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Opening of the TAR hairpin in the HIV-1 genome causes aberrant RNA dimerization and packaging

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Das Atze T

2012-07-01

Full Text Available Abstract Background The TAR hairpin is present at both the 5′ and 3′ end of the HIV-1 RNA genome. The 5′ element binds the viral Tat protein and is essential for Tat-mediated activation of transcription. We recently observed that complete TAR deletion is allowed in the context of an HIV-1 variant that does not depend on this Tat-TAR axis for transcription. Mutations that open the 5′ stem-loop structure did however affect the leader RNA conformation and resulted in a severe replication defect. In this study, we set out to analyze which step of the HIV-1 replication cycle is affected by this conformational change of the leader RNA. Results We demonstrate that opening the 5′ TAR structure through a deletion in either side of the stem region caused aberrant dimerization and reduced packaging of the unspliced viral RNA genome. In contrast, truncation of the TAR hairpin through deletions in both sides of the stem did not affect RNA dimer formation and packaging. Conclusions These results demonstrate that, although the TAR hairpin is not essential for RNA dimerization and packaging, mutations in TAR can significantly affect these processes through misfolding of the relevant RNA signals.
Inhibition of HIV Replication by Cyclic and Hairpin PNAs Targeting the HIV-1 TAR RNA Loop

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Upert, Gregory; Di Giorgio, Audrey; Upadhyay, Alok; Manvar, Dinesh; Pandey, Nootan; Pandey, Virendra N.; Patino, Nadia

2012-01-01

Human immunodeficiency virus-1 (HIV-1) replication and gene expression entails specific interaction of the viral protein Tat with its transactivation responsive element (TAR), to form a highly stable stem-bulge-loop structure. Previously, we described triphenylphosphonium (TPP) cation-based vectors that efficiently deliver nucleotide analogs (PNAs) into the cytoplasm of cells. In particular, we showed that the TPP conjugate of a linear 16-mer PNA targeting the apical stem-loop region of TAR impedes Tat-mediated transactivation of the HIV-1 LTR in vitro and also in cell culture systems. In this communication, we conjugated TPP to cyclic and hairpin PNAs targeting the loop region of HIV-1 TAR and evaluated their antiviral efficacy in a cell culture system. We found that TPP-cyclic PNAs containing only 8 residues, showed higher antiviral potency compared to hairpin PNAs of 12 or 16 residues. We further noted that the TPP-conjugates of the 8-mer cyclic PNA as well as the 16-mer linear PNA displayed similar antiviral efficacy. However, cyclic PNAs were shown to be highly specific to their target sequences. This communication emphasizes on the importance of small constrained cyclic PNAs over both linear and hairpin structures for targeting biologically relevant RNA hairpins. PMID:23029603
Inhibition of HIV Replication by Cyclic and Hairpin PNAs Targeting the HIV-1 TAR RNA Loop

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Gregory Upert

2012-01-01

Full Text Available Human immunodeficiency virus-1 (HIV-1 replication and gene expression entails specific interaction of the viral protein Tat with its transactivation responsive element (TAR, to form a highly stable stem-bulge-loop structure. Previously, we described triphenylphosphonium (TPP cation-based vectors that efficiently deliver nucleotide analogs (PNAs into the cytoplasm of cells. In particular, we showed that the TPP conjugate of a linear 16-mer PNA targeting the apical stem-loop region of TAR impedes Tat-mediated transactivation of the HIV-1 LTR in vitro and also in cell culture systems. In this communication, we conjugated TPP to cyclic and hairpin PNAs targeting the loop region of HIV-1 TAR and evaluated their antiviral efficacy in a cell culture system. We found that TPP-cyclic PNAs containing only 8 residues, showed higher antiviral potency compared to hairpin PNAs of 12 or 16 residues. We further noted that the TPP-conjugates of the 8-mer cyclic PNA as well as the 16-mer linear PNA displayed similar antiviral efficacy. However, cyclic PNAs were shown to be highly specific to their target sequences. This communication emphasizes on the importance of small constrained cyclic PNAs over both linear and hairpin structures for targeting biologically relevant RNA hairpins.
Inhibition of both HIV-1 reverse transcription and gene expression by a cyclic peptide that binds the Tat-transactivating response element (TAR RNA.

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Matthew S Lalonde

2011-05-01

Full Text Available The RNA response element TAR plays a critical role in HIV replication by providing a binding site for the recruitment of the viral transactivator protein Tat. Using a structure-guided approach, we have developed a series of conformationally-constrained cyclic peptides that act as structural mimics of the Tat RNA binding region and block Tat-TAR interactions at nanomolar concentrations in vitro. Here we show that these compounds block Tat-dependent transcription in cell-free systems and in cell-based reporter assays. The compounds are also cell permeable, have low toxicity, and inhibit replication of diverse HIV-1 strains, including both CXCR4-tropic and CCR5-tropic primary HIV-1 isolates of the divergent subtypes A, B, C, D and CRF01_AE. In human peripheral blood mononuclear cells, the cyclic peptidomimetic L50 exhibited an IC(50 ∼250 nM. Surprisingly, inhibition of LTR-driven HIV-1 transcription could not account for the full antiviral activity. Timed drug-addition experiments revealed that L-50 has a bi-phasic inhibition curve with the first phase occurring after HIV-1 entry into the host cell and during the initiation of HIV-1 reverse transcription. The second phase coincides with inhibition of HIV-1 transcription. Reconstituted reverse transcription assays confirm that HIV-1 (- strand strong stop DNA synthesis is blocked by L50-TAR RNA interactions in-vitro. These findings are consistent with genetic evidence that TAR plays critical roles both during reverse transcription and during HIV gene expression. Our results suggest that antiviral drugs targeting TAR RNA might be highly effective due to a dual inhibitory mechanism.
Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings.

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Al-Hashimi, Hashim M; Gosser, Yuying; Gorin, Andrey; Hu, Weidong; Majumdar, Ananya; Patel, Dinshaw J

2002-01-11

Ground-state dynamics in RNA is a critical precursor for structural adaptation observed ubiquitously in protein-RNA recognition. A tertiary conformational analysis of the stem-loop structural element in the transactivation response element (TAR) from human immunodeficiency virus type 1 (HIV-I) RNA is presented using recently introduced NMR methods that rely on the measurement of residual dipolar couplings (RDC) in partially oriented systems. Order matrix analysis of RDC data provides evidence for inter-helical motions that are of amplitude 46(+/-4) degrees, of random directional character, and that are executed about an average conformation with an inter-helical angle between 44 degrees and 54 degrees. The generated ensemble of TAR conformations have different organizations of functional groups responsible for interaction with the trans-activator protein Tat, including conformations similar to the previously characterized bound-state conformation. These results demonstrate the utility of RDC-NMR for simultaneously characterizing RNA tertiary dynamics and average conformation, and indicate an avenue for TAR complex formation involving tertiary structure capture. Copyright 2001 Academic Press.
Thermodynamic studies of a series of homologous HIV-1 TAR RNA ligands reveal that loose binders are stronger Tat competitors than tight ones.

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Pascale, Lise; Azoulay, Stéphane; Di Giorgio, Audrey; Zenacker, Laura; Gaysinski, Marc; Clayette, Pascal; Patino, Nadia

2013-06-01

RNA is a major drug target, but the design of small molecules that modulate RNA function remains a great challenge. In this context, a series of structurally homologous 'polyamide amino acids' (PAA) was studied as HIV-1 trans-activating response (TAR) RNA ligands. An extensive thermodynamic study revealed the occurence of an enthalpy-entropy compensation phenomenon resulting in very close TAR affinities for all PAA. However, their binding modes and their ability to compete with the Tat fragment strongly differ according to their structure. Surprisingly, PAA that form loose complexes with TAR were shown to be stronger Tat competitors than those forming tight ones, and thermal denaturation studies demonstrated that loose complexes are more stable than tight ones. This could be correlated to the fact that loose and tight ligands induce distinct RNA conformational changes as revealed by circular dichroism experiments, although nuclear magnetic resonance (NMR) experiments showed that the TAR binding site is the same in all cases. Finally, some loose PAA also display promising inhibitory activities on HIV-infected cells. Altogether, these results lead to a better understanding of RNA interaction modes that could be very useful for devising new ligands of relevant RNA targets.
Molecular dynamics and MM/GBSA-integrated protocol probing the correlation between biological activities and binding free energies of HIV-1 TAR RNA inhibitors.

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Peddi, Saikiran Reddy; Sivan, Sree Kanth; Manga, Vijjulatha

2018-02-01

The interaction of HIV-1 transactivator protein Tat with its cognate transactivation response (TAR) RNA has emerged as a promising target for developing antiviral compounds and treating HIV infection, since it is a crucial step for efficient transcription and replication. In the present study, molecular dynamics (MD) simulations and MM/GBSA calculations have been performed on a series of neamine derivatives in order to estimate appropriate MD simulation time for acceptable correlation between ΔG bind and experimental pIC 50 values. Initially, all inhibitors were docked into the active site of HIV-1 TAR RNA. Later to explore various conformations and examine the docking results, MD simulations were carried out. Finally, binding free energies were calculated using MM/GBSA method and were correlated with experimental pIC 50 values at different time scales (0-1 to 0-10 ns). From this study, it is clear that in case of neamine derivatives as simulation time increased the correlation between binding free energy and experimental pIC 50 values increased correspondingly. Therefore, the binding energies which can be interpreted at longer simulation times can be used to predict the bioactivity of new neamine derivatives. Moreover, in this work, we have identified some plausible critical nucleotide interactions with neamine derivatives that are responsible for potent inhibitory activity. Furthermore, we also provide some insights into a new class of oxadiazole-based back bone cyclic peptides designed by incorporating the structural features of neamine derivatives. On the whole, this approach can provide a valuable guidance for designing new potent inhibitors and modify the existing compounds targeting HIV-1 TAR RNA.
A proteomic study of TAR-RNA binding protein (TRBP-associated factors

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Chi Ya-Hui

2011-02-01

Full Text Available Abstract Background The human TAR RNA-binding protein, TRBP, was first identified and cloned based on its high affinity binding to the small hairpin trans-activation responsive (TAR RNA of HIV-1. TRBP has more recently been found to be a constituent of the RNA-induced silencing complex (RISC serving as a Dicer co-factor in the processing of the ~70 nucleotide pre-microRNAs(miRNAs to 21-25 nucleotide mature miRNAs. Findings Using co-immunoprecipitation and protein-identification by mass spectrometry, we characterized intracellular proteins that complex with TRBP. These interacting proteins include those that have been described to act in protein synthesis, RNA modifications and processing, DNA transcription, and cell proliferation. Conclusions Our findings provide a proteome of factors that may cooperate with TRBP in activities such as miRNA processing and in RNA interference by the RISC complex.
Structural and dynamic characterization of the upper part of the HIV-1 cTAR DNA hairpin

OpenAIRE

Zargarian, Loussin?; Kanevsky, Igor; Bazzi, Ali; Boynard, Jonathan; Chaminade, Fran?oise; Foss?, Philippe; Mauffret, Olivier

2009-01-01

First strand transfer is essential for HIV-1 reverse transcription. During this step, the TAR RNA hairpin anneals to the cTAR DNA hairpin; this annealing reaction is promoted by the nucleocapsid protein and involves an initial loop?loop interaction between the apical loops of TAR and cTAR. Using NMR and probing methods, we investigated the structural and dynamic properties of the top half of the cTAR DNA (mini-cTAR). We show that the upper stem located between the apical and the internal loop...
APOBEC3G inhibits HIV-1 RNA elongation by inactivating the viral trans-activation response element.

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Nowarski, Roni; Prabhu, Ponnandy; Kenig, Edan; Smith, Yoav; Britan-Rosich, Elena; Kotler, Moshe

2014-07-29

Deamination of cytidine residues in viral DNA is a major mechanism by which APOBEC3G (A3G) inhibits vif-deficient human immunodeficiency virus type 1 (HIV-1) replication. dC-to-dU transition following RNase-H activity leads to viral cDNA degradation, production of non-functional proteins, formation of undesired stop codons and decreased viral protein synthesis. Here, we demonstrate that A3G provides an additional layer of defense against HIV-1 infection dependent on inhibition of proviral transcription. HIV-1 transcription elongation is regulated by the trans-activation response (TAR) element, a short stem-loop RNA structure required for elongation factors binding. Vif-deficient HIV-1-infected cells accumulate short viral transcripts and produce lower amounts of full-length HIV-1 transcripts due to A3G deamination of the TAR apical loop cytidine, highlighting the requirement for TAR loop integrity in HIV-1 transcription. We further show that free single-stranded DNA (ssDNA) termini are not essential for A3G activity and a gap of CCC motif blocked with juxtaposed DNA or RNA on either or 3'+5' ends is sufficient for A3G deamination. These results identify A3G as an efficient mutator and that deamination of (-)SSDNA results in an early block of HIV-1 transcription. Copyright © 2014 Elsevier Ltd. All rights reserved.
DeepMirTar: a deep-learning approach for predicting human miRNA targets.

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Wen, Ming; Cong, Peisheng; Zhang, Zhimin; Lu, Hongmei; Li, Tonghua

2018-06-01

MicroRNAs (miRNAs) are small noncoding RNAs that function in RNA silencing and post-transcriptional regulation of gene expression by targeting messenger RNAs (mRNAs). Because the underlying mechanisms associated with miRNA binding to mRNA are not fully understood, a major challenge of miRNA studies involves the identification of miRNA-target sites on mRNA. In silico prediction of miRNA-target sites can expedite costly and time-consuming experimental work by providing the most promising miRNA-target-site candidates. In this study, we reported the design and implementation of DeepMirTar, a deep-learning-based approach for accurately predicting human miRNA targets at the site level. The predicted miRNA-target sites are those having canonical or non-canonical seed, and features, including high-level expert-designed, low-level expert-designed, and raw-data-level, were used to represent the miRNA-target site. Comparison with other state-of-the-art machine-learning methods and existing miRNA-target-prediction tools indicated that DeepMirTar improved overall predictive performance. DeepMirTar is freely available at https://github.com/Bjoux2/DeepMirTar_SdA. lith@tongji.edu.cn, hongmeilu@csu.edu.cn. Supplementary data are available at Bioinformatics online.
A Tat-grafted anti-nucleic acid antibody acquires nuclear-localization property and a preference for TAR RNA

International Nuclear Information System (INIS)

Jeong, Jong-Geun; Kim, Dong-Sik; Kim, Yong-Sung; Kwon, Myung-Hee

2011-01-01

Highlights: → We generate ' H3 Tat-3D8' by grafting Tat 48-60 peptide to VH CDR of 3D8 scFv antibody. → H3 Tat-3D8 antibody retains nucleic acid binding and hydrolyzing activities. → H3 Tat-3D8 acquires a preference for TAR RNA structure. → Properties of Tat 48-60 is transferred to an antibody via Tat-grafting into a CDR. -- Abstract: The 3D8 single chain variable fragment (3D8 scFv) is an anti-nucleic acid antibody that can hydrolyze nucleic acids and enter the cytosol of cells without reaching the nucleus. The Tat peptide, derived from the basic region of the HIV-1 Tat protein, translocates to cell nuclei and has TAR RNA binding activity. In this study, we generated a Tat-grafted antibody ( H3 Tat-3D8) by replacing complementarity-determining region 3 (CDR3) within the VH domain of the 3D8 scFv with a Tat 48-60 peptide (GRKKRRQRRRPPQ). H3 Tat-3D8 retained the DNA-binding and DNA-hydrolyzing activity of the scFv, and translocated to the nuclei of HeLa cells and preferentially recognized TAR RNA. Thus, the properties associated with the Tat peptide were transferred to the antibody via Tat-grafting without loss of the intrinsic DNA-binding and hydrolyzing activities of the 3D8 scFv antibody.
Forced evolution of a regulatory RNA helix in the HIV-1 genome

NARCIS (Netherlands)

Berkhout, B.; Klaver, B.; Das, A. T.

1997-01-01

The 5'and 3'end of the HIV-1 RNA genome forms a repeat (R) element that encodes a double stem-loop structure (the TAR and polyA hairpins). Phylogenetic analysis of the polyA hairpin in different human and simian immunodeficiency viruses suggests that the thermodynamic stability of the helix is
Traditional African Religions (TARs): on HIV/AIDS, health and ...

African Journals Online (AJOL)

This is because the moral guidance put forward by. African religions is underestimated; hence making HIV/AIDS more of a moral problem. Rethinking the dialogue with TARs, will help in setting appropriate means of enhancing health in a broad sense and living in human dignity in Africa. Mtafiti Mwafrika Vol. 15 2005: pp.
Deciphering structure-activity relationships in a series of Tat/TAR inhibitors.

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Pascale, Lise; González, Alejandro López; Di Giorgio, Audrey; Gaysinski, Marc; Teixido Closa, Jordi; Tejedor, Roger Estrada; Azoulay, Stéphane; Patino, Nadia

2016-11-01

A series of pentameric "Polyamide Amino Acids" (PAAs) compounds derived from the same trimeric precursor have been synthesized and investigated as HIV TAR RNA ligands, in the absence and in the presence of a Tat fragment. All PAAs bind TAR with similar sub-micromolar affinities but their ability to compete efficiently with the Tat fragment strongly differs, IC50 ranging from 35 nM to >2 μM. While NMR and CD studies reveal that all PAA interact with TAR at the same site and induce globally the same RNA conformational change upon binding, a comparative thermodynamic study of PAA/TAR equilibria highlights distinct TAR binding modes for Tat competitor and non-competitor PAAs. This led us to suggest two distinct interaction modes that have been further validated by molecular modeling studies. While the binding of Tat competitor PAAs induces a contraction at the TAR bulge region, the binding of non-competitor ones widens it. This could account for the distinct PAA ability to compete with Tat fragment. Our work illustrates how comparative thermodynamic studies of a series of RNA ligands of same chemical family are of value for understanding their binding modes and for rationalizing structure-activity relationships.
A real-time view of the TAR:Tat:P-TEFb complex at HIV-1 transcription sites

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Knezevich Anna

2007-05-01

Full Text Available Abstract HIV-1 transcription is tightly regulated: silent in long-term latency and highly active in acutely-infected cells. Transcription is activated by the viral protein Tat, which recruits the elongation factor P-TEFb by binding the TAR sequence present in nascent HIV-1 RNAs. In this study, we analyzed the dynamic of the TAR:Tat:P-TEFb complex in living cells, by performing FRAP experiments at HIV-1 transcription sites. Our results indicate that a large fraction of Tat present at these sites is recruited by Cyclin T1. We found that in the presence of Tat, Cdk9 remained bound to nascent HIV-1 RNAs for 71s. In contrast, when transcription was activated by PMA/ionomycin, in the absence of Tat, Cdk9 turned-over rapidly and resided on the HIV-1 promoter for only 11s. Thus, the mechanism of trans-activation determines the residency time of P-TEFb at the HIV-1 gene, possibly explaining why Tat is such a potent transcriptional activator. In addition, we observed that Tat occupied HIV-1 transcription sites for 55s, suggesting that the TAR:Tat:P-TEFb complex dissociates from the polymerase following transcription initiation, and undergoes subsequent cycles of association/dissociation.
Endogenous MCM7 microRNA cluster as a novel platform to multiplex small interfering and nucleolar RNAs for combinational HIV-1 gene therapy.

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Chung, Janet; Zhang, Jane; Li, Haitang; Ouellet, Dominique L; DiGiusto, David L; Rossi, John J

2012-11-01

Combinational therapy with small RNA inhibitory agents against multiple viral targets allows efficient inhibition of viral production by controlling gene expression at critical time points. Here we explore combinations of different classes of therapeutic anti-HIV-1 RNAs expressed from within the context of an intronic MCM7 (minichromosome maintenance complex component-7) platform that naturally harbors 3 microRNAs (miRNAs). We replaced the endogenous miRNAs with anti-HIV small RNAs, including small interfering RNAs (siRNAs) targeting HIV-1 tat and rev messages that function to induce post-transcriptional gene silencing by the RNA interference pathway, a nucleolar-localizing RNA ribozyme that targets the conserved U5 region of HIV-1 transcripts for degradation, and finally nucleolar trans-activation response (TAR) and Rev-binding element (RBE) RNA decoys designed to sequester HIV-1 Tat and Rev proteins inside the nucleolus. We demonstrate the versatility of the MCM7 platform in expressing and efficiently processing the siRNAs as miRNA mimics along with nucleolar small RNAs. Furthermore, three of the combinatorial constructs tested potently suppressed viral replication during a 1-month HIV challenge, with greater than 5-log inhibition compared with untransduced, HIV-1-infected CEM T lymphocytes. One of the most effective constructs contains an anti-HIV siRNA combined with a nucleolar-localizing U5 ribozyme and TAR decoy. This represents the first efficacious example of combining Drosha-processed siRNAs with small nucleolar ribonucleoprotein (snoRNP)-processed nucleolar RNA chimeras from a single intron platform for effective inhibition of viral replication. Moreover, we demonstrated enrichment/selection for cells expressing levels of the antiviral RNAs that provide optimal inhibition under the selective pressure of HIV. The combinations of si/snoRNAs represent a new paradigm for combinatorial RNA-based gene therapy applications.
Site-selective probing of cTAR destabilization highlights the necessary plasticity of the HIV-1 nucleocapsid protein to chaperone the first strand transfer

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Godet, Julien; Kenfack, Cyril; Przybilla, Frédéric; Richert, Ludovic; Duportail, Guy; Mély, Yves

2013-01-01

The HIV-1 nucleocapsid protein (NCp7) is a nucleic acid chaperone required during reverse transcription. During the first strand transfer, NCp7 is thought to destabilize cTAR, the (−)DNA copy of the TAR RNA hairpin, and subsequently direct the TAR/cTAR annealing through the zipping of their destabilized stem ends. To further characterize the destabilizing activity of NCp7, we locally probe the structure and dynamics of cTAR by steady-state and time resolved fluorescence spectroscopy. NC(11–55), a truncated NCp7 version corresponding to its zinc-finger domain, was found to bind all over the sequence and to preferentially destabilize the penultimate double-stranded segment in the lower part of the cTAR stem. This destabilization is achieved through zinc-finger–dependent binding of NC to the G10 and G50 residues. Sequence comparison further revealed that C•A mismatches close to the two G residues were critical for fine tuning the stability of the lower part of the cTAR stem and conferring to G10 and G50 the appropriate mobility and accessibility for specific recognition by NC. Our data also highlight the necessary plasticity of NCp7 to adapt to the sequence and structure variability of cTAR to chaperone its annealing with TAR through a specific pathway. PMID:23511968
Structural determinants of HIV-1 nucleocapsid protein for cTAR DNA binding and destabilization, and correlation with inhibition of self-primed DNA synthesis.

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Beltz, Hervé; Clauss, Céline; Piémont, Etienne; Ficheux, Damien; Gorelick, Robert J; Roques, Bernard; Gabus, Caroline; Darlix, Jean-Luc; de Rocquigny, Hugues; Mély, Yves

2005-05-20

The nucleocapsid protein (NC) of human immunodeficiency virus type 1 (HIV-1) is formed of two highly conserved CCHC zinc fingers flanked by small basic domains. NC is required for the two obligatory strand transfers in viral DNA synthesis through its nucleic acid chaperoning properties. The first DNA strand transfer relies on NC's ability to bind and destabilize the secondary structure of complementary transactivation response region (cTAR) DNA, to inhibit self-priming, and to promote the annealing of cTAR to TAR RNA. To further investigate NC chaperone properties, our aim was to identify by fluorescence spectroscopy and gel electrophoresis, the NC structural determinants for cTAR binding and destabilization, and for the inhibition of self-primed DNA synthesis on a model system using a series of NC mutants and HIV-1 reverse transcriptase. NC destabilization and self-priming inhibition properties were found to be supported by the two fingers in their proper context and the basic (29)RAPRKKG(35) linker. The strict requirement of the native proximal finger suggests that its hydrophobic platform (Val13, Phe16, Thr24 and Ala25) is crucial for binding, destabilization and inhibition of self-priming. In contrast, only partial folding of the distal finger is required, probably for presenting the Trp37 residue in an appropriate orientation. Also, Trp37 and the hydrophobic residues of the proximal finger appear to be essential for the propagation of the melting from the cTAR ends up to the middle of the stem. Finally, both N-terminal and C-terminal basic domains contribute to cTAR binding but not to its destabilization.
HuMiTar: A sequence-based method for prediction of human microRNA targets

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Chen Ke

2008-12-01

Full Text Available Abstract Background MicroRNAs (miRs are small noncoding RNAs that bind to complementary/partially complementary sites in the 3' untranslated regions of target genes to regulate protein production of the target transcript and to induce mRNA degradation or mRNA cleavage. The ability to perform accurate, high-throughput identification of physiologically active miR targets would enable functional characterization of individual miRs. Current target prediction methods include traditional approaches that are based on specific base-pairing rules in the miR's seed region and implementation of cross-species conservation of the target site, and machine learning (ML methods that explore patterns that contrast true and false miR-mRNA duplexes. However, in the case of the traditional methods research shows that some seed region matches that are conserved are false positives and that some of the experimentally validated target sites are not conserved. Results We present HuMiTar, a computational method for identifying common targets of miRs, which is based on a scoring function that considers base-pairing for both seed and non-seed positions for human miR-mRNA duplexes. Our design shows that certain non-seed miR nucleotides, such as 14, 18, 13, 11, and 17, are characterized by a strong bias towards formation of Watson-Crick pairing. We contrasted HuMiTar with several representative competing methods on two sets of human miR targets and a set of ten glioblastoma oncogenes. Comparison with the two best performing traditional methods, PicTar and TargetScanS, and a representative ML method that considers the non-seed positions, NBmiRTar, shows that HuMiTar predictions include majority of the predictions of the other three methods. At the same time, the proposed method is also capable of finding more true positive targets as a trade-off for an increased number of predictions. Genome-wide predictions show that the proposed method is characterized by 1.99 signal

Controlling cellular P-TEFb activity by the HIV-1 transcriptional transactivator Tat.

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Lisa Muniz

Full Text Available The human immunodeficiency virus 1 (HIV-1 transcriptional transactivator (Tat is essential for synthesis of full-length transcripts from the integrated viral genome by RNA polymerase II (Pol II. Tat recruits the host positive transcription elongation factor b (P-TEFb to the HIV-1 promoter through binding to the transactivator RNA (TAR at the 5'-end of the nascent HIV transcript. P-TEFb is a general Pol II transcription factor; its cellular activity is controlled by the 7SK small nuclear RNA (snRNA and the HEXIM1 protein, which sequester P-TEFb into transcriptionally inactive 7SK/HEXIM/P-TEFb snRNP. Besides targeting P-TEFb to HIV transcription, Tat also increases the nuclear level of active P-TEFb through promoting its dissociation from the 7SK/HEXIM/P-TEFb RNP by an unclear mechanism. In this study, by using in vitro and in vivo RNA-protein binding assays, we demonstrate that HIV-1 Tat binds with high specificity and efficiency to an evolutionarily highly conserved stem-bulge-stem motif of the 5'-hairpin of human 7SK snRNA. The newly discovered Tat-binding motif of 7SK is structurally and functionally indistinguishable from the extensively characterized Tat-binding site of HIV TAR and importantly, it is imbedded in the HEXIM-binding elements of 7SK snRNA. We show that Tat efficiently replaces HEXIM1 on the 7SK snRNA in vivo and therefore, it promotes the disassembly of the 7SK/HEXIM/P-TEFb negative transcriptional regulatory snRNP to augment the nuclear level of active P-TEFb. This is the first demonstration that HIV-1 specifically targets an important cellular regulatory RNA, most probably to promote viral transcription and replication. Demonstration that the human 7SK snRNA carries a TAR RNA-like Tat-binding element that is essential for the normal transcriptional regulatory function of 7SK questions the viability of HIV therapeutic approaches based on small drugs blocking the Tat-binding site of HIV TAR.
HIV RNA and proviral HIV DNA can be detected in semen after 6 months of antiretroviral therapy although HIV RNA is undetectable in blood.

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Du, Peiwei; Liu, An; Jiao, Yanmei; Liu, Cuie; Jiang, Taiyi; Zhu, Weijun; Zhu, Yunxia; Wu, Hao; Sun, Lijun

2016-03-01

The risk of sexual transmission of HIV is strongly correlated with amounts of genital HIV RNA. Few studies have reported amounts of HIV RNA and HIV DNA in semen in HIV-infected Chinese patients undergoing antiviral treatment (ART). In this observational study, the amounts of HIV RNA and HIV DNA in semen were assessed after six months of ART in HIV-infected Chinese individuals, when HIV RNA was undetectable in blood . This study included 19 HIV-infected Chinese men undergoing ART for six months. Amounts of HIV in paired semen and blood samples were assessed using real-time PCR. The C2-V5 region of the HIV envelope (env) genes was cloned and sequenced and genotype and co-receptor usage predicted based on the sequence. It was found that HIV RNA was undetectable in the plasma of most patients (17/19), whereas HIV RNA could be detected in the semen of most patients (16/19). HIV DNA could be detected in both semen and blood. Genetic diversity of HIV between the seminal and blood compartments was identified. Thus, amounts of HIV RNA and HIV DNA remain high in semen of HIV-infected Chinese patients after six months of ART treatment, even when HIV RNA was undetectable in blood. © 2016 The Societies and John Wiley & Sons Australia, Ltd.
Evidence for conformational flexibility in the Tat-TAR recognition motif of cyclin T1

International Nuclear Information System (INIS)

Das, Chandreyee; Edgcomb, Stephen P.; Peteranderl, Ralph; Chen, Lily; Frankel, Alan D.

2004-01-01

Cyclin T1 (CycT1) is a cellular transcription elongation factor that also participates in Tat-mediated activation of several lentiviral promoters. In human immunodeficiency virus (HIV), CycT1 is required for Tat to bind tightly to TAR and interacts in the ternary complex via its Tat-TAR recognition motif (TRM). In the related bovine immunodeficiency virus (BIV), Tat recognizes its cognate TAR element with high affinity and specificity in the absence of CycT1. At both promoters, CycT1 recruits the Cdk9 kinase, which phosphorylates RNA polymerase II to generate processive transcription complexes. To examine the physical properties of CycT1, we purified a functional domain corresponding to residues 1-272 and found that it possesses a stably folded core, as judged by partial proteolysis and circular dichroism experiments. Interestingly, the C-terminal 20 residues corresponding to the TRM appear conformationally flexible or disordered. The TRM of the bovine CycT1 (bCycT1) is similarly sensitive to proteolysis yet differs in sequence from the human protein. In particular, bCycT1 lacks a cysteine at residue 261 known to be critical for HIV but not BIV ternary complex formation, and mutagenesis data are consistent with a proposed role for this cysteine in metal binding. The apparent flexibility of the TRM suggests that conformational rearrangements may accompany formation of CycT1-Tat-TAR ternary complexes and may contribute to different TAR recognition strategies in different lentiviruses
Exploring the impact of the side-chain length on peptide/RNA binding events.

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Sbicca, Lola; González, Alejandro López; Gresika, Alexandra; Di Giorgio, Audrey; Closa, Jordi Teixido; Tejedor, Roger Estrada; Andréola, Marie-Line; Azoulay, Stéphane; Patino, Nadia

2017-07-19

The impact of the amino-acid side-chain length on peptide-RNA binding events has been investigated using HIV-1 Tat derived peptides as ligands and the HIV-1 TAR RNA element as an RNA model. Our studies demonstrate that increasing the length of all peptide side-chains improves unexpectedly the binding affinity (K D ) but reduces the degree of compactness of the peptide-RNA complex. Overall, the side-chain length appears to modulate in an unpredictable way the ability of the peptide to compete with the cognate TAR RNA partner. Beyond the establishment of non-intuitive fundamental relationships, our results open up new perspectives in the design of effective RNA ligand competitors, since a large number of them have already been identified but few studies report on the modulation of the biological activity by modifying in the same way the length of all chains connecting RNA recognition motives to the central scaffold of a ligand.
Detection of HIV-RNA-positive monocytes in peripheral blood of HIV-positive patients by simultaneous flow cytometric analysis of intracellular HIV RNA and cellular immunophenotype.

Science.gov (United States)

Patterson, B K; Mosiman, V L; Cantarero, L; Furtado, M; Bhattacharya, M; Goolsby, C

1998-04-01

Determinations of plasma HIV viral RNA copy numbers help to define the kinetics of HIV-1 infection in vivo and to monitor antiretroviral therapy. However, questions remain regarding the identity of various infected cell types contributing to this free virus pool and to the in vivo lifecycle of HIV during disease progression. Characterization of a novel fluorescence in situ hybridization (FISH) assay employing a pool of labeled oligonucleotide probes directed against HIV RNA was done followed by coupling of the FISH assay with simultaneous surface immunophenotyping to address these questions. In vitro characterizations of this assay using tumor necrosis factor-alpha stimulated and unstimulated ACH-2 cells demonstrated the ability to detect < 5% HIV RNA positive cells with a sensitivity of < 30 RNA copies per cell. Peripheral blood mononuclear cells from 39 HIV-seropositive patients on no, single, combination, or triple drug therapy and 8 HIV-seronegative patients were examined. The majority of HIV-positive patients (24/39) harbored monocytes positive for HIV RNA and a significantly higher fraction of patients with high plasma viral load carried positive monocytes (13/16) than did patients in the low plasma viral load group (11/23). These results demonstrate the effectiveness of a novel FISH assay for identifying and monitoring HIV-infected cell populations in the peripheral blood of HIV-positive patients. In addition, monocytes are a major source of cellular HIV virus in the peripheral blood of HIV patients, even with progression of disease.
Micro RNA in Exosomes from HIV-Infected Macrophages

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William W. Roth

2015-12-01

Full Text Available Exosomes are small membrane-bound vesicles secreted by cells that function to shuttle RNA and proteins between cells. To examine the role of exosomal micro RNA (miRNA during the early stage of HIV-1 infection we characterized miRNA in exosomes from HIV-infected macrophages, compared with exosomes from non-infected macrophages. Primary human monocytes from uninfected donors were differentiated to macrophages (MDM which were either mock-infected or infected with the macrophage-tropic HIV-1 BaL strain. Exosomes were recovered from culture media and separated from virus particles by centrifugation on iodixanol density gradients. The low molecular weight RNA fraction was prepared from purified exosomes. After pre-amplification, RNA was hybridized to microarrays containing probes for 1200 miRNA species of known and unknown function. We observed 48 miRNA species in both infected and uninfected MDM exosomes. Additionally, 38 miRNAs were present in infected-cell exosomes but not uninfected-cell exosomes. Of these, 13 miRNAs were upregulated in exosomes from HIV-infected cells, including 4 miRNA species that were increased by more than 10-fold. Though numerous miRNA species have been identified in HIV-infected cells, relatively little is known about miRNA content in exosomes from these cells. In the future, we plan to investigate whether the upregulated miRNA species we identified are increased in exosomes from HIV-1-positive patients.
Recognition of DNA/RNA bulges by antimicrobial and antitumor metallohelices

Czech Academy of Sciences Publication Activity Database

Malina, Jaroslav; Scott, P.; Brabec, Viktor

2015-01-01

Roč. 44, č. 33 (2015), s. 14656-14665 ISSN 1477-9226 R&D Projects: GA ČR(CZ) GAP205/11/0856 Institutional support: RVO:68081707 Keywords : CONTAINING DEOXYTRIDECANUCLEOTIDE DUPLEXES * HIV -1 TAR RNA * METALLOSUPRAMOLECULAR CYLINDERS Subject RIV: BO - Biophysics Impact factor: 4.177, year: 2015
Interactions between the HIV-1 Unspliced mRNA and Host mRNA Decay Machineries

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Daniela Toro-Ascuy

2016-11-01

Full Text Available The human immunodeficiency virus type-1 (HIV-1 unspliced transcript is used both as mRNA for the synthesis of structural proteins and as the packaged genome. Given the presence of retained introns and instability AU-rich sequences, this viral transcript is normally retained and degraded in the nucleus of host cells unless the viral protein REV is present. As such, the stability of the HIV-1 unspliced mRNA must be particularly controlled in the nucleus and the cytoplasm in order to ensure proper levels of this viral mRNA for translation and viral particle formation. During its journey, the HIV-1 unspliced mRNA assembles into highly specific messenger ribonucleoproteins (mRNPs containing many different host proteins, amongst which are well-known regulators of cytoplasmic mRNA decay pathways such as up-frameshift suppressor 1 homolog (UPF1, Staufen double-stranded RNA binding protein 1/2 (STAU1/2, or components of miRNA-induced silencing complex (miRISC and processing bodies (PBs. More recently, the HIV-1 unspliced mRNA was shown to contain N6-methyladenosine (m6A, allowing the recruitment of YTH N6-methyladenosine RNA binding protein 2 (YTHDF2, an m6A reader host protein involved in mRNA decay. Interestingly, these host proteins involved in mRNA decay were shown to play positive roles in viral gene expression and viral particle assembly, suggesting that HIV-1 interacts with mRNA decay components to successfully accomplish viral replication. This review summarizes the state of the art in terms of the interactions between HIV-1 unspliced mRNA and components of different host mRNA decay machineries.
Semen Bacterial Concentrations and HIV-1 RNA Shedding Among HIV-1-Seropositive Kenyan Men.

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Korhonen, Christine J; Srinivasan, Sujatha; Huang, Dandi; Ko, Daisy L; Sanders, Eduard J; Peshu, Norbert M; Krieger, John N; Muller, Charles H; Coombs, Robert W; Fredricks, David N; Graham, Susan M

2017-03-01

HIV-1 is transmitted through semen from men to their sexual partners. Genital infections can increase HIV-1 RNA shedding in semen, but shedding also occurs in the absence of typical pathogens. We hypothesized that higher bacterial concentrations in semen would be associated with higher HIV-1 RNA levels. We analyzed semen samples from 42 HIV-1-seropositive Kenyan men using quantitative polymerase chain reaction (PCR) to assess bacterial concentrations and real-time PCR to measure HIV-1 RNA levels. Generalized estimation equations were used to evaluate associations between these 2 measures. Broad-range 16S rRNA gene PCR with pyrosequencing was performed on a subset of 13 samples to assess bacterial community composition. Bacteria were detected in 96.6% of 88 samples by quantitative PCR. Semen bacterial concentration and HIV-1 RNA levels were correlated 0.30 (P = 0.01). The association between bacterial concentration and HIV-1 RNA detection was not significant after adjustment for antiretroviral therapy (ART) (adjusted odds ratio: 1.27, 95% CI: 0.84 to 1.91). Factors associated with semen bacterial concentration included insertive anal sex (adjusted beta 0.92, 95% CI: 0.12 to 1.73) and ART use (adjusted beta: -0.77, 95% CI: -1.50 to 0.04). Among 13 samples with pyrosequencing data, Corynebacterium spp., Staphylococcus spp., and Streptococcus spp. were most frequently detected. Most of these HIV-1-infected men had bacteria in their semen. ART use was associated with undetectable semen HIV-1 RNA and lower semen bacterial concentrations, whereas insertive anal sex was associated with higher bacterial concentrations. Additional studies evaluating the relationship between semen bacteria, inflammation, mucosal immunity, and HIV-1 shedding are needed to understand implications for HIV-1 transmission.
Screening Yield of HIV Antigen/Antibody Combination and Pooled HIV RNA Testing for Acute HIV Infection in a High-Prevalence Population.

