. The content of Fe in nanoparticles was found to be 40%, in addition to other elements like C (16%), O (19%) and Cl (23%). FT-IR study suggested that functional groups like -NH, -C=O, -C=N and -C=C were involved in particle formation. The removal efficiency of GnIP-chitosan composite for As(III) and As(V) was found to be 98.79 and 99.65%. Regeneration of adsorbent suggested that synthesised green GnIP may work as an effective tool for removal of arsenic from contaminated water.

  18. Synthesis of green nano iron particles (GnIP) and their application in adsorptive removal of As(III) and As(V) from aqueous solution

    International Nuclear Information System (INIS)

    Prasad, Kumar Suranjit; Gandhi, Pooja; Selvaraj, Kaliaperumal

    2014-01-01

    Graphical abstract: - Highlights: • Colloidal GnIP synthesised using extract of Mint leaves were entrapped in chitosan beads. • GnIP loaded beads were employed for removal of As ions, showed excellent removal efficiency. • Iron and chitosan are cost effective materials hence can be a good adsorbent for removal of arsenic. - Abstract: The present study reports a new approach to synthesise nano iron particles using leaf extract of Mint (Mentha spicata L.) plant. The synthesised GnIPs were subjected to detailed adsorption studies for removal of arsenite and arsenate from aqueous solution of defined concentration. Iron nanoparticles synthesised using leaf extract showed UV–vis absorption peaks at 360 and 430 nm. TEM result showed the formation of polydispersed nanoparticles of size ranging from 20 to 45 nm. Nanoparticles were found to have core–shell structure. The planer reflection of selected area electron diffraction (SAED) and XRD analysis suggested that iron particles were crystalline and belonged to fcc (face centred cubic) type. Energy-dispersive X-ray analysis (EDAX) shows that Fe was an integral component of synthesised nanoparticles. The content of Fe in nanoparticles was found to be 40%, in addition to other elements like C (16%), O (19%) and Cl (23%). FT-IR study suggested that functional groups like -NH, -C=O, -C=N and -C=C were involved in particle formation. The removal efficiency of GnIP-chitosan composite for As(III) and As(V) was found to be 98.79 and 99.65%. Regeneration of adsorbent suggested that synthesised green GnIP may work as an effective tool for removal of arsenic from contaminated water

  19. Bioavailability and ecotoxicity of arsenic species in solution culture and soil system: implications to remediation.

    Science.gov (United States)

    Bolan, Nanthi; Mahimairaja, Santiago; Kunhikrishnan, Anitha; Seshadri, Balaji; Thangarajan, Ramya

    2015-06-01

    In this work, bioavailability and ecotoxicity of arsenite (As(III)) and arsenate (As(V)) species were compared between solution culture and soil system. Firstly, the adsorption of As(III) and As(V) was compared using a number of non-allophanic and allophanic soils. Secondly, the bioavailability and ecotoxicity were examined using germination, phytoavailability, earthworm, and soil microbial activity tests. Both As-spiked soils and As-contaminated sheep dip soils were used to test bioavailability and ecotoxicity. The sheep dip soil which contained predominantly As(V) species was subject to flooding to reduce As(V) to As(III) and then used along with the control treatment soil to compare the bioavailability between As species. Adsorption of As(V) was much higher than that of As(III), and the difference in adsorption between these two species was more pronounced in the allophanic than non-allophanic soils. In the solution culture, there was no significant difference in bioavailability and ecotoxicity, as measured by germination and phytoavailability tests, between these two As species. Whereas in the As-spiked soils, the bioavailability and ecotoxicity were higher for As(III) than As(V), and the difference was more pronounced in the allophanic than non-allophanic soils. Bioavailability of As increased with the flooding of the sheep dip soils which may be attributed to the reduction of As(V) to As(III) species. The results in this study have demonstrated that while in solution, the bioavailability and ecotoxicity do not vary between As(III) and As(V), in soils, the latter species is less bioavailable than the former species because As(V) is more strongly retained than As(III). Since the bioavailability and ecotoxicity of As depend on the nature of As species present in the environment, risk-based remediation approach should aim at controlling the dynamics of As transformation.

  20. Direct in situ measurement of dissolved zinc in the presence of zinc oxide nanoparticles using anodic stripping voltammetry.

    Science.gov (United States)

    Jiang, Chuanjia; Hsu-Kim, Heileen

    2014-11-01

    The wide use of metal-based nanomaterials such as zinc oxide (ZnO) nanoparticles (NPs) has generated concerns regarding their environmental and health risks. For ZnO NPs, their toxicity in aquatic systems often depends on the release of dissolved zinc species, and the rate of dissolution is influenced by water chemistry, including the presence of zinc-chelating ligands. A challenge, however, remains in quantifying the dissolution of ZnO NPs, particularly for time scales that are short enough to determine rates. This paper reports the application of anodic stripping voltammetry (ASV) with a hanging mercury drop electrode to directly measure the concentration of dissolved zinc in ZnO NP suspensions, without separation of the ZnO NPs from the aqueous phase. The effects of the deposition time and the electrochemical potential scan rate on the ASV measurement were consistent with expectations for dissolved phase measurements. The dissolved zinc concentration measured by ASV ([Zn]ASV) was compared with that measured by inductively coupled plasma mass spectrometry (ICP-MS) after ultracentrifugation ([Zn]ICP-MS), for four types of ZnO NPs with different coatings and primary particle diameters. For small ZnO NPs (4-5 nm), [Zn]ASV was 20% higher than [Zn]ICP-MS, suggesting that these small NPs contributed to the voltammetric measurement. For larger ZnO NPs (approximately 20 nm), [Zn]ASV was (79 ± 19)% of [Zn]ICP-MS, despite the high concentrations of ZnO NPs in suspension. Using ASV, the dissolution of ZnO NPs was studied, with or without Suwannee River Fulvic Acid (SRFA). Although SRFA diminished the ASV stripping current, dissolution of 20 nm ZnO NPs was significantly promoted at high fulvic acid to ZnO NP ratios. The ASV method described in this paper provides a useful tool for studying the dissolution kinetics of ZnO NPs in complex environmental matrices.

  1. Cost-effectiveness of daclatasvir plus asunaprevir for chronic hepatitis C genotype 1b treatment-naïve patients in China.

    Science.gov (United States)

    Lu, Yun; Jin, Xiuze; Duan, Cheng-A-Xin; Chang, Feng

    2018-01-01

    Hepatitis C is the second fastest growing infectious disease in China. The standard-of-care for chronic hepatitis C in China is Pegylated interferon plus ribavirin (PR), which is associated with tolerability and efficacy issues. An interferon- and ribavirin-free, all-oral regimen comprising daclatasvir (DCV) and asunaprevir (ASV), which displays higher efficacy and tolerability, has recently been approved in China. This study is to estimate the cost-effectiveness of DCV+ASV (24 weeks) for chronic hepatitis C genotype 1b treatment-naïve patients compared with PR regimen (48 weeks) in China. A cohort-based Markov model was developed from Chinese payer perspective to project the lifetime outcomes of treating 10,000 patients with an average age of 44.5 with two hypothetical regimens, DCV+ASV and PR. Chinese-specific health state costs and efficacy data were used. The annual discount rate was 5%. Base-case analysis and sensitivity analysis were conducted. For HCV Genotype 1b treatment-naïve patients, DCV+ASV proved to be dominant over PR, with a cost saving of ¥33,480(5,096 USD) and gains in QALYs and life years of 1.29 and 0.85, respectively. The lifetime risk of compensated cirrhosis, decompensated cirrhosis, hepatocellular carcinoma and liver-related death was greatly reduced with DCV+ASV. Univariate sensitivity analysis demonstrated that key influencers were the discount rate, time horizon, initial disease severity and sustained virological response rate of DCV+ASV, with all scenarios resulting in additional benefit. Probabilistic sensitivity analysis demonstrated that DCV+ASV has a high likelihood (100%) of being cost-effective. DCV+ASV is not only an effective and well-tolerated regimen to treat chronic HCV genotype 1b infection treatment-naïve patients, but also is more cost-effective than PR regimen. DCV+ASV can benefit both the public health and reimbursement system in China.

  2. Cyclic GMP-AMP Synthase is an Innate Immune Sensor of HIV and Other Retroviruses

    OpenAIRE

    Gao, Daxing; Wu, Jiaxi; Wu, You-Tong; Du, Fenghe; Aroh, Chukwuemika; Yan, Nan; Sun, Lijun; Chen, Zhijian J.

    2013-01-01

    Retroviruses, including HIV, can activate innate immune responses, but the host sensors for retroviruses are largely unknown. Here we show that HIV infection activates cyclic-GMP-AMP (cGAMP) synthase (cGAS) to produce cGAMP, which binds to and activates the adaptor protein STING to induce type-I interferons and other cytokines. Inhibitors of HIV reverse transcriptase, but not integrase, abrogated interferon-β induction by the virus, suggesting that the reverse transcribed HIV DNA triggers the...

  3. Arsenic Removal from Water by Adsorption on Iron-Contaminated Cryptocrystalline Graphite

    Science.gov (United States)

    Yang, Qiang; Yang, Lang; Song, Shaoxian; Xia, Ling

    This work aimed to study the feasibility of using iron-contaminated graphite as an adsorbent for As(V) removal from water. The adsorbent was prepared by grinding graphite concentrate with steel ball. The study was performed through the measurements of adsorption capacity, BET surface area and XPS analysis. The experimental results showed that the iron-contaminated graphite exhibited significantly high adsorption capacity of As(V). The higher the iron contaminated on the graphite surface, the higher the adsorption capacity of As(V) on the material obtained. It was suggested that the ion-contaminated graphite was a good adsorbent for As(V) removal.

  4. Study on Roll Instability Mechanism and Stability Index of Articulated Steering Vehicles

    Directory of Open Access Journals (Sweden)

    Xuefei Li

    2016-01-01

    Full Text Available This study examines the roll instability mechanism and stability index of articulated steering vehicles (ASVs by taking wheel loaders as the research object. A seven-degree-of-freedom nonlinear dynamics model of the ASVs is built on the basis of multibody dynamics. A physical prototype model of an ASV is designed and manufactured to validate the dynamic model. Test results reasonably agree with the simulation results, which indicates that the established dynamic model can reasonably describe ASV movements. Detailed analysis of the rollover stability of the wheel loader is performed with the use of the established dynamic model. Analysis results show that rollover will occur when the roll angular velocity exceeds a critical threshold, which is affected by lateral acceleration and slope angle. On this basis, a dynamic stability index applicable to the ASVs is presented.

  5. Large Diversity of Nonstandard Genes and Dynamic Evolution of Chloroplast Genomes in Siphonous Green Algae (Bryopsidales, Chlorophyta).

    Science.gov (United States)

    Cremen, Ma Chiela M; Leliaert, Frederik; Marcelino, Vanessa R; Verbruggen, Heroen

    2018-04-01

    Chloroplast genomes have undergone tremendous alterations through the evolutionary history of the green algae (Chloroplastida). This study focuses on the evolution of chloroplast genomes in the siphonous green algae (order Bryopsidales). We present five new chloroplast genomes, which along with existing sequences, yield a data set representing all but one families of the order. Using comparative phylogenetic methods, we investigated the evolutionary dynamics of genomic features in the order. Our results show extensive variation in chloroplast genome architecture and intron content. Variation in genome size is accounted for by the amount of intergenic space and freestanding open reading frames that do not show significant homology to standard plastid genes. We show the diversity of these nonstandard genes based on their conserved protein domains, which are often associated with mobile functions (reverse transcriptase/intron maturase, integrases, phage- or plasmid-DNA primases, transposases, integrases, ligases). Investigation of the introns showed proliferation of group II introns in the early evolution of the order and their subsequent loss in the core Halimedineae, possibly through RT-mediated intron loss.

  6. Real-life prevalence of resistance-associated variants against non-structural protein 5A inhibitors and efficiency of Daclatasvir + Asunaprevir therapy in Korean patients with genotype 1b hepatitis C.

    Science.gov (United States)

    Yu, Jung Hwan; Lee, Jung Il; Lee, Kwan Sik; Kim, Ja Kyung

    2017-08-24

    Direct-acting antivirals (DAAs) for chronic hepatitis C (CHC) treatment are tolerable and highly effective in a shorter period of time than before. However, resistance-associated variants (RAVs) can affect the efficacy of DAAs. The aim of this study was to investigate the real-life prevalence of RAVs against non-structural protein 5A (NS5A) inhibitors in Korean patients with genotype 1b chronic hepatitis C. All consecutive patients with CHC genotype 1b who underwent a RAV test at a single referral hospital were enrolled. A total of 142 patients (male 53, female 89) were tested for RAVs. The average age of the patients was 58 years. Liver cirrhosis was found in 34.5% (49/142) of patients, and 19.0% (29/142) of patients had previously undergone interferon-based treatment. Twenty-nine patients (20.4%) had RAVs (Y93 or L31). Y93H, L31, or Y93H with L31 were detected in 22 (15.5%), 8 (5.6%), and 1 (0.7%) patients, respectively. The presence of RAV was not affected by previous interferon-based treatment or by the existence of liver cirrhosis. Among 113 patients without baseline NS5A RAVs, 72 patients started daclatasvir (DCV) + asunaprevir (ASV) treatment and 95% (68/72) patients achieved virologic response at week 4. Virologic response at end of treatment and sustained virologic response at 12 weeks after treatment were achieved by 94% (68/72) and 94% (68/72), respectively. In Korean patients with genotype 1b CHC, 20.4% (29 of 142) of patients showed RAVs against NS5A inhibitors. Patient without RAVs who received treatment with DCV + ASV showed high virologic response rates in Korea.

  7. 5-Hydroxypyrido[2,3-b]pyrazin-6(5H)-one derivatives as novel dual inhibitors of HIV-1 reverse transcriptase-associated ribonuclease H and integrase.

    Science.gov (United States)

    Sun, Lin; Gao, Ping; Dong, Guanyu; Zhang, Xujie; Cheng, Xiqiang; Ding, Xiao; Wang, Xueshun; Daelemans, Dirk; De Clercq, Erik; Pannecouque, Christophe; Menéndez-Arias, Luis; Zhan, Peng; Liu, Xinyong

    2018-06-18

    We reported herein the design, synthesis and biological evaluation of a series of 5-hydroxypyrido[2,3-b]pyrazin-6(5H)-one derivatives as HIV-1 reverse transcriptase (RT) ribonuclease H (RNase H) inhibitors using a privileged structure-guided scaffold refining strategy. In view of the similarities between the pharmacophore model of RNase H and integrase (IN) inhibitors as well as their catalytic sites, we also performed IN inhibition assays. Notably, the majority of these derivatives inhibited RNase H and IN at micromolar concentrations. Among them, compound 7a exhibited similar inhibitory activity against RNase H and IN (IC 50 RNase H  = 1.77 μM, IC 50 IN  = 1.18 μM, ratio = 1.50). To the best of our knowledge, this is the first reported dual HIV-1 RNase H-IN inhibitor based on a 5-hydroxypyrido[2,3-b]pyrazin-6(5H)-one structure. Molecular modeling has been used to predict the binding mode of 7a in complex with the catalytic cores of HIV-1 RNase H and IN. Taken together these results strongly support the feasibility of developing HIV-1 dual inhibitors from analog-based optimization of divalent metal ion chelators. Recently, the identification of dual inhibitors proved to be a highly effective strategy for novel antivirals discovery. Therefore, these compounds appear to be useful leads that can be further modified to develop more valuable anti-HIV-1 molecules with suitable drug profiles. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

  8. Removal of arsenic from groundwater by using a native isolated arsenite-oxidizing bacterium.

    Science.gov (United States)

    Kao, An-Chieh; Chu, Yu-Ju; Hsu, Fu-Lan; Liao, Vivian Hsiu-Chuan

    2013-12-01

    Arsenic (As) contamination of groundwater is a significant public health concern. In this study, the removal of arsenic from groundwater using biological processes was investigated. The efficiency of arsenite (As(III)) bacterial oxidation and subsequent arsenate (As(V)) removal from contaminated groundwater using bacterial biomass was examined. A novel As(III)-oxidizing bacterium (As7325) was isolated from the aquifer in the blackfoot disease (BFD) endemic area in Taiwan. As7325 oxidized 2300μg/l As(III) using in situ As(III)-contaminated groundwater under aerobic conditions within 1d. After the oxidation of As(III) to As(V), As(V) removal was further examined using As7325 cell pellets. The results showed that As(V) could be adsorbed efficiently by lyophilized As7325 cell pellets, the efficiency of which was related to lyophilized cell pellet concentration. Our study conducted the examination of an alternative technology for the removal of As(III) and As(V) from groundwater, indicating that the oxidation of As(III)-contaminated groundwater by native isolated bacterium, followed by As(V) removal using bacterial biomass is a potentially effective technology for the treatment of As(III)-contaminated groundwater. © 2013.

  9. A microarray study of gene and protein regulation in human and rat brain following middle cerebral artery occlusion

    Science.gov (United States)

    Mitsios, Nick; Saka, Mohamad; Krupinski, Jerzy; Pennucci, Roberta; Sanfeliu, Coral; Wang, Qiuyu; Rubio, Francisco; Gaffney, John; Kumar, Pat; Kumar, Shant; Sullivan, Matthew; Slevin, Mark

    2007-01-01

    Background Altered gene expression is an important feature of ischemic cerebral injury and affects proteins of many functional classes. We have used microarrays to investigate the changes in gene expression at various times after middle cerebral artery occlusion in human and rat brain. Results Our results demonstrated a significant difference in the number of genes affected and the time-course of expression between the two cases. The total number of deregulated genes in the rat was 335 versus 126 in the human, while, of 393 overlapping genes between the two array sets, 184 were changed only in the rat and 36 in the human with a total of 41 genes deregulated in both cases. Interestingly, the mean fold changes were much higher in the human. The expression of novel genes, including p21-activated kinase 1 (PAK1), matrix metalloproteinase 11 (MMP11) and integrase interactor 1, was further analyzed by RT-PCR, Western blotting and immunohistochemistry. Strong neuronal staining was seen for PAK1 and MMP11. Conclusion Our findings confirmed previous studies reporting that gene expression screening can detect known and unknown transcriptional features of stroke and highlight the importance of research using human brain tissue in the search for novel therapeutic agents. PMID:17997827

  10. Effects of adaptive servo-ventilation therapy on cardiac function and remodeling in patients with chronic heart failure (SAVIOR-C): study protocol for a randomized controlled trial.

    Science.gov (United States)

    Seino, Yoshihiko; Momomura, Shin-Ichi; Kihara, Yasuki; Adachi, Hitoshi; Yasumura, Yoshio; Yokoyama, Hiroyuki

    2015-01-16

    Adaptive servo-ventilation (ASV) therapy, which is a form of noninvasive positive pressure ventilation therapy and uses an innovative ventilator that has simple operability and provides good patient adherence, potentially has therapeutic benefits-suppression of the deterioration and progression of chronic heart failure (CHF) and a reduction in the number of repeated hospitalizations. Therefore, ASV therapy draws attention as a novel, noninvasive nonpharmacotherapy for patients with CHF owing to its hemodynamics-improving effect, and it is currently being accepted in real-world clinical settings in Japan. However, clinical evidence sufficient for treatment recommendation is lacking because a multicenter, randomized, controlled study of ASV therapy has never been conducted. The present study is a confirmatory, prospective, multicenter, collaborative, open-label, blinded-endpoint, parallel-group, randomized, controlled study. At 40 medical institutions in Japan, 200 Japanese outpatients with mild to severe CHF (age: ≥ 20 years; New York Heart Association classification: greater than or equal to class II) will be randomly assigned to either of the following two study groups: the ASV group, in which 100 outpatients undergo guideline-directed medical therapy and ASV therapy for 24 weeks; and the control group, in which 100 outpatients undergo only guideline-directed medical therapy for 24 weeks. The objective of the present study is to confirm whether the ASV group is superior to the control group concerning the improvement of left ventricular contractility and remodeling, both assessed by two-dimensional echocardiography. Furthermore, the present study will also secondarily examine the effects of ASV therapy on the prognosis and quality of life of patients with CHF. ASV therapy using the device has the potential to provide therapeutic benefits based on its simple operability and good patient adherence and possesses the potential to improve left ventricular

  11. Speciation of inorganic arsenic by electrochemical hydride generation atomic absorption spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Li Xun [Department of Chemistry, Beijing Normal University, Beijing 100875 (China); Department of Chemistry and Life Science, Gannan Teachers College, Ganzhou 341000 (China); Jia Jing [Department of Chemistry, Beijing Normal University, Beijing 100875 (China); Wang Zhenghao [Department of Chemistry, Beijing Normal University, Beijing 100875 (China)]. E-mail: zhwang@bnu.edu.cn

    2006-02-23

    A simple procedure was developed for the speciation of inorganic arsenic by electrochemical hydride generation atomic absorption spectrometry (EcHG-AAS), without pre-reduction of As(V). Glassy carbon was selected as cathode material in the flow cell. An optimum catholyte concentration for simultaneous generation of arsine from As(III) and As(V) was 0.06 mol l{sup -1} H{sub 2}SO{sub 4}. Under the optimized conditions, adequate sensitivity and difference in ratio of slopes of the calibration curves for As(III) and As(V) can be achieved at the electrolytic currents of 0.6 and 1 A. The speciation of inorganic arsenic can be performed by controlling the electrolytic currents, and the concentration of As(III) and As(V) in the sample can be calculated according to the equations of absorbance additivity obtained at two selected electrolytic currents. The calibration curves were linear up to 50 ng ml{sup -1} for both As(III) and As(V) at 0.6 and 1 A. The detection limits of the method were 0.2 and 0.5 ng ml{sup -1} for As(III) and As(V) at 0.6 A, respectively. The relative standard deviations were of 2.1% for 20 ng ml{sup -1} As(III) and 2.5% for 20 ng ml{sup -1} As(V). The method was validated by the analysis of human hair certified reference material and successfully applied to speciation of soluble inorganic arsenic in Chinese medicine.

  12. Speciation of inorganic arsenic by electrochemical hydride generation atomic absorption spectrometry

    International Nuclear Information System (INIS)

    Li Xun; Jia Jing; Wang Zhenghao

    2006-01-01

    A simple procedure was developed for the speciation of inorganic arsenic by electrochemical hydride generation atomic absorption spectrometry (EcHG-AAS), without pre-reduction of As(V). Glassy carbon was selected as cathode material in the flow cell. An optimum catholyte concentration for simultaneous generation of arsine from As(III) and As(V) was 0.06 mol l -1 H 2 SO 4 . Under the optimized conditions, adequate sensitivity and difference in ratio of slopes of the calibration curves for As(III) and As(V) can be achieved at the electrolytic currents of 0.6 and 1 A. The speciation of inorganic arsenic can be performed by controlling the electrolytic currents, and the concentration of As(III) and As(V) in the sample can be calculated according to the equations of absorbance additivity obtained at two selected electrolytic currents. The calibration curves were linear up to 50 ng ml -1 for both As(III) and As(V) at 0.6 and 1 A. The detection limits of the method were 0.2 and 0.5 ng ml -1 for As(III) and As(V) at 0.6 A, respectively. The relative standard deviations were of 2.1% for 20 ng ml -1 As(III) and 2.5% for 20 ng ml -1 As(V). The method was validated by the analysis of human hair certified reference material and successfully applied to speciation of soluble inorganic arsenic in Chinese medicine

  13. Human versus Computer Controlled Selection of Ventilator Settings: An Evaluation of Adaptive Support Ventilation and Mid-Frequency Ventilation

    Directory of Open Access Journals (Sweden)

    Eduardo Mireles-Cabodevila

    2012-01-01

    Full Text Available Background. There are modes of mechanical ventilation that can select ventilator settings with computer controlled algorithms (targeting schemes. Two examples are adaptive support ventilation (ASV and mid-frequency ventilation (MFV. We studied how different clinician-chosen ventilator settings are from these computer algorithms under different scenarios. Methods. A survey of critical care clinicians provided reference ventilator settings for a 70 kg paralyzed patient in five clinical/physiological scenarios. The survey-derived values for minute ventilation and minute alveolar ventilation were used as goals for ASV and MFV, respectively. A lung simulator programmed with each scenario’s respiratory system characteristics was ventilated using the clinician, ASV, and MFV settings. Results. Tidal volumes ranged from 6.1 to 8.3 mL/kg for the clinician, 6.7 to 11.9 mL/kg for ASV, and 3.5 to 9.9 mL/kg for MFV. Inspiratory pressures were lower for ASV and MFV. Clinician-selected tidal volumes were similar to the ASV settings for all scenarios except for asthma, in which the tidal volumes were larger for ASV and MFV. MFV delivered the same alveolar minute ventilation with higher end expiratory and lower end inspiratory volumes. Conclusions. There are differences and similarities among initial ventilator settings selected by humans and computers for various clinical scenarios. The ventilation outcomes are the result of the lung physiological characteristics and their interaction with the targeting scheme.

  14. Extraction techniques for arsenic species in rice flour and their speciation by HPLC-ICP-MS.

    Science.gov (United States)

    Narukawa, Tomohiro; Suzuki, Toshihiro; Inagaki, Kazumi; Hioki, Akiharu

    2014-12-01

    The extraction of arsenic (As) species present in rice flour samples was investigated using different extracting solvents, and the concentration of each species was determined by HPLC-ICP-MS after heat-assisted extraction. The extraction efficiencies for total arsenic species and especially for arsenite [As(III)] and arsenate [As(V)] were investigated. As(III), As(V) and dimethylarsinic acid (DMAA) were found in the samples, and the concentration of DMAA did not vary with treatment conditions. However, the concentrations of extracted total arsenic and those of As(III) and As(V) depended on the extracting solvents. When an extracting solvent was highly acidic, the concentrations of extracted total arsenic were in good agreement with the total arsenic concentration determined by ICP-MS after microwave-assisted digestion, though a part of the As(V) was reduced to As(III) during the highly acidic extraction process. Extraction under neutral conditions increased the extracted As(V), but extracted total arsenic was decreased because a part of the As(III) could not be extracted. Optimum conditions for the extraction of As(III) and As(V) from rice flour samples are discussed to allow the accurate determinations of As(III), As(V) and DMAA in the rice flour samples. Heat block extraction techniques using 0.05 mol L(-1) HClO4 and silver-containing 0.15 mol L(-1) HNO3 were also developed. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. Evaluation of the effect of short-term treatment with the integrase inhibitor raltegravir (Isentress) on the course of progressive feline leukemia virus infection.

    Science.gov (United States)

    Boesch, Andrea; Cattori, Valentino; Riond, Barbara; Willi, Barbara; Meli, Marina L; Rentsch, Katharina M; Hosie, Margaret J; Hofmann-Lehmann, Regina; Lutz, Hans

    2015-02-25

    Cats persistently infected with the gammaretrovirus feline leukemia virus (FeLV) are at risk to die within months to years from FeLV-associated disease, such as immunosuppression, anemia or lymphoma/leukemia. The integrase inhibitor raltegravir has been demonstrated to reduce FeLV replication in vitro. The aim of the present study was to investigate raltegravir in vivo for its safety and efficacy to suppress FeLV replication. The safety was tested in three naïve specified pathogen-free (SPF) cats during a 15 weeks treatment period (initially 20mg then 40mg orally b.i.d.). No adverse effects were noted. The efficacy was tested in seven persistently FeLV-infected SPF cats attained from 18 cats experimentally exposed to FeLV-A/Glasgow-1. The seven cats were treated during nine weeks (40mg then 80mg b.i.d.). Raltegravir was well tolerated even at the higher dose. A significant decrease in plasma viral RNA loads (∼5×) was found; however, after treatment termination a rebound effect was observed. Only one cat developed anti-FeLV antibodies and viral RNA loads remained decreased after treatment termination. Of note, one of the untreated FeLV-A infected cats developed fatal FeLV-C associated anemia within 5 weeks of FeLV-A infection. Moreover, progressive FeLV infection was associated with significantly lower enFeLV loads prior to infection supporting that FeLV susceptibility may be related to the genetic background of the cat. Overall, our data demonstrate the ability of raltegravir to reduce viral replication also in vivo. However, no complete control of viremia was achieved. Further investigations are needed to find an optimized treatment against FeLV. (250 words). Copyright © 2014 Elsevier B.V. All rights reserved.

  16. Geometrically and conformationally restrained cinnamoyl compounds as inhibitors of HIV-1 integrase: synthesis, biological evaluation, and molecular modeling.

    Science.gov (United States)

    Artico, M; Di Santo, R; Costi, R; Novellino, E; Greco, G; Massa, S; Tramontano, E; Marongiu, M E; De Montis, A; La Colla, P

    1998-10-08

    Various cinnammoyl-based structures were synthesized and tested in enzyme assays as inhibitors of the HIV-1 integrase (IN). The majority of compounds were designed as geometrically or conformationally constrained analogues of caffeic acid phenethyl ester (CAPE) and were characterized by a syn disposition of the carbonyl group with respect to the vinylic double bond. Since the cinnamoyl moiety present in flavones such as quercetin (inactive on HIV-1-infected cells) is frozen in an anti arrangement, it was hoped that fixing our compounds in a syn disposition could favor anti-HIV-1 activity in cell-based assays. Geometrical and conformational properties of the designed compounds were taken into account through analysis of X-ray structures available from the Cambridge Structural Database. The polyhydroxylated analogues were prepared by reacting 3,4-bis(tetrahydropyran-2-yloxy)benzaldehyde with various compounds having active methylene groups such as 2-propanone, cyclopentanone, cyclohexanone, 1,3-diacetylbenzene, 2, 4-dihydroxyacetophenone, 2,3-dihydro-1-indanone, 2,3-dihydro-1, 3-indandione, and others. While active against both 3'-processing and strand-transfer reactions, the new compounds, curcumin included, failed to inhibit the HIV-1 multiplication in acutely infected MT-4 cells. Nevertheless, they specifically inhibited the enzymatic reactions associated with IN, being totally inactive against other viral (HIV-1 reverse transcriptase) and cellular (RNA polymerase II) nucleic acid-processing enzymes. On the other hand, title compounds were endowed with remarkable antiproliferative activity, whose potency correlated neither with the presence of catechols (possible source of reactive quinones) nor with inhibition of topoisomerases. The SARs developed for our compounds led to novel findings concerning the molecular determinants of IN inhibitory activity within the class of cinnamoyl-based structures. We hypothesize that these compounds bind to IN featuring the

  17. Auditoria da segurança viária

    Directory of Open Access Journals (Sweden)

    Christine Tessele Nodari

    2009-12-01

    Full Text Available

    A Auditoria de Segurança Viária - ASV, originada no Reino Unido na década de 80, tem por objetivo diminuir a probabilidade de ocorrência de acidentes de trânsito por meio da realização de vistorias periódicas com foco nas questões de segurança. Este artigo objetiva revisar a ASV, apresentando seus principais conceitos, objetivos, resultados alcançados, aplicabilidade, aspectos legais, custos e benefícios.

    A realização de ASV no Brasil é ainda muito incipiente. Por outro lado, em países como a Inglaterra, Dinamarca, Canadá, Austrália e Nova Zelândia, que possuem índices de acidentes substancialmente menores que os brasileiros, a realização de ASV já é prática obrigatória.

    A adoção da ASV possibilita economias significativas de recursos. A experiência resultante de duas décadas de condução de ASV sugere que os custos associados à sua execução representam um aumento de apenas 4 a 10% no custo total do projeto. Embora os benefícios gerados sejam de difícil quantificação, estima-se que a condução de ASV resulte em relações benefício-custo na ordem de 15:1; estimativas mais otimistas avaliam essa relação em 20:1. Essas estimativas indicam o grande potencial de retorno social e econômico decorrente da sua aplicação, o que referenda a difusão atual da prática de ASV por diversos países do mundo.

  18. Effects of auto-servo ventilation on patients with sleep-disordered breathing, stable systolic heart failure and concomitant diastolic dysfunction: subanalysis of a randomized controlled trial.

    Science.gov (United States)

    Birner, Christoph; Series, Frederic; Lewis, Keir; Benjamin, Amit; Wunderlich, Silke; Escourrou, Pierre; Zeman, Florian; Luigart, Ruth; Pfeifer, Michael; Arzt, Michael

    2014-01-01

    Systolic heart failure (HF) is frequently accompanied by diastolic dysfunction and sleep-disordered breathing (SDB). The objective of this subset analysis was to determine effect sizes of auto-servo ventilation (ASV and biphasic positive airway pressure ASV) on echocardiographic measures of diastolic function in patients with systolic HF and SDB. Thirty-two patients with stable systolic HF, concomitant diastolic dysfunction [age 66 ± 9 years old, left ventricular (LV) ejection fraction: 30 ± 7% and New York Heart Association class II: 72%] and SDB (apnea-hypopnea index, AHI: 48 ± 19/h; 53% had predominantly obstructive sleep apnea) receiving either ASV (n = 19) or optimal medical treatment (control, n = 13) were analyzed in a randomized controlled clinical trial. Polysomnographic and echocardiographic measurements were obtained at baseline and after 12 weeks. AHI significantly improved in the ASV group compared to the control group (-39 ± 18 vs. -0.2 ± 13.2/h, p control visit, diastolic function assessed by the isovolumetric relaxation time (-10.3 ± 26.1 vs. 9.3 ± 49.1, p = 0.48) and deceleration time (-43.9 ± 88.8 vs. 12.4 ± 68.8, p = 0.40) tended to improve after ASV treatment, but did not reach statistical significance. Likewise, the proportion of patients whose diastolic dysfunction improved was nonsignificantly higher in the ASV than in the control group, respectively (37 vs. 15%, p = 0.25). ASV treatment efficiently abolishes SDB in patients with stable systolic HF and concomitant diastolic dysfunction, and was associated with a statistically nonsignificant improvement in measures of diastolic dysfunction. Thus, these data provide estimates of effect size and justify the evaluation of the effects of ASV on diastolic function in larger randomized controlled trials. Copyright © 2013 S. Karger AG, Basel.

  19. Gene Expression in Class 2 Integrons Is SOS-Independent and Involves Two Pc Promoters.

    Science.gov (United States)

    Jové, Thomas; Da Re, Sandra; Tabesse, Aurore; Gassama-Sow, Amy; Ploy, Marie-Cécile

    2017-01-01

    Integrons are powerful bacterial genetic elements that permit the expression and dissemination of antibiotic-resistance gene cassettes. They contain a promoter Pc that allows the expression of gene cassettes captured through site-specific recombination catalyzed by IntI, the integron-encoded integrase. Class 1 and 2 integrons are found in both clinical and environmental settings. The regulation of intI and of Pc promoters has been extensively studied in class 1 integrons and the regulatory role of the SOS response on intI expression has been shown. Here we investigated class 2 integrons. We characterized the P intI2 promoter and showed that intI2 expression is not regulated via the SOS response. We also showed that, unlike class 1 integrons, class 2 integrons possess not one but two active Pc promoters that are located within the attI2 region that seem to contribute equally to gene cassette expression. Class 2 integrons mostly encode an inactive truncated integrase, but the rare class 2 integrons that encode an active integrase are associated with less efficient Pc2 promoter variants. We propose an evolutionary model for class 2 integrons in which the absence of repression of the integrase gene expression led to mutations resulting in either inactive integrase or Pc variants of weaker activity, thereby reducing the potential fitness cost of these integrons.

  20. 1,4-Bis(5-(naphthalen-1-yl)thiophen-2-yl)naphthalene, a small molecule, functions as a novel anti-HIV-1 inhibitor targeting the interaction between integrase and cellular Lens epithelium-derived growth factor.

    Science.gov (United States)

    Gu, Wan-gang; Ip, Denis Tsz-Ming; Liu, Si-jie; Chan, Joseph H; Wang, Yan; Zhang, Xuan; Zheng, Yong-tang; Wan, David Chi-Cheong

    2014-04-25

    Translocation of viral integrase (IN) into the nucleus is a critical precondition of integration during the life cycle of HIV, a causative agent of Acquired Immunodeficiency Syndromes (AIDS). As the first discovered cellular factor to interact with IN, Lens epithelium-derived growth factor (LEDGF/p75) plays an important role in the process of integration. Disruption of the LEDGF/p75-IN interaction has provided a great interest for anti-HIV agent discovery. In this work, we reported that one small molecular compound, 1,4-bis(5-(naphthalen-1-yl)thiophen-2-yl)naphthalene(Compound 15), potently inhibit the IN-LEDGF/p75 interaction and affect the HIV-1 IN nuclear distribution at 1 μM. The putative binding mode of Compound 15 was constructed by a molecular docking simulation to provide structural insights into the ligand-binding mechanism. Compound 15 suppressed viral replication by measuring p24 antigen production in HIV-1IIIB acute infected C8166 cells with EC50 value of 11.19 μM. Compound 15 might supply useful structural information for further anti-HIV agent discovery. Copyright © 2014. Published by Elsevier Ireland Ltd.

  1. Intelligent ventilation in the intensive care unit

    Directory of Open Access Journals (Sweden)

    Sigal Sviri

    2012-08-01

    Full Text Available Objectives. Automated, microprocessor-controlled, closed-loop mechanical ventilation has been used in our Medical Intensive Care Unit (MICU at the Hadassah Hebrew-University Medical Center for the past 15 years; for 10 years it has been the primary (preferred ventilator modality. Design and setting. We describe our clinical experience with adaptive support ventilation (ASV over a 6-year period, during which time ASV-enabled ventilators became more readily available and were used as the primary (preferred ventilators for all patients admitted to the MICU. Results. During the study period, 1 220 patients were ventilated in the MICU. Most patients (84% were ventilated with ASV on admission. The median duration of ventilation with ASV was 6 days. The weaning success rate was 81%, and tracheostomy was required in 13%. Sixty-eight patients (6% with severe hypoxia and high inspiratory pressures were placed on pressure-controlled ventilation, in most cases to satisfy a technical requirement for precise and conservative administration of inhaled nitric oxide. The overall pneumothorax rate was less than 3%, and less than 1% of patients who were ventilated only using ASV developed pneumothorax. Conclusions. ASV is a safe and acceptable mode of ventilation for complicated medical patients, with a lower than usual ventilation complication rate.

  2. Co-adsorption of Trichloroethylene and Arsenate by Iron-Impregnated Granular Activated Carbon.

    Science.gov (United States)

    Deng, Baolin; Kim, Eun-Sik

    2016-05-01

    Co-adsorption of trichloroethylene (TCE) and arsenate [As(V)] was investigated using modified granular activated carbons (GAC): untreated, sodium hypochlorite-treated (NaClO-GAC), and NaClO with iron-treated GAC (NaClO/Fe-GAC). Batch experiments of single- [TCE or As(V)] and binary- [TCE and As(V)] components solutions are evaluated through Langmuir and Freundlich isotherm models and adsorption kinetic tests. In the single-component system, the adsorption capacity of As(V) was increased by the NaClO-GAC and the NaClO/Fe-GAC. The untreated GAC showed a low adsorption capacity for As(V). Adsorption of TCE by the NaClO/Fe-GAC was maximized, with an increased Freundlich constant. Removal of TCE in the binary-component system was decreased 15% by the untreated GAC, and NaClO- and NaClO/Fe-GAC showed similar efficiency to the single-component system because of the different chemical status of the GAC surfaces. Results of the adsorption isotherms of As(V) in the binary-component system were similar to adsorption isotherms of the single-component system. The adsorption affinities of single- and binary-component systems corresponded with electron transfer, competitive adsorption, and physicochemical properties.

  3. Temporal transcription of the lactococcal temperate phage TP901-1 and DNA sequence of the early promoter region

    DEFF Research Database (Denmark)

    Madsen, Hans Peter Lynge; Hammer, Karin

    1998-01-01

    to a phage repressor, a single-stranded DNA-binding protein, a topoisomerase, a Cro-like protein and two other phage proteins of unknown function were detected. The gene arrangement in the early transcribed region of TP901-1 thus consists of two transcriptional units: one from PR containing four genes......, of which at least two (the integrase gene and putative repressor) are needed for lysogeny, and the divergent and longer transcriptional unit from PL, presumably encoding functions required for the lytic life cycle. ORFs with homology to proteins involved in DNA replication were identified on the latter......Transcriptional analysis by Northern blotting identified clusters of early, middle and late transcribed regions of the temperate lactococcal bacteriophage TP901-1 during one-step growth experiments. The latent period was found to be 65 min and the burst size 40 +/- 10. The eight early transcripts...

  4. Single helically folded aromatic oligoamides that mimic the charge surface of double-stranded B-DNA

    Science.gov (United States)

    Ziach, Krzysztof; Chollet, Céline; Parissi, Vincent; Prabhakaran, Panchami; Marchivie, Mathieu; Corvaglia, Valentina; Bose, Partha Pratim; Laxmi-Reddy, Katta; Godde, Frédéric; Schmitter, Jean-Marie; Chaignepain, Stéphane; Pourquier, Philippe; Huc, Ivan

    2018-05-01

    Numerous essential biomolecular processes require the recognition of DNA surface features by proteins. Molecules mimicking these features could potentially act as decoys and interfere with pharmacologically or therapeutically relevant protein-DNA interactions. Although naturally occurring DNA-mimicking proteins have been described, synthetic tunable molecules that mimic the charge surface of double-stranded DNA are not known. Here, we report the design, synthesis and structural characterization of aromatic oligoamides that fold into single helical conformations and display a double helical array of negatively charged residues in positions that match the phosphate moieties in B-DNA. These molecules were able to inhibit several enzymes possessing non-sequence-selective DNA-binding properties, including topoisomerase 1 and HIV-1 integrase, presumably through specific foldamer-protein interactions, whereas sequence-selective enzymes were not inhibited. Such modular and synthetically accessible DNA mimics provide a versatile platform to design novel inhibitors of protein-DNA interactions.

  5. CRISPR-Cas and Contact-Dependent Secretion Systems Present on Excisable Pathogenicity Islands with Conserved Recombination Modules.

    Science.gov (United States)

    Carpenter, Megan R; Kalburge, Sai S; Borowski, Joseph D; Peters, Molly C; Colwell, Rita R; Boyd, E Fidelma

    2017-05-15

    Pathogenicity islands (PAIs) are mobile integrated genetic elements that contain a diverse range of virulence factors. PAIs integrate into the host chromosome at a tRNA locus that contains their specific bacterial attachment site, attB , via integrase-mediated site-specific recombination generating attL and attR sites. We identified conserved recombination modules (integrases and att sites) previously described in choleragenic Vibrio cholerae PAIs but with novel cargo genes. Clustered regularly interspaced short palindromic repeat (CRISPR)-associated proteins (Cas proteins) and a type VI secretion system (T6SS) gene cluster were identified at the Vibrio pathogenicity island 1 (VPI-1) insertion site in 19 V. cholerae strains and contained the same recombination module. Two divergent type I-F CRISPR-Cas systems were identified, which differed in Cas protein homology and content. The CRISPR repeat sequence was identical among all V. cholerae strains, but the CRISPR spacer sequences and the number of spacers varied. In silico analysis suggests that the CRISPR-Cas systems were active against phages and plasmids. A type III secretion system (T3SS) was present in 12 V. cholerae strains on a 68-kb island inserted at the same tRNA-serine insertion site as VPI-2 and contained the same recombination module. Bioinformatics analysis showed that two divergent T3SSs exist among the strains examined. Both the CRISPR and T3SS islands excised site specifically from the bacterial chromosome as complete units, and the cognate integrases were essential for this excision. These data demonstrated that identical recombination modules that catalyze integration and excision from the chromosome can acquire diverse cargo genes, signifying a novel method of acquisition for both CRISPR-Cas systems and T3SSs. IMPORTANCE This work demonstrated the presence of CRISPR-Cas systems and T3SSs on PAIs. Our work showed that similar recombination modules can associate with different cargo genes and

  6. Factor Analysis, AMMI Stability Value (ASV Parameter and GGE Bi-Plot Graphical Method of Quantitative and Qualitative Traits in Potato Genotypes

    Directory of Open Access Journals (Sweden)

    Davood Hassanpanah

    2016-10-01

    Full Text Available Quantitative and qualitative traits and stability of marketable tuber yield of 14 promising potato clones, along with three commercial cultivars (Agria, Marfona and Savalan as checks, were evaluated at the Ardabil Agricultural and Natural Resources Research Station during 2013 and 2014. The experiment was based on a randomized complete block design with four replications. During growing period and after harvest, traits like main stem number per plant, plant height, tuber number and weight per plant, total and marketable tuber yield, dry matter percentage, baking type, hollow heart, tuber inner ring and discoloration of raw tuber flesh after 24 hours were measured. Combined ANONA for quantitative traits showed that there were significant differences among promising clones as to total and marketable tuber yield, tuber number and weight per plant, plant height, tuber mean weight, main stem number per plant and dry matter percentage and their interactions with year in total and marketable tuber yield. The clone 9 (397078-3 with the least amount of marketable tuber yield had significant difference with clones 4 (397045-13, 1 (397031-16, 3 (397031-11, 6 (397009-8 and 12 (397067-6 in 2013 and with clone 4 (397045-13 and Agria cultivar in 2014. The clones 4(397045-13, 1 (397031-16 and 12 (397067-6 had uniform tuber, yellow to dark-yellow skin and light-yellow to yellow flesh color, tuber shape of oval round and round, shallow to mid shallow eyes, no tuber inner ring, hollow heart and tuber inner crack and mid-late maturity. They were selected for home consumption of chips, french-fries and frying. Based on the results of factor analysis, "tuber yield", "number of tuber" and "plant structural and quality "were named as first, second and third quality determining factors respectively. In this experiment, GGE Bi-plot model and AMMI Stability Value (ASV parameter, were acceptable methods for the selection of marketable tuber yield stability which found to

  7. Simultaneous Oxidation and Sequestration of As(III) from Water by Using Redox Polymer-Based Fe(III) Oxide Nanocomposite.

    Science.gov (United States)

    Zhang, Xiaolin; Wu, Mengfei; Dong, Hao; Li, Hongchao; Pan, Bingcai

    2017-06-06

    Water decontamination from As(III) is an urgent but still challenging task. Herein, we fabricated a bifunctional nanocomposite HFO@PS-Cl for highly efficient removal of As(III), with active chlorine covalently binding spherical polystyrene host for in situ oxidation of As(III) to As(V), and Fe(III) hydroxide (HFO) nanoparticles (NPs) embedded inside for specific As(V) removal. HFO@PS-Cl could work effectively in a wide pH range (5-9), and other substances like sulfate, chloride, bicarbonate, silicate, and humic acid exert insignificant effect on As(III) removal. As(III) sequestration is realized via two pathways, that is, oxidation to As(V) by the active chlorine followed by specific As(V) adsorption onto HFO NPs, and As(III) adsorption onto HFO NPs followed by oxidation to As(V). The exhausted HFO@PS-Cl could be refreshed for cyclic runs with insignificant capacity loss by the combined regeneration strategy, that is, alkaline solution to rinse the adsorbed As(V) and NaClO solution to renew the host oxidation capability. In addition, fixed-bed experiments demonstrated that the HFO@PS-Cl column could generate >1760 bed volume (BV) effluent from a synthetic As(III)-containing groundwater to meet the drinking water standard (nanocomposites, HFO@PS-N and HFO@D201 could only generate 450 and 600 BV effluents under otherwise identical conditions.

  8. Effect of weak magnetic field on arsenate and arsenite removal from water by zerovalent iron: an XAFS investigation.

    Science.gov (United States)

    Sun, Yuankui; Guan, Xiaohong; Wang, Jianmin; Meng, Xiaoguang; Xu, Chunhua; Zhou, Gongming

    2014-06-17

    In this study, a weak magnetic field (WMF), superimposed with a permanent magnet, was utilized to improve ZVI corrosion and thereby enhance As(V)/As(III) removal by ZVI at pHini 3.0-9.0. The experiment with real arsenic-bearing groundwater revealed that WMF could greatly improve arsenic removal by ZVI even in the presence of various cations and anions. The WMF-induced improvement in As(V)/As(III) removal by ZVI should be primarily associated with accelerated ZVI corrosion, as evidenced by the pH variation, Fe(2+) release, and the formation of corrosion products as characterized with X-ray absorption fine structure spectroscopy. The arsenic species analysis in solution/solid phases at pHini 3.0 revealed that As(III) oxidation to As(V) in aqueous phase preceded its subsequent sequestration by the newly formed iron (hydr)oxides. However, both As(V) adsorption following As(III) oxidation to As(V) in solution and As(III) adsorption preceding its conversion to As(V) in solid phase were observed at pHini 5.0-9.0. The application of WMF accelerated the transformation of As(III) to As(V) in both aqueous and solid phases at pHini 5.0-9.0 and enhanced the oxidation of As(III) to As(V) in solution at pHini 3.0.

  9. Evaluation and comparison of aluminum-coated pumice and zeolite in arsenic removal from water resources

    Directory of Open Access Journals (Sweden)

    Heidari Masoumeh

    2012-12-01

    Full Text Available Abstract In this research the potential of aluminum-coated pumice and zeolite in arsenic, As (V removal was investigated and compared. Scanning Electron Microscopy (SEM, X-Ray Diffraction (XRD and X-Ray Flaorescence Spectrometry (XRF were carried out to determine the properties of the adsorbents. Several parameters including adsorbent dosage] pH, contact time, and initial As(V concentration were studied. The optimum pH obtained for both adsorbents was pH = 7. As(V adsorption by both adsorbents followed the Freundlich isotherm (for aluminum-coated pumice and zeolite respectively with R2 > 0.98 and R2 > 0.99. The obtained data from kinetics showed that the pseudo-second order model could better explain As(V adsorption for both aluminum-coated pumice and zeolite (R2 > 0.98 and R2 > 0.99 respectively. Because of low cost, both adsorbents may be economically used, but aluminum-coated zeolite showed high efficiency of, due to its porosity and surface area. More than 96% of As(V with initial concentration of 250 μg/L was removed by 10 g/L aluminum-coated zeolite at pH = 7 and in 60 minutes to achieve As(V concentration of 10 μg/L, while only 71% of As(V could be removed by aluminum-coated pumice.

  10. Manganese-modified activated carbon fiber (Mn-ACF): Novel efficient adsorbent for Arsenic

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Zhumei; Yu, Yichang; Pang, Shiyu; Du, Dongyun, E-mail: dydu666@yahoo.com.cn

    2013-11-01

    In this paper, a novel adsorbent, manganese-modified activated carbon fiber (Mn-ACF), was prepared and used for removal of As(V) from aqueous solution. The adsorbent was characterized by scanning electron microscopy (SEM) and X-ray photoelectron spectroscopy (XPS). Adsorption of As(V) onto the as-prepared adsorbent from aqueous solutions was investigated and discussed. The adsorption kinetic data were modeled using the pseudo-first-order and pseudo-second order, respectively. The experimental results indicate that the pseudo-second-order kinetic equation can better describe the adsorption kinetics. Furthermore, adsorption equilibrium data of As(V) on the as-prepared adsorbent were analyzed by Langmuir and Freundlich models, which suggested that the Langmuir model provides a better correlation of the experimental data. The adsorption capacities (q{sub max}) of As(V) on Mn-ACF at various temperatures, determined using the Langmuir equation, are 23.77, 33.23 and 36.53 mg g{sup −1} at 303, 313 and 323 K, respectively. To the best of our knowledge, this adsorption capacity for As(V) is much larger than those reported in literatures (7.50–16.58 mg g{sup −1}). Notably, the q{sub max} increases with increasing temperature, suggesting that adsorption of As(V) on Mn-ACF surface is an endothermic process, which is further confirmed by the calculated thermodynamic parameters including free energy, enthalpy, and entropy of adsorption process. The effect of experimental parameters such as pH and dosage of adsorbent on adsorption of As(V) were also studied. The present work will be useful in purification of groundwater.

  11. Efficacy and safety of daclatasvir and asunaprevir for hepatitis C virus genotype 1b infection

    Directory of Open Access Journals (Sweden)

    Hee Chul Nam

    2016-06-01

    Full Text Available Background/Aims: The treatment strategy for hepatitis C virus (HCV has been changing rapidly since the introduction of direct-acting antivirals such as daclatasvir (DCV and asunaprevir (ASV. We evaluated the efficacy and safety of DCV and ASV for HCV in real-life practice. Methods: Patients were treated with 60 mg of DCV once daily plus 200 mg of ASV twice daily for 24 weeks, and followed for 12 weeks. The primary endpoint was a sustained virological response at 12 weeks after treatment (SVR12 and safety. Results: This retrospective study included eight patients with chronic HCV genotype 1b infection. All of the enrolled patients were diagnosed with liver cirrhosis, and their mean age was 65.75 years. One patient was a nonresponder and two patients relapsed with previous pegylated interferon (PegIFN and ribavirin (RBV treatment. None of the patient showed NS5A mutation. An SVR12 was achieved in 88% of cases by the DCV and ASV combination therapy. The serum transaminase level and the aspartate-aminotransferase-to-platelet ratio were improved after the treatment. DCV and ASV were well tolerated in most of the patients, with treatment discontinuation due to adverse events (elevated liver enzyme and decompensation occurring in two patients. Conclusion: In this study, combination of DCV and ASV treatment achieved a high sustained virological response with few adverse events even in those with cirrhosis, advanced age, and nonresponse/relapse to previous interferon-based therapy. Close monitoring of safety issues may be necessary when treating chronic HCV patients receiving DCV and ASV, especially in older patient and those with cirrhosis.

  12. Experimental effects of exposure to pornography

    DEFF Research Database (Denmark)

    Hald, Gert Martin; Malamuth, Neil N

    2015-01-01

    Using a randomly selected community sample of 200 Danish young adult men and women in a randomized experimental design, the study investigated the effects of a personality trait (agreeableness), past pornography consumption, and experimental exposure to non-violent pornography on attitudes...... supporting violence against women (ASV). We found that lower levels of agreeableness and higher levels of past pornography consumption significantly predicted ASV. In addition, experimental exposure to pornography increased ASV but only among men low in agreeableness. This relationship was found...

  13. Guidelines for Quality Management of Apallic Syndrome / Vegetative State.

    Science.gov (United States)

    von Wild, Klaus; Gerstenbrand, Franz; Dolce, Giuliano; Binder, Heinrich; Vos, Pieter E; Saltuari, Leopold; Alekseenko, Yuri; Formisano, Rita; Ritz, Annegret; Ortega-Suhrkamp, Erika; Jörg, Johannes R; Potapov, Alexander A; León-Carrión, José; Vilcinis, Rimantas; Zitnay, George A

    2007-06-01

    Epidemiology in Europe shows constantly increasing figures for the apallic syndrome (AS)/vegetative state (VS) as a consequence of advanced rescue, emergency services, intensive care treatment after acute brain damage and high-standard activating home nursing for completely dependent end-stage cases secondary to progressive neurological disease. Management of patients in irreversible permanent AS/VS has been the subject of sustained scientific and moral-legal debate over the past decade. A task force on guidelines for quality management of AS/VS was set up under the auspices of the Scientific Panel Neurotraumatology of the European Federation of Neurological Societies to address key issues relating to AS/VS prevalence and quality management. Collection and analysis of scientific data on class II (III) evidence from the literature and recommendations based on the best practice as resulting from the task force members' expertise are in accordance with EFNS Guidance regulations. The overall incidence of new AS/VS full stage cases all etiology is 0.5-2/100.000 population per year. About one third are traumatic and two thirds non traumatic cases. Increasing figures for hypoxic brain damage and progressive neurological disease have been noticed. The main conceptual criticism is based on the assessment and diagnosis of all different AS/VS stages based solely on behavioural findings without knowing the exact or uniform pathogenesis or neuropathological findings and the uncertainty of clinical assessment due to varying inclusion criteria. No special diagnostics, no specific medical management can be recommended for class II or III AS treatment and rehabilitation. This is why sine qua non diagnostics of the clinical features and appropriate treatment of AS/VS patients of "AS full, remission, defect and end stages" require further professional training and expertise for doctors and rehabilitation personnel. Management of AS aims at the social reintegration of patients or has

  14. Arsenic sorption to nanoparticulate mackinawite (FeS): An examination of phosphate competition.

    Science.gov (United States)

    Niazi, Nabeel Khan; Burton, Edward D

    2016-11-01

    Nanoparticulate mackinawite (FeS) can be an important host-phase for arsenic (As) in sulfidic, subsurface environments. Although not previously investigated, phosphate (PO 4 3- ) may compete with As for available sorption sites on FeS, thereby enhancing As mobility in FeS-bearing soils, sediments and groundwater systems. In this study, we examine the effect of PO 4 3- on sorption of arsenate (As(V)) and arsenite (As(III)) to nanoparticulate FeS at pH 6, 7 and 9. Results show that PO 4 3- (at 0.01-1.0 mM P) did not significantly affect sorption of either As(V) or As(III) to nanoparticulate FeS at initial aqueous As concentrations ranging from 0.01 to 1.0 mM. At pH 9 and 7, sorption of both As(III) and As(V) to nanoparticulate FeS was similar, with distribution coefficient (K d ) values spanning 0.76-15 L g -1 (which corresponds to removal of 87-98% of initial aqueous As(III) and As(V) concentrations). Conversely, at pH 6, the sorption of As(III) was characterized by substantially higher K d values (6.3-93.4 L g -1 ) than those for As(V) (K d  = 0.21-0.96 L g -1 ). Arsenic K-edge X-ray absorption near edge structure (XANES) spectroscopy indicated that up to 52% of the added As(V) was reduced to As(III) in As(V) sorption experiments, as well as the formation of minor amounts of an As 2 S 3 -like species. In As(III) sorption experiments, XANES spectroscopy also demonstrated the formation of an As 2 S 3 -like species and the partial oxidation of As(III) to As(V) (despite the strictly O 2 -free experimental conditions). Overall, the XANES data indicate that As sorption to nanoparticulate FeS involves several redox transformations and various sorbed species, which display a complex dependency on pH and As loading but that are not influenced by the co-occurrence of PO 4 3- . This study shows that nanoparticulate FeS can help to immobilize As(III) and As(V) in sulfidic subsurface environments where As co-exists with PO 4 3- . Copyright © 2016 Elsevier Ltd. All

  15. Effects of solution chemistry on arsenic(V) removal by low-cost adsorbents.

    Science.gov (United States)

    Wang, Yuru; Tsang, Daniel C W

    2013-11-01

    Natural and anthropogenic arsenic (As) contamination of water sources pose serious health concerns, especially for small communities in rural areas. This study assessed the applicability of three industrial byproducts (coal fly ash, lignite, and green waste compost) as the low-cost adsorbents for As(V) removal under various field-relevant conditions (dissolved oxygen, As(V)/Fe ratio, solution pH, and presence of competing species). The physico-chemical properties of the adsorbents were characterized by XRD, XRF, FT-IR, and NMR analysis. Batch experiments demonstrated that coal fly ash could provide effective As(V) removal (82.1%-95%) because it contained high content of amorphous iron/aluminium hydroxides for As(V) adsorption and dissolvable calcium minerals for calcium arsenate precipitation. However, the addition of lignite and green waste compost was found unfavourable since they hindered the As(V) removal by 10%-42% possibly due to dissolution of organic matter and ternary arsenate-iron-organic matter complexes. On the other hand, higher concentrations of dissolved iron (comparing As(V)/Fe ratios of 1:1 and 1:10) and dissolved oxygen (comparing 0.2 and 6 mg/L) only marginally enhanced the As(V) removal at pH 6 and 8. Thus, addition of dissolved iron, water aeration, or pH adjustment became unnecessary because coal fly ash was able to provide effective As(V) removal under the natural range of geochemical conditions. Moreover, the presence of low levels of background competing (0.8 or 8 mg/L of humic acid, phosphate, and silicate) imposed little influence on As(V) removal, possibly because the high adsorption capacity of coal fly ash was far from exhaustion. These results suggested that coal fly ash was a potentially promising adsorbent that warranted further investigation.

  16. Remediation of groundwater contaminated with arsenic through enhanced natural attenuation: Batch and column studies.

    Science.gov (United States)

    Hafeznezami, Saeedreza; Zimmer-Faust, Amity G; Jun, Dukwoo; Rugh, Megyn B; Haro, Heather L; Park, Austin; Suh, Jae; Najm, Tina; Reynolds, Matthew D; Davis, James A; Parhizkar, Tarannom; Jay, Jennifer A

    2017-10-01

    Batch and column laboratory experiments were conducted on natural sediment and groundwater samples from a contaminated site in Maine, USA with the aim of lowering the dissolved arsenate [As(V)] concentrations through chemical enhancement of natural attenuation capacity. In batch factorial experiments, two levels of treatment for three parameters (pH, Ca, and Fe) were studied at different levels of phosphate to evaluate their impact on As(V) solubility. Results illustrated that lowering pH, adding Ca, and adding Fe significantly increased the sorption capacity of sediments. Overall, Fe amendment had the highest individual impact on As(V) levels. To provide further evidence for the positive impact of Ca on As(V) adsorption, isotherm experiments were conducted at three different levels of Ca concentrations. A consistent increase in adsorption capacity (26-37%) of sediments was observed with the addition of Ca. The observed favorable effect of Ca on As(V) adsorption is likely caused by an increase in the surface positive charges due to surface accumulation of Ca 2+ ions. Column experiments were conducted by flowing contaminated groundwater with elevated pH, As(V), and phosphate through both uncontaminated and contaminated sediments. Potential in-situ remediation scenarios were simulated by adding a chemical amendment feed to the columns injecting Fe(II) or Ca as well as simultaneous pH adjustment. Results showed a temporary and limited decrease in As(V) concentrations under the Ca treatment (39-41%) and higher levels of attenuation in Fe(II) treated columns (50-91%) but only after a certain number of pore volumes (18-20). This study illustrates the importance of considering geochemical parameters including pH, redox potential, presence of competing ions, and sediment chemical and physical characteristics when considering enhancing the natural attenuation capacity of sediments to mitigate As contamination in natural systems. Copyright © 2017 Elsevier Ltd. All rights

  17. Arsenate reduction and methylation in the cells of Trichoderma asperellum SM-12F1, Penicillium janthinellum SM-12F4, and Fusarium oxysporum CZ-8F1 investigated with X-ray absorption near edge structure

    Energy Technology Data Exchange (ETDEWEB)

    Su, S.M., E-mail: shimingsu@163.com [Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Environment, Ministry of Agriculture, Beijing (China); Zeng, X.B., E-mail: zengxb@ieda.org.cn [Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Environment, Ministry of Agriculture, Beijing (China); Li, L.F.; Duan, R.; Bai, L.Y. [Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Environment, Ministry of Agriculture, Beijing (China); Li, A.G.; Wang, J.; Jiang, S. [Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai (China)

    2012-12-15

    Highlights: Black-Right-Pointing-Pointer Three fungal strains are capable of As(V) reduction and methylation. Black-Right-Pointing-Pointer As(V) reduction might be more easily processed than the methylation in fungal cells. Black-Right-Pointing-Pointer As sequestration and speciation transformation might be the detoxification processes. - Abstract: Synchrotron radiation-based X-ray absorption near edge structure (XANES) was introduced to directly analysis chemical species of arsenic (As) in the cells of Trichoderma asperellum SM-12F1, Penicillium janthinellum SM-12F4, and Fusarium oxysporum CZ-8F1 capable of As accumulation and volatilisation. After exposure to As(V) of 500 mg L{sup -1} for 15 days, a total of 60.5% and 65.3% of the accumulated As in the cells of T. asperellum SM-12F1 and P. janthinellum SM-12F4, respectively, was As(III), followed by 31.3% and 32.4% DMA (dimethylarsinic acid), 8.3% and 2.3% MMA (monomethylarsonic acid), respectively. However, for F. oxysporum CZ-8F1, 54.5% of the accumulated As was As(III), followed by 37.8% MMA and 7.7% As(V). The reduction and methylation of As(V) formed As(III), MMA, and DMA as the primacy products, and the reduction of As(V) might be more easily processed than the methylation. These results will help to understanding the mechanisms of As detoxification and its future application in bioremediation.

  18. Comparing the effects of adaptive support ventilation and synchronized intermittent mandatory ventilation on intubation duration and hospital stay after coronary artery bypass graft surgery

    Directory of Open Access Journals (Sweden)

    Ahmadreza Yazdannik

    2016-01-01

    Full Text Available Background: Different modes of mechanical ventilation are used for respiratory support after coronary artery bypass graft (CABG. This study aimed to compare the effect(s of using adaptive support ventilation (ASV and synchronized intermittent mandatory ventilation (SIMV on the length of mechanical ventilation (intubation duration and hospital stay after coronary artery bypass graft surgery. Materials and Methods: In a randomized control trial, 64 patients were ventilated with ASV as the experiment group or with SIMV as the control group after CABG surgery in Chamran Hospital of Isfahan University of Medical Sciences. The time of tracheal intubation and the length of hospital stay were compared between the two groups. Data were analyzed and described using statistical analysis (independent t-test. Results: The mean time of intubation duration was significantly lower in ASV group compared with SIMV group. (4.83 h vs 6.71 h, P < 0.001. The lengths of hospital stay in the ASV and the SIMV groups were 140.6 h and 145.1 h, respectively. This difference was significant between the two groups (P = 0.006. Conclusions: According to the results of this study, using ASV mode for mechanical ventilation after CABG led to a decrease in intubation duration and also hospital stay in comparison with the SIMV group. It is recommended to use ASV mode on ventilators for respiratory support of patients undergoing coronary artery bypass graft surgery.

  19. Arsenate reduction and methylation in the cells of Trichoderma asperellum SM-12F1, Penicillium janthinellum SM-12F4, and Fusarium oxysporum CZ-8F1 investigated with X-ray absorption near edge structure

    International Nuclear Information System (INIS)

    Su, S.M.; Zeng, X.B.; Li, L.F.; Duan, R.; Bai, L.Y.; Li, A.G.; Wang, J.; Jiang, S.

    2012-01-01

    Highlights: ► Three fungal strains are capable of As(V) reduction and methylation. ► As(V) reduction might be more easily processed than the methylation in fungal cells. ► As sequestration and speciation transformation might be the detoxification processes. - Abstract: Synchrotron radiation-based X-ray absorption near edge structure (XANES) was introduced to directly analysis chemical species of arsenic (As) in the cells of Trichoderma asperellum SM-12F1, Penicillium janthinellum SM-12F4, and Fusarium oxysporum CZ-8F1 capable of As accumulation and volatilisation. After exposure to As(V) of 500 mg L −1 for 15 days, a total of 60.5% and 65.3% of the accumulated As in the cells of T. asperellum SM-12F1 and P. janthinellum SM-12F4, respectively, was As(III), followed by 31.3% and 32.4% DMA (dimethylarsinic acid), 8.3% and 2.3% MMA (monomethylarsonic acid), respectively. However, for F. oxysporum CZ-8F1, 54.5% of the accumulated As was As(III), followed by 37.8% MMA and 7.7% As(V). The reduction and methylation of As(V) formed As(III), MMA, and DMA as the primacy products, and the reduction of As(V) might be more easily processed than the methylation. These results will help to understanding the mechanisms of As detoxification and its future application in bioremediation.

  20. Remediation of Organic and Inorganic Arsenic Contaminated Groundwater using a Nonocrystalline TiO2 Based Adsorbent

    Energy Technology Data Exchange (ETDEWEB)

    Jing, C.; Meng, X; Calvache, E; Jiang, G

    2009-01-01

    A nanocrystalline TiO2-based adsorbent was evaluated for the simultaneous removal of As(V), As(III), monomethylarsonic acid (MMA), and dimethylarsinic acid (DMA) in contaminated groundwater. Batch experimental results show that As adsorption followed pseudo-second order rate kinetics. The competitive adsorption was described with the charge distribution multi-site surface complexation model (CD-MUSIC). The groundwater containing an average of 329 ?g L-1 As(III), 246 ?g L-1 As(V), 151 ?g L-1 MMA, and 202 ?g L-1 DMA was continuously passed through a TiO2 filter at an empty bed contact time of 6 min for 4 months. Approximately 11 000, 14 000, and 9900 bed volumes of water had been treated before the As(III), As(V), and MMA concentration in the effluent increased to 10 ?g L-1. However, very little DMA was removed. The EXAFS results demonstrate the existence of a bidentate binuclear As(V) surface complex on spent adsorbent, indicating the oxidation of adsorbed As(III). A nanocrystalline TiO2-based adsorbent could be used for the simultaneous removal of As(V), As(III), MMA, and DMA in contaminated groundwater.

  1. Arsenic transformation and plant growth promotion characteristics of As-resistant endophytic bacteria from As-hyperaccumulator Pteris vittata.

    Science.gov (United States)

    Xu, Jia-Yi; Han, Yong-He; Chen, Yanshan; Zhu, Ling-Jia; Ma, Lena Q

    2016-02-01

    The ability of As-resistant endophytic bacteria in As transformation and plant growth promotion was determined. The endophytes were isolated from As-hyperaccumulator Pteris vittata (PV) after growing for 60 d in a soil containing 200 mg kg(-1) arsenate (AsV). They were isolated in presence of 10 mM AsV from PV roots, stems, and leaflets, representing 4 phyla and 17 genera. All endophytes showed at least one plant growth promoting characteristics including IAA synthesis, siderophore production and P solubilization. The root endophytes had higher P solubilization ability than the leaflet (60.0 vs. 18.3 mg L(-1)). In presence of 10 mM AsV, 6 endophytes had greater growth than the control, suggesting As-stimulated growth. Furthermore, root endophytes were more resistant to AsV while the leaflet endophytes were more tolerant to arsenite (AsIII), which corresponded to the dominant As species in PV tissues. Bacterial As resistance was positively correlated to their ability in AsV reduction but not AsIII oxidation. The roles of those endophytes in promoting plant growth and As resistance in P. vittata warrant further investigation. Published by Elsevier Ltd.

  2. Adsorption characteristics of arsenic from micro-polluted water by an innovative coal-based mesoporous activated carbon.

    Science.gov (United States)

    Li, Wei-Guang; Gong, Xu-Jin; Wang, Ke; Zhang, Xin-Ran; Fan, Wen-Biao

    2014-08-01

    An innovative coal-based mesoporous activated carbon (NCPAC) was prepared by re-agglomeration, oxidation and two-step activation using coal-blending as precursor. Adsorption capacities of As(III) and As(V) ions (<0.5mg/L) onto NCPAC as a function of pH, adsorbent dose, initial arsenic concentrations, contact time, and adsorption isotherms at 7°C was investigated. The innovative methods promoted total pore volume (1.087cm(3)/g), mesoporosity (64.31%), iodine numbers (1104mg/g), methylene blue (251.8mg/g) and ash contents (15.26%). The adsorption capacities of NCPAC for As(III) and As(V) were found to be strongly dependent on pH and contact time. The optimal pH value was 6. The equilibrium time was 60min for adsorption of As(III) and As(V) by NCPAC. The Langmuir model fitted the experimental data well for both As(III) (R(2)=0.9980) and As(V) (R(2)=0.9988). Maximum adsorption capacities of As(III) and As(V) (C0=0.50mg/L) by NCPAC were 1.491 and 1.760mg/g, respectively. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. 360-Degree Visual Detection and Target Tracking on an Autonomous Surface Vehicle

    Science.gov (United States)

    Wolf, Michael T; Assad, Christopher; Kuwata, Yoshiaki; Howard, Andrew; Aghazarian, Hrand; Zhu, David; Lu, Thomas; Trebi-Ollennu, Ashitey; Huntsberger, Terry

    2010-01-01

    This paper describes perception and planning systems of an autonomous sea surface vehicle (ASV) whose goal is to detect and track other vessels at medium to long ranges and execute responses to determine whether the vessel is adversarial. The Jet Propulsion Laboratory (JPL) has developed a tightly integrated system called CARACaS (Control Architecture for Robotic Agent Command and Sensing) that blends the sensing, planning, and behavior autonomy necessary for such missions. Two patrol scenarios are addressed here: one in which the ASV patrols a large harbor region and checks for vessels near a fixed asset on each pass and one in which the ASV circles a fixed asset and intercepts approaching vessels. This paper focuses on the ASV's central perception and situation awareness system, dubbed Surface Autonomous Visual Analysis and Tracking (SAVAnT), which receives images from an omnidirectional camera head, identifies objects of interest in these images, and probabilistically tracks the objects' presence over time, even as they may exist outside of the vehicle's sensor range. The integrated CARACaS/SAVAnT system has been implemented on U.S. Navy experimental ASVs and tested in on-water field demonstrations.

  4. Adverse drug reaction profile of anti-snake venom in a rural tertiary care teaching hospital

    Science.gov (United States)

    Deshpande, Rushikesh Prabhakar; Motghare, Vijay Motiram; Padwal, Sudhir Laxman; Pore, Rakesh Ramkrishna; Bhamare, Chetanraj Ghanshyam; Deshmukh, Vinod Shivaji; Pise, Harshal Nutan

    2013-01-01

    Objectives The study was carried out with the aim of evaluation of the adverse drug reaction profile of anti-snake venom serum (ASV) in a rural tertiary care hospital. Methods An observational study was conducted in SRTR Medical College, Ambajogai, Maharashtra, India. A total number of 296 indoor case papers of snake bite from February to September 2011 and June to August 2012 were retrieved from the record section and the antivenom reactions were assessed. In addition, basic epidemiological data and prescribing practices of ASV were also analyzed. Results Vasculotoxic snake bites were more common (50.61%) than neuroparalytic ones (22.56%). Mild envenomation was the commonest presentation. A total of 92 (56.10%) patients who received ASV suffered from antivenom reactions. The most common nature of reaction was chills, rigors (69.56%) followed by nausea and vomiting (34.8%). 10-15% patients suffered from moderate to severe reactions like hypotension and sudden respiratory arrest. We did not find any dose response relationship of ASV to risk of reactions (odds ratio 0.37). Intradermal sensitivity test was performed in about 72% cases. Conclusion Our study showed a higher incidence of reactions to ASV at our institute. PMID:24396245

  5. pH modulates arsenic toxicity in Bacillus licheniformis DAS-2.

    Science.gov (United States)

    Tripti, K; Shardendu

    2016-08-01

    The toxic characteristics of arsenic species, As(V) and As(III) result in ecological risks. Arsenic tolerant bacterium was isolated and identified as the Bacillus licheniformis DAS-2 through 16SrDNA sequencing. B. licheniformis DAS-2 was efficient to tolerate and remove both the As(V)[MIC 8mM] and As(III)[MIC 6mM] from the growth medium. The potential for the removal/uptake of arsenic from the 3, 5 and 7mM As(V) enriched growth media was 100%, 60% and 35% respectively and from the 1, 3 and 5mM As(III) enrichment it was 100%, 99% and 58% respectively at neutral pH. 80% of uptake As(V) was reduced to As(III) in 3mM As(V) enrichment which was gradually decreased to only 17% at 7mM As(V) enrichment at neutral pH. The arsenic toxicity in B. licheniformis DAS-2 was found modulated by pH and was examined through alteration in growth, uptake/removal, reduction and measurement of chemical toxicity. Copyright © 2016 Elsevier Inc. All rights reserved.

  6. Sensitive Bioanalysis Based on in-Situ Droplet Anodic Stripping Voltammetric Detection of CdS Quantum Dots Label after Enhanced Cathodic Preconcentration

    Directory of Open Access Journals (Sweden)

    Xiaoli Qin

    2016-08-01

    Full Text Available We report a protocol of CdS-labeled sandwich-type amperometric bioanalysis with high sensitivity, on the basis of simultaneous chemical-dissolution/cathodic-enrichment of the CdS quantum dot biolabel and anodic stripping voltammetry (ASV detection of Cd directly on the bioelectrode. We added a microliter droplet of 0.1 M aqueous HNO3 to dissolve CdS on the bioelectrode and simultaneously achieved the potentiostatic cathodic preconcentration of Cd by starting the potentiostatic operation before HNO3 addition, which can largely increase the ASV signal. Our protocol was used for immunoanalysis and aptamer-based bioanalysis of several proteins, giving limits of detection of 4.5 fg·mL−1 for human immunoglobulin G, 3.0 fg·mL−1 for human carcinoembryonic antigen (CEA, 4.9 fg·mL−1 for human α-fetoprotein (AFP, and 0.9 fM for thrombin, which are better than many reported results. The simultaneous and sensitive analysis of CEA and AFP at two screen-printed carbon electrodes was also conducted by our protocol.

  7. Identification and Characterization of Putative Integron-Like Elements of the Heavy-Metal-Hypertolerant Strains of Pseudomonas spp.

    Science.gov (United States)

    Ciok, Anna; Adamczuk, Marcin; Bartosik, Dariusz; Dziewit, Lukasz

    2016-11-28

    Pseudomonas strains isolated from the heavily contaminated Lubin copper mine and Zelazny Most post-flotation waste reservoir in Poland were screened for the presence of integrons. This analysis revealed that two strains carried homologous DNA regions composed of a gene encoding a DNA_BRE_C domain-containing tyrosine recombinase (with no significant sequence similarity to other integrases of integrons) plus a three-component array of putative integron gene cassettes. The predicted gene cassettes encode three putative polypeptides with homology to (i) transmembrane proteins, (ii) GCN5 family acetyltransferases, and (iii) hypothetical proteins of unknown function (homologous proteins are encoded by the gene cassettes of several class 1 integrons). Comparative sequence analyses identified three structural variants of these novel integron-like elements within the sequenced bacterial genomes. Analysis of their distribution revealed that they are found exclusively in strains of the genus Pseudomonas .

  8. Adsorption of arsenic(V) by iron-oxide-coated diatomite (IOCD).

    Science.gov (United States)

    Pan, Yi-Fong; Chiou, Cary T; Lin, Tsair-Fuh

    2010-09-01

    PURPOSES AND AIMS: Economically efficient methods for removing arsenic from the drinking water supply are urgently needed in many parts of the world. Iron oxides are known to have a strong affinity for arsenic in water. However, they are commonly present in the forms of fine powder or floc, which limits their utility in water treatment. In this study, a novel granular adsorbent, iron-oxide-coated diatomite (IOCD), was developed and examined for its adsorption of arsenic from water. An industrial-grade diatomite was used as the iron oxide support. The diatomite was first acidified and dried and then coated with iron oxide up to five times. The prepared IOCD samples were characterized for their morphology, composition, elemental content, and crystal properties by various instruments. Experiments of equilibrium and kinetic adsorption of As(V) on IOCD were conducted using 0.1- and 2-L polyethylene bottles, respectively, at different pH and temperatures. Iron oxide (alpha-Fe(2)O(3) hematite) coated onto diatomite greatly improves (by about 30 times) the adsorption of As(V) from water by IOCD as compared to using raw diatomite. This improvement was attributed to increases in both surface affinity and surface area of the IOCD. The surface area of IOCD increased to an optimal value. However, as the IOCD surface area (93 m(2)/g) was only 45% higher than that of raw diatomite (51 m(2)/g), the enhanced As(V) adsorption resulted primarily from the enhanced association of negatively charged As(V) ions with the partial positive surface charge of the iron oxide. The As(V) adsorption decreased when the solution pH was increased from 3.5 to 9.5, as expected from the partial charge interaction between As(V) and IOCD. The adsorption data at pH 5.5 and 7.5 could be well fitted to the Freundlich equation. A moderately high exothermic heat was observed for the As(V) adsorption, with the calculated molar isosteric heat ranging from -4 to -9 kcal/mol. The observed heats fall between those

  9. Mapping of immunogenic and protein-interacting regions at the surface of the seven-bladed β-propeller domain of the HIV-1 cellular interactor EED

    Directory of Open Access Journals (Sweden)

    Gouet Patrice

    2008-02-01

    Full Text Available Abstract Background The human EED protein, a member of the superfamily of Polycomb group proteins, is involved in multiple cellular protein complexes. Its C-terminal domain, which is common to the four EED isoforms, contains seven repeats of a canonical WD-40 motif. EED is an interactor of three HIV-1 proteins, matrix (MA, integrase (IN and Nef. An antiviral activity has been found to be associated with isoforms EED3 and EED4 at the late stage of HIV-1 replication, due to a negative effect on virus assembly and genomic RNA packaging. The aim of the present study was to determine the regions of the EED C-terminal core domain which were accessible and available to protein interactions, using three-dimensional (3D protein homology modelling with a WD-40 protein of known structure, and epitope mapping of anti-EED antibodies. Results Our data suggested that the C-terminal domain of EED was folded as a seven-bladed β-propeller protein. During the completion of our work, crystallographic data of EED became available from co-crystals of the EED C-terminal core with the N-terminal domain of its cellular partner EZH2. Our 3D-model was in good congruence with the refined structural model determined from crystallographic data, except for a unique α-helix in the fourth β-blade. More importantly, the position of flexible loops and accessible β-strands on the β-propeller was consistent with our mapping of immunogenic epitopes and sites of interaction with HIV-1 MA and IN. Certain immunoreactive regions were found to overlap with the EZH2, MA and IN binding sites, confirming their accessibility and reactivity at the surface of EED. Crystal structure of EED showed that the two discrete regions of interaction with MA and IN did not overlap with each other, nor with the EZH2 binding pocket, but were contiguous, and formed a continuous binding groove running along the lateral face of the β-propeller. Conclusion Identification of antibody-, MA-, IN- and EZH2

  10. Ce-Fe-modified zeolite-rich tuff to remove Ba(2+)-like (226)Ra(2+) in presence of As(V) and F(-) from aqueous media as pollutants of drinking water.

    Science.gov (United States)

    Olguín, María Teresa; Deng, Shuguang

    2016-01-25

    The sorption behavior of the Ba(2+)-like (226)Ra(2+) in the presence of H2AsO4(-)/HAsO4(2-) and F(-) from aqueous media using Ce-Fe-modified zeolite-rich tuff was investigated in this work. The Na-modified zeolite-rich tuff was also considered for comparison purposes. The zeolite-rich tuff collected from Wyoming (US) was in contact with NaCl and CeCl3-FeCl3 solutions to obtain the Na- and Ce-Fe-modified zeolite-rich tuffs (ZUSNa and ZUSCeFe). These zeolites were characterized by scanning electron microscopy and X-ray diffraction. The BET-specific surface and the points of zero charge were determined as well as the content of Na, Ce and Fe by neutron activation analysis. The textural characteristics and the point of zero charge were changed by the presence of Ce and Fe species in the zeolitic network. A linear model described the Ba(2+)-like (226)Ra(2+) sorption isotherms and the distribution coefficients (Kd) varied with respect to the metallic species present in the zeolitic material. The As(V) oxianionic chemical species and F(-) affected this parameter when the Ba(2+)-like (226)Ra(2+)-As(V)-F(-) solutions were in contact with ZUSCeFe. The H2AsO4(-)/HAsO4(2-) and F(-) were adsorbed by ZUSCeFe in the same amount, independent of the concentration of Ba(2+)-like (226)Ra(2+) in the initial solution. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. Effects of pH and Competing Anions on the Solution Speciation of Arsenic by Ion Exchange Resins

    Energy Technology Data Exchange (ETDEWEB)

    Impellitteri, Christopher A.; Ryan, JAmes A.; Al-Abed, Souhail R.; Scheckel, Kirk G.; Randall, Paul M.; Richardson, Collin A.

    2003-03-26

    Anion-exchange resins (AER) are used to differentiate As(V) and As(III) by retaining As(V) and allowing As(III) to pass through. AERs allow rapid speciation of As in the field which precludes the effects of sample preservation on As speciation. Aqueous environmental samples contain anions that may interfere with the speciation of As. This study compares the speciation of As by two commercially available AERs. A silica-based AER was selected for further study. As(V) and As(III) were passed through the AER in the presence of NO3 -, SO4 2-, HPO4 2-, Cl- and HCO3 - at pH 4, 6 and 8. Recoveries of As species in mixed systems range between 90 to 100%. Breakthrough curves for As(V) are presented which allow calculation of loading rates. HPO4 2- has the greatest effect on the speciation of As by AER.

  12. A prospective multicenter clinical feasibility study of a new automatic speaking valve for postlaryngectomy voice rehabilitation

    NARCIS (Netherlands)

    Lansaat, L.; de Kleijn, B. J.; Hilgers, F. J. M.; van der Laan, B. F. A. M.; van den Brekel, M. W. M.

    Evaluation of short- and long-term clinical feasibility and exploration of limitations and advantages of a new automatic speaking valve (ASV) for laryngectomized patients with integrated HME, the Provox FreeHands FlexiVoice (FlexiVoice). This ASV not only enables automatic, but also manual closure

  13. Arsenic speciation in water by precipitation with APDC and EDXRF measurements

    International Nuclear Information System (INIS)

    Valcarcel, L.; Estevez, J.; Montero, A.; Pupo, I.

    2006-01-01

    A method for the determination of As (III) by precipitation with APDC and EDXRF measurements was developed. A reduction step with sodium thiosulphate is necessary in order to determine the As(V) concentration. Recoveries of As(III) and As(V) were approximately 95-96%

  14. Remediation of organic and inorganic arsenic contaminated groundwater using a nanocrystalline TiO{sub 2}-based adsorbent

    Energy Technology Data Exchange (ETDEWEB)

    Jing Chuanyong, E-mail: cyjing@rcees.ac.c [State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing 100085 (China); Center for Environmental Systems, Stevens Institute of Technology, Hoboken, NJ 07030 (United States); Meng Xiaoguang; Calvache, Edwin [Center for Environmental Systems, Stevens Institute of Technology, Hoboken, NJ 07030 (United States); Jiang Guibin [State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing 100085 (China)

    2009-08-15

    A nanocrystalline TiO{sub 2}-based adsorbent was evaluated for the simultaneous removal of As(V), As(III), monomethylarsonic acid (MMA), and dimethylarsinic acid (DMA) in contaminated groundwater. Batch experimental results show that As adsorption followed pseudo-second order rate kinetics. The competitive adsorption was described with the charge distribution multi-site surface complexation model (CD-MUSIC). The groundwater containing an average of 329 mug L{sup -1} As(III), 246 mug L{sup -1} As(V), 151 mug L{sup -1} MMA, and 202 mug L{sup -1} DMA was continuously passed through a TiO{sub 2} filter at an empty bed contact time of 6 min for 4 months. Approximately 11 000, 14 000, and 9900 bed volumes of water had been treated before the As(III), As(V), and MMA concentration in the effluent increased to 10 mug L{sup -1}. However, very little DMA was removed. The EXAFS results demonstrate the existence of a bidentate binuclear As(V) surface complex on spent adsorbent, indicating the oxidation of adsorbed As(III). - A nanocrystalline TiO{sub 2}-based adsorbent could be used for the simultaneous removal of As(V), As(III), MMA, and DMA in contaminated groundwater.

  15. [Efficacy of dolutegravir in treatment-experienced patients: the SAILING and VIKING trials].

    Science.gov (United States)

    Moreno, Santiago; Berenguer, Juan

    2015-03-01

    Dolutegravir is an HIV integrase inhibitor with a high genetic barrier to resistance and is active against raltegravir- and/or elvitegravir-resistant strains. The clinical development of dolutegravir for HIV infection rescue therapy is based on 3 clinical trials. In the SAILING trial, dolutegravir (5 mg once daily) in combination with 2 other antiretroviral agents was well tolerated and showed greater virological effect than raltegravir (400 mg twice daily) in the treatment of integrase inhibitor-naïve adults with virological failure infected with HIV strains with at least two-class drug resistance. The VIKING studies were designed to evaluate the efficacy of dolutegravir as rescue therapy in treatment-experienced patients infected with HIV strains with resistance mutations to raltegravir and/or elvitegravir. VIKING-1-2 was a dose-ranging phase IIb trial. VIKING-3 was a phase III trial in which dolutegravir (50 mg twice daily) formed part of an optimized regimen and proved safe and effective in this difficult-to-treat group of patients. Dolutegravir is the integrase inhibitor of choice for rescue therapy in multiresistant HIV infection, both in integrase inhibitor-naïve patients and in those previously treated with raltegravir or elvitegravir. Copyright © 2015 Elsevier España, S.L.U. All rights reserved.

  16. Requirement for Vibrio cholerae integration host factor in conjugative DNA transfer.

    Science.gov (United States)

    McLeod, Sarah M; Burrus, Vincent; Waldor, Matthew K

    2006-08-01

    The requirement for host factors in the transmission of integrative and conjugative elements (ICEs) has not been extensively explored. Here we tested whether integration host factor (IHF) or Fis, two host-encoded nucleoid proteins, are required for transfer of SXT, a Vibrio cholerae-derived ICE that can be transmitted to many gram-negative species. Fis did not influence the transfer of SXT to or from V. cholerae. In contrast, IHF proved to be required for V. cholerae to act as an SXT donor. In the absence of IHF, V. cholerae displayed a modest defect for serving as an SXT recipient. Surprisingly, SXT integration into or excision from the V. cholerae chromosome, which requires an SXT-encoded integrase related to lambda integrase, did not require IHF. Therefore, the defect in SXT transmission in the V. cholerae IHF mutant is probably not related to IHF's ability to promote DNA recombination. The V. cholerae IHF mutant was also highly impaired as a donor of RP4, a broad-host-range conjugative plasmid. Thus, the V. cholerae IHF mutant appears to have a general defect in conjugation. Escherichia coli IHF mutants were not impaired as donors or recipients of SXT or RP4, indicating that IHF is a V. cholerae-specific conjugation factor.

  17. Rapid arsenic(V)-reduction by fire in schwertmannite-rich soil enhances arsenic mobilisation

    DEFF Research Database (Denmark)

    Johnston, Scott G.; Bennett, William W.; Burton, Edward D.

    2018-01-01

    (III) formation (∼90%) within 5–10 min at 400–600 °C, followed by partial re-oxidation to As(V) thereafter. In contrast, heating As(V)-schwertmannite in the absence of soil-organic matter did not cause reduction of As(V) or Fe(III), nor form maghemite; thus highlighting the critical role of organic matter......Arsenic in acid sulfate soil (ASS) landscapes commonly associates with schwertmannite, a poorly crystalline Fe(III) mineral. Fires in ASS landscapes can thermally transform Fe(III) minerals to more crystalline phases, such as maghemite (γFe2O3). Although thermal genesis of maghemite requires...... and hematite at temperatures above 300–400 °C, with some transitory formation of magnetite, and electrons are readily transferred to both Fe(III) and As(V). As(V) reduction to As(III) is influenced by a combination of temperature, heating duration and carbon content and is significantly (P

  18. Digital simulation of anodic stripping voltammetry from thin film electrodes

    International Nuclear Information System (INIS)

    Magallanes, J.F.

    1984-01-01

    The anodic stripping voltammetry (ASV) is routinely applied to control of Cu(II) in heavy water in the primary cooling loop of the Nuclear Power Reactor. The anodic stripping voltammetry (ASV) is a very well-known technique in electroanalytical chemistry. However, due to the complexity of the phenomena, it is practised with the fundamentals of empiric considerations. A geometric model for the anodic stripping voltammetry (ASV) from thin film electrodes which can be calculated by explicit digital simulation method is proposed as a possibility of solving the electrochemically reversible, cuasi-reversible and irreversible reactions under linear potential scan and multiple potential scans. (Until now the analytical mathematical method was applied to reversible reactions). All the results are compared with analytical solutions and experimental results and it permits to conclude that the anodic stripping voltammetry (ASV) can be studied with the simplicity and potentialities of explicit digital simulation methods. (M.E.L.) [es

  19. Cost Effectiveness of Daclatasvir/Asunaprevir Versus Peginterferon/Ribavirin and Protease Inhibitors for the Treatment of Hepatitis c Genotype 1b Naïve Patients in Chile.