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Peters, Philip J; Westheimer, Emily; Cohen, Stephanie; Hightow-Weidman, Lisa B; Moss, Nicholas; Tsoi, Benjamin; Hall, Laura; Fann, Charles; Daskalakis, Demetre C; Beagle, Steve; Patel, Pragna; Radix, Asa; Foust, Evelyn; Kohn, Robert P; Marmorino, Jenni; Pandori, Mark; Fu, Jie; Samandari, Taraz; Gay, Cynthia L

2016-02-16

Although acute HIV infection contributes disproportionately to onward HIV transmission, HIV testing has not routinely included screening for acute HIV infection. To evaluate the performance of an HIV antigen/antibody (Ag/Ab) combination assay to detect acute HIV infection compared with pooled HIV RNA testing. Multisite, prospective, within-individual comparison study conducted between September 2011 and October 2013 in 7 sexually transmitted infection clinics and 5 community-based programs in New York, California, and North Carolina. Participants were 12 years or older and seeking HIV testing, without known HIV infection. All participants with a negative rapid HIV test result were screened for acute HIV infection with an HIV Ag/Ab combination assay (index test) and pooled human immunodeficiency virus 1 (HIV-1) RNA testing. HIV RNA testing was the reference standard, with positive reference standard result defined as detectable HIV-1 RNA on an individual RNA test. Number and proportion with acute HIV infections detected. Among 86,836 participants with complete test results (median age, 29 years; 75.0% men; 51.8% men who have sex with men), established HIV infection was diagnosed in 1158 participants (1.33%) and acute HIV infection was diagnosed in 168 participants (0.19%). Acute HIV infection was detected in 134 participants with HIV Ag/Ab combination testing (0.15% [95% CI, 0.13%-0.18%]; sensitivity, 79.8% [95% CI, 72.9%-85.6%]; specificity, 99.9% [95% CI, 99.9%-99.9%]; positive predictive value, 59.0% [95% CI, 52.3%-65.5%]) and in 164 participants with pooled HIV RNA testing (0.19% [95% CI, 0.16%-0.22%]; sensitivity, 97.6% [95% CI, 94.0%-99.4%]; specificity, 100% [95% CI, 100%-100%]; positive predictive value, 96.5% [95% CI, 92.5%-98.7%]; sensitivity comparison, P testing detected 82% of acute HIV infections detectable by pooled HIV RNA testing. Compared with rapid HIV testing alone, HIV Ag/Ab combination testing increased the relative HIV diagnostic yield (both
DBR1 siRNA inhibition of HIV-1 replication

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Naidu Yathi

2005-10-01

Full Text Available Abstract Background HIV-1 and all retroviruses are related to retroelements of simpler organisms such as the yeast Ty elements. Recent work has suggested that the yeast retroelement Ty1 replicates via an unexpected RNA lariat intermediate in cDNA synthesis. The putative genomic RNA lariat intermediate is formed by a 2'-5' phosphodiester bond, like that found in pre-mRNA intron lariats and it facilitates the minus-strand template switch during cDNA synthesis. We hypothesized that HIV-1 might also form a genomic RNA lariat and therefore that siRNA-mediated inhibition of expression of the human RNA lariat de-branching enzyme (DBR1 expression would specifically inhibit HIV-1 replication. Results We designed three short interfering RNA (siRNA molecules targeting DBR1, which were capable of reducing DBR1 mRNA expression by 80% and did not significantly affect cell viability. We assessed HIV-1 replication in the presence of DBR1 siRNA and found that DBR1 knockdown led to decreases in viral cDNA and protein production. These effects could be reversed by cotransfection of a DBR1 cDNA indicating that the inhibition of HIV-1 replication was a specific effect of DBR1 underexpression. Conclusion These data suggest that DBR1 function may be needed to debranch a putative HIV-1 genomic RNA lariat prior to completion of reverse transcription.
HIV-1 nef suppression by virally encoded microRNA

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Brisibe Ebiamadon

2004-12-01

Full Text Available Abstract Background MicroRNAs (miRNAs are 21~25-nucleotides (nt long and interact with mRNAs to trigger either translational repression or RNA cleavage through RNA interference (RNAi, depending on the degree of complementarity with the target mRNAs. Our recent study has shown that HIV-1 nef dsRNA from AIDS patients who are long-term non-progressors (LTNPs inhibited the transcription of HIV-1. Results Here, we show the possibility that nef-derived miRNAs are produced in HIV-1 persistently infected cells. Furthermore, nef short hairpin RNA (shRNA that corresponded to a predicted nef miRNA (~25 nt, miR-N367 can block HIV-1 Nef expression in vitro and the suppression by shRNA/miR-N367 would be related with low viremia in an LTNP (15-2-2. In the 15-2-2 model mice, the weight loss, which may be rendered by nef was also inhibited by shRNA/miR-N367 corresponding to suppression of nef expression in vivo. Conclusions These data suggest that nef/U3 miRNAs produced in HIV-1-infected cells may suppress both Nef function and HIV-1 virulence through the RNAi pathway.
Profile of HIV-1 RNA viral load among HIV-TB co-infected patients in ...

African Journals Online (AJOL)

Profile of HIV-1 RNA viral load among HIV-TB co-infected patients in a tertiary health facility in Maiduguri, Northeastern Nigeria. ... This study aims to estimate the HIV-1 RNA viral load and impact of anti TB therapy (ATT) ... HOW TO USE AJOL.
Semen Bacterial Concentrations and HIV-1 RNA Shedding Among HIV-1–Seropositive Kenyan Men

Science.gov (United States)

Srinivasan, Sujatha; Huang, Dandi; Ko, Daisy L.; Sanders, Eduard J.; Peshu, Norbert M.; Krieger, John N.; Muller, Charles H.; Coombs, Robert W.; Fredricks, David N.; Graham, Susan M.

2017-01-01

Introduction: HIV-1 is transmitted through semen from men to their sexual partners. Genital infections can increase HIV-1 RNA shedding in semen, but shedding also occurs in the absence of typical pathogens. We hypothesized that higher bacterial concentrations in semen would be associated with higher HIV-1 RNA levels. Methods: We analyzed semen samples from 42 HIV-1–seropositive Kenyan men using quantitative polymerase chain reaction (PCR) to assess bacterial concentrations and real-time PCR to measure HIV-1 RNA levels. Generalized estimation equations were used to evaluate associations between these 2 measures. Broad-range 16S rRNA gene PCR with pyrosequencing was performed on a subset of 13 samples to assess bacterial community composition. Results: Bacteria were detected in 96.6% of 88 samples by quantitative PCR. Semen bacterial concentration and HIV-1 RNA levels were correlated 0.30 (P = 0.01). The association between bacterial concentration and HIV-1 RNA detection was not significant after adjustment for antiretroviral therapy (ART) (adjusted odds ratio: 1.27, 95% CI: 0.84 to 1.91). Factors associated with semen bacterial concentration included insertive anal sex (adjusted beta 0.92, 95% CI: 0.12 to 1.73) and ART use (adjusted beta: −0.77, 95% CI: −1.50 to 0.04). Among 13 samples with pyrosequencing data, Corynebacterium spp., Staphylococcus spp., and Streptococcus spp. were most frequently detected. Conclusion: Most of these HIV-1–infected men had bacteria in their semen. ART use was associated with undetectable semen HIV-1 RNA and lower semen bacterial concentrations, whereas insertive anal sex was associated with higher bacterial concentrations. Additional studies evaluating the relationship between semen bacteria, inflammation, mucosal immunity, and HIV-1 shedding are needed to understand implications for HIV-1 transmission. PMID:27861240
Distribution of HIV RNA in CSF and Blood is linked to CD4/CD8 Ratio During Acute HIV.

Science.gov (United States)

Chan, Phillip; Patel, Payal; Hellmuth, Joanna; Colby, Donn J; Kroon, Eugène; Sacdalan, Carlo; Pinyakorn, Suteeraporn; Jagodzinski, Linda; Krebs, Shelly; Ananworanich, Jintanat; Valcour, Victor; Spudich, Serena

2018-05-07

HIV RNA levels in the plasma and cerebrospinal fluid (CSF) are correlated in chronic HIV infection but their dynamics have not been characterized during acute infection. This study analyzed predictors of CSF HIV RNA and relative degree of CNS viral transmigration expressed as plasma minus CSF HIV log10 RNA (PCratio) during untreated acute HIV infection. CSF immune markers were compared between groups with different PCratio. 117 mostly male (97%) participants in the RV254 cohort in Bangkok, Thailand, had median age 28 years and an estimated median 18 days duration of infection; forty-three (37%) were Fiebig stages I/II. Twenty-seven (23%) had CSF HIV RNA CSF HIV RNA and PCratio of 3.76 and 2.36 Log10 copies/mL, respectively. HIV RNA peaked at Fiebig III in plasma and Fiebig IV in CSF. In multivariable analyses, plasma HIV RNA and CD4/CD8 ratio independently correlated with CSF HIV RNA (pCSF neopterin, sCD163, IL-6 and sCD14 levels (all pCSF HIV RNA and PCratio, suggesting that immune responses modulate CNS viral entry at early infection.
Development of antibody-modified chitosan nanoparticles for the targeted delivery of siRNA across the blood-brain barrier as a strategy for inhibiting HIV replication in astrocytes.

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Gu, Jijin; Al-Bayati, Karam; Ho, Emmanuel A

2017-08-01

R-mediated transcytosis of nanoparticles across the epithelial cells. c B2R-mediated endocytosis of nanoparticles in astrocytes. d The molecular interactions between HIV-1 Tat protein and Cyclin T1 and Tip110 cellular proteins. e A schematic representation of chitosan nanoparticles with its components. RNAPII RNA polymerase II, TAR transactivation response RNA element, LTR long terminal repeat, Ab antibody, CS chitosan, TPP tripolyphosphate.
Diversity of 16S rRNA and dioxygenase genes detected in coal-tar-contaminated site undergoing active bioremediation

Energy Technology Data Exchange (ETDEWEB)

Kumar, M; Khanna, S [NIIT Univ, Neemrana (India). Dept. of Biotechnology & Bioinformation

2010-04-15

In order to develop effective bioremediation strategies for polyaromatic hydrocarbons (PAHs) degradation, the composition and metabolic potential of microbial communities need to be better understood, especially in highly PAH contaminated sites in which little information on the cultivation-independent communities is available. Coal-tar-contaminated soil was collected, which consisted of 122-122.5 mg g{sup -1} total extractable PAH compounds. Biodegradation studies with this soil indicated the presence of microbial community that is capable of degrading the model PAH compounds viz naphthalene, phenanthrene and pyrene at 50 ppm each. PCR clone libraries were established from the DNA of the coal-tar-contaminated soil, targeting the 16S rRNA to characterize (I) the microbial communities, (ii) partial gene fragment encoding the Rieske iron sulfur center {alpha}-subunit) common to all PAH dioxygenase enzymes and (iii) {beta}-subunit of dioxygenase. Phylotypes related to Proteobacteria ({Alpha}-, {Epsilon}- and Gammaproteobacteria), Acidobacteria, Actinobacteria, Firmicutes, Gemmatimonadetes and Deinococci were detected in 16S rRNA derived clone libraries. Many of the gene fragment sequences of alpha-subunit and beta-subunit of dioxygenase obtained from the respective clone libraries fell into clades that are distinct from the reference dioxygenase gene sequences. Presence of consensus sequence of the Rieske type (2Fe2S) cluster binding site suggested that these gene fragments encode for {alpha}-subunit of dioxygenase gene. Sequencing of the cloned libraries representing {alpha}-subunit gene fragments (Rf1) and beta-subunit of dioxygenase showed the presence of hitherto unidentified dioxygenase in coal-tar-contaminated soil.
Similarities and differences in the nucleic acid chaperone activity of HIV-2 and HIV-1 nucleocapsid proteins in vitro.

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Pachulska-Wieczorek, Katarzyna; Stefaniak, Agnieszka K; Purzycka, Katarzyna J

2014-07-03

The nucleocapsid domain of Gag and mature nucleocapsid protein (NC) act as nucleic acid chaperones and facilitate folding of nucleic acids at critical steps of retroviral replication cycle. The basic N-terminus of HIV-1 NC protein was shown most important for the chaperone activity. The HIV-2 NC (NCp8) and HIV-1 NC (NCp7) proteins possess two highly conserved zinc fingers, flanked by basic residues. However, the NCp8 N-terminal domain is significantly shorter and contains less positively charged residues. This study characterizes previously unknown, nucleic acid chaperone activity of the HIV-2 NC protein. We have comparatively investigated the in vitro nucleic acid chaperone properties of the HIV-2 and HIV-1 NC proteins. Using substrates derived from the HIV-1 and HIV-2 genomes, we determined the ability of both proteins to chaperone nucleic acid aggregation, annealing and strand exchange in duplex structures. Both NC proteins displayed comparable, high annealing activity of HIV-1 TAR DNA and its complementary nucleic acid. Interesting differences between the two NC proteins were discovered when longer HIV substrates, particularly those derived from the HIV-2 genome, were used in chaperone assays. In contrast to NCp7, NCp8 weakly facilitates annealing of HIV-2 TAR RNA to its complementary TAR (-) DNA. NCp8 is also unable to efficiently stimulate tRNALys3 annealing to its respective HIV-2 PBS motif. Using truncated NCp8 peptide, we demonstrated that despite the fact that the N-terminus of NCp8 differs from that of NCp7, this domain is essential for NCp8 activity. Our data demonstrate that the HIV-2 NC protein displays reduced nucleic acid chaperone activity compared to that of HIV-1 NC. We found that NCp8 activity is limited by substrate length and stability to a greater degree than that of NCp7. This is especially interesting in light of the fact that the HIV-2 5'UTR is more structured than that of HIV-1. The reduced chaperone activity observed with NCp8 may
Levels and patterns of HIV RNA viral load in untreated pregnant women

DEFF Research Database (Denmark)

NN, NN; Patel, Deven; Thorne, Claire

2008-01-01

OBJECTIVE: To assess pregnancy levels and patterns of HIV RNA in the absence of antiretroviral therapy, while appropriately adjusting for potential confounders, including maternal immune status and race. METHODS: Data on > or = 1 antenatal HIV RNA measurements were available for 333 untreated HIV......-infected pregnant women enrolled in the European Collaborative Study. CD4 counts and HIV RNA measurements were routinely collected from 1992 and 1998, respectively. Linear mixed effects models based on 246 women for whom complete data were available examined changes in HIV RNA levels over pregnancy, with a nested...... random effects term accounting for measurement variability within women and period of sample collection. RESULTS: The change in HIV RNA over pregnancy varied significantly by race (p=0.005): from the second trimester until delivery, HIV RNA decreased significantly by an estimated 0.019 log(10) copies...
Dynamics of HIV-1 RNA Near the Plasma Membrane during Virus Assembly.

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Sardo, Luca; Hatch, Steven C; Chen, Jianbo; Nikolaitchik, Olga; Burdick, Ryan C; Chen, De; Westlake, Christopher J; Lockett, Stephen; Pathak, Vinay K; Hu, Wei-Shau

2015-11-01

To increase our understanding of the events that lead to HIV-1 genome packaging, we examined the dynamics of viral RNA and Gag-RNA interactions near the plasma membrane by using total internal reflection fluorescence microscopy. We labeled HIV-1 RNA with a photoconvertible Eos protein via an RNA-binding protein that recognizes stem-loop sequences engineered into the viral genome. Near-UV light exposure causes an irreversible structural change in Eos and alters its emitted fluorescence from green to red. We studied the dynamics of HIV-1 RNA by photoconverting Eos near the plasma membrane, and we monitored the population of photoconverted red-Eos-labeled RNA signals over time. We found that in the absence of Gag, most of the HIV-1 RNAs stayed near the plasma membrane transiently, for a few minutes. The presence of Gag significantly increased the time that RNAs stayed near the plasma membrane: most of the RNAs were still detected after 30 min. We then quantified the proportion of HIV-1 RNAs near the plasma membrane that were packaged into assembling viral complexes. By tagging Gag with blue fluorescent protein, we observed that only a portion, ∼13 to 34%, of the HIV-1 RNAs that reached the membrane were recruited into assembling particles in an hour, and the frequency of HIV-1 RNA packaging varied with the Gag expression level. Our studies reveal the HIV-1 RNA dynamics on the plasma membrane and the efficiency of RNA recruitment and provide insights into the events leading to the generation of infectious HIV-1 virions. Nascent HIV-1 particles assemble on plasma membranes. During the assembly process, HIV-1 RNA genomes must be encapsidated into viral complexes to generate infectious particles. To gain insights into the RNA packaging and virus assembly mechanisms, we labeled and monitored the HIV-1 RNA signals near the plasma membrane. Our results showed that most of the HIV-1 RNAs stayed near the plasma membrane for only a few minutes in the absence of Gag, whereas

An RNA-binding compound that stabilizes the HIV-1 gRNA packaging signal structure and specifically blocks HIV-1 RNA encapsidation.

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Ingemarsdotter, Carin K; Zeng, Jingwei; Long, Ziqi; Lever, Andrew M L; Kenyon, Julia C

2018-03-14

NSC260594, a quinolinium derivative from the NCI diversity set II compound library, was previously identified in a target-based assay as an inhibitor of the interaction between the HIV-1 (ψ) stem-loop 3 (SL3) RNA and Gag. This compound was shown to exhibit potent antiviral activity. Here, the effects of this compound on individual stages of the viral lifecycle were examined by qRT-PCR, ELISA and Western blot, to see if its actions were specific to the viral packaging stage. The structural effects of NSC260594 binding to the HIV-1 gRNA were also examined by SHAPE and dimerization assays. Treatment of cells with NSC260594 did not reduce the number of integration events of incoming virus, and treatment of virus producing cells did not affect the level of intracellular Gag protein or viral particle release as determined by immunoblot. However, NSC260594 reduced the incorporation of gRNA into virions by up to 82%, without affecting levels of gRNA inside the cell. This reduction in packaging correlated closely with the reduction in infectivity of the released viral particles. To establish the structural effects of NSC260594 on the HIV-1 gRNA, we performed SHAPE analyses to pinpoint RNA structural changes. NSC260594 had a stabilizing effect on the wild type RNA that was not confined to SL3, but that was propagated across the structure. A packaging mutant lacking SL3 did not show this effect. NSC260594 acts as a specific inhibitor of HIV-1 RNA packaging. No other viral functions are affected. Its action involves preventing the interaction of Gag with SL3 by stabilizing this small RNA stem-loop which then leads to stabilization of the global packaging signal region (psi or ψ). This confirms data, previously only shown in analyses of isolated SL3 oligonucleotides, that SL3 is structurally labile in the presence of Gag and that this is critical for the complete psi region to be able to adopt different conformations. Since replication is otherwise unaffected by NSC260594
Comparison of HIV DNA and RNA in gut-associated lymphoid tissue of HIV-infected controllers and noncontrollers.

Science.gov (United States)

Hatano, Hiroyu; Somsouk, Ma; Sinclair, Elizabeth; Harvill, Kara; Gilman, Lee; Cohen, Michelle; Hoh, Rebecca; Hunt, Peter W; Martin, Jeffrey N; Wong, Joseph K; Deeks, Steven G; Yukl, Steven A

2013-09-10

HIV-infected controllers have provided novel insights into mechanisms of viral control. We investigated the degree to which HIV DNA and RNA are present in gut-associated lymphoid tissue (GALT) of controllers. Cross-sectional cohort study. Colorectal biopsy pieces were obtained from five untreated noncontrollers, five ART-suppressed patients, and nine untreated controllers. Rectal HIV DNA was lower in controllers (median 496 copies/10(6) CD4 T cells) than in untreated noncontrollers (117483 copies/10(6) CD4+ T cells, P = 0.001) and ART-suppressed patients (6116 copies/10(6) CD4 T cells, P = 0.004). Similarly, rectal HIV RNA was lower in controllers (19 copies/10(6) CD4 T cells) than in noncontrollers (15210 copies/10(6) CD4+ T cells, P = 0.001) and ART-suppressed patients (1625 copies/10(6) CD4+ T cells, P = 0.0599). Rectal HIV RNA/DNA ratios were not statistically different between the three groups. Despite being able to maintain very low plasma HIV RNA levels in the absence of antiretroviral therapy (ART), HIV-infected controllers have readily measurable levels of HIV DNA and RNA in GALT. As expected, controllers had lower rectal HIV DNA and RNA compared with untreated noncontrollers and ART-suppressed individuals. Compared with the mechanisms of 'natural' viral control of controllers, long-term ART does not reduce the total HIV reservoir to the level of controllers.
Dynamics of breast milk HIV-1 RNA with unilateral mastitis or abscess.

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Semrau, Katherine; Kuhn, Louise; Brooks, Daniel R; Cabral, Howard; Sinkala, Moses; Kankasa, Chipepo; Thea, Donald M; Aldrovandi, Grace M

2013-03-01

Mastitis and abscess in HIV-infected women increase the risk of breastfeeding transmission of HIV. Guidelines encourage women to stop breastfeeding on the affected breast and feed on the contralateral breast. However, impact of breast pathology on breast milk HIV dynamics is unknown. HIV RNA was quantified in 211 breast milk samples collected before, during, and after a clinical mastitis or an abscess diagnosis from 38 HIV-infected women participating in a Zambian breastfeeding study. HIV RNA quantity was compared between affected and unaffected breasts over time using generalized estimating equation models. A sample of 115 women without breast pathology was selected as a control group. In the affected breast, breast milk HIV RNA quantity increased from the pre- to during-pathology period by log(10) 0.45 copies per milliliter [95% confidence interval (CI): 0.16 to 0.74], and after symptom resolution, HIV RNA levels were no different from prepathology levels (log10 -0.04 copies per milliliter 95% CI: -0.33 to 0.25). In the contralateral, unaffected breast, HIV RNA quantity did not significantly increase (log(10) 0.15 copies per milliliter, 95% CI: -0.41 to 0.10). Increase was more marked in women with abscess or with a greater number of mastitis symptoms. HIV RNA was not significantly different between affected and unaffected women, except at the time of diagnosis. Breast milk HIV RNA increased modestly in the affected breast with unilateral mastitis or abscess and returned to prepathology levels with symptom resolution. Contralateral HIV RNA was not affected. Results support guidelines encouraging feeding from the contralateral breast to minimize the risk of HIV transmission associated with unilateral breast pathology.
Impact of collection method on assessment of semen HIV RNA viral load.

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Brendan J W Osborne

Full Text Available The blood HIV RNA viral load is the best-defined predictor of HIV transmission, in part due to ease of measurement and the correlation of blood and genital tract (semen or cervico-vaginal viral load, although recent studies found semen HIV RNA concentration to be a stronger predictor of HIV transmission. There is currently no standardized method for semen collection when measuring HIV RNA concentration. Therefore, we compared two collection techniques in order to study of the impact of antiretroviral therapy on the semen viral load.Semen was collected by masturbation from HIV-infected, therapy-naïve men who have sex with men (MSM either undiluted (Visit 1 or directly into transport medium (Visit 2. Seminal plasma was then isolated, and the HIV RNA concentration obtained with each collection technique was measured and corrected for dilution if necessary. Collection of semen directly into transport medium resulted in a median HIV RNA viral load that was 0.4 log10 higher than undiluted samples.The method of semen collection is an important consideration when quantifying the HIV RNA viral load in this compartment.
Coal Tar and Coal-Tar Pitch

Science.gov (United States)

Learn about coal-tar products, which can raise your risk of skin cancer, lung cancer, and other types of cancer. Examples of coal-tar products include creosote, coal-tar pitch, and certain preparations used to treat skin conditions such as eczema, psoriasis, and dandruff.
Full Viral Suppression, Low-Level Viremia, and Quantifiable Plasma HIV-RNA at the End of Pregnancy in HIV-Infected Women on Antiretroviral Treatment.

Science.gov (United States)

Baroncelli, Silvia; Pirillo, Maria F; Tamburrini, Enrica; Guaraldi, Giovanni; Pinnetti, Carmela; Degli Antoni, Anna; Galluzzo, Clementina M; Stentarelli, Chiara; Amici, Roberta; Floridia, Marco

2015-07-01

There is limited information on full viral suppression and low-level HIV-RNA viremia in HIV-infected women at the end of pregnancy. We investigated HIV-RNA levels close to delivery in women on antiretroviral treatment in order to define rates of complete suppression, low-level viremia, and quantifiable HIV-RNA, exploring as potential determinants some clinical and viroimmunological variables. Plasma samples from a national study in Italy, collected between 2003 and 2012, were used. According to plasma HIV-RNA levels, three groups were defined: full suppression (target not detected), low-level viremia (target detected but HIV-RNA (≥37 copies/ml). Multivariable logistic regression was used to define determinants of full viral suppression and of quantifiable HIV-RNA. Among 107 women evaluated at a median gestational age of 35 weeks, 90 (84.1%) had HIV-RNA HIV-RNA was 109 copies/ml (IQR 46-251), with only one case showing resistance (mutation M184V; rate: 9.1%). In multivariable analyses, women with higher baseline HIV-RNA levels and with hepatitis C virus (HCV) coinfection were significantly more likely to have quantifiable HIV-RNA in late pregnancy. Full viral suppression was significantly more likely with nonnucleoside reverse transcriptase inhibitor (NNRTI)-based regimens and significantly less likely with higher HIV-RNA in early pregnancy. No cases of HIV transmission occurred. In conclusion, HIV-infected pregnant women showed a high rate of viral suppression and a low resistance rate before delivery. In most cases no target HIV-RNA was detected in plasma, suggesting a low risk of subsequent virological rebound and development of resistance. Women with high levels of HIV-RNA in early pregnancy and those who have concomitant HCV infection should be considered at higher risk of having quantifiable HIV-RNA at the end of pregnancy.
Cell-associated HIV DNA measured early during infection has prognostic value independent of serum HIV RNA measured concomitantly

DEFF Research Database (Denmark)

Katzenstein, Terese L; Oliveri, Roberto S; Benfield, Thomas

2002-01-01

Using data from the Danish AIDS Cohort of HIV-infected homosexual men established in the 1980s, the prognostic value of early HIV DNA loads was evaluated. In addition to DNA measurements, concomitant serum HIV RNA levels, CD4 cell counts and CCR5 genotypes were determined. The patients were divided...... of serum HIV RNA (p normal allele (p
Interactions Between HIV-1 Gag and Viral RNA Genome Enhance Virion Assembly

DEFF Research Database (Denmark)

Dilley, Kari A; Nikolaitchik, Olga A; Galli, Andrea

2017-01-01

between Gag and viral RNA are required for the enhancement of particle production. Taken together, these studies are consistent with our previous hypothesis that specific dimeric viral RNA:Gag interactions are the nucleation event of infectious virion assembly, ensuring that one RNA dimer is packaged......Most HIV-1 virions contain two copies of full-length viral RNA, indicating that genome packaging is efficient and tightly regulated. However, the structural protein Gag is the only component required for the assembly of noninfectious virus-like particles and the viral RNA is dispensable...... in this process. The mechanism that allows HIV-1 to achieve such high efficiency of genome packaging when a packageable viral RNA is not required for virus assembly is currently unknown. In this report, we examined the role of HIV-1 RNA in virus assembly and found that packageable HIV-1 RNA enhances particle...
Bacterial vaginosis, human papilloma virus and herpes viridae do not predict vaginal HIV RNA shedding in women living with HIV in Denmark.

Science.gov (United States)

Wessman, Maria; Thorsteinsson, Kristina; Jensen, Jørgen S; Storgaard, Merete; Rönsholt, Frederikke F; Johansen, Isik S; Pedersen, Gitte; Nørregård Nielsen, Lars; Bonde, Jesper; Katzenstein, Terese L; Weis, Nina; Lebech, Anne-Mette

2017-05-31

Bacterial vaginosis (BV) has been found to be associated with HIV acquisition and transmission. This is suggested to be due to higher HIV RNA levels in cervicovaginal fluids in women living with HIV (WLWH) with BV, as bacteria associated with BV may induce viral replication and shedding in the genital tract despite undetectable HIV RNA plasma viral load. We examined the prevalence and diagnostic predictors of BV and HIV-1 RNA vaginal shedding in women living with HIV (WLWH) in Denmark, taking into account the presence of human papillomavirus (HPV) and herpes viridae. WLWH between 18-51 years were recruited from six Departments of Infectious Diseases in Denmark during enrolment in the SHADE cohort; a prospective cohort study of WLWH attending regular outpatient care. BV was diagnosed by microscopy of vaginal swabs and PCR was used for detection of BV-associated bacteria, HPV, herpes viridae, and vaginal HIV viral load. Median age of the 150 included women was 41 years; ethnicity was predominantly White (35%) or Black (47%). The majority (96%) was on ART and had undetectable (85%) plasma HIV RNA (<40 copies/mL). BV was diagnosed in 32%. Overall, 11% had detectable vaginal HIV RNA. Both before and after adjustment for BV, age, ethnicity, plasma HIV RNA, CD4 cell count, herpes viridae and HPV, we found no significant predictors of HIV RNA vaginal shedding. In well-treated WLWH, BV, herpes viridae or HPV do not predict vaginal HIV RNA shedding. This implies that HIV shedding does not seem to be increased by BV.
RNA interference-based therapeutics for human immunodeficiency virus HIV-1 treatment: synthetic siRNA or vector-based shRNA?

Science.gov (United States)

Subramanya, Sandesh; Kim, Sang-Soo; Manjunath, N; Shankar, Premlata

2010-02-01

Despite the clinical benefits of highly active antiretroviral therapy (HAART), the prospect of life-long antiretroviral treatment poses significant problems, which has spurred interest in developing new drugs and strategies to treat HIV infection and eliminate persistent viral reservoirs. RNAi has emerged as a therapeutic possibility for HIV. We discuss progress in overcoming hurdles to translating transient and stable RNAi enabling technologies to clinical application for HIV; covering the past 2 - 3 years. HIV inhibition can be achieved by transfection of chemically or enzymatically synthesized siRNAs or by DNA-based vector systems expressing short hairpin RNAs (shRNAs) that are processed intracellularly into siRNA. We compare these approaches, focusing on technical and safety issues that will guide the choice of strategy for clinical use. Introduction of synthetic siRNA into cells or its stable endogenous production using vector-driven shRNA have been shown to suppress HIV replication in vitro and, in some instances, in vivo. Each method has advantages and limitations in terms of ease of delivery, duration of silencing, emergence of escape mutants and potential toxicity. Both appear to have potential as future therapeutics for HIV, once the technical and safety issues of each approach are overcome.
The thermodynamics of Pr55Gag-RNA interaction regulate the assembly of HIV.

Directory of Open Access Journals (Sweden)

Hanumant S Tanwar

2017-02-01

Full Text Available The interactions that occur during HIV Pr55Gag oligomerization and genomic RNA packaging are essential elements that facilitate HIV assembly. However, mechanistic details of these interactions are not clearly defined. Here, we overcome previous limitations in producing large quantities of full-length recombinant Pr55Gag that is required for isothermal titration calorimetry (ITC studies, and we have revealed the thermodynamic properties of HIV assembly for the first time. Thermodynamic analysis showed that the binding between RNA and HIV Pr55Gag is an energetically favourable reaction (ΔG<0 that is further enhanced by the oligomerization of Pr55Gag. The change in enthalpy (ΔH widens sequentially from: (1 Pr55Gag-Psi RNA binding during HIV genome selection; to (2 Pr55Gag-Guanosine Uridine (GU-containing RNA binding in cytoplasm/plasma membrane; and then to (3 Pr55Gag-Adenosine(A-containing RNA binding in immature HIV. These data imply the stepwise increments of heat being released during HIV biogenesis may help to facilitate the process of viral assembly. By mimicking the interactions between A-containing RNA and oligomeric Pr55Gag in immature HIV, it was noted that a p6 domain truncated Pr50Gag Δp6 is less efficient than full-length Pr55Gag in this thermodynamic process. These data suggest a potential unknown role of p6 in Pr55Gag-Pr55Gag oligomerization and/or Pr55Gag-RNA interaction during HIV assembly. Our data provide direct evidence on how nucleic acid sequences and the oligomeric state of Pr55Gag regulate HIV assembly.
Bacterial vaginosis, human papilloma virus and herpes viridae do not predict vaginal HIV RNA shedding in women living with HIV in Denmark

DEFF Research Database (Denmark)

Wessman, Maria; Thorsteinsson, Kristina; Jensen, Jørgen S

2017-01-01

in the genital tract despite undetectable HIV RNA plasma viral load. We examined the prevalence and diagnostic predictors of BV and HIV-1 RNA vaginal shedding in women living with HIV (WLWH) in Denmark, taking into account the presence of human papillomavirus (HPV) and herpes viridae. METHODS: WLWH between 18......-51 years were recruited from six Departments of Infectious Diseases in Denmark during enrolment in the SHADE cohort; a prospective cohort study of WLWH attending regular outpatient care. BV was diagnosed by microscopy of vaginal swabs and PCR was used for detection of BV-associated bacteria, HPV, herpes...... RNA. Both before and after adjustment for BV, age, ethnicity, plasma HIV RNA, CD4 cell count, herpes viridae and HPV, we found no significant predictors of HIV RNA vaginal shedding. CONCLUSION: In well-treated WLWH, BV, herpes viridae or HPV do not predict vaginal HIV RNA shedding. This implies...
Molecular mimicry of human tRNALys anti-codon domain by HIV-1 RNA genome facilitates tRNA primer annealing.

Science.gov (United States)

Jones, Christopher P; Saadatmand, Jenan; Kleiman, Lawrence; Musier-Forsyth, Karin

2013-02-01

The primer for initiating reverse transcription in human immunodeficiency virus type 1 (HIV-1) is tRNA(Lys3). Host cell tRNA(Lys) is selectively packaged into HIV-1 through a specific interaction between the major tRNA(Lys)-binding protein, human lysyl-tRNA synthetase (hLysRS), and the viral proteins Gag and GagPol. Annealing of the tRNA primer onto the complementary primer-binding site (PBS) in viral RNA is mediated by the nucleocapsid domain of Gag. The mechanism by which tRNA(Lys3) is targeted to the PBS and released from hLysRS prior to annealing is unknown. Here, we show that hLysRS specifically binds to a tRNA anti-codon-like element (TLE) in the HIV-1 genome, which mimics the anti-codon loop of tRNA(Lys) and is located proximal to the PBS. Mutation of the U-rich sequence within the TLE attenuates binding of hLysRS in vitro and reduces the amount of annealed tRNA(Lys3) in virions. Thus, LysRS binds specifically to the TLE, which is part of a larger LysRS binding domain in the viral RNA that includes elements of the Psi packaging signal. Our results suggest that HIV-1 uses molecular mimicry of the anti-codon of tRNA(Lys) to increase the efficiency of tRNA(Lys3) annealing to viral RNA.
Coal tar phototherapy for psoriasis reevaluated: erythemogenic versus suberythemogenic ultraviolet with a tar extract in oil and crude coal tar

International Nuclear Information System (INIS)

Lowe, N.J.; Wortzman, M.S.; Breeding, J.; Koudsi, H.; Taylor, L.

1983-01-01

Recent studies have questioned the therapeutic value of coal tar versus ultraviolet (UV) radiation and their relative necessity in phototherapy for psoriasis. In this investigation, different aspects of tar phototherapy have been studied in single-blind bilateral paired comparison studies. The effects of 1% crude coal tar were compared with those of petrolatum in conjunction with erythemogenic and suberythemogenic doses of ultraviolet light (UVB) using a FS72 sunlamp tubed cabinet. Crude coal tar was clinically superior to petrolatum with suberythemogenic ultraviolet. With the erythemogenic UVB, petrolatum was equal in efficacy to crude coal tar. Suberythemogenic UVB was also used adjunctively to compare the effects of a 5% concentration of a tar extract in an oil base to 5% crude coal tar in petrolatum or the oil base without tar. The tar extract in oil plus suberythemogenic UVB produced significantly more rapid improvement than the oil base plus UVB. The direct bilateral comparison of equal concentrations of tar extract in oil base versus crude coal tar in petrolatum in a suberythemogenic UV photo regimen revealed no statistical differences between treatments. In a study comparing tar extract in oil and the oil base without ultraviolet radiation, the tar extract in oil side responded more rapidly
Receptor-targeted aptamer-siRNA conjugate-directed transcriptional regulation of HIV-1

Science.gov (United States)

Zhou, Jiehua; Lazar, Daniel; Li, Haitang; Xia, Xin; Satheesan, Sangeetha; Charlins, Paige; O'Mealy, Denis; Akkina, Ramesh; Saayman, Sheena; Weinberg, Marc S.; Rossi, John J.; Morris, Kevin V.

2018-01-01

Gene-based therapies represent a promising therapeutic paradigm for the treatment of HIV-1, as they have the potential to maintain sustained viral inhibition with reduced treatment interventions. Such an option may represent a long-term treatment alternative to highly active antiretroviral therapy. Methods: We previously described a therapeutic approach, referred to as transcriptional gene silencing (TGS), whereby small noncoding RNAs directly inhibit the transcriptional activity of HIV-1 by targeting sites within the viral promoter, specifically the 5' long terminal repeat (LTR). TGS differs from traditional RNA interference (RNAi) in that it is characterized by concomitant silent-state epigenetic marks on histones and DNA. To deliver TGS-inducing RNAs, we developed functional RNA conjugates based on the previously reported dual function of the gp120 (A-1) aptamer conjugated to 27-mer Dicer-substrate anti-HIV-1 siRNA (dsiRNA), LTR-362. Results: We demonstrate here that high levels of processed guide RNAs localize to the nucleus in infected T lymphoblastoid CEM cell line and primary human CD4+ T-cells. Treatment of the aptamer-siRNA conjugates induced TGS with an ~10-fold suppression of viral p24 levels as measured at day 12 post infection. To explore the silencing efficacy of aptamer-siRNA conjugates in vivo, HIV-1-infected humanized NOD/SCID/IL2 rγnull mice (hu-NSG) were treated with the aptamer-siRNA conjugates. Systemic delivery of the A-1-stick-LTR-362 27-mer siRNA conjugates suppressed HIV-1 infection and protected CD4+ T cell levels in viremia hu-NSG mice. Principle conclusions: Collectively these data suggest that the gp120 aptamer-dsiRNA conjugate design is suitable for systemic delivery of small RNAs that can be used to suppress HIV-1. PMID:29556342
Analytical Performances of Human Immunodeficiency Virus Type 1 RNA-Based Amplix® Real-Time PCR Platform for HIV-1 RNA Quantification

Directory of Open Access Journals (Sweden)

Christian Diamant Mossoro-Kpinde

2016-01-01

Full Text Available Objectives. We evaluated the performances of Amplix real-time PCR platform developed by Biosynex (Strasbourg, France, combining automated station extraction (Amplix station 16 Dx and real-time PCR (Amplix NG, for quantifying plasma HIV-1 RNA by lyophilized HIV-1 RNA-based Amplix reagents targeting gag and LTR, using samples from HIV-1-infected adults from Central African Republic. Results. Amplix real-time PCR assay showed low limit of detection (28 copies/mL, across wide dynamic range (1.4–10 log copies/mL, 100% sensitivity and 99% specificity, high reproducibility, and accuracy with mean bias < 5%. The assay showed excellent correlations and concordance of 95.3% with the reference HIV-1 RNA load assay (Roche, with mean absolute bias of +0.097 log copies/mL by Bland-Altman analysis. The assay was able to detect and quantify the most prevalent HIV-1 subtype strains and the majority of non-B subtypes, CRFs of HIV-1 group M, and HIV-1 groups N and O circulating in Central Africa. The Amplix assay showed 100% sensitivity and 99.6% specificity to diagnose virological failure in clinical samples from antiretroviral drug-experienced patients. Conclusions. The HIV-1 RNA-based Amplix real-time PCR platform constitutes sensitive and reliable system for clinical monitoring of HIV-1 RNA load in HIV-1-infected children and adults, particularly adapted to intermediate laboratory facilities in sub-Saharan Africa.
Cell-associated HIV DNA measured early during infection has prognostic value independent of serum HIV RNA measured concomitantly

DEFF Research Database (Denmark)

Katzenstein, Terese L; Oliveri, Roberto S; Benfield, Thomas

2002-01-01

Using data from the Danish AIDS Cohort of HIV-infected homosexual men established in the 1980s, the prognostic value of early HIV DNA loads was evaluated. In addition to DNA measurements, concomitant serum HIV RNA levels, CD4 cell counts and CCR5 genotypes were determined. The patients were divided...... into 3 groups, according to whether their cell-associated HIV DNA load was or = 2,500 DNA copies/10(6) peripheral blood mononuclear cells. Clinical progression rates differed significantly between the groups (p value independent...... of serum HIV RNA (p value. Patients heterozygous for the CCR5 delta 32 allele had significantly lower HIV DNA loads than those homozygous for the normal allele (p
Diagnosing acute HIV infection: The performance of quantitative HIV-1 RNA testing (viral load) in the 2014 laboratory testing algorithm.

Science.gov (United States)

Wu, Hsiu; Cohen, Stephanie E; Westheimer, Emily; Gay, Cynthia L; Hall, Laura; Rose, Charles; Hightow-Weidman, Lisa B; Gose, Severin; Fu, Jie; Peters, Philip J

2017-08-01

New recommendations for laboratory diagnosis of HIV infection in the United States were published in 2014. The updated testing algorithm includes a qualitative HIV-1 RNA assay to resolve discordant immunoassay results and to identify acute HIV-1 infection (AHI). The qualitative HIV-1 RNA assay is not widely available; therefore, we evaluated the performance of a more widely available quantitative HIV-1 RNA assay, viral load, for diagnosing AHI. We determined that quantitative viral loads consistently distinguished AHI from a false-positive immunoassay result. Among 100 study participants with AHI and a viral load result, the estimated geometric mean viral load was 1,377,793copies/mL. Copyright © 2017 Elsevier B.V. All rights reserved.
Impact of tuberculosis treatment on CD4 cell count, HIV RNA, and p24 antigen in patients with HIV and tuberculosis

DEFF Research Database (Denmark)

Wejse, Christian; Furtado, A.; Camara, C.

2013-01-01

To describe HIV RNA levels during tuberculosis (TB) infection in patients co-infected with TB and HIV. Moreover, to examine the p24 antigen profile during TB treatment.......To describe HIV RNA levels during tuberculosis (TB) infection in patients co-infected with TB and HIV. Moreover, to examine the p24 antigen profile during TB treatment....
What do we measure when we measure cell-associated HIV RNA.

Science.gov (United States)

Pasternak, Alexander O; Berkhout, Ben

2018-01-29

Cell-associated (CA) HIV RNA has received much attention in recent years as a surrogate measure of the efficiency of HIV latency reversion and because it may provide an estimate of the viral reservoir size. This review provides an update on some recent insights in the biology and clinical utility of this biomarker. We discuss a number of important considerations to be taken into account when interpreting CA HIV RNA measurements, as well as different methods to measure this biomarker.

The HIV-1 leader RNA conformational switch regulates RNA dimerization but does not regulate mRNA translation

NARCIS (Netherlands)

Abbink, Truus E. M.; Ooms, Marcel; Haasnoot, P. C. Joost; Berkhout, Ben

2005-01-01

The untranslated leader RNA is the most conserved part of the human immunodeficiency virus type I (HIV-1) genome. It contains many regulatory motifs that mediate a variety of steps in the viral life cycle. Previous work showed that the full-length leader RNA can adopt two alternative structures: a
Editing of HIV-1 RNA by the double-stranded RNA deaminase ADAR1 stimulates viral infection

Science.gov (United States)

Doria, Margherita; Neri, Francesca; Gallo, Angela; Farace, Maria Giulia; Michienzi, Alessandro

2009-01-01

Adenosine deaminases that act on dsRNA (ADARs) are enzymes that target double-stranded regions of RNA converting adenosines into inosines (A-to-I editing) thus contributing to genome complexity and fine regulation of gene expression. It has been described that a member of the ADAR family, ADAR1, can target viruses and affect their replication process. Here we report evidence showing that ADAR1 stimulates human immuno deficiency virus type 1 (HIV-1) replication by using both editing-dependent and editing-independent mechanisms. We show that over-expression of ADAR1 in HIV-1 producer cells increases viral protein accumulation in an editing-independent manner. Moreover, HIV-1 virions generated in the presence of over-expressed ADAR1 but not an editing-inactive ADAR1 mutant are released more efficiently and display enhanced infectivity, as demonstrated by challenge assays performed with T cell lines and primary CD4+ T lymphocytes. Finally, we report that ADAR1 associates with HIV-1 RNAs and edits adenosines in the 5′ untranslated region (UTR) and the Rev and Tat coding sequence. Overall these results suggest that HIV-1 has evolved mechanisms to take advantage of specific RNA editing activity of the host cell and disclose a stimulatory function of ADAR1 in the spread of HIV-1. PMID:19651874
A DEVICE AND METHOD FOR MEASURING TAR IN A TAR-ENVIRONMENT

DEFF Research Database (Denmark)

2017-01-01

The present disclosure describes a device and corresponding method for measuring tar in a tar environment, e.g., a tar producing environment such as a stove or a combustion engine, based on UV absorption spectroscopy. A first measurement along an optical path in the tar environment is performed...
Discordant CSF/plasma HIV-1 RNA in individuals on virologically suppressive antiretroviral therapy in Western India.