    Directory of Open Access Journals (Sweden)

    Constanza L Vargas

    Full Text Available Daclatasvir and Asunaprevir (DCV/ASV have recently been approved for the treatment of chronic hepatitis C virus infection. In association, they are more effective and safer than previous available treatments, but more expensive. It is unclear if paying for the additional costs is an efficient strategy considering limited resources.A Markov model was built to estimate the expected costs in Chilean pesos (CL$ and converted to US dollars (US$ and benefits in quality adjusted life years (QALYs in a hypothetic cohort of naive patients receiving DCV/ASV compared to protease inhibitors (PIs and Peginterferon plus Ribavirin (PR. Efficacy was obtained from a mixed-treatment comparison study and costs were estimated from local sources. Utilities were obtained applying the EQ-5D survey to local patients and then valued with the Chilean tariff. A time horizon of 46 years and a discount rate of 3% for costs and outcomes was considered. The ICERs were estimated for a range of DCV/ASV prices. Deterministic and probabilistic sensitivity analyses were performed.PIs were extendedly dominated by DCV/ASV. The ICER of DCV/ASV compared to PR was US$ 16,635/QALY at a total treatment price of US$ 77,419; US$11,581 /QALY at a price of US$ 58,065; US$ 6,375/QALY at a price of US$ 38,710; and US$ 1,364 /QALY at a price of US$ 19,355. The probability of cost-effectiveness at a price of US$ 38,710 was 91.6% while there is a 21.43% probability that DCV/ASV dominates PR if the total treatment price was US$ 19,355. Although the results are sensitive to certain parameters, the ICER did not increase above the suggested threshold of 1 GDP per capita.DCV/ASV can be considered cost-effective at any price of the range studied. These results provide decision makers useful information about the value of incorporating these drugs into the public Chilean healthcare system.

  20. Association between Childhood Sexual Abuse and Adult Sexual Victimization in a Representative Sample in Hong Kong Chinese

    Science.gov (United States)

    Chan, Ko Ling

    2011-01-01

    Objective: The current study investigated the prevalence and impact of childhood sexual abuse (CSA) on adult sexual victimization (ASV) in Hong Kong, China. This study also examines correlates of demographic characteristics, depression, suicidal ideation, and self-esteem with ASV. Methods: A total of 5,049 Chinese adult respondents were…

  1. Towards novel therapeutics for HIV through fragment-based screening and drug design.

    Science.gov (United States)

    Tiefendbrunn, Theresa; Stout, C David

    2014-01-01

    Fragment-based drug discovery has been applied with varying levels of success to a number of proteins involved in the HIV (Human Immunodeficiency Virus) life cycle. Fragment-based approaches have led to the discovery of novel binding sites within protease, reverse transcriptase, integrase, and gp41. Novel compounds that bind to known pockets within CCR5 have also been identified via fragment screening, and a fragment-based approach to target the TAR-Tat interaction was explored. In the context of HIV-1 reverse transcriptase (RT), fragment-based approaches have yielded fragment hits with mid-μM activity in an in vitro activity assay, as well as fragment hits that are active against drug-resistant variants of RT. Fragment-based drug discovery is a powerful method to elucidate novel binding sites within proteins, and the method has had significant success in the context of HIV proteins.

  2. Impacts of environmental factors on arsenate biotransformation and release in Microcystis aeruginosa using the Taguchi experimental design approach.

    Science.gov (United States)

    Wang, Zhenhong; Luo, Zhuanxi; Yan, Changzhou; Xing, Baoshan

    2017-07-01

    Very limited information is available on how and to what extent environmental factors influence arsenic (As) biotransformation and release in freshwater algae. These factors include concentrations of arsenate (As(V)), dissolved inorganic nitrogen (N), phosphate (P), and ambient pH. This study conducted a series of experiments using Taguchi methods to determine optimum conditions for As biotransformation. We assessed principal effective factors of As(V), N, P, and pH and determined that As biotransformation and release actuate at 10.0 μM As(V) in dead alga cells, the As efflux ratio and organic As efflux content actuate at 1.0 mg/L P, algal growth and intracellular arsenite (As(III)) content actuate at 10.0 mg/L N, and the total sum of As(III) efflux from dead alga cells actuates at a pH level of 10. Moreover, N is the critical component for As(V) biotransformation in M. aeruginosa, specifically for As(III) transformation, because N can accelerate algal growth, subsequently improving As(III) accumulation and its efflux, which results in an As(V) to As(III) reduction. Furthermore, low P concentrations in combination with high N concentrations promote As accumulation. Following As(V), P was the primary impacting factor for As accumulation. In addition, small amounts of As accumulation under low concentrations of As and high P were securely stored in living algal cells and were easily released after cell death. Results from this study will help to assess practical applications and the overall control of key environmental factors, particularly those associated with algal bioremediation in As polluted water. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Outcomes of treatment with daclatasvir and asunaprevir for recurrent hepatitis C after liver transplantation.

    Science.gov (United States)

    Honda, Masaki; Sugawara, Yasuhiko; Watanabe, Takehisa; Tateyama, Masakuni; Tanaka, Motohiko; Uchida, Koushi; Kawabata, Seiichi; Yoshii, Daiki; Miura, Kouhei; Isono, Kaori; Hayashida, Shintaro; Ohya, Yuki; Yamamoto, Hidekazu; Sasaki, Yutaka; Inomata, Yukihiro

    2017-10-01

    The development of direct-acting oral agents has dramatically changed the treatment strategy of hepatitis C virus (HCV) infection. Here we aimed to reveal the efficacy and safety of daclatasvir (DCV) and asunaprevir (ASV) for recurrent HCV genotype 1 infection after liver transplantation (LT). A retrospective study was undertaken on nine patients who underwent a 24-week DCV/ASV treatment regimen for recurrent HCV genotype 1 infection. Five of the patients were men; four had failed treatment with pegylated interferon (Peg-IFN)/ribavirin, two had failed simeprevir/Peg-IFN/ribavirin, one had the resistance-associated variant Y93H in the NS5A region, and one underwent maintenance dialysis. Median time to treatment initiation following LT was 70 months. Of the nine patients treated with DCV/ASV, eight (88.9%) achieved a sustained viral response 12 weeks after completion of therapy (SVR12). The patient with virologic failure had failed simeprevir/Peg-interferon/ribavirin therapy 4 months before undergoing the DCV/ASV treatment regimen. In addition, a resistance-associated variant D168E in the NS3 region was detected in the patient after discontinuation of the DCV/ASV regimen. The trough level of tacrolimus tended to decrease, and renal function showed no significant changes during treatment. Adverse events occurred in two patients (22.2%), but no severe adverse events occurred during treatment. The DCV/ASV regimen was well tolerated, resulting in high rates of sustained viral response 12 weeks after completion of therapy for LT patients with recurrent HCV genotype 1 infection. © 2016 The Japan Society of Hepatology.

  4. Treatment of sleep apnea in chronic heart failure patients with auto-servo ventilation improves sleep fragmentation: a randomized controlled trial.

    Science.gov (United States)

    Hetzenecker, Andrea; Escourrou, Pierre; Kuna, Samuel T; Series, Frederic; Lewis, Keir; Birner, Christoph; Pfeifer, Michael; Arzt, Michael

    2016-01-01

    Impaired sleep efficiency is independently associated with worse prognosis in patients with chronic heart failure (CHF). Therefore, a test was conducted on whether auto-servo ventilation (ASV, biphasic positive airway pressure [BiPAP]-ASV, Philips Respironics) reduces sleep fragmentation and improves sleep efficiency in CHF patients with central sleep apnea (CSA) or obstructive sleep apnea (OSA). In this multicenter, randomized, parallel group trial, a study was conducted on 63 CHF patients (age 64 ± 10 years; left ventricular ejection fraction 29 ± 7%) with CSA or OSA (apnea-hypopnea Index, AHI 47 ± 18/h; 46% CSA) referred to sleep laboratories of the four participating centers. Participants were randomized to either ASV (n = 32) or optimal medical treatment alone (control, n = 31). Polysomnography (PSG) and actigraphy at home (home) with centralized blinded scoring were obtained at baseline and 12 weeks. ASV significantly reduced sleep fragmentation (total arousal indexPSG: -16.4 ± 20.6 vs. -0.6 ± 13.2/h, p = 0.001; sleep fragmentation indexhome: -7.6 ± 15.6 versus 4.3 ± 13.9/h, p = 0.003, respectively) and significantly increased sleep efficiency assessed by actigraphy (SEhome) compared to controls (2.3 ± 10.1 vs. -2.1 ± 6.9%, p = 0.002). Effects of ASV on sleep fragmentation and efficiency were similar in patients suffering from OSA and CSA. At home, ASV treatment modestly improves sleep fragmentation as well as sleep efficiency in CHF patients having either CSA or OSA. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. Low dose versus high dose anti-snake venom therapy in the treatment of haematotoxic snake bite in South India.

    Science.gov (United States)

    Joseph, Imanto M; Kuriakose, Cijoy K; Dev, Anand Vimal; Philip, George A

    2017-10-01

    Most of the studies on the appropriate dose of anti-snake venom (ASV) are from tertiary hospitals and the guidelines are unclear. Our observational study compared the outcomes of two prevalent treatment regimes for haematotoxic snake bite in a secondary care hospital in South India. The time to normalisation of whole blood clotting time, mortality and complications were not different between the groups. The average dose of ASV required in the low and high dose groups were 106 mL and 246 mL, respectively. Consequently, patients who received low dose ASV incurred approximately 50% less expense. Urticarial rashes were also significantly fewer in the low dose group.

  6. A prospective comparison of the efficacy and safety of fully closed ...

    African Journals Online (AJOL)

    We conducted a within-group comparison of three modes of ventilation, ASV, Intellivent-ASV and SIMV, using a Hamilton S1 ventilator (Hamilton Medical, Switzerland). Subjects were ventilated for 2 hours on each mode, and at the end of each 2-hour period, parameters of ventilation and haemodynamics were measured.

  7. Inverse correlation between promoter strength and excision activity in class 1 integrons.

    Directory of Open Access Journals (Sweden)

    Thomas Jové

    2010-01-01

    Full Text Available Class 1 integrons are widespread genetic elements that allow bacteria to capture and express gene cassettes that are usually promoterless. These integrons play a major role in the dissemination of antibiotic resistance among Gram-negative bacteria. They typically consist of a gene (intI encoding an integrase (that catalyzes the gene cassette movement by site-specific recombination, a recombination site (attI1, and a promoter (Pc responsible for the expression of inserted gene cassettes. The Pc promoter can occasionally be combined with a second promoter designated P2, and several Pc variants with different strengths have been described, although their relative distribution is not known. The Pc promoter in class 1 integrons is located within the intI1 coding sequence. The Pc polymorphism affects the amino acid sequence of IntI1 and the effect of this feature on the integrase recombination activity has not previously been investigated. We therefore conducted an extensive in silico study of class 1 integron sequences in order to assess the distribution of Pc variants. We also measured these promoters' strength by means of transcriptional reporter gene fusion experiments and estimated the excision and integration activities of the different IntI1 variants. We found that there are currently 13 Pc variants, leading to 10 IntI1 variants, that have a highly uneven distribution. There are five main Pc-P2 combinations, corresponding to five promoter strengths, and three main integrases displaying similar integration activity but very different excision efficiency. Promoter strength correlates with integrase excision activity: the weaker the promoter, the stronger the integrase. The tight relationship between the aptitude of class 1 integrons to recombine cassettes and express gene cassettes may be a key to understanding the short-term evolution of integrons. Dissemination of integron-driven drug resistance is therefore more complex than previously thought.

  8. Spectrophotometric determination of low levels arsenic species in beverages after ion-pairing vortex-assisted cloud-point extraction with acridine red.

    Science.gov (United States)

    Altunay, Nail; Gürkan, Ramazan; Kır, Ufuk

    2016-01-01

    A new, low-cost, micellar-sensitive and selective spectrophotometric method was developed for the determination of inorganic arsenic (As) species in beverage samples. Vortex-assisted cloud-point extraction (VA-CPE) was used for the efficient pre-concentration of As(V) in the selected samples. The method is based on selective and sensitive ion-pairing of As(V) with acridine red (ARH(+)) in the presence of pyrogallol and sequential extraction into the micellar phase of Triton X-45 at pH 6.0. Under the optimised conditions, the calibration curve was highly linear in the range of 0.8-280 µg l(-1) for As(V). The limits of detection and quantification of the method were 0.25 and 0.83 µg l(-1), respectively. The method was successfully applied to the determination of trace As in the pre-treated and digested samples under microwave and ultrasonic power. As(V) and total As levels in the samples were spectrophotometrically determined after pre-concentration with VA-CPE at 494 nm before and after oxidation with acidic KMnO4. The As(III) levels were calculated from the difference between As(V) and total As levels. The accuracy of the method was demonstrated by analysis of two certified reference materials (CRMs) where the measured values for As were statistically within the 95% confidence limit for the certified values.

  9. Arsenate biotransformation by Microcystis aeruginosa under different nitrogen and phosphorus levels.

    Science.gov (United States)

    Che, Feifei; Du, Miaomiao; Yan, Changzhou

    2018-04-01

    The arsenate (As(V)) biotransformation by Microcystis aeruginosa in a medium with different concentrations of nitrogen (N) and phosphorus (P) has been studied under laboratory conditions. When 15μg/L As(V) was added, N and P in the medium showed effective regulation on arsenic (As) metabolism in M. aeruginosa, resulting in significant differences in the algal growth among different N and P treatments. Under 0.2mg/L P treatment, increases in N concentration (4-20mg/L) significantly stimulated the cell growth and therefore indirectly enhanced the production of dimethylarsinic acid (DMA), the main As metabolite, accounting for 71%-79% of the total As in the medium. Meanwhile, 10-20mg/L N treatments accelerated the ability of As metabolization by M. aeruginosa, leading to higher contents of DMA per cell. However, As(V) uptake by M. aeruginosa was significantly impeded by 0.5-1.0mg/L P treatment, resulting in smaller rates of As transformation in M. aeruginosa as well as lower contents of As metabolites in the medium. Our data demonstrated that As(V) transformation by M. aeruginosa was significantly accelerated by increasing N levels, while it was inhibited by increasing P levels. Overall, both P and N play key roles in As(V) biotransformation processes. Copyright © 2017. Published by Elsevier B.V.

  10. Indirect spectrophotometric determination of small amounts of selenium(IV) and arsenic(V) by simple extraction using flotation columns.

    Science.gov (United States)

    Mostafa, G A; Ghazy, S E

    2001-10-01

    A simple, rapid and selective procedure for the indirect spectrophotometric determination of Se(IV) and As(V) has been developed. It is based on the reduction of Se(IV) to Se(0) and As(V) to As(III) with hydroiodic acid (KI + HCl). The liberated iodine, equivalent to each analyte, is quantitatively extracted with oleic acid (HOL) surfactant. The iodine-HOL system exhibits its maximum absorbance at 435 nm. The different analytical parameters affecting the extraction and determination processes have been examined. The calibration graphs were found to be linear over the ranges 5-120 and 0.25-20 ppm of Se(IV) and As(V), with lower detection limits of 2.5 and 0.15 ppm and molar absorptivities of 1 x 10(4) and 0.5 x 10(4) dm3 mol(-1) cm(-1), respectively. Sandell's sensitivity was calculated to be 0.0078 and 0.0149 microg/cm2 in the same order. The relative standard deviation for five replicate analyses of 40 ppm Se(IV) and 4 ppm As(V) were 1.0 and 0.9%, respectively. The proposed procedure in the presence of EDTA as a masking agent for foreign ions has been successfully applied to the determination of Se(IV) in a reference sample and As(V) in copper metal, in addition to their determination in spiked and polluted water samples.

  11. Arsenic Removal from Aqueous Solutions Using Modified and Unmodified Oak Sawdust

    Directory of Open Access Journals (Sweden)

    Ali Reza Rahmani

    2016-01-01

    Full Text Available In this research, oak sawdust, in both modified and unmodified forms, was used as an economical and low-cost material for the removal of arsenic from aqueous solutions. For this purpose, arsenic synthetic samples were prepared using NaAsO2 in distilled water and the effects of pH, adsorbent dosage, contact time, and initial As(V concentration were investigated on As(V adsorption using the adsorbents prepared. The results showed that modified sawdust achieved the highest efficiency (>91% over a contact time of 60 min and at pH 7 when the adsorbent dosage was 4gr/L and the initial As(V concentration was 150 µg/L. The data from both adsorbents fitted well to the Langmuir isotherm. Under optimum conditions (an initial As(V concentration of 150 µg/L and optimal absorption pH, contact time, and adsorbent dosage, maximum As(V removal efficiencies were 93.85% and 91.034% with the modified  and unmodified sawdust adsorbents, respectively. Given the availability and low cost of the adsorbent used and the high removal efficiency obtained at  lower adsorbent dosages and contact times, the modified oak sawdust may be recommended as an effective adsorbent for the removal of arsenic (v from aqueous solutions, especially since it requires no need for pH modification.

  12. Molecular study on some antibiotic resistant genes in Salmonella spp. isolates

    Science.gov (United States)

    Nabi, Ari Q.

    2017-09-01

    Studying the genes related with antimicrobial resistance in Salmonella spp. is a crucial step toward a correct and faster treatment of infections caused by the pathogen. In this work Integron mediated antibiotic resistant gene IntI1 (Class I Integrase IntI1) and some plasmid mediated antibiotic resistance genes (Qnr) were scanned among the isolated non-Typhoid Salmonellae strains with known resistance to some important antimicrobial drugs using Sybr Green real time PCR. The aim of the study was to correlate the multiple antibiotics and antimicrobial resistance of Salmonella spp. with the presence of integrase (IntI1) gene and plasmid mediated quinolone resistant genes. Results revealed the presence of Class I Integrase gene in 76% of the isolates with confirmed multiple antibiotic resistances. Moreover, about 32% of the multiple antibiotic resistant serotypes showed a positive R-PCR for plasmid mediated qnrA gene encoding for nalidixic acid and ciprofloxacin resistance. No positive results could be revealed form R-PCRs targeting qnrB or qnrS. In light of these results we can conclude that the presence of at least one of the qnr genes and/or the presence of Integrase Class I gene were responsible for the multiple antibiotic resistance to for nalidixic acid and ciprofloxacin from the studied Salmonella spp. and further studies required to identify the genes related with multiple antibiotic resistance of the pathogen.

  13. Arsenic and fluoride removal from contaminated drinking water with Haix-Fe-Zr and Haix-Zr resin beads.

    Science.gov (United States)

    Phillips, Debra H; Sen Gupta, Bhaskar; Mukhopadhyay, Soumyadeep; Sen Gupta, Arup K

    2018-06-01

    The objective of the study was to carry-out batch tests to examine the effectiveness of Haix-Fe-Zr and Haix-Zr resin beads in the removal of As(III), As(V) and F - from groundwater with a similar geochemistry to a site where a community-based drinking water plant has been installed in West Bengal, India. The groundwater was spiked separately with ∼200 μg/L As(III) and As(V) and 5 mg/L F - . Haix-Zr resin beads were more effective than Haix-Fe-Zr resin beads in removing As(III) and As(V). Haix-Zr resin beads showed higher removal of As(V) compared to As(III). Haix-Zr resin beads removed As(V) below the WHO (10 μg/L) drinking water standards at 8.79 μg/L after 4 h of shaking, while As(III) was reduced to 7.72 μg/L after 8 h of shaking. Haix-Fe-Zr resin beads were more effective in removing F - from the spiked groundwater compared to Haix-Zr resin beads. Concentrations of F - decreased from 6.27 mg/L to 1.26 mg/L, which is below the WHO drinking water standards (1.5 mg/L) for F - , after 15 min of shaking with Haix-Fe-Zr resin beads. After 20 min of shaking in groundwater treated with Haix-Zr resin beads, F - concentrations decreased from 6.27 mg/L to 1.43 mg/L. In the removal of As(III), As(V), and F - from the groundwater, Haix-Fe-Zr and Haix-Zr resin beads fit the parabolic diffusion equation (PDE) suggesting that adsorption of these contaminants was consistent with inter-particle diffusion. Copyright © 2018 Elsevier Ltd. All rights reserved.

  14. Interactions between arsenic species and marine algae

    Energy Technology Data Exchange (ETDEWEB)

    Sanders, J.G.

    1978-01-01

    The arsenic concentration and speciation of marine algae varies widely, from 0.4 to 23 ng.mg/sup -1/, with significant differences in both total arsenic content and arsenic speciation occurring between algal classes. The Phaeophyceae contain more arsenic than other algal classes, and a greater proportion of the arsenic is organic. The concentration of inorganic arsenic is fairly constant in macro-algae, and may indicate a maximum level, with the excess being reduced and methylated. Phytoplankton take up As(V) readily, and incorporate a small percentage of it into the cell. The majority of the As(V) is reduced, methylated, and released to the surrounding media. The arsenic speciation in phytoplankton and Valonia also changes when As(V) is added to cultures. Arsenate and phosphate compete for uptake by algal cells. Arsenate inhibits primary production at concentrations as low as 5 ..mu..g.1/sup -1/ when the phosphate concentration is low. The inhibition is competitive. A phosphate enrichment of > 0.3 ..mu..M alleviates this inhibition; however, the As(V) stress causes an increase in the cell's phosphorus requirement. Arsenite is also toxic to phytoplankton at similar concentrations. Methylated arsenic species did not affect cell productivity, even at concentrations of 25 ..mu..g.1/sup -1/. Thus, the methylation of As(V) by the cell produces a stable, non-reactive compound which is nontoxic. The uptake and subsequent reduction and methylation of As(V) is a significant factor in determining the arsenic biogeochemistry of productive systems, and also the effect that the arsenic may have on algal productivity. Therefore, the role of marine algae in determining the arsenic speciation of marine systems cannot be ignored. (ERB)

  15. Comparison of two modes of ventilation after fast-track cardiac surgery: Adaptive support ventilation versus synchronized intermittent mandatory ventilation

    International Nuclear Information System (INIS)

    Aghadavoudi, O.

    2012-01-01

    Objective: There is substantial debate regarding the appropriate protocol for ventilatory management in fast-track cardiac anesthesia (FTCA). This study was carried out to assess and compare the risks and benefits of respiratory weaning based on adaptive support ventilation (ASV) and synchronized intermittent mandatory ventilation (SIMV) after uncomplicated cardiac surgery. Methodology: In a randomized clinical trial, after receiving approval of the Department Research Committee and informed consent from study subjects, 100 patients undergoing elective coronary artery bypass graft (CABG) surgery with cardiopulmonary bypass (CPB) were enrolled during a 4-month period at a university-based hospital. After surgery and admission to the intensive care unit (ICU), patients were randomized to ASV and SIMV groups. Arterial blood gas (ABG) and hemodynamic variables, respiratory and ventilator characteristics including lung compliance, rapid shallow breathing index (RSBI), tidal volume (TV), respiratory rate (RR), peak inspiratory pressure (P peak), mean airway pressure (p mean), Pao2/FIo2, duration of mechanical ventilation and tracheal intubation, and length of ICU stay were recorded and compared between the two groups. The data were analyzed in 82 patients after considering the exclusion criteria. Results: There were no differences between ASV and SIMV groups in demographics and preoperative characteristics. The duration of tracheal intubation and the length of ICU stay were similar in both groups. There were no statistically and clinically relevant differences between the two groups in ABG, hemodynamic changes, and respiratory and ventilator characteristics during ICU stay. Conclusion: Although ASV may facilitate postoperative respiratory management in FTCA, both ASV and SIMV provide similarly safe and practicable respiratory weaning in the cardiac ICU. The evaluation of potential advantages in patient outcomes and resource utilization of respiratory weaning based on ASV

  16. Preparation and certification of hijiki reference material, NMIJ CRM 7405-a, from the edible marine algae hijiki (Hizikia fusiforme).

    Science.gov (United States)

    Narukawa, Tomohiro; Inagaki, Kazumi; Zhu, Yanbei; Kuroiwa, Takayoshi; Narushima, Izumi; Chiba, Koichi; Hioki, Akiharu

    2012-02-01

    A certified reference material, NMIJ CRM 7405-a, for the determination of trace elements and As(V) in algae was developed from the edible marine hijiki (Hizikia fusiforme) and certified by the National Metrology Institute of Japan (NMIJ), the National Institute of Advanced Industrial Science and Technology (AIST). Hijiki was collected from the Pacific coast in the Kanto area of Japan, and was washed, dried, powdered, and homogenized. The hijiki powder was placed in 400 bottles (ca. 20 g each). The concentrations of 18 trace elements and As(V) were determined by two to four independent analytical techniques, including (ID)ICP-(HR)MS, ICP-OES, GFAAS, and HPLC-ICP-MS using calibration solutions prepared from the elemental standard solution of Japan calibration service system (JCSS) and the NMIJ CRM As(V) solution, and whose concentrations are certified and SI traceable. The uncertainties of all the measurements and preparation procedures were evaluated. The values of 18 trace elements and As(V) in the CRM were certified with uncertainty (k = 2).

  17. Extraction and determination of arsenic species in leafy vegetables: Method development and application.

    Science.gov (United States)

    Ma, Li; Yang, Zhaoguang; Kong, Qian; Wang, Lin

    2017-02-15

    Extraction of arsenic (As) species in leafy vegetables was investigated by different combinations of methods and extractants. The extracted As species were separated and determined by HPLC-ICP-MS method. The microwave assisted method using 1% HNO3 as the extractant exhibited satisfactory efficiency (>90%) at 90°C for 1.5h. The proposed method was applied for extracting As species from real leafy vegetables. Thirteen cultivars of leafy vegetables were collected and analyzed. The predominant species in all the investigated vegetable samples were As(III) and As(V). Moreover, both As(III) and As(V) concentrations were positive significant (p<0.01) correlated with total As (tAs) concentration. However, the percentage of As(V) reduced with tAs concentration increasing probably due to the conversion and transformation of As(V) to As(III) after uptake. The hazard quotient results indicated no particular risk to 94.6% of local consumers. Considerably carcinogenic risk by consumption of the leafy vegetables was observed. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. Effects of root anatomy and Fe plaque on arsenic uptake by rice seedlings grown in solution culture

    Energy Technology Data Exchange (ETDEWEB)

    Deng, Dan [Department of Environmental Sciences, East China Normal University, Shanghai (China); Croucher Institute for Environmental Sciences, and Department of Biology, Hong Kong Baptist University (Hong Kong); Wu Shengchun; Wu Fuyong [Croucher Institute for Environmental Sciences, and Department of Biology, Hong Kong Baptist University (Hong Kong); Deng Hong, E-mail: lilac_deng@yahoo.com.c [Department of Environmental Sciences, East China Normal University, Shanghai (China); Tiantong National Station of Forest Ecosystem, Key Laboratory of Urbanization and Ecological Restoration, East China Normal University, Shanghai 200062 (China); Wong Minghung, E-mail: mhwong@hkbu.edu.h [Croucher Institute for Environmental Sciences, and Department of Biology, Hong Kong Baptist University (Hong Kong)

    2010-08-15

    Hydroponic experiments were carried out to investigate the effects of root anatomy, induced by aeration and stagnation, and Fe plaque on arsenic (III and V) uptake and translocation by rice plants. The results showed that As uptake in rice plants (Gui Chao-2) treated by aeration was decreased due to lower root specific surface area. Rice roots with larger specific surface area tended to form more Fe plaque, and Fe plaque affected As uptake kinetics by changing As influx curves from linear to hyperbolic for As(III) and from hyperbolic to S-curve for As(V). Fe plaque increased As(III and V) adsorption and minimized the effects of root anatomy characteristics on As uptake into roots and subsequently translocation to shoots. Fe plaque increased As(III) uptake rate at As(III) concentrations of 0.5{approx}8 mg L{sup -1}, reduced As(V) uptake rate at low As(V) concentrations (<2 mg L{sup -1}), but increased As uptake rate at high As(V) concentrations (>6 mg L{sup -1}). - Rice root anatomy and Fe plaque affect As uptake.

  19. Metal accumulation, growth, antioxidants and oil yield of Brassica juncea L. exposed to different metals.

    Science.gov (United States)

    Sinha, Sarita; Sinam, Geetgovind; Mishra, Rohit Kumar; Mallick, Shekhar

    2010-09-01

    In agricultural fields, heavy metal contamination is responsible for limiting the crop productivity and quality. This study reports that the plants of Brassica juncea L. cv. Pusa bold grown on contaminated substrates [Cu, Cr(VI), As(III), As(V)] under simulated field conditions have shown translocation of metals to the upper part and its sequestration in the leaves without significantly affecting on oil yield, except for Cr and higher concentration of As(V), compared to control. Decrease in the oil content in As(V) treated plants was observed in a dose dependent manner; however, maximum decrease was recorded in Cr treated plants. Among all the metal treatments, Cr was the most toxic as evident from the decrease in oil content, growth parameters and antioxidants. The accumulation of metals was below the detection limit in the seeds grown on 10 and 30 mg kg(-1) As(III) and Cr(VI); 10 mg kg(-1) As(V)) and thus can be recommended only for oil cultivation. Copyright (c) 2010 Elsevier Inc. All rights reserved.

  20. Investigation of mechanism and critical parameters for removal of arsenic from water using Zr-TiO2 composite.

    Science.gov (United States)

    Anđelković, I; Amaizah, N R R; Marković, S B; Stanković, D; Marković, M; Kuzmanović, D; Roglić, G

    2017-09-01

    Using the microwave-hydrothermal method for the synthesis of composite, high surface density of hydroxyl groups, as an active adsorption sites for arsenic, was obtained. Adsorption mechanisms of As(III) and As(V) onto zirconium-doped titanium dioxide (Zr-TiO 2 ) were investigated and proposed using macroscopic and microscopic methods. Obtained results are suggesting inner-sphere and outer-sphere adsorption mechanisms for As(III) and As(V), respectively. This allowed us to identify parameters that are critical for the successful removal of arsenic from water, which is essential information for further optimization of the removal process. The composite was further applied for the removal of As(III) and As(V) from water in a dynamic flow through the reactor. Column study proved that the removal of both arsenic species below the value recommended by WHO can be achieved. Elution of As(III) and As(V) from the composite can be done by using small amounts of 0.01 M NaOH solution resulting in preconcentration of arsenic species and possible multiple usage of composite.

  1. Adaptive servo-ventilation therapy for patients with chronic heart failure in a confirmatory, multicenter, randomized, controlled study.

    Science.gov (United States)

    Momomura, Shin-Ichi; Seino, Yoshihiko; Kihara, Yasuki; Adachi, Hitoshi; Yasumura, Yoshio; Yokoyama, Hiroyuki; Wada, Hiroshi; Ise, Takayuki; Tanaka, Koichi

    2015-01-01

    Adaptive servo-ventilation (ASV) therapy is expected to be novel nonpharmacotherapy with hemodynamic effects on patients with chronic heart failure (CHF), but sufficient evidence has not been obtained. A 24-week, open-label, randomized, controlled study was performed to confirm the cardiac function-improving effect of ASV therapy on CHF patients. At 39 institutions, 213 outpatients with CHF, whose left ventricular ejection fraction (LVEF) was control group], respectively. The primary endpoint was LVEF, and the secondary endpoints were HF deterioration, B-type natriuretic peptide (BNP), and clinical composite response (CCR: NYHA class+HF deterioration). LVEF and BNP improved significantly at completion against the baseline values in the 2 groups. However, no significant difference was found between these groups. HF deterioration tended to be suppressed. The ASV group showed a significant improvement in CCR corroborated by significant improvements in NYHA class and ADL against the control group. Under the present study's conditions, ASV therapy was not superior to GDMT in the cardiac function-improving effect but showed a clinical status-improving effect, thus indicating a given level of clinical benefit.

  2. Investigation of arsenic removal in batch wise water treatments by means of sequential hydride generation flow injection analysis.

    Science.gov (United States)

    Toda, Kei; Takaki, Mari; Hashem, Md Abul

    2008-08-01

    Arsenic water pollution is a big issue worldwide. Determination of inorganic arsenic in each oxidation state is important because As(III) is much more toxic than As(V). An automated arsenic measurement system was developed based on complete vaporization of As by a sequential procedure and collection/preconcentration of the vaporized AsH(3), which was subsequently measured by a flow analysis. The automated sensitive method was applied to monitoring As(III) and As(V) concentrations in contaminated water standing overnight. Behaviors of arsenics were investigated in different conditions, and unique time dependence profiles were obtained. For example, in the standing of anaerobic water samples, the As(III) concentration immediately began decreasing whereas dead time was observed in the removal of As(V). In normal groundwater conditions, most arsenic was removed from the water simply by standing overnight. To obtain more effective removal, the addition of oxidants and use of steel wools were investigated. Simple batch wise treatments of arsenic contaminated water were demonstrated, and detail of the transitional changes in As(III) and As(V) were investigated.

  3. Effects of root anatomy and Fe plaque on arsenic uptake by rice seedlings grown in solution culture

    International Nuclear Information System (INIS)

    Deng, Dan; Wu Shengchun; Wu Fuyong; Deng Hong; Wong Minghung

    2010-01-01

    Hydroponic experiments were carried out to investigate the effects of root anatomy, induced by aeration and stagnation, and Fe plaque on arsenic (III and V) uptake and translocation by rice plants. The results showed that As uptake in rice plants (Gui Chao-2) treated by aeration was decreased due to lower root specific surface area. Rice roots with larger specific surface area tended to form more Fe plaque, and Fe plaque affected As uptake kinetics by changing As influx curves from linear to hyperbolic for As(III) and from hyperbolic to S-curve for As(V). Fe plaque increased As(III and V) adsorption and minimized the effects of root anatomy characteristics on As uptake into roots and subsequently translocation to shoots. Fe plaque increased As(III) uptake rate at As(III) concentrations of 0.5∼8 mg L -1 , reduced As(V) uptake rate at low As(V) concentrations ( -1 ), but increased As uptake rate at high As(V) concentrations (>6 mg L -1 ). - Rice root anatomy and Fe plaque affect As uptake.

  4. Insights and inferences about integron evolution from genomic data

    Directory of Open Access Journals (Sweden)

    Martin Andrew P

    2008-05-01

    Full Text Available Abstract Background Integrons are mechanisms that facilitate horizontal gene transfer, allowing bacteria to integrate and express foreign DNA. These are important in the exchange of antibiotic resistance determinants, but can also transfer a diverse suite of genes unrelated to pathogenicity. Here, we provide a systematic analysis of the distribution and diversity of integron intI genes and integron-containing bacteria. Results We found integrons in 103 different pathogenic and non-pathogenic bacteria, in six major phyla. Integrons were widely scattered, and their presence was not confined to specific clades within bacterial orders. Nearly 1/3 of the intI genes that we identified were pseudogenes, containing either an internal stop codon or a frameshift mutation that would render the protein product non-functional. Additionally, 20% of bacteria contained more than one integrase gene. dN/dS ratios revealed mutational hotspots in clades of Vibrio and Shewanella intI genes. Finally, we characterized the gene cassettes associated with integrons in Methylobacillus flagellatus KT and Dechloromonas aromatica RCB, and found a heavy metal efflux gene as well as genes involved in protein folding and stability. Conclusion Our analysis suggests that the present distribution of integrons is due to multiple losses and gene transfer events. While, in some cases, the ability to integrate and excise foreign DNA may be selectively advantageous, the gain, loss, or rearrangment of gene cassettes could also be deleterious, selecting against functional integrases. Thus, such a high fraction of pseudogenes may suggest that the selective impact of integrons on genomes is variable, oscillating between beneficial and deleterious, possibly depending on environmental conditions.

  5. Adsorção de arsênio(V pela quitosana ferro - III reticulada Asorption of arsenic (V by crosslinked iron-III-chitosan

    Directory of Open Access Journals (Sweden)

    Tathyane Fagundes

    2008-01-01

    Full Text Available The removal of As(V by a crosslinked iron(III-chitosan adsorbent was evaluated under various conditions. The adsorption capacity of CH-FeCL was around 54 mg/g of As(V. The kinetics of adsorption obeys a pseudo-first-order model with rate constants equal to 0.022, 0.028, and 0.033 min-1 at 15, 25 and 35 ºC respectively. Adsorption data were well described by the Langmuir model, although they could be modeled also by the Langmuir-Freundlich equation. The maximum adsorption capacity, calculated with the Langmuir model, was 127 mg g-1 of As(V. The inhibition by competing anions is dependant on their kind and valence.

  6. What is the Optimal Strategy for Adaptive Servo-Ventilation Therapy?

    Science.gov (United States)

    Imamura, Teruhiko; Kinugawa, Koichiro

    2018-05-23

    Clinical advantages in the adaptive servo-ventilation (ASV) therapy have been reported in selected heart failure patients with/without sleep-disorder breathing, whereas multicenter randomized control trials could not demonstrate such advantages. Considering this discrepancy, optimal patient selection and device setting may be a key for the successful ASV therapy. Hemodynamic and echocardiographic parameters indicating pulmonary congestion such as elevated pulmonary capillary wedge pressure were reported as predictors of good response to ASV therapy. Recently, parameters indicating right ventricular dysfunction also have been reported as good predictors. Optimal device setting with appropriate pressure setting during appropriate time may also be a key. Large-scale prospective trial with optimal patient selection and optimal device setting is warranted.

  7. Prediction of the binding mode and resistance profile for a dual-target pyrrolyl diketo acid scaffold against HIV-1 integrase and reverse-transcriptase-associated ribonuclease H.

    Science.gov (United States)

    Yang, Fengyuan; Zheng, Guoxun; Fu, Tingting; Li, Xiaofeng; Tu, Gao; Li, Ying Hong; Yao, Xiaojun; Xue, Weiwei; Zhu, Feng

    2018-06-27

    The rapid emergence of drug-resistant variants is one of the most common causes of highly active antiretroviral therapeutic (HAART) failure in patients infected with HIV-1. Compared with the existing HAART, the recently developed pyrrolyl diketo acid scaffold targeting both HIV-1 integrase (IN) and reverse transcriptase-associated ribonuclease H (RNase H) is an efficient approach to counteract the failure of anti-HIV treatment due to drug resistance. However, the binding mode and potential resistance profile of these inhibitors with important mechanistic principles remain poorly understood. To address this issue, an integrated computational method was employed to investigate the binding mode of inhibitor JMC6F with HIV-1 IN and RNase H. By using per-residue binding free energy decomposition analysis, the following residues: Asp64, Thr66, Leu68, Asp116, Tyr143, Gln148 and Glu152 in IN, Asp443, Glu478, Trp536, Lys541 and Asp549 in RNase H were identified as key residues for JMC6F binding. And then computational alanine scanning was carried to further verify the key residues. Moreover, the resistance profile of the currently known major mutations in HIV-1 IN and 2 mutations in RNase H against JMC6F was predicted by in silico mutagenesis studies. The results demonstrated that only three mutations in HIV-1 IN (Y143C, Q148R and N155H) and two mutations in HIV-1 RNase H (Y501R and Y501W) resulted in a reduction of JMC6F potency, thus indicating their potential role in providing resistance to JMC6F. These data provided important insights into the binding mode and resistance profile of the inhibitors with a pyrrolyl diketo acid scaffold in HIV-1 IN and RNase H, which would be helpful for the development of more effective dual HIV-1 IN and RNase H inhibitors.

  8. Time for an alternative perspective: the eternal problem of supply and quality of anti snake venom in the developing world--"it's the economy, stupid".

    Science.gov (United States)

    Simpson, Ian D

    2008-01-01

    The "crisis in anti snake venom supply" has been an enduring problem. Despite the frequency with which it appears in the literature, it remains unquantified and an enigma. If there is a serious shortage of anti snake venom (ASV), why has this not been resolved? Anti snake venoms are produced, and yet many suppliers are described as leaving the market. There appears to be a problem in the call for highly effective, high-quality, and cheap anti venoms that contributes to this result of suppliers leaving the market. Private companies are tasked with achieving adequate shareholder returns and by doing so ensure continued supply. Efforts should therefore target a means of lowering production cost by introducing whole immunoglobulin G (IgG) antivenoms with greater antibody yields, reducing the drive to eliminate adverse reactions, for which there are other more cost-effective treatments, as well as a means of introducing good manufacturing processes, with care based on demonstrable need. In order to ensure sustainability of supply, a private company supplier providing a whole IgG antivenom that effectively neutralizes venom is the most credible option. The need for ASV in areas of shortage mandates the need for clear decisions regarding the type of ASV and the recognition that the market requires acceptable returns for producers if supply is to be sustainable. This paper reviews the economic realities of ASV production and suggests a pragmatic, sustainable approach to the problem of supplying ASV to developing countries.

  9. Removal of arsenate by ferrihydrite via surface complexation and surface precipitation

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Xiuli [Department of Environment Engineering, College of the Environment and Ecology, and The Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, Xiamen University, Xiamen (China); Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, and The Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen (China); Peng, Changjun; Fu, Dun; Chen, Zheng [Department of Environment Engineering, College of the Environment and Ecology, and The Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, Xiamen University, Xiamen (China); Shen, Liang [Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, and The Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen (China); Li, Qingbiao [Department of Environment Engineering, College of the Environment and Ecology, and The Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, Xiamen University, Xiamen (China); Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, and The Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen (China); Ouyang, Tong, E-mail: yz3t@xmu.edu.cn [Department of Environment Engineering, College of the Environment and Ecology, and The Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, Xiamen University, Xiamen (China); Wang, Yuanpeng, E-mail: wypp@xmu.edu.cn [Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, and The Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen (China)

    2015-10-30

    Graphical abstract: - Highlights: • Surface complexation and surface precipitation of As on ferrihydrite happen at pH 3–6. • The formation of surface precipitation enhanced As(V) adsorption. • The dissolved Fe{sup 3+} had a good linear relationship with the amount of arsenate re-adsorption. - Abstract: In this study, macroscopic and spectroscopic experimental methods accurately modeled the sorption process of arsenate on ferrihydrite. EXAFS, X-ray diffraction and infrared (IR) spectroscopy indicated that the behavior of As(V) adsorption onto ferrihydrite took place mainly via surface complexation and surface precipitation at acidic pH (3.0–6.0), while the surface precipitation was dominated at longer time intervals and higher Fe{sup 3+} concentration. The macroscopic competitive adsorption experiment between arsenate with phosphate indicated two types of adsorption sites existing on the surface of ferrihydrite, i.e., non-exchangeable sites, which are responsible for a rapid surface complex formation; and exchangeable sites for a slow build-up of surface precipitates. In the slow build-up precipitates, the As(V) surface coverage (mmol/g) exhibited a good linear relationship (R{sup 2} = 0.952) with the amount of dissolved Fe{sup 3+}. Three steps are involved during the process of surface precipitation, i.e., (1) an initial uptake of As(V) via surface complexation; (2) re-adsorption of Fe{sup 3+} leaching from ferrihydrite on the surface complex; and (3) As(V) adsorption via surface complexation again and finally forming the surface precipitate.

  10. A novel genetic tool for metabolic optimization of Corynebacterium glutamicum: efficient and repetitive chromosomal integration of synthetic promoter-driven expression libraries

    DEFF Research Database (Denmark)

    Shen, Jing; Chen, Jun; Jensen, Peter Ruhdal

    2017-01-01

    readily could integrate into the attB site in this strain providing expression of the corresponding integrase. Subsequent expression of the Cre recombinase promoted recombination between the modified loxP sites, resulting in a strain only retaining the target insertions and an attB site. To simplify...... the procedure, non-replicating circular expression units for the phage integrase and the Cre recombinase were used. As a showcase, we used the tool to construct a battery of strains simultaneously expressing the two reporter genes, lacZ (encoding β-galactosidase) and gusA (encoding β...

  11. Emerging contaminants and nutrients synergistically affect the spread of class 1 integron-integrase (intI1) and sul1 genes within stable streambed bacterial communities.

    Science.gov (United States)

    Subirats, Jèssica; Timoner, Xisca; Sànchez-Melsió, Alexandre; Balcázar, José Luis; Acuña, Vicenç; Sabater, Sergi; Borrego, Carles M

    2018-07-01

    Wastewater effluents increase the nutrient load of receiving streams while introducing a myriad of anthropogenic chemical pollutants that challenge the resident aquatic (micro)biota. Disentangling the effects of both kind of stressors and their potential interaction on the dissemination of antibiotic resistance genes in bacterial communities requires highly controlled manipulative experiments. In this work, we investigated the effects of a combined regime of nutrients (at low, medium and high concentrations) and a mixture of emerging contaminants (ciprofloxacin, erythromycin, sulfamethoxazole, diclofenac, and methylparaben) on the bacterial composition, abundance and antibiotic resistance profile of biofilms grown in artificial streams. In particular, we investigated the effect of this combined stress on genes encoding resistance to ciprofloxacin (qnrS), erythromycin (ermB), sulfamethoxazole (sul1 and sul2) as well as the class 1 integron-integrase gene (intI1). Only genes conferring resistance to sulfonamides (sul1 and sul2) and intI1 gene were detected in all treatments during the study period. Besides, bacterial communities exposed to emerging contaminants showed higher copy numbers of sul1 and intI1 genes than those not exposed, whereas nutrient amendments did not affect their abundance. However, bacterial communities exposed to both emerging contaminants and a high nutrient concentration (1, 25 and 1 mg L -1 of phosphate, nitrate and ammonium, respectively) showed the highest increase on the abundance of sul1 and intI1 genes thus suggesting a factors synergistic effect of both stressors. Since none of the treatments caused a significant change on the composition of bacterial communities, the enrichment of sul1 and intI1 genes within the community was caused by their dissemination under the combined pressure exerted by nutrients and emerging contaminants. To the best of our knowledge, this is the first study demonstrating the contribution of nutrients on

  12. Role of competing ions in the mobilization of arsenic in groundwater of Bengal Basin: insight from surface complexation modeling.

    Science.gov (United States)

    Biswas, Ashis; Gustafsson, Jon Petter; Neidhardt, Harald; Halder, Dipti; Kundu, Amit K; Chatterjee, Debashis; Berner, Zsolt; Bhattacharya, Prosun

    2014-05-15

    This study assesses the role of competing ions in the mobilization of arsenic (As) by surface complexation modeling of the temporal variability of As in groundwater. The potential use of two different surface complexation models (SCMs), developed for ferrihydrite and goethite, has been explored to account for the temporal variation of As(III) and As(V) concentration, monitored in shallow groundwater of Bengal Basin over a period of 20 months. The SCM for ferrihydrite appears as the better predictor of the observed variation in both As(III) and As(V) concentrations in the study sites. It is estimated that among the competing ions, PO4(3-) is the major competitor of As(III) and As(V) adsorption onto Fe oxyhydroxide, and the competition ability decreases in the order PO4(3-) ≫ Fe(II) > H4SiO4 = HCO3(-). It is further revealed that a small change in pH can also have a significant effect on the mobility of As(III) and As(V) in the aquifers. A decrease in pH increases the concentration of As(III), whereas it decreases the As(V) concentration and vice versa. The present study suggests that the reductive dissolution of Fe oxyhydroxide alone cannot explain the observed high As concentration in groundwater of the Bengal Basin. This study supports the view that the reductive dissolution of Fe oxyhydroxide followed by competitive sorption reactions with the aquifer sediment is the processes responsible for As enrichment in groundwater. Copyright © 2014 Elsevier Ltd. All rights reserved.

  13. Therapeutical options for the treatment of Cheyne-Stokes respiration.

    Science.gov (United States)

    Randerath, Winfried J

    2009-03-07

    The awareness of Cheyne-Stokes respiration (CSR) and of the co-existence of the obstructive sleep apnoea syndrome and central breathing disturbances has rapidly grown in recent years. CSR is defined by a waxing and waning pattern of the breathing amplitude. Sleep related breathing disorders in patients with heart failure are associated with impaired clinical outcome and survival. While continuous positive airway pressure treatment (CPAP) is widely used to treat CSR, it has failed to improve overall survival of heart failure patients. Nevertheless, it has been shown that CPAP reduces mortality if breathing disturbances were sufficiently eliminated. Therefore, optimal suppression of CSR is critical. While CPAP reduces CSR by 50% on average, adaptive servoventilation (ASV) normalises CSR in most patients. ASV devices apply different levels of pressure support: during periods of hypoventilation the inspiratory pressure is increased while it is reduced to the lowest possible level during hyperventilation. The devices deliver an expiratory pressure to overcome upper airways obstruction. Pressure support is defined by the difference between expiratory and inspiratory pressure. Thus, while pressure support is fixed in bilevel devices, it varies under ASV. However, the hypothesis that ASV might improve survival in CSR patients has to be proved in prospective studies in CPAP nonresponders. There is a lack of evidence on the use of bilevel devices in CSR. However, ASV has proven both to effectively treat CSR and to be superior to CPAP in respiratory and sleep parameters in short term and medium term studies. Nevertheless, data on the long term use and the influence on cardiac parameters are necessary.

  14. Biosorptive removal of inorganic arsenic species and fluoride from aqueous medium by the stem of Tecomella undulate.

    Science.gov (United States)

    Brahman, Kapil Dev; Kazi, Tasneem Gul; Baig, Jameel Ahmed; Afridi, Hassan Imran; Arain, Sadaf Sadia; Saraj, Saima; Arain, Muhammad B; Arain, Salma Aslam

    2016-05-01

    Simultaneous removal of fluoride (F(-)), inorganic arsenic species, As(III) and As(V), from aqueous samples has been performed using an economic indigenous biosorbent (Stem of Tecomella undulata). The inorganic As species in water samples before and after biosorption were determined by cloud point and solid phase extraction methods, while F(-) was determined by ion chromatography. Batch experiments were carried out to evaluate the equilibrium adsorption isotherm studies for As(III), As(V) and F(-) in aqueous solutions. Several parameters of biosorption were optimized such as pH, biomass dosage, analytes concentration, time and temperature. The surface of biosorbent was characterized by SEM and FTIR. The FTIR study indicated the presence of carbonyl and amine functional groups which may have important role in the sorption/removal of these ions. Thermodynamic and kinetic study indicated that the biosorption of As(III), As(V) and F(-) were spontaneous, exothermic and followed by pseudo-second-order. Meanwhile, the interference study revealed that there was no significant effect of co-existing ions for the removal of inorganic As species and F(-) from aqueous samples (p > 0.05). It was observed that the indigenous biosorbent material simultaneously adsorbed As(III) (108 μg g(-1)), As(V) (159 μg g(-1)) and F(-) (6.16 mg g(-1)) from water at optimized conditions. The proposed biosorbent was effectively regenerated and efficiently used for several experiments, to remove the As(III), As(V) and F(-) from real water sample collected from endemic area of Pakistan. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Toxicity of arsenic (III) and (V) on plant growth, element uptake, and total amylolytic activity of mesquite (Prosopis juliflora x P. velutina).

    Science.gov (United States)

    Mokgalaka-Matlala, Ntebogeng S; Flores-Tavizón, Edith; Castillo-Michel, Hiram; Peralta-Videa, Jose R; Gardea-Torresdey, Jorge L

    2008-01-01

    The effects of arsenite [As(III)] and arsenate [As(V)] on the growth of roots, stems, and leaves and the uptake of arsenic (As), micro- and macronutrients, and total amylolytic activity were investigated to elucidate the phytotoxicity of As to the mesquite plant (Prosopis juliflora x P. velutina). The plant growth was evaluated by measuring the root and shoot length, and the element uptake was determined using inductively coupled plasma optical emission spectroscopy. The root and leaf elongation decreased significantly with increasing As(III) and As(V) concentrations; whereas, stem elongation remained unchanged. The As uptake increased with increasing As(III) or As(V) concentrations in the medium. Plants treated with 50 mg/L As(III) accumulated up to 920 mg/kg dry weight (d wt) in roots and 522 mg/kg d wt in leaves, while plants exposed to 50 mg/L As(V) accumulated 1980 and 210 mg/kg d wt in roots and leaves, respectively. Increasing the As(V) concentration up to 20 mg/L resulted in a decrease in the total amylolytic activity. On the contrary, total amylolytic activity in As(III)-treated plants increased with increasing As concentration up to 20 mg/L. The macro- and micronutrient concentrations changed in As-treated plants. In shoots, Mo and K were reduced but Ca was increased, while in roots Fe and Ca were increased but K was reduced. These changes reduced the size of the plants, mainly in the As(III)-treated plants; however, there were no visible sign of As toxicity.

  16. Metagenomic exploration reveals a marked change in the river resistome and mobilome after treated wastewater discharges.

    Science.gov (United States)

    Lekunberri, Itziar; Balcázar, José Luis; Borrego, Carles M

    2018-03-01

    Mobile genetic elements (MGEs) are key agents in the spread of antibiotic resistance genes (ARGs) across environments. Here we used metagenomics to compare the river resistome (collection of all ARGs) and mobilome (e.g., integrases, transposases, integron integrases and insertion sequence common region "ISCR" elements) between samples collected upstream (n = 6) and downstream (n = 6) of an urban wastewater treatment plant (UWWTP). In comparison to upstream metagenomes, downstream metagenomes showed a drastic increase in the abundance of ARGs, as well as markers of MGEs, particularly integron integrases and ISCR elements. These changes were accompanied by a concomitant prevalence of 16S rRNA gene signatures of bacteria affiliated to families encompassing well-known human and animal pathogens. Our results confirm that chronic discharges of treated wastewater severely impact the river resistome affecting not only the abundance and diversity of ARGs but also their potential spread by enriching the river mobilome in a wide variety of MGEs. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Rice-arsenate interactions in hydroponics: whole genome transcriptional analysis.

    Science.gov (United States)

    Norton, Gareth J; Lou-Hing, Daniel E; Meharg, Andrew A; Price, Adam H

    2008-01-01

    Rice (Oryza sativa) varieties that are arsenate-tolerant (Bala) and -sensitive (Azucena) were used to conduct a transcriptome analysis of the response of rice seedlings to sodium arsenate (AsV) in hydroponic solution. RNA extracted from the roots of three replicate experiments of plants grown for 1 week in phosphate-free nutrient with or without 13.3 muM AsV was used to challenge the Affymetrix (52K) GeneChip Rice Genome array. A total of 576 probe sets were significantly up-regulated at least 2-fold in both varieties, whereas 622 were down-regulated. Ontological classification is presented. As expected, a large number of transcription factors, stress proteins, and transporters demonstrated differential expression. Striking is the lack of response of classic oxidative stress-responsive genes or phytochelatin synthases/synthatases. However, the large number of responses from genes involved in glutathione synthesis, metabolism, and transport suggests that glutathione conjugation and arsenate methylation may be important biochemical responses to arsenate challenge. In this report, no attempt is made to dissect differences in the response of the tolerant and sensitive variety, but analysis in a companion article will link gene expression to the known tolerance loci available in the BalaxAzucena mapping population.

  18. Rice–arsenate interactions in hydroponics: whole genome transcriptional analysis

    Science.gov (United States)

    Norton, Gareth J.; Lou-Hing, Daniel E.; Meharg, Andrew A.; Price, Adam H.

    2008-01-01

    Rice (Oryza sativa) varieties that are arsenate-tolerant (Bala) and -sensitive (Azucena) were used to conduct a transcriptome analysis of the response of rice seedlings to sodium arsenate (AsV) in hydroponic solution. RNA extracted from the roots of three replicate experiments of plants grown for 1 week in phosphate-free nutrient with or without 13.3 μM AsV was used to challenge the Affymetrix (52K) GeneChip Rice Genome array. A total of 576 probe sets were significantly up-regulated at least 2-fold in both varieties, whereas 622 were down-regulated. Ontological classification is presented. As expected, a large number of transcription factors, stress proteins, and transporters demonstrated differential expression. Striking is the lack of response of classic oxidative stress-responsive genes or phytochelatin synthases/synthatases. However, the large number of responses from genes involved in glutathione synthesis, metabolism, and transport suggests that glutathione conjugation and arsenate methylation may be important biochemical responses to arsenate challenge. In this report, no attempt is made to dissect differences in the response of the tolerant and sensitive variety, but analysis in a companion article will link gene expression to the known tolerance loci available in the Bala×Azucena mapping population. PMID:18453530

  19. Facile measurement of {sup 1}H-{sup 15}N residual dipolar couplings in larger perdeuterated proteins

    Energy Technology Data Exchange (ETDEWEB)

    Fitzkee, Nicholas C.; Bax, Ad, E-mail: bax@nih.go [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

    2010-10-15

    We present a simple method, ARTSY, for extracting {sup 1}J{sub NH} couplings and {sup 1}H-{sup 15}N RDCs from an interleaved set of two-dimensional {sup 1}H-{sup 15}N TROSY-HSQC spectra, based on the principle of quantitative J correlation. The primary advantage of the ARTSY method over other methods is the ability to measure couplings without scaling peak positions or altering the narrow line widths characteristic of TROSY spectra. Accuracy of the method is demonstrated for the model system GB3. Application to the catalytic core domain of HIV integrase, a 36 kDa homodimer with unfavorable spectral characteristics, demonstrates its practical utility. Precision of the RDC measurement is limited by the signal-to-noise ratio, S/N, achievable in the 2D TROSY-HSQC spectrum, and is approximately given by 30/(S/N) Hz.

  20. Microcomputer-Assisted Flow-Through ASV System.

    Science.gov (United States)

    1979-09-01

    FXVAL AND LPTNO,LXVAL *RETURN I-TRUE 0-FALSE IN ACCA *T VALUE ON LINE IS LEFT IN Y 0390 FE 0033 D AELINE LDX FPTNO /GET Ti 0393 09 DIX 1ST Y VALUE 0394...64D6 9 DEX 04D7 26 F3 04D4 SNE CLSA1 04D9 39 RTS *SAVE THE INTEGRATION RESULTS IN PROPER BUFFER ***** ** *** k******* 04DA 36 6633 D SAYRES LDAA ELN

  1. Dredging Operations Technical Support Program. Transformation, Fixation, and Mobilization of Arsenic and Antimony in Contaminated Sediments.

    Science.gov (United States)

    1984-01-01

    and Edwards (1977) reported that whole cells of :ethaogenic bacteria in variod anaerobic environments ( rumen fluid, sewage sludge) nproduced...sediments were studied with emphasis placed on short- and long-term 14 leaching and sediment conditions that affect mobilization. -; Under anaerobic ...conditions, arsenate [As(V)] was reduced to arsenite [As(III)] in a wide range of sediments. In anaerobic Texas City sediment slur- ries, 70% of added As(V

  2. Effects of Combined CCR5/Integrase Inhibitors-Based Regimen on Mucosal Immunity in HIV-Infected Patients Naïve to Antiretroviral Therapy: A Pilot Randomized Trial.

    Directory of Open Access Journals (Sweden)

    Sergio Serrano-Villar

    2016-01-01

    Full Text Available Whether initiation of antiretroviral therapy (ART regimens aimed at achieving greater concentrations within gut associated lymphoid tissue (GALT impacts the level of mucosal immune reconstitution, inflammatory markers and the viral reservoir remains unknown. We included 12 HIV- controls and 32 ART-naïve HIV patients who were randomized to efavirenz, maraviroc or maraviroc+raltegravir, each with fixed-dose tenofovir disoproxil fumarate/emtricitabine. Rectal and duodenal biopsies were obtained at baseline and at 9 months of ART. We performed a comprehensive assay of T-cell subsets by flow cytometry, T-cell density in intestinal biopsies, plasma and tissue concentrations of antiretroviral drugs by high-performance liquid chromatography/mass spectroscopy, and plasma interleukin-6 (IL-6, lipoteichoic acid (LTA, soluble CD14 (sCD14 and zonulin-1 each measured by ELISA. Total cell-associated HIV DNA was measured in PBMC and rectal and duodenal mononuclear cells. Twenty-six HIV-infected patients completed the follow-up. In the duodenum, the quadruple regimen resulted in greater CD8+ T-cell density decline, greater normalization of mucosal CCR5+CD4+ T-cells and increase of the naïve/memory CD8+ T-cell ratio, and a greater decline of sCD14 levels and duodenal HIV DNA levels (P = 0.004 and P = 0.067, respectively, with no changes in HIV RNA in plasma or tissue. Maraviroc showed the highest drug distribution to the gut tissue, and duodenal concentrations correlated well with other T-cell markers in duodenum, i.e., the CD4/CD8 ratio, %CD4+ and %CD8+ HLA-DR+CD38+ T-cells. Maraviroc use elicited greater activation of the mucosal naïve CD8+ T-cell subset, ameliorated the distribution of the CD8+ T-cell maturational subsets and induced higher improvement of zonulin-1 levels. These data suggest that combined CCR5 and integrase inhibitor based combination therapy in ART treatment naïve patients might more effectively reconstitute duodenal immunity, decrease

  3. Murine leukemia viruses: objects and organisms.

    Science.gov (United States)

    Rein, Alan

    2011-01-01

    Murine leukemia viruses (MLVs) are among the simplest retroviruses. Prototypical gammaretroviruses encode only the three polyproteins that will be used in the assembly of progeny virus particles. These are the Gag polyprotein, which is the structural protein of a retrovirus particle, the Pol protein, comprising the three retroviral enzymes-protease, which catalyzes the maturation of the particle, reverse transcriptase, which copies the viral RNA into DNA upon infection of a new host cell, and integrase, which inserts the DNA into the chromosomal DNA of the host cell, and the Env polyprotein, which induces the fusion of the viral membrane with that of the new host cell, initiating infection. In general, a productive MLV infection has no obvious effect upon host cells. Although gammaretroviral structure and replication follow the same broad outlines as those of other retroviruses, we point out a number of significant differences between different retroviral genera.

  4. Adsorptive properties of alluvial soil for arsenic(V) and its potential for protection of the shallow groundwater among Changsha, Zhuzhou, and Xiangtan cities, China.

    Science.gov (United States)

    Chen, Hongwei; Mei, Jinhua; Luo, Yueping; Qiu, Anni; Wang, Huan

    2017-02-01

    The study area is among Changsha, Zhuzhou, and Xiangtan cities, which was under agricultural use and natural conditions about 10 years ago and now is becoming part of the metropolis because of the urban expansion. This study aims to investigate the mechanisms and capabilities of the local alluvial soil layer for protecting the local shallow groundwater from arsenic pollution by field surveys and batch experiments. The field surveys showed that there was an acidic tendency of the groundwater, and phosphate, nitrate, and arsenic in the groundwater significantly increased comparing to their reference values. It indicates that the disturbance of the former agricultural land due to the change of land use may be responsible for these changes. From the experimental results, the maximum adsorption capacity of the soil for As(V) was as low as 0.334 mg/g, and lower As(V) adsorption capacities were obtained at higher As(V) concentration, higher pH, and lower temperature. The presence of H 2 PO 4 - and SiO 3 2- posed negative, while HCO 3 - slight positive, and SO 4 2- , NO 3 - and Cl - negligible influences on the As(V) adsorption. The surface-derived organic matter played a negative role in the adsorption process, and low specific surface area influenced adsorption capacity of the soil. The study reveals that the local soil layer shows poor potential for protection of the local shallow groundwater from As(V) pollution, and the change trends of the groundwater environments due to more intensive anthropogenic activities will further weaken this potential and increase the risk of the groundwater contamination.

  5. Effect of iron oxide reductive dissolution on the transformation and immobilization of arsenic in soils: New insights from X-ray photoelectron and X-ray absorption spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Fan, Jian-Xin [Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008 (China); School of River and Ocean Engineering, Chongqing Jiaotong University, Chongqing 400074 (China); Wang, Yu-Jun, E-mail: yjwang@issas.ac.cn [Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008 (China); Liu, Cun [Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008 (China); Wang, Li-Hua; Yang, Ke [Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of sciences, Shanghai 201204 (China); Zhou, Dong-Mei, E-mail: dmzhou@issas.ac.cn [Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008 (China); Li, Wei; Sparks, Donald L. [Environmental Soil Chemistry Group, Delaware Environmental Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19717-1303 United States (United States)

    2014-08-30

    Graphical abstract: - Highlights: • Immobility and transformation of As on different Eh soils were investigated. • μ-XRF, XANES, and XPS were used to gain As distribution and speciation in soil. • Sorption capacity of As on anaerobic soil was much higher than that on oxic soil. • Fe oxides reductive dissolution is a key factor for As sorption and transformation. - Abstract: The geochemical behavior and speciation of arsenic (As) in paddy soils is strongly controlled by soil redox conditions and the sequestration by soil iron oxyhydroxides. Hence, the effects of iron oxide reductive dissolution on the adsorption, transformation and precipitation of As(III) and As(V) in soils were investigated using batch experiments and synchrotron based techniques to gain a deeper understanding at both macroscopic and microscopic scales. The results of batch sorption experiments revealed that the sorption capacity of As(V) on anoxic soil was much higher than that on control soil. Synchrotron based X-ray fluorescence (μ-XRF) mapping studies indicated that As was heterogeneously distributed and was mainly associated with iron in the soil. X-ray absorption near edge structure (XANES), micro-X-ray absorption near edge structure (μ-XANES) and X-ray photoelectron spectroscopy (XPS) analyses revealed that the primary speciation of As in the soil is As(V). These results further suggested that, when As(V) was introduced into the anoxic soil, the rapid coprecipitation of As(V) with ferric/ferrous ion prevented its reduction to As(III), and was the main mechanism controlling the immobilization of As. This research could improve the current understanding of soil As chemistry in paddy and wetland soils.

  6. Effect of iron oxide reductive dissolution on the transformation and immobilization of arsenic in soils: New insights from X-ray photoelectron and X-ray absorption spectroscopy

    International Nuclear Information System (INIS)

    Fan, Jian-Xin; Wang, Yu-Jun; Liu, Cun; Wang, Li-Hua; Yang, Ke; Zhou, Dong-Mei; Li, Wei; Sparks, Donald L.

    2014-01-01

    Graphical abstract: - Highlights: • Immobility and transformation of As on different Eh soils were investigated. • μ-XRF, XANES, and XPS were used to gain As distribution and speciation in soil. • Sorption capacity of As on anaerobic soil was much higher than that on oxic soil. • Fe oxides reductive dissolution is a key factor for As sorption and transformation. - Abstract: The geochemical behavior and speciation of arsenic (As) in paddy soils is strongly controlled by soil redox conditions and the sequestration by soil iron oxyhydroxides. Hence, the effects of iron oxide reductive dissolution on the adsorption, transformation and precipitation of As(III) and As(V) in soils were investigated using batch experiments and synchrotron based techniques to gain a deeper understanding at both macroscopic and microscopic scales. The results of batch sorption experiments revealed that the sorption capacity of As(V) on anoxic soil was much higher than that on control soil. Synchrotron based X-ray fluorescence (μ-XRF) mapping studies indicated that As was heterogeneously distributed and was mainly associated with iron in the soil. X-ray absorption near edge structure (XANES), micro-X-ray absorption near edge structure (μ-XANES) and X-ray photoelectron spectroscopy (XPS) analyses revealed that the primary speciation of As in the soil is As(V). These results further suggested that, when As(V) was introduced into the anoxic soil, the rapid coprecipitation of As(V) with ferric/ferrous ion prevented its reduction to As(III), and was the main mechanism controlling the immobilization of As. This research could improve the current understanding of soil As chemistry in paddy and wetland soils

  7. Evaluation of stone volume distribution in renal collecting system as a predictor of stone-free rate after percutaneous nephrolithotomy: a retrospective single-center study.

    Science.gov (United States)

    Atalay, Hasan Anıl; Canat, Lutfi; Bayraktarlı, Recep; Alkan, Ilter; Can, Osman; Altunrende, Fatih

    2017-06-23

    We analyzed our stone-free rates of PNL with regard to stone burden and its ratio to the renal collecting system volume. Data of 164 patients who underwent PNL were analyzed retrospectively. Volume segmentation of renal collecting system and stones were done using 3D segmentation software with the images obtained from CT data. Analyzed stone volume (ASV) and renal collecting system volume (RCSV) were measured and the ASV-to-RCSV ratio was calculated after the creation of a 3D surface volume rendering of renal stones and the collecting system. Univariate and multivariate statistical analyses were performed to determine factors affecting stone-free rates; also we assessed the predictive accuracy of the ASV-to-RCSV ratio using the receiving operating curve (ROC) and AUC. The stone-free rate of PNL monotherapy was 53% (164 procedures).The ASV-to-RCSV ratio and calyx number with stones were the most influential predictors of stone-free status (OR 4.15, 95% CI 2.24-7.24, renal collecting system, which is calculated using the 3D volume segmentation method, is a significant determinant of the stone-free rate before PCNL surgery. It could be used as a single guide variable by the clinician before renal stone surgery to predict extra requirements for stone clearance.

  8. Mobilisation and Bioavailability of Arsenic Around Mesothermal Gold Deposits in a Semiarid Environment, Otago, New Zealand

    Directory of Open Access Journals (Sweden)

    D. Craw

    2002-01-01

    Full Text Available Arsenopyrite (FeAsS is the principal arsenic (As mineral in mineralised mesothermal veins (typically 5,000 mg/kg As in southeastern New Zealand. Groundwater in contact with arsenopyrite-bearing rocks has elevated As concentrations (up to 0.1 mg/l. The arsenopyrite decomposes slowly on oxidation in soils and historic mine workings in a cool semiarid climate. Dissolved As is predominantly As(III in association with arsenopyrite, but this is rapidly oxidised over days to weeks to As(V in the vadose zone. Oxidation is facilitated by particulate Fe and/or Mn oxyhydroxides, and by bacteria in surface waters. Evaporative concentration of dissolved As(V in the vadose zone causes precipitation of scorodite (Fe(IIIAs(VO4.2H2O. Adsorption of As(V to Fe oxyhydroxides in soils and groundwater pathways lowers dissolved As concentrations. Soils over mineralised veins typically have <200 mg/kg As, as most As is removed in solution on geological time scales. Most plants on the mineralised rocks and soils do not take up As, although some inedible species can fix up to 18 mg/kg As. Hence, bioavailability of As(V is low in this environment, despite the substantial As flux.

  9. Experimental effects of exposure to pornography: the moderating effect of personality and mediating effect of sexual arousal.

    Science.gov (United States)

    Hald, Gert Martin; Malamuth, Neil N

    2015-01-01

    Using a randomly selected community sample of 200 Danish young adult men and women in a randomized experimental design, the study investigated the effects of a personality trait (agreeableness), past pornography consumption, and experimental exposure to non-violent pornography on attitudes supporting violence against women (ASV). We found that lower levels of agreeableness and higher levels of past pornography consumption significantly predicted ASV. In addition, experimental exposure to pornography increased ASV but only among men low in agreeableness. This relationship was found to be significantly mediated by sexual arousal with sexual arousal referring to the subjective assessment of feeling sexually excited, ready for sexual activities, and/or bodily sensations associated with being sexually aroused. In underscoring the importance of individual differences, the results supported the hierarchical confluence model of sexual aggression and the media literature on affective engagement and priming effects.

  10. Arsenic removal from water using low-cost adsorbents: A comparative study

    Directory of Open Access Journals (Sweden)

    Rajaković Ljubinka V.

    2011-01-01

    Full Text Available Inorganic arsenic removal from water using low-cost adsorbents is presented in this paper. Selective removal of As(III and As(V from water was performed with natural materials (zeolite, bentonite, sepiolite, pyrolusite and limonite and industrial by-products (waste filter sand as a water treatment residual and blast furnace slag from steel production; all inexpensive and locally available. Kinetic and equilibrium studies were realized using batch system techniques under conditions that are likely to occur in real water treatment systems. The natural zeolite and the industrial by-products were found to be good and inexpensive sorbents for arsenic while bentonite and sepiolite clays showed little affinity towards arsenic. The highest maximum sorption capacities were obtained for natural zeolite, 4.07 mg As(V g-1, and waste iron slag, 4.04 mg As(V g-1.

  11. Availability of Acute and/or Subacute Toxicokinetic Data for Select Compounds for the Rat and Physiologically Based Pharmacokinetic (PBPK) Models for Rats and Humans for Those Compounds

    Science.gov (United States)

    2017-05-04

    DMA, and total As in urine Mouse: radioactivity in feces, liver, kidneys, lungs, and carcass (DMA), DMA in urine; after arsenate dose...radioactivity in urine, feces, liver, kidneys, lungs, skin, carcass and blood and AsV, AsIII, MMA and DMA excreted in urine; after arsenite dose, AsV, AsIII...Pharmacokinetic parameter values were taken from a variety of sources, including animal studies (e.g., oral absorption rate), in vitro kinetic

  12. Integron gene cassettes and degradation of compounds associated with industrial waste: the case of the Sydney tar ponds.

    Directory of Open Access Journals (Sweden)

    Jeremy E Koenig

    Full Text Available Integrons are genetic platforms that accelerate lateral gene transfer (LGT among bacteria. They were first detected on plasmids bearing single and multiple drug resistance determinants in human pathogens, and it is abundantly clear that integrons have played a major role in the evolution of this public health menace. Similar genetic elements can be found in nonpathogenic environmental bacteria and in metagenomic environmental DNA samples, and it is reasonable to suppose that integrons have facilitated microbial adaptation through LGT in niches outside infectious disease wards. Here we show that a heavily impacted estuary, exposed for almost a century to products of coal and steel industries, has developed a rich and unique cassette metagenome, containing genes likely to aid in the catabolism of compounds associated with industrial waste found there. In addition, we report that the most abundant cassette recovered in this study is one that encodes a putative LysR protein. This autoregulatory transcriptional regulator is known to activate transcription of linked target genes or unlinked regulons encoding diverse functions including chlorocatechol and dichlorophenol catabolism. Finally, only class 1 integrase genes were amplified in this study despite using different primer sets, and it may be that the cassettes present in the Tar Ponds will prove to be associated with class 1 integrase genes. Nevertheless, our cassette library provides a snapshot of a complex evolutionary process involving integron-meditated LGT likely to be important in natural bioremediation.

  13. Family values in the age of genomics: comparative analyses of temperate bacteriophage HK022.

    Science.gov (United States)

    Weisberg, R A; Gottesmann, M E; Hendrix, R W; Little, J W

    1999-01-01

    HK022 is a temperate coliphage related to phage lambda. Its chromosome has been completely sequenced, and several aspects of its life cycle have been intensively studied. In the overall arrangement, expression, and function of most of its genes, HK022 broadly resembles lambda and other members of the lambda family. Upon closer view, significant differences emerge. The differences reveal alternative strategies used by related phages to cope with similar problems and illuminate previously unknown regulatory and structural motifs. HK022 prophages protect lysogens from superinfection by producing a sequence-specific RNA binding protein that prematurely terminates nascent transcripts of infecting phage. It uses a novel RNA-based mechanism to antiterminate its own early transcription. The HK022 protein shell is strengthened by a complex pattern of covalent subunit interlinking to form a unitary structure that resembles chain-mail armour. Its integrase and repressor proteins are similar to those of lambda, but the differences provide insights into the evolution of biological specificity and the elements needed for construction of a stable genetic switch.

  14. Humic substances and the biogeochemical arsenic cycle in groundwater of the Blackfoot Disease endemic area, southwestern Taiwan

    Science.gov (United States)

    Kulp, T. R.; Jean, J.

    2009-12-01

    Blackfoot Disease (BFD) is a peripheral vascular disease that is endemic to the Chianan Plain area on the southwestern coast of Taiwan. The disease has been linked to long term ingestion of arsenic-contaminated groundwater derived from deep (>100 m) wells that were drilled in the region during the early 1900’s. Victims of BFD typically exhibit symptoms that include ulceration and gangrene in the extremities, which are unique compared to cases of arsenic toxicosis arising in other As-impacted areas. While the exact etiology of BFD is still a subject of some debate, many workers suggest that elevated arsenic in combination with high concentrations of dissolved fluorescent humic compounds in the region’s groundwater are primary causative factors. Despite considerable research over the past 30 years into the occurrence and distribution of As in the region’s groundwater, few studies have been conducted to investigate the geochemical and microbiological processes that influence the element’s speciation and mobility in this aquifer. We measured the concentration and speciation of As associated with sediments and groundwater from wells drilled in the BFD endemic area and conducted sediment microcosm bioassays to investigate the potential for reductive desorption and mobilization of As from the aquifer sediments by endogenous populations of As(V)-reducing bacteria. Samples from 100 -120 m depth were characterized by the highest As concentrations in sediment (1.4 mg/kg) and water (175.4 μg/L). Sediment-adsorbed As was present primarily as As(V) (>87%), whereas ground water samples contained no measurable aqueous As(V). Instead, arsenic in the groundwater samples was present in organo-arsenic complexes and was detectable by hydride generation - atomic absorption spectrophotometry only after oxidative treatments to convert all As to As(V). Biological As(V) reduction was observed in live slurries of aquifer sediment from 120 and 140 m sediment depth. Microbial As(V

  15. Comparing side chain packing in soluble proteins, protein-protein interfaces, and transmembrane proteins.

    Science.gov (United States)

    Gaines, J C; Acebes, S; Virrueta, A; Butler, M; Regan, L; O'Hern, C S

    2018-05-01

    We compare side chain prediction and packing of core and non-core regions of soluble proteins, protein-protein interfaces, and transmembrane proteins. We first identified or created comparable databases of high-resolution crystal structures of these 3 protein classes. We show that the solvent-inaccessible cores of the 3 classes of proteins are equally densely packed. As a result, the side chains of core residues at protein-protein interfaces and in the membrane-exposed regions of transmembrane proteins can be predicted by the hard-sphere plus stereochemical constraint model with the same high prediction accuracies (>90%) as core residues in soluble proteins. We also find that for all 3 classes of proteins, as one moves away from the solvent-inaccessible core, the packing fraction decreases as the solvent accessibility increases. However, the side chain predictability remains high (80% within 30°) up to a relative solvent accessibility, rSASA≲0.3, for all 3 protein classes. Our results show that ≈40% of the interface regions in protein complexes are "core", that is, densely packed with side chain conformations that can be accurately predicted using the hard-sphere model. We propose packing fraction as a metric that can be used to distinguish real protein-protein interactions from designed, non-binding, decoys. Our results also show that cores of membrane proteins are the same as cores of soluble proteins. Thus, the computational methods we are developing for the analysis of the effect of hydrophobic core mutations in soluble proteins will be equally applicable to analyses of mutations in membrane proteins. © 2018 Wiley Periodicals, Inc.

  16. The Conjugative Relaxase TrwC Promotes Integration of Foreign DNA in the Human Genome.

    Science.gov (United States)

    González-Prieto, Coral; Gabriel, Richard; Dehio, Christoph; Schmidt, Manfred; Llosa, Matxalen

    2017-06-15

    Bacterial conjugation is a mechanism of horizontal DNA transfer. The relaxase TrwC of the conjugative plasmid R388 cleaves one strand of the transferred DNA at the oriT gene, covalently attaches to it, and leads the single-stranded DNA (ssDNA) into the recipient cell. In addition, TrwC catalyzes site-specific integration of the transferred DNA into its target sequence present in the genome of the recipient bacterium. Here, we report the analysis of the efficiency and specificity of the integrase activity of TrwC in human cells, using the type IV secretion system of the human pathogen Bartonella henselae to introduce relaxase-DNA complexes. Compared to Mob relaxase from plasmid pBGR1, we found that TrwC mediated a 10-fold increase in the rate of plasmid DNA transfer to human cells and a 100-fold increase in the rate of chromosomal integration of the transferred DNA. We used linear amplification-mediated PCR and plasmid rescue to characterize the integration pattern in the human genome. DNA sequence analysis revealed mostly reconstituted oriT sequences, indicating that TrwC is active and recircularizes transferred DNA in human cells. One TrwC-mediated site-specific integration event was detected, proving that TrwC is capable of mediating site-specific integration in the human genome, albeit with very low efficiency compared to the rate of random integration. Our results suggest that TrwC may stabilize the plasmid DNA molecules in the nucleus of the human cell, probably by recircularization of the transferred DNA strand. This stabilization would increase the opportunities for integration of the DNA by the host machinery. IMPORTANCE Different biotechnological applications, including gene therapy strategies, require permanent modification of target cells. Long-term expression is achieved either by extrachromosomal persistence or by integration of the introduced DNA. Here, we studied the utility of conjugative relaxase TrwC, a bacterial protein with site

  17. Arsenic removal by perilla leaf biochar in aqueous solutions and groundwater: An integrated spectroscopic and microscopic examination.

    Science.gov (United States)

    Niazi, Nabeel Khan; Bibi, Irshad; Shahid, Muhammad; Ok, Yong Sik; Burton, Edward D; Wang, Hailong; Shaheen, Sabry M; Rinklebe, Jörg; Lüttge, Andreas

    2018-01-01

    In this study, we examined the removal of arsenite (As(III)) and arsenate (As(V)) by perilla leaf-derived biochars produced at 300 and 700 °C (referred as BC300 and BC700) in aqueous environments. Results revealed that the Langmuir isotherm model provided the best fit for As(III) and As(V) sorption, with the sorption affinity following the order: BC700-As(III) > BC700-As(V) > BC300-As(III) > BC300-As(V) (Q L  = 3.85-11.01 mg g -1 ). In general, As removal decreased (76-60%) with increasing pH from 7 to 10 except for the BC700-As(III) system, where notably higher As removal (88-90%) occurred at pH from 7 to 9. Surface functional moieties contributed to As sequestration by the biochars examined here. However, significantly higher surface area and aromaticity of BC700 favored a greater As removal compared to BC300, suggesting that surface complexation/precipitation dominated As removal by BC700. Arsenic K-edge X-ray absorption near edge structure (XANES) spectroscopy demonstrated that up to 64% of the added As(V) was reduced to As(III) in BC700- and BC300-As(V) sorption experiments, and in As(III) sorption experiments, partial oxidation of As(III) to As(V) occurred (37-39%). However, XANES spectroscopy was limited to precisely quantify As binding with sulfur species as As 2 S 3 -like phase. Both biochars efficiently removed As from natural As-contaminated groundwater (As: 23-190 μg L -1 ; n = 12) despite in the presence of co-occurring anions (e.g., CO 3 2- , PO 4 3- , SO 4 2- ) with the highest levels of As removal observed for BC700 (97-100%). Overall, this study highlights that perilla leaf biochars, notably BC700, possessed the greatest ability to remove As from solution and groundwater (drinking water). Significantly, the integrated spectroscopic techniques advanced our understanding to examine complex redox transformation of As(III)/As(V) with biochar, which are crucial to determine fate of As on biochar in aquatic environments. Copyright

  18. Kinetic Modeling of Arsenic Cycling by a Freshwater Cyanobacterium as Influenced by N:P Ratios: A Potential Biologic Control in an Iron-Limited Drainage Basin

    Science.gov (United States)

    Markley, C. T.; Herbert, B. E.

    2004-12-01

    Elevated As levels are common in South Texas surface waters, where As is derived from the natural weathering of geogenic sources and a byproduct of historical uranium mining. The impacted surface waters of the Nueces River drainage basin supply Lake Corpus Christi (LCC), a major drinking water reservoir for the Corpus Christi area. The soils and sediments of the Nueces River drainage basin generally have low levels of reactive iron (average concentration of 2780 mg/kg), limiting the control of iron oxyhydroxides on As geochemistry and bioavailability. Given these conditions, biologic cycling of As may have a large influence on As fate and transport in LCC. Sediment cores from LCC show evidence for cyanobacterial blooms after reservoir formation based upon stable isotopes, total organic matter and specific elemental correlations. While algae have been shown to accumulate and reduce inorganic As(V), few studies have reported biologic cycling of As by cyanobacteria. Therefore, As(V) uptake, accumulation, reduction, and excretion in a 1.0 μ M As(V) solution by the freshwater cyanobacterium, Anabaena sp. Strain PCC 7120, was measured over time as a function of low, middle and high N:P ratios (1.2, 12, 120) to determine nutrient effects on As cycling by the cyanobacterium. Total As(V) reduction was observed in all three conditions upon completion of the ten-day experiment. Maximum As(V) reduction rates ranged from (0.013 mmol g C-1 day-1) in the low N:P solution to (0.398 mmol g C-1 day-1) in the high N:P solution. Increased cell biomass in the low N:P ratio solution compensated for the low maximum reduction rate to allow total As(V) reduction. Kinetic equations commonly used to model algal-nutrient interactions were utilized in modeling the current data. The Michaelis-Menten enzyme saturation equation modified with a competitive inhibition term adequately modeled As(III) excretion in the high and middle N:P ratio test conditions. The low N:P test condition further

  19. Arsenic bioaccumulation in a marine juvenile fish Terapon jarbua

    International Nuclear Information System (INIS)

    Zhang Wei; Huang Liangmin; Wang Wenxiong

    2011-01-01

    Highlights: Radiotracer technique was used to quantify the biokinetics of As(V) in a marine fish. As(V) had a low bioavailability to Terapon jarbua. Dietary assimilation of As was only 3.1–7.4% for fish fed with different preys. Dietary uptake could be the primary route for As bioaccumulation in fish. - Abstract: Arsenic (As) is a ubiquitous toxic metalloid that is causing widespread public concern. Recent measurements have indicated that some marine fish in China might be seriously contaminated with As. Yet the biokinetics and bioaccumulation pathway of As in fish remain little understood. In this study, we employed a radiotracer technique to quantify the dissolved uptake, dietary assimilation and subsequent efflux of As(V) in a marine predatory fish, Terapon jarbua. The dissolved uptake of As showed a linear pattern over a range of dissolved concentrations from 0.5 to 50 μg L −1 , with a corresponding uptake rate constant of 0.0015 L g −1 d −1 . The assimilation efficiencies (AEs) of dietary As were only 3.1–7.4% for fish fed with copepods, clams, prey fish, or artificial diets, and were much lower than the As that entered the trophically available metal fraction in the prey. The dietary AEs were independent of the As(V) concentrations in the artificial diets. The efflux rate constant of As in fish following the dietary exposure was 0.03 d −1 . Modeling calculations showed that dietary uptake could be the primary route for As bioaccumulation in fish, and the corresponding contributions of waterborne and dietary uptakes were related to the bioconcentration factor (BCF) of the prey and the ingestion rate of fish. This study demonstrates that As(V) has a low bioavailability to T. jarbua.

  20. Vast diversity of prokaryotic virus genomes encoding double jelly-roll major capsid proteins uncovered by genomic and metagenomic sequence analysis.

    Science.gov (United States)

    Yutin, Natalya; Bäckström, Disa; Ettema, Thijs J G; Krupovic, Mart; Koonin, Eugene V

    2018-04-10

    Analysis of metagenomic sequences has become the principal approach for the study of the diversity of viruses. Many recent, extensive metagenomic studies on several classes of viruses have dramatically expanded the visible part of the virosphere, showing that previously undetected viruses, or those that have been considered rare, actually are important components of the global virome. We investigated the provenance of viruses related to tail-less bacteriophages of the family Tectiviridae by searching genomic and metagenomics sequence databases for distant homologs of the tectivirus-like Double Jelly-Roll major capsid proteins (DJR MCP). These searches resulted in the identification of numerous genomes of virus-like elements that are similar in size to tectiviruses (10-15 kilobases) and have diverse gene compositions. By comparison of the gene repertoires, the DJR MCP-encoding genomes were classified into 6 distinct groups that can be predicted to differ in reproduction strategies and host ranges. Only the DJR MCP gene that is present by design is shared by all these genomes, and most also encode a predicted DNA-packaging ATPase; the rest of the genes are present only in subgroups of this unexpectedly diverse collection of DJR MCP-encoding genomes. Only a minority encode a DNA polymerase which is a hallmark of the family Tectiviridae and the putative family "Autolykiviridae". Notably, one of the identified putative DJR MCP viruses encodes a homolog of Cas1 endonuclease, the integrase involved in CRISPR-Cas adaptation and integration of transposon-like elements called casposons. This is the first detected occurrence of Cas1 in a virus. Many of the identified elements are individual contigs flanked by inverted or direct repeats and appear to represent complete, extrachromosomal viral genomes, whereas others are flanked by bacterial genes and thus can be considered as proviruses. These contigs come from metagenomes of widely different environments, some dominated by

  1. Protein docking prediction using predicted protein-protein interface

    Directory of Open Access Journals (Sweden)

    Li Bin

    2012-01-01

    Full Text Available Abstract Background Many important cellular processes are carried out by protein complexes. To provide physical pictures of interacting proteins, many computational protein-protein prediction methods have been developed in the past. However, it is still difficult to identify the correct docking complex structure within top ranks among alternative conformations. Results We present a novel protein docking algorithm that utilizes imperfect protein-protein binding interface prediction for guiding protein docking. Since the accuracy of protein binding site prediction varies depending on cases, the challenge is to develop a method which does not deteriorate but improves docking results by using a binding site prediction which may not be 100% accurate. The algorithm, named PI-LZerD (using Predicted Interface with Local 3D Zernike descriptor-based Docking algorithm, is based on a pair wise protein docking prediction algorithm, LZerD, which we have developed earlier. PI-LZerD starts from performing docking prediction using the provided protein-protein binding interface prediction as constraints, which is followed by the second round of docking with updated docking interface information to further improve docking conformation. Benchmark results on bound and unbound cases show that PI-LZerD consistently improves the docking prediction accuracy as compared with docking without using binding site prediction or using the binding site prediction as post-filtering. Conclusion We have developed PI-LZerD, a pairwise docking algorithm, which uses imperfect protein-protein binding interface prediction to improve docking accuracy. PI-LZerD consistently showed better prediction accuracy over alternative methods in the series of benchmark experiments including docking using actual docking interface site predictions as well as unbound docking cases.

  2. Protein docking prediction using predicted protein-protein interface.

    Science.gov (United States)

    Li, Bin; Kihara, Daisuke

    2012-01-10

    Many important cellular processes are carried out by protein complexes. To provide physical pictures of interacting proteins, many computational protein-protein prediction methods have been developed in the past. However, it is still difficult to identify the correct docking complex structure within top ranks among alternative conformations. We present a novel protein docking algorithm that utilizes imperfect protein-protein binding interface prediction for guiding protein docking. Since the accuracy of protein binding site prediction varies depending on cases, the challenge is to develop a method which does not deteriorate but improves docking results by using a binding site prediction which may not be 100% accurate. The algorithm, named PI-LZerD (using Predicted Interface with Local 3D Zernike descriptor-based Docking algorithm), is based on a pair wise protein docking prediction algorithm, LZerD, which we have developed earlier. PI-LZerD starts from performing docking prediction using the provided protein-protein binding interface prediction as constraints, which is followed by the second round of docking with updated docking interface information to further improve docking conformation. Benchmark results on bound and unbound cases show that PI-LZerD consistently improves the docking prediction accuracy as compared with docking without using binding site prediction or using the binding site prediction as post-filtering. We have developed PI-LZerD, a pairwise docking algorithm, which uses imperfect protein-protein binding interface prediction to improve docking accuracy. PI-LZerD consistently showed better prediction accuracy over alternative methods in the series of benchmark experiments including docking using actual docking interface site predictions as well as unbound docking cases.