Science.gov (United States)

Dravid, Ameet N; Natrajan, Kartik; Kulkarni, Milind M; Saraf, Chinmay K; Mahajan, Uma S; Kore, Sachin D; Rathod, Niranjan M; Mahajan, Umakant S; Wadia, Rustom S

2018-02-01

Aim of this study was to estimate the prevalence of cerebrospinal fluid (CSF)/Plasma HIV-1 RNA discordance in virologically suppressed individuals presenting with incident neurologic symptoms.In this retrospective cohort study conducted between March 1, 2009, and March 1, 2017, HIV-1 infected adults exposed to atleast 12 months of antiretroviral therapy (ART) and having plasma viral load (VL) CSF/Plasma HIV-1 RNA discordance by measuring HIV-1 RNA in collected plasma and CSF samples. CSF/plasma HIV-1 RNA discordance was defined as either detectable CSF HIV-1 RNA (VL > 20 copies/mL) with an undetectable plasma RNA (complete viral suppression, VL ≤20 copies/mL) or CSF HIV-1 RNA ≥ 0.5 log10 higher than plasma RNA when plasma VL was between 20 and 1000 copies/mL (low-level viremia, LLV).Out of 1584 virologically suppressed patients, 71 (4.4%) presented with incident neurologic symptoms. Twenty out of 71 (28.2%) patients were diagnosed with CSF/Plasma HIV-1 discordance. Median plasma and CSF VL in patients with discordance was 120 [interquartile range (IQR): CSF HIV-1 genotypic resistance testing was done showed mutations that would compromise efficacy of prescribed ART regimen. Prevalence of CSF/plasma HIV-1 RNA discordance was higher among neurologically symptomatic patients with plasma LLV as compared with those with complete viral suppression (70% vs 11.8%, P CSF/plasma HIV-1 RNA discordance indicates replication of HIV-1 that has adapted to the CNS or has developed antiretroviral drug resistance. Larger studies should be performed to study incidence of discordance in India. This will help in managing patients presenting with neurologic symptoms on suppressive ART with appropriate neuroeffective therapy.
Increasing cerebrospinal fluid chemokine concentrations despite undetectable cerebrospinal fluid HIV RNA in HIV-1-infected patients receiving antiretroviral therapy

NARCIS (Netherlands)

Gisolf, E. H.; van Praag, R. M.; Jurriaans, S.; Portegies, P.; Goudsmit, J.; Danner, S. A.; Lange, J. M.; Prins, J. M.

2000-01-01

Only limited data on cerebrospinal fluid (CSF) HIV-1 RNA responses and markers of local inflammation in CSF during antiretroviral therapy are available. HIV-RNA, soluble tumor necrosis factor (TNF)-receptor (sTNFr)-II, monocyte chemoattractant protein (MCP)-1, and interferon-gamma-inducible protein
RNA interactions in the 5' region of the HIV-1 genome

DEFF Research Database (Denmark)

Damgaard, Christian Kroun; Andersen, Ebbe Sloth; Knudsen, Bjarne

2004-01-01

The untranslated leader of the dimeric HIV-1 RNA genome is folded into a complex structure that plays multiple and essential roles in the viral replication cycle. Here, we have investigated secondary and tertiary structural elements within the 5' 744 nucleotides of the HIV-1 genome using...... a combination of bioinformatics, enzymatic probing, native gel electrophoresis, and UV-crosslinking experiments. We used a recently developed RNA folding algorithm (Pfold) to predict the common secondary structure of an alignment of 20 divergent HIV-1 sequences. Combining this analysis with biochemical data, we...
Full Viral Suppression, Low-Level Viremia, and Quantifiable Plasma HIV-RNA at the End of Pregnancy in HIV-Infected Women on Antiretroviral Treatment

OpenAIRE

Baroncelli, Silvia; Pirillo, Maria F.; Tamburrini, Enrica; Guaraldi, Giovanni; Pinnetti, Carmela; Antoni, Anna Degli; Galluzzo, Clementina M.; Stentarelli, Chiara; Amici, Roberta; Floridia, Marco

2015-01-01

There is limited information on full viral suppression and low-level HIV-RNA viremia in HIV-infected women at the end of pregnancy. We investigated HIV-RNA levels close to delivery in women on antiretroviral treatment in order to define rates of complete suppression, low-level viremia, and quantifiable HIV-RNA, exploring as potential determinants some clinical and viroimmunological variables. Plasma samples from a national study in Italy, collected between 2003 and 2012, were used. According ...
HIV-1 RNAs are Not Part of the Argonaute 2 Associated RNA Interference Pathway in Macrophages.

Directory of Open Access Journals (Sweden)

Valentina Vongrad

Full Text Available MiRNAs and other small noncoding RNAs (sncRNAs are key players in post-transcriptional gene regulation. HIV-1 derived small noncoding RNAs (sncRNAs have been described in HIV-1 infected cells, but their biological functions still remain to be elucidated. Here, we approached the question whether viral sncRNAs may play a role in the RNA interference (RNAi pathway or whether viral mRNAs are targeted by cellular miRNAs in human monocyte derived macrophages (MDM.The incorporation of viral sncRNAs and/or their target RNAs into RNA-induced silencing complex was investigated using photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP as well as high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP, which capture Argonaute2-bound miRNAs and their target RNAs. HIV-1 infected monocyte-derived macrophages (MDM were chosen as target cells, as they have previously been shown to express HIV-1 sncRNAs. In addition, we applied small RNA deep sequencing to study differential cellular miRNA expression in HIV-1 infected versus non-infected MDMs.PAR-CLIP and HITS-CLIP data demonstrated the absence of HIV-1 RNAs in Ago2-RISC, although the presence of a multitude of HIV-1 sncRNAs in HIV-1 infected MDMs was confirmed by small RNA sequencing. Small RNA sequencing revealed that 1.4% of all sncRNAs were of HIV-1 origin. However, neither HIV-1 derived sncRNAs nor putative HIV-1 target sequences incorporated into Ago2-RISC were identified suggesting that HIV-1 sncRNAs are not involved in the canonical RNAi pathway nor is HIV-1 targeted by this pathway in HIV-1 infected macrophages.
Viral protein Nef is detected in plasma of half of HIV-infected adults with undetectable plasma HIV RNA.

Directory of Open Access Journals (Sweden)

Jana Ferdin

Full Text Available To address the role of translationally active HIV reservoir in chronic inflammation and non-AIDS related disorders, we first need a simple and accurate assay to evaluate viral protein expression in virally suppressed subjects.We optimized an HIV Nef enzyme-linked immunosorbent assay (ELISA and used it to quantify plasma Nef levels as an indicator of the leaky HIV reservoir in an HIV-infected cohort.This study accessed 134 plasma samples from a well-characterized cohort study of HIV-infected and uninfected adults in San Francisco (the SCOPE cohort. We optimized an ELISA for detection of plasma Nef in HIV-negative subjects and HIV-infected non-controllers, and evaluated its utility to quantify plasma Nef levels in a cross-sectional study of ART-suppressed and elite controller HIV-infected subjects.Here, we describe the performance of an optimized HIV Nef ELISA. When we applied this assay to the study cohort we found that plasma Nef levels were correlated with plasma HIV RNA levels in untreated disease. However, we were able to detect Nef in plasma of approximately half of subjects on ART or with elite control, despite the lack of detectable plasma HIV RNA levels using standard assays. Plasma Nef levels were not consistently associated with CD4+ T-cell count, CD8+ T-cell count, self-reported nadir CD4+ T-cell count or the CD4+/CD8+ T-cell ratio in HIV-infected subjects.Since plasma HIV RNA levels are undetectable in virally suppressed subjects, it is reasonable to assume that viral protein expression in leaky reservoir, and not plasma virions, is the source of Nef accumulating in plasma. To examine this further, improvements of the assay sensitivity, by lowering the background through improvements in the quality of Nef antibodies, and detailed characterization of the HIV reservoirs are needed.
Hydration dependent dynamics in RNA

International Nuclear Information System (INIS)

Olsen, Greg L.; Bardaro, Michael F.; Echodu, Dorothy C.; Drobny, Gary P.; Varani, Gabriele

2009-01-01

The essential role played by local and collective motions in RNA function has led to a growing interest in the characterization of RNA dynamics. Recent investigations have revealed that even relatively simple RNAs experience complex motions over multiple time scales covering the entire ms-ps motional range. In this work, we use deuterium solid-state NMR to systematically investigate motions in HIV-1 TAR RNA as a function of hydration. We probe dynamics at three uridine residues in different structural environments ranging from helical to completely unrestrained. We observe distinct and substantial changes in 2 H solid-state relaxation times and lineshapes at each site as hydration levels increase. By comparing solid-state and solution state 13 C relaxation measurements, we establish that ns-μs motions that may be indicative of collective dynamics suddenly arise in the RNA as hydration reaches a critical point coincident with the onset of bulk hydration. Beyond that point, we observe smaller changes in relaxation rates and lineshapes in these highly hydrated solid samples, compared to the dramatic activation of motion occurring at moderate hydration
Chimeric peptide-mediated siRNA transduction to inhibit HIV-1 infection.

Science.gov (United States)

Bivalkar-Mehla, Shalmali; Mehla, Rajeev; Chauhan, Ashok

2017-04-01

Persistent human immunodeficiency virus 1 (HIV-1) infection provokes immune activation and depletes CD4 + lymphocytes, leading to acquired immunodeficiency syndrome. Uninterrupted administration of combination antiretroviral therapy (cART) in HIV-infected patients suppresses viral replication to below the detectable level and partially restores the immune system. However, cART-unresponsive residual HIV-1 infection and elusive transcriptionally silent but reactivatable viral reservoirs maintain a permanent viral DNA blue print. The virus rebounds within a few weeks after interruption of suppressive therapy. Adjunct gene therapy to control viral replication by ribonucleic acid interference (RNAi) is a post-transcriptional gene silencing strategy that could suppress residual HIV-1 burden and overcome viral resistance. Small interfering ribonucleic acids (siRNAs) are efficient transcriptional inhibitors, but need delivery systems to reach inside target cells. We investigated the potential of chimeric peptide (FP-PTD) to deliver specific siRNAs to HIV-1-susceptible and permissive cells. Chimeric FP-PTD peptide was designed with an RNA binding domain (PTD) to bind siRNA and a cell fusion peptide domain (FP) to enter cells. FP-PTD-siRNA complex entered and inhibited HIV-1 replication in susceptible cells, and could be a candidate for in vivo testing.
HIV Infection Status as a Predictor of Hepatitis C Virus RNA Testing in Primary Care

Science.gov (United States)

Yartel, Anthony K.; Morgan, Rebecca L.; Rein, David B.; Brown, Kimberly Ann; Kil, Natalie B.; Massoud, Omar I.; Fallon, Michael B.; Smith, Bryce D.

2015-01-01

Introduction Receipt of hepatitis C virus (HCV) RNA testing following a positive HCV antibody (anti-HCV+) test result to establish current infection is a quality indicator for HCV-related care. This study examines HIV infection status as a predictor of HCV RNA test receipt after an anti-HCV+ result in the primary care setting. Methods Electronic medical records of anti-HCV+ patients from a multisite retrospective study of patients aged ≥18 years who utilized one or more primary care outpatient services during 2005–2010 were analyzed in 2014. A multivariable logistic regression model examined the independent relationships between patient characteristics and receipt of HCV RNA testing. Results Among 1,115 anti-HCV+ patients, 133 (11.9%) were also HIV-positive. Of these, 77.4% (n=103) underwent HCV RNA testing to determine current infection status. By contrast, 66.7% (n=654/980) of anti-HCV+ patients who were HIV-negative received HCV RNA testing. Following multivariable adjustment, the odds of receiving HCV RNA testing were higher among anti-HCV+ patients who were also HIV-positive (AOR=1.9, 95% CI=1.2, 3.0), compared with their HIV-negative counterparts. Elevated alanine aminotransferase level was also associated with receipt of HCV RNA testing (AOR=1.9, 95% CI=1.4, 2.4). Black race was associated with decreased odds of receiving HCV RNA testing (AOR=0.7, 95% CI=0.5, 1.0). Conclusions HIV infection status is independently associated with the likelihood of receiving HCV RNA testing following an anti-HCV+ result. One quarter of anti-HCV+ patients who were also HIV-positive and one third of their HIV-negative counterparts, respectively, did not receive testing to establish active HCV infection, which is imperative for appropriate care and treatment. PMID:25896194
The HIV-1 Rev/RRE system is required for HIV-1 5' UTR cis elements to augment encapsidation of heterologous RNA into HIV-1 viral particles

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Ma Hong

2011-06-01

Full Text Available Abstract Background The process of HIV-1 genomic RNA (gRNA encapsidation is governed by a number of viral encoded components, most notably the Gag protein and gRNA cis elements in the canonical packaging signal (ψ. Also implicated in encapsidation are cis determinants in the R, U5, and PBS (primer binding site from the 5' untranslated region (UTR. Although conventionally associated with nuclear export of HIV-1 RNA, there is a burgeoning role for the Rev/RRE in the encapsidation process. Pleiotropic effects exhibited by these cis and trans viral components may confound the ability to examine their independent, and combined, impact on encapsidation of RNA into HIV-1 viral particles in their innate viral context. We systematically reconstructed the HIV-1 packaging system in the context of a heterologous murine leukemia virus (MLV vector RNA to elucidate a mechanism in which the Rev/RRE system is central to achieving efficient and specific encapsidation into HIV-1 viral particles. Results We show for the first time that the Rev/RRE system can augment RNA encapsidation independent of all cis elements from the 5' UTR (R, U5, PBS, and ψ. Incorporation of all the 5' UTR cis elements did not enhance RNA encapsidation in the absence of the Rev/RRE system. In fact, we demonstrate that the Rev/RRE system is required for specific and efficient encapsidation commonly associated with the canonical packaging signal. The mechanism of Rev/RRE-mediated encapsidation is not a general phenomenon, since the combination of the Rev/RRE system and 5' UTR cis elements did not enhance encapsidation into MLV-derived viral particles. Lastly, we show that heterologous MLV RNAs conform to transduction properties commonly associated with HIV-1 viral particles, including in vivo transduction of non-dividing cells (i.e. mouse neurons; however, the cDNA forms are episomes predominantly in the 1-LTR circle form. Conclusions Premised on encapsidation of a heterologous RNA into
Bacterial vaginosis, human papilloma virus and herpes viridae do not predict vaginal HIV RNA shedding in women living with HIV in Denmark

DEFF Research Database (Denmark)

Wessman, Maria; Thorsteinsson, Kristina; Jensen, Jørgen S

2017-01-01

in the genital tract despite undetectable HIV RNA plasma viral load. We examined the prevalence and diagnostic predictors of BV and HIV-1 RNA vaginal shedding in women living with HIV (WLWH) in Denmark, taking into account the presence of human papillomavirus (HPV) and herpes viridae. Methods: WLWH between 18...
Hepatitis C virus (HCV) RNA profiles among chronic HIV/HCV-coinfected individuals in ESPRIT; spontaneous HCV RNA clearance observed in nine individuals.

Science.gov (United States)

Grint, D; Tedaldi, E; Peters, L; Mocroft, A; Edlin, B; Gallien, S; Klinker, H; Boesecke, C; Kokordelis, P; Rockstroh, J K

2017-07-01

Studies have shown that hepatitis C virus (HCV) RNA levels remain stable over time in HIV/HCV-coinfected individuals taking combination antiretroviral therapy (cART), while spontaneous clearance of HCV RNA during the persistent infection phase has been documented only rarely among those with the CC interleukin (IL)-28B genotype. This study describes HCV RNA profiles and factors associated with changes over time in HCV RNA levels in the ESPRIT study. HIV/HCV-coinfected individuals positive for HCV RNA were included in the study. Follow-up was counted from the first HCV RNA positive test and censored at the initiation of interferon-based treatment. HCV RNA and IL-28B measurements were performed in the same reference laboratory. Random effects mixed models were used to analyse changes over time in HCV RNA. A total of 312 ESPRIT patients were included in the study (151 in the arm receiving subcutaneous recombinant IL-2 and 161 in the control arm). Most of the patients were white (89%) and male (76%), and they had a median of 5 HCV RNA measurements per person [interquartile range (IQR) 3-6; range 1-9]. Median follow-up was 5 years (IQR: 2-6 years). At baseline, 96% of patients were taking cART and 93% had undetectable HIV RNA. Mean HCV RNA levels decreased by 13% per year over the study period [95% confidence interval (CI) 8-18%; P < 0.0001]. Baseline HCV RNA levels and the change over time in HCV RNA did not differ by randomization arm (P = 0.16 and P = 0.56, respectively). Nine individuals spontaneously cleared HCV RNA during follow-up [IL-28B genotypes: CC, five patients (56%); CT, four patients (44%)]. HCV RNA levels decreased over time in this population with well-controlled HIV infection. Spontaneous clearance of HCV RNA was documented in five individuals with IL-28B genotype CC and four with the CT genotype. © 2016 British HIV Association.
RRE-dependent HIV-1 Env RNA effects on Gag protein expression, assembly and release

International Nuclear Information System (INIS)

López, Claudia S.; Sloan, Rachel; Cylinder, Isabel; Kozak, Susan L.; Kabat, David; Barklis, Eric

2014-01-01

The HIV-1 Gag proteins are translated from the full-length HIV-1 viral RNA (vRNA), whereas the envelope (Env) protein is translated from incompletely spliced Env mRNAs. Nuclear export of vRNAs and Env mRNAs is mediated by the Rev accessory protein which binds to the rev-responsive element (RRE) present on these RNAs. Evidence has shown there is a direct or indirect interaction between the Gag protein, and the cytoplasmic tail (CT) of the Env protein. Our current work shows that env gene expression impacts HIV-1 Gag expression and function in two ways. At the protein level, full-length Env expression altered Gag protein expression, while Env CT-deletion proteins did not. At the RNA level, RRE-containing Env mRNA expression reduced Gag expression, processing, and virus particle release from cells. Our results support models in which Gag is influenced by the Env CT, and Env mRNAs compete with vRNAs for nuclear export. - Highlights: • At the protein level, full-length HIV-1 Env alters Gag protein expression. • HIV-1 Env RNA expression reduces Gag levels and virus release. • Env RNA effects on Gag are dependent on the RRE. • RRE-containing Env RNAs compete with vRNAs for nuclear export
Damaging the Integrated HIV Proviral DNA with TALENs.

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Christy L Strong

Full Text Available HIV-1 integrates its proviral DNA genome into the host genome, presenting barriers for virus eradication. Several new gene-editing technologies have emerged that could potentially be used to damage integrated proviral DNA. In this study, we use transcription activator-like effector nucleases (TALENs to target a highly conserved sequence in the transactivation response element (TAR of the HIV-1 proviral DNA. We demonstrated that TALENs cleave a DNA template with the HIV-1 proviral target site in vitro. A GFP reporter, under control of HIV-1 TAR, was efficiently inactivated by mutations introduced by transfection of TALEN plasmids. When infected cells containing the full-length integrated HIV-1 proviral DNA were transfected with TALENs, the TAR region accumulated indels. When one of these mutants was tested, the mutated HIV-1 proviral DNA was incapable of producing detectable Gag expression. TALEN variants engineered for degenerate recognition of select nucleotide positions also cleaved proviral DNA in vitro and the full-length integrated proviral DNA genome in living cells. These results suggest a possible design strategy for the therapeutic considerations of incomplete target sequence conservation and acquired resistance mutations. We have established a new strategy for damaging integrated HIV proviral DNA that may have future potential for HIV-1 proviral DNA eradication.
Cerebrospinal fluid HIV-1 RNA levels in asymptomatic patients with early stage chronic HIV-1 infection: support for the hypothesis of local virus replication.

Science.gov (United States)

García, F; Niebla, G; Romeu, J; Vidal, C; Plana, M; Ortega, M; Ruiz, L; Gallart, T; Clotet, B; Miró, J M; Pumarola, T; Gatell, J M

1999-08-20

To assess HIV-1 RNA levels in cerebrospinal fluid (CSF) and their potential correlation with plasma viral load and central nervous system (CNS) HIV-1 infection markers in stable asymptomatic patients with a CD4 T cell count >500x10(6) cells/l. Consecutive patients screened for two trials were eligible for lumbar puncture assessment. At day 0, simultaneous samples of CSF and plasma were obtained and levels of total proteins, albumin, IgG, antibodies against HIV-1 p24 antigen, HIV-1 RNA (using the polymerase chain technique) and white cells were measured. The integrity of the blood-brain barrier was preserved (albumin index > or =7) in 59 out of 70 patients (84%). Intrathecal production of antibodies against HIV-1 p24 antigen was demonstrated in 55 out of 70 individuals (78%). Viral load in CSF was significantly lower than plasma values (3.13+/-0.95 versus 4.53+/-0.53, P = 0.0001). HIV-1 RNA was not detected in CSF in only three of the 70 patients (4%). Overall, there was a significant correlation between plasma and CSF HIV-1 RNA levels (r = 0.43, P = 0.0001); however, in 29 patients (41%) there were significant differences (>1.5 log10 copies/ml) between the viral loads in plasma and CSF. In the multivariate analysis, a high level of protein and white cells in CSF, but not the HIV-1 RNA plasma level, were factors independently associated with a higher level of HIV-1 RNA in CSF (P = 0.0001). HIV-1 RNA can be detected almost always in CSF of asymptomatic patients in early stages of HIV-1 infection including those with a preserved integrity of the blood-brain barrier. The important discrepancies between plasma and CSF viral load, and the independent association between CSF abnormalities and CSF viral load, support the hypothesis of local production of HIV-1.
Promiscuous RNA binding ensures effective encapsidation of APOBEC3 proteins by HIV-1.

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Luis Apolonia

2015-01-01

Full Text Available The apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3 proteins are cell-encoded cytidine deaminases, some of which, such as APOBEC3G (A3G and APOBEC3F (A3F, act as potent human immunodeficiency virus type-1 (HIV-1 restriction factors. These proteins require packaging into HIV-1 particles to exert their antiviral activities, but the molecular mechanism by which this occurs is incompletely understood. The nucleocapsid (NC region of HIV-1 Gag is required for efficient incorporation of A3G and A3F, and the interaction between A3G and NC has previously been shown to be RNA-dependent. Here, we address this issue in detail by first determining which RNAs are able to bind to A3G and A3F in HV-1 infected cells, as well as in cell-free virions, using the unbiased individual-nucleotide resolution UV cross-linking and immunoprecipitation (iCLIP method. We show that A3G and A3F bind many different types of RNA, including HIV-1 RNA, cellular mRNAs and small non-coding RNAs such as the Y or 7SL RNAs. Interestingly, A3G/F incorporation is unaffected when the levels of packaged HIV-1 genomic RNA (gRNA and 7SL RNA are reduced, implying that these RNAs are not essential for efficient A3G/F packaging. Confirming earlier work, HIV-1 particles formed with Gag lacking the NC domain (Gag ΔNC fail to encapsidate A3G/F. Here, we exploit this system by demonstrating that the addition of an assortment of heterologous RNA-binding proteins and domains to Gag ΔNC efficiently restored A3G/F packaging, indicating that A3G and A3F have the ability to engage multiple RNAs to ensure viral encapsidation. We propose that the rather indiscriminate RNA binding characteristics of A3G and A3F promote functionality by enabling recruitment into a wide range of retroviral particles whose packaged RNA genomes comprise divergent sequences.
Coal tar in dermatology

Energy Technology Data Exchange (ETDEWEB)

Roelofzen, J.H.J.; Aben, K.K.H.; Van Der Valk, P.G.M.; Van Houtum, J.L.M.; Van De Kerkhof, P.C.M.; Kiemeney, L.A.L.M. [Radboud University Nijmegen Medical Center, Nijmegen (Netherlands). Dept. of Dermatology

2007-07-01

Coal tar is one of the oldest treatments for psoriasis and eczema. It has anti-inflammatory, antibacterial, antipruritic and antimitotic effects. The short-term side effects are folliculitis, irritation and contact allergy. Coal tar contains carcinogens. The carcinogenicity of coal tar has been shown in animal studies and studies in occupational settings. There is no clear evidence of an increased risk of skin tumors or internal tumors. Until now, most studies have been fairly small and they did not investigate the risk of coal tar alone, but the risk of coal tar combined with other therapies. New, well-designed, epidemiological studies are necessary to assess the risk of skin tumors and other malignancies after dermatological use of coal tar.

Cis elements and trans-acting factors involved in the RNA dimerization of the human immunodeficiency virus HIV-1.

Science.gov (United States)

Darlix, J L; Gabus, C; Nugeyre, M T; Clavel, F; Barré-Sinoussi, F

1990-12-05

The retroviral genome consists of two identical RNA molecules joined at their 5' ends by the Dimer Linkage Structure (DLS). To study the mechanism of dimerization and the DLS of HIV-1 RNA, large amounts of bona fide HIV-1 RNA and of mutants have been synthesized in vitro. We report that HIV-1 RNA forms dimeric molecules and that viral nucleocapsid (NC) protein NCp15 greatly activates dimerization. Deletion mutagenesis in the RNA 5' 1333 nucleotides indicated that a small domain of 100 nucleotides, located between positions 311 to 415 from the 5' end, is necessary and sufficient to promote HIV-1 RNA dimerization. This dimerization domain encompasses an encapsidation element located between the 5' splice donor site and initiator AUG of gag and shows little sequence variations in different strains of HIV-1. Furthermore, cross-linking analysis of the interactions between NC and HIV-1 RNA (311 to 415) locates a major contact site in the encapsidation element of HIV-1 RNA. The genomic RNA dimer is tightly associated with nucleocapsid protein molecules in avian and murine retroviruses, and this ribonucleoprotein structure is believed to be the template for reverse transcription. Genomic RNA-protein interactions have been analyzed in human immunodeficiency virus (HIV) virions and results showed that NC protein molecules are tightly bound to the genomic RNA dimer. Since retroviral RNA dimerization and packaging appear to be under the control of the same cis element, the encapsidation sequences, and trans-acting factor, the NC protein, they are probably related events in the course of virion assembly.
Expression of Herpes Simplex Virus Thymidine Kinase/Ganciclovir by RNA Trans-Splicing Induces Selective Killing of HIV-Producing Cells

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Carin K. Ingemarsdotter

2017-06-01

Full Text Available Antiviral strategies targeting hijacked cellular processes are less easily evaded by the virus than viral targets. If selective for viral functions, they can have a high therapeutic index. We used RNA trans-splicing to deliver the herpes simplex virus thymidine kinase-ganciclovir (HSV-tk/GCV cell suicide system into HIV-producing cells. Using an extensive in silico bioinformatics and RNA structural analysis approach, ten HIV RNA trans-splicing constructs were designed targeting eight different HIV splice donor or acceptor sites and were tested in cells expressing HIV. Trans-spliced mRNAs were identified in HIV-expressing cells using qRT-PCR with successful detection of fusion RNA transcripts between HIV RNA and the HSV-tk RNA transcripts from six of ten candidate RNA trans-splicing constructs. Conventional PCR and Sanger sequencing confirmed RNA trans-splicing junctions. Measuring cell viability in the presence or absence of GCV expression of HSV-tk by RNA trans-splicing led to selective killing of HIV-producing cells using either 3′ exon replacement or 5′ exon replacement in the presence of GCV. Five constructs targeting four HIV splice donor and acceptor sites, D4, A5, A7, and A8, involved in regulating the generation of multiple HIV RNA transcripts proved to be effective for trans-splicing mediated selective killing of HIV-infected cells, within which individual constructs targeting D4 and A8 were the most efficient.
HIV-1 matrix dependent membrane targeting is regulated by Gag mRNA trafficking.

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Jing Jin

Full Text Available Retroviral Gag polyproteins are necessary and sufficient for virus budding. Productive HIV-1 Gag assembly takes place at the plasma membrane. However, little is known about the mechanisms by which thousands of Gag molecules are targeted to the plasma membrane. Using a bimolecular fluorescence complementation (BiFC assay, we recently reported that the cellular sites and efficiency of HIV-1 Gag assembly depend on the precise pathway of Gag mRNA export from the nucleus, known to be mediated by Rev. Here we describe an assembly deficiency in human cells for HIV Gag whose expression depends on hepatitis B virus (HBV post-transcriptional regulatory element (PRE mediated-mRNA nuclear export. PRE-dependent HIV Gag expressed well in human cells, but assembled with slower kinetics, accumulated intracellularly, and failed to associate with a lipid raft compartment where the wild-type Rev-dependent HIV-1 Gag efficiently assembles. Surprisingly, assembly and budding of PRE-dependent HIV Gag in human cells could be rescued in trans by co-expression of Rev-dependent Gag that provides correct membrane targeting signals, or in cis by replacing HIV matrix (MA with other membrane targeting domains. Taken together, our results demonstrate deficient membrane targeting of PRE-dependent HIV-1 Gag and suggest that HIV MA function is regulated by the trafficking pathway of the encoding mRNA.
Relationship between hunger, adherence to antiretroviral therapy and plasma HIV RNA suppression among HIV-positive illicit drug users in a Canadian setting.

Science.gov (United States)

Anema, Aranka; Kerr, Thomas; Milloy, M-J; Feng, Cindy; Montaner, Julio S G; Wood, Evan

2014-04-01

Food insecurity may be a barrier to achieving optimal HIV treatment-related outcomes among illicit drug users. This study therefore, aimed to assess the impact of severe food insecurity, or hunger, on plasma HIV RNA suppression among illicit drug users receiving antiretroviral therapy (ART). A cross-sectional Multivariate logistic regression model was used to assess the potential relationship between hunger and plasma HIV RNA suppression. A sample of n = 406 adults was derived from a community-recruited open prospective cohort of HIV-positive illicit drug users, in Vancouver, British Columbia (BC), Canada. A total of 235 (63.7%) reported "being hungry and unable to afford enough food," and 241 (59.4%) had plasma HIV RNA hunger was associated with lower odds of plasma HIV RNA suppression (Odds Ratio = 0.59, 95% confidence interval [CI]: 0.39-0.90, p = 0.015). In multivariate analyses, this association was no longer significant after controlling for socio-demographic, behavioral, and clinical characteristics, including 95% adherence (Adjusted Odds Ratio [AOR] = 0.65, 95% CI: 0.37-1.10, p = 0.105). Multivariate models stratified by 95% adherence found that the direction and magnitude of this association was not significantly altered by the adherence level. Hunger was common among illicit drug users in this setting. Although, there was an association between hunger and lower likelihood of plasma HIV RNA suppression, this did not persist in adjusted analyses. Further research is warranted to understand the social-structural, policy, and physical factors shaping the HIV outcomes of illicit drug users.
Deciphering the role of the Gag-Pol ribosomal frameshift signal in HIV-1 RNA genome packaging.

Science.gov (United States)

Nikolaitchik, Olga A; Hu, Wei-Shau

2014-04-01

A key step of retroviral replication is packaging of the viral RNA genome during virus assembly. Specific packaging is mediated by interactions between the viral protein Gag and elements in the viral RNA genome. In HIV-1, similar to most retroviruses, the packaging signal is located within the 5' untranslated region and extends into the gag-coding region. A recent study reported that a region including the Gag-Pol ribosomal frameshift signal plays an important role in HIV-1 RNA packaging; deletions or mutations that affect the RNA structure of this signal lead to drastic decreases (10- to 50-fold) in viral RNA packaging and virus titer. We examined here the role of the ribosomal frameshift signal in HIV-1 RNA packaging by studying the RNA packaging and virus titer in the context of proviruses. Three mutants with altered ribosomal frameshift signal, either through direct deletion of the signal, mutation of the 6U slippery sequence, or alterations of the secondary structure were examined. We found that RNAs from all three mutants were packaged efficiently, and they generate titers similar to that of a virus containing the wild-type ribosomal frameshift signal. We conclude that although the ribosomal frameshift signal plays an important role in regulating the replication cycle, this RNA element is not directly involved in regulating RNA encapsidation. To generate infectious viruses, HIV-1 must package viral RNA genome during virus assembly. The specific HIV-1 genome packaging is mediated by interactions between the structural protein Gag and elements near the 5' end of the viral RNA known as packaging signal. In this study, we examined whether the Gag-Pol ribosomal frameshift signal is important for HIV-1 RNA packaging as recently reported. Our results demonstrated that when Gag/Gag-Pol is supplied in trans, none of the tested ribosomal frameshift signal mutants has defects in RNA packaging or virus titer. These studies provide important information on how HIV-1
Treatment of lignite tars, etc

Energy Technology Data Exchange (ETDEWEB)

1936-08-07

A process is described for treating tars such as lignite tar, shale tar, or peat tar, and similar tars, characterized by the fact that the tar is rectified to about 240/sup 0/C and the residue brought to a temperature above 50/sup 0/C after diluting with a product of the type of gasoline or ligroin at about 30/sup 0/C and treated with selective solvents preferably low-boiling phenols and eventually with water.
Fast prediction of RNA-RNA interaction using heuristic algorithm.

Science.gov (United States)

Montaseri, Soheila

2015-01-01

Interaction between two RNA molecules plays a crucial role in many medical and biological processes such as gene expression regulation. In this process, an RNA molecule prohibits the translation of another RNA molecule by establishing stable interactions with it. Some algorithms have been formed to predict the structure of the RNA-RNA interaction. High computational time is a common challenge in most of the presented algorithms. In this context, a heuristic method is introduced to accurately predict the interaction between two RNAs based on minimum free energy (MFE). This algorithm uses a few dot matrices for finding the secondary structure of each RNA and binding sites between two RNAs. Furthermore, a parallel version of this method is presented. We describe the algorithm's concurrency and parallelism for a multicore chip. The proposed algorithm has been performed on some datasets including CopA-CopT, R1inv-R2inv, Tar-Tar*, DIS-DIS, and IncRNA54-RepZ in Escherichia coli bacteria. The method has high validity and efficiency, and it is run in low computational time in comparison to other approaches.
Indian coal tars. II

Energy Technology Data Exchange (ETDEWEB)

Basu, A N; Bhatnagar, J N; Roy, A K

1954-01-01

Laboratory experiments were carried out on these efforts: (1) rank and specific-gravity fractions on tar yield; (2) addition of water to the coal charge, or steam during carbonization, on yield of tar and tar acids; (3) the presence of a cracking agent (shale) with and without steam addition on the yield of tar and tar acids (the particular shale used without steam reduced the yield, and the restricted use of steam brought the yield to the former noncatalyzed level); and (4) catalytic effect of three different samples of shale, firebrick, quartz, coke, and silica-alumina on the cracking of tar acids (the most active were two of the shales, a freshly-prepared coke, and the Al/sub 2/O/sub 3/-SiO/sub 2/ catalysts that gave conversion up to 98%). The products were mainly carbon, aromatic hydrocarbons of the naphthalene series and gases (CO and H/sub 2/). The yield of the tar becomes less as coal of lower specific gravity is used or when higher temperatures are used for carbonization. The mineral matter associated with Indian coals acts as a decomposition catalyst for tar acids, as shown by experiments on the decomposition of PhOH at temperatures above 800/sup 0/.
Tar bases in low-temperature coal tar

Energy Technology Data Exchange (ETDEWEB)

Sugiura, S; Ueno, H; Yokoyama, H

1951-01-01

Tar bases were extracted from three fractions, that boil below 260/sup 0/ at 260/sup 0/ to 280/sup 0/, and 280/sup 0/ to 330/sup 0/, respectively, of the low-temperature tar obtained by the carbonization of Ube coal in a Koppers' vertical retort at approximately 750/sup 0/. These were divided, respectively, into three groups, acetate-forming amine, HCl salt-forming bases (I), and CHCl/sub 3/-soluble bases (II), and further fractionally distilled. From the physical and chemical properties of the fractions thus obtained, it was concluded that low-temperature coal tar contained no low boiling pyridine homologues and that, besides higher homologues of pyridine, nonaromatic, more saturated, and less basic compounds of larger atomic weight and smaller refractive index, such as derivatives of pyrrole and indole, also existed as in crude petroleum.
Human Immunodeficiency Virus-Type 1 LTR DNA contains an intrinsic gene producing antisense RNA and protein products

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Hsiao Chiu-Bin

2006-11-01

Full Text Available Abstract Background While viruses have long been shown to capitalize on their limited genomic size by utilizing both strands of DNA or complementary DNA/RNA intermediates to code for viral proteins, it has been assumed that human retroviruses have all their major proteins translated only from the plus or sense strand of RNA, despite their requirement for a dsDNA proviral intermediate. Several studies, however, have suggested the presence of antisense transcription for both HIV-1 and HTLV-1. More recently an antisense transcript responsible for the HTLV-1 bZIP factor (HBZ protein has been described. In this study we investigated the possibility of an antisense gene contained within the human immunodeficiency virus type 1 (HIV-1 long terminal repeat (LTR. Results Inspection of published sequences revealed a potential transcription initiator element (INR situated downstream of, and in reverse orientation to, the usual HIV-1 promoter and transcription start site. This antisense initiator (HIVaINR suggested the possibility of an antisense gene responsible for RNA and protein production. We show that antisense transcripts are generated, in vitro and in vivo, originating from the TAR DNA of the HIV-1 LTR. To test the possibility that protein(s could be translated from this novel HIV-1 antisense RNA, recombinant HIV antisense gene-FLAG vectors were designed. Recombinant protein(s were produced and isolated utilizing carboxy-terminal FLAG epitope (DYKDDDDK sequences. In addition, affinity-purified antisera to an internal peptide derived from the HIV antisense protein (HAP sequences identified HAPs from HIV+ human peripheral blood lymphocytes. Conclusion HIV-1 contains an antisense gene in the U3-R regions of the LTR responsible for both an antisense RNA transcript and proteins. This antisense transcript has tremendous potential for intrinsic RNA regulation because of its overlap with the beginning of all HIV-1 sense RNA transcripts by 25 nucleotides. The
Seminal Plasma HIV-1 RNA Concentration Is Strongly Associated with Altered Levels of Seminal Plasma Interferon-γ, Interleukin-17, and Interleukin-5

Science.gov (United States)

Hoffman, Jennifer C.; Anton, Peter A.; Baldwin, Gayle Cocita; Elliott, Julie; Anisman-Posner, Deborah; Tanner, Karen; Grogan, Tristan; Elashoff, David; Sugar, Catherine; Yang, Otto O.

2014-01-01

Abstract Seminal plasma HIV-1 RNA level is an important determinant of the risk of HIV-1 sexual transmission. We investigated potential associations between seminal plasma cytokine levels and viral concentration in the seminal plasma of HIV-1-infected men. This was a prospective, observational study of paired blood and semen samples from 18 HIV-1 chronically infected men off antiretroviral therapy. HIV-1 RNA levels and cytokine levels in seminal plasma and blood plasma were measured and analyzed using simple linear regressions to screen for associations between cytokines and seminal plasma HIV-1 levels. Forward stepwise regression was performed to construct the final multivariate model. The median HIV-1 RNA concentrations were 4.42 log10 copies/ml (IQR 2.98, 4.70) and 2.96 log10 copies/ml (IQR 2, 4.18) in blood and seminal plasma, respectively. In stepwise multivariate linear regression analysis, blood HIV-1 RNA level (pplasma HIV-1 RNA level. After controlling for blood HIV-1 RNA level, seminal plasma HIV-1 RNA level was positively associated with interferon (IFN)-γ (p=0.03) and interleukin (IL)-17 (p=0.03) and negatively associated with IL-5 (p=0.0007) in seminal plasma. In addition to blood HIV-1 RNA level, cytokine profiles in the male genital tract are associated with HIV-1 RNA levels in semen. The Th1 and Th17 cytokines IFN-γ and IL-17 are associated with increased seminal plasma HIV-1 RNA, while the Th2 cytokine IL-5 is associated with decreased seminal plasma HIV-1 RNA. These results support the importance of genital tract immunomodulation in HIV-1 transmission. PMID:25209674
A Conserved Target Site in HIV-1 Gag RNA is Accessible to Inhibition by Both an HDV Ribozyme and a Short Hairpin RNA

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Robert J Scarborough

2014-01-01

Full Text Available Antisense-based molecules targeting HIV-1 RNA have the potential to be used as part of gene or drug therapy to treat HIV-1 infection. In this study, HIV-1 RNA was screened to identify more conserved and accessible target sites for ribozymes based on the hepatitis delta virus motif. Using a quantitative screen for effects on HIV-1 production, we identified a ribozyme targeting a highly conserved site in the Gag coding sequence with improved inhibitory potential compared to our previously described candidates targeting the overlapping Tat/Rev coding sequence. We also demonstrate that this target site is highly accessible to short hairpin directed RNA interference, suggesting that it may be available for the binding of antisense RNAs with different modes of action. We provide evidence that this target site is structurally conserved in diverse viral strains and that it is sufficiently different from the human transcriptome to limit off-target effects from antisense therapies. We also show that the modified hepatitis delta virus ribozyme is more sensitive to a mismatch in its target site compared to the short hairpin RNA. Overall, our results validate the potential of a new target site in HIV-1 RNA to be used for the development of antisense therapies.
Co-occurrence of Trichomonas vaginalis and bacterial vaginosis and vaginal shedding of HIV-1 RNA.