  3. Prediction of Protein-Protein Interactions Related to Protein Complexes Based on Protein Interaction Networks

    Directory of Open Access Journals (Sweden)

    Peng Liu

    2015-01-01

    Full Text Available A method for predicting protein-protein interactions based on detected protein complexes is proposed to repair deficient interactions derived from high-throughput biological experiments. Protein complexes are pruned and decomposed into small parts based on the adaptive k-cores method to predict protein-protein interactions associated with the complexes. The proposed method is adaptive to protein complexes with different structure, number, and size of nodes in a protein-protein interaction network. Based on different complex sets detected by various algorithms, we can obtain different prediction sets of protein-protein interactions. The reliability of the predicted interaction sets is proved by using estimations with statistical tests and direct confirmation of the biological data. In comparison with the approaches which predict the interactions based on the cliques, the overlap of the predictions is small. Similarly, the overlaps among the predicted sets of interactions derived from various complex sets are also small. Thus, every predicted set of interactions may complement and improve the quality of the original network data. Meanwhile, the predictions from the proposed method replenish protein-protein interactions associated with protein complexes using only the network topology.

  4. Not so bad after all: retroviruses and long terminal repeat retrotransposons as a source of new genes in vertebrates.

    Science.gov (United States)

    Naville, M; Warren, I A; Haftek-Terreau, Z; Chalopin, D; Brunet, F; Levin, P; Galiana, D; Volff, J-N

    2016-04-01

    Viruses and transposable elements, once considered as purely junk and selfish sequences, have repeatedly been used as a source of novel protein-coding genes during the evolution of most eukaryotic lineages, a phenomenon called 'molecular domestication'. This is exemplified perfectly in mammals and other vertebrates, where many genes derived from long terminal repeat (LTR) retroelements (retroviruses and LTR retrotransposons) have been identified through comparative genomics and functional analyses. In particular, genes derived from gag structural protein and envelope (env) genes, as well as from the integrase-coding and protease-coding sequences, have been identified in humans and other vertebrates. Retroelement-derived genes are involved in many important biological processes including placenta formation, cognitive functions in the brain and immunity against retroelements, as well as in cell proliferation, apoptosis and cancer. These observations support an important role of retroelement-derived genes in the evolution and diversification of the vertebrate lineage. Copyright © 2016 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

  5. Characterization of the SOS meta-regulon in the human gut microbiome.

    Science.gov (United States)

    Cornish, Joseph P; Sanchez-Alberola, Neus; O'Neill, Patrick K; O'Keefe, Ronald; Gheba, Jameel; Erill, Ivan

    2014-05-01

    Data from metagenomics projects remain largely untapped for the analysis of transcriptional regulatory networks. Here, we provide proof-of-concept that metagenomic data can be effectively leveraged to analyze regulatory networks by characterizing the SOS meta-regulon in the human gut microbiome. We combine well-established in silico and in vitro techniques to mine the human gut microbiome data and determine the relative composition of the SOS network in a natural setting. Our analysis highlights the importance of translesion synthesis as a primary function of the SOS response. We predict the association of this network with three novel protein clusters involved in cell wall biogenesis, chromosome partitioning and restriction modification, and we confirm binding of the SOS response transcriptional repressor to sites in the promoter of a cell wall biogenesis enzyme, a phage integrase and a death-on-curing protein. We discuss the implications of these findings and the potential for this approach for metagenome analysis.

  6. The prophages of Lactobacillus johnsonii NCC 533: comparative genomics and transcription analysis

    International Nuclear Information System (INIS)

    Ventura, Marco; Canchaya, Carlos; Pridmore, R. David; Bruessow, Harald

    2004-01-01

    Two non-inducible, but apparently complete prophages were identified in the genome of the sequenced Lactobacillus johnsonii strain NCC 533. The 38- and 40-kb-long prophages Lj928 and Lj965 represent distinct lineages of Sfi11-like pac-site Siphoviridae unrelated at the DNA sequence level. The deduced structural proteins from Lj928 demonstrated aa sequence identity with Lactococcus lactis phage TP901-1, while Lj965 shared sequence links with Streptococcus thermophilus phage O1205. With the exception of tRNA genes, inserted between DNA replication and DNA packaging genes, the transcription of the prophage was restricted to the genome segments near both attachment sites. Transcribed genes unrelated to phage functions were inserted between the phage repressor and integrase genes; one group of genes shared sequence relatedness with a mobile DNA element in Staphylococcus aureus. A short, but highly transcribed region was located between the phage lysin and right attachment site; it lacked a protein-encoding function in one prophage

  7. Ionic liquid-assisted multiwalled carbon nanotube-dispersive micro-solid phase extraction for sensitive determination of inorganic As species in garlic samples by electrothermal atomic absorption spectrometry

    Science.gov (United States)

    Grijalba, Alexander Castro; Escudero, Leticia B.; Wuilloud, Rodolfo G.

    2015-08-01

    A highly sensitive dispersive micro-solid phase extraction (D-μ-SPE) method combining an ionic liquid (IL) and multi-walled carbon nanotubes (MWCNTs) for inorganic As species (As(III) and As(V)) species separation and determination in garlic samples by electrothermal atomic absorption spectrometry (ETAAS) was developed. Trihexyl(tetradecil)phosphonium chloride IL was used to form an ion pair with the arsenomolybdate complex obtained by reaction of As(V) with molybdate ion. Afterwards, 1.0 mg of MWCNTs was dispersed for As(V) extraction and the supernatant was separated by centrifugation. MWCNTs were re-dispersed with tetradecyltrimethylammonium bromide surfactant and ultrasound followed by direct injection into the graphite furnace of ETAAS for As determination. Pyrolysis and atomization conditions were carefully studied for complete decomposition of MWCNTs and IL matrices. Under optimum conditions, an extraction efficiency of 100% and a preconcentration factor of 70 were obtained with 5 mL of garlic extract. The detection limit was 7.1 ng L- 1 and the relative standard deviations (RSDs) for six replicate measurements at 5 μg L- 1 of As were 5.4% and 4.8% for As(III) and As(V), respectively. The proposed D-μ-SPE method allowed the efficient separation and determination of inorganic As species in a complex matrix such as garlic extract.

  8. Preconcentration of Arsenic in Water Samples Using the Composition-Induced Phase Separation Method and Determination by ETAAS

    Directory of Open Access Journals (Sweden)

    Güçoğlu M.

    2013-04-01

    Full Text Available A new phase transition microextraction method was developed for determination of trace amount of arsenic ions in water samples in this work. The method is based on the critical point of miscibility of solvents. In this method the mixed solution of sample and organic solvent is initially homogeneous but is separated into two phases by adding a secondary solvent (modifier. In acidic medium As(V was complexed with ammonium molybdate, this complex was quantitatively extracted to the mixture of organic solvent (acetonitrile/methyl isobutyl ketone before ETAAS determination. Total inorganic arsenic (III, V was extracted similarly after oxidation of As(III to As(V with nitric acid. Concentration of As(III was calculated by difference in the concentration between total arsenic and As(V. Optimization of the experimental conditions and instrumental parameters was investigated in detail. A detection limit of 0.05 μgL−1 with enrichment factor of 85 was achieved for only 5 mL of sample. The analytical curve was linear in the concentration range of 0.25-4.00 μgL−1. Relative standard deviation (RSD for 10 replicate determinations of 2.0 μgL−1 of As(V was 4,1%. The method was successfully applied to preconcentration and determination of arsenic in real water samples.

  9. A Bacteriophage-Related Chimeric Marine Virus Infecting Abalone

    Science.gov (United States)

    Zhuang, Jun; Cai, Guiqin; Lin, Qiying; Wu, Zujian; Xie, Lianhui

    2010-01-01

    Marine viruses shape microbial communities with the most genetic diversity in the sea by multiple genetic exchanges and infect multiple marine organisms. Here we provide proof from experimental infection that abalone shriveling syndrome-associated virus (AbSV) can cause abalone shriveling syndrome. This malady produces histological necrosis and abnormally modified macromolecules (hemocyanin and ferritin). The AbSV genome is a 34.952-kilobase circular double-stranded DNA, containing putative genes with similarity to bacteriophages, eukaryotic viruses, bacteria and endosymbionts. Of the 28 predicted open reading frames (ORFs), eight ORF-encoded proteins have identifiable functional homologues. The 4 ORF products correspond to a predicted terminase large subunit and an endonuclease in bacteriophage, and both an integrase and an exonuclease from bacteria. The other four proteins are homologous to an endosymbiont-derived helicase, primase, single-stranded binding (SSB) protein, and thymidylate kinase, individually. Additionally, AbSV exhibits a common gene arrangement similar to the majority of bacteriophages. Unique to AbSV, the viral genome also contains genes associated with bacterial outer membrane proteins and may lack the structural protein-encoding ORFs. Genomic characterization of AbSV indicates that it may represent a transitional form of microbial evolution from viruses to bacteria. PMID:21079776

  10. A bacteriophage-related chimeric marine virus infecting abalone.

    Directory of Open Access Journals (Sweden)

    Jun Zhuang

    Full Text Available Marine viruses shape microbial communities with the most genetic diversity in the sea by multiple genetic exchanges and infect multiple marine organisms. Here we provide proof from experimental infection that abalone shriveling syndrome-associated virus (AbSV can cause abalone shriveling syndrome. This malady produces histological necrosis and abnormally modified macromolecules (hemocyanin and ferritin. The AbSV genome is a 34.952-kilobase circular double-stranded DNA, containing putative genes with similarity to bacteriophages, eukaryotic viruses, bacteria and endosymbionts. Of the 28 predicted open reading frames (ORFs, eight ORF-encoded proteins have identifiable functional homologues. The 4 ORF products correspond to a predicted terminase large subunit and an endonuclease in bacteriophage, and both an integrase and an exonuclease from bacteria. The other four proteins are homologous to an endosymbiont-derived helicase, primase, single-stranded binding (SSB protein, and thymidylate kinase, individually. Additionally, AbSV exhibits a common gene arrangement similar to the majority of bacteriophages. Unique to AbSV, the viral genome also contains genes associated with bacterial outer membrane proteins and may lack the structural protein-encoding ORFs. Genomic characterization of AbSV indicates that it may represent a transitional form of microbial evolution from viruses to bacteria.

  11. Cyclic GMP-AMP synthase is an innate immune sensor of HIV and other retroviruses.

    Science.gov (United States)

    Gao, Daxing; Wu, Jiaxi; Wu, You-Tong; Du, Fenghe; Aroh, Chukwuemika; Yan, Nan; Sun, Lijun; Chen, Zhijian J

    2013-08-23

    Retroviruses, including HIV, can activate innate immune responses, but the host sensors for retroviruses are largely unknown. Here we show that HIV infection activates cyclic guanosine monophosphate-adenosine monophosphate (cGAMP) synthase (cGAS) to produce cGAMP, which binds to and activates the adaptor protein STING to induce type I interferons and other cytokines. Inhibitors of HIV reverse transcriptase, but not integrase, abrogated interferon-β induction by the virus, suggesting that the reverse-transcribed HIV DNA triggers the innate immune response. Knockout or knockdown of cGAS in mouse or human cell lines blocked cytokine induction by HIV, murine leukemia virus, and simian immunodeficiency virus. These results indicate that cGAS is an innate immune sensor of HIV and other retroviruses.

  12. Use of novel composite coagulants for arsenic removal from waters : experimental insight for the application of polyferric sulfate (PFS)

    OpenAIRE

    Katsoyiannis, Ioannis A.; Tzollas, Nikolaos M.; Tolkou, Athanasia K.; Mitrakas, Manassis; Ernst, Mathias; Zouboulis, Anastasios I.

    2017-01-01

    In the present study, several pre-polymerized coagulants of iron and aluminum were tested for their efficiency towards As(V) and As(III) removal from water sources. The results showed that the pre-polymerized coagulants of iron, such as poly-ferric sulfate and poly-ferric silicate chloride, were very efficient for As(V) removal. With regard to As(III) removal, among all examined coagulants, including the conventional ferric chloride, only the poly-ferric sulfate (PFS) was able to reduce As(II...

  13. Efficacy of three treatment protocols for adolescents with social anxiety disorder: a 5-year follow-up assessment.

    Science.gov (United States)

    Garcia-Lopez, Luis-Joaquin; Olivares, Jose; Beidel, Deborah; Albano, Anne-Marie; Turner, Samuel; Rosa, Ana I

    2006-01-01

    Few studies have reported long-term follow-up data in adults and even fewer in adolescents. The purpose of this work is to report on the longest follow-up assessment in the literature on treatments for adolescents with social phobia. A 5-year follow-up assessment was conducted with subjects who originally received either Cognitive Behavioral Group Therapy for Adolescents (CBGT-A), Social Effectiveness Therapy for Adolescents--Spanish version (SET-Asv), or Intervención en Adolescentes con Fobia Social--Treatment for Adolescents with Social Phobia (IAFS) in a controlled clinical trial. Twenty-three subjects completing the treatment conditions were available for the 5-year follow-up. Results demonstrate that subjects treated either with CBGT-A, SET-Asv and IAFS continued to maintain their gains after treatments were terminated. Either the CBGT-A, SET-Asv and IAFS can provide lasting effects to the majority of adolescents with social anxiety. Issues that may contribute to future research and clinical implications are discussed.

  14. Characterization of the extremely arsenic-resistant Brevibacterium linens strain AE038-8 isolated from contaminated groundwater in Tucumán, Argentina

    Science.gov (United States)

    Maizel, Daniela; Blum, Jodi S.; Ferrero, Marcela A.; Utturkar, Sagar M.; Brown, Steven D.; Rosen, Barry P.; Oremland, Ronald S.

    2015-01-01

    Brevibacterium linens AE038-8, isolated from As-contaminated groundwater in Tucumán (Argentina), is highly resistant to arsenic oxyanions, being able to tolerate up to 1 M As(V) and 75 mM As(III) in a complex medium. Strain AE038-8 was also able to reduce As(V) to As(III) when grown in complex medium but paradoxically it could not do this in a defined minimal medium with sodium acetate and ammonium sulfate as carbon and nitrogen sources, respectively. No oxidation of As(III) to As(V) was observed under any conditions. Three copies of the ars operon comprising arsenic resistance genes were found on B. linens AE038-8 genome. In addition to the well known arsC, ACR3 andarsR, two copies of the arsO gene of unknown function were detected.

  15. Confocal μ-XRF, μ-XAFS, and μ-XRD Studies of Sediment from a Nuclear Waste Disposal Natural Analogue Site and Fractured Granite Following a Radiotracer Migration Experiment

    International Nuclear Information System (INIS)

    Denecke, Melissa A.; Brendebach, Boris; Rothe, Joerg; Simon, Rolf; Janssens, Koen; Nolf, Wout de; Vekemans, Bart; Falkenberg, Gerald; Somogyi, Andrea; Noseck, Ulrich

    2007-01-01

    Combined μ-XRF, μ-XAFS, and μ-XRD investigations of a uranium-rich tertiary sediment, from a nuclear repository natural analogue site, and a fractured granite bore core section after a column tracer experiment using a Np(V) containing cocktail have been performed. Most μ-XRF/μ-XAFS measurements are recorded in a confocal geometry to provide added depth information. The U-rich sediment results show uranium to be present as a tetravalent phosphate and that U(IV) is associated with As(V). Arsenic present is either As(V) or As(0). The As(0) forms thin coatings on the surface of pyrite nodules. A hypothesis for the mechanism of uranium immobilization is proposed, where arsenopyrite acted as reductant of ground water dissolved U(VI) leading to precipitation of less soluble U(IV) and thereby forming As(V). Results for the granite sample show the immobilized Np to be tetravalent and associated with facture material

  16. Thermodynamics of complexes formation by ITC in methanol/water = 9/1 (v/v) solution: A case study

    Energy Technology Data Exchange (ETDEWEB)

    Fisicaro, Emilia, E-mail: emilia.fisicaro@unipr.it [University of Parma, Department of Pharmacy, Parco Area delle Scienze, 27/A, 43124 Parma (Italy); Compari, Carlotta; Bacciottini, Franco; Contardi, Laura [University of Parma, Department of Pharmacy, Parco Area delle Scienze, 27/A, 43124 Parma (Italy); Carcelli, Mauro; Rispoli, Gabriele; Rogolino, Dominga [University of Parma, Department of Chemistry, Parco Area delle Scienze, 17/A, 43124 Parma (Italy)

    2014-06-01

    Graphical abstract: Integrase strand transfert inhibitors chelate the metal ions in the active site of HIV integrase. - Highlights: • Development of inhibitors acting against those viral enzymes operating via a cooperative two-metal ion mechanism, such as HIV integrase (IN), requires optimizing the binding affinity to the target. • We have defined an experimental procedure for obtaining reliable thermodynamic data by ITC in methanol/water = 9/1 (v/v) as solvent. • Formation heats in mixed solvent of the complexes formed by a ligand, model of Raltegravir, with Mg(II), Mn(II), Co(II) and Zn(II) are here reported. - Abstract: Most enzymes that participate in the biochemistry of nucleic acids require divalent metal ion cofactors to promote activity. Development of potent inhibitors, acting against those viral enzymes operating via a cooperative two-metal ion mechanism, such as HIV integrase (IN) and RNase H, hepatitis C virus polymerase and influenza endonuclease, requires optimizing the binding affinity to the target, which is dictated by the binding free energy composed of both enthalpic and entropic contributions. They can be obtained by using isothermal titration microcalorimetry. We have defined an experimental procedure for obtaining reliable thermodynamic data in methanol/water = 9/1 0.1 M KCl as solvent, used to overcome solubility problems. In this way we have measured the heats of formation of the complexes formed by N-(4-fluorobenzyl)-5-hydroxy-2-isopropyl-1-methyl-6-oxo-1, 6-dihydroxypyrimidine-4-carboxylate (HL, a model of Raltegravir, the antiretroviral drug produced by Merck and Co.), and a series of divalent metal ions of biological interest (Mg(II), Mn(II), Co(II) and Zn(II)), whose speciation was previously determined by potentiometry.

  17. [Mechanisms of action, pharmacology and interactions of dolutegravir].

    Science.gov (United States)

    Ribera, Esteban; Podzamczer, Daniel

    2015-03-01

    Dolutegravir is a second-generation integrase strand transfer inhibitor (INSTI), whose potential and binding half-life in the integrase are far superior to those of raltegravir and elvitegravir, conferring it with unique characteristics in terms of its genetic barrier to resistance and activity against viruses with one or more mutations in the integrase. The pharmacokinetic properties of dolutegravir allow once-daily dosing (50 mg), with or without food, maintaining concentrations far above those effective against wild-type viruses. If integrase resistance mutations are present, the recommended dosing regimen is 50 mg/12 h. The distribution of dolutegravir in cerebrospinal fluid is good and effective concentrations are also reached in the male and female genital tracts. Dolutegravir is metabolized by UGT1A1 and, to a lesser extent, by CYP3A4, without being an inducer or inhibitor of the usual metabolic systems. It has a very low potential for drug interactions and can be administered in routine doses with most drugs. Dose adjustment is not required, even in patients with renal insufficiency or mild or moderate liver failure. Increasing the dose of dolutegravir (50 mg/12 h) is only recommended when administered with efavirenz, nevirapine, fosamprenavir/r, tipranavir/r, rifampicin, carbamazepine, phenytoin and phenobarbital. Coadministration of dolutegravir with etravirine is not recommended without a protease inhibitor or with Hypericum perforatum. Dolutegravir should be administered 2 h before or 6 h after antacids or products with polyvalent cations. Dolutegravir can reduce renal tubule secretion of substances excreted via OCT2, with a slight initial increase in creatinine, with no risk of renal toxicity. The drug can also increase metformin concentrations and consequently monitoring is recommended in case dose adjustment is required. In summary, dolutegravir has excellent pharmacokinetic and drug interaction profiles. Copyright © 2015 Elsevier España, S

  18. A new activity of anti-HIV and anti-tumor protein GAP31: DNA adenosine glycosidase - Structural and modeling insight into its functions

    Energy Technology Data Exchange (ETDEWEB)

    Li, Hui-Guang [Department of Biochemistry, New York University School of Medicine, New York, NY 10016 (United States); Huang, Philip L. [American Biosciences, Boston, MA 02114 (United States); Zhang, Dawei; Sun, Yongtao [Department of Biochemistry, New York University School of Medicine, New York, NY 10016 (United States); Chen, Hao-Chia [Endocrinology and Reproduction Research Branch, National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892 (United States); Zhang, John [Department of Chemistry, New York University, New York, NY 10003 (United States); Huang, Paul L. [Department of Medicine, Harvard Medical School and Massachusetts General Hospital, Boston, MA 02114 (United States); Kong, Xiang-Peng, E-mail: xiangpeng.kong@med.nyu.edu [Department of Biochemistry, New York University School of Medicine, New York, NY 10016 (United States); Lee-Huang, Sylvia, E-mail: sylvia.lee-huang@med.nyu.edu [Department of Biochemistry, New York University School of Medicine, New York, NY 10016 (United States)

    2010-01-01

    We report here the high-resolution atomic structures of GAP31 crystallized in the presence of HIV-LTR DNA oligonucleotides systematically designed to examine the adenosine glycosidase activity of this anti-HIV and anti-tumor plant protein. Structural analysis and molecular modeling lead to several novel findings. First, adenine is bound at the active site in the crystal structures of GAP31 to HIV-LTR duplex DNA with 5' overhanging adenosine ends, such as the 3'-processed HIV-LTR DNA but not to DNA duplex with blunt ends. Second, the active site pocket of GAP31 is ideally suited to accommodate the 5' overhanging adenosine of the 3'-processed HIV-LTR DNA and the active site residues are positioned to perform the adenosine glycosidase activity. Third, GAP31 also removes the 5'-end adenine from single-stranded HIV-LTR DNA oligonucleotide as well as any exposed adenosine, including that of single nucleotide dAMP but not from AMP. Fourth, GAP31 does not de-purinate guanosine from di-nucleotide GT. These results suggest that GAP31 has DNA adenosine glycosidase activity against accessible adenosine. This activity is distinct from the generally known RNA N-glycosidase activity toward the 28S rRNA. It may be an alternative function that contributes to the antiviral and anti-tumor activities of GAP31. These results provide molecular insights consistent with the anti-HIV mechanisms of GAP31 in its inhibition on the integration of viral DNA into the host genome by HIV-integrase as well as irreversible topological relaxation of the supercoiled viral DNA.

  19. Oligomeric protein structure networks: insights into protein-protein interactions

    Directory of Open Access Journals (Sweden)

    Brinda KV

    2005-12-01

    Full Text Available Abstract Background Protein-protein association is essential for a variety of cellular processes and hence a large number of investigations are being carried out to understand the principles of protein-protein interactions. In this study, oligomeric protein structures are viewed from a network perspective to obtain new insights into protein association. Structure graphs of proteins have been constructed from a non-redundant set of protein oligomer crystal structures by considering amino acid residues as nodes and the edges are based on the strength of the non-covalent interactions between the residues. The analysis of such networks has been carried out in terms of amino acid clusters and hubs (highly connected residues with special emphasis to protein interfaces. Results A variety of interactions such as hydrogen bond, salt bridges, aromatic and hydrophobic interactions, which occur at the interfaces are identified in a consolidated manner as amino acid clusters at the interface, from this study. Moreover, the characterization of the highly connected hub-forming residues at the interfaces and their comparison with the hubs from the non-interface regions and the non-hubs in the interface regions show that there is a predominance of charged interactions at the interfaces. Further, strong and weak interfaces are identified on the basis of the interaction strength between amino acid residues and the sizes of the interface clusters, which also show that many protein interfaces are stronger than their monomeric protein cores. The interface strengths evaluated based on the interface clusters and hubs also correlate well with experimentally determined dissociation constants for known complexes. Finally, the interface hubs identified using the present method correlate very well with experimentally determined hotspots in the interfaces of protein complexes obtained from the Alanine Scanning Energetics database (ASEdb. A few predictions of interface hot

  20. A combined experimental study of vivianite and As (V) reactivity in the pH range 2-11

    International Nuclear Information System (INIS)

    Thinnappan, V.; Merrifield, C.M.; Islam, F.S.; Polya, D.A.; Wincott, P.; Wogelius, R.A.

    2008-01-01

    Four different sets of experiments were completed in order to constrain vivianite [Fe 3 (PO 4 ) 2 . 8H 2 O] reactivity under conditions pertinent to As(V)-bearing groundwater systems. Firstly, titration experiments were undertaken in the pH range 4-9 to determine the zero point of charge (ZPC) of vivianite; showing that the ZPC lies at a pH of approximately 5.3. Secondly, the steady state dissolution rates of vivianite far from equilibrium were measured in aqueous solutions in the pH range 2-10 at 18.5 d eg. C (±3 deg. C) using a fluidized bed reactor. The rate of vivianite dissolution, R, is given by (1)R(moless -1 cm -2 )=1.18x10 -10 a H+ 0.77 +1x10 -15 +6.92x10 -24 a H+ -1 The dissolution rate exhibits an exponential increase with increase in the activity of the H + ion (a H+ ) in solution at 2 8. Thirdly, the sorption of arsenate [As(V)] onto natural well-crystallized vivianite in the pH range 3-11 under static flow conditions was determined. 25-40% of As(V) from a starting concentration (C 0 ) of 100 μM was adsorbed onto vivianite. Static adsorption experiments were also completed at two lower As(V) concentrations (C 0 = 10 and 1 μM). Sorption was determined to be only weakly dependent on pH. Fourthly, the final part of this study investigated the sorption of As(V) onto vivianite at pH 9 under dynamic flow conditions. An input solution of 4 mM As(V) was applied to water saturated columns, followed by leaching with deionised water (DIW). Breakthrough curves show that the retention and exchangeability of As within the column is enhanced with vivianite present, consistent with solid phase analysis of unreacted and reacted solid materials. A simple calculation based on a model shallow Bengal sediment having about 0.2 wt% of vivianite and total initial dissolved As concentrations of 100 μM showed that under such conditions 88% of dissolved As(V) could potentially be adsorbed onto vivianite. These results will help to better understand As mobility in the

  1. New and investigational antiretroviral drugs for HIV infection: mechanisms of action and early research findings.

    Science.gov (United States)

    Saag, Michael S

    2012-12-01

    Numerous investigational antiretroviral agents are in clinical development. Among them are festinavir (BMS986001), a thymidine analogue similar to stavudine with reduced potential for toxicity; GS-7340, a prodrug of tenofovir that achieves greater intracellular concentrations; MK-1439, a nonnucleoside analogue reverse transcriptase inhibitor (NNRTI) that retains activity against common NNRTI-associated resistance mutations; and albuvirtide, a long-acting parenteral fusion inhibitor. Investigational integrase strand transfer inhibitors (InSTIs) include elvitegravir, recently approved by the US Food and Drug Administration (FDA) as part of a once-daily, single-tablet formulation with cobicistat/tenofovir/emtricitabine; dolutegravir, which maintains some activity against raltegravir- and elvitegravir-resistant mutants; and S/GSK1265744, which also maintains some activity against resistance mutations in the integrase gene and is being developed as a long-lasting parenteral agent. Novel 2-(quinolin-3-yl)acetic acid derivatives (LEDGINs), agents that were originally thought to inhibit the interaction of integrase with its cofactor lens epithelium-derived growth factor p75 (LEDGF/p75), be active against InSTI-resistant mutants and to have additive activity when combined with InSTIs. This article summarizes a presentation by Michael S. Saag, MD, at the IAS-USA live Improving the Management of HCV Disease continuing medical education program held in New York in October 2012.

  2. Protein nanoparticles for therapeutic protein delivery.

    Science.gov (United States)

    Herrera Estrada, L P; Champion, J A

    2015-06-01

    Therapeutic proteins can face substantial challenges to their activity, requiring protein modification or use of a delivery vehicle. Nanoparticles can significantly enhance delivery of encapsulated cargo, but traditional small molecule carriers have some limitations in their use for protein delivery. Nanoparticles made from protein have been proposed as alternative carriers and have benefits specific to therapeutic protein delivery. This review describes protein nanoparticles made by self-assembly, including protein cages, protein polymers, and charged or amphipathic peptides, and by desolvation. It presents particle fabrication and delivery characterization for a variety of therapeutic and model proteins, as well as comparison of the features of different protein nanoparticles.

  3. A novel highly efficient adsorbent {[Co4(L)2(μ3-OH)2(H2O)3(4,4‧-bipy)2]·(H2O)2}n: Synthesis, crystal structure, magnetic and arsenic (V) absorption capacity

    Science.gov (United States)

    Zhang, Chong; Xiao, Yu; Qin, Yan; Sun, Quanchun; Zhang, Shuhua

    2018-05-01

    A novel highly efficient adsorbent-microporous tetranuclear Co(II)-based polymer, {[Co4(L)2(μ3-OH)2(H2O)3(4,4‧-bipy)2]·(H2O)2}n (1, H3L = 4-(N,N‧-bis(4-carboxybenzyl)amino) benzenesulfonic acid, 4,4‧-bipy = 4,4‧-bipyridine), was hydrothermally synthesized. The complex 1 is a metal-organic framework (MOF) material which was characterized by single-crystal X-ray diffraction, BET and platon software. Co-MOF (complex 1) reveals excellent adsorption property. The capacity of Co-MOF to remove arsenic As(V) from sodium arsenate aqueous solutions was investigated (The form of As(V) is AsO43-). The experimental results showed that Co-MOF had a higher stable and relatively high As(V) removal rate (> 98%) at pH 4-10. The adsorption kinetics followed a pseudo-second-order kinetic model, and the adsorption isotherm followed the Langmuir equation. Co-MOF exhibits a very high adsorption capacity of As(V) in aqueous solution (Qmax of 96.08 mg/g). Finally, the optimal adsorption conditions for the model were obtained through a Box-Behnken response surface experiment which was designed with adsorption time, dose, temperature and rotational speed of the shaker as the influencing factors to determine two-factor interaction effects. Co-MOF was further characterized using FTIR, PXRD, X-ray photoelectron spectroscopy before and after adsorption As (V). The magnetism of Co-MOF was also discussed.

  4. The sorption of inorganic arsenic on modified sepiolite: Effect of hydrated iron(III-oxide

    Directory of Open Access Journals (Sweden)

    Ilić Nikola I.

    2014-01-01

    Full Text Available The sorption of inorganic arsenic species, As(III and As(V, from water by sepiolite modified with hydrated iron(III oxide was investigated at 25 °C through batch studies. The influence of the initial pH value, the initial As concentrations, the contact time and types of water on the sorption capacity was investigated. Two types of water were used, deionized and groundwater. The maximal sorption capacity for As(III from deionized water was observed at initial and final pH value 7.0, while the bonding of As(V was observed to be almost pH independent for pH value in the range from 2.0 to 7.0, and the significant decrease in the sorption capacity was observed at pH values above 7.0. The sorption capacity at initial pH 7.0 was about 10 mg gˉ1 for As(III and 4.2 mg gˉ1 for As(V in deionized water. The capacity in groundwater was decreased by 40 % for As(III and by 20 % for As(V. The Langmuir model and pseudo-second order kinetic model revealed good agreement with the experimental results. The results show that Fe(III-modified sepiolite exhibits significant affinity for arsenic removal and it has a potential for the application in water purification processes. [Projekat Ministarstva nauke Republike Srbije, br. III 45019, III 43009 i TR 37010

  5. Synthesis and characterization of anionic/nonionic surfactant-interceded iron-doped TiO{sub 2} to enhance sorbent/photo-catalytic properties

    Energy Technology Data Exchange (ETDEWEB)

    Sharma, Ajit; Lee, Byeong-Kyu, E-mail: bklee@ulsan.ac.kr

    2015-09-15

    We investigated the synthesis, characterization, and application of surfactant-interceded Fe nanoparticle-doped TiO{sub 2} (TiO{sub 2}/Fe-S1 and TiO{sub 2}/Fe-S2) that were used as adsorbents and photo-catalysts for the removal of As(V) ions from aqueous media. Two types of surfactant (anionic (sodium dodecyl sulfate), S1 and non-ionic (Triton X-100), S2) were used to obtain the separation and mono-dispersion of Fe(III) ions in the reaction solution. The nanocomposites were characterized by Fourier transform infrared (FTIR) spectroscopy, X-ray photoelectron spectroscopy (XPS), UV–vis, scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM/EDX) and elemental mapping analysis before and after As(V) removal. The Langmuir capacities (q{sub e}, mg/g) of the sodium dodecyl sulfate (SDS) and Triton X-100 interceded nanocomposites (TiO{sub 2}/Fe-S1 and TiO{sub 2}/Fe-S2, respectively) for arsenic removal were determined to be 65.79 and 50.76 mg/g, respectively, in aqueous media with As(V) concentration ranges of 0–10 mg/L at pH 6.5. - Highlights: • Fe(III) doped TiO{sub 2} nanocomposite was prepared with surfactant. • Anionic surfactant SDS enhanced the transfer of Fe(III) ions to TiO{sub 2}. • Surfactant-interceded nanocomposite enhanced As(V) removal. • Arsenic removal efficiency was as follows: dark phase>visible phase>UV region.

  6. Long-term effect of adaptive servo ventilation on patients with chronic heart failure and sleep-disordered breathing: Meta analysis

    Directory of Open Access Journals (Sweden)

    Yu-xing FEI

    2017-02-01

    Full Text Available Objective To evaluate the long-tem effect of adaptive servo ventilation (ASV on patients with chronic heart failure (CHF and sleep-disordered breathing (SDB. Methods The controlled clinical articles were searched included in PubMed, Cochrane, EMBASE and CBM, CJFD, WangFang Database from Jan. 1970 to Dec. 2015. Included standard: left ventricular ejection fraction (LVEF ≤55%, apnea hypopnea index (AHI ≥15/h, follow up period over 4 weeks. After quality assessment (modified Jadad score and data extraction by two independent reviewers, mete analysis was performed with RevMan 5.3 software. Results Thirteen studies were recruited including 442 cases being followed over 4 weeks [ASV group 233 cases and control group 216 cases (corssover design 7]. Compared to control group, LVEF increased [weighted mean difference (WMD=3.72, 95%CI: 1.80-5.64, P<0.01] and AHI decreased significantly (WMD=–18.63, 95%CI: –26.19-–11.08, the distance walked in 6 minutes increased (WMD=28.72, 95%CI: 2.26-55.18, P=0.03 and plasma N terminal brain natriuretic peptide precursor (NT-pro BNP decreased significantly (WMD=–744.03, 95%CI: –1262.45-–225.62, P<0.05 in ASV group. Conclusion Over 4 weeks ASV may improve LVEF and AHI, increase 6-min walking distance and decrease NT-pro BNP in patients with CHF and SDB. DOI: 10.11855/j.issn.0577-7402.2016.12.12

  7. Selected Fe and Mn (nano)oxides as perspective amendments for the stabilization of As in contaminated soils.

    Science.gov (United States)

    Michálková, Zuzana; Komárek, Michael; Veselská, Veronika; Číhalová, Sylva

    2016-06-01

    An amorphous Mn oxide (AMO), nanomaghemite, and nanomagnetite were used as potential amendments reducing the mobility of As in three contrasting contaminated soils differing in origin of As contamination. Adsorption experiments and XPS analyses combined with incubation batch experiments and pH-static leaching tests were used. The AMO showed excellent adsorption capacity for As(V) reaching a maximum of 1.79 mmol g(-1) at pH 7 and 8. Interestingly, the adsorption capacity in this case decreases with decreasing pH, probably as a result of AMO dissolution at lower pH values. Chemical sorption of As(V) onto AMO was further confirmed with XPS. Both Fe nano-oxides proved the highest adsorption capacity at pH 4 reaching 11 mg g(-1) of adsorbed As(V). The AMO was also the most efficient amendment for decreasing As concentrations in soil solutions during 8 weeks of incubation. Additionally, pH-static leaching tests were performed at pH 4, 5, 6, 7, and natural pH (not adjusted) and AMO again proved the highest ability to decrease As content in leachate. On the other hand, strong dissolution of this amendment at lower pH values (especially pH 4) was observed. For that reason, AMO appears as a promising stabilizing agent for As, especially in neutral, alkaline, or slightly acidic soils, where As(V) species are expected to be more mobile.

  8. Marine ASV Range Surveillance System, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — United States spaceports carry out the impressive task of launching and recovering spacecrafts and payloads which represent extremely unique and expensive assets....

  9. Marine ASV Range Surveillance System, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — United States spaceports carry out the critical task of launching and recovering vehicles and payloads. These are extremely unique and expensive assets, and their...

  10. Protein-protein interactions: an application of Tus-Ter mediated protein microarray system.

    Science.gov (United States)

    Sitaraman, Kalavathy; Chatterjee, Deb K

    2011-01-01

    In this chapter, we present a novel, cost-effective microarray strategy that utilizes expression-ready plasmid DNAs to generate protein arrays on-demand and its use to validate protein-protein interactions. These expression plasmids were constructed in such a way so as to serve a dual purpose of synthesizing the protein of interest as well as capturing the synthesized protein. The microarray system is based on the high affinity binding of Escherichia coli "Tus" protein to "Ter," a 20 bp DNA sequence involved in the regulation of DNA replication. The protein expression is carried out in a cell-free protein synthesis system, with rabbit reticulocyte lysates, and the target proteins are detected either by labeled incorporated tag specific or by gene-specific antibodies. This microarray system has been successfully used for the detection of protein-protein interaction because both the target protein and the query protein can be transcribed and translated simultaneously in the microarray slides. The utility of this system for detecting protein-protein interaction is demonstrated by a few well-known examples: Jun/Fos, FRB/FKBP12, p53/MDM2, and CDK4/p16. In all these cases, the presence of protein complexes resulted in the localization of fluorophores at the specific sites of the immobilized target plasmids. Interestingly, during our interactions studies we also detected a previously unknown interaction between CDK2 and p16. Thus, this Tus-Ter based system of protein microarray can be used for the validation of known protein interactions as well as for identifying new protein-protein interactions. In addition, it can be used to examine and identify targets of nucleic acid-protein, ligand-receptor, enzyme-substrate, and drug-protein interactions.

  11. Bioenergetics of transient and steady-state anaerobic redox processes relevant to groundwater contamination

    DEFF Research Database (Denmark)

    Heimann, Axel Colin

    I afhandlingen undersøges anaerob mikrobiel respiration for to forskellige typer af kontaminanter i grundvandet, klorerede ethener og arsen. En kombination af ren- og blandkultur eksperimenter, sedimentmikrokosmos studier og termodynamiske beregninger blev benyttet, for at belyse energetiske......). Ligeledes viste sediment mikrokosmer fra en arsen forurenet aquifer i Vietnam hurtig omsætning af As(V) til As(III) ledsaget af forholdsvis lave steady state brint niveauer. Sammen, tyder data på, at As(V) reduktion, mistænkt for at spille en rolle i arsen kontaminering i grundvandsystemer, er en meget...

  12. Truly Absorbed Microbial Protein Synthesis, Rumen Bypass Protein, Endogenous Protein, and Total Metabolizable Protein from Starchy and Protein-Rich Raw Materials

    NARCIS (Netherlands)

    Parand, Ehsan; Vakili, Alireza; Mesgaran, Mohsen Danesh; Duinkerken, Van Gert; Yu, Peiqiang

    2015-01-01

    This study was carried out to measure truly absorbed microbial protein synthesis, rumen bypass protein, and endogenous protein loss, as well as total metabolizable protein, from starchy and protein-rich raw feed materials with model comparisons. Predictions by the DVE2010 system as a more

  13. Field and laboratory arsenic speciation methods and their application to natural-water analysis

    Science.gov (United States)

    Bednar, A.J.; Garbarino, J.R.; Burkhardt, M.R.; Ranville, J.F.; Wildeman, T.R.

    2004-01-01

    The toxic and carcinogenic properties of inorganic and organic arsenic species make their determination in natural water vitally important. Determination of individual inorganic and organic arsenic species is critical because the toxicology, mobility, and adsorptivity vary substantially. Several methods for the speciation of arsenic in groundwater, surface-water, and acid mine drainage sample matrices using field and laboratory techniques are presented. The methods provide quantitative determination of arsenite [As(III)], arsenate [As(V)], monomethylarsonate (MMA), dimethylarsinate (DMA), and roxarsone in 2-8min at detection limits of less than 1??g arsenic per liter (??g AsL-1). All the methods use anion exchange chromatography to separate the arsenic species and inductively coupled plasma-mass spectrometry as an arsenic-specific detector. Different methods were needed because some sample matrices did not have all arsenic species present or were incompatible with particular high-performance liquid chromatography (HPLC) mobile phases. The bias and variability of the methods were evaluated using total arsenic, As(III), As(V), DMA, and MMA results from more than 100 surface-water, groundwater, and acid mine drainage samples, and reference materials. Concentrations in test samples were as much as 13,000??g AsL-1 for As(III) and 3700??g AsL-1 for As(V). Methylated arsenic species were less than 100??g AsL-1 and were found only in certain surface-water samples, and roxarsone was not detected in any of the water samples tested. The distribution of inorganic arsenic species in the test samples ranged from 0% to 90% As(III). Laboratory-speciation method variability for As(III), As(V), MMA, and DMA in reagent water at 0.5??g AsL-1 was 8-13% (n=7). Field-speciation method variability for As(III) and As(V) at 1??g AsL-1 in reagent water was 3-4% (n=3). ?? 2003 Elsevier Ltd. All rights reserved.

  14. Aqueous arsenite removal by simultaneous ultraviolet photocatalytic oxidation-coagulation of titanium sulfate

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yuxia [Key Laboratory of Northwest Water Resources, Environment and Ecology, MOE, School of Environmental & Municipal Engineering, Xi’an University of Architecture and Technology (China); Duan, Jinming, E-mail: jinmingduan@xauat.edu.cn [Key Laboratory of Northwest Water Resources, Environment and Ecology, MOE, School of Environmental & Municipal Engineering, Xi’an University of Architecture and Technology (China); Centre for Water Management and Reuse, School of Natural and Built Environments, University of South Australia, Mawson Lakes Campus, South Australia (Australia); Li, Wei [Key Laboratory of Northwest Water Resources, Environment and Ecology, MOE, School of Environmental & Municipal Engineering, Xi’an University of Architecture and Technology (China); Beecham, Simon; Mulcahy, Dennis [Centre for Water Management and Reuse, School of Natural and Built Environments, University of South Australia, Mawson Lakes Campus, South Australia (Australia)

    2016-02-13

    Highlights: • A simultaneous UV catalysed oxidation–coagulation for As(III) removal is proposed. • As(III) was effectively oxidised to As(V) by the UV catalysed coagulation. • >99% removal for As(III) in pH 4–6 at low doses of Ti(SO{sub 4}){sub 2} was achieved. • Concurrent UV radiation in massive small crystal formation facilitate the effects. • Reaction mechanisms involve both hydroxyl radicals and superoxide radicals. - Abstract: This study explored the efficacy and efficiency of a simultaneous UV-catalyzed oxidation–coagulation process of titanium sulfate (UV/Ti(SO{sub 4}){sub 2}) for efficient removal of As(III) from water. It revealed that, As(III) could be oxidized to As(V) during the UV catalyzed coagulation of Ti(SO{sub 4}){sub 2} with highly efficient As(III) removal in the pH range 4–6{sub .} The UV catalyzed oxidation–coagulation showed surprisingly effective oxidation of As(III) to As(V) within a short time. XPS indicated that 84.7% of arsenic on the coagulated precipitate was in the oxidized form of As(V) after the UV/Ti(SO{sub 4}){sub 2} treatment of As(III) aqueous solutions at pH 5. Arsenic remaining in solution at high pH was in the oxidized form As(V). Removal efficiencies of As(III) were investigated as a function of pH, Ti(SO{sub 4}){sub 2} dosage, initial As(III) concentration and irradiation energy. As(III) could almost completely be removed (>99%) by the photocatalytic oxidation–coagulation process with a moderate dose of Ti(SO{sub 4}){sub 2} in the pH range 4–6 at an initial arsenic concentration of 200 μg/L. The mechanisms of the photocatalytic coagulation oxidation of Ti(SO{sub 4}){sub 2} are similar to those of UV/crystalline TiO{sub 2} particles, involving the formation and reactions of the hydroxyl radical OH· and superoxide HO{sub 2}·/O{sub 2}{sup ·−}.

  15. Composition of Overlapping Protein-Protein and Protein-Ligand Interfaces.

    Directory of Open Access Journals (Sweden)

    Ruzianisra Mohamed

    Full Text Available Protein-protein interactions (PPIs play a major role in many biological processes and they represent an important class of targets for therapeutic intervention. However, targeting PPIs is challenging because often no convenient natural substrates are available as starting point for small-molecule design. Here, we explored the characteristics of protein interfaces in five non-redundant datasets of 174 protein-protein (PP complexes, and 161 protein-ligand (PL complexes from the ABC database, 436 PP complexes, and 196 PL complexes from the PIBASE database and a dataset of 89 PL complexes from the Timbal database. In all cases, the small molecule ligands must bind at the respective PP interface. We observed similar amino acid frequencies in all three datasets. Remarkably, also the characteristics of PP contacts and overlapping PL contacts are highly similar.

  16. Protein- protein interaction detection system using fluorescent protein microdomains

    Science.gov (United States)

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2010-02-23

    The invention provides a protein labeling and interaction detection system based on engineered fragments of fluorescent and chromophoric proteins that require fused interacting polypeptides to drive the association of the fragments, and further are soluble and stable, and do not change the solubility of polypeptides to which they are fused. In one embodiment, a test protein X is fused to a sixteen amino acid fragment of GFP (.beta.-strand 10, amino acids 198-214), engineered to not perturb fusion protein solubility. A second test protein Y is fused to a sixteen amino acid fragment of GFP (.beta.-strand 11, amino acids 215-230), engineered to not perturb fusion protein solubility. When X and Y interact, they bring the GFP strands into proximity, and are detected by complementation with a third GFP fragment consisting of GFP amino acids 1-198 (strands 1-9). When GFP strands 10 and 11 are held together by interaction of protein X and Y, they spontaneous association with GFP strands 1-9, resulting in structural complementation, folding, and concomitant GFP fluorescence.