Science.gov (United States)

Fastring, Danielle R; Amedee, Angela; Gatski, Megan; Clark, Rebecca A; Mena, Leandro A; Levison, Judy; Schmidt, Norine; Rice, Janet; Gustat, Jeanette; Kissinger, Patricia

2014-03-01

Trichomonas vaginalis (TV) and bacterial vaginosis (BV) are independently associated with increased risk of vaginal shedding in HIV-positive women. Because these 2 conditions commonly co-occur, this study was undertaken to examine the association between TV/BV co-occurrence and vaginal shedding of HIV-1 RNA. HIV-positive women attending outpatient HIV clinics in 3 urban US cities underwent a clinical examination; were screened for TV, BV, Neisseria gonorrhoeae, Chlamydia trachomatis, and vulvovaginal candidiasis; and completed a behavioral survey. Women shedding HIV-1 RNA vaginally (≥50 copies/mL) were compared with women who had an undetectable (women who were TV positive and BV positive or had co-occurrence of TV/BV had higher odds of shedding vaginally when compared with women who did not have these conditions. In this sample of 373 HIV-positive women, 43.1% (n = 161) had co-occurrence of TV/BV and 33.2% (n = 124) were shedding HIV-1 RNA vaginally. The odds of shedding HIV vaginally in the presence of TV alone or BV alone and when TV/BV co-occurred were 4.07 (95% confidence interval [CI], 1.78-9.37), 5.65 (95% CI, 2.64-12.01), and 18.63 (95% CI, 6.71-51.72), respectively, when compared with women with no diagnosis of TV or BV, and after adjusting for age, antiretroviral therapy status, and plasma viral load. T. vaginalis and BV were independently and synergistically related to vaginal shedding of HIV-1 RNA. Screening and prompt treatment of these 2 conditions among HIV-positive women are important not only clinically but for HIV prevention, as well.
Cervical Shedding of HIV-1 RNA Among Women With Low Levels of Viremia While Receiving Highly Active Antiretroviral Therapy

Science.gov (United States)

Neely, Michael N.; Benning, Lorie; Xu, Jiaao; Strickler, Howard D.; Greenblatt, Ruth M.; Minkoff, Howard; Young, Mary; Bremer, James; Levine, Alexandra M.; Kovacs, Andrea

2011-01-01

Background Among women with low o r undetectable quantities of HIV-1 RNA in plasma, factors associated with genital HIV-1 RNA shedding, including choice of treatment regimen, are poorly characterized. Methods We measured HIV-1 RNA in cervical swab specimens obtained from participants in the Women’s Interagency HIV Study who had concurrent plasma viral RNA levels <500 copies/mL, and we assessed factors associated with genital HIV shedding. The study was powered to determine the relative effects of antiretroviral protease inhibitors (PIs) versus nonnucleoside reverse transcriptase inhibitors (NNRTIs) on viral RNA shedding. Results Overall, 44 (15%) of 290 women had detectable HIV-1 RNA in cervical specimens. In the final multivariate model, shedding was independently associated with NNRTI (vs. PI) use (odds ratio [OR], 95% confidence interval [CI]: 2.24, 1.13 to 4.45) and illicit drug use (OR, 95% CI: 2.41, 0.96 to 5.69). Conclusions This is the largest study to define risks for genital HIV-1 RNA shedding in women with low/undetectable plasma virus. Shedding in this population was common, and NNRTI-based highly active antiretroviral therapy (HAART) (vs. PI-based HAART) was associated with genital HIV shedding. Further study is required to determine the impact of these findings on transmission of HIV from mother to child or to sexual partners. PMID:17106279
Process of treating tars

Energy Technology Data Exchange (ETDEWEB)

Hansen, C; Hempel, H; Weissenburger, H

1955-05-05

A process is described for treating tars or tar oils, especially carbonization tars, characterized in that the tars or tar oils are mixed with benzene or light oils which contain no aromatic material or only slight amounts, or with gas oil in such amounts that the asphalt precipitates, and after separation of the precipitated material the mixture is treated with caustic solution for separation of the phenols, and after separation of the phenolate liquor the mixture is subjected to heating for removal of the dilution medium, then the remaining oil can be used as heating oil or it is submitted to distillation for the purpose of recovering a fuel suitable for diesel motors, while the phenolate liquor is worked up into phenols.
Cold Preparation of Heroin in a Black Tar Market.

Science.gov (United States)

Roth, Alexis M; Armenta, Richard F; Wagner, Karla D; Strathdee, Steffanie A; Goldshear, Jesse L; Cuevas-Mota, Jazmine; Garfein, Richard S

2017-07-29

Black tar heroin is typically prepared for injection with heat which decreases the risk of HIV transmission by inactivating the virus. We received reports that persons who inject drugs (PWID) in Tijuana, Baja California, Mexico, a black tar heroin market, were using only water to dissolve heroin. Because Tijuana abuts San Diego County, CA, United States, we undertook the present analyses to determine the prevalence of this practice among PWID in San Diego, California. PWID completed quarterly behavioral assessments and serological testing for blood-borne viruses. Bivariate and multivariable logistic regression models were constructed to assess for individual, social, and structural correlates of preparing heroin without heat within the preceding 6 months. Nearly half of black tar heroin users (149/305) reported they had prepared heroin without heat within 6 months. In multivariable analysis, cold preparation was independently associated with younger age (10 year decrease; AOR = 1.25; 95% CI 1.03, 1.53), more drug injecting acquaintances (per 5 acquaintance increase; AOR = 1.05; 95% CI 1.01, 1.09) and prefilled syringe use (injecting drugs from syringes that are already filled with drugs before purchase; AOR = 1.86; 95% CI 1.14, 3.02). Conclusions/Importance: To our knowledge, this is the first paper to report that PWID living in a black tar heroin market are preparing heroin without heat. Additional research is needed to determine whether this is an endemic practice or PWID are engaging in new forms of drug preparation in response to changes in the environment.
Nuclear retention of multiply spliced HIV-1 RNA in resting CD4+ T cells.

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Kara G Lassen

2006-07-01

Full Text Available HIV-1 latency in resting CD4+ T cells represents a major barrier to virus eradication in patients on highly active antiretroviral therapy (HAART. We describe here a novel post-transcriptional block in HIV-1 gene expression in resting CD4+ T cells from patients on HAART. This block involves the aberrant localization of multiply spliced (MS HIV-1 RNAs encoding the critical positive regulators Tat and Rev. Although these RNAs had no previously described export defect, we show that they exhibit strict nuclear localization in resting CD4+ T cells from patients on HAART. Overexpression of the transcriptional activator Tat from non-HIV vectors allowed virus production in these cells. Thus, the nuclear retention of MS HIV-1 RNA interrupts a positive feedback loop and contributes to the non-productive nature of infection of resting CD4+ T cells. To define the mechanism of nuclear retention, proteomic analysis was used to identify proteins that bind MS HIV-1 RNA. Polypyrimidine tract binding protein (PTB was identified as an HIV-1 RNA-binding protein differentially expressed in resting and activated CD4+ T cells. Overexpression of PTB in resting CD4+ T cells from patients on HAART allowed cytoplasmic accumulation of HIV-1 RNAs. PTB overexpression also induced virus production by resting CD4+ T cells. Virus culture experiments showed that overexpression of PTB in resting CD4+ T cells from patients on HAART allowed release of replication-competent virus, while preserving a resting cellular phenotype. Whether through effects on RNA export or another mechanism, the ability of PTB to reverse latency without inducing cellular activation is a result with therapeutic implications.
Maternal characteristics during pregnancy and risk factors for positive HIV RNA at delivery: a single-cohort observational study (Brescia, Northern Italy

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Magoni Michele

2011-02-01

Full Text Available Abstract Background Detectable HIV RNA in mothers at delivery is an important risk factor for HIV transmission to newborns. Our hypothesis was that, in migrant women, the risk of detectable HIV RNA at delivery is greater owing to late HIV diagnosis. Therefore, we examined pregnant women by regional provenance and measured variables that could be associated with detectable HIV RNA at delivery. Methods A observational retrospective study was conducted from January 1999 to May 2008. Univariate and multivariable regression analyses (generalized linear models were used, with detectable HIV RNA at delivery as dependent variable. Results The overall population comprised 154 women (46.8% migrants. Presentation was later in migrant women than Italians, as assessed by CD4-T-cell count at first contact (mean 417/mm3 versus 545/mm3, respectively; p = 0.003. Likewise, HIV diagnosis was made before pregnancy and HAART was already prescribed at the time of pregnancy in more Italians (91% and 75%, respectively than migrants (61% and 42.8%, respectively. A subgroup of women with available HIV RNA close to term (i.e., ≤30 days before labour was studied for risk factors of detectable HIV RNA (≥50 copies/ml at delivery. Among 93 women, 25 (26.9% had detectable HIV RNA. A trend toward an association between non-Italian nationality and detectable HIV RNA at delivery was demonstrated by univariate analysis (relative risk, RR = 1.86; p = 0.099. However, by multivariable regression analysis, the following factors appeared to be more important: lack of stable (i.e., ≥14 days antiretroviral therapy at the time of HIV RNA testing (RR = 4.3; p 3, RR = 0.94; p = 0.038. Conclusions These results reinforce the importance of extensive screening for HIV infection, earlier initiation of antiretroviral therapy and stricter monitoring of pregnant women to reduce the risk of detectable HIV RNA at delivery. Public health interventions should be particularly targeted to migrant
Dried blood spot HIV-1 RNA quantification using open real-time systems in South Africa and Burkina Faso.

Science.gov (United States)

Viljoen, Johannes; Gampini, Sandrine; Danaviah, Sivapragashini; Valéa, Diane; Pillay, Sureshnee; Kania, Dramane; Méda, Nicolas; Newell, Marie-Louise; Van de Perre, Philippe; Rouet, François

2010-11-01

There is an urgent need to assess the accuracy/feasibility of using dried blood spots (DBS) for monitoring of HIV-1 viral load in resource-limited settings. A total of 892 DBS from HIV-1-positive pregnant women and their neonates enrolled in the Kesho Bora prevention of mother-to-child transmission trial conducted in Durban (South Africa) and Bobo-Dioulasso (Burkina Faso) between May 2005 and July 2008 were tested for HIV-1 RNA. The combination Nuclisens extraction method (BioMérieux)/Generic HIV Viral Load assay (Biocentric) was performed using one DBS (in Durban) versus 2 DBS (in Bobo-Dioulasso) on 2 distinct open real-time polymerase chain reaction instruments. DBS HIV-1 RNA results were compared with plasma HIV-1 RNA and HIV serology results used as the gold standards. The limits of detection of assays on DBS were 3100 and 1550 copies per milliliter in Durban and Bobo-Dioulasso, respectively. DBS HIV-1 RNA values correlated significantly with plasma levels (n = 327; R = 0.7351) and were uniformly distributed according to duration of DBS storage at -20°C (median duration, 280 days). For early infant diagnosis, the sensitivity and specificity were 100% (95% confidence interval: 97.2 to 100.0 and 96.5 to 100.0, respectively). HIV-1 viral load kinetics in DNase-pretreated DBS were similar to those obtained in plasma specimens among 13 patients receiving antiretroviral treatment. HIV-1 RNA findings from serial infant DBS collected prospectively (n = 164) showed 100% concordance with HIV serology at 18 months of life. Our findings strongly advocate the implementation of DBS HIV-1 RNA testing in remote areas from low-income and middle-income countries.
Topical tar: Back to the future

Energy Technology Data Exchange (ETDEWEB)

Paghdal, K.V.; Schwartz, R.A. [University of Medicine & Dentistry of New Jersey, Newark, NJ (United States)

2009-08-15

The use of medicinal tar for dermatologic disorders dates back to the ancient times. Although coal tar is utilized more frequently in modern dermatology, wood tars have also been widely employed. Tar is used mainly in the treatment of chronic stable plaque psoriasis, scalp psoriasis, atopic dermatitis, and seborrheic dermatitis, either alone or in combination therapy with other medications, phototherapy, or both. Many modifications have been made to tar preparations to increase their acceptability, as some dislike its odor, messy application, and staining of clothing. One should consider a tried and true treatment with tar that has led to clearing of lesions and prolonged remission times. Occupational studies have demonstrated the carcinogenicity of tar; however, epidemiologic studies do not confirm similar outcomes when used topically. This article will review the pharmacology, formulations, efficacy, and adverse effects of crude coal tar and other tars in the treatment of selected dermatologic conditions.

Physician experience and rates of plasma HIV-1 RNA suppression among illicit drug users: an observational study

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Sangsari Sassan

2012-01-01

Full Text Available Abstract Background Despite the availability of antiretroviral therapy (ART, suboptimal treatment outcomes have been observed among HIV-seropositive illicit drug users. As there is an urgent need to improve responses to antiretroviral therapy among this population, we undertook this study to evaluate the role of physician experience on rates of plasma HIV-1 RNA suppression following initiation of ART. Methods Using data from a community-recruited cohort of HIV-positive illicit drug users, we used Cox proportional hazards regression to model the time to plasma viral HIV RNA Results Between May 1996 and December 2008, 267 individuals initiated ART among whom 227 (85% achieved a plasma HIV RNA Conclusions In this setting of universal HIV/AIDS care, illicit drug users with more experienced physicians exhibited faster rates of plasma viral load suppression. These findings argue for specialized services to help optimize HIV treatment outcomes among this population.
Cytoplasmic HIV-1 RNA is mainly transported by diffusion in the presence or absence of Gag protein

DEFF Research Database (Denmark)

Chen, Jianbo; Grunwald, David; Sardo, Luca

2014-01-01

. In this report, we visualized HIV-1 RNA and monitored its movement in the cytoplasm by using single-molecule tracking. We observed that most of the HIV-1 RNA molecules move in a nondirectional, random-walk manner, which does not require an intact cytoskeletal structure, and that the mean-squared distance...... traveled by the RNA increases linearly with time, indicative of diffusive movement. We also observed that a single HIV-1 RNA molecule can move at various speeds when traveling through the cytoplasm, indicating that its movement is strongly affected by the immediate environment. To examine the effect of Gag...
Removing tar information from cigarette packages may reduce South Korean smokers' misconceptions about low-tar cigarettes

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Hye-Jin Paek

2018-03-01

Full Text Available Background Many smokers still have misconceptions about “light” or “low tar” cigarettes. In South Korea, low-tar (< 3 mg cigarette sales have increased sharply from 1.8% in 2002 to 49.2% in 2015. Although government regulations forbid cigarette packages from displaying messages such as “mild,” “low-tar,” and “light,” numbers indicating tar amounts are still permitted. This study examines whether removing tar information from packaging altogether reduces people's misconceptions about low tar cigarettes. Methods An online experiment was conducted among 531 smokers who were randomly assigned to one of two conditions. In the “tar” condition, 271 participants were shown in random order three cigarette packages for three major brands (Esse, The One, Marlboro with different tar amounts. In the “no-tar” condition, 260 participants were shown the same packages without tar information. Next, participants evaluated which type of cigarette was mildest, least harmful, easier for nonsmokers to start smoking, and easier for smokers to quit. After descriptive statistics were checked, twelve sets of chi-square tests were performed. Results Average age of the participants was 26.22 (14 - 62 years; 53.5% were male. All 12 chi-square tests were statistically significant. Participants in the tar condition judged the lowest-tar cigarette to be mildest, least harmful, easier to start, and easier to quit. In the no-tar condition, for the Korean brands Esse and The One, most respondents evaluated all cigarette types to be the same only for harm, ease of starting, and ease of quitting; for Marlboro, judgments were the same as those in the tar condition except that “easier to quit” was judged to be the same across the three types. Conclusions Banning tar information from cigarette packages may help reduce smokers' misconceptions about low-tar cigarettes. People have inconsistent judgments about differently packaged cigarettes when tar
RNA glycosidase and other agents target Tat to inhibit HIV-1 transcription.

Science.gov (United States)

Harrich, David; Jin, Hongping

2018-03-20

The HIV-1 tat gene encodes a small 86-104 amino acid protein depending on the HIV-1 strain. Tat is essential for HIV-1 replication through interactions with numerous cellular transcription factors. The interaction between Tat and P-TEFb, which is a cellular protein complex composed of cyclin T1 and CDK9, delivers P-TEFb to the newly transcribed viral mRNAs where phosphorylation of RNA polymerase II by CDK9 leads to highly efficient mRNA transcription. It has long been recognized that Tat is a potential anti-HIV-1 target and possibly a viral Achilles' heel. However, specifically targeting Tat without affecting normal host cell functions has been challenging. Means to inactivate Tat have been reported that includes small compounds, transdominant negative Tat proteins, and by plant-derived antivirals. Investigations of these agents have reported encouraging outcomes that inform and may hopefully affect strategies for a functional HIV-1 cure. © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.
Distilling tar; distillation, destructive

Energy Technology Data Exchange (ETDEWEB)

Brash, P; Young, W

1866-09-17

The tarry residue, which separates on treating crude shale oil with sulfuric acid, is redistilled, in the manner described in Specification No. 1278, A.D. 1866, together with shale. Previous to the distillation, the acid is neutralized with lime, or may be separated by blowing steam into the tar and adding salt. The purified tar thus obtained is absorbed by ashes, or is mixed with lime or other alkaline matter, or the shale may be mixed with lime and distilled with the tar, which is allowed to flow over and through the shale during the process. The tar obtained in the purification of natural paraffin may be similarly utilized.
Comparison of droplet digital PCR and seminested real-time PCR for quantification of cell-associated HIV-1 RNA

NARCIS (Netherlands)

Kiselinova, Maja; Pasternak, Alexander O.; de Spiegelaere, Ward; Vogelaers, Dirk; Berkhout, Ben; Vandekerckhove, Linos

2014-01-01

Cell-associated (CA) HIV-1 RNA is considered a potential marker for assessment of viral reservoir dynamics and antiretroviral therapy (ART) response in HIV-infected patients. Recent studies employed sensitive seminested real-time quantitative (q)PCR to quantify CA HIV-1 RNA. Digital PCR has been
NF90 una proteína celular que se une a RNAds inhibe la transactivación del LTR del HIV-1 mediada por TAT

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Silvio Urcuqui Inchima

2001-04-01

Full Text Available
La transactivación del LTR de HIV-1 requiere la interacción de la proteína Tat ( trans-activation transcription con la estructura TAR ( trans-activation response, que se encuentra localizada en el extremo 5’ de todos los transcriptos virales. La interacción de la proteína Tat con TAR forma un precomplejo transcripcional indispensable para la eficiente transcripción del genoma viral.
La interacción de diferentes factores celulares (cdk9 y ciclina T, entre otros con el precomplejo Tat-TAR, constituye un complejo estable que facilita la fosforilación de la subunidad mayor de la RNA polimerasa II, asegurando una eficiente elongación de los transcriptos virales. No se han descripto proteínas capaces de regular negativamente la función de Tat con resultados nefastos para la replicación viral. También se ha descrito otro tipo de proteínas celulares con capacidad de interactuar con TAR. El ejemplo mejor caracterizado es la proteína-kinasa dependiente de RNA (PKR, se autofosforila y mediante fosforilación del factor eIF2, inhibe la síntesis de proteínas. Con el presente trabajo se
pretendió aislar y caracterizar otras proteínas celulares capaces de interactuar con la estructura TAR y estudiar su efecto en la función de Tat.
A prospective study of the effect of pregnancy on CD4 counts and plasma HIV-1 RNA concentrations of antiretroviral-naive HIV-1-infected women.

Science.gov (United States)

Heffron, Renee; Donnell, Deborah; Kiarie, James; Rees, Helen; Ngure, Kenneth; Mugo, Nelly; Were, Edwin; Celum, Connie; Baeten, Jared M

2014-02-01

In HIV-1-infected women, CD4 count declines occur during pregnancy, which has been attributed to hemodilution. However, for women who have not initiated antiretroviral therapy, it is unclear if CD4 declines are sustained beyond pregnancy and accompanied by increased viral levels, which could indicate an effect of pregnancy on accelerating HIV-1 disease progression. In a prospective study among 2269 HIV-1-infected antiretroviral therapy-naive women from 7 African countries, we examined the effect of pregnancy on HIV-1 disease progression. We used linear mixed models to compare CD4 counts and plasma HIV-1 RNA concentrations between pregnant, postpartum, and nonpregnant periods. Women contributed 3270 person-years of follow-up, during which time 476 women became pregnant. In adjusted analysis, CD4 counts were an average of 56 (95% confidence interval: 39 to 73) cells/mm lower during pregnant compared with nonpregnant periods and 70 (95% confidence interval: 53 to 88) cells/mm lower during pregnant compared with postpartum periods; these results were consistent when restricted to the subgroup of women who became pregnant. Plasma HIV-1 RNA concentrations were not different between pregnant and nonpregnant periods (P = 0.9) or pregnant and postpartum periods (P = 0.3). Neither CD4 counts nor plasma HIV-1 RNA levels were significantly different in postpartum compared with nonpregnant periods. CD4 count declines among HIV-1-infected women during pregnancy are temporary and not sustained in postpartum periods. Pregnancy does not have a short-term impact on plasma HIV-1 RNA concentrations.
Engineering and Validation of a Vector for Concomitant Expression of Rare Transfer RNA (tRNA and HIV-1 nef Genes in Escherichia coli.

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Siti Aisyah Mualif

Full Text Available Relative ease in handling and manipulation of Escherichia coli strains make them primary candidate to express proteins heterologously. Overexpression of heterologous genes that contain codons infrequently used by E. coli is related with difficulties such as mRNA instability, early termination of transcription and/or translation, deletions and/or misincorporation, and cell growth inhibition. These codon bias -associated problems are addressed by co-expressing ColE1-compatible, rare tRNA expressing helper plasmids. However, this approach has inadequacies, which we have addressed by engineering an expression vector that concomitantly expresses the heterologous protein of interest, and rare tRNA genes in E. coli. The expression vector contains three (argU, ileY, leuW rare tRNA genes and a useful multiple cloning site for easy in-frame cloning. To maintain the overall size of the parental plasmid vector, the rare tRNA genes replaced the non-essential DNA segments in the vector. The cloned gene is expressed under the control of T7 promoter and resulting recombinant protein has a C-terminal 6His tag for IMAC-mediated purification. We have evaluated the usefulness of this expression vector by expressing three HIV-1 genes namely HIV-1 p27 (nef, HIV-1 p24 (ca, and HIV-1 vif in NiCo21(DE3 E.coli and demonstrated the advantages of using expression vector that concomitantly expresses rare tRNA and heterologous genes.
Technology unlocks tar sands energy

Energy Technology Data Exchange (ETDEWEB)

Law, C

1967-09-25

Tar sand processing technology has been developed primarily in the categories of extraction techniques and in-situ processing. In October, a $235 million venture into tar sand processing will be inspected by visitors from many points on the globe. A synthetic crude of premium quality will be flowing through a 16-in. pipeline from the Tar Island plant site of Great Canadian Oil Sands to Edmonton. This processing plant uses an extractive mining technique. The tar sand pay zone in this area averages approximately 150 ft in thickness with a 50-ft overburden. It has been estimated that the tar sands cannot be exploited when the formation thickness is less than 100 ft and overburden exceeds the same amount. This indicates that extraction techniques can only be used to recover approximately 15% of the tar sand deposits. An in-situ recovery technique developed by Shell of Canada is discussed in detail. In essence it is selective hydraulic fracturing, followed by the injection of emulsifying chemicals and steam.
Single-Cell RNA-Seq Reveals Transcriptional Heterogeneity in Latent and Reactivated HIV-Infected Cells.

Science.gov (United States)

Golumbeanu, Monica; Cristinelli, Sara; Rato, Sylvie; Munoz, Miguel; Cavassini, Matthias; Beerenwinkel, Niko; Ciuffi, Angela

2018-04-24

Despite effective treatment, HIV can persist in latent reservoirs, which represent a major obstacle toward HIV eradication. Targeting and reactivating latent cells is challenging due to the heterogeneous nature of HIV-infected cells. Here, we used a primary model of HIV latency and single-cell RNA sequencing to characterize transcriptional heterogeneity during HIV latency and reactivation. Our analysis identified transcriptional programs leading to successful reactivation of HIV expression. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.
A prospective study of the effect of pregnancy on CD4 counts and plasma HIV-1 RNA concentrations of antiretroviral-naive HIV-1 infected women

Science.gov (United States)

Heffron, Renee; Donnell, Deborah; Kiarie, James; Rees, Helen; Ngure, Kenneth; Mugo, Nelly; Were, Edwin; Celum, Connie; Baeten, Jared M.

2014-01-01

Background In HIV-1 infected women, CD4 count declines occur during pregnancy, which has been attributed to hemodilution. However, for women who have not initiated antiretroviral therapy (ART), it is unclear if CD4 declines are sustained beyond pregnancy and accompanied by increased viral levels, which could indicate an effect of pregnancy on accelerating HIV-1 disease progression. Methods In a prospective study among 2269 HIV-1 infected ART-naïve women from 7 African countries, we examined the effect of pregnancy on HIV-1 disease progression. We used linear mixed models to compare CD4 counts and plasma HIV-1 RNA concentrations between pregnant, postpartum and non-pregnant periods. Results Women contributed 3270 person-years of follow-up, during which time 476 women became pregnant. In adjusted analysis, CD4 counts were an average of 56 (95% CI 39-73) cells/mm3 lower during pregnant compared to non-pregnant periods and 70 (95% CI 53-88) cells/mm3 lower during pregnant compared to postpartum periods; these results were consistent when restricted to the subgroup of women who became pregnant. Plasma HIV-1 RNA concentrations were not different between pregnant and non-pregnant periods (p=0.9) or pregnant and postpartum periods (p=0.3). Neither CD4 counts nor plasma HIV-1 RNA levels were significantly different in postpartum compared to non-pregnant periods. Conclusion CD4 count declines among HIV-1 infected women during pregnancy are temporary and not sustained in postpartum periods. Pregnancy does not have a short term impact on plasma HIV-1 RNA concentrations. PMID:24442226
Upgrading of hydropyrolysis coal tar by hydroprocessing

Energy Technology Data Exchange (ETDEWEB)

Haglund, R.; Otterstedt, J.E.; Sterte, J. (Chalmers Univ. of Tech., Goeteborg (Sweden). 1. Dept. of Engineering Chemistry)

1991-05-01

Upgrading of a hydropyrolysis coal tar by hydroprocessing was investigated using different process conditions. The response of the hydropyrolysis tar to hydroprocessing was compared to those of a conventional coal tar and two heavy oil fractions. At comparable conditions, the removal of heteroatoms from the hydropyrolysis tar was more effective than from the conventional tar and, in particular, than from the oil fractions. Using conditions typical for hydroprocessing of heavy oil fractions, the contents of N, O as well as S in the hydropyrolysis tar were reduced by more than 90%. Hydroprocessing also resulted in a considerable increase in the gasoline fraction of the tar. (orig.).
MicroRNA profile changes in human immunodeficiency virus type 1 (HIV-1 seropositive individuals

Directory of Open Access Journals (Sweden)

Smith Stephen M

2008-12-01

Full Text Available Abstract MicroRNAs (miRNAs play diverse roles in regulating cellular and developmental functions. We have profiled the miRNA expression in peripheral blood mononuclear cells from 36 HIV-1 seropositive individuals and 12 normal controls. The HIV-1-positive individuals were categorized operationally into four classes based on their CD4+ T-cell counts and their viral loads. We report that specific miRNA signatures can be observed for each of the four classes.
Distinct binding interactions of HIV-1 Gag to Psi and non-Psi RNAs: Implications for viral genomic RNA packaging

OpenAIRE

Webb, Joseph A.; Jones, Christopher P.; Parent, Leslie J.; Rouzina, Ioulia; Musier-Forsyth, Karin

2013-01-01

The mechanism underlying the selective packaging of genomic RNA into HIV-1 virions is not known. This paper provides important new biophysical insights into the nature of protein–RNA interactions responsible for HIV-1 genome packaging by quantifying the electrostatic and hydrophobic contributions to specific and nonspecific RNA.
Nuclear Factor 90, a cellular dsRNA binding protein inhibits the HIV Rev-export function

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St-Laurent Georges

2006-11-01

Full Text Available Abstract Background The HIV Rev protein is known to facilitate export of incompletely spliced and unspliced viral transcripts to the cytoplasm, a necessary step in virus life cycle. The Rev-mediated nucleo-cytoplasmic transport of nascent viral transcripts, dependents on interaction of Rev with the RRE RNA structural element present in the target RNAs. The C-terminal variant of dsRNA-binding nuclear protein 90 (NF90ctv has been shown to markedly attenuate viral replication in stably transduced HIV-1 target cell line. Here we examined a mechanism of interference of viral life cycle involving Rev-NF90ctv interaction. Results Since Rev:RRE complex formations depend on protein:RNA and protein:protein interactions, we investigated whether the expression of NF90ctv might interfere with Rev-mediated export of RRE-containing transcripts. When HeLa cells expressed both NF90ctv and Rev protein, we observed that NF90ctv inhibited the Rev-mediated RNA transport. In particular, three regions of NF90ctv protein are involved in blocking Rev function. Moreover, interaction of NF90ctv with the RRE RNA resulted in the expression of a reporter protein coding sequences linked to the RRE structure. Moreover, Rev influenced the subcellular localization of NF90ctv, and this process is leptomycin B sensitive. Conclusion The dsRNA binding protein, NF90ctv competes with HIV Rev function at two levels, by competitive protein:protein interaction involving Rev binding to specific domains of NF90ctv, as well as by its binding to the RRE-RNA structure. Our results are consistent with a model of Rev-mediated HIV-1 RNA export that envisions Rev-multimerization, a process interrupted by NF90ctv.
Decrease in Seminal HIV-1 RNA Load After Praziquantel Treatment of Urogenital Schistosomiasis Coinfection in HIV-Positive Men—An Observational Study

DEFF Research Database (Denmark)

Midzi, Nicholas; Mduluza, Takafira; Mudenge, Boniface

2017-01-01

BACKGROUND: Urogenital schistosomiasis due to Schistosoma hematobium infection is hypothesized to cause increased HIV-1 RNA shedding in semen in HIV co-infected men as result of chronic egg-induced inflammation in the prostate and the seminal vesicles. The effect of treatment with the antihelmint...... targeting praziquantel as a supplementary preventive measure of sexual transmission of HIV-1 in S. haematobium endemic areas in sub-Saharan Africa....
Combinatorial RNA-based gene therapy for the treatment of HIV/AIDS.

Science.gov (United States)

Chung, Janet; DiGiusto, David L; Rossi, John J

2013-03-01

HIV/AIDS continues to be a worldwide health problem and viral eradication has been an elusive goal. HIV+ patients are currently treated with combination antiretroviral therapy (cART) which is not curative. For many patients, cART is inaccessible, intolerable or unaffordable. Therefore, a new class of therapeutics for HIV is required to overcome these limitations. Cell and gene therapy for HIV has been proposed as a way to provide a functional cure for HIV in the form of a virus/infection resistant immune system. In this review, the authors describe the standard therapy for HIV/AIDS, its limitations, current areas of investigation and the potential of hematopoietic stem cells modified with anti-HIV RNAs as a means to affect a functional cure for HIV. Cell and gene therapy for HIV/AIDS is a promising alternative to antiviral drug therapy and may provide a functional cure. In order to show clinical benefit, multiple mechanisms of inhibition of HIV entry and lifecycle are likely to be required. Among the most promising antiviral strategies is the use of transgenic RNA molecules that provide protection from HIV infection. When these molecules are delivered as gene-modified hematopoietic stem and progenitor cells, long-term repopulation of the patient's immune system with gene-modified progeny has been observed.
Probing the HIV-1 genomic RNA trafficking pathway and dimerization by genetic recombination and single virion analyses.

Directory of Open Access Journals (Sweden)

Michael D Moore

2009-10-01

Full Text Available Once transcribed, the nascent full-length RNA of HIV-1 must travel to the appropriate host cell sites to be translated or to find a partner RNA for copackaging to form newly generated viruses. In this report, we sought to delineate the location where HIV-1 RNA initiates dimerization and the influence of the RNA transport pathway used by the virus on downstream events essential to viral replication. Using a cell-fusion-dependent recombination assay, we demonstrate that the two RNAs destined for copackaging into the same virion select each other mostly within the cytoplasm. Moreover, by manipulating the RNA export element in the viral genome, we show that the export pathway taken is important for the ability of RNA molecules derived from two viruses to interact and be copackaged. These results further illustrate that at the point of dimerization the two main cellular export pathways are partially distinct. Lastly, by providing Gag in trans, we have demonstrated that Gag is able to package RNA from either export pathway, irrespective of the transport pathway used by the gag mRNA. These findings provide unique insights into the process of RNA export in general, and more specifically, of HIV-1 genomic RNA trafficking.
Preparation of pure phenols from tars

Energy Technology Data Exchange (ETDEWEB)

Meyer, J

1933-02-07

A process is disclosed for the preparation of pure phenols from brown coal tar, shale tar, or primary tar, characterized in that the raw oil obtained from the tar is carefully fractionated, in a suitable way without or with a slight pressure decrease, or before the fractionation the raw oil is heated to free the prepared phenolate solution from impurities after successful oxidation by passing in steam at a temperature between 100 and 120/sup 0/C.

Analysis of tars produced in biomass gasification

Energy Technology Data Exchange (ETDEWEB)

Zhou, J.; Wang, Y.; Kinoshita, C.M. [Univ. of Hawaii, Honolulu, HI (United States)

1993-12-31

Parametric tests on tar formation, varying temperature, equivalence ratio, and residence time, are performed on a bench-scale, indirectly-heated fluidized bed gasifier. Prepared tar samples are analyzed in a gas chromatograph (GC) with a flame ionization detector, using a capillary column. Standards containing dominant tar species have been prepared for GC calibration. The identified peaks include single-ring hydrocarbons, such as benzene, to five-ring hydrocarbons, such as perylene; depending on the gasification conditions, the identified species represent about 70 to 90% (mass basis) of the tar constituents. Under all conditions tested, benzene and naphthalene were the most dominant species. Temperature and equivalence ratio have significant effect on tar yield and tar composition. Tar yield decreases with increasing temperature or equivalence ratio. The test results suggest that lower temperature favors the formation of more aromatic tar species with diversified substituent groups, while higher temperature favors the formation of fewer aromatic tar species without substituent groups. Higher temperature or equivalence ratio favors the formation of polyaromatic compounds. Oxygen-containing compounds exist in significant quantities only at temperature below 800{degrees}C and decrease with increasing temperature, equivalence ratio, or residence time.
Determination of phenol in tar

Energy Technology Data Exchange (ETDEWEB)

Dierichs, A; Heinichen, G

1955-01-01

During low-temperature carbonization of lignite, the phenols and other oxygenated compounds appear both in the aqueous-process liquor and in the tar. Measurements of these oxygenated components resulting from low-temperature carbonization may serve as a parameter for the classification of lignites. However, such measurements are complicated by the instability of the tar and the complex nature of some of the acidic substances. Difficulties with the previous methods of analysis are reviewed. The present method outlines separation of aqueous-process liquor from lignite tar in a Fischer retort, followed by determination of phenols and fatty acids in the tar phase. The jacketed tar receiver is washed with 300 milliliter xylol and treated with aqueous caustic washes. Neutral oils are separated from the aqueous alkali solution. It is then extracted with ether and finally acidified with HCl. Solids are filtered off, and phenols and fatty acids are separated by Na/sub 2/CO/sub 3/ solution.
High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states.

Directory of Open Access Journals (Sweden)

Kevin A Wilkinson

2008-04-01

Full Text Available Replication and pathogenesis of the human immunodeficiency virus (HIV is tightly linked to the structure of its RNA genome, but genome structure in infectious virions is poorly understood. We invent high-throughput SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension technology, which uses many of the same tools as DNA sequencing, to quantify RNA backbone flexibility at single-nucleotide resolution and from which robust structural information can be immediately derived. We analyze the structure of HIV-1 genomic RNA in four biologically instructive states, including the authentic viral genome inside native particles. Remarkably, given the large number of plausible local structures, the first 10% of the HIV-1 genome exists in a single, predominant conformation in all four states. We also discover that noncoding regions functioning in a regulatory role have significantly lower (p-value < 0.0001 SHAPE reactivities, and hence more structure, than do viral coding regions that function as the template for protein synthesis. By directly monitoring protein binding inside virions, we identify the RNA recognition motif for the viral nucleocapsid protein. Seven structurally homologous binding sites occur in a well-defined domain in the genome, consistent with a role in directing specific packaging of genomic RNA into nascent virions. In addition, we identify two distinct motifs that are targets for the duplex destabilizing activity of this same protein. The nucleocapsid protein destabilizes local HIV-1 RNA structure in ways likely to facilitate initial movement both of the retroviral reverse transcriptase from its tRNA primer and of the ribosome in coding regions. Each of the three nucleocapsid interaction motifs falls in a specific genome domain, indicating that local protein interactions can be organized by the long-range architecture of an RNA. High-throughput SHAPE reveals a comprehensive view of HIV-1 RNA genome structure, and further
Associations between HIV-RNA-based indicators and virological and clinical outcomes

DEFF Research Database (Denmark)

Laut, Kamilla G; Shepherd, Leah C; Pedersen, Court

2016-01-01

OBJECTIVES: To evaluate and compare the performance of six HIV-RNA-based quality of care indicators for predicting short-term and long-term outcomes. DESIGN: Multinational cohort study. METHODS: We included EuroSIDA patients on antiretroviral therapy (ART) with at least three viral load measureme......OBJECTIVES: To evaluate and compare the performance of six HIV-RNA-based quality of care indicators for predicting short-term and long-term outcomes. DESIGN: Multinational cohort study. METHODS: We included EuroSIDA patients on antiretroviral therapy (ART) with at least three viral load...... measurements after baseline (the latest of 01/01/2001 or entry into EuroSIDA). Using multivariate Poisson regression, we modelled the association between short-term (resistance, triple-class failure) and long-term (all-cause mortality, any AIDS/non-AIDS clinical event) outcomes and the indicators: viraemia...
Hydroconversion of coal tars: effect of the temperature of pyrolysis on the reactivity of tars

Energy Technology Data Exchange (ETDEWEB)

Lemberton, J.L.; Touzeyidio, M.; Guisnet, M.

1988-12-01

The hydroconversion of a low-temperature and of a high-temperature tar was carried out in the presence of a sulfided Ni and Mo on alumina catalyst - pure or mixed with an acid catalyst (HY zeolite). Significant amounts of light products can be obtained from low temperature tar, formed however through a non-catalytic process. On the contrary, there is a slight catalytic effect during the hydroprocessing of high temperature tar, but the yield in light products is very low. These results can be explained by an extensive poisoning of the NiMo on alumina catalyst by coke which is initiated by the O- and N-containing compounds of the tars. 10 refs., 1 fig., 3 tabs.
Undetectable hepatitis C virus RNA during syphilis infection in two HIV/HCV-co-infected patients

DEFF Research Database (Denmark)

Salado-Rasmussen, Kirsten; Knudsen, Andreas; Krarup, Henrik Bygum

2014-01-01

BACKGROUND: Treponema pallidum, the causative agent of syphilis, elicits a vigorous immune response in the infected host. This study sought to describe the impact of syphilis infection on hepatitis C virus (HCV) RNA levels in patients with HIV and chronic HCV infection. METHODS: Patients......-α), interferon gamma (IFN-γ), and IFN-γ-inducible protein 10 kDa (IP-10). RESULTS: Undetectable HCV RNA at the time of early latent syphilis infection was observed in 2 patients with HIV and chronic HCV infection. After treatment of the syphilis infection, HCV RNA levels increased again in patient 1, whereas...... patient 2 initiated HCV therapy and remained HCV RNA-negative. Available plasma samples obtained before and after the episode with undetectable HCV RNA were phylogenetically identical, making the possibility of spontaneous clearance and HCV reinfection less likely. The IL-10, TNF-α, and IP-10 levels...
HIV-Infected Ugandan Women on Antiretroviral Therapy Maintain HIV-1 RNA Suppression Across Periconception, Pregnancy, and Postpartum Periods.

Science.gov (United States)

Matthews, Lynn T; Ribaudo, Heather B; Kaida, Angela; Bennett, Kara; Musinguzi, Nicholas; Siedner, Mark J; Kabakyenga, Jerome; Hunt, Peter W; Martin, Jeffrey N; Boum, Yap; Haberer, Jessica E; Bangsberg, David R

2016-04-01

HIV-infected women risk sexual and perinatal HIV transmission during conception, pregnancy, childbirth, and breastfeeding. We compared HIV-1 RNA suppression and medication adherence across periconception, pregnancy, and postpartum periods, among women on antiretroviral therapy (ART) in Uganda. We analyzed data from women in a prospective cohort study, aged 18-49 years, enrolled at ART initiation and with ≥1 pregnancy between 2005 and 2011. Participants were seen quarterly. The primary exposure of interest was pregnancy period, including periconception (3 quarters before pregnancy), pregnancy, postpartum (6 months after pregnancy outcome), or nonpregnancy related. Regression models using generalized estimating equations compared the likelihood of HIV-1 RNA ≤400 copies per milliliter, pregnancy, and 89% of postpartum visits, and was more likely during periconception (adjusted odds ratio, 2.15) compared with nonpregnant periods. Average ART adherence was 90% [interquartile range (IQR), 70%-98%], 93% (IQR, 82%-98%), 92% (IQR, 72%-98%), and 88% (IQR, 63%-97%) during nonpregnant, periconception, pregnant, and postpartum periods, respectively. Average adherence pregnancy were virologically suppressed at most visits, with an increased likelihood of suppression and high adherence during periconception follow-up. Increased frequency of 72-hour gaps suggests a need for increased adherence support during postpartum periods.
Dissection of specific binding of HIV-1 Gag to the 'packaging signal' in viral RNA.