  17. Amplifying genetic logic gates.

    Science.gov (United States)

    Bonnet, Jerome; Yin, Peter; Ortiz, Monica E; Subsoontorn, Pakpoom; Endy, Drew

    2013-05-03

    Organisms must process information encoded via developmental and environmental signals to survive and reproduce. Researchers have also engineered synthetic genetic logic to realize simpler, independent control of biological processes. We developed a three-terminal device architecture, termed the transcriptor, that uses bacteriophage serine integrases to control the flow of RNA polymerase along DNA. Integrase-mediated inversion or deletion of DNA encoding transcription terminators or a promoter modulates transcription rates. We realized permanent amplifying AND, NAND, OR, XOR, NOR, and XNOR gates actuated across common control signal ranges and sequential logic supporting autonomous cell-cell communication of DNA encoding distinct logic-gate states. The single-layer digital logic architecture developed here enables engineering of amplifying logic gates to control transcription rates within and across diverse organisms.

  18. Identification of Protein-Protein Interactions with Glutathione-S-Transferase (GST) Fusion Proteins.

    Science.gov (United States)

    Einarson, Margret B; Pugacheva, Elena N; Orlinick, Jason R

    2007-08-01

    INTRODUCTIONGlutathione-S-transferase (GST) fusion proteins have had a wide range of applications since their introduction as tools for synthesis of recombinant proteins in bacteria. GST was originally selected as a fusion moiety because of several desirable properties. First and foremost, when expressed in bacteria alone, or as a fusion, GST is not sequestered in inclusion bodies (in contrast to previous fusion protein systems). Second, GST can be affinity-purified without denaturation because it binds to immobilized glutathione, which provides the basis for simple purification. Consequently, GST fusion proteins are routinely used for antibody generation and purification, protein-protein interaction studies, and biochemical analysis. This article describes the use of GST fusion proteins as probes for the identification of protein-protein interactions.

  19. Protein-protein interaction network-based detection of functionally similar proteins within species.

    Science.gov (United States)

    Song, Baoxing; Wang, Fen; Guo, Yang; Sang, Qing; Liu, Min; Li, Dengyun; Fang, Wei; Zhang, Deli

    2012-07-01

    Although functionally similar proteins across species have been widely studied, functionally similar proteins within species showing low sequence similarity have not been examined in detail. Identification of these proteins is of significant importance for understanding biological functions, evolution of protein families, progression of co-evolution, and convergent evolution and others which cannot be obtained by detection of functionally similar proteins across species. Here, we explored a method of detecting functionally similar proteins within species based on graph theory. After denoting protein-protein interaction networks using graphs, we split the graphs into subgraphs using the 1-hop method. Proteins with functional similarities in a species were detected using a method of modified shortest path to compare these subgraphs and to find the eligible optimal results. Using seven protein-protein interaction networks and this method, some functionally similar proteins with low sequence similarity that cannot detected by sequence alignment were identified. By analyzing the results, we found that, sometimes, it is difficult to separate homologous from convergent evolution. Evaluation of the performance of our method by gene ontology term overlap showed that the precision of our method was excellent. Copyright © 2012 Wiley Periodicals, Inc.

  20. Protein-Protein Docking in Drug Design and Discovery.

    Science.gov (United States)

    Kaczor, Agnieszka A; Bartuzi, Damian; Stępniewski, Tomasz Maciej; Matosiuk, Dariusz; Selent, Jana

    2018-01-01

    Protein-protein interactions (PPIs) are responsible for a number of key physiological processes in the living cells and underlie the pathomechanism of many diseases. Nowadays, along with the concept of so-called "hot spots" in protein-protein interactions, which are well-defined interface regions responsible for most of the binding energy, these interfaces can be targeted with modulators. In order to apply structure-based design techniques to design PPIs modulators, a three-dimensional structure of protein complex has to be available. In this context in silico approaches, in particular protein-protein docking, are a valuable complement to experimental methods for elucidating 3D structure of protein complexes. Protein-protein docking is easy to use and does not require significant computer resources and time (in contrast to molecular dynamics) and it results in 3D structure of a protein complex (in contrast to sequence-based methods of predicting binding interfaces). However, protein-protein docking cannot address all the aspects of protein dynamics, in particular the global conformational changes during protein complex formation. In spite of this fact, protein-protein docking is widely used to model complexes of water-soluble proteins and less commonly to predict structures of transmembrane protein assemblies, including dimers and oligomers of G protein-coupled receptors (GPCRs). In this chapter we review the principles of protein-protein docking, available algorithms and software and discuss the recent examples, benefits, and drawbacks of protein-protein docking application to water-soluble proteins, membrane anchoring and transmembrane proteins, including GPCRs.

  1. A comparison of the determination and speciation of inorganic arsenic using general HPLC methodology with UV, MS and MS/MS detection.

    Science.gov (United States)

    Gilmartin, Gregory; Gingrich, Diane

    2018-04-15

    The determination and speciation of arsenic in natural resources such as drinking water and agricultural soils has been a growing concern in recent years due to its many toxicological effects [1-3]. To speciate and quantitate concentrations of arsenic, typically an ion chromatograph (IC) interfaced to an inductively coupled plasma mass spectrometer (ICP-MS) is employed [4-9]. This methodology may be very robust and sensitive, but it is expensive and not as ubiquitous as high performance liquid chromatography (HPLC) with ultraviolet (UV) absorbance detection or electrospray ionization mass spectrometry (ESI-MS). Anion exchange chromatography is a well-documented means of speciating arsenite (As(III), As 2 O 3 ) and arsenate (As(V), AsO 4 ) using UV [10], conductivity [11], or ESI-MS detection [12,13]. This paper demonstrates the utilization of common liquid chromatographic instrumentation to speciate and determines inorganic Arsenic compounds using UV or MS via selected ion recording (SIR) or multiple reaction monitoring (MRM) detection. This paper describes the analysis of arsenite and arsenate samples prepared using both deionized and ground water. The limit of quantitation for the techniques described in this paper for samples spiked in ground water were 454 ppb (As(III)) and 562 ppb (As(V)) for UV detection, 45.4 ppb (As(III)) and 56.2 ppb (As(V)) for SIR detection, and 4.54 ppb (As(III)) and 5.62 ppb (As(V)) for MRM detection. Copyright © 2018 Elsevier B.V. All rights reserved.

  2. Microbial Community Structure and Arsenic Biogeochemistry in Two Arsenic-Impacted Aquifers in Bangladesh

    Directory of Open Access Journals (Sweden)

    Edwin T. Gnanaprakasam

    2017-11-01

    Full Text Available Long-term exposure to trace levels of arsenic (As in shallow groundwater used for drinking and irrigation puts millions of people at risk of chronic disease. Although microbial processes are implicated in mobilizing arsenic from aquifer sediments into groundwater, the precise mechanism remains ambiguous. The goal of this work was to target, for the first time, a comprehensive suite of state-of-the-art molecular techniques in order to better constrain the relationship between indigenous microbial communities and the iron and arsenic mineral phases present in sediments at two well-characterized arsenic-impacted aquifers in Bangladesh. At both sites, arsenate [As(V] was the major species of As present in sediments at depths with low aqueous As concentrations, while most sediment As was arsenite [As(III] at depths with elevated aqueous As concentrations. This is consistent with a role for the microbial As(V reduction in mobilizing arsenic. 16S rRNA gene analysis indicates that the arsenic-rich sediments were colonized by diverse bacterial communities implicated in both dissimilatory Fe(III and As(V reduction, while the correlation analyses involved phylogenetic groups not normally associated with As mobilization. Findings suggest that direct As redox transformations are central to arsenic fate and transport and that there is a residual reactive pool of both As(V and Fe(III in deeper sediments that could be released by microbial respiration in response to hydrologic perturbation, such as increased groundwater pumping that introduces reactive organic carbon to depth.

  3. Inorganic species of arsenic in soil solution determined by microcartridges and ferrihydrite-based diffusive gradient in thin films (DGT).

    Science.gov (United States)

    Moreno-Jiménez, Eduardo; Six, Laetitia; Williams, Paul N; Smolders, Erik

    2013-01-30

    The bioavailability of soil arsenic (As) is determined by its speciation in soil solution, i.e., arsenite [As(III)] or arsenate [As(V)]. Soil bioavailability studies require suitable methods to cope with small volumes of soil solution that can be speciated directly after sampling, and thereby minimise any As speciation change during sample collection. In this study, we tested a self-made microcartridge to separate both As species and compared it to a commercially available cartridge. In addition, the diffusive gradient in thin films technique (DGT), in combination with the microcartridges, was applied to synthetic solutions and to a soil spiked with As. This combination was used to improve the assessment of available inorganic As species with ferrihydrite(FH)-DGT, in order to validate the technique for environmental analysis, mainly in soils. The self-made microcartridge was effective in separating As(III) from As(V) in solution with detection by inductively coupled plasma optical emission spectrometry (ICP-OES) in volumes of only 3 ml. The DGT study also showed that the FH-based binding gels are effective for As(III) and As(V) assessment, in solutions with As and P concentrations and ionic strength commonly found in soils. The FH-DGT was tested on flooded and unflooded As spiked soils and recoveries of As(III) and As(V) were 85-104% of the total dissolved As. This study shows that the DGT with FH-based binding gel is robust for assessing inorganic species of As in soils. Copyright © 2012 Elsevier B.V. All rights reserved.

  4. Emerging trends in biosensing using stripping voltammetric detection of metal-containing nanolabels – A review

    Energy Technology Data Exchange (ETDEWEB)

    Kokkinos, Christos; Economou, Anastasios, E-mail: aeconomo@chem.uoa.gr

    2017-04-08

    Over the last years, nanomaterials have found many applications in the development of electrochemical biosensors. Among other functions, metal nanoparticles (NPs) and quantum dots (QDs) (semiconducting nanocrystals composed of metal salts) are increasingly being used as voltammetric labels in affinity biosensing. Labeling is based on the attachment of the label(s) on the target biomolecules or on a biorecognition reporting probe. After an appropriate specific affinity interaction between the target and the reporting probe, the metallic nanolabels are converted to the respective cations which are quantified by a voltammetric technique. The very use of metal-containing nanoprobes as labels provides a first amplification step since each nanoprobe can release a very significant number of detectable cations. When anodic stripping voltammetry (ASV) (in which a preconcentration step precedes the actual voltammetric scan) is further employed as the detection format, ultra-sensitive bioassays can be developed. The present paper reviews the emerging trends in affinity biosensing using ASV detection of metal-containing nanolabels. It provides a critical discussion of recent developments in ASV transduction and electrodes, novel strategies for signal enhancement, approaches for multiplexed detection as well as fluidics, paper-based and lab-on-a-chip devices. - Highlights: • This paper reviews the use of ASV for affinity biosensing with metal-containing nanolabels. • Both metal nanoparticles and quantum dots applications are considered. • Transducers and new electrode materials are covered. • Signal enhancement and multiplexing strategies are discussed. • Sensor arrays, paper-based, fluidic and lab-on-chip applications are described.

  5. Evolution of protein-protein interactions

    Indian Academy of Sciences (India)

    Evolution of protein-protein interactions · Our interests in protein-protein interactions · Slide 3 · Slide 4 · Slide 5 · Slide 6 · Slide 7 · Slide 8 · Slide 9 · Slide 10 · Slide 11 · Slide 12 · Slide 13 · Slide 14 · Slide 15 · Slide 16 · Slide 17 · Slide 18 · Slide 19 · Slide 20.

  6. Protein function prediction using neighbor relativity in protein-protein interaction network.

    Science.gov (United States)

    Moosavi, Sobhan; Rahgozar, Masoud; Rahimi, Amir

    2013-04-01

    There is a large gap between the number of discovered proteins and the number of functionally annotated ones. Due to the high cost of determining protein function by wet-lab research, function prediction has become a major task for computational biology and bioinformatics. Some researches utilize the proteins interaction information to predict function for un-annotated proteins. In this paper, we propose a novel approach called "Neighbor Relativity Coefficient" (NRC) based on interaction network topology which estimates the functional similarity between two proteins. NRC is calculated for each pair of proteins based on their graph-based features including distance, common neighbors and the number of paths between them. In order to ascribe function to an un-annotated protein, NRC estimates a weight for each neighbor to transfer its annotation to the unknown protein. Finally, the unknown protein will be annotated by the top score transferred functions. We also investigate the effect of using different coefficients for various types of functions. The proposed method has been evaluated on Saccharomyces cerevisiae and Homo sapiens interaction networks. The performance analysis demonstrates that NRC yields better results in comparison with previous protein function prediction approaches that utilize interaction network. Copyright © 2012 Elsevier Ltd. All rights reserved.

  7. Protein Structure Prediction by Protein Threading

    Science.gov (United States)

    Xu, Ying; Liu, Zhijie; Cai, Liming; Xu, Dong

    The seminal work of Bowie, Lüthy, and Eisenberg (Bowie et al., 1991) on "the inverse protein folding problem" laid the foundation of protein structure prediction by protein threading. By using simple measures for fitness of different amino acid types to local structural environments defined in terms of solvent accessibility and protein secondary structure, the authors derived a simple and yet profoundly novel approach to assessing if a protein sequence fits well with a given protein structural fold. Their follow-up work (Elofsson et al., 1996; Fischer and Eisenberg, 1996; Fischer et al., 1996a,b) and the work by Jones, Taylor, and Thornton (Jones et al., 1992) on protein fold recognition led to the development of a new brand of powerful tools for protein structure prediction, which we now term "protein threading." These computational tools have played a key role in extending the utility of all the experimentally solved structures by X-ray crystallography and nuclear magnetic resonance (NMR), providing structural models and functional predictions for many of the proteins encoded in the hundreds of genomes that have been sequenced up to now.

  8. Specificity and affinity quantification of protein-protein interactions.

    Science.gov (United States)

    Yan, Zhiqiang; Guo, Liyong; Hu, Liang; Wang, Jin

    2013-05-01

    Most biological processes are mediated by the protein-protein interactions. Determination of the protein-protein structures and insight into their interactions are vital to understand the mechanisms of protein functions. Currently, compared with the isolated protein structures, only a small fraction of protein-protein structures are experimentally solved. Therefore, the computational docking methods play an increasing role in predicting the structures and interactions of protein-protein complexes. The scoring function of protein-protein interactions is the key responsible for the accuracy of the computational docking. Previous scoring functions were mostly developed by optimizing the binding affinity which determines the stability of the protein-protein complex, but they are often lack of the consideration of specificity which determines the discrimination of native protein-protein complex against competitive ones. We developed a scoring function (named as SPA-PP, specificity and affinity of the protein-protein interactions) by incorporating both the specificity and affinity into the optimization strategy. The testing results and comparisons with other scoring functions show that SPA-PP performs remarkably on both predictions of binding pose and binding affinity. Thus, SPA-PP is a promising quantification of protein-protein interactions, which can be implemented into the protein docking tools and applied for the predictions of protein-protein structure and affinity. The algorithm is implemented in C language, and the code can be downloaded from http://dl.dropbox.com/u/1865642/Optimization.cpp.

  9. Assessment of Integration-defective HIV-1 and EIAV Vectors In Vitro and In Vivo

    Directory of Open Access Journals (Sweden)

    Scott Ellis

    2012-01-01

    Full Text Available The interest in integrase-defective lentiviral vectors (IDLVs stems from their potential advantage of large cloning capacity and broad cell tropism while avoiding the possibility of insertional mutagenesis. Here, we directly compared the transducing potential of IDLVs based on the equine infectious anemia virus (EIAV to the more commonly described HIV-1 IDLVs. IDLVs were constructed by introducing equivalent single/triple mutations into the integrase catalytic triad. We show that both the single and the triple mutant HIV-1 IDLVs transduce the PC12 cells, but not the C2C12 cells, with similar efficiency to their parental HIV-1 vector. In contrast, the single and triple EIAV IDLVs did not efficiently transduce either differentiated cell line. Moreover, this HIV-1 IDLV-mediated expression was independent of any residual integration activity because reporter expression was lost when cell cycling was restored. Four weeks following stereotactic administration into adult rat brains, only the single HIV-1 IDLV mutant displayed a comparable transduction profile to the parental HIV-1 vector. In contrast, neither EIAV IDLV mutants showed significant reporter gene expression. This work indicates that the transducing potential of IDLVs appears to depend not only on the choice of integrase mutation and type of target cell, but also on the nature of the lentiviral vector.

  10. The Wave Glider°: A New Autonomous Surface Vehicle to Augment MBARI's Growing Fleet of Ocean Observing Systems

    Science.gov (United States)

    Tougher, B. B.

    2011-12-01

    Monterey Bay Aquarium Research Institute's (MBARI) evolving fleet of ocean observing systems has made it possible to collect information and data about a wide variety of ocean parameters, enabling researchers to better understand marine ecosystems. In collaboration with Liquid Robotics Inc, the designer of the Wave Glider autonomous surface vehicle (ASV), MBARI is adding a new capability to its suite of ocean observing tools. This new technology will augment MBARI research programs that use satellites, ships, moorings, drifters, autonomous underwater vehicles (AUVs) and remotely operated vehicles (ROVs) to improve data collection of temporally and spatially variable oceanographic features. The Wave Glider ASV derives its propulsion from wave energy, while sensors and communications are powered through the use of two solar panels and batteries, enabling it to remain at sea indefinitely. Wave Gliders are remotely controlled via real-time Iridium burst communications, which also permit real-time data telemetry. MBARI has developed Ocean Acidification (OA) moorings to continuously monitor the chemical and physical changes occurring in the ocean as a result of increased levels of atmospheric carbon dioxide (CO2). The moorings are spatially restricted by being anchored to the seafloor, so during the summer of 2011 the ocean acidification sensor suite designed for moorings was integrated into a Wave Glider ASV to increase both temporal and spatial ocean observation capabilities. The OA sensor package enables the measurement of parameters essential to better understanding the changing acidity of the ocean, specifically pCO2, pH, oxygen, salinity and temperature. The Wave Glider will also be equipped with a meteorological sensor suite that will measure air temperature, air pressure, and wind speed and direction. The OA sensor integration into a Wave Glider was part of MBARI's 2011 summer internship program. This project involved designing a new layout for the OA sensors

  11. Detection of protein complex from protein-protein interaction network using Markov clustering

    International Nuclear Information System (INIS)

    Ochieng, P J; Kusuma, W A; Haryanto, T

    2017-01-01

    Detection of complexes, or groups of functionally related proteins, is an important challenge while analysing biological networks. However, existing algorithms to identify protein complexes are insufficient when applied to dense networks of experimentally derived interaction data. Therefore, we introduced a graph clustering method based on Markov clustering algorithm to identify protein complex within highly interconnected protein-protein interaction networks. Protein-protein interaction network was first constructed to develop geometrical network, the network was then partitioned using Markov clustering to detect protein complexes. The interest of the proposed method was illustrated by its application to Human Proteins associated to type II diabetes mellitus. Flow simulation of MCL algorithm was initially performed and topological properties of the resultant network were analysed for detection of the protein complex. The results indicated the proposed method successfully detect an overall of 34 complexes with 11 complexes consisting of overlapping modules and 20 non-overlapping modules. The major complex consisted of 102 proteins and 521 interactions with cluster modularity and density of 0.745 and 0.101 respectively. The comparison analysis revealed MCL out perform AP, MCODE and SCPS algorithms with high clustering coefficient (0.751) network density and modularity index (0.630). This demonstrated MCL was the most reliable and efficient graph clustering algorithm for detection of protein complexes from PPI networks. (paper)

  12. Coarse-grain modelling of protein-protein interactions

    NARCIS (Netherlands)

    Baaden, Marc; Marrink, Siewert J.

    2013-01-01

    Here, we review recent advances towards the modelling of protein-protein interactions (PPI) at the coarse-grained (CG) level, a technique that is now widely used to understand protein affinity, aggregation and self-assembly behaviour. PPI models of soluble proteins and membrane proteins are

  13. A role for the budding yeast separase, Esp1, in Ty1 element retrotransposition.

    Directory of Open Access Journals (Sweden)

    Krystina L Ho

    2015-03-01

    Full Text Available Separase/Esp1 is a protease required at the onset of anaphase to cleave cohesin and thereby enable sister chromatid separation. Esp1 also promotes release of the Cdc14 phosphatase from the nucleolus to enable mitotic exit. To uncover other potential roles for separase, we performed two complementary genome-wide genetic interaction screens with a strain carrying the budding yeast esp1-1 separase mutation. We identified 161 genes that when mutated aggravate esp1-1 growth and 44 genes that upon increased dosage are detrimental to esp1-1 viability. In addition to the expected cell cycle and sister chromatid segregation genes that were identified, 24% of the genes identified in the esp1-1 genetic screens have a role in Ty1 element retrotransposition. Retrotransposons, like retroviruses, replicate through reverse transcription of an mRNA intermediate and the resultant cDNA product is integrated into the genome by a conserved transposon or retrovirus encoded integrase protein. We purified Esp1 from yeast and identified an interaction between Esp1 and Ty1 integrase using mass spectrometry that was subsequently confirmed by co-immunoprecipitation analysis. Ty1 transposon mobility and insertion upstream of the SUF16 tRNA gene are both reduced in an esp1-1 strain but increased in cohesin mutant strains. Securin/Pds1, which is required for efficient localization of Esp1 to the nucleus, is also required for efficient Ty1 transposition. We propose that Esp1 serves two roles to mediate Ty1 transposition - one to remove cohesin and the second to target Ty1-IN to chromatin.

  14. Origins of the Xylella fastidiosa prophage-like regions and their impact in genome differentiation.

    Directory of Open Access Journals (Sweden)

    Alessandro de Mello Varani

    Full Text Available Xylella fastidiosa is a Gram negative plant pathogen causing many economically important diseases, and analyses of completely sequenced X. fastidiosa genome strains allowed the identification of many prophage-like elements and possibly phage remnants, accounting for up to 15% of the genome composition. To better evaluate the recent evolution of the X. fastidiosa chromosome backbone among distinct pathovars, the number and location of prophage-like regions on two finished genomes (9a5c and Temecula1, and in two candidate molecules (Ann1 and Dixon were assessed. Based on comparative best bidirectional hit analyses, the majority (51% of the predicted genes in the X. fastidiosa prophage-like regions are related to structural phage genes belonging to the Siphoviridae family. Electron micrograph reveals the existence of putative viral particles with similar morphology to lambda phages in the bacterial cell in planta. Moreover, analysis of microarray data indicates that 9a5c strain cultivated under stress conditions presents enhanced expression of phage anti-repressor genes, suggesting switches from lysogenic to lytic cycle of phages under stress-induced situations. Furthermore, virulence-associated proteins and toxins are found within these prophage-like elements, thus suggesting an important role in host adaptation. Finally, clustering analyses of phage integrase genes based on multiple alignment patterns reveal they group in five lineages, all possessing a tyrosine recombinase catalytic domain, and phylogenetically close to other integrases found in phages that are genetic mosaics and able to perform generalized and specialized transduction. Integration sites and tRNA association is also evidenced. In summary, we present comparative and experimental evidence supporting the association and contribution of phage activity on the differentiation of Xylella genomes.

  15. Detection of protein-protein interactions by ribosome display and protein in situ immobilisation.

    Science.gov (United States)

    He, Mingyue; Liu, Hong; Turner, Martin; Taussig, Michael J

    2009-12-31

    We describe a method for identification of protein-protein interactions by combining two cell-free protein technologies, namely ribosome display and protein in situ immobilisation. The method requires only PCR fragments as the starting material, the target proteins being made through cell-free protein synthesis, either associated with their encoding mRNA as ribosome complexes or immobilised on a solid surface. The use of ribosome complexes allows identification of interacting protein partners from their attached coding mRNA. To demonstrate the procedures, we have employed the lymphocyte signalling proteins Vav1 and Grb2 and confirmed the interaction between Grb2 and the N-terminal SH3 domain of Vav1. The method has promise for library screening of pairwise protein interactions, down to the analytical level of individual domain or motif mapping.

  16. Coevolution study of mitochondria respiratory chain proteins: toward the understanding of protein--protein interaction.

    Science.gov (United States)

    Yang, Ming; Ge, Yan; Wu, Jiayan; Xiao, Jingfa; Yu, Jun

    2011-05-20

    Coevolution can be seen as the interdependency between evolutionary histories. In the context of protein evolution, functional correlation proteins are ever-present coordinated evolutionary characters without disruption of organismal integrity. As to complex system, there are two forms of protein--protein interactions in vivo, which refer to inter-complex interaction and intra-complex interaction. In this paper, we studied the difference of coevolution characters between inter-complex interaction and intra-complex interaction using "Mirror tree" method on the respiratory chain (RC) proteins. We divided the correlation coefficients of every pairwise RC proteins into two groups corresponding to the binary protein--protein interaction in intra-complex and the binary protein--protein interaction in inter-complex, respectively. A dramatical discrepancy is detected between the coevolution characters of the two sets of protein interactions (Wilcoxon test, p-value = 4.4 × 10(-6)). Our finding reveals some critical information on coevolutionary study and assists the mechanical investigation of protein--protein interaction. Furthermore, the results also provide some unique clue for supramolecular organization of protein complexes in the mitochondrial inner membrane. More detailed binding sites map and genome information of nuclear encoded RC proteins will be extraordinary valuable for the further mitochondria dynamics study. Copyright © 2011. Published by Elsevier Ltd.

  17. A Novel Approach for Protein-Named Entity Recognition and Protein-Protein Interaction Extraction

    Directory of Open Access Journals (Sweden)

    Meijing Li

    2015-01-01

    Full Text Available Many researchers focus on developing protein-named entity recognition (Protein-NER or PPI extraction systems. However, the studies about these two topics cannot be merged well; then existing PPI extraction systems’ Protein-NER still needs to improve. In this paper, we developed the protein-protein interaction extraction system named PPIMiner based on Support Vector Machine (SVM and parsing tree. PPIMiner consists of three main models: natural language processing (NLP model, Protein-NER model, and PPI discovery model. The Protein-NER model, which is named ProNER, identifies the protein names based on two methods: dictionary-based method and machine learning-based method. ProNER is capable of identifying more proteins than dictionary-based Protein-NER model in other existing systems. The final discovered PPIs extracted via PPI discovery model are represented in detail because we showed the protein interaction types and the occurrence frequency through two different methods. In the experiments, the result shows that the performances achieved by our ProNER and PPI discovery model are better than other existing tools. PPIMiner applied this protein-named entity recognition approach and parsing tree based PPI extraction method to improve the performance of PPI extraction. We also provide an easy-to-use interface to access PPIs database and an online system for PPIs extraction and Protein-NER.

  18. Arsenic speciation for the phytoremediation by the Chinese brake fern, Pteris vittata.

    Science.gov (United States)

    Shoji, R; Yajima, R; Yano, Y

    2008-01-01

    Arsenic (As) speciation for the phytoremediation by the Chinese brake fern was studied. In particular, the mechanism of how plants induce compounds containing thiol (SH) and proteins by As exposure in terms of the relationship between As and phosphate uptaken into plant cells was examined. Pteris vittata callus could efficiently reduce As(V) to As(III) by the rapid introduction of reductase and synthesize thiols leading to phytochelatins production. Furthermore, Pteris vittata could control phosphate concentration in the cells corresponding to the concentration of arsenite and arsenate. To our best knowledge, this is the first report to show the mechanisms of such high As tolerance of Pteris vittata using their callus in terms of in vitro approach for the analysis of As speciation and metabolism route.

  19. Protein complex prediction in large ontology attributed protein-protein interaction networks.

    Science.gov (United States)

    Zhang, Yijia; Lin, Hongfei; Yang, Zhihao; Wang, Jian; Li, Yanpeng; Xu, Bo

    2013-01-01

    Protein complexes are important for unraveling the secrets of cellular organization and function. Many computational approaches have been developed to predict protein complexes in protein-protein interaction (PPI) networks. However, most existing approaches focus mainly on the topological structure of PPI networks, and largely ignore the gene ontology (GO) annotation information. In this paper, we constructed ontology attributed PPI networks with PPI data and GO resource. After constructing ontology attributed networks, we proposed a novel approach called CSO (clustering based on network structure and ontology attribute similarity). Structural information and GO attribute information are complementary in ontology attributed networks. CSO can effectively take advantage of the correlation between frequent GO annotation sets and the dense subgraph for protein complex prediction. Our proposed CSO approach was applied to four different yeast PPI data sets and predicted many well-known protein complexes. The experimental results showed that CSO was valuable in predicting protein complexes and achieved state-of-the-art performance.

  20. Protein surface shielding agents in protein crystallization

    International Nuclear Information System (INIS)

    Hašek, J.

    2011-01-01

    The crystallization process can be controlled by protein surface shielding agents blocking undesirable competitive adhesion modes during non-equilibrium processes of deposition of protein molecules on the surface of growing crystalline blocks. The hypothesis is based on a number of experimental proofs from diffraction experiments and also retrieved from the Protein Data Bank. The molecules adhering temporarily on the surface of protein molecules change the propensity of protein molecules to deposit on the crystal surface in a definite position and orientation. The concepts of competitive adhesion modes and protein surface shielding agents acting on the surface of molecules in a non-equilibrium process of protein crystallization provide a useful platform for the control of crystallization. The desirable goal, i.e. a transient preference of a single dominating adhesion mode between protein molecules during crystallization, leads to uniform deposition of proteins in a crystal. This condition is the most important factor for diffraction quality and thus also for the accuracy of protein structure determination. The presented hypothesis is a generalization of the experimentally well proven behaviour of hydrophilic polymers on the surface of protein molecules of other compounds

  1. Retrotransposons. An RNA polymerase III subunit determines sites of retrotransposon integration.

    Science.gov (United States)

    Bridier-Nahmias, Antoine; Tchalikian-Cosson, Aurélie; Baller, Joshua A; Menouni, Rachid; Fayol, Hélène; Flores, Amando; Saïb, Ali; Werner, Michel; Voytas, Daniel F; Lesage, Pascale

    2015-05-01

    Mobile genetic elements are ubiquitous. Their integration site influences genome stability and gene expression. The Ty1 retrotransposon of the yeast Saccharomyces cerevisiae integrates upstream of RNA polymerase III (Pol III)-transcribed genes, yet the primary determinant of target specificity has remained elusive. Here we describe an interaction between Ty1 integrase and the AC40 subunit of Pol III and demonstrate that AC40 is the predominant determinant targeting Ty1 integration upstream of Pol III-transcribed genes. Lack of an integrase-AC40 interaction dramatically alters target site choice, leading to a redistribution of Ty1 insertions in the genome, mainly to chromosome ends. The mechanism of target specificity allows Ty1 to proliferate and yet minimizes genetic damage to its host. Copyright © 2015, American Association for the Advancement of Science.

  2. The Development of Protein Microarrays and Their Applications in DNA-Protein and Protein-Protein Interaction Analyses of Arabidopsis Transcription Factors

    Science.gov (United States)

    Gong, Wei; He, Kun; Covington, Mike; Dinesh-Kumar, S. P.; Snyder, Michael; Harmer, Stacey L.; Zhu, Yu-Xian; Deng, Xing Wang

    2009-01-01

    We used our collection of Arabidopsis transcription factor (TF) ORFeome clones to construct protein microarrays containing as many as 802 TF proteins. These protein microarrays were used for both protein-DNA and protein-protein interaction analyses. For protein-DNA interaction studies, we examined AP2/ERF family TFs and their cognate cis-elements. By careful comparison of the DNA-binding specificity of 13 TFs on the protein microarray with previous non-microarray data, we showed that protein microarrays provide an efficient and high throughput tool for genome-wide analysis of TF-DNA interactions. This microarray protein-DNA interaction analysis allowed us to derive a comprehensive view of DNA-binding profiles of AP2/ERF family proteins in Arabidopsis. It also revealed four TFs that bound the EE (evening element) and had the expected phased gene expression under clock-regulation, thus providing a basis for further functional analysis of their roles in clock regulation of gene expression. We also developed procedures for detecting protein interactions using this TF protein microarray and discovered four novel partners that interact with HY5, which can be validated by yeast two-hybrid assays. Thus, plant TF protein microarrays offer an attractive high-throughput alternative to traditional techniques for TF functional characterization on a global scale. PMID:19802365

  3. Protein sequence comparison and protein evolution

    Energy Technology Data Exchange (ETDEWEB)

    Pearson, W.R. [Univ. of Virginia, Charlottesville, VA (United States). Dept. of Biochemistry

    1995-12-31

    This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. This tutorial examines how the information conserved during the evolution of a protein molecule can be used to infer reliably homology, and thus a shared proteinfold and possibly a shared active site or function. The authors start by reviewing a geological/evolutionary time scale. Next they look at the evolution of several protein families. During the tutorial, these families will be used to demonstrate that homologous protein ancestry can be inferred with confidence. They also examine different modes of protein evolution and consider some hypotheses that have been presented to explain the very earliest events in protein evolution. The next part of the tutorial will examine the technical aspects of protein sequence comparison. Both optimal and heuristic algorithms and their associated parameters that are used to characterize protein sequence similarities are discussed. Perhaps more importantly, they survey the statistics of local similarity scores, and how these statistics can both be used to improve the selectivity of a search and to evaluate the significance of a match. They them examine distantly related members of three protein families, the serine proteases, the glutathione transferases, and the G-protein-coupled receptors (GCRs). Finally, the discuss how sequence similarity can be used to examine internal repeated or mosaic structures in proteins.

  4. On the analysis of protein-protein interactions via knowledge-based potentials for the prediction of protein-protein docking

    DEFF Research Database (Denmark)

    Feliu, Elisenda; Aloy, Patrick; Oliva, Baldo

    2011-01-01

    Development of effective methods to screen binary interactions obtained by rigid-body protein-protein docking is key for structure prediction of complexes and for elucidating physicochemical principles of protein-protein binding. We have derived empirical knowledge-based potential functions for s...... and with independence of the partner. This information is encoded at the residue level and could be easily incorporated in the initial grid scoring for Fast Fourier Transform rigid-body docking methods.......Development of effective methods to screen binary interactions obtained by rigid-body protein-protein docking is key for structure prediction of complexes and for elucidating physicochemical principles of protein-protein binding. We have derived empirical knowledge-based potential functions...... for selecting rigid-body docking poses. These potentials include the energetic component that provides the residues with a particular secondary structure and surface accessibility. These scoring functions have been tested on a state-of-art benchmark dataset and on a decoy dataset of permanent interactions. Our...

  5. Proteins interacting with cloning scars: a source of false positive protein-protein interactions.

    Science.gov (United States)

    Banks, Charles A S; Boanca, Gina; Lee, Zachary T; Florens, Laurence; Washburn, Michael P

    2015-02-23

    A common approach for exploring the interactome, the network of protein-protein interactions in cells, uses a commercially available ORF library to express affinity tagged bait proteins; these can be expressed in cells and endogenous cellular proteins that copurify with the bait can be identified as putative interacting proteins using mass spectrometry. Control experiments can be used to limit false-positive results, but in many cases, there are still a surprising number of prey proteins that appear to copurify specifically with the bait. Here, we have identified one source of false-positive interactions in such studies. We have found that a combination of: 1) the variable sequence of the C-terminus of the bait with 2) a C-terminal valine "cloning scar" present in a commercially available ORF library, can in some cases create a peptide motif that results in the aberrant co-purification of endogenous cellular proteins. Control experiments may not identify false positives resulting from such artificial motifs, as aberrant binding depends on sequences that vary from one bait to another. It is possible that such cryptic protein binding might occur in other systems using affinity tagged proteins; this study highlights the importance of conducting careful follow-up studies where novel protein-protein interactions are suspected.

  6. Arsenic removal from aqueous solutions using Fe3O4-HBC composite: effect of calcination on adsorbents performance.

    Directory of Open Access Journals (Sweden)

    Shams Ali Baig

    Full Text Available The presence of elevated concentration of arsenic in water sources is considered to be health hazard globally. Calcination process is known to change the surface efficacy of the adsorbent. In current study, five adsorbent composites: uncalcined and calcined Fe3O4-HBC prepared at different temperatures (400°C and 1000°C and environment (air and nitrogen were investigated for the adsorptive removal of As(V and As(III from aqueous solutions determining the influence of solution's pH, contact time, temperature, arsenic concentration and phosphate anions. Characterizations from FTIR, XRD, HT-XRD, BET and SEM analyses revealed that the Fe3O4-HBC composite at higher calcination temperature under nitrogen formed a new product (fayalite, Fe2SiO4 via phase transformation. In aqueous medium, ligand exchange between arsenic and the effective sorbent site ( = FeOOH was established from the release of hydroxyl group. Langmuir model suggested data of the five adsorbent composites follow the order: Fe3O4-HBC-1000°C(N2>Fe3O4-HBC (uncalcined>Fe3O4-HBC-400°C(N2>Fe3O4-HBC-400°C(air>Fe3O4-HBC-1000°C(air and the maximum As(V and As(III adsorption capacities were found to be about 3.35 mg g(-1 and 3.07 mg g(-1, respectively. The adsorption of As(V and As(III remained stable in a wider pH range (4-10 using Fe3O4-HBC-1000°C(N2. Additionally, adsorption data fitted well in pseudo-second-order (R2>0.99 rather than pseudo-first-order kinetics model. The adsorption of As(V and As(III onto adsorbent composites increase with increase in temperatures indicating that it is an endothermic process. Phosphate concentration (0.0l mM or higher strongly inhibited As(V and As(III removal through the mechanism of competitive adsorption. This study suggests that the selective calcination process could be useful to improve the adsorbent efficiency for enhanced arsenic removal from contaminated water.

  7. Arsenic removal from aqueous solutions using Fe3O4-HBC composite: effect of calcination on adsorbents performance.

    Science.gov (United States)

    Baig, Shams Ali; Sheng, TianTian; Sun, Chen; Xue, XiaoQin; Tan, LiSha; Xu, XinHua

    2014-01-01

    The presence of elevated concentration of arsenic in water sources is considered to be health hazard globally. Calcination process is known to change the surface efficacy of the adsorbent. In current study, five adsorbent composites: uncalcined and calcined Fe3O4-HBC prepared at different temperatures (400°C and 1000°C) and environment (air and nitrogen) were investigated for the adsorptive removal of As(V) and As(III) from aqueous solutions determining the influence of solution's pH, contact time, temperature, arsenic concentration and phosphate anions. Characterizations from FTIR, XRD, HT-XRD, BET and SEM analyses revealed that the Fe3O4-HBC composite at higher calcination temperature under nitrogen formed a new product (fayalite, Fe2SiO4) via phase transformation. In aqueous medium, ligand exchange between arsenic and the effective sorbent site ( = FeOOH) was established from the release of hydroxyl group. Langmuir model suggested data of the five adsorbent composites follow the order: Fe3O4-HBC-1000°C(N2)>Fe3O4-HBC (uncalcined)>Fe3O4-HBC-400°C(N2)>Fe3O4-HBC-400°C(air)>Fe3O4-HBC-1000°C(air) and the maximum As(V) and As(III) adsorption capacities were found to be about 3.35 mg g(-1) and 3.07 mg g(-1), respectively. The adsorption of As(V) and As(III) remained stable in a wider pH range (4-10) using Fe3O4-HBC-1000°C(N2). Additionally, adsorption data fitted well in pseudo-second-order (R2>0.99) rather than pseudo-first-order kinetics model. The adsorption of As(V) and As(III) onto adsorbent composites increase with increase in temperatures indicating that it is an endothermic process. Phosphate concentration (0.0l mM or higher) strongly inhibited As(V) and As(III) removal through the mechanism of competitive adsorption. This study suggests that the selective calcination process could be useful to improve the adsorbent efficiency for enhanced arsenic removal from contaminated water.

  8. The effect of protein-protein and protein-membrane interactions on membrane fouling in ultrafiltration

    NARCIS (Netherlands)

    Huisman, I.H.; Prádanos, P.; Hernández, A.

    2000-01-01

    It was studied how protein-protein and protein-membrane interactions influence the filtration performance during the ultrafiltration of protein solutions over polymeric membranes. This was done by measuring flux, streaming potential, and protein transmission during filtration of bovine serum albumin

  9. Complete genome sequence of the Pectobacterium carotovorum subsp. carotovorum virulent bacteriophage PM1.

    Science.gov (United States)

    Lim, Jeong-A; Shin, Hakdong; Lee, Dong Hwan; Han, Sang-Wook; Lee, Ju-Hoon; Ryu, Sangryeol; Heu, Sunggi

    2014-08-01

    PM1, a novel virulent bacteriophage that infects Pectobacterium carotovorum subsp. carotovorum, was isolated. Its morphological features were examined by electron microscopy, which indicated that this phage belongs to the family Myoviridae. It has a 55,098-bp genome, including a 2,665-bp terminal repeat. A total of 63 open reading frames (ORFs) were predicted, but only 20 ORFs possessed homology with functional proteins. There is one tRNA coding region, and the GC-content of the genome is 44.9 %. Most ORFs in bacteriophage PM1 showed high homology to enterobacteria phage ΦEcoM-GJ1 and Erwinia phage νB EamM-Y2. Like these bacteriophages, PM1 encodes an RNA polymerase, which is a hallmark of T7-like phages. There is no integrase or repressor, suggesting that PM1 is a virulent bacteriophage.

  10. Fluorogen-activating proteins: beyond classical fluorescent proteins

    Directory of Open Access Journals (Sweden)

    Shengnan Xu

    2018-05-01

    Full Text Available Fluorescence imaging is a powerful technique for the real-time noninvasive monitoring of protein dynamics. Recently, fluorogen activating proteins (FAPs/fluorogen probes for protein imaging were developed. Unlike the traditional fluorescent proteins (FPs, FAPs do not fluoresce unless bound to their specific small-molecule fluorogens. When using FAPs/fluorogen probes, a washing step is not required for the removal of free probes from the cells, thus allowing rapid and specific detection of proteins in living cells with high signal-to-noise ratio. Furthermore, with different fluorogens, living cell multi-color proteins labeling system was developed. In this review, we describe about the discovery of FAPs, the design strategy of FAP fluorogens, the application of the FAP technology and the advances of FAP technology in protein labeling systems. KEY WORDS: Fluorogen activating proteins, Fluorogens, Genetically encoded sensors, Fluorescence imaging, Molecular imaging

  11. Bioaccumulation of Fe2O3(magnetic) nanoparticles in Ceriodaphnia dubia

    International Nuclear Information System (INIS)

    Hu Ji; Wang Demin; Wang Jiangtao; Wang Jianmin

    2012-01-01

    While nano-Fe 2 O 3 (magnetic) is generally considered non-toxic, it could serve as a carrier of other toxic chemicals such as As(V) and enhance their toxicity. The bioaccumulation of nano-Fe 2 O 3 (m) with different exposure times, NP concentrations, and pH conditions was investigated using Ceriodaphnia dubia (C. dubia) as the model organism. Under natural pH conditions, C. dubia significantly accumulated nano-Fe 2 O 3 (m) in the gut, with the maximum accumulation being achieved after 6 h of exposure. The concentration of nano-Fe 2 O 3 also impacted its accumulation, with the maximum uptake occurring at 20 mg/L or more. In addition, the highest bioaccumulation occurred in a pH range of 7–8 where the highest feeding rate was reported, confirming that the ingestion of NPs is the main route of nano-Fe 2 O 3 (m) bioaccumulation. In a clean environment without NPs, depuration of nano-Fe 2 O 3 (m) occurred, and food addition accelerated the depuration process. - Highlights: ► Nano-Fe 2 O 3 (m) enhances the toxicity of As(V). ► C. dubia significantly accumulate nano-Fe 2 O 3 (m) through ingestion. ► The bioaccumulation of nano-Fe 2 O 3 (m) is affected by time, NP concentration, and pH. ► Food addition accelerates the depuration process of accumulated nano-Fe 2 O 3 (m). - Nano-Fe 2 O 3 (m) could enhance the toxicity of As(V) due to the significant accumulation of nano-Fe 2 O 3 (m) along with sorbed As(V) by C. dubia through ingestion.

  12. Ionic liquid-assisted multiwalled carbon nanotube-dispersive micro-solid phase extraction for sensitive determination of inorganic As species in garlic samples by electrothermal atomic absorption spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Grijalba, Alexander Castro; Escudero, Leticia B.; Wuilloud, Rodolfo G., E-mail: rwuilloud@mendoza-conicet.gob.ar

    2015-08-01

    A highly sensitive dispersive micro-solid phase extraction (D-μ-SPE) method combining an ionic liquid (IL) and multi-walled carbon nanotubes (MWCNTs) for inorganic As species (As(III) and As(V)) species separation and determination in garlic samples by electrothermal atomic absorption spectrometry (ETAAS) was developed. Trihexyl(tetradecil)phosphonium chloride IL was used to form an ion pair with the arsenomolybdate complex obtained by reaction of As(V) with molybdate ion. Afterwards, 1.0 mg of MWCNTs was dispersed for As(V) extraction and the supernatant was separated by centrifugation. MWCNTs were re-dispersed with tetradecyltrimethylammonium bromide surfactant and ultrasound followed by direct injection into the graphite furnace of ETAAS for As determination. Pyrolysis and atomization conditions were carefully studied for complete decomposition of MWCNTs and IL matrices. Under optimum conditions, an extraction efficiency of 100% and a preconcentration factor of 70 were obtained with 5 mL of garlic extract. The detection limit was 7.1 ng L{sup −1} and the relative standard deviations (RSDs) for six replicate measurements at 5 μg L{sup −1} of As were 5.4% and 4.8% for As(III) and As(V), respectively. The proposed D-μ-SPE method allowed the efficient separation and determination of inorganic As species in a complex matrix such as garlic extract. - Highlights: • Efficient retention and preconcentration of As by combining an IL with MWCNTs • Determination of As by ETAAS with direct injection of MWCNTs • Thermal degradation of MWCNTs in the graphite furnace of ETAAS • Highly sensitive speciation and determination of As in garlic.