Science.gov (United States)

Comas-Garcia, Mauricio; Datta, Siddhartha Ak; Baker, Laura; Varma, Rajat; Gudla, Prabhakar R; Rein, Alan

2017-07-20

Selective packaging of HIV-1 genomic RNA (gRNA) requires the presence of a cis -acting RNA element called the 'packaging signal' (Ψ). However, the mechanism by which Ψ promotes selective packaging of the gRNA is not well understood. We used fluorescence correlation spectroscopy and quenching data to monitor the binding of recombinant HIV-1 Gag protein to Cy5-tagged 190-base RNAs. At physiological ionic strength, Gag binds with very similar, nanomolar affinities to both Ψ-containing and control RNAs. We challenged these interactions by adding excess competing tRNA; introducing mutations in Gag; or raising the ionic strength. These modifications all revealed high specificity for Ψ. This specificity is evidently obscured in physiological salt by non-specific, predominantly electrostatic interactions. This nonspecific activity was attenuated by mutations in the MA, CA, and NC domains, including CA mutations disrupting Gag-Gag interaction. We propose that gRNA is selectively packaged because binding to Ψ nucleates virion assembly with particular efficiency.
Selective translational repression of HIV-1 RNA by Sam68DeltaC occurs by altering PABP1 binding to unspliced viral RNA

Directory of Open Access Journals (Sweden)

Soros Vanessa

2008-10-01

Full Text Available Abstract HIV-1 structural proteins are translated from incompletely spliced 9 kb and 4 kb mRNAs, which are transported to the cytoplasm by Crm1. It has been assumed that once in the cytoplasm, translation of incompletely spliced HIV-1 mRNAs occurs in the same manner as host mRNAs. Previous analyses have demonstrated that Sam68 and a mutant thereof, Sam68ΔC, have dramatic effects on HIV gene expression, strongly enhancing and inhibiting viral structural protein synthesis, respectively. While investigating the inhibition of incompletely spliced HIV-1 mRNAs by Sam68ΔC, we determined that the effect was independent of the perinuclear bundling of the viral RNA. Inhibition was dependent upon the nuclear export pathway used, as translation of viral RNA exported via the Tap/CTE export pathway was not blocked by Sam68ΔC. We demonstrate that inhibition of HIV expression by Sam68ΔC is correlated with a loss of PABP1 binding with no attendant change in polyadenosine tail length of the affected RNAs. The capacity of Sam68ΔC to selectively inhibit translation of HIV-1 RNAs exported by Crm1 suggests that it is able to recognize unique characteristics of these viral RNPs, a property that could lead to new therapeutic approaches to controlling HIV-1 replication.
Dehydration of hydrated low-temperature tar

Energy Technology Data Exchange (ETDEWEB)

Yoshida, T

1949-01-01

Yoshida examined the mechanism of the dehydration of hydrated low-temperature tar with a microscope. The tar containing free carbon and coal dust is so stable that the removal of the above substances and water by a physical method is very difficult. Addition of light oil produced by fractionation of low-temperature tar facilitates the operations. Yoshida tried using the separate acid, neutral, and basic components of the light oil; the acid oil proved to be most effective. For many reasons it is convenient to use light oil as it is. In this method the quantity of light oil required is 2 to 3 times that of tar. But in supplementing the centrifugal method, the quantity of light oil needed might be only half the amount of tar.
Low levels of HIV-1 RNA detected in the cerebrospinal fluid after up to 10 years of suppressive therapy are associated with local immune activation.

Science.gov (United States)

Dahl, Viktor; Peterson, Julia; Fuchs, Dietmar; Gisslen, Magnus; Palmer, Sarah; Price, Richard W

2014-09-24

Though combination antiretroviral therapy reduces the concentration of HIV-1 RNA in both plasma and cerebrospinal fluid (CSF) below the detection limit of clinical assays, low levels of HIV-1 RNA are frequently detectable in plasma using more sensitive assays. We examined the frequency and magnitude of persistent low-level HIV-1 RNA in CSF and its relation to the central nervous system (CNS) immune activation. CSF and plasma HIV-1 RNA were measured using the single-copy assay with a detection limit of 0.3 copies/ml in 70 CSF and 68 plasma samples from 45 treated HIV-1-infected patients with less than 40 copies/ml of HIV-1 RNA in both fluids by standard clinical assays. We also measured CSF neopterin to assess intrathecal immune activation. Theoretical drug exposure was estimated using the CNS penetration-efficacy score of treatment regimens. CSF HIV-1 RNA was detected in 12 of the 70 CSF samples (17%) taken after up to 10 years of suppressive therapy, compared to 39 of the 68 plasma samples (57%) with a median concentration of less than 0.3 copies/ml in CSF compared to 0.3 copies/ml in plasma (P < 0.0001). CSF samples with detectable HIV-1 RNA had higher CSF neopterin levels (mean 8.2 compared to 5.7 nmol/l; P = 0.0085). Patients with detectable HIV-1 RNA in CSF did not differ in pretreatment plasma HIV-1 RNA levels, nadir CD4 cell count or CNS penetration-efficacy score. Low-level CSF HIV-1 RNA and its association with elevated CSF neopterin highlight the potential for the CNS to serve as a viral reservoir and for persistent infection to cause subclinical CNS injury.
Separating cresote from tars, mineral oils, etc

Energy Technology Data Exchange (ETDEWEB)

Erdmann, E

1921-01-07

Phenolic bodies are extracted from tars such as lignite, shale, peat, coal, producer and low temperature tars, and from tar distillates and residues and from mineral oils and distillates by washing with a mixture of acetone and water. Acetone extracts of the tars etc., may be mixed with water or aqueous acetone to cause the separation of the oils, while the creosote remains in solution.
Neurocognitive and neuroinflammatory correlates of PDYN and OPRK1 mRNA expression in the anterior cingulate in postmortem brain of HIV-infected subjects.

Science.gov (United States)

Yuferov, Vadim; Butelman, Eduardo R; Ho, Ann; Morgello, Susan; Kreek, Mary Jeanne

2014-01-09

Chronic inflammation may contribute to neuropsychological impairments in individuals with HIV, and modulation of this inflammatory response by opiate receptor ligands is important in light of the prevalence of drug use in HIV populations. Exogenous MOR and KOR agonists have differential effects on central nervous system (CNS) immunity and, while some data suggest KOR agonists are immunosuppressive, the KOR agonist dynorphin has been shown to stimulate human monocyte chemotaxis. In this study, we examined mRNA levels of endogenous opioid receptors OPRK1 and OPRM1, prodynorphin (PDYN), macrophage scavenger receptor CD163, and microglia/macrophage marker CD68 in the caudate and anterior cingulate of postmortem brains from HIV-positive and HIV-negative subjects. Brain tissues of HIV-infected (n = 24) and control subjects (n = 15) were obtained from the Manhattan HIV Brain Bank. Quantification of the gene mRNA was performed using SYBR Green RT-PCR. CD68 and CD163 were increased in HIV-positive (HIV+) compared to HIV-negative (HIV-) individuals in both brain regions. There were higher OPRK1 (P <0.005), and lower PDYN mRNA (P <0.005) levels in the anterior cingulate of HIV+ compared to HIV- subjects. This difference between the clinical groups was not found in the caudate. There was no difference in the levels of OPRM1 mRNA between HIV+ and HIV- subjects. Using linear regression analysis, we examined the relationship of OPRK1 and PDYN mRNA levels in the HIV+ subjects with seven cognitive domain T scores of a neuropsychological test battery. Within the HIV+ subjects, there was a positive correlation between anterior cingulate PDYN mRNA levels and better T-scores in the motor domain. Within the HIV+ subjects there were also positive correlations of both OPRK1 and PDYN mRNA levels with the anti-inflammatory marker CD163, but not with proinflammatory CD68 levels. In this setting, decreased PDYN mRNA may reflect a homeostatic mechanism to reduce monocyte
Hepatitis C virus (HCV) RNA profiles among chronic HIV/HCV-coinfected individuals in ESPRIT; spontaneous HCV RNA clearance observed in nine individuals

DEFF Research Database (Denmark)

Grint, D; Tedaldi, Ellen; Peters, L

2017-01-01

OBJECTIVES: Studies have shown that hepatitis C virus (HCV) RNA levels remain stable over time in HIV/HCV-coinfected individuals taking combination antiretroviral therapy (cART), while spontaneous clearance of HCV RNA during the persistent infection phase has been documented only rarely among tho...
The relative prognostic value of plasma HIV RNA levels and CD4 lymphocyte counts in advanced HIV infection

DEFF Research Database (Denmark)

Cozzi-Lepri, A; Katzenstein, T L; Ullum, H

1998-01-01

. RESULTS: The plasma HIV RNA (median 101410 copies/ml; range (range 200-7200000) and the CD4 lymphocyte count (median 250 cells x 10(6)/l; range 1-1247) were negatively correlated (Pearson r = -0.53; P
Inhibition of HIV transmission in human cervicovaginal explants and humanized mice using CD4 aptamer-siRNA chimeras

Science.gov (United States)

Wheeler, Lee Adam; Trifonova, Radiana; Vrbanac, Vladimir; Basar, Emre; McKernan, Shannon; Xu, Zhan; Seung, Edward; Deruaz, Maud; Dudek, Tim; Einarsson, Jon Ivar; Yang, Linda; Allen, Todd M.; Luster, Andrew D.; Tager, Andrew M.; Dykxhoorn, Derek M.; Lieberman, Judy

2011-01-01

The continued spread of the HIV epidemic underscores the need to interrupt transmission. One attractive strategy is a topical vaginal microbicide. Sexual transmission of herpes simplex virus type 2 (HSV-2) in mice can be inhibited by intravaginal siRNA application. To overcome the challenges of knocking down gene expression in immune cells susceptible to HIV infection, we used chimeric RNAs composed of an aptamer fused to an siRNA for targeted gene knockdown in cells bearing an aptamer-binding receptor. Here, we showed that CD4 aptamer-siRNA chimeras (CD4-AsiCs) specifically suppress gene expression in CD4+ T cells and macrophages in vitro, in polarized cervicovaginal tissue explants, and in the female genital tract of humanized mice. CD4-AsiCs do not activate lymphocytes or stimulate innate immunity. CD4-AsiCs that knock down HIV genes and/or CCR5 inhibited HIV infection in vitro and in tissue explants. When applied intravaginally to humanized mice, CD4-AsiCs protected against HIV vaginal transmission. Thus, CD4-AsiCs could be used as the active ingredient of a microbicide to prevent HIV sexual transmission. PMID:21576818
Novel RNA Duplex Locks HIV-1 in a Latent State via Chromatin-mediated Transcriptional Silencing

Directory of Open Access Journals (Sweden)

Chantelle Ahlenstiel

2015-01-01

Full Text Available Transcriptional gene silencing (TGS of mammalian genes can be induced by short interfering RNA (siRNA targeting promoter regions. We previously reported potent TGS of HIV-1 by siRNA (PromA, which targets tandem NF-κB motifs within the viral 5′LTR. In this study, we screened a siRNA panel with the aim of identifying novel 5′LTR targets, to provide multiplexing potential with enhanced viral silencing and application toward developing alternate therapeutic strategies. Systematic examination identified a novel siRNA target, si143, confirmed to induce TGS as the silencing mechanism. TGS was prolonged with virus suppression >12 days, despite a limited ability to induce post- TGS. Epigenetic changes associated with silencing were suggested by partial reversal by histone deacetylase inhibitors and confirmed by chromatin immunoprecipitation analyses, which showed induction of H3K27me3 and H3K9me3, reduction in H3K9Ac, and recruitment of argonaute-1, all characteristic marks of heterochromatin and TGS. Together, these epigenetic changes mimic those associated with HIV-1 latency. Further, robust resistance to reactivation was observed in the J-Lat 9.2 cell latency model, when transduced with shPromA and/or sh143. These data support si/shRNA-mediated TGS approaches to HIV-1 and provide alternate targets to pursue a functional cure, whereby the viral reservoir is locked in latency following antiretroviral therapy cessation.
Rational design of micro-RNA-like bifunctional siRNAs targeting HIV and the HIV coreceptor CCR5.

Science.gov (United States)

Ehsani, Ali; Saetrom, Pål; Zhang, Jane; Alluin, Jessica; Li, Haitang; Snøve, Ola; Aagaard, Lars; Rossi, John J

2010-04-01

Small-interfering RNAs (siRNAs) and micro-RNAs (miRNAs) are distinguished by their modes of action. SiRNAs serve as guides for sequence-specific cleavage of complementary mRNAs and the targets can be in coding or noncoding regions of the target transcripts. MiRNAs inhibit translation via partially complementary base-pairing to 3' untranslated regions (UTRs) and are generally ineffective when targeting coding regions of a transcript. In this study, we deliberately designed siRNAs that simultaneously direct cleavage and translational suppression of HIV RNAs, or cleavage of the mRNA encoding the HIV coreceptor CCR5 and suppression of translation of HIV. These bifunctional siRNAs trigger inhibition of HIV infection and replication in cell culture. The design principles have wide applications throughout the genome, as about 90% of genes harbor sites that make the design of bifunctional siRNAs possible.
Bioremediation potential of coal-tar-oil-contaminated soil

International Nuclear Information System (INIS)

Lajoie, C.A.

1991-01-01

The bioremediation of coal tar oil contaminated soil was investigated in 90 day laboratory simulation experiments. The effect of soil moisture, humic acid amendment, and coal tar oil concentration on the rate of disappearance of individual coal tar oil constituents (PAHs and related compounds) was determined by methylene chloride extraction and gas chromatography. Mass balance experiments determined the fate of both the individual 14 C-labeled PAHs phenanthrene, pyrene, and benzo(a)pyrene, and the total coal tar oil carbon. Mineralization, volatilization, incorporation into microbial biomass, disappearance of individual coal tar oil constitutents, and the distribution of residual 14 C-activity in different soil fractions were measured. The rate of disappearance of coal tar oil constituents increased with increasing soil moisture over the experimental range. Humic acid amendment initially enhanced the rate of disappearance, but decreased the extent of disappearance. The amount of contamination removed decreased at higher coal tar oil concentrations. The practical limit for biodegradation in the system tested appeared to be between 1.0 and 2.5% coal tar oil. Mineralization accounted for 40 to 50% of the applied coal tar oil. Volatilization was a minor pathway of disappearance
The prion protein has RNA binding and chaperoning properties characteristic of nucleocapsid protein NCP7 of HIV-1.

Science.gov (United States)

Gabus, C; Derrington, E; Leblanc, P; Chnaiderman, J; Dormont, D; Swietnicki, W; Morillas, M; Surewicz, W K; Marc, D; Nandi, P; Darlix, J L

2001-06-01

Transmissible spongiform encephalopathies are fatal neurodegenerative diseases associated with the accumulation of a protease-resistant form of the prion protein (PrP). Although PrP is conserved in vertebrates, its function remains to be identified. In vitro PrP binds large nucleic acids causing the formation of nucleoprotein complexes resembling human immunodeficiency virus type 1 (HIV-1) nucleocapsid-RNA complexes and in vivo MuLV replication accelerates the scrapie infectious process, suggesting possible interactions between retroviruses and PrP. Retroviruses, including HIV-1 encode a major nucleic acid binding protein (NC protein) found within the virus where 2000 NC protein molecules coat the dimeric genome. NC is required in virus assembly and infection to chaperone RNA dimerization and packaging and in proviral DNA synthesis by reverse transcriptase (RT). In HIV-1, 5'-leader RNA/NC interactions appear to control these viral processes. This prompted us to compare and contrast the interactions of human and ovine PrP and HIV-1 NCp7 with HIV-1 5'-leader RNA. Results show that PrP has properties characteristic of NCp7 with respect to viral RNA dimerization and proviral DNA synthesis by RT. The NC-like properties of huPrP map to the N-terminal region of huPrP. Interestingly, PrP localizes in the membrane and cytoplasm of PrP-expressing cells. These findings suggest that PrP is a multifunctional protein possibly participating in nucleic acid metabolism.

Factors influencing cerebrospinal fluid and plasma HIV-1 RNA detection rate in patients with and without opportunistic neurological disease during the HAART era

Directory of Open Access Journals (Sweden)

Aleixo Agdemir W

2007-12-01

Full Text Available Abstract Background In the central nervous system, HIV replication can occur relatively independent of systemic infection, and intrathecal replication of HIV-1 has been observed in patients with HIV-related and opportunistic neurological diseases. The clinical usefulness of HIV-1 RNA detection in the cerebrospinal fluid (CSF of patients with opportunistic neurological diseases, or the effect of opportunistic diseases on CSF HIV levels in patients under HAART has not been well defined. We quantified CSF and plasma viral load in HIV-infected patients with and without different active opportunistic neurological diseases, determined the characteristics that led to a higher detection rate of HIV RNA in CSF, and compared these two compartments. Methods A prospective study was conducted on 90 HIV-infected patients submitted to lumbar puncture as part of a work-up for suspected neurological disease. Seventy-one patients had active neurological diseases while the remaining 19 did not. Results HIV-1 RNA was quantified in 90 CSF and 70 plasma samples. The HIV-1 RNA detection rate in CSF was higher in patients with neurological diseases, in those with a CD4 count lower than 200 cells/mm3, and in those not receiving antiretroviral therapy, as well as in patients with detectable plasma HIV-1 RNA. Median viral load was lower in CSF than in plasma in the total population, in patients without neurological diseases, and in patients with toxoplasmic encephalitis, while no significant difference between the two compartments was observed for patients with cryptococcal meningitis and HIV-associated dementia. CSF viral load was lower in patients with cryptococcal meningitis and neurotoxoplasmosis under HAART than in those not receiving HAART. Conclusion Detection of HIV-1 RNA in CSF was more frequent in patients with neurological disease, a CD4 count lower than 200 cells/mm3 and detectable plasma HIV-1. Median HIV-1 RNA levels were generally lower in CSF than in
In situ recovery of oil from Utah tar sand: a summary of tar sand research at the Laramie Energy Technology Center

Energy Technology Data Exchange (ETDEWEB)

Marchant, L.C.; Westhoff, J.D.

1985-10-01

This report describes work done by the United States Department of Energy's Laramie Energy Technology Center from 1971 through 1982 to develop technology for future recovery of oil from US tar sands. Work was concentrated on major US tar sand deposits that are found in Utah. Major objectives of the program were as follows: determine the feasibility of in situ recovery methods applied to tar sand deposits; and establish a system for classifying tar sand deposits relative to those characteristics that would affect the design and operation of various in situ recovery processes. Contents of this report include: (1) characterization of Utah tar sand; (2) laboratory extraction studies relative to Utah tar sand in situ methods; (3) geological site evaluation; (4) environmental assessments and water availability; (5) reverse combustion field experiment, TS-1C; (6) a reverse combustion followed by forward combustion field experiment, TS-2C; (7) tar sand permeability enhancement studies; (8) two-well steam injection experiment; (9) in situ steam-flood experiment, TS-1S; (10) design of a tar sand field experiment for air-stream co-injection, TS-4; (11) wastewater treatment and oil analyses; (12) economic evaluation of an in situ tar sand recovery process; and (13) appendix I (extraction studies involving Utah tar sands, surface methods). 70 figs., 68 tabs.
Marcadores virológicos no convencionales en pacientes infectados con el virus de la inmunodeficiencia humana: ADN HIV-T, ADN HIV- 2LTR y ARN de HIV Non conventional virological markers in HIV-infected patients: T-HIV DNA, 2LTR-HIV DNA and HIV RNA

Directory of Open Access Journals (Sweden)

Rosana Gariglio

2004-10-01

study, we analyzed the presence of total HIV DNA (T-HIV DNA, non-integrated DNA with 2LTR (2LTR-HIV DNA and HIV RNA in a group of 55 HIV-positive subjects from Rosario City, with different clinical stages, with and without HAART. All markers were evaluated by PCR assays optimized in our laboratory that included colorimetric detection in microplate. HIV RNA clinical sensitivity was compared with a reference test, bDNA, resulting in 74% and 64% respectively, with an 85% of agreement. Thus, our HIV RNA assay could be used to monitor patients under HAART and at risk of infection. The 2LTR-HIV DNA was 54% positive although it was absent in patients with high VL. This marker was considered a labile product therefore its presence was associated with recent infection. However, current evidences question its stability. Thus, its clinical significance should be reconsidered. The absence of 2LTR-HIV DNA in patients with detectable VL may relate to the heterogeneity of the sequence used for its detection. T-HIV DNA was present in 100% of the samples and could be a relevant remission marker when therapies that effectively eradicate the infection became available.
HIV-1 Tat C-mediated regulation of tumor necrosis factor receptor-associated factor-3 by microRNA 32 in human microglia

Directory of Open Access Journals (Sweden)

Mishra Ritu

2012-06-01

Full Text Available Abstract Background HIV-1 Tat protein is known to be associated with neuroinflammation, a condition that develops in almost half of patients infected with HIV-1. HIV-1 Tat can alter glial neuroprotective functions, leading to neurotoxicity within the CNS. HIV-1 Tat is known to be secreted from productively infected cells and can affect neighboring uninfected cells by modulating cellular gene expression in a bystander fashion. Methods We were interested to study whether exogenous exposure to HIV-1 Tat-C protein perturbs the microRNA (miRNA expression profile of human microglial cells, leading to altered protein expression. We used protein expression and purification, miRNA overexpression, miRNA knockdown, transfection, site-directed mutagenesis, real-time PCR, luciferase assay and western blotting techniques to perform our study. Results HIV-1 Tat-C treatment of human microglial cells resulted in a dose-dependent increase in miR-32 expression. We found that tumor necrosis factor-receptor–associated factor 3 TRAF3 is a direct target for miR-32, and overexpression of miR-32 in CHME3 cells decreased TRAF3 both at the mRNA and the protein level. Recovery of TRAF3 protein expression after transfection of anti-miR-32 and the results of the luciferase reporter assay provided direct evidence of TRAF3 regulation by miR-32. We found that the regulation of interferon regulatory factor 3 (IRF3 and IRF7 is controlled by cellular levels of TRAF3 protein in microglial cells, as after overexpression of miR-32 and application of anti-miR-32, expression levels of IRF3 and IRF7 were inversely regulated by expression levels of TRAF3. Thus, our results suggest a novel miRNA mediated mechanism for regulation of TRAF3 in human microglial cells exposed to HIV-1 Tat C protein. These results may help to elucidate the detrimental neuroinflammatory consequences of HIV-1 Tat C protein in bystander fashion. Conclusion HIV-1 Tat protein can modulate TRAF3 expression through
Centrifuge treatment of coal tar

Energy Technology Data Exchange (ETDEWEB)

L.A. Kazak; V.Z. Kaidalov; L.F. Syrova; O.S. Miroshnichenko; A.S. Minakov [Giprokoks, the State Institute for the Design of Coke-Industry Enterprises, Kharkov (Ukraine)

2009-07-15

New technology is required for the removal of water and heavy fractions from regular coal tar. Centrifuges offer the best option. Purification of coal tar by means of centrifuges at OAO NLMK permits the production of pitch coke or electrode pitch that complies with current standards.
Short communication: identification of a novel HIV type 1 subtype H/J recombinant in Canada with discordant HIV viral load (RNA) values in three different commercial assays.

Science.gov (United States)

Kim, John E; Beckthold, Brenda; Chen, Zhaoxia; Mihowich, Jennifer; Malloch, Laurie; Gill, Michael John

2007-11-01

The presence of HIV-1 non-B subtypes is increasing worldwide. This poses challenges to commercial diagnostic and viral load (RNA) monitoring tests that are predominantly based on HIV-1 subtype B strains. Based on phylogenetic analysis of the gag, pol, and env gene regions, we describe the first HIV-1 H/J recombinant in Canada that presented divergent viral load values. DNA sequence analysis of the gag gene region further revealed that genetic diversity between this H/J recombinant and the primers and probes used in the bio-Merieux Nuclisens HIV-1 QT (Nuclisens) and Roche Amplicor Monitor HIV-1, v1.5 (Monitor) viral RNA assays can erroneously lead to undetectable viral load values. This observation appears to be more problematic in the Nuclisens assay. In light of increasing genetic diversity in HIV worldwide we recommend that DNA sequencing of HIV, especially in the gag gene region targeted by primers and probes used in molecular diagnostic and viral load tests, be incorporated into clinical monitoring practices.
A Multiple siRNA-Based Anti-HIV/SHIV Microbicide Shows Protection in Both In Vitro and In Vivo Models.

Directory of Open Access Journals (Sweden)

Sandhya Boyapalle

Full Text Available Human immunodeficiency virus (HIV types 1 and 2 (HIV-1 and HIV-2 are the etiologic agents of AIDS. Most HIV-1 infected individuals worldwide are women, who acquire HIV infections during sexual contact. Blocking HIV mucosal transmission and local spread in the female lower genital tract is important in preventing infection and ultimately eliminating the pandemic. Microbicides work by destroying the microbes or preventing them from establishing an infection. Thus, a number of different types of microbicides are under investigation, however, the lack of their solubility and bioavailability, and toxicity has been major hurdles. Herein, we report the development of multifunctional chitosan-lipid nanocomplexes that can effectively deliver plasmids encoding siRNA(s as microbicides without adverse effects and provide significant protection against HIV in both in vitro and in vivo models. Chitosan or chitosan-lipid (chlipid was complexed with a cocktail of plasmids encoding HIV-1-specific siRNAs (psiRNAs and evaluated for their efficacy in HEK-293 cells, PBMCs derived from nonhuman primates, 3-dimensional human vaginal ectocervical tissue (3D-VEC model and also in non-human primate model. Moreover, prophylactic administration of the chlipid to deliver a psiRNA cocktail intravaginally with a cream formulation in a non-human primate model showed substantial reduction of SHIV (simian/human immunodeficiency virus SF162 viral titers. Taken together, these studies demonstrate the potential of chlipid-siRNA nanocomplexes as a potential genetic microbicide against HIV infections.
The Regulatory and Kinase Domains but Not the Interdomain Linker Determine Human Double-stranded RNA-activated Kinase (PKR) Sensitivity to Inhibition by Viral Non-coding RNAs.

Science.gov (United States)

Sunita, S; Schwartz, Samantha L; Conn, Graeme L

2015-11-20

Double-stranded RNA (dsRNA)-activated protein kinase (PKR) is an important component of the innate immune system that presents a crucial first line of defense against viral infection. PKR has a modular architecture comprising a regulatory N-terminal dsRNA binding domain and a C-terminal kinase domain interposed by an unstructured ∼80-residue interdomain linker (IDL). Guided by sequence alignment, we created IDL deletions in human PKR (hPKR) and regulatory/kinase domain swap human-rat chimeric PKRs to assess the contributions of each domain and the IDL to regulation of the kinase activity by RNA. Using circular dichroism spectroscopy, limited proteolysis, kinase assays, and isothermal titration calorimetry, we show that each PKR protein is properly folded with similar domain boundaries and that each exhibits comparable polyinosinic-cytidylic (poly(rI:rC)) dsRNA activation profiles and binding affinities for adenoviral virus-associated RNA I (VA RNAI) and HIV-1 trans-activation response (TAR) RNA. From these results we conclude that the IDL of PKR is not required for RNA binding or mediating changes in protein conformation or domain interactions necessary for PKR regulation by RNA. In contrast, inhibition of rat PKR by VA RNAI and TAR RNA was found to be weaker than for hPKR by 7- and >300-fold, respectively, and each human-rat chimeric domain-swapped protein showed intermediate levels of inhibition. These findings indicate that PKR sequence or structural elements in the kinase domain, present in hPKR but absent in rat PKR, are exploited by viral non-coding RNAs to accomplish efficient inhibition of PKR. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.
Coal tar pitch. Interrelations between properties and utilization of coal tar pitch

Energy Technology Data Exchange (ETDEWEB)

Collin, G; Koehler, H [Ruetgerswerke A.G., Duisburg (Germany, F.R.)

1977-06-01

Coal tar pitch is won as a highly aromatic, thermoplastic residue by destillating coal tar. In this paper the structure as well as the chemical and physical data of this pitch are introduced. In addition to this the actual as well as possible applications are indicated. For example, the pitch can be used for the production of binders, e.g. for electrodes and road construction as well as in combination with plastics for the production of insulating material and corrosion protection material.
The RNA helicase DDX1 is involved in restricted HIV-1 Rev function in human astrocytes

International Nuclear Information System (INIS)

Fang Jianhua; Acheampong, Edward; Dave, Rajnish; Wang Fengxiang; Mukhtar, Muhammad; Pomerantz, Roger J.

2005-01-01

Productive infection by human immunodeficiency virus type I (HIV-1) in the central nervous system (CNS) involves mainly macrophages and microglial cells. A frequency of less than 10% of human astrocytes is estimated to be infectable with HIV-1. Nonetheless, this relatively low percentage of infected astrocytes, but associated with a large total number of astrocytic cells in the CNS, makes human astrocytes a critical part in the analyses of potential HIV-1 reservoirs in vivo. Investigations in astrocytic cell lines and primary human fetal astrocytes revealed that limited HIV-1 replication in these cells resulted from low-level viral entry, transcription, viral protein processing, and virion maturation. Of note, a low ratio of unspliced versus spliced HIV-1-specific RNA was also investigated, as Rev appeared to act aberrantly in astrocytes, via loss of nuclear and/or nucleolar localization and diminished Rev-mediated function. Host cellular machinery enabling Rev function has become critical for elucidation of diminished Rev activity, especially for those factors leading to RNA metabolism. We have recently identified a DEAD-box protein, DDX1, as a Rev cellular co-factor and now have explored its potential importance in astrocytes. Cells were infected with HIV-1 pseudotyped with envelope glycoproteins of amphotropic murine leukemia viruses (MLV). Semi-quantitative reverse transcriptase-polymerase chain reactions (RT-PCR) for unspliced, singly-spliced, and multiply-spliced RNA clearly showed a lower ratio of unspliced/singly-spliced over multiply-spliced HIV-1-specific RNA in human astrocytes as compared to Rev-permissive, non-glial control cells. As well, the cellular localization of Rev in astrocytes was cytoplasmically dominant as compared to that of Rev-permissive, non-glial controls. This endogenous level of DDX1 expression in astrocytes was demonstrated directly to lead to a shift of Rev sub-cellular distribution dominance from nuclear and/or nucleolar to
Coal tar: past, present and future

Energy Technology Data Exchange (ETDEWEB)

Thami, G.P.; Sarkar, R. [Government Medical College & Hospital, Chandigarh (India). Dept. of Dermatology & Venerology

2002-03-01

Crude coal tar has been used in the treatment of dermatoses for many decades. In the last few years its use has been limited to skin diseases such as psoriasis and chronic dermatitis. Newer topical modalities for psoriasis are being used increasingly for treatment, but have failed to replace crude coal tar as a first-line treatment of psoriasis. The authors review the pharmacology, chemistry and use of crude coal tar in order to reappraise its role as a therapeutic agent in dermatology.
Distillation of tar and tar fractions in the presence of surface-active coke

Energy Technology Data Exchange (ETDEWEB)

Jaeppelt, A; Klaus, J

1943-01-01

The tar obtained by low-temperature carbonization of Upper Silesian gas coke and fractions from this tar were distilled in the presence of different grades of coke dust with varying surface activity; the coke had been activated by steam in the course of its production by low-temperature carbonization. The surface activity of the coke dusts was measured by determining the heat of wetting with C/sub 6/H/sub 6/. Tar and coke dust, both anhydrous, were mixed in a kneading machine in such proportions that the capillaries of the dust were saturated and enough ''externally'' bound tar was present to permit briquetting. The briquets were distilled without cracking and with steam as heating medium. The yield and quality of the distillate depended on the magnitude of the internal surface of the coke dust used; a mixture of a very active coke from brown coal and tar yielded a distillate with Conradson carbon residue of 1.34 percent, asphalt content 6.1 percent and eta/sub 20/ 5.4/sup 0/ E. as compared with C residue of 10.95 percent, asphalt content 33.5 percent and eta/sub 20/ 123.6/sup 0/ E. of the distillate obtained in the absence of surface-active coke. Even higher-boiling fractions can be improved by this treatment, although it is preferable to use oils with an initial boiling point below 300/sup 0/. The ratio of oil to adsorbent is not critical, but better results were obtained with higher percentages of added coke dust. The process in its present form is not suited for the conversion of crude creosote to useful phenols.
Dried blood spot HIV-1 RNA quantification: A useful tool for viral load monitoring among HIV-infected individuals in India

Science.gov (United States)

Neogi, Ujjwal; Gupta, Soham; Rodridges, Rashmi; Sahoo, Pravat Nalini; Rao, Shwetha D.; Rewari, Bharat B.; Shastri, Suresh; De Costa, Ayesha; Shet, Anita

2012-01-01

Background & objectives: Monitoring of HIV-infected individuals on antiretroviral treatment (ART) ideally requires periodic viral load measurements to ascertain adequate response to treatment. While plasma viral load monitoring is widely available in high-income settings, it is rarely used in resource-limited regions because of high cost and need for sophisticated sample transport. Dried blood spot (DBS) as source specimens for viral load measurement has shown promise as an alternative to plasma specimens and is likely to be a useful tool for Indian settings. The present study was undertaken to investigate the performance of DBS in HIV-1 RNA quantification against the standard plasma viral load assay. Methods: Between April-June 2011, 130 samples were collected from HIV-1-infected (n=125) and non-infected (n=5) individuals in two district clinics in southern India. HIV-1 RNA quantification was performed from DBS and plasma using Abbott m2000rt system after manual RNA extraction. Statistical analysis included correlation, regression and Bland-Altman analysis. Results: The sensitivity of DBS viral load was 97 per cent with viral loads >3.0 log10 copies/ml. Measurable viral load (>3.0 log 10 copies/ml) results obtained for the 74 paired plasma-DBS samples showed positive correlation between both the assays (r=0.96). For clinically acceptable viral load threshold values of >5,000 copies/ml, Bland-Altman plots showed acceptable limits of agreement (−0.21 to +0.8 log10 copies/ml). The mean difference was 0.29 log10 copies/ml. The cost of DBS was $2.67 lower compared to conventional plasma viral load measurement in the setting Interpretation & conclusions: The significant positive correlation with standard plasma-based assay and lower cost of DBS viral load monitoring suggest that DBS sampling can be a feasible and economical means of viral load monitoring in HIV-infected individual in India and in other resource-limited settings globally. PMID:23391790
The role of Vif oligomerization and RNA chaperone activity in HIV-1 replication.

Science.gov (United States)

Batisse, Julien; Guerrero, Santiago; Bernacchi, Serena; Sleiman, Dona; Gabus, Caroline; Darlix, Jean-Luc; Marquet, Roland; Tisné, Carine; Paillart, Jean-Christophe

2012-11-01

The viral infectivity factor (Vif) is essential for the productive infection and dissemination of HIV-1 in non-permissive cells that involve most natural HIV-1 target cells. Vif counteracts the packaging of two cellular cytidine deaminases named APOBEC3G (A3G) and A3F by diverse mechanisms including the recruitment of an E3 ubiquitin ligase complex and the proteasomal degradation of A3G/A3F, the inhibition of A3G mRNA translation or by a direct competition mechanism. In addition, Vif appears to be an active partner of the late steps of viral replication by participating in virus assembly and Gag processing, thus regulating the final stage of virion formation notably genomic RNA dimerization and by inhibiting the initiation of reverse transcription. Vif is a small pleiotropic protein with multiple domains, and recent studies highlighted the importance of Vif conformation and flexibility in counteracting A3G and in binding RNA. In this review, we will focus on the oligomerization and RNA chaperone properties of Vif and show that the intrinsic disordered nature of some Vif domains could play an important role in virus assembly and replication. Experimental evidence demonstrating the RNA chaperone activity of Vif will be presented. Copyright © 2012 Elsevier B.V. All rights reserved.
Flash hydropyrolysis of bituminous coal . III. Research on flash hydropyrolysis tar

Energy Technology Data Exchange (ETDEWEB)

Dong, M.; Zhu, Z.; He, Y.; Ding, N.; Tang, L. [East China University of Science and Technology, Shanghai (China)

2000-02-01

Tar sample obtained by flash hydropyrolysis (FHP) from Dongshen coal at high pressure entrained reactor was investigated. An effect of flash hydropyrolysis temperature on the main components in tar was studied and the quality of the tar was compared with high temperature coke oven tar. The results showed that: the yields of liquid hydrocarbon in FHP tar were more than 15%, which is twofold of that in coke oven tar; the FHP tar has high oil fraction and low pitch; high phenol components and pure condensed polycyclic aromatic hydrocarbon, and low aliphatic hydrocarbon. The components of the FHP tar were simpler than that of high temperature coke oven tar. Therefore, FHP has improved the quantity and quality of tar. 11 refs., 3 figs., 5 tabs.
Physical and performance properties of coal tar urethanes - pipe

International Nuclear Information System (INIS)

Hickney, J.; Hendry, M.

1984-01-01

The purpose of this paper is to review certain physical properties of coal tar extended urethane coatings designed specifically for use in the pipe coatings market. The blend of coal tar and urethane resins provides a novel finished product with properties cumulatively inherent in its constituents. Typically, coal tar and coal tar pitch offer exceptional water resistance and cathodic alkali resistance when blended with other resins. An example is the standard coal tar epoxies used for many years in the marine markets for shipbottoms
Characterization of acid tar waste from benzol purification | Danha ...

African Journals Online (AJOL)

The use of concentrated sulphuric acid to purify benzene, toluene and xylene produces acidic waste known as acid tar. The characterization of the acid tar to determine the composition and physical properties to device a way to use the waste was done. There were three acid tars two from benzene (B acid tar), toluene and ...
Nanoparticles containing siRNA to silence CD4 and CCR5 reduce expression of these receptors and inhibit HIV-1 infection in human female reproductive tract tissue explants

Directory of Open Access Journals (Sweden)

Susan K. Eszterhas

2011-09-01

Full Text Available Human Immunodeficiency Virus-type 1 (HIV- 1 binds to CD4 and CCR5 receptors on target cells in the human female reproductive tract. We sought to determine whether reducing levels of messenger RNA (mRNA transcripts that encode these receptors in female reproductive tract cells could protect mucosal tissue explants from HIV- 1 infection. Explants prepared from the endometrium, endocervix, and ectocervix of hysterectomy tissues from HIV-1 sero-negative women were exposed to nanoparticles containing CD4- and CCR5-specific short-interfering RNA (siRNA sequences. Explants were then exposed two days later to HIV-1, and HIV-1 reverse transcripts were measured five days post-infection. Explants treated with nanoparticles containing CD4- and CCR5-specific siRNA showed reduced levels of CD4 and CCR5 transcripts, and significantly lower levels of HIV-1 reverse transcripts compared to those treated with an irrelevant siRNA. In female reproductive tract explants and in peripheral blood cell cultures, siRNA transfection induced the secretion of IFN-alpha (IFN-α, a potent antiviral cytokine. In female mice, murine-specific Cd4-siRNA nanoparticles instilled within the uterus significantly reduced murine Cd4 transcripts by day 3. Our findings demonstrate that siRNA nanoparticles reduce expression of HIV-1 infectivity receptors in human female reproductive tract tissues and also inhibit HIV-1 infection. Murine studies demonstrate that nanoparticles can penetrate the reproductive tract tissues in vivo and silence gene expression. The induction of IFN-α after siRNA transfection can potentially contribute to the antiviral effect. These findings support the therapeutic development of nanoparticles to deliver siRNA molecules to silence host cell receptors in the female reproductive tract as a novel microbicide to inhibit mucosal HIV-1 transmission.
The temporal relationship between advertising and sales of low-tar cigarettes.

Science.gov (United States)

Reed, Mark B; Anderson, Christy M; Burns, David M

2006-12-01

To determine whether a temporal relationship exists between the advertising and sales of low-tar cigarettes. It was hypothesised that increases in the advertising of low-tar cigarettes would precede increases in sales for these cigarettes. The themes of cigarette advertisements were reviewed and coded for 20 low-tar cigarette brands advertised in 13 widely read magazines in the US between 1960 and 1996. These 20 brands represented most of the low-tar cigarette advertisements and cigarette sales from 1967 to 1996. Cigarette sales data were obtained from the 1994 Maxwell report that summarises all cigarette sales from 1925 to 1990. If the advertisement referred to the low-tar attributes of the cigarette advertised, the advertisement was coded as having a low-tar theme and was included in the analysis. Five different graphical presentations of the relationship between the advertising and sales of the 20 low-tar cigarette brands showed a temporal relationship between low-tar advertising and sales for these brands. This relationship was observed for brands that introduced a low-tar alternative into an existing brand family (eg, Marlboro Light) and for new exclusively low-tar brands (eg, Carlton). Despite large increases in the advertising for the exclusively low-tar brands, sales of these brands remained low relative to sales of the low-tar alternative brands. Increases in print advertising of 20 of the most popular low-tar cigarette brands were followed by increases in sales for these cigarettes. Despite increases in the advertising of exclusively low-tar brands in the mid-1970s and early 1980s, the sales of these brands never matched the sales of the low-tar alternative brands. This suggests that it may have been easier to get smokers to switch to low-tar brands within a brand family compared with entirely new low-tar brands. Over the past 30 years, the marketing of low-tar cigarettes as a healthier alternative to higher-tar cigarettes has resulted in these brands
Cancer fear over coal tar products

Energy Technology Data Exchange (ETDEWEB)

NONE

1995-01-01

Discusses a report by Dutch researchers which suggests that the regular use of coal tar shampoos may significantly increase the risk of cancer due to the high levels of polynuclear aromatic hydrocarbons (PAHs) in the products. The PAH exposure of volunteers using a coal tar anti-dandruff shampoo was studied by measuring the amount of hydroxypyrene, a PAH breakdown product in their urine. Volunteers who had used the shampoo excreted high levels of hydroxypyrene the day after exposure. Excretion by the control group using a non-coal tar anti-dandruff shampoo remained constant. 1 ref., 1 fig.

Detection of HIV and HCV RNA in semen from Brazilian coinfected men using multiplex PCR before and after semen washing Detecção do RNA do HIV e HCV em sêmen de homens brasileiros, usando PCR multiplex antes e depois do "semen washing"

Directory of Open Access Journals (Sweden)

Cynthia Liliane Motta do Canto

2006-08-01

Full Text Available INTRODUCTION: Prolonged survival of patients under HAART has resulted in new demands for assisted reproductive technologies. HIV serodiscordant couples wish to make use of assisted reproduction techniques in order to avoid viral transmission to the partner or to the newborn. It is therefore essential to test the effectiveness of techniques aimed at reducing HIV and HCV loads in infected semen using molecular biology tests. METHODS: After seminal analysis, semen samples from 20 coinfected patients were submitted to cell fractioning and isolation of motile spermatozoa by density gradient centrifugation and swim-up. HIV and HCV RNA detection tests were performed with RNA obtained from sperm, seminal plasma and total semen. RESULTS: In pre-washing semen, HIV RNA was detected in 100% of total semen samples, whereas HCV RNA was concomitantly amplified in only one specimen. Neither HIV nor HCV were detected either in the swim-up or in the post-washing semen fractions. CONCLUSIONS: Reduction of HIV and/or HCV shedding in semen by density gradient centrifugation followed by swim-up is an efficient method. These findings lead us to believe that, although semen is rarely found to contain HCV, semen processing is highly beneficial for HIV/HCV coinfected individuals.O aumento da sobrevida dos pacientes que utilizam terapêutica antiretroviral altamente eficaz (HAART- Highly Active Antiretroviral Therapy trouxe uma nova demanda de casais sorodiscordantes que desejam filhos. Como esses casais não podem abandonar o uso de preservativos, torna-se indispensável tratar o sêmen infectado com técnicas laboratoriais eficazes que além de isolar os melhores espermatozóides, reduzam a carga viral do HIV e HCV a níveis indetectáveis. Para isso, são utilizadas técnicas de semen washing, associadas a testes ultra sensíveis de biologia molecular. Após análise seminal, sêmen de 20 pacientes co-infectados HIV-HCV foram submetidos a fracionamento celular e
HIV-1 resistance conferred by siRNA cosuppression of CXCR4 and CCR5 coreceptors by a bispecific lentiviral vector

Directory of Open Access Journals (Sweden)

Akkina Ramesh

2005-01-01

Full Text Available Abstract Background RNA interference (RNAi mediated by small interfering RNAs (siRNAs has proved to be a highly effective gene silencing mechanism with great potential for HIV/AIDS gene therapy. Previous work with siRNAs against cellular coreceptors CXCR4 and CCR5 had shown that down regulation of these surface molecules could prevent HIV-1 entry and confer viral resistance. Since monospecific siRNAs targeting individual coreceptors are inadequate in protecting against both T cell tropic (X4 and monocyte tropic (R5 viral strains simultaneously, bispecific constructs with dual specificity are required. For effective long range therapy, the bispecific constructs need to be stably transduced into HIV-1 target cells via integrating viral vectors. Results To achieve this goal, lentiviral vectors incorporating both CXCR4 and CCR5 siRNAs of short hairpin design were constructed. The CXCR4 siRNA was driven by a U6 promoter whereas the CCR5 siRNA was driven by an H1 promoter. A CMV promoter driven EGFP reporter gene is also incorporated in the bispecific construct. High efficiency transduction into coreceptor expressing Magi and Ghost cell lines with a concomitant down regulation of respective coreceptors was achieved with lentiviral vectors. When the siRNA expressing transduced cells were challenged with X4 and R5 tropic HIV-1, they demonstrated marked viral resistance. HIV-1 resistance was also observed in bispecific lentiviral vector transduced primary PBMCs. Conclusions Both CXCR4 and CCR5 coreceptors could be simultaneously targeted for down regulation by a single combinatorial lentiviral vector incorporating respective anti-coreceptor siRNAs. Stable down regulation of both the coreceptors protects cells against infection by both X4 and R5 tropic HIV-1. Stable down regulation of cellular molecules that aid in HIV-1 infection will be an effective strategy for long range HIV gene therapy.
Comparison of sampling methods to measure HIV RNA viral load in female genital tract secretions.

Science.gov (United States)

Jaumdally, Shameem Z; Jones, Heidi E; Hoover, Donald R; Gamieldien, Hoyam; Kriek, Jean-Mari; Langwenya, Nontokozo; Myer, Landon; Passmore, Jo-Ann S; Todd, Catherine S

2017-03-01

How does menstrual cup (MC) compare to other genital sampling methods for HIV RNA recovery? We compared HIV RNA levels between MC, endocervical swab (ECS), and ECS-enriched cervicovaginal lavage (eCVL) specimens in 51 HIV-positive, antiretroviral therapy-naive women at enrollment, 3 and 6 months, with order rotated by visit. Paired comparisons were analyzed with McNemar's exact tests, signed-rank tests, and an extension of Somer's D for pooled analyses across visits. MC specimens had the highest proportion of quantifiable HIV VL at enrollment and month 3, but more MC specimens (n=12.8%) were insufficient for testing, compared with ECS (2%, P=0.006) and eCVL (0%, P<0.001). Among sufficient specimens, median VL was significantly higher for MC (2.62 log 10 copies/mL) compared to ECS (1.30 log 10 copies/mL, P<0.001) and eCVL (1.60 log 10 copies/mL, P<0.001) across visits. MC may be more sensitive than eCVL and CVS, provided insufficient specimens are reduced. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.
Engineering HIV-1-resistant T-cells from short-hairpin RNA-expressing hematopoietic stem/progenitor cells in humanized BLT mice.

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Gene-Errol E Ringpis

Full Text Available Down-regulation of the HIV-1 coreceptor CCR5 holds significant potential for long-term protection against HIV-1 in patients. Using the humanized bone marrow/liver/thymus (hu-BLT mouse model which allows investigation of human hematopoietic stem/progenitor cell (HSPC transplant and immune system reconstitution as well as HIV-1 infection, we previously demonstrated stable inhibition of CCR5 expression in systemic lymphoid tissues via transplantation of HSPCs genetically modified by lentiviral vector transduction to express short hairpin RNA (shRNA. However, CCR5 down-regulation will not be effective against existing CXCR4-tropic HIV-1 and emergence of resistant viral strains. As such, combination approaches targeting additional steps in the virus lifecycle are required. We screened a panel of previously published shRNAs targeting highly conserved regions and identified a potent shRNA targeting the R-region of the HIV-1 long terminal repeat (LTR. Here, we report that human CD4(+ T-cells derived from transplanted HSPC engineered to co-express shRNAs targeting CCR5 and HIV-1 LTR are resistant to CCR5- and CXCR4- tropic HIV-1-mediated depletion in vivo. Transduction with the combination vector suppressed CXCR4- and CCR5- tropic viral replication in cell lines and peripheral blood mononuclear cells in vitro. No obvious cytotoxicity or interferon response was observed. Transplantation of combination vector-transduced HSPC into hu-BLT mice resulted in efficient engraftment and subsequent stable gene marking and CCR5 down-regulation in human CD4(+ T-cells within peripheral blood and systemic lymphoid tissues, including gut-associated lymphoid tissue, a major site of robust viral replication, for over twelve weeks. CXCR4- and CCR5- tropic HIV-1 infection was effectively inhibited in hu-BLT mouse spleen-derived human CD4(+ T-cells ex vivo. Furthermore, levels of gene-marked CD4(+ T-cells in peripheral blood increased despite systemic infection with either
The temporal relationship between advertising and sales of low‐tar cigarettes

Science.gov (United States)

Reed, Mark B; Anderson, Christy M; Burns, David M

2006-01-01

Objective and hypothesis To determine whether a temporal relationship exists between the advertising and sales of low‐tar cigarettes. It was hypothesised that increases in the advertising of low‐tar cigarettes would precede increases in sales for these cigarettes. Methods The themes of cigarette advertisements were reviewed and coded for 20 low‐tar cigarette brands advertised in 13 widely read magazines in the US between 1960 and 1996. These 20 brands represented most of the low‐tar cigarette advertisements and cigarette sales from 1967 to 1996. Cigarette sales data were obtained from the 1994 Maxwell report that summarises all cigarette sales from 1925 to 1990. If the advertisement referred to the low‐tar attributes of the cigarette advertised, the advertisement was coded as having a low‐tar theme and was included in the analysis. Results Five different graphical presentations of the relationship between the advertising and sales of the 20 low‐tar cigarette brands showed a temporal relationship between low‐tar advertising and sales for these brands. This relationship was observed for brands that introduced a low‐tar alternative into an existing brand family (eg, Marlboro Light) and for new exclusively low‐tar brands (eg, Carlton). Despite large increases in the advertising for the exclusively low‐tar brands, sales of these brands remained low relative to sales of the low‐tar alternative brands. Conclusions Increases in print advertising of 20 of the most popular low‐tar cigarette brands were followed by increases in sales for these cigarettes. Despite increases in the advertising of exclusively low‐tar brands in the mid‐1970s and early 1980s, the sales of these brands never matched the sales of the low‐tar alternative brands. This suggests that it may have been easier to get smokers to switch to low‐tar brands within a brand family compared with entirely new low‐tar brands. Over the past 30 years, the marketing of low‐tar
Structure and Mechanism of Staphylococcus aureus TarS, the Wall Teichoic Acid β-glycosyltransferase Involved in Methicillin Resistance.

Directory of Open Access Journals (Sweden)

Solmaz Sobhanifar

2016-12-01

Full Text Available In recent years, there has been a growing interest in teichoic acids as targets for antibiotic drug design against major clinical pathogens such as Staphylococcus aureus, reflecting the disquieting increase in antibiotic resistance and the historical success of bacterial cell wall components as drug targets. It is now becoming clear that β-O-GlcNAcylation of S. aureus wall teichoic acids plays a major role in both pathogenicity and antibiotic resistance. Here we present the first structure of S. aureus TarS, the enzyme responsible for polyribitol phosphate β-O-GlcNAcylation. Using a divide and conquer strategy, we obtained crystal structures of various TarS constructs, mapping high resolution overlapping N-terminal and C-terminal structures onto a lower resolution full-length structure that resulted in a high resolution view of the entire enzyme. Using the N-terminal structure that encapsulates the catalytic domain, we furthermore captured several snapshots of TarS, including the native structure, the UDP-GlcNAc donor complex, and the UDP product complex. These structures along with structure-guided mutants allowed us to elucidate various catalytic features and identify key active site residues and catalytic loop rearrangements that provide a valuable platform for anti-MRSA drug design. We furthermore observed for the first time the presence of a trimerization domain composed of stacked carbohydrate binding modules, commonly observed in starch active enzymes, but adapted here for a poly sugar-phosphate glycosyltransferase.
Liver stiffness is not associated with short- and long-term plasma HIV RNA replication in immunocompetent patients with HIV infection and with HIV/HCV coinfection

Science.gov (United States)

Parisi, Saverio Giuseppe; Basso, Monica; Mengoli, Carlo; Scaggiante, Renzo; Andreis, Samantha; Franzetti, Marzia Maria; Cattelan, Anna Maria; Zago, Daniela; Cruciani, Mario; Andreoni, Massimo; Piovesan, Sara; Palù, Giorgio; Alberti, Alfredo

2017-01-01

Background Human immunodeficiency virus (HIV) may be directly responsible for liver damage but there are contrasting data regarding the influence of detectable plasma viremia. We analyzed the influence of plasma HIV RNA (pHIV) detectability and of other clinical and viro-immunological variables on liver stiffness (LS) measurement in adult immunocompetent HIV-monoinfected patients and in patients coinfected with hepatitis C virus (HCV). Methods Logistic regression analysis was performed using the value of LS>7.1 kPa as the dependent variable. A linear regression model was applied using LS measurement after log10 transformation (lkpa) as the dependent variable and we analyzed the predicted values versus the observed lkpa values; pHIV was classified as detectable or undetectable in the 12- and 36-month study periods before LS measurement. Results We studied 251 patients (178 with HIV monoinfection), most of whom were on antiviral treatment; 36-month study time was available for 154 subjects. The mean CD4+ cell count was 634 cells/mm3 in HIV-monoinfected patients and 606 cells/mm3 in coinfected patients. No difference in LS was found between patients with detectable or undetectable pHIV in either the 12- or the 36-month study period before transient elastography. The mean LS was higher in HIV/HCV coinfected patients (P<0.0001) than in the HIV-monoinfected subjects; lkpa was positively correlated with HCV coinfection (P<0.0001) and aspartate aminotransferase levels (P<0.0001). Detectable pHIV failed to reach significance. Eight HIV-monoinfected patients had a predicted LS measurement lower than the observed one, while eight patients had the opposite result. Conclusion LS was not correlated with ongoing HIV replication during the 12- and 36-month study periods in immunocompetent HIV-monoinfected and HIV/HCV-coinfected patients. PMID:28845109
Stability of hepatitis C virus (HCV) RNA levels among interferon-naïve HIV/HCV-coinfected individuals treated with combination antiretroviral therapy

DEFF Research Database (Denmark)

Grint, D; Peters, L; Reekie, J

2013-01-01

Infection with hepatitis C virus (HCV) is a major cause of chronic liver disease. High HCV RNA levels have been associated with poor treatment response. This study aimed to examine the natural history of HCV RNA in chronically HCV/HIV-coinfected individuals.......Infection with hepatitis C virus (HCV) is a major cause of chronic liver disease. High HCV RNA levels have been associated with poor treatment response. This study aimed to examine the natural history of HCV RNA in chronically HCV/HIV-coinfected individuals....
Ebola Virus RNA in Semen from an HIV-Positive Survivor of Ebola.

Science.gov (United States)

Purpura, Lawrence J; Rogers, Emerson; Baller, April; White, Stephen; Soka, Moses; Choi, Mary J; Mahmoud, Nuha; Wasunna, Christine; Massaquoi, Moses; Kollie, Jomah; Dweh, Straker; Bemah, Philip; Ladele, Victor; Kpaka, Jonathan; Jawara, Mary; Mugisha, Margaret; Subah, Onyekachi; Faikai, Mylene; Bailey, Jeff A; Rollin, Pierre; Marston, Barbara; Nyenswah, Tolbert; Gasasira, Alex; Knust, Barbara; Nichol, Stuart; Williams, Desmond

2017-04-01

Ebola virus is known to persist in semen of male survivors of Ebola virus disease (EVD). However, maximum duration of, or risk factors for, virus persistence are unknown. We report an EVD survivor with preexisting HIV infection, whose semen was positive for Ebola virus RNA 565 days after recovery from EVD.
Characterization of Tar Deposits, Extraction and Sorption Properties

Directory of Open Access Journals (Sweden)

Pryszcz Adrian

2016-06-01

Full Text Available The main goal of this paper was to characterize and find a useful solution for the decomposition of tar deposits. For the experimental part, tar deposits, formed by polymerization and condensation reactions, were chosen from a storage tank for tars. At first the initial analyses of tar deposits (elemental, thermogravimetric, and calorimetric analyses were performed. After the characterization, the tar deposits were extracted in the Soxhlet extractor by acetone, toluene, and quinolone and activated with potassium hydroxide. As the final step of this work, the sorption characterization on the 3Flex Surface Characterization Analyzer (Micromeritics was performed. The specific surface area of the samples was evaluated using two methods - a single point measurement at p/p0=0.2 and BET method. Micropore and external surface areas were calculated based on a t-plot analysis (carbon black model.
A miRNA Signature for Cognitive Deficits and Alcohol Use Disorder in Persons Living with HIV/AIDS

Directory of Open Access Journals (Sweden)

Dorota Wyczechowska

2017-11-01

Full Text Available HIV-associated neurocognitive disorders (HAND affects more than half of persons living with HIV-1/AIDS (PLWHA. Identification of biomarkers representing the cognitive status of PLWHA is a critical step for implementation of successful cognitive, behavioral and pharmacological strategies to prevent onset and progression of HAND. However, the presence of co-morbidity factors in PLWHA, the most common being substance abuse, can prevent the identification of such biomarkers. We have optimized a protocol to profile plasma miRNAs using quantitative RT-qPCR and found a miRNA signature with very good discriminatory ability to distinguish PLWHA with cognitive impairment from those without cognitive impairment. Here, we have evaluated this miRNA signature in PLWHA with alcohol use disorder (AUD at LSU Health Sciences Center (LSUHSC. The results show that AUD is a potential confounding factor for the miRNAs associated with cognitive impairment in PLWHA. Furthermore, we have investigated the miRNA signature associated with cognitive impairment in an independent cohort of PLWHA using plasma samples from the CNS HIV Antiretroviral Therapy Effects Research (CHARTER program. Despite differences between the two cohorts in socioeconomic status, AUD, and likely misuse of illicit or prescription drugs, we validated a miRNA signature for cognitive deficits found at LSUHSC in the CHARTER samples.
Combinatorial microRNA target predictions

DEFF Research Database (Denmark)

Krek, Azra; Grün, Dominic; Poy, Matthew N.

2005-01-01

MicroRNAs are small noncoding RNAs that recognize and bind to partially complementary sites in the 3' untranslated regions of target genes in animals and, by unknown mechanisms, regulate protein production of the target transcript1, 2, 3. Different combinations of microRNAs are expressed...... in different cell types and may coordinately regulate cell-specific target genes. Here, we present PicTar, a computational method for identifying common targets of microRNAs. Statistical tests using genome-wide alignments of eight vertebrate genomes, PicTar's ability to specifically recover published micro......RNA targets, and experimental validation of seven predicted targets suggest that PicTar has an excellent success rate in predicting targets for single microRNAs and for combinations of microRNAs. We find that vertebrate microRNAs target, on average, roughly 200 transcripts each. Furthermore, our results...
Persistent CSF but not Plasma HIV RNA, is Associated with Increased Risk of New-onset Moderate-to-Severe Depressive Symptoms; A Prospective Cohort Study

Science.gov (United States)

Hammond, Edward R.; Crum, Rosa M.; Treisman, Glenn J.; Mehta, Shruti H.; Clifford, David B.; Ellis, Ronald J.; Gelman, Benjamin B.; Grant, Igor; Letendre, Scott L.; Marra, Christina M; Morgello, Susan; Simpson, David M.; McArthur, Justin C.

2016-01-01

Major depressive disorder is the most common neuropsychiatric complication in human immunodeficiency virus (HIV) infections and is associated with worse clinical outcomes. We determined if detectable cerebrospinal fluid (CSF) HIV ribonucleic acid (RNA) at threshold ≥50 copies/ml is associated with increased risk of depression. The CNS HIV Anti-Retroviral Therapy Effects Research (CHARTER) cohort is a six-center US-based prospective cohort with bi-annual follow-up 674 participants. We fit linear mixed models (N=233) and discrete-time survival models (N=154; 832 observations), to evaluate trajectories of Beck Depression Inventory (BDI) II scores, and the incidence of new-onset moderate-to-severe depressive symptoms (BDI≥17) among participants, on combination antiretroviral therapy (cART), who were free of depression at study entry, and received a minimum of three CSF examinations over 2,496 person-months follow-up. Detectable CSF HIV RNA (threshold ≥50 copies/ml) at any visit was associated with a 4.7-fold increase in new-onset depression at subsequent visits adjusted for plasma HIV RNA and treatment adherence; hazard ratio (HR)=4.76, (95% CI: 1.58–14.3); P=0.006. Depression (BDI) scores were 2.53 points higher (95% CI: 0.47–4.60; P=0.02) over 6 months if CSF HIV RNA was detectable at a prior study visit in fully adjusted models including age, sex, race, education, plasma HIV RNA, duration and adherence of cART, and lifetime depression diagnosis by DSM-IV criteria. Persistent CSF but not plasma HIV RNA, is associated with an increased risk for new-onset depression. Further research evaluating the role of immune activation and inflammatory markers may improve our understanding of this association. PMID:26727907
Preparation of pure phenols from tars

Energy Technology Data Exchange (ETDEWEB)

Meyer, J

1929-06-18

A process is disclosed for preparing pure phenols from brown coal and shale tar, characterized in that the alkaline extract obtained from the tar is oxidized and concurrently the alkaline solution is separated from the existing impurities by heating with steam at high temperature, which finally reaches at least 150/sup 0/C.
New method for the exact determination of phenols in low-temperature tar and tar oils

Energy Technology Data Exchange (ETDEWEB)

Lambris, G; Haferkorn, H

1949-01-01

A 3-gram sample of water-free tar or tar oil containing approximately 50% phenols is dissolved in a mixture of benzene and xylene and a known excess of a 20% KOH solution of known normality saturated with benzene and xylene is added. Weight of the KOH is determined by difference. This mixture is shaken repeatedly in a 300-milliliter separatory funnel. After standing for 0.5 h, the dark or almost black phenolate solution containing the major portion is separated and weighed. Care must be taken to prevent the induction of solids. The phenolate in the residue is extracted with hot water and titrated with 0.2N HCl and 1 ml. Congo red (1:100). If water is present in the tar or tar oil, 100 ml of xylene is added immediately after weighing and the water separated by distillation the weight of which must be determined. Any phenols carried over are dissolved in the small quantity of xylene in the distillate. This quantity is added to the bulk of the xylene. After any remaining phenols are extracted from the tar residue with boiling benzene, the benzene-xylene mixture is treated with KOH as above. The accuracy of the method is estimated to be +-1% as shown by experiments with phenol; o-, m-, and p-cresol; cresol mixture; and pyrocatechol. The weight of the dissolved phenols X is determined by X = c - a + cd/(ab - d) where a = weight of KOH, b = HCl used per gram of KOH, C = weight of major portion of phenolate solution, which is formed by shaking the phenol solution with KOH, d = HCl used for titration of phenolate residue.
Schistosomiasis and HIV-1 infection in rural Zimbabwe: effect of treatment of schistosomiasis on CD4 cell count and plasma HIV-1 RNA load

DEFF Research Database (Denmark)

Kallestrup, Per; Zinyama, Rutendo; Gomo, Exnevia

2005-01-01

To determine whether treatment of schistosomiasis has an effect on the course of human immunodeficiency virus type 1 (HIV-1) infection, individuals with schistosomiasis and with or without HIV-1 infection were randomized to receive praziquantel treatment at inclusion or after a delay of 3 months......; 287 participants were included in the study, and 227 (79%) were followed up. Among the 130 participants who were coinfected, those who received early treatment (n=64) had a significantly lower increase in plasma HIV-1 RNA load than did those who received delayed treatment (n=66) (P...
Infrared absorption characteristics of hydroxyl groups in coal tars

Energy Technology Data Exchange (ETDEWEB)

Cannon, S A; Chu, C J; Hange, R H; Margrave, J L

1987-01-01

Tar evolution was observed over a temperature range of 150-600 C for four coals. Pittsburgh bituminous, Illinois No.6, Rawhide subbituminous, and Texas lignite. Isolation of the evolved tars in a nitrogen matrix at 15 degrees K produced better resolved infrared spectra than those in a coal matrix, thus enhancing structural characterization of the tar molecules. Two distinct hydroxyl functional groups in the tar molecules free of hydrogen bonding were identified for the first time without interference from H/sub 2/O absorptions. These absorptions at 3626.5 cm/sup -1/ have been assigned to phenolic hydroxyls. It is suggested that carboxylic and aliphatic hydroxyl groups do not survive the vaporization process. Tars from Illinois No.6 were found to contain the largest amount of phenolic hydroxyl; Pittsburgh No. 8 tar contains approximately half of that for Illinois No.6 while Rawhide and Texas lignite contain much less phenolic than either of the other coals. 10 references, 6 figures, 1 table.
Sunflower oil in the treatment of hot tar burns.

Science.gov (United States)

Türegün, M; Oztürk, S; Selmanpakoğlu, N

1997-08-01

Hot tar burns compose a unique class of thermal injury, because removal of this highly sticky compound may be very difficult without inflicting additional tissue damage. Early removal of tar facilitates assessment of the burn and improves patient comfort. Although the use of many substances for the painless removal of tar has been described, we used sunflower oil effectively in the treatment of four tar burn patients. This first report describes the practical and successful use of sunflower oil which was easily obtained from the hospital kitchen.
Tar dew point analyser as a tool in biomass gasification

Energy Technology Data Exchange (ETDEWEB)

Vreugdenhil, B.J.; Kuipers, J. [ECN Biomass, Coal and Environmental Research, Petten (Netherlands)

2008-08-15

Application of the Tar Dew point Analyzer (TDA) in different biomass based gasification systems and subsequent gas cleaning setups has been proven feasible. Such systems include BFB gasifiers, CFB gasifier and fixed bed gasifiers, with tar crackers or different scrubbers for tar removal. Tar dew points obtained with the TDA give direct insight in the performance of the gas cleaning section and help prevent any tar related problems due to condensation. The current TDA is capable of measuring tar dew points between -20 to 200C. This manuscript will present results from 4 different gasification setups. The range of measured tar dew points is -7 to 164C with comparable results from the calculated dew points based on the SPA measurements. Further detail will be presented on the differences between TDA and SPA results and explanations will be given for deviations that occurred. Improvements for the TDA regarding future work will be presented.
The catalytic cracking mechanism of lignite pyrolysis char on tar

International Nuclear Information System (INIS)

Lei, Z.; Huibin, H.; Xiangling, S.; Zhenhua, M.; Lei, Z.

2017-01-01

The influence of different pyrolysis conditions for tar catalytic cracking will be analyzed according to the lignite pyrolysis char as catalyst on pyrolytic tar in this paper. The pyrolysis char what is the by-product of the cracking of coal has an abundant of pore structure and it has good catalytic activity. On this basis, making the modified catalyst when the pyrolysis char is activation and loads Fe by impregnation method. The cracking mechanism of lignite pyrolytic tar is explored by applying gas chromatograph to analyze splitting products of tar. The experimental results showed that: (1) The effect of tar cracking as the pyrolysis temperature, the heating rate, the volatilization of pyrolysis char and particle size increasing is better and better. The effect of the catalytic and cracking of lignite pyrolysis char in tar is best when the heating rate, the pyrolysis temperature, the volatiles of pyrolysis char, particle size is in specific conditions.(2) The activation of pyrolysis char can improve the catalytic effect of pyrolysis char on the tar cracking. But it reduces the effect of the tar cracking when the pyrolysis char is activation loading Fe. (author)

Low-temperature tar and oil: properties and applications

Energy Technology Data Exchange (ETDEWEB)

Heinze, R

1942-01-01

In Germany the value of low-temperature tar is largely dependent on its fuel fractions; these vary with the coal and the method of carbonization (external heating or recirculated gases). Brown-coal tars can be processed by distillation, cracking under pressure, hydrogenation under pressure (largest volume of tar is processed by this method) and by solvent extraction, with EtOH, SO/sub 2/, or phenol. Each of these processes is discussed in detail. In the pressure-hydrogenation process, 1.25 kilogram of brown-coal tar yields approximately 1 kilogram of gasoline with an octane number of 60 to 70. Low-temperature tars from bituminous coals can be hydrogenated readily but are not well adapted to solvent extraction. Attempts should be made to produce tar approximating the desired characteristics for fuel directly from the carbonizing apparatus. For laboratory carbonization tests, an approximation to results secured by externally heated retorts is secured by using an insert consisting of a series of perforated trays in the 200-gram Fischer aluminum retort; this reduces the capacity to 100 gram. Fractional condensation is used to separate heavy oil, middle oil, and liquor; low-boiling products are condensed at -20/sup 0/ by solid CO/sub 2/.
Anti-HIV Antibody Responses and the HIV Reservoir Size during Antiretroviral Therapy.

Directory of Open Access Journals (Sweden)

Sulggi A Lee

Full Text Available A major challenge to HIV eradication strategies is the lack of an accurate measurement of the total burden of replication-competent HIV (the "reservoir". We assessed the association of anti-HIV antibody responses and the estimated size of the reservoir during antiretroviral therapy (ART.We evaluated anti-HIV antibody profiles using luciferase immunoprecipitation systems (LIPS assay in relation to several blood-based HIV reservoir measures: total and 2-LTR DNA (rtPCR or droplet digital PCR; integrated DNA (Alu PCR; unspliced RNA (rtPCR, multiply-spliced RNA (TILDA, residual plasma HIV RNA (single copy PCR, and replication-competent virus (outgrowth assay. We also assessed total HIV DNA and RNA in gut-associated lymphoid tissue (rtPCR. Spearman correlations and linear regressions were performed using log-transformed blood- or tissue-based reservoir measurements as predictors and log-transformed antibody levels as outcome variables.Among 51 chronically HIV-infected ART-suppressed participants (median age = 57, nadir CD4+ count = 196 cells/mm3, ART duration = 9 years, the most statistically significant associations were between antibody responses to integrase and HIV RNA in gut-associated lymphoid tissue (1.17 fold-increase per two-fold RNA increase, P = 0.004 and between antibody responses to matrix and integrated HIV DNA in resting CD4+ T cells (0.35 fold-decrease per two-fold DNA increase, P = 0.003. However, these associations were not statistically significant after a stringent Bonferroni-adjustment of P<0.00045. Multivariate models including age and duration of ART did not markedly alter results.Our findings suggest that anti-HIV antibody responses may reflect the size of the HIV reservoir during chronic treated HIV disease, possibly via antigen recognition in reservoir sites. Larger, prospective studies are needed to validate the utility of antibody levels as a measure of the total body burden of HIV during treatment.
Chemical-composition studies of low-temperature-carbonization coal tar

Energy Technology Data Exchange (ETDEWEB)

Edel' shtein, N G; Lanin, V A

1955-01-01

Pintsch-oven low-temperature tar was separated into its constituents by conventional methods, and the average of 2 results was neutral asphaltenes 12.56, basic asphaltenes 2.61, acid asphaltenes 18.82, phenols 13.23, bases 2.31, neutral oil 17.66, crystalline paraffins 7.34, silica-gel tars (I) (benzene extract) 15.40, I (acetone extract) 2.47, carbenes 0.45, and carbides and dust 1.44%. The low-temperature-tar asphaltenes and tars differ from shale-oil tars by being lower in C and higher in H, with a considerably higher C:H ratio. Their specific gravity is somewhat higher, and they are cyclic in structure. The asphaltenes and silica-gel tars of coal tar and shale oil were hydrogenated, molecular weights d/sub 4//sup 20/ and n/sub 4//sup 20/ of the separated compounds were determined, and empirical formulas of the hydrogenated compounds calculated. The neutral oil was separated into saturated, intermediate (iodine number 23), unsaturated (iodine number 51), a small quantity of a mixture of unsaturated and aromatic hydrocarbons, and 44.9% aromatic hydrocarbons. While naphthenes seem to be predominantly present in the neutral-oil fraction of shale oil, aromatic hydrocarbons are predominant in coal oil.
Process of transforming tars, etc

Energy Technology Data Exchange (ETDEWEB)

1929-04-11

A process is described for treating tars obtained by carbonization, at high or low temperature, of coals, lignites, shales, and other carbonaceous materials or fractions of these tars, for obtaining products of greater value, consisting of polymerizing or saturating the unstable hydrocarbons in the presence of catalyzers by the progressing action particularly of halogenated metals, such as titanium tetrachloride, iron chloride, etc. and applying a known process of recovery, the disclosed process leading to an important reduction of final losses.
Mineral oils, tars. [British patent

Energy Technology Data Exchange (ETDEWEB)

O' Brien, A M; Handmarch, E

1933-08-11

Hydrocarbon materials such as mineral oils and tars from coal, shale, lignite, or peat are freed from phenols and like oxy-bodies by heating under pressure in a closed vessel to a temperature and for a time sufficient to effect reduction of the oxy-bodies, and then removing the water formed by the reaction. 350/sup 0/ to 400/sup 0/C. for 30 to 60 minutes is suitable. Any wax-like constituents are converted to liquids of lower viscosity and settling point. The product may be fractionated to give light oils and a residue of aviation Diesel fuel. In an example, oil from the low-temperature distillation of coal and having a tar acid content of 30 per cent is treated in a tubular converter at 380/sup 0/C. and 400 lb. per sq. in for 40 min., and the benzine toluol, and xylol distilled; the residue has a tar acid content of only 7.6 per cent.
Production of HIV-1 vif mRNA Is Modulated by Natural Nucleotide Variations and SLSA1 RNA Structure in SA1D2prox Genomic Region

Directory of Open Access Journals (Sweden)

Masako Nomaguchi

2017-12-01

Full Text Available Genomic RNA of HIV-1 contains localized structures critical for viral replication. Its structural analysis has demonstrated a stem-loop structure, SLSA1, in a nearby region of HIV-1 genomic splicing acceptor 1 (SA1. We have previously shown that the expression level of vif mRNA is considerably altered by some natural single-nucleotide variations (nSNVs clustering in SLSA1 structure. In this study, besides eleven nSNVs previously identified by us, we totally found nine new nSNVs in the SLSA1-containing sequence from SA1, splicing donor 2, and through to the start codon of Vif that significantly affect the vif mRNA level, and designated the sequence SA1D2prox (142 nucleotides for HIV-1 NL4-3. We then examined by extensive variant and mutagenesis analyses how SA1D2prox sequence and SLSA1 secondary structure are related to vif mRNA level. While the secondary structure and stability of SLSA1 was largely changed by nSNVs and artificial mutations introduced to restore the original NL4-3 form from altered ones by nSNVs, no clear association of the two SLSA1 properties with vif mRNA level was observed. In contrast, when naturally occurring SA1D2prox sequences that contain multiple nSNVs were examined, we attained significant inverse correlation between the vif level and SLSA1 stability. These results may suggest that SA1D2prox sequence adapts over time, and also that the altered SA1D2prox sequence, SLSA1 stability, and vif level are mutually related. In total, we show here that the entire SA1D2prox sequence and SLSA1 stability critically contribute to the modulation of vif mRNA level.
Reaction Mechanism of Tar Evolution in Biomass Steam Gasification for Hydrogen Production

International Nuclear Information System (INIS)

Shingo Katayama; Masahiro Suzuki; Atsushi Tsutsumi

2006-01-01

Reaction mechanism of tar evolution in steam gasification of biomass was investigated with a continuous cross-flow moving bed type differential reactor, in which tar and gases can be fractionated according to reaction time. We estimated that time profile of tar and gas evolution in the gasification of cellulose, xylan, and lignin, and compared it with experimental product time profile of real biomass gasification. The experimental tar evolution rate is different from estimated tar evolution rate. The estimated tar evolution rate has a peak at 20 s. On the other hand, the experimental tar evolution rate at 20 s is little, and tar at initial stage includes more water-soluble and water-insoluble compounds. It can be concluded that in the real biomass steam gasification the evolution of tar from cellulose and lignin component was found to be precipitated by that from hemi-cellulose component. (authors)
Intracellular interactions between APOBEC3G, RNA, and HIV-1 Gag: APOBEC3G multimerization is dependent on its association with RNA

OpenAIRE

Friew, Yeshitila N; Boyko, Vitaly; Hu, Wei-Shau; Pathak, Vinay K

2009-01-01

Abstract Background Host restriction factor APOBEC3G (A3G) blocks human immunodeficiency virus type 1 (HIV-1) replication by G-to-A hypermutation, and by inhibiting DNA synthesis and provirus formation. Previous reports have suggested that A3G is a dimer and its virion incorporation is mediated through interactions with viral or nonviral RNAs and/or HIV-1 Gag. We have now employed a bimolecular fluorescence complementation assay (BiFC) to analyze the intracellular A3G-A3G, A3G-RNA, and A3G-Ga...
DECOMPOSITION OF TARS IN MICROWAVE PLASMA – PRELIMINARY RESULTS

Directory of Open Access Journals (Sweden)

Mateusz Wnukowski

2014-07-01

Full Text Available The paper refers to the main problem connected with biomass gasification - a presence of tar in a product gas. This paper presents preliminary results of tar decomposition in a microwave plasma reactor. It gives a basic insight into the construction and work of the plasma reactor. During the experiment, researches were carried out on toluene as a tar surrogate. As a carrier gas for toluene and as a plasma agent, nitrogen was used. Flow rates of the gases and the microwave generator’s power were constant during the whole experiment. Results of the experiment showed that the decomposition process of toluene was effective because the decomposition efficiency attained above 95%. The main products of tar decomposition were light hydrocarbons and soot. The article also gives plans for further research in a matter of tar removal from the product gas.
Independent alignment of RNA for dynamic studies using residual dipolar couplings

Energy Technology Data Exchange (ETDEWEB)

Bardaro, Michael F.; Varani, Gabriele, E-mail: varani@chem.washington.edu [University of Washington, Department of Chemistry (United States)

2012-09-15

Molecular motion and dynamics play an essential role in the biological function of many RNAs. An important source of information on biomolecular motion can be found in residual dipolar couplings which contain dynamics information over the entire ms-ps timescale. However, these methods are not fully applicable to RNA because nucleic acid molecules tend to align in a highly collinear manner in different alignment media. As a consequence, information on dynamics that can be obtained with this method is limited. In order to overcome this limitation, we have generated a chimeric RNA containing both the wild type TAR RNA, the target of our investigation of dynamics, as well as the binding site for U1A protein. When U1A protein was bound to the portion of the chimeric RNA containing its binding site, we obtained independent alignment of TAR by exploiting the physical chemical characteristics of this protein. This technique can allow the extraction of new information on RNA dynamics, which is particularly important for time scales not covered by relaxation methods where important RNA motions occur.
The connection domain in reverse transcriptase facilitates the in vivo annealing of tRNALys3 to HIV-1 genomic RNA

Directory of Open Access Journals (Sweden)

Niu Meijuan

2004-10-01

Full Text Available Abstract The primer tRNA for reverse transcription in HIV-1, tRNALys3, is selectively packaged into the virus during its assembly, and annealed to the viral genomic RNA. The ribonucleoprotein complex that is involved in the packaging and annealing of tRNALys into HIV-1 consists of Gag, GagPol, tRNALys, lysyl-tRNA synthetase (LysRS, and viral genomic RNA. Gag targets tRNALys for viral packaging through Gag's interaction with LysRS, a tRNALys-binding protein, while reverse transcriptase (RT sequences within GagPol (the thumb domain bind to tRNALys. The further annealing of tRNALys3 to viral RNA requires nucleocapsid (NC sequences in Gag, but not the NC sequences GagPol. In this report, we further show that while the RT connection domain in GagPol is not required for tRNALys3 packaging into the virus, it is required for tRNALys3 annealing to the viral RNA genome.
Recovery of very viscous lubricating oils from shale-tar, etc

Energy Technology Data Exchange (ETDEWEB)

Erdmann, E

1918-01-22

A process is disclosed for the recovery of very viscous lubricating oils from brown-coal tar and shale tar, consisting in driving off from the crude tar or the tar freed from volatile constituents after removal of paraffin by precipitation with a volatile solvent such as acetone or one of its homologs, the light oils more or less completely with superheated steam from about 200 to 250/sup 0/C without any outside heating over a free flame.
VAPOR PRESSURES AND HEATS OF VAPORIZATION OF PRIMARY COAL TARS

Energy Technology Data Exchange (ETDEWEB)

Eric M. Suuberg; Vahur Oja

1997-07-01

This project had as its main focus the determination of vapor pressures of coal pyrolysis tars. It involved performing measurements of these vapor pressures and from them, developing vapor pressure correlations suitable for use in advanced pyrolysis models (those models which explicitly account for mass transport limitations). This report is divided into five main chapters. Each chapter is a relatively stand-alone section. Chapter A reviews the general nature of coal tars and gives a summary of existing vapor pressure correlations for coal tars and model compounds. Chapter B summarizes the main experimental approaches for coal tar preparation and characterization which have been used throughout the project. Chapter C is concerned with the selection of the model compounds for coal pyrolysis tars and reviews the data available to us on the vapor pressures of high boiling point aromatic compounds. This chapter also deals with the question of identifying factors that govern the vapor pressures of coal tar model materials and their mixtures. Chapter D covers the vapor pressures and heats of vaporization of primary cellulose tars. Chapter E discusses the results of the main focus of this study. In summary, this work provides improved understanding of the volatility of coal and cellulose pyrolysis tars. It has resulted in new experimentally verified vapor pressure correlations for use in pyrolysis models. Further research on this topic should aim at developing general vapor pressure correlations for all coal tars, based on their molecular weight together with certain specific chemical characteristics i.e. hydroxyl group content.
Microstructure and properties of lignite tar and pitch. Part II

Energy Technology Data Exchange (ETDEWEB)

Walther, H

1954-01-01

Photomicrographs reveal the presence of crystalline wax which affects the working properties in lignite tars and pitch. The crystals are large needles after slow cooling and small after rapid cooling. The crystals are paraffinic in character. All samples were nonhomogeneous. Thus the properties of lignite tar and pitch are varied by the source of the lignite and history of the specimen, neither softening point nor dropping point seems to satisfactorily characterize these tars. The samples exhibit thixotropic behavior characteristic of a structural viscosity and show hysteresis loops on varying the working rate. The variations have hindered use of lignite tars and pitches except where solubility in a solvent such as coal tar oil can be used to advantage.
Catalytic destruction of tar in biomass derived producer gas

International Nuclear Information System (INIS)

Zhang Ruiqin; Brown, Robert C.; Suby, Andrew; Cummer, Keith

2004-01-01

The purpose of this study is to investigate catalytic destruction of tar formed during gasification of biomass, with the goal of improving the quality of the producer gas. This work focuses on nickel based catalysts treated with alkali in an effort to promote steam gasification of the coke that deposits on catalyst surfaces. A tar conversion system consisting of a guard bed and catalytic reactor was designed to treat the producer gas from an air blown, fluidized bed biomass gasifier. The guard bed used dolomite to crack the heavy tars. The catalytic reactor was used to evaluate three commercial steam reforming catalysts. These were the ICI46-1 catalyst from Imperial Chemical Industry and Z409 and RZ409 catalysts from Qilu Petrochemical Corp. in China. A 0.5-3 l/min slipstream from a 5 tpd biomass gasifier was used to test the tar conversion system. Gas and tar were sampled before and after the tar conversion system to evaluate the effectiveness of the system. Changes in gas composition as functions of catalytic bed temperature, space velocity and steam/TOC (total organic carbon) ratio are presented. Structural changes in the catalysts during the tests are also described
Characterization of acid tars

Energy Technology Data Exchange (ETDEWEB)

Leonard, Sunday A., E-mail: sunday.leonard@ucl.ac.uk [Department of Civil Environmental and Geomatic Engineering, University College London, Chadwick Building, Gower Street, London, WC1E 6BT (United Kingdom); Stegemann, Julia A. [Department of Civil Environmental and Geomatic Engineering, University College London, Chadwick Building, Gower Street, London, WC1E 6BT (United Kingdom); Roy, Amitava [J. Bennett Johnston, Sr., Centre for Advance Microstructures and Devices (CAMD), 6980 Jefferson Highway, Louisiana State University, Baton Rouge, LA, 70806 (United States)

2010-03-15

Acid tars from the processing of petroleum and petrochemicals using sulfuric acid were characterized by gas chromatography/mass spectrometry (GC/MS), inductively coupled plasma/optical emission spectrometry (ICP/OES), differential scanning calorimetry (DSC), Fourier transform infrared (FTIR) spectrometry, and scanning electron microscopy/energy dispersive X-ray (SEM/EDX) micro-analysis. Leaching of contaminants from the acid tars in 48 h batch tests with distilled water at a liquid-to-solid ratio 10:1 was also studied. GC/MS results show that the samples contained aliphatic hydrocarbons, cyclic hydrocarbons, up to 12 of the 16 USEPA priority polycyclic aromatic hydrocarbons (PAHs), and numerous other organic groups, including organic acids (sulfonic acids, carboxylic acids and aromatic acids), phenyl, nitrile, amide, furans, thiophenes, pyrroles, and phthalates, many of which are toxic. Metals analysis shows that Pb was present in significant concentration. DSC results show different transition peaks in the studied samples, demonstrating their complexity and variability. FTIR analysis further confirmed the presence of the organic groups detected by GC/MS. The SEM/EDX micro-analysis results provided insight on the surface characteristics of the samples and show that contaminants distribution was heterogeneous. The results provide useful data on the composition, complexity, and variability of acid tars; information which hitherto have been scarce in public domain.
Characterization of acid tars

International Nuclear Information System (INIS)

Leonard, Sunday A.; Stegemann, Julia A.; Roy, Amitava

2010-01-01

Acid tars from the processing of petroleum and petrochemicals using sulfuric acid were characterized by gas chromatography/mass spectrometry (GC/MS), inductively coupled plasma/optical emission spectrometry (ICP/OES), differential scanning calorimetry (DSC), Fourier transform infrared (FTIR) spectrometry, and scanning electron microscopy/energy dispersive X-ray (SEM/EDX) micro-analysis. Leaching of contaminants from the acid tars in 48 h batch tests with distilled water at a liquid-to-solid ratio 10:1 was also studied. GC/MS results show that the samples contained aliphatic hydrocarbons, cyclic hydrocarbons, up to 12 of the 16 USEPA priority polycyclic aromatic hydrocarbons (PAHs), and numerous other organic groups, including organic acids (sulfonic acids, carboxylic acids and aromatic acids), phenyl, nitrile, amide, furans, thiophenes, pyrroles, and phthalates, many of which are toxic. Metals analysis shows that Pb was present in significant concentration. DSC results show different transition peaks in the studied samples, demonstrating their complexity and variability. FTIR analysis further confirmed the presence of the organic groups detected by GC/MS. The SEM/EDX micro-analysis results provided insight on the surface characteristics of the samples and show that contaminants distribution was heterogeneous. The results provide useful data on the composition, complexity, and variability of acid tars; information which hitherto have been scarce in public domain.
Ultrasound assisted, thermally activated persulfate oxidation of coal tar DNAPLs.