  13. Energy sources for chemolithotrophs in an arsenic- and iron-rich shallow-sea hydrothermal system.

    Science.gov (United States)

    Akerman, N H; Price, R E; Pichler, T; Amend, J P

    2011-09-01

    The hydrothermally influenced sediments of Tutum Bay, Ambitle Island, Papua New Guinea, are ideal for investigating the chemolithotrophic activities of micro-organisms involved in arsenic cycling because hydrothermal vents there expel fluids with arsenite (As(III)) concentrations as high as 950 μg L(-1) . These hot (99 °C), slightly acidic (pH ~6), chemically reduced, shallow-sea vent fluids mix with colder, oxidized seawater to create steep gradients in temperature, pH, and concentrations of As, N, Fe, and S redox species. Near the vents, iron oxyhydroxides precipitate with up to 6.2 wt% arsenate (As(V)). Here, chemical analyses of sediment porewaters from 10 sites along a 300-m transect were combined with standard Gibbs energies to evaluate the energy yields (-ΔG(r)) from 19 potential chemolithotrophic metabolisms, including As(V) reduction, As(III) oxidation, Fe(III) reduction, and Fe(II) oxidation reactions. The 19 reactions yielded 2-94 kJ mol(-1) e(-) , with aerobic oxidation of sulphide and arsenite the two most exergonic reactions. Although anaerobic As(V) reduction and Fe(III) reduction were among the least exergonic reactions investigated, they are still potential net metabolisms. Gibbs energies of the arsenic redox reactions generally correlate linearly with pH, increasing with increasing pH for As(III) oxidation and decreasing with increasing pH for As(V) reduction. The calculated exergonic energy yields suggest that micro-organisms could exploit diverse energy sources in Tutum Bay, and examples of micro-organisms known to use these chemolithotrophic metabolic strategies are discussed. Energy modeling of redox reactions can help target sampling sites for future microbial collection and cultivation studies. © 2011 Blackwell Publishing Ltd.

  14. Ionic liquid-assisted multiwalled carbon nanotube-dispersive micro-solid phase extraction for sensitive determination of inorganic As species in garlic samples by electrothermal atomic absorption spectrometry

    International Nuclear Information System (INIS)

    Grijalba, Alexander Castro; Escudero, Leticia B.; Wuilloud, Rodolfo G.

    2015-01-01

    A highly sensitive dispersive micro-solid phase extraction (D-μ-SPE) method combining an ionic liquid (IL) and multi-walled carbon nanotubes (MWCNTs) for inorganic As species (As(III) and As(V)) species separation and determination in garlic samples by electrothermal atomic absorption spectrometry (ETAAS) was developed. Trihexyl(tetradecil)phosphonium chloride IL was used to form an ion pair with the arsenomolybdate complex obtained by reaction of As(V) with molybdate ion. Afterwards, 1.0 mg of MWCNTs was dispersed for As(V) extraction and the supernatant was separated by centrifugation. MWCNTs were re-dispersed with tetradecyltrimethylammonium bromide surfactant and ultrasound followed by direct injection into the graphite furnace of ETAAS for As determination. Pyrolysis and atomization conditions were carefully studied for complete decomposition of MWCNTs and IL matrices. Under optimum conditions, an extraction efficiency of 100% and a preconcentration factor of 70 were obtained with 5 mL of garlic extract. The detection limit was 7.1 ng L −1 and the relative standard deviations (RSDs) for six replicate measurements at 5 μg L −1 of As were 5.4% and 4.8% for As(III) and As(V), respectively. The proposed D-μ-SPE method allowed the efficient separation and determination of inorganic As species in a complex matrix such as garlic extract. - Highlights: • Efficient retention and preconcentration of As by combining an IL with MWCNTs • Determination of As by ETAAS with direct injection of MWCNTs • Thermal degradation of MWCNTs in the graphite furnace of ETAAS • Highly sensitive speciation and determination of As in garlic

  15. Precipitation of organic arsenic compounds and their degradation products during struvite formation

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Jin-Biao; Yuan, Shoujun [School of Civil Engineering, Hefei University of Technology, Hefei 230009 (China); Institute of Water Treatment and Wastes Reutilization, Hefei University of Technology, Hefei 230009 (China); Wang, Wei, E-mail: dwhit@126.com [School of Civil Engineering, Hefei University of Technology, Hefei 230009 (China); Institute of Water Treatment and Wastes Reutilization, Hefei University of Technology, Hefei 230009 (China); Hu, Zhen-Hu, E-mail: zhhu@hfut.edu.cn [School of Civil Engineering, Hefei University of Technology, Hefei 230009 (China); Institute of Water Treatment and Wastes Reutilization, Hefei University of Technology, Hefei 230009 (China); Yu, Han-Qing [Department of Chemistry, University of Science & Technology of China, Hefei 230026 (China)

    2016-11-05

    Highlights: • Organic and inorganic arsenic compounds precipitated during struvite formation. • Precipitation of organic arsenic compounds in struvite decreased with increasing pH. • Arsenate easily precipitate in struvite as compared to organic arsenic compounds. • Arsenic compounds in solution affected the shape of struvite crystallization products. - Abstract: Roxarsone (ROX) and arsanilic acid (ASA) have been extensively used as organoarsenic animal feed additives. Organic arsenic compounds and their degradation products, arsenate (As(V)) and arsenite (As(III)), exist in the effluent from anaerobic reactors treating animal manure contaminated by ROX or ASA with ammonium (NH{sub 4}{sup +}-N) and phosphate (PO{sub 4}{sup 3−}-P) together. Therefore, arsenic species in the effluent might be involved in the struvite formation process. In this study, the involvement of organic arsenic compounds and their degradation products As(V) and As(III) in the struvite crystallization was investigated. The results demonstrated that arsenic compounds did not substantially affect the PO{sub 4}{sup 3−}-P recovery, but confirmed the precipitation of arsenic during struvite formation. The precipitation of arsenic compounds in struvite was considerably affected by a solution pH from 9.0 to 11.0. With an increase in pH, the content of ASA and ROX in the precipitation decreased, but the contents of As(III) and As(V) increased. In addition, the arsenic content of As(V) in the struvite was higher than that of As(III), ASA and ROX. The results indicated that the struvite could be contaminated when the solution contains arsenic species, but that could be minimized by controlling the solution pH and maintaining anaerobic conditions during struvite formation.

  16. Cloud Point Extraction for Electroanalysis: Anodic Stripping Voltammetry of Cadmium.

    Science.gov (United States)

    Rusinek, Cory A; Bange, Adam; Papautsky, Ian; Heineman, William R

    2015-06-16

    Cloud point extraction (CPE) is a well-established technique for the preconcentration of hydrophobic species from water without the use of organic solvents. Subsequent analysis is then typically performed via atomic absorption spectroscopy (AAS), UV-vis spectroscopy, or high performance liquid chromatography (HPLC). However, the suitability of CPE for electroanalytical methods such as stripping voltammetry has not been reported. We demonstrate the use of CPE for electroanalysis using the determination of cadmium (Cd(2+)) by anodic stripping voltammetry (ASV). Rather than using the chelating agents which are commonly used in CPE to form a hydrophobic, extractable metal complex, we used iodide and sulfuric acid to neutralize the charge on Cd(2+) to form an extractable ion pair. This offers good selectivity for Cd(2+) as no interferences were observed from other heavy metal ions. Triton X-114 was chosen as the surfactant for the extraction because its cloud point temperature is near room temperature (22-25 °C). Bare glassy carbon (GC), bismuth-coated glassy carbon (Bi-GC), and mercury-coated glassy carbon (Hg-GC) electrodes were compared for the CPE-ASV. A detection limit for Cd(2+) of 1.7 nM (0.2 ppb) was obtained with the Hg-GC electrode. ASV with CPE gave a 20x decrease (4.0 ppb) in the detection limit compared to ASV without CPE. The suitability of this procedure for the analysis of tap and river water samples was demonstrated. This simple, versatile, environmentally friendly, and cost-effective extraction method is potentially applicable to a wide variety of transition metals and organic compounds that are amenable to detection by electroanalytical methods.

  17. Fe3O4 and MnO2 assembled on honeycomb briquette cinders (HBC) for arsenic removal from aqueous solutions.

    Science.gov (United States)

    Zhu, Jin; Baig, Shams Ali; Sheng, Tiantian; Lou, Zimo; Wang, Zhuoxing; Xu, Xinhua

    2015-04-09

    In this study, a novel composite adsorbent (HBC-Fe3O4-MnO2) was synthesized by combining honeycomb briquette cinders (HBC) with Fe3O4 and MnO2 through a co-precipitation process. The purpose was to make the best use of the oxidative property of MnO2 and the adsorptive ability of magnetic Fe3O4 for enhanced As(III) and As(V) removal from aqueous solutions. Experimental results showed that the adsorption capacity of As(III) was observed to be much higher than As(V). The maximum adsorption capacity (2.16 mg/g) was achieved for As(III) by using HBC-Fe3O4-MnO2 (3:2) as compared to HBC-Fe3O4-MnO2 (2:1) and HBC-Fe3O4-MnO2 (1:1). The experimental data of As(V) adsorption fitted well with the Langmuir isotherm model, whereas As(III) data was described perfectly by Freundlich model. The pseudo-second-order kinetic model was fitted well for the entire adsorption process of As(III) and As(V) suggesting that the adsorption is a rate-controlling step. Aqueous solution pH was found to greatly affect the adsorption behavior. Furthermore, co-ions including HCO3(-) and PO4(3-) exhibited greater influence on arsenic removal efficiency, whereas Cl(-), NO3(-), SO4(2-) were found to have negligible effects on arsenic removal. Five consecutive adsorption-regeneration cycles confirmed that the adsorbent could be reusable for successive arsenic treatment and can be used in real treatment applications. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. Adaptive servo-ventilation for central sleep apnoea in systolic heart failure: results of the major substudy of SERVE-HF.

    Science.gov (United States)

    Cowie, Martin R; Woehrle, Holger; Wegscheider, Karl; Vettorazzi, Eik; Lezius, Susanne; Koenig, Wolfgang; Weidemann, Frank; Smith, Gillian; Angermann, Christiane; d'Ortho, Marie-Pia; Erdmann, Erland; Levy, Patrick; Simonds, Anita K; Somers, Virend K; Zannad, Faiez; Teschler, Helmut

    2018-03-01

    The SERVE-HF trial investigated the impact of treating central sleep apnoea (CSA) with adaptive servo-ventilation (ASV) in patients with systolic heart failure. A preplanned substudy was conducted to provide insight into mechanistic changes underlying the observed effects of ASV, including assessment of changes in left ventricular function, ventricular remodelling, and cardiac, renal and inflammatory biomarkers. In a subset of the 1325 randomised patients, echocardiography, cardiac magnetic resonance imaging (cMRI) and biomarker analysis were performed at baseline, and 3 and 12 months. In secondary analyses, data for patients with baseline and 12-month values were evaluated; 312 patients participated in the substudy. The primary endpoint, change in echocardiographically determined left ventricular ejection fraction from baseline to 12 months, did not differ significantly between the ASV and the control groups. There were also no significant between-group differences for changes in left ventricular dimensions, wall thickness, diastolic function or right ventricular dimensions and ejection fraction (echocardiography), and on cMRI (in small patient numbers). Plasma N-terminal pro B-type natriuretic peptide concentration decreased in both groups, and values were similar at 12 months. There were no significant between-group differences in changes in cardiac, renal and systemic inflammation biomarkers. In patients with systolic heart failure and CSA, addition of ASV to guideline-based medical management had no statistically significant effect on cardiac structure and function, or on cardiac biomarkers, renal function and systemic inflammation over 12 months. The increased cardiovascular mortality reported in SERVE-HF may not be related to adverse remodelling or worsening heart failure. © 2017 The Authors. European Journal of Heart Failure © 2017 European Society of Cardiology.

  19. Regulation of arsenic mobility on basaltic glass surfaces by speciation and pH.

    Science.gov (United States)

    Sigfusson, Bergur; Meharg, Andrew A; Gislason, Sigurdur R

    2008-12-01

    The importance of geothermal energy as a source for electricity generation and district heating has increased over recent decades. Arsenic can be a significant constituent of the geothermal fluids pumped to the surface during power generation. Dissolved As exists in different oxidation states, mainly as As(III) and As(V), and the charge of individual species varies with pH. Basaltic glass is one of the most important rock types in many high-temperature geothermal fields. Static batch and dynamic column experiments were combined to generate and validate sorption coefficients for As(III) and As(V) in contact with basaltic glass at pH 3-10. Validation was carried out by two empirical kinetic models and a surface complexation model (SCM). The SCM provided a better fit to the experimental column data than kinetic models at high pH values. However, in certain circumstances, an adequate estimation of As transport in the column could not be attained without incorporation of kinetic reactions. The varying mobility with pH was due to the combined effects of the variable charge of the basaltic glass with the pH point of zero charge at 6.8 and the individual As species as pH shifted, respectively. The mobility of As(III) decreased with increasing pH. The opposite was true for As(V), being nearly immobile at pH 3 to being highly mobile at pH 10. Incorporation of appropriate sorption constants, based on the measured pH and Eh of geothermal fluids, into regional groundwater-flow models should allow prediction of the As(III) and As(V) transport from geothermal systems to adjacent drinking water sources and ecosystems.

  20. Removal of heavy metals from water using multistage functionalized multiwall carbon nanotubes

    Directory of Open Access Journals (Sweden)

    Budimirović Dragoslav

    2017-01-01

    Full Text Available The multistage synthesis of the multi-wall carbon nanotubes (MWCNT modified with polyamidoamine dendrimers, A1/ and A2/MWCNT, capable of cation removal, is presented in this work, as well as novel adsorbents based on these precursor materials and modified with goethite nano-deposit, α-FeOOH, A1/ and A2/MWCNT–α-FeO(OH adsorbents used for As(V removal. In a batch test, the influence of pH, contact time, initial ion concentration and temperature on adsorption efficiency were studied. Adsorption data modelling by the Langmuir isotherm, revealed good adsorption capacities (in mg g-1 of 18.8 for As(V and 60.1 and 44.2 for Pb2+ and Cd2+ on A2/MWCNT, respectively. Also, 27.6 and 29.8 mg g-1 of As(V on A1/ and A2/MWCNT–α-FeO(OH, respectively, were removed. Thermodynamic parameters showed that the adsorption is spontaneous and endothermic processes. Results of the study of influences of competitive ions: bicarbonate, sulfate, phosphate, silicate, chromate, fluoride and natural organic matter (NOM, i.e., humic acid (HA, showed the highest effect of phosphate on the decrease of arsenate adsorption. Time-dependent adsorption was best described by pseudo-second-order kinetic model and Weber–Morris model which predicted intra-particle diffusion as a rate-controlling step. Also, activation energy (Ea / kJ mol-1: 8.85 for Cd2+, 9.25 for Pb2+ and 7.98 for As(V, were obtained from kinetic data. [Project of the Serbian Ministry of Education, Science and Technological Development, Grant no. III45019 and Grant no. OI 172057

  1. When four become one

    OpenAIRE

    Craigie, Robert

    2010-01-01

    Every machine is made of parts. But, as the new structure of the HIV integrase enzyme in complex with viral DNA shows, one could not have predicted from the individual parts just how this machine works.

  2. Urinary arsenic speciation profile in ethnic group of the Atacama desert (Chile) exposed to variable arsenic levels in drinking water.

    Science.gov (United States)

    Yáñez, Jorge; Mansilla, Héctor D; Santander, I Paola; Fierro, Vladimir; Cornejo, Lorena; Barnes, Ramón M; Amarasiriwardena, Dulasiri

    2015-01-01

    Ethnic groups from the Atacama Desert (known as Atacameños) have been exposed to natural arsenic pollution for over 5000 years. This work presents an integral study that characterizes arsenic species in water used for human consumption. It also describes the metabolism and arsenic elimination through urine in a chronically exposed population in northern Chile. In this region, water contained total arsenic concentrations up to 1250 μg L(-1), which was almost exclusively As(V). It is also important that this water was ingested directly from natural water sources without any treatment. The ingested arsenic was extensively methylated. In urine 93% of the arsenic was found as methylated arsenic species, such as monomethylarsonic acid [MMA(V)] and dimethylarsinic acid [DMA(V)]. The original ingested inorganic species [As(V)], represent less than 1% of the total urinary arsenic. Methylation activity among individuals can be assessed by measuring primary [inorganic As/methylated As] and secondary methylation [MMA/DMA] indexes. Both methylation indexes were 0.06, indicating a high biological converting capability of As(V) into MMA and then MMA into DMA, compared with the control population and other arsenic exposed populations previously reported.

  3. Reassessing the role of sulfur geochemistry on arsenic speciation in reducing environments

    KAUST Repository

    Couture, Raoul-Marie

    2011-05-01

    Recent evidence suggests that the oxidation of arsenite by zero-valent sulfur (S(0)) may produce stable aqueous arsenate species under highly reducing conditions. The speciation of arsenic (As) in reducing soils, sediments and aquifers may therefore be far more complex than previously thought. We illustrate this by presenting updated Eh-pH diagrams of As speciation in sulfidic waters that include the most recently reported formation constants for sulfide complexes of As(III) and As(V). The results show that the stability fields of As(III) and As(V) (oxy)thioanions cover a large pH range, from pH 5 to 10. In particular, As(V)-S(-II) complexes significantly enhance the predicted solubility of As under reducing conditions. Equilibrium calculations further show that, under conditions representative of sulfidic pore waters and in the presence of solid-phase elemental sulfur, the S0 (aq)/HS- couple yields a redox potential (Eh)~0.1V higher than the SO4 2-/HS- couple. S(0) may thus help stabilize aqueous As(V) not only by providing an electron acceptor for As(III) but also by contributing to a more oxidizing redox state. © 2011 Elsevier B.V.

  4. X-ray absorption spectroscopy as a tool investigating arsenic(III) and arsenic(V) sorption by an aluminum-based drinking-water treatment residual.

    Science.gov (United States)

    Makris, Konstantinos C; Sarkar, Dibyendu; Parsons, Jason G; Datta, Rupali; Gardea-Torresdey, Jorge L

    2009-11-15

    Historic applications of arsenical pesticides to agricultural land have resulted in accumulation of residual arsenic (As) in such soils. In situ immobilization represents a cost-effective and least ecological disrupting treatment technology for soil As. Earlier work in our laboratory showed that drinking-water treatment residuals (WTRs), a low-cost, waste by-product of the drinking-water treatment process exhibit a high affinity for As. Wet chemical experiments (sorption kinetics and desorption) were coupled with X-ray absorption spectroscopy measurements to elucidate the bonding strength and type of As(V) and As(III) sorption by an aluminum-based WTR. A fast (1h), followed by a slower sorption stage resulted in As(V) and As(III) sorption capacities of 96% and 77%, respectively. Arsenic desorption with a 5mM oxalate from the WTR was minimal, being always absorption spectroscopy data showed inner-sphere complexation between As and surface hydroxyls. Reaction time (up to 48h) had no effect on the initial As oxidation state for sorbed As(V) and As(III). A combination of inner-sphere bonding types occurred between As and Al on the WTR surface because mixed surface geometries and interatomic distances were observed.

  5. Ground water pollution by arsenic and its effects on health. Removal of arsenic from water; Suichu karano hiso no jokyo gijutsu

    Energy Technology Data Exchange (ETDEWEB)

    Tokunaga, S.

    1997-07-10

    Recently environmental standard for ground water is established. It is pointed out that the need of arsenic`s removal from water is expected in high level. Present condition of removal techniques of inorganic nitrogen and problems are explained. For example, ferro (III) chloride method is effective in As(V) and most suitable range is pH4{approx}5. Removal is possible until 0.005 when initial concentration is 0.2 mg{center_dot}l{sup -1}. As far as secondary problems are, there are dry treatment of generated sludge and disposal. Earth adsorbent as a new adsorbent is adsorption method is expected. Lanthanum and yttrium compounds possess adsorption for As(III) and As(V) and re-generation use is also possible. For example, removal of As(V) with initial concentration 19 mg{center_dot}l{sup -1} until 0.01 is possible at pH5{approx}77 range when hydroxide lanthanum is used as an adsorbent. Further special characteristics of each method are explained. It is concluded that a good removal method should be selected by considering raw water`s quality, capacity of treatment water, use of treatment water and economics. 29 refs., 2 figs.

  6. Arsenic uptake and speciation in vegetables grown under greenhouse conditions.

    Science.gov (United States)

    Smith, E; Juhasz, A L; Weber, J

    2009-04-01

    The accumulation of arsenic (As) by vegetables is a potential human exposure pathway. The speciation of As in vegetables is an important consideration due to the varying toxicity of different As species. In this study, common Australian garden vegetables were hydroponically grown with As-contaminated irrigation water to determine the uptake and species of As present in vegetable tissue. The highest concentrations of total As were observed in the roots of all vegetables and declined in the aerial portions of the plants. Total As accumulation in the edible portions of the vegetables decreased in the order radish > mung bean > lettuce = chard. Arsenic was present in the roots of radish, chard, and lettuce as arsenate (As(V)) and comprised between 77 and 92% of the total As present, whereas in mung beans, arsenite (As(III)) comprised 90% of the total As present. In aerial portions of the vegetables, As was distributed equally between both As(V) and As(III) in radish and chard but was present mainly as As(V) in lettuce. The presence of elevated As in vegetable roots suggests that As species may be complexed by phytochelatins, which limits As translocation to aerial portions of the plant.

  7. Reassessing the role of sulfur geochemistry on arsenic speciation in reducing environments

    KAUST Repository

    Couture, Raoul-Marie; Van Cappellen, Philippe

    2011-01-01

    Recent evidence suggests that the oxidation of arsenite by zero-valent sulfur (S(0)) may produce stable aqueous arsenate species under highly reducing conditions. The speciation of arsenic (As) in reducing soils, sediments and aquifers may therefore be far more complex than previously thought. We illustrate this by presenting updated Eh-pH diagrams of As speciation in sulfidic waters that include the most recently reported formation constants for sulfide complexes of As(III) and As(V). The results show that the stability fields of As(III) and As(V) (oxy)thioanions cover a large pH range, from pH 5 to 10. In particular, As(V)-S(-II) complexes significantly enhance the predicted solubility of As under reducing conditions. Equilibrium calculations further show that, under conditions representative of sulfidic pore waters and in the presence of solid-phase elemental sulfur, the S0 (aq)/HS- couple yields a redox potential (Eh)~0.1V higher than the SO4 2-/HS- couple. S(0) may thus help stabilize aqueous As(V) not only by providing an electron acceptor for As(III) but also by contributing to a more oxidizing redox state. © 2011 Elsevier B.V.

  8. Efficient removal of arsenic from water using a granular adsorbent: Fe-Mn binary oxide impregnated chitosan bead.

    Science.gov (United States)

    Qi, Jianying; Zhang, Gaosheng; Li, Haining

    2015-10-01

    A novel sorbent of Fe-Mn binary oxide impregnated chitosan bead (FMCB) was fabricated through impregnating Fe-Mn binary oxide into chitosan matrix. The FMCB is sphere-like with a diameter of 1.6-1.8 mm, which is effective for both As(V) and As(III) sorption. The maximal sorption capacities are 39.1 and 54.2 mg/g, respectively, outperforming most of reported granular sorbents. The arsenic was mainly removed by adsorbing onto the Fe-Mn oxide component. The coexisting SO4(2-), HCO3(-) and SiO3(2-) have no great influence on arsenic sorption, whereas, the HPO4(2-) shows negative effects. The arsenic-loaded FMCB could be effectively regenerated using NaOH solution and repeatedly used. In column tests, about 1500 and 3200 bed volumes of simulated groundwater containing 233 μg/L As(V) and As(III) were respectively treated before breakthrough. These results demonstrate the superiority of the FMCB in removing As(V) and As(III), indicating that it is a promising candidate for arsenic removal from real drinking water. Copyright © 2015 Elsevier Ltd. All rights reserved.

  9. Clustered epitopes within the Gag-Pol fusion protein DNA vaccine enhance immune responses and protection against challenge with recombinant vaccinia viruses expressing HIV-1 Gag and Pol antigens

    International Nuclear Information System (INIS)

    Bolesta, Elizabeth; Gzyl, Jaroslaw; Wierzbicki, Andrzej; Kmieciak, Dariusz; Kowalczyk, Aleksandra; Kaneko, Yutaro; Srinivasan, Alagarsamy; Kozbor, Danuta

    2005-01-01

    We have generated a codon-optimized hGagp17p24-Polp51 plasmid DNA expressing the human immunodeficiency virus type 1 (HIV-1) Gag-Pol fusion protein that consists of clusters of highly conserved cytotoxic T lymphocyte (CTL) epitopes presented by multiple MHC class I alleles. In the hGagp17p24-Polp51 construct, the ribosomal frameshift site had been deleted together with the potentially immunosuppressive Gag nucleocapsid (p15) as well as Pol protease (p10) and integrase (p31). Analyses of the magnitude and breadth of cellular responses demonstrated that immunization of HLA-A2/K b transgenic mice with the hGagp17p24-Polp51 construct induced 2- to 5-fold higher CD8 + T-cell responses to Gag p17-, p24-, and Pol reverse transcriptase (RT)-specific CTL epitopes than the full-length hGag-PolΔFsΔPr counterpart. The increases were correlated with higher protection against challenge with recombinant vaccinia viruses (rVVs) expressing gag and pol gene products. Consistent with the profile of Gag- and Pol-specific CD8 + T cell responses, an elevated level of type 1 cytokine production was noted in p24- and RT-stimulated splenocyte cultures established from hGagp17p24-Polp51-immunized mice compared to responses induced with the hGag-PolΔFsΔPr vaccine. Sera of mice immunized with the hGagp17p24-Polp51 vaccine also exhibited an increased titer of p24- and RT-specific IgG2 antibody responses. The results from our studies provide insights into approaches for boosting the breadth of Gag- and Pol-specific immune responses

  10. Protein immobilization strategies for protein biochips

    NARCIS (Netherlands)

    Rusmini, F.; Rusmini, Federica; Zhong, Zhiyuan; Feijen, Jan

    2007-01-01

    In the past few years, protein biochips have emerged as promising proteomic and diagnostic tools for obtaining information about protein functions and interactions. Important technological innovations have been made. However, considerable development is still required, especially regarding protein

  11. Bringing SASI back: Single session selective arterial secretin injection and transarterial embolization of intrahepatic pancreatic neuroendocrine metastasis in a MEN-1 patient

    Directory of Open Access Journals (Sweden)

    Jawad S. Hussain, MD, MS

    2018-04-01

    Full Text Available SASI (selective arterial secretin injection is a form of ASVS (arterial stimulation and venous sampling used to localize pancreatic gastrinomas. This report aims to review the protocol for SASI and demonstrate its utility in localizing functional and nonfunctional gastrinomas. Even if a patient has a pancreatic mass and a laboratory profile fitting a specific endocrine syndrome, these may or may not be associated as has been previously demonstrated with adrenal vein sampling. We present a case where a patient underwent simultaneous SASI and bland embolization of a hepatic metastasis to facilitate partial pancreatectomy for Zollinger-Ellison syndrome. Keywords: SASI, ASVS, Gastrinoma, Sampling

  12. Tooele Army Depot Revised Final Site-Wide Ecological Risk Assessment. Volume IV.

    Science.gov (United States)

    1998-02-01

    SS!5!55 "^ **i "i *n Q ti ti d ci *»S «S «n *n «n 6 Ö Ö «*$ «ri «r> *r) Wj «1 «rj o c> o <a fr^ «•! *rj f) rrj «*j fry ...Venugopal and Luckey 1978. Arsenic 0.94 (mouse, AsIII and AsV) 0.95 (dog, AsV) 60 - 90 (rat) 2.5 ( chicken ) 2.4 (dog) 0.0077-0.012 0.277 0.288...reservation. A pan of that investigation involves a search for rare plant species, those that might be included under stipulations of the Endangered

  13. Protein Molecular Structures, Protein SubFractions, and Protein Availability Affected by Heat Processing: A Review

    International Nuclear Information System (INIS)

    Yu, P.

    2007-01-01

    The utilization and availability of protein depended on the types of protein and their specific susceptibility to enzymatic hydrolysis (inhibitory activities) in the gastrointestine and was highly associated with protein molecular structures. Studying internal protein structure and protein subfraction profiles leaded to an understanding of the components that make up a whole protein. An understanding of the molecular structure of the whole protein was often vital to understanding its digestive behavior and nutritive value in animals. In this review, recently obtained information on protein molecular structural effects of heat processing was reviewed, in relation to protein characteristics affecting digestive behavior and nutrient utilization and availability. The emphasis of this review was on (1) using the newly advanced synchrotron technology (S-FTIR) as a novel approach to reveal protein molecular chemistry affected by heat processing within intact plant tissues; (2) revealing the effects of heat processing on the profile changes of protein subfractions associated with digestive behaviors and kinetics manipulated by heat processing; (3) prediction of the changes of protein availability and supply after heat processing, using the advanced DVE/OEB and NRC-2001 models, and (4) obtaining information on optimal processing conditions of protein as intestinal protein source to achieve target values for potential high net absorbable protein in the small intestine. The information described in this article may give better insight in the mechanisms involved and the intrinsic protein molecular structural changes occurring upon processing.

  14. Retroviral DNA integration: viral and cellular determinants of target-site selection.

    Directory of Open Access Journals (Sweden)

    Mary K Lewinski

    2006-06-01

    Full Text Available Retroviruses differ in their preferences for sites for viral DNA integration in the chromosomes of infected cells. Human immunodeficiency virus (HIV integrates preferentially within active transcription units, whereas murine leukemia virus (MLV integrates preferentially near transcription start sites and CpG islands. We investigated the viral determinants of integration-site selection using HIV chimeras with MLV genes substituted for their HIV counterparts. We found that transferring the MLV integrase (IN coding region into HIV (to make HIVmIN caused the hybrid to integrate with a specificity close to that of MLV. Addition of MLV gag (to make HIVmGagmIN further increased the similarity of target-site selection to that of MLV. A chimeric virus with MLV Gag only (HIVmGag displayed targeting preferences different from that of both HIV and MLV, further implicating Gag proteins in targeting as well as IN. We also report a genome-wide analysis indicating that MLV, but not HIV, favors integration near DNase I-hypersensitive sites (i.e., +/- 1 kb, and that HIVmIN and HIVmGagmIN also favored integration near these features. These findings reveal that IN is the principal viral determinant of integration specificity; they also reveal a new role for Gag-derived proteins, and strengthen models for integration targeting based on tethering of viral IN proteins to host proteins.

  15. Probable secondary transmission of antimicrobial-resistant Escherichia coli between people living with and without pets.

    Science.gov (United States)

    Chung, Yeon Soo; Park, Young Kyung; Park, Yong Ho; Park, Kun Taek

    2017-03-18

    Companion animals are considered as one of the reservoirs of antimicrobial-resistant (AR) bacteria that can be cross-transmitted to humans. However, limited information is available on the possibility of AR bacteria originating from companion animals being transmitted secondarily from owners to non-owners sharing the same space. To address this issue, the present study investigated clonal relatedness among AR E. coli isolated from dog owners and non-owners in the same college classroom or household. Anal samples (n=48) were obtained from 14 owners and 34 non-owners; 31 E. coli isolates were collected (nine from owners and 22 from non-owners). Of 31 E. coli, 20 isolates (64.5%) were resistant to at least one antimicrobial, and 16 isolates (51.6%) were determined as multi-drug resistant E. coli. Six isolates (19.4%) harbored integrase genes (five harbored class I integrase gene and one harbored class 2 integrase gene, respectively). Pulsed-field gel electrophoretic analysis identified three different E. coli clonal sets among isolates, indicating that cross-transmission of AR E. coli can easily occur between owners and non-owners. The findings emphasize a potential risk of spread of AR bacteria originating from pets within human communities, once they are transferred to humans. Further studies are needed to evaluate the exact risk and identify the risk factors of secondarily transmission by investigating larger numbers of isolates from pets, their owners and non-owners in a community.

  16. HIV-1 resistance dynamics in patients failing dolutegravir maintenance monotherapy.

    Science.gov (United States)

    Wijting, Ingeborg E A; Lungu, Cynthia; Rijnders, Bart J A; van der Ende, Marchina E; Pham, Hanh T; Mesplede, Thibault; Pas, Suzan D; Voermans, Jolanda J C; Schuurman, Rob; van de Vijver, David A M C; Boers, Patrick H M; Gruters, Rob A; Boucher, Charles A B; van Kampen, Jeroen J A

    2018-03-29

    A high genetic resistance barrier to the integrase-strand-transfer-inhibitor (INSTI) dolutegravir has been reported in vitro and in vivo. We describe the dynamics of INSTI-resistance-associated-mutations (INSTI-RAMs) and mutations in the 3'-polypurine tract (3'-PPT) in relation to virological failure (VF) observed in the randomized dolutegravir maintenance monotherapy study (DOMONO, NCT02401828). From ten patients with VF plasma samples prior to start cART and during VF were used to generate Sanger sequences of integrase, the 5' terminal bases of the 3'- LTR, and the 3'-PPT. Median HIV-RNA (IQR) at VF was 3,490 (1,440-4,990) c/mL. INSTI-RAMs were detected in 4/10 patients (S230R, R263K, N155H, E92Q+N155H) and in 4/10 patients no INSTI-RAMs were detected (2/10 patients integrase sequencing was unsuccessful). The time-to-VF ranged from 4 weeks to 72 weeks. In one patient, mutations developed in the highly conserved 3'-PPT. No changes in the terminal bases of the 3'-LTR were observed. The genetic barrier to resistance is too low to justify dolutegravir maintenance monotherapy as single INSTI-RAMs are sufficient to cause VF. The large variation in time-to-VF suggests that stochastic reactivation of a pre-existing provirus containing a single INSTI-RAM is the mechanism for failure. Changes in the 3'-PPT point to a new dolutegravir resistance mechanism in vivo.

  17. Rheumatic diseases in HIV-infected patients in the post-antiretroviral therapy era: a tertiary care center experience.

    Science.gov (United States)

    Parperis, Konstantinos; Abdulqader, Yasir; Myers, Robert; Bhattarai, Bikash; Al-Ani, Muhsen

    2018-04-04

    The aim of the study was to calculate the proportion of rheumatic diseases in HIV patients who were receiving ART and to identify association of the HIV medications with the development of rheumatologic diseases. We conducted a retrospective chart review during the period of 2010 to 2016. We identified 2996 patients as having chronic HIV infection and on ART, and we collected data regarding patient's demographic characteristics, comorbidities, CD 4 count, HIV viral load, and ART. One hundred thirteen out of 2996 HIV patients (3.8%) were found to have a rheumatic condition (mean age of 48.6 years, 83% male). The most frequent musculoskeletal condition was avascular necrosis (AVN) in 39 (1.3%), and the most frequent autoimmune condition was psoriasis in 28 patients (1%). Compared with the 200 HIV patients without any diagnosis of rheumatic disease were the older patients with rheumatic conditions (mean age of 48.9 vs. 42.7 years; p rheumatic conditions were 1.7 times higher in males (relative to females). Those who received integrase inhibitors were more likely (63.3%) to develop rheumatologic manifestations relative to those who never received integrase inhibitors (21.6%; p rheumatic diseases in HIV patients appears to be comparable to the prevalence in the US population. Older age, longer duration of HIV infection, and the use of ART regimens containing integrase inhibitors, appear to increase the risk of developing a rheumatic condition.

  18. Information assessment on predicting protein-protein interactions

    Directory of Open Access Journals (Sweden)

    Gerstein Mark

    2004-10-01

    Full Text Available Abstract Background Identifying protein-protein interactions is fundamental for understanding the molecular machinery of the cell. Proteome-wide studies of protein-protein interactions are of significant value, but the high-throughput experimental technologies suffer from high rates of both false positive and false negative predictions. In addition to high-throughput experimental data, many diverse types of genomic data can help predict protein-protein interactions, such as mRNA expression, localization, essentiality, and functional annotation. Evaluations of the information contributions from different evidences help to establish more parsimonious models with comparable or better prediction accuracy, and to obtain biological insights of the relationships between protein-protein interactions and other genomic information. Results Our assessment is based on the genomic features used in a Bayesian network approach to predict protein-protein interactions genome-wide in yeast. In the special case, when one does not have any missing information about any of the features, our analysis shows that there is a larger information contribution from the functional-classification than from expression correlations or essentiality. We also show that in this case alternative models, such as logistic regression and random forest, may be more effective than Bayesian networks for predicting interactions. Conclusions In the restricted problem posed by the complete-information subset, we identified that the MIPS and Gene Ontology (GO functional similarity datasets as the dominating information contributors for predicting the protein-protein interactions under the framework proposed by Jansen et al. Random forests based on the MIPS and GO information alone can give highly accurate classifications. In this particular subset of complete information, adding other genomic data does little for improving predictions. We also found that the data discretizations used in the

  19. Mapping Protein-Protein Interactions by Quantitative Proteomics

    DEFF Research Database (Denmark)

    Dengjel, Joern; Kratchmarova, Irina; Blagoev, Blagoy

    2010-01-01

    spectrometry (MS)-based proteomics in combination with affinity purification protocols has become the method of choice to map and track the dynamic changes in protein-protein interactions, including the ones occurring during cellular signaling events. Different quantitative MS strategies have been used...... to characterize protein interaction networks. In this chapter we describe in detail the use of stable isotope labeling by amino acids in cell culture (SILAC) for the quantitative analysis of stimulus-dependent dynamic protein interactions.......Proteins exert their function inside a cell generally in multiprotein complexes. These complexes are highly dynamic structures changing their composition over time and cell state. The same protein may thereby fulfill different functions depending on its binding partners. Quantitative mass...

  20. Integrating Multiple Autonomous Underwater Vessels, Surface Vessels and Aircraft into Oceanographic Research Vessel Operations

    Science.gov (United States)

    McGillivary, P. A.; Borges de Sousa, J.; Martins, R.; Rajan, K.

    2012-12-01

    Autonomous platforms are increasingly used as components of Integrated Ocean Observing Systems and oceanographic research cruises. Systems deployed can include gliders or propeller-driven autonomous underwater vessels (AUVs), autonomous surface vessels (ASVs), and unmanned aircraft systems (UAS). Prior field campaigns have demonstrated successful communication, sensor data fusion and visualization for studies using gliders and AUVs. However, additional requirements exist for incorporating ASVs and UASs into ship operations. For these systems to be optimally integrated into research vessel data management and operational planning systems involves addressing three key issues: real-time field data availability, platform coordination, and data archiving for later analysis. A fleet of AUVs, ASVs and UAS deployed from a research vessel is best operated as a system integrated with the ship, provided communications among them can be sustained. For this purpose, Disruptive Tolerant Networking (DTN) software protocols for operation in communication-challenged environments help ensure reliable high-bandwidth communications. Additionally, system components need to have considerable onboard autonomy, namely adaptive sampling capabilities using their own onboard sensor data stream analysis. We discuss Oceanographic Decision Support System (ODSS) software currently used for situational awareness and planning onshore, and in the near future event detection and response will be coordinated among multiple vehicles. Results from recent field studies from oceanographic research vessels using AUVs, ASVs and UAS, including the Rapid Environmental Picture (REP-12) cruise, are presented describing methods and results for use of multi-vehicle communication and deliberative control networks, adaptive sampling with single and multiple platforms, issues relating to data management and archiving, and finally challenges that remain in addressing these technological issues. Significantly, the

  1. Transferable integrons of Gram-negative bacteria isolated from the gut of a wild boar in the buffer zone of a national park.

    Science.gov (United States)

    Mokracka, Joanna; Koczura, Ryszard; Kaznowski, Adam

    2012-06-01

    The aim of this study was to determine the presence of integron-bearing Gram-negative bacteria in the gut of a wild boar (Sus scrofa L.) shot in the buffer zone of a national park. Five Gram-negative strains of Escherichia coli, Serratia odorifera, Hafnia alvei and Pseudomonas sp. were isolated. Four of these strains had class 2 integrase (intI2), and one harbored class 1 integrase (intI1). The integron-positive strains were multiresistant, i.e., resistant to at least three unrelated antibiotics. All of the integrons were transferred to E. coli J-53 (Rif(R)) in a conjugation assay. The results showed that a number of multiresistant, integron-containing bacterial strains of different genera may inhabit a single individual of a wild animal, allowing the possibility of transfer of antimicrobial resistance genes.

  2. ProDis-ContSHC: learning protein dissimilarity measures and hierarchical context coherently for protein-protein comparison in protein database retrieval.

    Science.gov (United States)

    Wang, Jingyan; Gao, Xin; Wang, Quanquan; Li, Yongping

    2012-05-08

    The need to retrieve or classify protein molecules using structure or sequence-based similarity measures underlies a wide range of biomedical applications. Traditional protein search methods rely on a pairwise dissimilarity/similarity measure for comparing a pair of proteins. This kind of pairwise measures suffer from the limitation of neglecting the distribution of other proteins and thus cannot satisfy the need for high accuracy of the retrieval systems. Recent work in the machine learning community has shown that exploiting the global structure of the database and learning the contextual dissimilarity/similarity measures can improve the retrieval performance significantly. However, most existing contextual dissimilarity/similarity learning algorithms work in an unsupervised manner, which does not utilize the information of the known class labels of proteins in the database. In this paper, we propose a novel protein-protein dissimilarity learning algorithm, ProDis-ContSHC. ProDis-ContSHC regularizes an existing dissimilarity measure dij by considering the contextual information of the proteins. The context of a protein is defined by its neighboring proteins. The basic idea is, for a pair of proteins (i, j), if their context N(i) and N(j) is similar to each other, the two proteins should also have a high similarity. We implement this idea by regularizing dij by a factor learned from the context N(i) and N(j).Moreover, we divide the context to hierarchial sub-context and get the contextual dissimilarity vector for each protein pair. Using the class label information of the proteins, we select the relevant (a pair of proteins that has the same class labels) and irrelevant (with different labels) protein pairs, and train an SVM model to distinguish between their contextual dissimilarity vectors. The SVM model is further used to learn a supervised regularizing factor. Finally, with the new Supervised learned Dissimilarity measure, we update the Protein Hierarchial

  3. Biophysics of protein evolution and evolutionary protein biophysics

    Science.gov (United States)

    Sikosek, Tobias; Chan, Hue Sun

    2014-01-01

    The study of molecular evolution at the level of protein-coding genes often entails comparing large datasets of sequences to infer their evolutionary relationships. Despite the importance of a protein's structure and conformational dynamics to its function and thus its fitness, common phylogenetic methods embody minimal biophysical knowledge of proteins. To underscore the biophysical constraints on natural selection, we survey effects of protein mutations, highlighting the physical basis for marginal stability of natural globular proteins and how requirement for kinetic stability and avoidance of misfolding and misinteractions might have affected protein evolution. The biophysical underpinnings of these effects have been addressed by models with an explicit coarse-grained spatial representation of the polypeptide chain. Sequence–structure mappings based on such models are powerful conceptual tools that rationalize mutational robustness, evolvability, epistasis, promiscuous function performed by ‘hidden’ conformational states, resolution of adaptive conflicts and conformational switches in the evolution from one protein fold to another. Recently, protein biophysics has been applied to derive more accurate evolutionary accounts of sequence data. Methods have also been developed to exploit sequence-based evolutionary information to predict biophysical behaviours of proteins. The success of these approaches demonstrates a deep synergy between the fields of protein biophysics and protein evolution. PMID:25165599

  4. CLINICAL: ARt

    African Journals Online (AJOL)

    2008-12-17

    Dec 17, 2008 ... ral replication was thought to be a declining CD4 cell ... (NNRTIs), 10 protease inhibitors (PIs), and one each of the fusion, entry and integrase inhibitors to choose .... actions, side-effects and efavirenz teratogencity are un-.

  5. High quality protein microarray using in situ protein purification

    Directory of Open Access Journals (Sweden)

    Fleischmann Robert D

    2009-08-01

    Full Text Available Abstract Background In the postgenomic era, high throughput protein expression and protein microarray technologies have progressed markedly permitting screening of therapeutic reagents and discovery of novel protein functions. Hexa-histidine is one of the most commonly used fusion tags for protein expression due to its small size and convenient purification via immobilized metal ion affinity chromatography (IMAC. This purification process has been adapted to the protein microarray format, but the quality of in situ His-tagged protein purification on slides has not been systematically evaluated. We established methods to determine the level of purification of such proteins on metal chelate-modified slide surfaces. Optimized in situ purification of His-tagged recombinant proteins has the potential to become the new gold standard for cost-effective generation of high-quality and high-density protein microarrays. Results Two slide surfaces were examined, chelated Cu2+ slides suspended on a polyethylene glycol (PEG coating and chelated Ni2+ slides immobilized on a support without PEG coating. Using PEG-coated chelated Cu2+ slides, consistently higher purities of recombinant proteins were measured. An optimized wash buffer (PBST composed of 10 mM phosphate buffer, 2.7 mM KCl, 140 mM NaCl and 0.05% Tween 20, pH 7.4, further improved protein purity levels. Using Escherichia coli cell lysates expressing 90 recombinant Streptococcus pneumoniae proteins, 73 proteins were successfully immobilized, and 66 proteins were in situ purified with greater than 90% purity. We identified several antigens among the in situ-purified proteins via assays with anti-S. pneumoniae rabbit antibodies and a human patient antiserum, as a demonstration project of large scale microarray-based immunoproteomics profiling. The methodology is compatible with higher throughput formats of in vivo protein expression, eliminates the need for resin-based purification and circumvents

  6. Can infrared spectroscopy provide information on protein-protein interactions?

    Science.gov (United States)

    Haris, Parvez I

    2010-08-01

    For most biophysical techniques, characterization of protein-protein interactions is challenging; this is especially true with methods that rely on a physical phenomenon that is common to both of the interacting proteins. Thus, for example, in IR spectroscopy, the carbonyl vibration (1600-1700 cm(-1)) associated with the amide bonds from both of the interacting proteins will overlap extensively, making the interpretation of spectral changes very complicated. Isotope-edited infrared spectroscopy, where one of the interacting proteins is uniformly labelled with (13)C or (13)C,(15)N has been introduced as a solution to this problem, enabling the study of protein-protein interactions using IR spectroscopy. The large shift of the amide I band (approx. 45 cm(-1) towards lower frequency) upon (13)C labelling of one of the proteins reveals the amide I band of the unlabelled protein, enabling it to be used as a probe for monitoring conformational changes. With site-specific isotopic labelling, structural resolution at the level of individual amino acid residues can be achieved. Furthermore, the ability to record IR spectra of proteins in diverse environments means that isotope-edited IR spectroscopy can be used to structurally characterize difficult systems such as protein-protein complexes bound to membranes or large insoluble peptide/protein aggregates. In the present article, examples of application of isotope-edited IR spectroscopy for studying protein-protein interactions are provided.