Science.gov (United States)

Peng, Libin; Wang, Li; Hu, Xingting; Wu, Peihui; Wang, Xueqing; Huang, Chumei; Wang, Xiangyang; Deng, Dayi

2016-11-15

The feasibility of ultrasound assisted, thermally activated persulfate for effective oxidation of twenty 2-6 ringed coal tar PAHs in a biphasic tar/water system and a triphasic tar/soil/water system were investigated and established. The results indicate that ultrasonic assistance, persulfate and elevated reaction temperature are all required to achieve effective oxidation of coal tar PAHs, while the heating needed can be provided by ultrasonic induced heating as well. Further kinetic analysis reveals that the oxidation of individual PAH in the biphasic tar/water system follows the first-order kinetics, and individual PAH oxidation rate is primary determined by the mass transfer coefficients, tar/water interfacial areas, the aqueous solubility of individual PAH and its concentration in coal tar. Based on the kinetic analysis and experimental results, the contributions of ultrasound, persulfate and elevated reaction temperature to PAHs oxidation were characterized, and the effects of ultrasonic intensity and oxidant dosage on PAHs oxidation efficiency were investigated. In addition, the results indicate that individual PAH degradability is closely related to its reactivity as well, and the high reactivity of 4-6 ringed PAHs substantially improves their degradability. Copyright © 2016 Elsevier B.V. All rights reserved.
Production of oil from Intermountain West tar sands deposits

Energy Technology Data Exchange (ETDEWEB)

Glassett, J.M.; Glassett, J.A.

1976-03-01

Six tar sand deposits in the Intermountain West, each containing more than one billion barrels of oil in place, are identified. All of these deposits are in eastern Utah and contain a total of twenty-eight billion barrels of oil. The names of the six deposits arranged in descending order of desirability for large-scale surface-mining oil recovery operations are as follows: Sunnyside, Tar Sand Triangle, Asphalt Ridge, P.R. Spring, Circle Cliffs, and Hill Creek. An overview of each deposit is presented including geology, surface-mining variables, chemical processing variables, environmental aspects, and economics. A comparison of Utah tar sands and Athabasca, Alberta, Canada tar sands is also presented.
Detecting microRNA activity from gene expression data

LENUS (Irish Health Repository)

Madden, Stephen F

2010-05-18

Abstract Background MicroRNAs (miRNAs) are non-coding RNAs that regulate gene expression by binding to the messenger RNA (mRNA) of protein coding genes. They control gene expression by either inhibiting translation or inducing mRNA degradation. A number of computational techniques have been developed to identify the targets of miRNAs. In this study we used predicted miRNA-gene interactions to analyse mRNA gene expression microarray data to predict miRNAs associated with particular diseases or conditions. Results Here we combine correspondence analysis, between group analysis and co-inertia analysis (CIA) to determine which miRNAs are associated with differences in gene expression levels in microarray data sets. Using a database of miRNA target predictions from TargetScan, TargetScanS, PicTar4way PicTar5way, and miRanda and combining these data with gene expression levels from sets of microarrays, this method produces a ranked list of miRNAs associated with a specified split in samples. We applied this to three different microarray datasets, a papillary thyroid carcinoma dataset, an in-house dataset of lipopolysaccharide treated mouse macrophages, and a multi-tissue dataset. In each case we were able to identified miRNAs of biological importance. Conclusions We describe a technique to integrate gene expression data and miRNA target predictions from multiple sources.

Detecting microRNA activity from gene expression data.

LENUS (Irish Health Repository)

Madden, Stephen F

2010-01-01

BACKGROUND: MicroRNAs (miRNAs) are non-coding RNAs that regulate gene expression by binding to the messenger RNA (mRNA) of protein coding genes. They control gene expression by either inhibiting translation or inducing mRNA degradation. A number of computational techniques have been developed to identify the targets of miRNAs. In this study we used predicted miRNA-gene interactions to analyse mRNA gene expression microarray data to predict miRNAs associated with particular diseases or conditions. RESULTS: Here we combine correspondence analysis, between group analysis and co-inertia analysis (CIA) to determine which miRNAs are associated with differences in gene expression levels in microarray data sets. Using a database of miRNA target predictions from TargetScan, TargetScanS, PicTar4way PicTar5way, and miRanda and combining these data with gene expression levels from sets of microarrays, this method produces a ranked list of miRNAs associated with a specified split in samples. We applied this to three different microarray datasets, a papillary thyroid carcinoma dataset, an in-house dataset of lipopolysaccharide treated mouse macrophages, and a multi-tissue dataset. In each case we were able to identified miRNAs of biological importance. CONCLUSIONS: We describe a technique to integrate gene expression data and miRNA target predictions from multiple sources.
Application of organic geochemistry to coastal tar residues from central California

Energy Technology Data Exchange (ETDEWEB)

Kvenvolden, K.A.; Rosenbauer, R.J.; Hostettler, F.D.; Lorenson, T.D.

2000-01-01

Tar residues are common on the Monterey Bay National Marine Sanctuary. These coastal tar residues have been washed ashore and usually occur on headlands near the high-tide line. In this study, 18 coastal tar residues were collected and analyzed to determine their carbon isotopic compositions and values of selected biomarker ratios. All of the residues have very heavy ({sup 13}C-enriched) carbon isotopic compositions spanning a narrow range ({delta}{sup 13}C = {minus}22.2 to {minus}23.4{per{underscore}thousand}), and 28,30-bisnorhopane is present in all samples. These same geochemical characteristics are found in Monterey Formation oils from which the coastal tar residues were likely derived. These coastal residues could result from natural seeps or from accidental spills. Statistically the coastal tar residues can be organized into three groups, each of which may represent different spill or seep events. Seven samples of potential local representative sources for the tar residues were examined, but none could account for the coastal tars.
Study on tar generated from downdraft gasification of oil palm fronds.

Science.gov (United States)

Atnaw, Samson Mekbib; Kueh, Soo Chuan; Sulaiman, Shaharin Anwar

2014-01-01

One of the most challenging issues concerning the gasification of oil palm fronds (OPF) is the presence of tar and particulates formed during the process considering its high volatile matter content. In this study, a tar sampling train custom built based on standard tar sampling protocols was used to quantify the gravimetric concentration of tar (g/Nm3) in syngas produced from downdraft gasification of OPF. The amount of char, ash, and solid tar produced from the gasification process was measured in order to account for the mass and carbon conversion efficiency. Elemental analysis of the char and solid tar samples was done using ultimate analysis machine, while the relative concentration of the different compounds in the liquid tar was determined making use of a liquid gas chromatography (GC) unit. Average tar concentration of 4.928 g/Nm3 and 1.923 g/Nm3 was obtained for raw gas and cleaned gas samples, respectively. Tar concentration in the raw gas sample was found to be higher compared to results for other biomass materials, which could be attributed to the higher volatile matter percentage of OPF. Average cleaning efficiency of 61% which is comparable to that of sand bed filter and venturi scrubber cleaning systems reported in the literature was obtained for the cleaning system proposed in the current study.
Study on Tar Generated from Downdraft Gasification of Oil Palm Fronds

Directory of Open Access Journals (Sweden)

Samson Mekbib Atnaw

2014-01-01

Full Text Available One of the most challenging issues concerning the gasification of oil palm fronds (OPF is the presence of tar and particulates formed during the process considering its high volatile matter content. In this study, a tar sampling train custom built based on standard tar sampling protocols was used to quantify the gravimetric concentration of tar (g/Nm3 in syngas produced from downdraft gasification of OPF. The amount of char, ash, and solid tar produced from the gasification process was measured in order to account for the mass and carbon conversion efficiency. Elemental analysis of the char and solid tar samples was done using ultimate analysis machine, while the relative concentration of the different compounds in the liquid tar was determined making use of a liquid gas chromatography (GC unit. Average tar concentration of 4.928 g/Nm3 and 1.923 g/Nm3 was obtained for raw gas and cleaned gas samples, respectively. Tar concentration in the raw gas sample was found to be higher compared to results for other biomass materials, which could be attributed to the higher volatile matter percentage of OPF. Average cleaning efficiency of 61% which is comparable to that of sand bed filter and venturi scrubber cleaning systems reported in the literature was obtained for the cleaning system proposed in the current study.
Study on Tar Generated from Downdraft Gasification of Oil Palm Fronds

Science.gov (United States)

Atnaw, Samson Mekbib; Kueh, Soo Chuan; Sulaiman, Shaharin Anwar

2014-01-01

One of the most challenging issues concerning the gasification of oil palm fronds (OPF) is the presence of tar and particulates formed during the process considering its high volatile matter content. In this study, a tar sampling train custom built based on standard tar sampling protocols was used to quantify the gravimetric concentration of tar (g/Nm3) in syngas produced from downdraft gasification of OPF. The amount of char, ash, and solid tar produced from the gasification process was measured in order to account for the mass and carbon conversion efficiency. Elemental analysis of the char and solid tar samples was done using ultimate analysis machine, while the relative concentration of the different compounds in the liquid tar was determined making use of a liquid gas chromatography (GC) unit. Average tar concentration of 4.928 g/Nm3 and 1.923 g/Nm3 was obtained for raw gas and cleaned gas samples, respectively. Tar concentration in the raw gas sample was found to be higher compared to results for other biomass materials, which could be attributed to the higher volatile matter percentage of OPF. Average cleaning efficiency of 61% which is comparable to that of sand bed filter and venturi scrubber cleaning systems reported in the literature was obtained for the cleaning system proposed in the current study. PMID:24526899
Final Safety Assessment of Coal Tar as Used in Cosmetics

Energy Technology Data Exchange (ETDEWEB)

NONE

2008-07-01

Coal Tar is a semisolid by-product obtained in the destructive distillation of bituminous coal, which functions in cosmetic products as a cosmetic biocide and denaturant-antidandruff agent is also listed as a function, but this is considered an over-the-counter (OTC) drug use. In 2002, Coal Tar was reported to the Food and Drug Administration (FDA) to be used in four formulations, all of which appear to be OTC drug products. Coal Tar is monographed by the FDA as Category I (safe and effective) OTC drug ingredient for use in the treatment of dandruff, seborrhoea, and psoriasis. Coal Tar is absorbed through the skin of animals and humans and is systemically distributed. Although the Cosmetic Ingredient Review (CIR) Expert Panel believes that Coal Tar use as an antidandruff ingredient in OTC drug preparations is adequately addressed by the FDA regulations, the Panel also believes that the appropriate concentration of use of Coal Tar in cosmetic formulations should be that level that does not have a biological effect in the user. Additional data needed to make a safety assessment include product types in which Coal Tar is used (other than as an OTC drug ingredient), use concentrations, and the maximum concentration that does not induce a biological effect in users.
Improved detection of CXCR4-using HIV by V3 genotyping: application of population-based and "deep" sequencing to plasma RNA and proviral DNA.

Science.gov (United States)

Swenson, Luke C; Moores, Andrew; Low, Andrew J; Thielen, Alexander; Dong, Winnie; Woods, Conan; Jensen, Mark A; Wynhoven, Brian; Chan, Dennison; Glascock, Christopher; Harrigan, P Richard

2010-08-01

Tropism testing should rule out CXCR4-using HIV before treatment with CCR5 antagonists. Currently, the recombinant phenotypic Trofile assay (Monogram) is most widely utilized; however, genotypic tests may represent alternative methods. Independent triplicate amplifications of the HIV gp120 V3 region were made from either plasma HIV RNA or proviral DNA. These underwent standard, population-based sequencing with an ABI3730 (RNA n = 63; DNA n = 40), or "deep" sequencing with a Roche/454 Genome Sequencer-FLX (RNA n = 12; DNA n = 12). Position-specific scoring matrices (PSSMX4/R5) (-6.96 cutoff) and geno2pheno[coreceptor] (5% false-positive rate) inferred tropism from V3 sequence. These methods were then independently validated with a separate, blinded dataset (n = 278) of screening samples from the maraviroc MOTIVATE trials. Standard sequencing of HIV RNA with PSSM yielded 69% sensitivity and 91% specificity, relative to Trofile. The validation dataset gave 75% sensitivity and 83% specificity. Proviral DNA plus PSSM gave 77% sensitivity and 71% specificity. "Deep" sequencing of HIV RNA detected >2% inferred-CXCR4-using virus in 8/8 samples called non-R5 by Trofile, and <2% in 4/4 samples called R5. Triplicate analyses of V3 standard sequence data detect greater proportions of CXCR4-using samples than previously achieved. Sequencing proviral DNA and "deep" V3 sequencing may also be useful tools for assessing tropism.
UTILIZATION OF AQUEOUS-TAR CONDENSATES FORMED DURING GASIFICATION

Directory of Open Access Journals (Sweden)

Anna Kwiecińska

2016-11-01

Full Text Available Gasification of solid fuels is an alternative process for energy production using conventional and renewable fuels. Apart from desired compounds, i.e. carbon oxide, hydrogen and methane, the produced gas contains complex organic (tars and inorganic (carbonizate, ammonia contaminants. Those substances, together with water vapor, condensate during cooling of the process gas, what results in the formation of aqueous-tar condensate, which requires proper methods of utilization. The management of this stream is crucial for commercialization and application of the gasification technology. In the paper the treatment of aqueous-tar condensates formed during biomass gasification process is discussed. The removal of tars from the stream was based on their spontaneous separation. The aqueous stream was subjected to ultrafiltration operated at different pressures. Such a treatment configuration enabled to obtain highly concentrated retentate, which could be recycled to the gasifier, and filtrate, which could be subjected to further treatment.
Evaluation of lignite tar

Energy Technology Data Exchange (ETDEWEB)

Gossedin, A

1946-01-01

Tar from the low-temperature (450/sup 0/) carbonization of lignite from Bouches-du-Rhone was hydrogenated in the presence of a catalyst based on MoS/sub 2/ with a 3:1 H:N mixture. Processing (at 470/sup 0/ and 400 atmospheres) for maximum production of gasoline yielded 86 wt % of a product of boiling 55 to 186/sup 0/ and motor octane number 75. An alternative is to hydrogenate with a view to producing solvents and lubricants. For this purpose the tar was separated by distillation (at 20 millimeters, cutting at 220/sup 0/) into two fractions of equal volume. On hydrogenation (at 300/sup 0/ and 400 atmospheres) the light part yields a gasoline H/sub 2/O-soluble cut, a highly aromatic solvent fraction, a heavier cut (280/sup 0/ to 320/sup 0/) suitable as a plasticizer, and a phenol fraction. The heavier part of the tar is hydrogenated (at 380/sup 0/ and 400 atmospheres) to give spindle oil and lubricating oil of medium eta (11.2 centistokes at 98.2/sup 0/), moderate eta index (64), good pour point (-7/sup 0/), and good oxidizing characteristics. The overall yield of products from the two portions is 86.9% (gasoline and solvent 32, light phenols 9.7, spindle oil 14.2, medium lubricating oil 25.7, wax, 5.3%).
Modeling Tar Recirculation in Biomass Fluidized Bed Gasification

NARCIS (Netherlands)

Heineken, Wolfram; De la Cuesta de Cal, Daniel; Zobel, Nico

2016-01-01

A biomass gasification model is proposed and applied to investigate the benefits of tar recirculation within a gasification plant. In the model, tar is represented by the four species phenol, toluene, naphthalene, and benzene. The model is spatially one-dimensional, assuming plug flow for the
Repeat testing of low-level HIV-1 RNA: assay performance and implementation in clinical trials.

Science.gov (United States)

White, Kirsten; Garner, Will; Wei, Lilian; Eron, Joseph J; Zhong, Lijie; Miller, Michael D; Martin, Hal; Plummer, Andrew; Tran-Muchowski, Cecilia; Lindstrom, Kim; Porter, James; Piontkowsky, David; Light, Angela; Reiske, Heinz; Quirk, Erin

2018-05-15

Assess the performance of HIV-1 RNA repeat testing of stored samples in cases of low-level viremia during clinical trials. Prospective and retrospective analysis of randomized clinical trial samples and reference standards. To evaluate assay variability of the Cobas AmpliPrep/Cobas TaqMan HIV-1 Test, v2.0, three separate sources of samples were utilized: the World Health Organization (WHO) HIV reference standard (assayed using 50 independent measurements at six viral loads <200 copies/ml), retrospective analysis of four to six aliquots of plasma samples from four clinical trial participants, and prospective repeat testing of 120 samples from participants in randomized trials with low-level viremia. The TaqMan assay on the WHO HIV-1 RNA standards at viral loads <200 copies/ml performed within the expected variability according to assay specifications. However, standards with low viral loads of 36 and 18 copies/ml reported values of ≥ 50 copies/ml in 66 and 18% of tests, respectively. In participants treated with antiretrovirals who had unexpected viremia of 50-200 copies/ml after achieving <50 copies/ml, retesting of multiple aliquots of stored plasma found <50 copies/ml in nearly all cases upon retesting (14/15; 93%). Repeat testing was prospectively implemented in four clinical trials for all samples with virologic rebound of 50-200 copies/ml (n = 120 samples from 92 participants) from which 42% (50/120) had a retest result of less than 50 copies/ml and 58% (70/120) retested ≥ 50 copies/ml. The TaqMan HIV-1 RNA assay shows variability around 50 copies/ml that affects clinical trial results and may impact clinical practice. In participants with a history of viral load suppression, unexpected low-level viremia may be because of assay variability rather than low drug adherence or true virologic failure. Retesting a stored aliquot of the same sample may differentiate between assay variability and virologic failure as the source of viremia
Analysis of correlation between cerebrospinal fluid and plasma HIV-1 RNA levels in patients with neurological opportunistic diseases

Directory of Open Access Journals (Sweden)

Paulo Pereira Christo

2011-08-01

Full Text Available The question of whether HIV-1 RNA in cerebrospinal fluid (CSF is derived from viral replication in the central nervous system or simply reflects the transit of infected lymphocytes from the blood compartment has long been a matter of debate. Some studies found no correlation between CSF and plasma viral load, whereas others did. The lack of a correlation between the two compartments suggests that the presence of HIV-1 RNA is not simply due to the passive passage of the virus from blood to CSF but rather due to intrathecal replication. To evaluate the correlation between plasma and CSF HIV-1 RNA levels and to identify situations in which there is no correlation between the two compartments, seventy patients were prospectively studied. The association between CSF and plasma viral load was evaluated in the total population and in subgroups of patients with similar characteristics. A correlation between the CSF and plasma compartments was observed for patients undergoing highly active antiretroviral therapy (HAART, those with a CD4 T lymphocyte count lower than 200 cells/mm³, and those with increased CSF protein content. On the other hand, no correlation was observed for patients without adequate virological control, who had a CD4 count higher than 200 cells/mm³ and who did not use HAART. The correlation between the two compartments observed in some patients suggests that CSF HIV-1 RNA levels may reflect plasma levels in these subjects. In contrast, the lack of a correlation between the two compartments in patients who were not on HAART and who had normal CSF proteins and a poor virological control possibly indicates compartmentalization of the virus in CSF and, consequently, plasma-independent intrathecal viral replication.
Composition of coal tar from pyrolysis and hydropyrolysis of Shenmu coal macerals

Energy Technology Data Exchange (ETDEWEB)

Sun, Q.; Li, W.; Chen, H.; Li, B. [Shandong Academy of Sciences, Jinan (China)

2005-08-15

To understand the relationship of the tar compositions and the coal macerals, the tars obtained from the pyrolysis and hydropyrolysis of Shenmu coal macerals in a fixed-bed reactor were analysed using GC-MS. And the effects of petrographic component, atmosphere and pressure on the yield of aromatic hydrocarbon, phenols, hydrocarbons, oxygen-containing heterocycle and PAHs were systematically investigated. The results show that there is great difference in the composition and the relative content of long chain hydrocarbons, aromatic hydrocarbons, phenols, oxygen-containing heterocycle and PAHs in tars from vitrinite and inertinite pyrolysis. Vitrinite tar contains high content of hydrocarbon with long chain, and inertinite tar contains high content of aromatic hydrocarbons, phenols, oxygen-containing heterocycle and PAHs. It suggests that vitrinite has lower aromaticity and longer chain in its structure than inertinite, which is in well agreement with the result from {sup 13}C NMR and FT-IR test. The tar yield of hydropyrolysis is higher than that of pyrolysis. With increasing the hydrogen pressure, the yield of tar increases greatly. The content of phenols and naphthalene in vitrinite tar form hydropyrolysis under 0.1 MPa is much lower than that form pyrolysis, while that of inertinite tar changes a little. The difference of tar compositions and relative content during pyrolysis and hydropyrolysis reflects the effect of hydrogenation and hydrocracking reactions and the structure characteristics of the macerals. 12 refs., 3 figs.
HIV-1 pre-mRNA commitment to Rev mediated export through PSF and Matrin 3

International Nuclear Information System (INIS)

Kula, Anna; Gharu, Lavina; Marcello, Alessandro

2013-01-01

Human immunodeficiency virus gene expression and replication are regulated at several levels. Incompletely spliced viral RNAs and full-length genomic RNA contain the RRE element and are bound by the viral trans-acting protein Rev to be transported out of the nucleus. Previously we found that the nuclear matrix protein MATR3 was a cofactor of Rev-mediated RNA export. Here we show that the pleiotropic protein PSF binds viral RNA and is associated with MATR3. PSF is involved in the maintenance of a pool of RNA available for Rev activity. However, while Rev and PSF bind the viral pre-mRNA at the site of viral transcription, MATR3 interacts at a subsequent step. We propose that PSF and MATR3 define a novel pathway for RRE-containing HIV-1 RNAs that is hijacked by the viral Rev protein.
Distinct binding interactions of HIV-1 Gag to Psi and non-Psi RNAs: implications for viral genomic RNA packaging.

Science.gov (United States)

Webb, Joseph A; Jones, Christopher P; Parent, Leslie J; Rouzina, Ioulia; Musier-Forsyth, Karin

2013-08-01

Despite the vast excess of cellular RNAs, precisely two copies of viral genomic RNA (gRNA) are selectively packaged into new human immunodeficiency type 1 (HIV-1) particles via specific interactions between the HIV-1 Gag and the gRNA psi (ψ) packaging signal. Gag consists of the matrix (MA), capsid, nucleocapsid (NC), and p6 domains. Binding of the Gag NC domain to ψ is necessary for gRNA packaging, but the mechanism by which Gag selectively interacts with ψ is unclear. Here, we investigate the binding of NC and Gag variants to an RNA derived from ψ (Psi RNA), as well as to a non-ψ region (TARPolyA). Binding was measured as a function of salt to obtain the effective charge (Zeff) and nonelectrostatic (i.e., specific) component of binding, Kd(1M). Gag binds to Psi RNA with a dramatically reduced Kd(1M) and lower Zeff relative to TARPolyA. NC, GagΔMA, and a dimerization mutant of Gag bind TARPolyA with reduced Zeff relative to WT Gag. Mutations involving the NC zinc finger motifs of Gag or changes to the G-rich NC-binding regions of Psi RNA significantly reduce the nonelectrostatic component of binding, leading to an increase in Zeff. These results show that Gag interacts with gRNA using different binding modes; both the NC and MA domains are bound to RNA in the case of TARPolyA, whereas binding to Psi RNA involves only the NC domain. Taken together, these results suggest a novel mechanism for selective gRNA encapsidation.
48 CFR Appendix to Part 1252 - Tar Matrix

Science.gov (United States)

2010-10-01

... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Tar Matrix Appendix to Part 1252 Federal Acquisition Regulations System DEPARTMENT OF TRANSPORTATION CLAUSES AND FORMS SOLICITATION PROVISIONS AND CONTRACT CLAUSES Pt. 1252, App. Appendix to Part 1252—Tar Matrix ER27DE05.000...
Low-temperature tar from bituminous coal and its further treatment

Energy Technology Data Exchange (ETDEWEB)

Hansen, C J

1950-01-01

High-temperature carbonization of bituminous coal yields only 3 to 4 percent tar, as compared with 8 to 10 percent or even more for low-temperature carbonization. The yield of phenols is 20 to 30 times as great from the low-temperature tar. Five conditions that must be met by a satisfactory low-temperature carbonization process are listed. The only method that satisfies all of these conditions is the Brennstoff-Technik (BT) process, in which iron retorts with movable walls are used. One disadvantage of most of the other processes is the high-pitch content of the tar. These tars are processed further to a neutral oil and a phenol-containing oil which are good diesel fuels with high-cetane numbers; the neutral oil can be fractionated to give oils of high-, medium-, and low-cetane number. Attempts to fractionate the tar oil by solvents have not proved commercially useful. However, the tar can be diluted with low-temperature light oil and phenols extracted with NaOH solution without distillation. Some difficulty is found, owing to the simultaneous extraction of viscous resins and other products that are readily removed from the phenols by distillation.
Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain

DEFF Research Database (Denmark)

Sükösd, Zsuzsanna; Andersen, Ebbe Sloth; Seemann, Ernst Stefan

2015-01-01

of the HIV-1 genome is highly variable in most regions, with a limited number of stable and conserved RNA secondary structures. Most interesting, a set of long distance interactions form a core organizing structure (COS) that organize the genome into three major structural domains. Despite overlapping...
Evaluation of Gravimetric Tar Determination in Particle Samples

DEFF Research Database (Denmark)

Hindsgaul, Claus; Henriksen, Ulrik B.; Bentzen, Jens Dall

2000-01-01

A comparison of tar determination of particles from a down-draft gasifier using soxhlet extractions (with anisole, dichloromethane and acetone) and pyrolysis of the particles.......A comparison of tar determination of particles from a down-draft gasifier using soxhlet extractions (with anisole, dichloromethane and acetone) and pyrolysis of the particles....
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.

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.
Effect of antiretroviral drugs on maternal CD4 lymphocyte counts, HIV-1 RNA levels, and anthropometric parameters of their neonates Efeito das drogas anti-retrovirais sobre os valores dos linfócitos TCD4, RNA do HIV-1 e parâmetros antropométricos de neonatos de gestantes portadoras do HIV-1

Directory of Open Access Journals (Sweden)

Patrícia El Beitune

2005-06-01

Full Text Available PURPOSE: To study the effect of antiretroviral drugs administered during pregnancy on CD4 lymphocyte counts and HIV-1 RNA levels of pregnant women and on the anthropometric parameters of their neonates. METHODS: A prospective study was conducted on 57 pregnant women and their neonates divided into 3 groups: ZDV Group, HIV-infected mothers taking zidovudine (n = 20; triple therapy (TT Group, mothers taking zidovudine + lamivudine + nelfinavir (n = 25, and Control Group, normal women (n = 12. CD4 lymphocyte counts and HIV-1 RNA levels of pregnant women were analyzed during two periods of pregnancy. The perinatal prognosis took into account preterm rates, birth weight, intrauterine growth restriction, perinatal death, and vertical transmission of HIV-1. Data were analyzed statistically using the nonparametric chi-square, Mann-Whitney, Friedman, Kruskal-Wallis, and Wilcoxon matched pairs tests, with the level of significance set at P OBJETIVOS: Estudar o efeito das drogas anti-retrovirais sobre a quantificação dos linfócitos TCD4 e RNA do HIV-1 de gestantes portadoras do HIV-1 e parâmetros antropométricos de seus neonatos. MÉTODOS: Estudo prospectivo avaliando 57 gestantes e seus neonatos em três grupos: Grupo AZT, gestantes portadoras do HIV utilizando zidovudina (n=20; Grupo TT, mães utilizando zidovudina+lamivudina+nelfinavir (n=25, e Grupo Controle, mulheres saudáveis (n=12. A quantificação dos linfócitos TCD4 e RNA do HIV-1 de gestantes portadoras do HIV foi analisada em dois períodos durante a gestação. O prognóstico perinatal levou em consideração as taxas de pré-termos, restrição de crescimento intra-útero, mortalidade perinatal e transmissão vertical do HIV-1. Os dados foram analisados utilizando-se testes não paramétricos de qui-quadrado, Mann-Whitney, Friedman, Kruskal-Wallys e Wilcoxon para amostras pareadas, considerando-se significativos valores associados a p<0,05. RESULTADOS: Observou-se homogeneidade entre
Experimental comparison of biomass chars with other catalysts for tar reduction

NARCIS (Netherlands)

Abu El-Rub, Ziad; Bramer, Eduard A.; Brem, Gerrit

2008-01-01

In this paper the potential of using biomass char as a catalyst for tar reduction is discussed. Biomass char is compared with other known catalysts used for tar conversion. Model tar compounds, phenol and naphthalene, were used to test char and other catalysts. Tests were carried out in a fixed bed
Coal-tar based pavement sealant toxicity to freshwater macroinvertebrates

International Nuclear Information System (INIS)

Bryer, Pamela J.; Scoggins, Mateo; McClintock, Nancy L.

2010-01-01

Non-point-source pollution is a major source of ecological impairment in urban stream systems. Recent work suggests that coal-tar pavement sealants, used extensively to protect parking areas, may be contributing a large portion of the polycyclic aromatic hydrocarbon (PAH) loading seen in urban stream sediments. The hypothesis that dried coal-tar pavement sealant flake could alter the macroinvertebrate communities native to streams in Austin, TX was tested using a controlled outdoor laboratory type approach. The treatment groups were: control, low, medium, and high with total PAH concentrations (TPAH = sum of 16 EPA priority pollutant PAHs) of 0.1, 7.5, 18.4, and 300 mg/kg respectively. The low, medium, and high treatments were created via the addition of dried coal-tar pavement sealant to a sterile soil. At the start of the 24-day exposure, sediment from a minimally impacted local reference site containing a community of live sediment-dwelling benthic macroinvertebrates was added to each replicate. An exposure-dependent response was found for several stream health measures and for several individual taxa. There were community differences in abundance (P = 0.0004) and richness (P < 0.0001) between treatments in addition to specific taxa responses, displaying a clear negative relationship with the amount of coal-tar sealant flake. These results support the hypothesis that coal-tar pavement sealants contain bioavailable PAHs that may harm aquatic environments. - Coal-tar pavement sealants degrade stream invertebrate communities.
29 CFR 1910.1002 - Coal tar pitch volatiles; interpretation of term.

Science.gov (United States)

2010-07-01

... 29 Labor 6 2010-07-01 2010-07-01 false Coal tar pitch volatiles; interpretation of term. 1910.1002... Hazardous Substances § 1910.1002 Coal tar pitch volatiles; interpretation of term. As used in § 1910.1000 (Table Z-1), coal tar pitch volatiles include the fused polycyclic hydrocarbons which volatilize from the...
Isolation and characterization of 20'-F-RNA aptamers against whole HIV-1 subtype C envelope pseudovirus

CSIR Research Space (South Africa)

London, GM

2015-01-01

Full Text Available Aptamers, which are artificial nucleic acid ligands akin to antibodies in function, represent a new class of molecules that can prevent HIV infection. In this study, we isolated RNA aptamers against whole HV-1CAP45 enveloped pseudotyped virus...
Athabasca tar sand reservoir properties derived from cores and logs

International Nuclear Information System (INIS)

Woodhouse, R.

1976-01-01

Log interpretation parameters for the Athabasca Tar Sand Lease No. 24 have been determined by careful correlation with Dean and Stark core analysis data. Significant expansion of Athabasca cores occurs as overburden pressure is removed. In the more shaly sands the core analysis procedures remove adsorbed water from the clays leading to further overestimation of porosity and free water volume. Log interpretation parameters (R/sub w/ = 0.5 ohm . m and m = n = 1.5) were defined by correlation with the weight of tar as a fraction of the weight of rock solids (grain or dry weight fraction of tar). This quantity is independent of the water content of the cores, whereas porosity and the weight of tar as a fraction of the bulk weight of fluids plus solids (bulk weight fraction) are both dependent on water content. Charts are provided for the conversion of bulk weight fraction of fluids to porosity; grain weight fraction of fluids to porosity; log derived porosity and core grain weight tar to water saturation. Example results show that the core analysis grain weight fraction of tar is adequately matched by the log analyses. The log results provide a better representation of the reservoir fluid volumes than the core analysis data
Corrosion test by low-temperature coal tar

Energy Technology Data Exchange (ETDEWEB)

Ando, S; Yamamoto, S

1952-01-01

Corrosive actions of various fractions of low-temperature coal tar against mild steel or Cr 13-steel were compared at their boiling states. Corrosions became severe when the boiling points exceeded 240/sup 0/. The acidic fractions were more corrosive. In all instances, corrosion was excessive at the beginning of immersion testing and then gradually became mild; boiling accelerated the corrosion. Cr 13-steel was corrosion-resistant to low-temperature coal-tar fractions.
Mechanisms of human immunodeficiency virus type 2 RNA packaging

DEFF Research Database (Denmark)

Ni, Na; Nikolaitchik, Olga A; Dilley, Kari A

2011-01-01

do not support the cis-packaging hypothesis but instead indicate that trans packaging is the major mechanism of HIV-2 RNA packaging. To further characterize the mechanisms of HIV-2 RNA packaging, we visualized HIV-2 RNA in individual particles by using fluorescent protein-tagged RNA-binding proteins......Human immunodeficiency virus type 2 (HIV-2) has been reported to have a distinct RNA packaging mechanism, referred to as cis packaging, in which Gag proteins package the RNA from which they were translated. We examined the progeny generated from dually infected cell lines that contain two HIV-2...... proviruses, one with a wild-type gag/gag-pol and the other with a mutant gag that cannot express functional Gag/Gag-Pol. Viral titers and RNA analyses revealed that mutant viral RNAs can be packaged at efficiencies comparable to that of viral RNA from which wild-type Gag/Gag-Pol is translated. These results...
The RNA binding protein HuR does not interact directly with HIV-1 reverse transcriptase and does not affect reverse transcription in vitro

Directory of Open Access Journals (Sweden)

Gronenborn Angela M

2010-05-01

Full Text Available Abstract Background Lemay et al recently reported that the RNA binding protein HuR directly interacts with the ribonuclease H (RNase H domain of HIV-1 reverse transcriptase (RT and influences the efficiency of viral reverse transcription (Lemay et al., 2008, Retrovirology 5:47. HuR is a member of the embryonic lethal abnormal vision protein family and contains 3 RNA recognition motifs (RRMs that bind AU-rich elements (AREs. To define the structural determinants of the HuR-RT interaction and to elucidate the mechanism(s by which HuR influences HIV-1 reverse transcription activity in vitro, we cloned and purified full-length HuR as well as three additional protein constructs that contained the N-terminal and internal RRMs, the internal and C-terminal RRMs, or the C-terminal RRM only. Results All four HuR proteins were purified and characterized by biophysical methods. They are well structured and exist as monomers in solution. No direct protein-protein interaction between HuR and HIV-1 RT was detected using NMR titrations with 15N labeled HuR variants or the 15N labeled RNase H domain of HIV-1 RT. Furthermore, HuR did not significantly affect the kinetics of HIV-1 reverse transcription in vitro, even on RNA templates that contain AREs. Conclusions Our results suggest that HuR does not impact HIV-1 replication through a direct protein-protein interaction with the viral RT.
Effect of water addition in a microwave assisted thermal cracking of biomass tar models

International Nuclear Information System (INIS)

Warsita, Aris; Al-attab, K.A.; Zainal, Z.A.

2017-01-01

Highlights: • Effective tar thermal treatment with water addition using microwave is proposed. • The reactor temperature of 1200 °C can be reached quickly at bed height 120 mm. • The optimum water to tar ratio W/T was 0.3 for tar models. • Temperature greatly effect tar removal at various W/T rates. - Abstract: Producer gas from biomass gasification is plagued by the presence of tar which causes pipe blockages. Thermal and catalytic treatments in a microwave reactor have been shown to be effective methods in removing tar from producer gas. A question arises as to the possibility of enhancing the removal mechanism by adding water into the reactor. Toluene and naphthalene were used as tar models in the present study with N_2 as the carrier gas followed by the use of simulated producer gas. Thermal treatment with various amount of water was added at temperatures in the range of 800–1200 °C. The tar removal efficiency obtained 95.83% at the optimum temperature of 1200 °C for naphthalene in for toluene 96.32% at 1050 °C at water to tar ratio (W/T) of 0.3. This study shows that the removal of tar by microwave irradiation with water addition is a significant and effective method in tar cracking.
Sampling of tar from sewage sludge gasification using solid phase adsorption.

Science.gov (United States)

Ortiz González, Isabel; Pérez Pastor, Rosa Ma; Sánchez Hervás, José Ma

2012-06-01

Sewage sludge is a residue from wastewater treatment plants which is considered to be harmful to the environment and all living organisms. Gasification technology is a potential source of renewable energy that converts the sewage sludge into gases that can be used to generate energy or as raw material in chemical synthesis processes. But tar produced during gasification is one of the problems for the implementation of the gasification technology. Tar can condense on pipes and filters and may cause blockage and corrosion in the engines and turbines. Consequently, to minimize tar content in syngas, the ability to quantify tar levels in process streams is essential. The aim of this work was to develop an accurate tar sampling and analysis methodology using solid phase adsorption (SPA) in order to apply it to tar sampling from sewage sludge gasification gases. Four types of commercial SPA cartridges have been tested to determine the most suitable one for the sampling of individual tar compounds in such streams. Afterwards, the capacity, breakthrough volume and sample stability of the Supelclean™ ENVI-Carb/NH(2), which is identified as the most suitable, have been determined. Basically, no significant influences from water, H(2)S or NH(3) were detected. The cartridge was used in sampling real samples, and comparable results were obtained with the present and traditional methods.
Occupational coal tar dermatitis

Energy Technology Data Exchange (ETDEWEB)

Conde-Salazar, L; Guimaraens, D; Romero, L V; Gonzalez, M A

1987-04-01

The paper describes the allergic reaction to coal tar of a man handling it in a factory. The reaction appeared in the form of eczema on his trunk, arms and legs, but his hands were not affected as he had been wearing gloves. 1 ref.
Relationship of HIV Reservoir Characteristics with Immune Status and Viral Rebound Kinetics in an HIV Therapeutic Vaccine Study

Science.gov (United States)

Li, Jonathan Z.; Heisey, Andrea; Ahmed, Hayat; Wang, Hongying; Zheng, Lu; Carrington, Mary; Wrin, Terri; Schooley, Robert T.; Lederman, Michael M.; Kuritzkes, Daniel R.