  7. Protein and protein hydrolysates in sports nutrition.

    Science.gov (United States)

    van Loon, Luc J C; Kies, Arie K; Saris, Wim H M

    2007-08-01

    With the increasing knowledge about the role of nutrition in increasing exercise performance, it has become clear over the last 2 decades that amino acids, protein, and protein hydrolysates can play an important role. Most of the attention has been focused on their effects at a muscular level. As these nutrients are ingested, however, it also means that gastrointestinal digestibility and absorption can modulate their efficacy significantly. Therefore, discussing the role of amino acids, protein, and protein hydrolysates in sports nutrition entails holding a discussion on all levels of the metabolic route. On May 28-29, 2007, a small group of researchers active in the field of exercise science and protein metabolism presented an overview of the different aspects of the application of protein and protein hydrolysates in sports nutrition. In addition, they were asked to share their opinions on the future progress in their fields of research. In this overview, an introduction to the workshop and a short summary of its outcome is provided.

  8. ProDis-ContSHC: Learning protein dissimilarity measures and hierarchical context coherently for protein-protein comparison in protein database retrieval

    KAUST Repository

    Wang, Jim Jing-Yan

    2012-05-08

    Background: The need to retrieve or classify protein molecules using structure or sequence-based similarity measures underlies a wide range of biomedical applications. Traditional protein search methods rely on a pairwise dissimilarity/similarity measure for comparing a pair of proteins. This kind of pairwise measures suffer from the limitation of neglecting the distribution of other proteins and thus cannot satisfy the need for high accuracy of the retrieval systems. Recent work in the machine learning community has shown that exploiting the global structure of the database and learning the contextual dissimilarity/similarity measures can improve the retrieval performance significantly. However, most existing contextual dissimilarity/similarity learning algorithms work in an unsupervised manner, which does not utilize the information of the known class labels of proteins in the database.Results: In this paper, we propose a novel protein-protein dissimilarity learning algorithm, ProDis-ContSHC. ProDis-ContSHC regularizes an existing dissimilarity measure dij by considering the contextual information of the proteins. The context of a protein is defined by its neighboring proteins. The basic idea is, for a pair of proteins (i, j), if their context N (i) and N (j) is similar to each other, the two proteins should also have a high similarity. We implement this idea by regularizing dij by a factor learned from the context N (i) and N (j). Moreover, we divide the context to hierarchial sub-context and get the contextual dissimilarity vector for each protein pair. Using the class label information of the proteins, we select the relevant (a pair of proteins that has the same class labels) and irrelevant (with different labels) protein pairs, and train an SVM model to distinguish between their contextual dissimilarity vectors. The SVM model is further used to learn a supervised regularizing factor. Finally, with the new Supervised learned Dissimilarity measure, we update

  9. Targeting protein-protein interaction between MLL1 and reciprocal proteins for leukemia therapy.

    Science.gov (United States)

    Wang, Zhi-Hui; Li, Dong-Dong; Chen, Wei-Lin; You, Qi-Dong; Guo, Xiao-Ke

    2018-01-15

    The mixed lineage leukemia protein-1 (MLL1), as a lysine methyltransferase, predominantly regulates the methylation of histone H3 lysine 4 (H3K4) and functions in hematopoietic stem cell (HSC) self-renewal. MLL1 gene fuses with partner genes that results in the generation of MLL1 fusion proteins (MLL1-FPs), which are frequently detected in acute leukemia. In the progress of leukemogenesis, a great deal of proteins cooperate with MLL1 to form multiprotein complexes serving for the dysregulation of H3K4 methylation, the overexpression of homeobox (HOX) cluster genes, and the consequent generation of leukemia. Hence, disrupting the interactions between MLL1 and the reciprocal proteins has been considered to be a new treatment strategy for leukemia. Here, we reviewed potential protein-protein interactions (PPIs) between MLL1 and its reciprocal proteins, and summarized the inhibitors to target MLL1 PPIs. The druggability of MLL1 PPIs for leukemia were also discussed. Copyright © 2017. Published by Elsevier Ltd.

  10. Protein kinase substrate identification on functional protein arrays

    Directory of Open Access Journals (Sweden)

    Zhou Fang

    2008-02-01

    Full Text Available Abstract Background Over the last decade, kinases have emerged as attractive therapeutic targets for a number of different diseases, and numerous high throughput screening efforts in the pharmaceutical community are directed towards discovery of compounds that regulate kinase function. The emerging utility of systems biology approaches has necessitated the development of multiplex tools suitable for proteomic-scale experiments to replace lower throughput technologies such as mass spectroscopy for the study of protein phosphorylation. Recently, a new approach for identifying substrates of protein kinases has applied the miniaturized format of functional protein arrays to characterize phosphorylation for thousands of candidate protein substrates in a single experiment. This method involves the addition of protein kinases in solution to arrays of immobilized proteins to identify substrates using highly sensitive radioactive detection and hit identification algorithms. Results To date, the factors required for optimal performance of protein array-based kinase substrate identification have not been described. In the current study, we have carried out a detailed characterization of the protein array-based method for kinase substrate identification, including an examination of the effects of time, buffer compositions, and protein concentration on the results. The protein array approach was compared to standard solution-based assays for assessing substrate phosphorylation, and a correlation of greater than 80% was observed. The results presented here demonstrate how novel substrates for protein kinases can be quickly identified from arrays containing thousands of human proteins to provide new clues to protein kinase function. In addition, a pooling-deconvolution strategy was developed and applied that enhances characterization of specific kinase-substrate relationships and decreases reagent consumption. Conclusion Functional protein microarrays are an

  11. Protein kinesis: The dynamics of protein trafficking and stability

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-12-31

    The purpose of this conference is to provide a multidisciplinary forum for exchange of state-of-the-art information on protein kinesis. This volume contains abstracts of papers in the following areas: protein folding and modification in the endoplasmic reticulum; protein trafficking; protein translocation and folding; protein degradation; polarity; nuclear trafficking; membrane dynamics; and protein import into organelles.

  12. What to Start: Selecting a First HIV Regimen

    Science.gov (United States)

    ... CCR5 antagonists Integrase strand transfer inhibitors (INSTIs) Post-attachment inhibitors In general, a person's first HIV regimen includes two NRTIs plus an INSTI, an NNRTI, or a PI boosted with cobicistat (brand name: Tybost) or ritonavir (brand name: Norvir). Cobicistat ...

  13. Pharmacokinetic Drug-Drug Interaction Study Between Raltegravir and Atorvastatin 20 mg in Healthy Volunteers

    NARCIS (Netherlands)

    Blonk, M.I.; Beek, M. van; Colbers, A.; Schouwenberg, B.J.; Burger, D.M.

    2015-01-01

    BACKGROUND: Dyslipidemia is highly prevalent among patients with HIV infection and contributes to an increased risk of cardiovascular disease. We investigated the influence of a frequently used statin, atorvastatin, on the pharmacokinetics of the HIV-integrase inhibitor raltegravir and vice versa.

  14. Arsenate and fluoride enhanced each other's uptake in As-sensitive plant Pteris ensiformis.

    Science.gov (United States)

    Das, Suchismita; de Oliveira, Letuzia M; da Silva, Evandro; Ma, Lena Q

    2017-08-01

    We investigated the effects of arsenate (AsV) and fluoride (F) on each other's uptake in an As-sensitive plant Pteris ensiformis. Plants were exposed to 1) 0.1 × Hoagland solution control, 2) 3.75 mg L -1 As and 1.9, 3.8, or 7.6 mg L -1 F, or 3) 1 mg L -1 F and 3.75 mg L -1 or 7.5 mg L -1 As for 7 d in hydroponics. P. ensiformis accumulated 14.7-32.6 mg kg -1 As at 3.75 mg L -1 AsV, and 99-145 mg kg -1 F at 1 mg L -1 F. Our study revealed that AsV and F increased each other's uptake when co-present. At 1.9 mg L -1 , F increased frond As uptake from 14.7 to 40.3 mg kg -1 , while 7.5 mg L -1 As increased frond F uptake from 99 to 371 mg kg -1 . Although, AsV was the predominant As species in all tissues, F enhanced AsIII levels in the rhizomes and fronds, while the reverse was observed in the roots. Increasing As concentrations also enhanced TBARS and H 2 O 2 in tissues, indicating oxidative stress. However, F alleviated As stress by lowering their levels in the fronds. Frond and root membrane leakage were also evident due to As or F exposure. The results may facilitate better understanding of the mechanisms underlying the co-uptake of As and F in plants. However, the mechanisms of how they enhance each other's uptake in P. ensiformis need further investigation. Published by Elsevier Ltd.

  15. Assessing the mechanisms controlling the mobilization of arsenic in the arsenic contaminated shallow alluvial aquifer in the blackfoot disease endemic area

    International Nuclear Information System (INIS)

    Liao, Vivian Hsiu-Chuan; Chu, Yu-Ju; Su, Yu-Chen; Lin, Po-Cheng; Hwang, Yaw-Huei; Liu, Chen-Wuing; Liao, Chung-Min; Chang, Fi-John; Yu, Chan-Wei

    2011-01-01

    Highlights: ► Sedimentary microcosm showed simultaneous microbial reduction of Fe(III) and As(V). ► Addition of acetate caused a further increase in aqueous Fe(II) but not arsenic. ► An As(V)-reducing bacterium (ARS-3) native to aquifer sediments was isolated. ► ARS-3 showed microbial reduction of As(V) to As(III) in pore water in this aquifer. - Abstract: High levels of arsenic in groundwater and drinking water represent a major health problem worldwide. Drinking arsenic-contaminated groundwater is a likely cause of blackfoot disease (BFD) in Taiwan, but mechanisms controlling the mobilization of arsenic present at elevated concentrations within aquifers remain understudied. Microcosm experiments using sediments from arsenic contaminated shallow alluvial aquifers in the blackfoot disease endemic area showed simultaneous microbial reduction of Fe(III) and As(V). Significant soluble Fe(II) (0.23 ± 0.03 mM) in pore waters and mobilization of As(III) (206.7 ± 21.2 nM) occurred during the first week. Aqueous Fe(II) and As(III) respectively reached concentrations of 0.27 ± 0.01 mM and 571.4 ± 63.3 nM after 8 weeks. We also showed that the addition of acetate caused a further increase in aqueous Fe(II) but the dissolved arsenic did not increase. We further isolated an As(V)-reducing bacterium native to aquifer sediments which showed that the direct enzymatic reduction of As(V) to the potentially more-soluble As(III) in pore water is possible in this aquifer. Our results provide evidence that microorganisms can mediate the release of sedimentary arsenic to groundwater in this region and the capacity for arsenic release was not limited by the availability of electron donors in the sediments.

  16. Assessing the mechanisms controlling the mobilization of arsenic in the arsenic contaminated shallow alluvial aquifer in the blackfoot disease endemic area

    Energy Technology Data Exchange (ETDEWEB)

    Liao, Vivian Hsiu-Chuan, E-mail: vivianliao@ntu.edu.tw [Department of Bioenvironmental Systems Engineering, National Taiwan University, 1 Roosevelt Road, Sec. 4, Taipei 106, Taiwan (China); Chu, Yu-Ju; Su, Yu-Chen; Lin, Po-Cheng [Department of Bioenvironmental Systems Engineering, National Taiwan University, 1 Roosevelt Road, Sec. 4, Taipei 106, Taiwan (China); Hwang, Yaw-Huei [Institute of Occupational Medicine and Industrial Hygiene, College of Public Health, National Taiwan University, 17 Xu-Zhou Road, Taipei 100, Taiwan (China); Liu, Chen-Wuing; Liao, Chung-Min; Chang, Fi-John; Yu, Chan-Wei [Department of Bioenvironmental Systems Engineering, National Taiwan University, 1 Roosevelt Road, Sec. 4, Taipei 106, Taiwan (China)

    2011-12-15

    Highlights: Black-Right-Pointing-Pointer Sedimentary microcosm showed simultaneous microbial reduction of Fe(III) and As(V). Black-Right-Pointing-Pointer Addition of acetate caused a further increase in aqueous Fe(II) but not arsenic. Black-Right-Pointing-Pointer An As(V)-reducing bacterium (ARS-3) native to aquifer sediments was isolated. Black-Right-Pointing-Pointer ARS-3 showed microbial reduction of As(V) to As(III) in pore water in this aquifer. - Abstract: High levels of arsenic in groundwater and drinking water represent a major health problem worldwide. Drinking arsenic-contaminated groundwater is a likely cause of blackfoot disease (BFD) in Taiwan, but mechanisms controlling the mobilization of arsenic present at elevated concentrations within aquifers remain understudied. Microcosm experiments using sediments from arsenic contaminated shallow alluvial aquifers in the blackfoot disease endemic area showed simultaneous microbial reduction of Fe(III) and As(V). Significant soluble Fe(II) (0.23 {+-} 0.03 mM) in pore waters and mobilization of As(III) (206.7 {+-} 21.2 nM) occurred during the first week. Aqueous Fe(II) and As(III) respectively reached concentrations of 0.27 {+-} 0.01 mM and 571.4 {+-} 63.3 nM after 8 weeks. We also showed that the addition of acetate caused a further increase in aqueous Fe(II) but the dissolved arsenic did not increase. We further isolated an As(V)-reducing bacterium native to aquifer sediments which showed that the direct enzymatic reduction of As(V) to the potentially more-soluble As(III) in pore water is possible in this aquifer. Our results provide evidence that microorganisms can mediate the release of sedimentary arsenic to groundwater in this region and the capacity for arsenic release was not limited by the availability of electron donors in the sediments.

  17. Ceria modified activated carbon: an efficient arsenic removal adsorbent for drinking water purification

    Science.gov (United States)

    Sawana, Radha; Somasundar, Yogesh; Iyer, Venkatesh Shankar; Baruwati, Babita

    2017-06-01

    Ceria (CeO2) coated powdered activated carbon was synthesized by a single step chemical process and demonstrated to be a highly efficient adsorbent for the removal of both As(III) and As(V) from water without any pre-oxidation process. The formation of CeO2 on the surface of powdered activated carbon was confirmed by X-ray diffraction, Raman spectroscopy and X-ray photoelectron spectroscopy. The percentage of Ce in the adsorbent was confirmed to be 3.5 % by ICP-OES. The maximum removal capacity for As(III) and As(V) was found to be 10.3 and 12.2 mg/g, respectively. These values are comparable to most of the commercially available adsorbents. 80 % of the removal process was completed within 15 min of contact time in a batch process. More than 95 % removal of both As(III) and As(V) was achieved within an hour. The efficiency of removal was not affected by change in pH (5-9), salinity, hardness, organic (1-4 ppm of humic acid) and inorganic anions (sulphate, nitrate, chloride, bicarbonate and fluoride) excluding phosphate. Presence of 100 ppm phosphate reduced the removal significantly from 90 to 18 %. The equilibrium adsorption pattern of both As(III) and As(V) fitted well with the Freundlich model with R 2 values 0.99 and 0.97, respectively. The material shows reusability greater than three times in a batch process (arsenic concentration reduced below 10 ppb from 330 ppb) and a life of at least 100 L in a column study with 80 g material when tested under natural hard water (TDS 1000 ppm, pH 7.8, hardness 600 ppm as CaCO3) spiked with 330 ppb of arsenic.

  18. HKC: An Algorithm to Predict Protein Complexes in Protein-Protein Interaction Networks

    Directory of Open Access Journals (Sweden)

    Xiaomin Wang

    2011-01-01

    Full Text Available With the availability of more and more genome-scale protein-protein interaction (PPI networks, research interests gradually shift to Systematic Analysis on these large data sets. A key topic is to predict protein complexes in PPI networks by identifying clusters that are densely connected within themselves but sparsely connected with the rest of the network. In this paper, we present a new topology-based algorithm, HKC, to detect protein complexes in genome-scale PPI networks. HKC mainly uses the concepts of highest k-core and cohesion to predict protein complexes by identifying overlapping clusters. The experiments on two data sets and two benchmarks show that our algorithm has relatively high F-measure and exhibits better performance compared with some other methods.

  19. Molecular tweezers modulate 14-3-3 protein-protein interactions

    Science.gov (United States)

    Bier, David; Rose, Rolf; Bravo-Rodriguez, Kenny; Bartel, Maria; Ramirez-Anguita, Juan Manuel; Dutt, Som; Wilch, Constanze; Klärner, Frank-Gerrit; Sanchez-Garcia, Elsa; Schrader, Thomas; Ottmann, Christian

    2013-03-01

    Supramolecular chemistry has recently emerged as a promising way to modulate protein functions, but devising molecules that will interact with a protein in the desired manner is difficult as many competing interactions exist in a biological environment (with solvents, salts or different sites for the target biomolecule). We now show that lysine-specific molecular tweezers bind to a 14-3-3 adapter protein and modulate its interaction with partner proteins. The tweezers inhibit binding between the 14-3-3 protein and two partner proteins—a phosphorylated (C-Raf) protein and an unphosphorylated one (ExoS)—in a concentration-dependent manner. Protein crystallography shows that this effect arises from the binding of the tweezers to a single surface-exposed lysine (Lys214) of the 14-3-3 protein in the proximity of its central channel, which normally binds the partner proteins. A combination of structural analysis and computer simulations provides rules for the tweezers' binding preferences, thus allowing us to predict their influence on this type of protein-protein interactions.

  20. Application of Activated Carbon for Removal of Arsenic Ions from Aqueous Solutions

    Directory of Open Access Journals (Sweden)

    R. Ansari

    2007-01-01

    Full Text Available The activated carbon (AC was used for removal of As(III and As(V ions from aqueous solutions. Sorption experiments were conducted using both batch and column systems. The effect of some important parameters on sorption of these by AC was studied. It was found that among the different factors affecting sorption capacity and efficiency in removal of arsenic from aqueous solutions, the effect of pH and the oxidation state were the most prominent. The optimum pH values for removal of As(III and As(V from aqueous solutions using AC was found 12 and 3 respectively. Impregnation of AC with sulphur contain organic dyes, it is possible to improve As(III uptake considerably.

  1. Heat-assisted aqueous extraction of rice flour for arsenic speciation analysis.

    Science.gov (United States)

    Narukawa, Tomohiro; Chiba, Koichi

    2010-07-28

    A versatile heat-assisted pretreatment aqueous extraction method for the analysis of arsenic species in rice was developed. Rice flour certified reference materials NIST SRM1568a and NMIJ CRM 7503-a and a flour made from polished rice were used as samples, and HPLC-ICP-MS was employed for the determination of arsenic species. Arsenite [As(III)], arsenate [As(V)], monomethylarsonic acid (MMAA) and dimethylarsinic acid (DMAA) were detected in NIST SRM, and As(III), As(V) and DMAA were found in NMIJ CRM and the prepared polished rice flour. The sums of the concentrations of all species in each rice flour sample were 97-102% of the total arsenic concentration in each sample.

  2. Changes in protein composition and protein phosphorylation during ...

    African Journals Online (AJOL)

    Changes in protein profiles and protein phosphorylation were studied in various stages of germinating somatic and zygotic embryos. Many proteins, which were expressed in cotyledonary stage somatic embryos, were also present in the zygotic embryos obtained from mature dry seed. The intensity of 22 kDa protein was ...

  3. Naturally occurring Vpr inhibitors from medicinal plants of Myanmar.

    Science.gov (United States)

    Win, Nwet Nwet; Ngwe, Hla; Abe, Ikuro; Morita, Hiroyuki

    2017-10-01

    Human immunodeficiency virus type-1 (HIV-1) is a lentiviral family member that encodes the retroviral Gag, Pol, and Env proteins, along with six additional accessory proteins, Tat, Rev, Vpu, Vif, Nef, and Vpr. The currently approved anti-HIV drugs target the Pol and Env encoded proteins. However, these drugs are only effective in reducing viral replication. Furthermore, the drugs' toxicities and the emergence of drug-resistant strains have become serious worldwide problems. Resistance eventually arises to all of the approved anti-HIV drugs, including the newly approved drugs that target HIV integrase (IN). Drug resistance likely emerges because of spontaneous mutations that occur during viral replication. Therefore, new drugs that effectively block other viral components must be developed to reduce the rate of resistance and suppress viral replication with little or no long-term toxicity. The accessory proteins may expand treatment options. Viral protein R (Vpr) is one of the promising drug targets among the HIV accessory proteins. However, the search for inhibitors continues in anti-HIV drug discovery. In this review, we summarize the naturally occurring compounds discovered from two Myanmar medicinal plants as well as their structure-activity relationships. A total of 49 secondary metabolites were isolated from Kaempferia pulchra rhizomes and Picrasama javanica bark, and the types of compounds were identified as isopimarane diterpenoids and picrasane quassinoids, respectively. Among the isolates, 7 diterpenoids and 15 quassinoids were found to be Vpr inhibitors lacking detectable toxicity, and their potencies varied according to their respective functionalities.

  4. An ontology-based search engine for protein-protein interactions.

    Science.gov (United States)

    Park, Byungkyu; Han, Kyungsook

    2010-01-18

    Keyword matching or ID matching is the most common searching method in a large database of protein-protein interactions. They are purely syntactic methods, and retrieve the records in the database that contain a keyword or ID specified in a query. Such syntactic search methods often retrieve too few search results or no results despite many potential matches present in the database. We have developed a new method for representing protein-protein interactions and the Gene Ontology (GO) using modified Gödel numbers. This representation is hidden from users but enables a search engine using the representation to efficiently search protein-protein interactions in a biologically meaningful way. Given a query protein with optional search conditions expressed in one or more GO terms, the search engine finds all the interaction partners of the query protein by unique prime factorization of the modified Gödel numbers representing the query protein and the search conditions. Representing the biological relations of proteins and their GO annotations by modified Gödel numbers makes a search engine efficiently find all protein-protein interactions by prime factorization of the numbers. Keyword matching or ID matching search methods often miss the interactions involving a protein that has no explicit annotations matching the search condition, but our search engine retrieves such interactions as well if they satisfy the search condition with a more specific term in the ontology.

  5. Water-Protein Interactions: The Secret of Protein Dynamics

    Directory of Open Access Journals (Sweden)

    Silvia Martini

    2013-01-01

    Full Text Available Water-protein interactions help to maintain flexible conformation conditions which are required for multifunctional protein recognition processes. The intimate relationship between the protein surface and hydration water can be analyzed by studying experimental water properties measured in protein systems in solution. In particular, proteins in solution modify the structure and the dynamics of the bulk water at the solute-solvent interface. The ordering effects of proteins on hydration water are extended for several angstroms. In this paper we propose a method for analyzing the dynamical properties of the water molecules present in the hydration shells of proteins. The approach is based on the analysis of the effects of protein-solvent interactions on water protons NMR relaxation parameters. NMR relaxation parameters, especially the nonselective (R1NS and selective (R1SE spin-lattice relaxation rates of water protons, are useful for investigating the solvent dynamics at the macromolecule-solvent interfaces as well as the perturbation effects caused by the water-macromolecule interactions on the solvent dynamical properties. In this paper we demonstrate that Nuclear Magnetic Resonance Spectroscopy can be used to determine the dynamical contributions of proteins to the water molecules belonging to their hydration shells.

  6. Two Chimeric Regulators of G-protein Signaling (RGS) Proteins Differentially Modulate Soybean Heterotrimeric G-protein Cycle*

    Science.gov (United States)

    Roy Choudhury, Swarup; Westfall, Corey S.; Laborde, John P.; Bisht, Naveen C.; Jez, Joseph M.; Pandey, Sona

    2012-01-01

    Heterotrimeric G-proteins and the regulator of G-protein signaling (RGS) proteins, which accelerate the inherent GTPase activity of Gα proteins, are common in animals and encoded by large gene families; however, in plants G-protein signaling is thought to be more limited in scope. For example, Arabidopsis thaliana contains one Gα, one Gβ, three Gγ, and one RGS protein. Recent examination of the Glycine max (soybean) genome reveals a larger set of G-protein-related genes and raises the possibility of more intricate G-protein networks than previously observed in plants. Stopped-flow analysis of GTP-binding and GDP/GTP exchange for the four soybean Gα proteins (GmGα1–4) reveals differences in their kinetic properties. The soybean genome encodes two chimeric RGS proteins with an N-terminal seven transmembrane domain and a C-terminal RGS box. Both GmRGS interact with each of the four GmGα and regulate their GTPase activity. The GTPase-accelerating activities of GmRGS1 and -2 differ for each GmGα, suggesting more than one possible rate of the G-protein cycle initiated by each of the Gα proteins. The differential effects of GmRGS1 and GmRGS2 on GmGα1–4 result from a single valine versus alanine difference. The emerging picture suggests complex regulation of the G-protein cycle in soybean and in other plants with expanded G-protein networks. PMID:22474294

  7. Alignment of non-covalent interactions at protein-protein interfaces.

    Directory of Open Access Journals (Sweden)

    Hongbo Zhu

    Full Text Available BACKGROUND: The study and comparison of protein-protein interfaces is essential for the understanding of the mechanisms of interaction between proteins. While there are many methods for comparing protein structures and protein binding sites, so far no methods have been reported for comparing the geometry of non-covalent interactions occurring at protein-protein interfaces. METHODOLOGY/PRINCIPAL FINDINGS: Here we present a method for aligning non-covalent interactions between different protein-protein interfaces. The method aligns the vector representations of van der Waals interactions and hydrogen bonds based on their geometry. The method has been applied to a dataset which comprises a variety of protein-protein interfaces. The alignments are consistent to a large extent with the results obtained using two other complementary approaches. In addition, we apply the method to three examples of protein mimicry. The method successfully aligns respective interfaces and allows for recognizing conserved interface regions. CONCLUSIONS/SIGNIFICANCE: The Galinter method has been validated in the comparison of interfaces in which homologous subunits are involved, including cases of mimicry. The method is also applicable to comparing interfaces involving non-peptidic compounds. Galinter assists users in identifying local interface regions with similar patterns of non-covalent interactions. This is particularly relevant to the investigation of the molecular basis of interaction mimicry.

  8. The Ser/Thr Protein Kinase Protein-Protein Interaction Map of M. tuberculosis.

    Science.gov (United States)

    Wu, Fan-Lin; Liu, Yin; Jiang, He-Wei; Luan, Yi-Zhao; Zhang, Hai-Nan; He, Xiang; Xu, Zhao-Wei; Hou, Jing-Li; Ji, Li-Yun; Xie, Zhi; Czajkowsky, Daniel M; Yan, Wei; Deng, Jiao-Yu; Bi, Li-Jun; Zhang, Xian-En; Tao, Sheng-Ce

    2017-08-01

    Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, the leading cause of death among all infectious diseases. There are 11 eukaryotic-like serine/threonine protein kinases (STPKs) in Mtb, which are thought to play pivotal roles in cell growth, signal transduction and pathogenesis. However, their underlying mechanisms of action remain largely uncharacterized. In this study, using a Mtb proteome microarray, we have globally identified the binding proteins in Mtb for all of the STPKs, and constructed the first STPK protein interaction (KPI) map that includes 492 binding proteins and 1,027 interactions. Bioinformatics analysis showed that the interacting proteins reflect diverse functions, including roles in two-component system, transcription, protein degradation, and cell wall integrity. Functional investigations confirmed that PknG regulates cell wall integrity through key components of peptidoglycan (PG) biosynthesis, e.g. MurC. The global STPK-KPIs network constructed here is expected to serve as a rich resource for understanding the key signaling pathways in Mtb, thus facilitating drug development and effective control of Mtb. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  9. Protein-protein interaction site predictions with three-dimensional probability distributions of interacting atoms on protein surfaces.

    Directory of Open Access Journals (Sweden)

    Ching-Tai Chen

    Full Text Available Protein-protein interactions are key to many biological processes. Computational methodologies devised to predict protein-protein interaction (PPI sites on protein surfaces are important tools in providing insights into the biological functions of proteins and in developing therapeutics targeting the protein-protein interaction sites. One of the general features of PPI sites is that the core regions from the two interacting protein surfaces are complementary to each other, similar to the interior of proteins in packing density and in the physicochemical nature of the amino acid composition. In this work, we simulated the physicochemical complementarities by constructing three-dimensional probability density maps of non-covalent interacting atoms on the protein surfaces. The interacting probabilities were derived from the interior of known structures. Machine learning algorithms were applied to learn the characteristic patterns of the probability density maps specific to the PPI sites. The trained predictors for PPI sites were cross-validated with the training cases (consisting of 432 proteins and were tested on an independent dataset (consisting of 142 proteins. The residue-based Matthews correlation coefficient for the independent test set was 0.423; the accuracy, precision, sensitivity, specificity were 0.753, 0.519, 0.677, and 0.779 respectively. The benchmark results indicate that the optimized machine learning models are among the best predictors in identifying PPI sites on protein surfaces. In particular, the PPI site prediction accuracy increases with increasing size of the PPI site and with increasing hydrophobicity in amino acid composition of the PPI interface; the core interface regions are more likely to be recognized with high prediction confidence. The results indicate that the physicochemical complementarity patterns on protein surfaces are important determinants in PPIs, and a substantial portion of the PPI sites can be predicted

  10. Protein-Protein Interaction Site Predictions with Three-Dimensional Probability Distributions of Interacting Atoms on Protein Surfaces

    Science.gov (United States)

    Chen, Ching-Tai; Peng, Hung-Pin; Jian, Jhih-Wei; Tsai, Keng-Chang; Chang, Jeng-Yih; Yang, Ei-Wen; Chen, Jun-Bo; Ho, Shinn-Ying; Hsu, Wen-Lian; Yang, An-Suei

    2012-01-01

    Protein-protein interactions are key to many biological processes. Computational methodologies devised to predict protein-protein interaction (PPI) sites on protein surfaces are important tools in providing insights into the biological functions of proteins and in developing therapeutics targeting the protein-protein interaction sites. One of the general features of PPI sites is that the core regions from the two interacting protein surfaces are complementary to each other, similar to the interior of proteins in packing density and in the physicochemical nature of the amino acid composition. In this work, we simulated the physicochemical complementarities by constructing three-dimensional probability density maps of non-covalent interacting atoms on the protein surfaces. The interacting probabilities were derived from the interior of known structures. Machine learning algorithms were applied to learn the characteristic patterns of the probability density maps specific to the PPI sites. The trained predictors for PPI sites were cross-validated with the training cases (consisting of 432 proteins) and were tested on an independent dataset (consisting of 142 proteins). The residue-based Matthews correlation coefficient for the independent test set was 0.423; the accuracy, precision, sensitivity, specificity were 0.753, 0.519, 0.677, and 0.779 respectively. The benchmark results indicate that the optimized machine learning models are among the best predictors in identifying PPI sites on protein surfaces. In particular, the PPI site prediction accuracy increases with increasing size of the PPI site and with increasing hydrophobicity in amino acid composition of the PPI interface; the core interface regions are more likely to be recognized with high prediction confidence. The results indicate that the physicochemical complementarity patterns on protein surfaces are important determinants in PPIs, and a substantial portion of the PPI sites can be predicted correctly with

  11. Bioinformatic Prediction of WSSV-Host Protein-Protein Interaction

    Directory of Open Access Journals (Sweden)

    Zheng Sun

    2014-01-01

    Full Text Available WSSV is one of the most dangerous pathogens in shrimp aquaculture. However, the molecular mechanism of how WSSV interacts with shrimp is still not very clear. In the present study, bioinformatic approaches were used to predict interactions between proteins from WSSV and shrimp. The genome data of WSSV (NC_003225.1 and the constructed transcriptome data of F. chinensis were used to screen potentially interacting proteins by searching in protein interaction databases, including STRING, Reactome, and DIP. Forty-four pairs of proteins were suggested to have interactions between WSSV and the shrimp. Gene ontology analysis revealed that 6 pairs of these interacting proteins were classified into “extracellular region” or “receptor complex” GO-terms. KEGG pathway analysis showed that they were involved in the “ECM-receptor interaction pathway.” In the 6 pairs of interacting proteins, an envelope protein called “collagen-like protein” (WSSV-CLP encoded by an early virus gene “wsv001” in WSSV interacted with 6 deduced proteins from the shrimp, including three integrin alpha (ITGA, two integrin beta (ITGB, and one syndecan (SDC. Sequence analysis on WSSV-CLP, ITGA, ITGB, and SDC revealed that they possessed the sequence features for protein-protein interactions. This study might provide new insights into the interaction mechanisms between WSSV and shrimp.

  12. Protein subcellular localization assays using split fluorescent proteins

    Science.gov (United States)

    Waldo, Geoffrey S [Santa Fe, NM; Cabantous, Stephanie [Los Alamos, NM

    2009-09-08

    The invention provides protein subcellular localization assays using split fluorescent protein systems. The assays are conducted in living cells, do not require fixation and washing steps inherent in existing immunostaining and related techniques, and permit rapid, non-invasive, direct visualization of protein localization in living cells. The split fluorescent protein systems used in the practice of the invention generally comprise two or more self-complementing fragments of a fluorescent protein, such as GFP, wherein one or more of the fragments correspond to one or more beta-strand microdomains and are used to "tag" proteins of interest, and a complementary "assay" fragment of the fluorescent protein. Either or both of the fragments may be functionalized with a subcellular targeting sequence enabling it to be expressed in or directed to a particular subcellular compartment (i.e., the nucleus).

  13. Application of capillary electrophoresis to anion speciation in soil water extracts: 2. Arsenic

    Energy Technology Data Exchange (ETDEWEB)

    Naidu, R.; Smith, J.; McLaren, R.G.; Stevens, D.P.; Sumner, M.E.; Jackson, P.E.

    2000-02-01

    A method has been developed for the speciation of arsenic (AsO{sub 2}{sup {minus}}, AsO{sub 4}{sup 3{minus}}, and dimethylarsinic [DMA]) in natural soil solutions from contaminated sites in Australia. The separation of these anions was achieved by capillary zone electrophoresis (CZE) using a fused silica capillary with a basic chromate buffer and on-column indirect UV detection at 254 nm. Method parameters, such as electrolyte pH, run voltage, and capillary temperature were studied in order to establish suitable analytical conditions. The ideal separation for As(III) and DMA was achieved with a buffer pH of 8.0, a run voltage of 25 kV, and a capillary temperature of 30 C. Under these conditions, As(V) and orthophosphate ions comigrated. However, the use of a chromate buffer at pH 10, a run voltage of 20 kV, and capillary temperature of 20 C led to complete separation of As(V) and phosphate peaks. Results of these investigations together with recovery test data suggest that separation of the As species from soil solutions can be achieved in less than 5 min with detection limits of 0.50, 0.10, and 0.10 mg L{sup {minus}1} for As(III), As(V), and DMA, respectively.

  14. ARSENIC ADSORPTION AND REDUCTION IN IRON-RICH SOILS NEARBY LANDFILLS IN NORTHWEST FLORIDA

    Directory of Open Access Journals (Sweden)

    Hongqin Xue

    2016-01-01

    Full Text Available In Florida, soils are mainly composed of Myakka, an acid soil characterized by a subsurface accumulation of humus and Al(III and Fe(III oxides. Downgradient of the landfills in Northwest Florida, elevated levels of iron and arsenic observations had been made in the groundwater from monitoring wells, which was attributed to the geomicrobial iron and arsenic reduction. There is thus an immediate research need for a better understanding of the reduction reactions that are responsible for the mobilization of iron and arsenic in the subsurface soil nearby landfills. Owing to the high Fe(III oxide content, As(V adsorption reactions with Fe(III oxide surfaces are particularly important, which may control As(V reduction. This research focused on the investigation of the biogeochemical processes of the subsurface soil nearby landfills of Northwest Florida. Arsenic and iron reduction was studied in batch reactors and quantified based on Monod-type microbial kinetic growth simulations. As(V adsorption in iron-rich Northwest Floridian soils was further investigated to explain the reduction observations. It was demonstrated in this research that solubilization of arsenic in the subsurface soil nearby landfills in Northwest Florida would likely occur under conditions favoring Fe(III dissimilatory reduction.

  15. Distribution of inorganic arsenic species in groundwater from Central-West Part of Santa Fe Province, Argentina

    International Nuclear Information System (INIS)

    Sigrist, Mirna; Albertengo, Antonela; Brusa, Lucila; Beldoménico, Horacio; Tudino, Mabel

    2013-01-01

    Highlights: • Study on inorganic arsenic species in groundwater for drinking in Santa Fe Argentina. • This information is currently scarce or absent in the region. • An analytical methodology based on SPE-FI-HGAAS coupling was used for speciation. • Information is given for a more accurate interpretation of the toxicological impact. - Abstract: The distribution of inorganic arsenic species in groundwater used as drinking water supply by the peri-urban and rural population from central-western area of Santa Fe Province, Argentina, was studied. An analytical methodology based on an online system of atomic absorption spectrometry with hydride generation and flow injection (FI-HGAAS) was used for total inorganic arsenic determination. For speciation purposes, the distinction between As(V) and As(III) was performed through the on line coupling of FI-HGAAS to a solid phase system based on an anionic exchanger able to retain As(V) as oxyanion, allowing As(III) to be selectively determined. The concentration of As(V) was calculated as the difference between total arsenic and As(III) concentrations. Effects of matrix interference due to the nonselective behavior of the exchange resins were carefully laid. Results for 59 samples collected from 27 localities showed an almost exclusive predominance of pentavalent forms

  16. Da-KGM based GO-reinforced FMBO-loaded aerogels for efficient arsenic removal in aqueous solution.

    Science.gov (United States)

    Ye, Shuxin; Jin, Weiping; Huang, Qing; Hu, Ying; Li, Yan; Li, Jing; Li, Bin

    2017-01-01

    Composites based on deacetylated konjac glucomannan (Da-KGM) and graphene oxide (GO) aerogels with iron and manganese oxides (FMBO) for effective removal of arsenic from contaminated water. Da-KGM, which was used as supporting composite matrix here, were firstly treated with GO and loaded FMBO. The obtained Da-KGM/GO/FMBO composite aerogels were characterized by compression test, thermo gravimetric analysis (TGA), X-ray diffraction (XRD), fourier transform infrared spectroscopy (FTIR) and scanning electron microscope (SEM). The characteristic results showed that addition of GO exhibited enhanced mechanical properties towards Da-KGM aerogels. What's more, results of FTIR indicated the strong intermolecular hydrogen bond interaction between KGM and GO. Batch adsorption tests were used to evaluate arsenic removal capacity. Da-KGM/GO loaded FMBO composite aerogels exhibited high adsorption ability for arsenite [As(III)] and arsenate [As(V)]. The adsorption results showed that the arsenic for both arsenite [As(III)] and arsenate [As(V)] removal process followed a pseudo-second-order rate equation and Langmuir monolayer adsorption. The maximum As(III) and As(V) uptake capacity of Da-KGM/GO(10%)/FMBO composite aerogels reached 30.21mgg -1 and 12.08mgg -1 respectively according to Langmuir isotherm at pH 7 and 323K. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. Opportunities for Phytoremediation and Bioindication of Arsenic Contaminated Water Using a Submerged Aquatic Plant:Vallisneria natans (lour.) Hara.

    Science.gov (United States)

    Chen, Guoliang; Liu, Xingmei; Brookes, Philip C; Xu, Jianming

    2015-01-01

    The identification of plants with high arsenic hyperaccumulating efficiency from water is required to ensure the successful application of phytoremediation technology. Five dominant submerged plant species (Vallisneria natans (Lour.) Hara., Potamageton crispus L., Myriophyllum spicatum L., Ceratophyllum demersum L. and Hydrilla verticillata (L.f.) Royle) in China were used to determine their potential to remove As from contaminated water. V. natans had the highest accumulation of As among them. The characteristics of As accumulation, transformation and the effect of phosphate on As accumulation in V. natans were then further studied. The growth of V. natans was not inhibited even when the As concentration reached 2.0 mg L(-1). After 21 d of As treatment, the bioconcentration factor (BCF) reached 1300. The As concentration in the environment and exposure time are major factors controlling the As concentration in V. natans. After being absorbed, As(V) is efficiently reduced to As(III) in plants. The synthesis of non-enzymic antioxidants may play an important role under As stress and increase As detoxication. In addition, As(V) uptake by V. natans was negatively correlated with phosphate (P) uptake when P was sufficiently supplied. As(V) is probably taken up via P transporters in V. natans.

  18. CLINICO-EPIDEMIOLOGY AND THERAPEUTIC OUTCOME OF SNAKE BITE IN KONASEEMA REGION OF ANDHRA PRADESH

    Directory of Open Access Journals (Sweden)

    Sai Krishna

    2016-03-01

    Full Text Available INTRODUCTION Snake bite is a common and frequently devastating environmental and occupational problem, especially in rural areas of tropical developing countries. Snake bite incidence is high in Andhra Pradesh. With the onset of monsoon the incidence of snake bite used to increase. METHODS Present study is a retrospective study in which all the data of snake bite cases admitted in the Konaseema Institute of Medical Sciences was collected in last two years; details of the patient was obtained from bed head ticket. RESULTS In two years of data collection, 46 snake bite cases are found as per our record. Out of 46 patients, twenty seven were male and nineteen were female. Maximum twenty two (22 patients were between ages 20 to 40 years. Out of forty six patients, forty four recovered and only two patients died, cause of death was acute pulmonary oedema with cardiac arrhythmia. DISCUSSION Most of the patients were given ASV (anti-snake venom, out of that only four patients developed reaction to ASV. Most of the patients who have received ASV were recovered. Only two deaths were reported which was due to acute pulmonary oedema with cardiac arrhythmia. CONCLUSION Awareness and education about snake is required.

  19. Arsenic, chromium and mercury removal using mussel shell ash or a sludge/ashes waste mixture.

    Science.gov (United States)

    Seco-Reigosa, Natalia; Peña-Rodríguez, Susana; Nóvoa-Muñoz, Juan Carlos; Arias-Estévez, Manuel; Fernández-Sanjurjo, María J; Alvarez-Rodríguez, Esperanza; Núñez-Delgado, Avelino

    2013-04-01

    Different batches of valued mussel shell and waste mussel shell ash are characterised. Shell ash has pH > 12 and high electrical conductivities (between 16.01 and 27.27 dS m(-1)), while calcined shell shows pH values up to 10.7 and electrical conductivities between 1.19 and 3.55 dS m(-1). X-ray fluorescence, nitric acid digestion and water extractions show higher concentrations in shell ash for most parameters. Calcite is the dominant crystalline compound in this ash (95.6%), followed by aragonite. Adsorption/desorption trials were performed for mussel shell ash and for a waste mixture including shell ash, sewage sludge and wood ash, showing the following percentage adsorptions: Hg(II) >94%, As(V) >96% and Cr(VI) between 11 and 30% for shell ash; Hg(II) >98%, As(V) >88% and Cr(VI) between 30 and 88% for the waste mixture. Hg and As desorption was ash and the waste mixture, while Cr desorption was between 92 and 45% for shell ash, and between 19 and 0% for the mixture. In view of that, mussel shell ash and the mixture including shell ash, sewage sludge and wood ash could be useful for Hg(II) and As(V) removal.

  20. The new concept of hyphenated analytical system: Simultaneous determination of inorganic arsenic(III), arsenic(V), selenium(IV) and selenium(VI) by high performance liquid chromatography-hydride generation-(fast sequential) atomic absorption spectrometry during single analysis

    International Nuclear Information System (INIS)

    Niedzielski, P.

    2005-01-01

    The paper presents a new conception of determination of inorganic speciation forms of arsenic: As(III) and As(V) as well selenium Se(IV) and Se(VI) by means of the high performance liquid chromatography hyphenated with a detection by the atomic absorption spectrometry with hydride generation (HPLC-HG-AAS). The application of optimization procedure conditions of chromatographic separation of arsenic and selenium speciation forms (using anion-exchange Supelco LC-SAX1 column and phosphate buffer at pH 5.40 as a mobile phase) as well as the use of the atomic absorption spectrometry as a detector, which enables work in fast sequential mode, allowed to develop original detection methodology of simultaneous determination of arsenic As(III), As(V) and selenium Se(IV) and Se(VI) speciation forms within a 220 s single analysis. The obtained detection limits were 7.8 ng mL -1 for As(III); 12.0 ng mL -1 for As(V); 2.4 ng mL -1 for Se(IV) and 18.6 ng mL -1 for Se(VI) and precision 10.5%, 12.1%, 14.2% and 17.3%, respectively, for 100 ng mL -1 . The described method was used for ground water analysis