2014-01-01

Objectives To evaluate the impact of therapeutic HIV vaccination on the HIV reservoir, and assess the relationship of the viral reservoir with HIV-specific immune status and viral rebound kinetics. Design Retrospective analysis of ACTG A5197, a randomized, placebo-controlled trial of a therapeutic rAd5 HIV-1 gag vaccine. Methods Participants received vaccine/placebo at weeks 0, 4, and 26 prior to a 16-week analytic treatment interruption (ATI) at week 38. Cell-associated HIV-1 RNA and DNA (CA-RNA and CA-DNA) and HIV-1 residual viremia (RV) were quantified at weeks 0, 8, and 38. HIV-specific CD4+/CD8+ activity were assessed by an intracellular cytokine staining assay. Results At study entry, CA-RNA and CA-DNA levels were correlated inversely with the numbers of HIV-specific CD4+ interferon-γ-producing cells (CA-RNA: r = −0.23, P=0.03 and CA-DNA: r = −0.28, P<0.01, N=93). Therapeutic HIV vaccination induced HIV-specific CD4+ activity, but did not significantly affect levels of CA-RNA or CA-DNA. Vaccine recipients with undetectable RV at week 8 had higher frequencies of HIV-specific CD4+ and CD8+ interferon-γ-producing cells (undetectable versus detectable RV: 277 versus 161 CD4+ cells/106 lymphocytes, P=0.03 and 1326 versus 669 CD8+ cells/106 lymphocytes, P=0.04). Pre-ATI CA-RNA and CA-DNA were associated with post-ATI plasma HIV set point (CA-RNA: r = 0.51, P<0.01 and CA-DNA: r = 0.47, P<0.01). Conclusions Vaccine-induced T-cell responses were associated with a modest transient effect on RV, but more potent immune responses and/or combination treatment with latency-reversing agents are needed to reduce the HIV reservoir. HIV reservoir measures may act as biomarkers of post-ATI viral rebound kinetics. PMID:25254301
179 Extraction of Coal-tar Pitch by Supercritical Carbon Dioxide ...

African Journals Online (AJOL)

Meyer

Several extractions of coal-tar pitch were performed using supercritical fluid ..... pressure and temperature, unlike exhaustive extraction, which involves a change in ... mechanism that is operative on extracting coal-tar pitch components with.
Contact sensitivity to newsprint: a rare manifestation of coal tar allergy

Energy Technology Data Exchange (ETDEWEB)

Illchyshyn, A; Cartwright, P H; Smith, A G

1987-07-01

Contact dermatitis due to coal tar is infrequently reported in spite of the fact that it consists of a mixture of 10,000 constituents, and is still often used to treat both eczema and psoriasis. Discusses patient with coal tar sensitivity in whom the source of exacerbation of her dermatitis is shown to be newsprint, a common product containing coal tar-derived material. 6 refs.
A Method to Predict the Structure and Stability of RNA/RNA Complexes.

Science.gov (United States)

Xu, Xiaojun; Chen, Shi-Jie

2016-01-01

RNA/RNA interactions are essential for genomic RNA dimerization and regulation of gene expression. Intermolecular loop-loop base pairing is a widespread and functionally important tertiary structure motif in RNA machinery. However, computational prediction of intermolecular loop-loop base pairing is challenged by the entropy and free energy calculation due to the conformational constraint and the intermolecular interactions. In this chapter, we describe a recently developed statistical mechanics-based method for the prediction of RNA/RNA complex structures and stabilities. The method is based on the virtual bond RNA folding model (Vfold). The main emphasis in the method is placed on the evaluation of the entropy and free energy for the loops, especially tertiary kissing loops. The method also uses recursive partition function calculations and two-step screening algorithm for large, complicated structures of RNA/RNA complexes. As case studies, we use the HIV-1 Mal dimer and the siRNA/HIV-1 mutant (T4) to illustrate the method.
Coal tar phototoxicity: characteristics of the smarting reaction

International Nuclear Information System (INIS)

Diette, K.M.; Gange, R.W.; Stern, R.S.; Arndt, K.A.; Parrish, J.A.

1985-01-01

The properties and ultraviolet exposure parameters of tar smarts were examined in an effort to elucidate the mechanisms involved. It was show that irradiation with 1 minimal smarting dose (MSD) of UVA immediately following tar removal lowered the MSD for 6 h, demonstrated by subsequent challenge with UVA. Following 3 MSDs this memory effect was demonstrable for 24 h. The smarting reaction was area dependent--smaller areas of exposure require higher doses of UVA to induce smarting. Smarting followed reciprocity over a 6-fold range of irradiances (2-12.5 mW/cm2) but higher irradiances required higher doses of UVA, perhaps due to a delay in the recognition and reporting of smarting. The smarting reaction and delayed erythema due to UVA and tar were equally blocked by sunscreen
Activation of HIV Transcription with Short-Course Vorinostat in HIV-Infected Patients on Suppressive Antiretroviral Therapy

Science.gov (United States)

Solomon, Ajantha; Ghneim, Khader; Ahlers, Jeffrey; Cameron, Mark J.; Smith, Miranda Z.; Spelman, Tim; McMahon, James; Velayudham, Pushparaj; Brown, Gregor; Roney, Janine; Watson, Jo; Prince, Miles H.; Hoy, Jennifer F.; Chomont, Nicolas; Fromentin, Rémi; Procopio, Francesco A.; Zeidan, Joumana; Palmer, Sarah; Odevall, Lina; Johnstone, Ricky W.; Martin, Ben P.; Sinclair, Elizabeth; Deeks, Steven G.; Hazuda, Daria J.; Cameron, Paul U.; Sékaly, Rafick-Pierre; Lewin, Sharon R.

2014-01-01

Human immunodeficiency virus (HIV) persistence in latently infected resting memory CD4+ T-cells is the major barrier to HIV cure. Cellular histone deacetylases (HDACs) are important in maintaining HIV latency and histone deacetylase inhibitors (HDACi) may reverse latency by activating HIV transcription from latently infected CD4+ T-cells. We performed a single arm, open label, proof-of-concept study in which vorinostat, a pan-HDACi, was administered 400 mg orally once daily for 14 days to 20 HIV-infected individuals on suppressive antiretroviral therapy (ART). The primary endpoint was change in cell associated unspliced (CA-US) HIV RNA in total CD4+ T-cells from blood at day 14. The study is registered at ClinicalTrials.gov (NCT01365065). Vorinostat was safe and well tolerated and there were no dose modifications or study drug discontinuations. CA-US HIV RNA in blood increased significantly in 18/20 patients (90%) with a median fold change from baseline to peak value of 7.4 (IQR 3.4, 9.1). CA-US RNA was significantly elevated 8 hours post drug and remained elevated 70 days after last dose. Significant early changes in expression of genes associated with chromatin remodeling and activation of HIV transcription correlated with the magnitude of increased CA-US HIV RNA. There were no statistically significant changes in plasma HIV RNA, concentration of HIV DNA, integrated DNA, inducible virus in CD4+ T-cells or markers of T-cell activation. Vorinostat induced a significant and sustained increase in HIV transcription from latency in the majority of HIV-infected patients. However, additional interventions will be needed to efficiently induce virus production and ultimately eliminate latently infected cells. Trial Registration ClinicalTrials.gov NCT01365065 PMID:25393648
Activation of HIV transcription with short-course vorinostat in HIV-infected patients on suppressive antiretroviral therapy.

Directory of Open Access Journals (Sweden)

Julian H Elliott

2014-10-01

Full Text Available Human immunodeficiency virus (HIV persistence in latently infected resting memory CD4+ T-cells is the major barrier to HIV cure. Cellular histone deacetylases (HDACs are important in maintaining HIV latency and histone deacetylase inhibitors (HDACi may reverse latency by activating HIV transcription from latently infected CD4+ T-cells. We performed a single arm, open label, proof-of-concept study in which vorinostat, a pan-HDACi, was administered 400 mg orally once daily for 14 days to 20 HIV-infected individuals on suppressive antiretroviral therapy (ART. The primary endpoint was change in cell associated unspliced (CA-US HIV RNA in total CD4+ T-cells from blood at day 14. The study is registered at ClinicalTrials.gov (NCT01365065. Vorinostat was safe and well tolerated and there were no dose modifications or study drug discontinuations. CA-US HIV RNA in blood increased significantly in 18/20 patients (90% with a median fold change from baseline to peak value of 7.4 (IQR 3.4, 9.1. CA-US RNA was significantly elevated 8 hours post drug and remained elevated 70 days after last dose. Significant early changes in expression of genes associated with chromatin remodeling and activation of HIV transcription correlated with the magnitude of increased CA-US HIV RNA. There were no statistically significant changes in plasma HIV RNA, concentration of HIV DNA, integrated DNA, inducible virus in CD4+ T-cells or markers of T-cell activation. Vorinostat induced a significant and sustained increase in HIV transcription from latency in the majority of HIV-infected patients. However, additional interventions will be needed to efficiently induce virus production and ultimately eliminate latently infected cells.ClinicalTrials.gov NCT01365065.

Coal-tar based pavement sealant toxicity to freshwater macroinvertebrates

Energy Technology Data Exchange (ETDEWEB)

Bryer, P.J.; Scoggins, M.; McClintock, N.L. [Lamar University, Beaumont, TX (United States). Dept. of Biology

2010-05-15

Non-point-source pollution is a major source of ecological impairment in urban stream systems. Recent work suggests that coal-tar pavement sealants, used extensively to protect parking areas, may be contributing a large portion of the polycyclic aromatic hydrocarbon (PAH) loading seen in urban stream sediments. The hypothesis that dried coal-tar pavement sealant flake could alter the macroinvertebrate communities native to streams in Austin, TX was tested using a controlled outdoor laboratory type approach. The treatment groups were: control, low, medium, and high with total PAH concentrations (TPAH = sum of 16 EPA priority pollutant PAHs) of 0.1, 7.5, 18.4, & 300 mg/kg respectively. The low, medium, and high treatments were created via the addition of dried coal-tar pavement sealant to a sterile soil. At the start of the 24-day exposure, sediment from a minimally impacted local reference site containing a community of live sediment-dwelling benthic macroinvertebrates was added to each replicate. An exposure-dependent response was found for several stream health measures and for several individual taxa. There were community differences in abundance (P = 0.0004) and richness (P < 0.0001) between treatments in addition to specific taxa responses, displaying a clear negative relationship with the amount of coal-tar sealant flake. These results support the hypothesis that coal-tar pavement sealants contain bioavailable PAHs that may harm aquatic environments.
HIV RNA Suppression during and after Pregnancy among Women in the HIV Outpatient Study, 1996 to 2015.

Science.gov (United States)

Patel, Monita; Tedaldi, Ellen; Armon, Carl; Nesheim, Steven; Lampe, Margaret; Palella, Frank; Novak, Richard; Sutton, Madeline; Buchacz, Kate

2018-01-01

To examine HIV viral suppression during/after pregnancy. Prospective observational cohort. We identified pregnancies from 1996 to 2015. We examined HIV RNA viral load (VL), VL suppression (≤500 copies/mL), and antiretroviral therapy (ART) status at pregnancy start, end, and 6 months postpartum. We estimated risk ratios (RRs) and 95% confidence intervals (CIs) for VL nonsuppression. Among 253 pregnancies analyzed, 34.8% of women exhibited VL suppression at pregnancy start, 60.1% at pregnancy end, and 42.7% at 6 months postpartum. Median VL (log 10 copies/mL) was 2.80 (interquartile range [IQR]: 1.40-3.85) at pregnancy start, 1.70 (IQR: 1.40-2.82) at pregnancy end, and 2.30 (IQR: 1.40-3.86) at postpartum. Risk of postpartum VL nonsuppression was also lower among women on ART and with VL suppression at pregnancy end (versus those not; adjusted RR = 0.30, 95% CI: 0.17-0.53). Maintaining VL suppression among US women remains a challenge, particularly during postpartum. Achieving VL suppression earlier during pregnancy benefits women subsequently.
Chemical and physical characteristics of tar samples from selected Manufactured Gas Plant (MGP) sites

International Nuclear Information System (INIS)

Ripp, J.; Taylor, B.; Mauro, D.; Young, M.

1993-05-01

A multiyear, multidisciplinary project concerning the toxicity of former Manufactured Gas Plant (MGP) tarry residues was initiated by EPRI under the Environmental Behavior of Organic Substances (EBOS) Program. This report concerns one portion of that work -- the collection and chemical characterization of tar samples from several former MGP sites. META Environmental, Inc. and Atlantic Environmental Services, Inc. were contracted by EPRI to collect several samples of tarry residues from former MGP sites with varied historical gas production processes and from several parts of the country. The eight tars collected during this program were physically very different. Some tars were fluid and easily pumped from existing wells, while other tars were thicker, semi-solid, or solid. Although care was taken to collect only tar, the nature of the residues at several sites made it impossible not to collect other material, such as soil, gravel, and plant matter. After the samples were collected, they were analyzed for 37 organic compounds, 8 metals, and cyanide. In addition, elemental analysis was performed on the tar samples for carbon, hydrogen, oxygen, sulfur and nitrogen content and several physical/chemical properties were determined for each tar. The tars were mixed together in different batches and distributed to researchers for use in animal toxicity studies. The results of this work show that, although the tars were produced from different processes and stored in different manners, they had some chemical similarities. All of the tars, with the exception of one unusual solid tar, contained similar relative abundances of polycyclic aromatic hydrocarbons (PAHs)
Thermodynamic analysis of tar reforming through auto-thermal reforming process

Energy Technology Data Exchange (ETDEWEB)

Nurhadi, N., E-mail: nurhadi@tekmira.esdm.go.id; Diniyati, Dahlia; Efendi, M. Ade Andriansyah [R& D Centre for Mineral and Coal Technology, Jln. Jend.Sudirman no. 623, Bandung. Telp. 022-6030483 (Malaysia); Istadi, I. [Department of Chemical Engineering, Diponegoro University, Jln. Jl. Prof. Soedarto, SH, Semarang (Malaysia)

2015-12-29

Fixed bed gasification is a simple and suitable technology for small scale power generation. One of the disadvantages of this technology is producing tar. So far, tar is not utilized yet and being waste that should be treated into a more useful product. This paper presents a thermodynamic analysis of tar conversion into gas producer through non-catalytic auto-thermal reforming technology. Tar was converted into components, C, H, O, N and S, and then reacted with oxidant such as mixture of air or pure oxygen. Thus, this reaction occurred auto-thermally and reached chemical equilibrium. The sensitivity analysis resulted that the most promising process performance occurred at flow rate of air was reached 43% of stoichiometry while temperature of process is 1100°C, the addition of pure oxygen is 40% and preheating of oxidant flow is 250°C. The yield of the most promising process performance between 11.15-11.17 kmol/h and cold gas efficiency was between 73.8-73.9%.The results of this study indicated that thermodynamically the conversion of tar into producer gas through non-catalytic auto-thermal reformingis more promising.
Pelagic tar and plastic in the Gulf of Alaska and Bering Sea: 1975

Energy Technology Data Exchange (ETDEWEB)

Shaw, D G

1977-07-01

Seventy-one tows of 740 m/sup 2/ each were made in search of pelagic tar and plastics in the Gulf of Alaska and Bering Sea during the period October 1974 to October 1975. Tar was observed on nine occasions while plastics were found six times. The arithmetic mean value of tar abundance, 3.3 x 10/sup -3/ mg/m/sup 2/, is considerably lower than most other oceanic areas for which values have been reported. Gas chromatographic analysis of this tar indicates that it is more extensively weathered than tar from the north Atlantic. An estimate of the abundance of tar lumps too small to be sampled by net tows is made based on the assumption that there are equal weights of particles in logarithmetically equal size intervals. The abundance of pelagic plastics is also low.
Extraction of low-temperature tar by various alcohols

Energy Technology Data Exchange (ETDEWEB)

Hara, N; Osawa, M; Azuma, H

1948-01-01

MeOH was the most effective of the alcohols tested (MeOH to pentanol) in extracting acid components from low-temperature tar. The optimum concentrations of MeOH were 70 to 80% for 1 extraction and 70 to 75% for repeated or continuous extractions when the solvent-tar ratio was 1:1. By 2 to 3 extractions neutral oil could be separated in about 90% yield including > 3% acidic oil.
High rate of hepatitis C virus (HCV) recurrence in HIV-infected individuals with spontaneous HCV RNA clearance

DEFF Research Database (Denmark)

Peters, L; Mocroft, A; Soriano, V

2014-01-01

OBJECTIVES: Following resolution of hepatitis C virus (HCV) infection, recurrence has been shown to occur in some persons with repeated exposure to HCV. We aimed to investigate the rate and factors associated with HCV RNA recurrence among HIV-1-infected patients with prior spontaneous HCV RNA cle......-up. Our findings underline the importance of maintaining focus on preventive measures to reduce IDU and sharing of contaminated needles. Clinicians should maintain a high degree of vigilance to identify patients with new HCV infection early....
Alterations in HIV-1 LTR promoter activity during AIDS progression

International Nuclear Information System (INIS)

Hiebenthal-Millow, Kirsten; Greenough, Thomas C.; Bretttler, Doreen B.; Schindler, Michael; Wildum, Steffen; Sullivan, John L.; Kirchhoff, Frank

2003-01-01

HIV-1 variants evolving in AIDS patients frequently show increased replicative capacity compared to those present during early asymptomatic infection. It is known that late stage HIV-1 variants often show an expanded coreceptor tropism and altered Nef function. In the present study we investigated whether enhanced HIV-1 LTR promoter activity might also evolve during disease progression. Our results demonstrate increased LTR promoter activity after AIDS progression in 3 of 12 HIV-1-infected individuals studied. Further analysis revealed that multiple alterations in the U3 core-enhancer and in the transactivation-response (TAR) region seem to be responsible for the enhanced functional activity. Our findings show that in a subset of HIV-1-infected individuals enhanced LTR transcription contributes to the increased replicative potential of late stage virus isolates and might accelerate disease progression
Dermal uptake of polycyclic aromatic hydrocarbons after hairwash with coal-tar shampoo

Energy Technology Data Exchange (ETDEWEB)

Schooten, F.-J. van; Moonen, E.J.C.; Rhijnsburger, E.; Agen, B. van; Thijssen, H.H.W.; Kleinjans, J.C.S. [University of Limburg, Maastricht (Netherlands). Dept. of Health Risk Analysis and Toxicology

1994-11-26

Describes an experiment to assess the dermal uptake of polycyclic aromatic hydrocarbons (PAHs) after hairwashing with coal tar antidandruff shampoo. The urinary excretion of 1-hydroxypyrene (1-OH-P), a PAH metabolile was used to assess internal dose of PAH. A single use of coal tar shampoo resulted in increased 1-OH-P excretion in all members of the experimental group compared with the control group using a non-coal tar antidandruff shampoo. It is suggested that repeated use of coal tar shampoo would result in a high internal dose of carcinogenic PAH. 5 refs., 1 fig.
Iron-based materials as tar cracking catalyst in waste gasification

Energy Technology Data Exchange (ETDEWEB)

Nordgreen, Thomas

2011-07-01

The treatment of municipal solid waste (MSW) in Sweden has changed during the past decades due to national legislation and European Union directives. The former landfills have more or less been abandoned in favour of material recycling and waste incineration. On a yearly basis approximately 2.2 million tonnes waste are incinerated in Sweden with heat recovery and to some extent also with electricity generation, though at a low efficiency. It is desirable to alter this utilisation and instead employ MSW as fuel in a fluid bed gasification process. Then electrical energy may be produced at a much higher efficiency. However, MSW contain about 1 % chlorine in the form of ordinary table salt (NaCl) from food scraps. This implies that the tar cracking catalyst, dolomite, which is normally employed in gasification, will suffer from poisoning if applied under such conditions. Then the tar cracking capacity will be reduced or vanish completely with time. Consequently, an alternative catalyst, more resistant to chlorine, is needed. Preliminary research at KTH has indicated that iron in its metallic state may possess tar cracking ability. With this information at hand and participating in the project 'Energy from Waste' an experimental campaign was launched. Numerous experiments were conducted using iron as tar cracking catalyst. First iron sinter pellets from LKAB were employed. They were reduced in situ with a stream of hydrogen before they were applied. Later iron-based granules from Hoeganaes AB were tested. These materials were delivered in the metallic state. In all tests the KTH atmospheric fluidised bed gasifier with a secondary catalytic reactor housing the catalytic material was deployed. Mostly, the applied fuel was birch. The results show that metallic iron possesses an intrinsic ability, almost in the range of dolomite, to crack tars. Calculations indicate that iron may be more resistant to chlorine than dolomite. The exploration of metallic iron
Chemical Composition of Essential Oils from Thymus vulgaris, Cymbopogon citratus, and Rosmarinus officinalis, and Their Effects on the HIV-1 Tat Protein Function.

Science.gov (United States)

Feriotto, Giordana; Marchetti, Nicola; Costa, Valentina; Beninati, Simone; Tagliati, Federico; Mischiati, Carlo

2018-02-01

New drugs would be beneficial to fight resistant HIV strains, in particular those capable of interfering with essential viral functions other than those targeted by highly active antiretroviral therapy drugs. Despite the central role played by Tat protein in HIV transcription, a search for vegetable extracts able to hamper this important viral function was never carried out. In this work, we evaluated the chemical composition and possible interference of essential oil from Thymus vulgaris, Cananga odorata, Cymbopogon citratus, and Rosmarinus officinalis with the Tat/TAR-RNA interaction and with Tat-induced HIV-1 LTR transcription. GC/MS Analysis demonstrated the biodiversity of herbal species translated into essential oils composed of different blends of terpenes. In all of them, 4 - 6 constituents represent from 81.63% to 95.19% of the total terpenes. Essential oils of Thymus vulgaris, Cymbopogon citratus, and Rosmarinus officinalis were active in interfering with Tat functions, encouraging further studies to identify single terpenes responsible for the antiviral activity. In view of the quite different composition of these essential oils, we concluded that their interference on Tat function depends on specific terpene or a characteristic blend. © 2018 Wiley-VHCA AG, Zurich, Switzerland.
A predominance of R5-like HIV genotypes in vaginal secretions is associated with elevated plasma HIV-1 RNA levels and the absence of anti-retroviral therapy

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Lacour Nedra

2008-07-01

Full Text Available Abstract HIV expressed in genital secretions provides the inoculum from which transmitting variants are selected, both in sexual transmission and mother-to-infant transmission during partuition. Characterization of HIV levels and genotypes found in vaginal secretions and the impact of anti-retroviral therapy (ART on this virus can provide valuable insight for the prevention of HIV transmission. Vaginal HIV was evaluated in a cohort of 43 women attending a New Orleans HIV outpatient clinic. Predominant vaginal genotypes were characterized as R5- or X4-like by heteroduplex tracking analyses of the envelope V3 region. Most women (67.4% shed R5-like genotypes in vaginal secretions which was associated with elevated plasma HIV levels (≥ 10,000 copies HIV-RNA/mL and absence of ART. Because R5-like genotypes are more frequently associated with transmission, these observations suggest that the majority of women shedding HIV in genital secretions present a transmission risk. The levels of vaginal virus were similar between both groups, but shedding of X4-like genotypes was associated with lower plasma viral loads and the use of ART, suggesting that ART use may impact the genotypes of virus found in the female genital compartment.
Secondary reactions of tar during thermochemical biomass conversion[Dissertation 14341

Energy Technology Data Exchange (ETDEWEB)

Morf, P.O.

2001-07-01

This dissertation submitted to the Swiss Federal Institute of Technology in Zurich presents and discusses the results obtained during the examination of the processes involved in the formation and conversion of tar in biomass gasification plant. Details are given on the laboratory reactor system used to provide separated tar production and conversion for the purposes of the experiments carried out. The results of analyses made of the tar and the gaseous products obtained after its conversion at various temperatures are presented. The development of kinetic models using the results of the experiments that were carried out is described. The results of the experiments and modelling are compared with the corresponding results obtained using a full-scale down-draft, fixed-bed gasifier. The author is of the opinion that the reaction conditions found in full-scale gasifiers can be well simulated using heterogeneous tar conversion experiments using the lab reactor system.
HIV-1 splicing is controlled by local RNA structure and binding of splicing regulatory proteins at the major 5' splice site

NARCIS (Netherlands)

Mueller, Nancy; Berkhout, Ben; Das, Atze T.

2015-01-01

The 5' leader region of the human immunodeficiency virus 1 (HIV-1) RNA genome contains the major 5' splice site (ss) that is used in the production of the many spliced viral RNAs. This splice-donor (SD) region can fold into a stable stem-loop structure and the thermodynamic stability of this RNA
Tar loads on Omani beaches

International Nuclear Information System (INIS)

Badawy, M.I.; Al-Harthy, F.T.

1991-01-01

Owing to Oman's geographic position and long coastal line, the coastal areas of Oman are particularly vulnerable to oil pollution from normal tanker operations, illegal discharges, and accidental spills as well as local sources of oil input. UNEP carried out a survey on the coasts of Oman to determine the major sources of oil pollution and concluded that the major shoreline pollution problems in Oman arose from operational discharges of oil from passing vessels traffic. The oil, because of the high sea and air temperatures in the area, was subjected to relatively high rates of evaporation and photo-oxidation and tended to arrive at the coast as heavy petroleum particulate residues (tar balls). The aim of the present study was to measure the loads of tar balls in Omani coastal areas and to identify the source of oil pollutants on beaches
Decomposition of tar in gas from updraft gasifier by thermal cracking

DEFF Research Database (Denmark)

Brandt, Peder; Henriksen, Ulrik Birk

2000-01-01

Continuing earlier work with tar reduction by partial oxidation of pyrolysis gas [1] thermal cracking has been evaluated as a gas cleaning process. The work has been focusing on cleaning gas from updraft gasifiers, and the long term purpose is to develop a tar cleaning unit based on thermal...... cracking. An experimental set-up has been built, in which a flow of contaminated gas can be heated up to 1290°C in a reactor made of pure Al2O3. Four measurements were made. Three with gas from a pyrolysis unit simulating updraft gasifier, and one with gas from an updraft gasifier. Cracking temperatures...... was 1200, 1250 and 1290°C, and the residence time at this temperature was 0.5 second. The measurements show that at the selected residence time of 0.5 second, the gas flow in a thermal tar cracking unit has to be heated to at least 1250°C to achieve sufficient tar cleaning. At 1290°C, a tar content as low...
HIV shedding in cervico-vaginal secretions in pregnant women.

Science.gov (United States)

Gardella, Barbara; Roccio, Marianna; Maccabruni, Anna; Mariani, Bianca; Panzeri, Lucia; Zara, Francesca; Spinillo, Arsenio

2011-07-01

The purpose of this study was to evaluate the presence of HIV-1 in cervico-vaginal secretions of pregnant as compared to non-pregnant HIV-seropositive women. We compared 43 known HIV seropositive pregnant patients versus 241 age-matched (± 2 years) control non-pregnant HIV-seropositive subjects. In pregnant patients blood and cervico-vaginal samples were obtained during each trimester of pregnancy. In control subjects the same samples were obtained at enrolment. HIV-1 RNA was measured in plasma; proviral HIV-1 DNA, cell-associated and cell-free HIV-1 RNA in cervico-vaginal secretion by competitive polymerase chain reaction (cRT-PCR) and reverse transcriptase PCR. The genital shedding of HIV-DNA (22/43 as compared to 79/241, p = 0.02), and cell-free HIV-RNA detection (26/43 as compared to 72/241, p pregnant than in non pregnant women. Pregnancy correlated with a significant positive trend in the cervico-vaginal load of HIV-DNA (Spearman Rho= 0.149, p= 0.012), and cell-free HIV-RNA (Spearman Rho= 0.253, p HIV-RNA transcripts (Spearman Rho = 0.06, p= 0.31). After correction for potential confounders, first trimester pregnant women had increased rates of genital HIV- DNA (odds ratio = 1.94, 95% confidence interval = 1.01 3.78) and cell-free HIV-RNA (odds ratio = 4.07, 95% confidence interval = 1.97 8.41) detection compared to nonpregnant controls. The shedding of genital HIV was increased in pregnant compared to non pregnant subjects, even in patients with undetectable viremia. In this low-risk HIV-positive population the risks of vertical or horizontal transmissions should not be underestimated.
Use of human papillomavirus DNA, E6/E7 mRNA, and p16 immunocytochemistry to detect and predict anal high-grade squamous intraepithelial lesions in HIV-positive and HIV-negative men who have sex with men.

Directory of Open Access Journals (Sweden)

Nittaya Phanuphak

Full Text Available Men who have sex with men (MSM are at high risk of having anal cancer. Anal high-grade squamous intraepithelial lesion (HSIL is the precursor of anal cancer. We explored the use of different biomarkers associated with human papillomavirus (HPV infection and HPV-mediated cell transformation to detect and predict HSIL among HIV-positive and HIV-negative MSM.A total of 123 HIV-positive and 123 HIV-negative MSM were enrolled and followed for 12 months. High-resolution anoscopy (HRA with biopsies were performed at every visit along with anal sample collection for cytology, high-risk HPV DNA genotyping, HPV E6/E7 mRNA, and p16 immunocytochemistry. Performance characteristics and area under the receiver operator characteristics curve were calculated for these biomarkers at baseline, and Cox regression compared the usefulness of these biomarkers in predicting incident HSIL. High-risk HPV DNA, E6/E7 mRNA, and p16 immunocytochemistry each identified 43-46% of MSM whose baseline test positivity would trigger HRA referral. E6/E7 mRNA had the highest sensitivity (64.7% and correctly classified the highest number of prevalent HSIL cases. With the exception of p16 immunochemistry, most tests showed significant increases in sensitivity but decreases specificity versus anal cytology, while the overall number of correctly classified cases was not significantly different. Baseline or persistent type 16 and/or 18 HPV DNA was the only test significantly predicting incident histologic HSIL within 12 months in models adjusted for HIV status and low-grade squamous intraepithelial lesions at baseline.Countries with a high HIV prevalence among MSM and limited HRA resources may consider using biomarkers to identify individuals at high risk of HSIL. E6/E7 mRNA had the highest sensitivity for prevalent HSIL detection regardless of HIV status, whereas type 16 and/or 18 HPV DNA performed best in predicting development of incident HSIL within 12 months.
Novel HIV-1 knockdown targets identified by an enriched kinases/phosphatases shRNA library using a long-term iterative screen in Jurkat T-cells.

Directory of Open Access Journals (Sweden)

Sylvie Rato

2010-02-01

Full Text Available HIV-1 is a complex retrovirus that uses host machinery to promote its replication. Understanding cellular proteins involved in the multistep process of HIV-1 infection may result in the discovery of more adapted and effective therapeutic targets. Kinases and phosphatases are a druggable class of proteins critically involved in regulation of signal pathways of eukaryotic cells. Here, we focused on the discovery of kinases and phosphatases that are essential for HIV-1 replication but dispensable for cell viability. We performed an iterative screen in Jurkat T-cells with a short-hairpin-RNA (shRNA library highly enriched for human kinases and phosphatases. We identified 14 new proteins essential for HIV-1 replication that do not affect cell viability. These proteins are described to be involved in MAPK, JNK and ERK pathways, vesicular traffic and DNA repair. Moreover, we show that the proteins under study are important in an early step of HIV-1 infection before viral integration, whereas some of them affect viral transcription/translation. This study brings new insights for the complex interplay of HIV-1/host cell and opens new possibilities for antiviral strategies.
The export receptor Crm1 forms a dimer to promote nuclear export of HIV RNA.

Science.gov (United States)

Booth, David S; Cheng, Yifan; Frankel, Alan D

2014-12-08

The HIV Rev protein routes viral RNAs containing the Rev Response Element (RRE) through the Crm1 nuclear export pathway to the cytoplasm where viral proteins are expressed and genomic RNA is delivered to assembling virions. The RRE assembles a Rev oligomer that displays nuclear export sequences (NESs) for recognition by the Crm1-Ran(GTP) nuclear receptor complex. Here we provide the first view of an assembled HIV-host nuclear export complex using single-particle electron microscopy. Unexpectedly, Crm1 forms a dimer with an extensive interface that enhances association with Rev-RRE and poises NES binding sites to interact with a Rev oligomer. The interface between Crm1 monomers explains differences between Crm1 orthologs that alter nuclear export and determine cellular tropism for viral replication. The arrangement of the export complex identifies a novel binding surface to possibly target an HIV inhibitor and may point to a broader role for Crm1 dimerization in regulating host gene expression.

Viral dynamics in primary HIV-1 infection. Karolinska Institutet Primary HIV Infection Study Group.

Science.gov (United States)

Lindbäck, S; Karlsson, A C; Mittler, J; Blaxhult, A; Carlsson, M; Briheim, G; Sönnerborg, A; Gaines, H

2000-10-20

To study the natural course of viremia during primary HIV infection (PHI). Eight patients were followed from a median of 5 days from the onset of PHI illness. Plasma HIV-1 RNA levels were measured frequently and the results were fitted to mathematical models. HIV-1 RNA levels were also monitored in nine patients given two reverse transcriptase inhibitors and a protease inhibitor after a median of 7 days from the onset of PHI illness. HIV-1 RNA appeared in the blood during the week preceding onset of PHI illness and increased rapidly during the first viremic phase, reaching a peak at a mean of 7 days after onset of illness. This was followed by a phase of rapidly decreasing levels of HIV-1 RNA to an average of 21 days after onset. Viral density continued to decline thereafter but at a 5- to 50-fold lower rate; a steady-state level was reached at a median of 2 months after onset of PHI. Peak viral density levels correlated significantly with levels measured between days 50 and 600. Initiation of antiretroviral treatment during PHI resulted in rapidly declining levels to below 50 copies/mL. This study demonstrates the kinetic phases of viremia during PHI and indicates two new contributions to the natural history of HIV-1 infection: PHI peak levels correlate with steady-state levels and HIV-1 RNA declines biphasically; an initial rapid decay is usually followed by a slow decay, which is similar to the initial changes seen with antiviral treatment.
Monitoring of tar contents in gases. Final report

Energy Technology Data Exchange (ETDEWEB)

Petersen, Finn [ChimneyLab Europe ApS, Hadsten (Denmark); Houmann Jakobsen, H. [BioSynergi Proces ApS, Hoersholm (Denmark)

2012-08-15

The purpose of this project is to develop and test a relative cheap and simple online tar measuring method, which can monitor the tar content in product gas from thermal gasification. The measuring principle is absorption of tar from sample gas in Isopropanol (IPA), and measuring on this solution by UV-spectrophotometer. Continuous sampling of tar containing producer gas turned out to be a larger problem than earlier foreseen. The best solution was decided to be sampling with higher flows, and afterwards cleaning the IPA in activated carbon. The ambitions for continuous sampling had to be decreased to 1 week, where the IPA and the activated carbon is contaminated by tar and has to be replaced. However this requires larger amounts of IPA and activated carbon. For IPA the weekly consumption was 12-15 Litres and for activated carbon 10 Litres. The whole analyzer unit turned out to be more complex than first projected, mainly because of the increased amounts of IPA. The best mist filter, with respect to pressure drop, efficiency and retention time is a combination of glass wool and quarts wool. The unit has been tested on gas; 20 kW pellets burner for 116 hours. Harbooere updraft gasifier for 519 hours. Skive fluid bed gasifier for 879 hours. There have during the project period been several simple practical problems such as bubbles in the IPA, increasing pressure drop over the activated carbon bed, dropout of UV data acquisition program and increasing baseline. The principle showed from the beginning some good results, with the limitation of 1 week continuous operation, but at the 5. period in Skive the baseline was increasing all the time, and it was not possible to solve this problem. (LN)
Modelling the low-tar BIG gasification concept[Biomass Integrated gasification

Energy Technology Data Exchange (ETDEWEB)

Andersen, Lars; Elmegaard, B.; Qvale, B.; Henriksen, Ulrrik [Technical univ. of Denmark (Denmark); Bentzen, J.D.; Hummelshoej, R. [COWI A/S (Denmark)

2007-07-01

A low-tar, high-efficient biomass gasification concept for medium- to large-scale power plants has been designed. The concept is named 'Low-Tar BIG' (BIG = Biomass Integrated Gasification). The concept is based on separate pyrolysis and gasification units. The volatile gases from the pyrolysis (containing tar) are partially oxidised in a separate chamber, and hereby the tar content is dramatically reduced. Thus, the investment, and running cost of a gas cleaning system can be reduced, and the reliability can be increased. Both pyrolysis and gasification chamber are bubbling fluid beds, fluidised with steam. For moist fuels, the gasifier can be integrated with a steam drying process, where the produced steam is used in the pyrolysis/gasification chamber. In this paper, mathematical models and results from initial tests of a laboratory Low-Tar BIG gasifier are presented. Two types of models are presented: 1. The gasifier-dryer applied in different power plant systems: Gas engine, Simple cycle gas turbine, Recuperated gas turbine and Integrated Gasification and Combined Cycle (IGCC). The paper determines the differences in efficiency of these systems and shows that the gasifier will be applicable for very different fuels with different moisture contents, depending on the system. 2. A thermodynamic Low-Tar BIG model. This model is based on mass and heat balance between four reactors: Pyrolysis, partial oxidation, gasification, gas-solid mixer. The paper describes the results from this study and compares the results to actual laboratory tests. The study shows, that the Low-Tar BIG process can use very wet fuels (up to 65-70% moist) and still produce heat and power with a remarkable high electric efficiency. Hereby the process offers the unique combination of large scale gasification and low-cost gas cleaning and use of low-cost fuels which very likely is the necessary combination that will lead to a breakthrough of gasification technology. (au)
Creating fluid injectivity in tar sands formations

Science.gov (United States)

Stegemeier, George Leo; Beer, Gary Lee; Zhang, Etuan

2010-06-08

Methods for treating a tar sands formation are described herein. Methods for treating a tar sands may include heating a portion of a hydrocarbon layer in the formation from one or more heaters located in the portion. The heat may be controlled to increase the permeability of at least part of the portion to create an injection zone in the portion with an average permeability sufficient to allow injection of a fluid through the injection zone. A drive fluid and/or an oxidizing fluid may be provided into the injection zone. At least some hydrocarbons are produced from the portion.
HIVsirDB: a database of HIV inhibiting siRNAs.

Directory of Open Access Journals (Sweden)

Atul Tyagi

Full Text Available Human immunodeficiency virus (HIV is responsible for millions of deaths every year. The current treatment involves the use of multiple antiretroviral agents that may harm patients due to their toxic nature. RNA interference (RNAi is a potent candidate for the future treatment of HIV, uses short interfering RNA (siRNA/shRNA for silencing HIV genes. In this study, attempts have been made to create a database HIVsirDB of siRNAs responsible for silencing HIV genes.HIVsirDB is a manually curated database of HIV inhibiting siRNAs that provides comprehensive information about each siRNA or shRNA. Information was collected and compiled from literature and public resources. This database contains around 750 siRNAs that includes 75 partially complementary siRNAs differing by one or more bases with the target sites and over 100 escape mutant sequences. HIVsirDB structure contains sixteen fields including siRNA sequence, HIV strain, targeted genome region, efficacy and conservation of target sequences. In order to facilitate user, many tools have been integrated in this database that includes; i siRNAmap for mapping siRNAs on target sequence, ii HIVsirblast for BLAST search against database, iii siRNAalign for aligning siRNAs.HIVsirDB is a freely accessible database of siRNAs which can silence or degrade HIV genes. It covers 26 types of HIV strains and 28 cell types. This database will be very useful for developing models for predicting efficacy of HIV inhibiting siRNAs. In summary this is a useful resource for researchers working in the field of siRNA based HIV therapy. HIVsirDB database is accessible at http://crdd.osdd.net/raghava/hivsir/.
The separate effects of tar and nicotine on the cigarette smoking manoeuvre

International Nuclear Information System (INIS)

Woodman, G.; Newman, S.P.; Paiva, D.; Clarke, S.W.

1987-01-01

The separate effects of tar and nicotine on the cigarette smoking manoeuvre were investigated. Each of ten asymptomatic habitual smokers smoked three different commercially available cigarettes in a randomised order. The brands were chosen such that two had the same tar yield (10 mg) and two had the same nicotine yield (1.4 mg). The volume of smoke inhaled into the lungs was measured by tracing the smoke with the inert gas 81 Kr m . Puffing indices were recorded using an electronic smoking analyser and flowhead/cigarette holder. There was no difference in the total volume of smoke puffed from each of the cigarette brands. With cigarettes of the samme tar level, the total inhaled smoke volume was lower with the higher nicotine cigarette (P<0.05): by contrast, with cigarettes of the same nicotine level, the toal inhaled smoke volume was lower with the lower tar cigarette (P<0.02). Tar and nicotine appear to exercise independent control over the volume of smoke inhaled. (author)
Determination of HIV Status in African Adults With Discordant HIV Rapid Tests.

Science.gov (United States)

Fogel, Jessica M; Piwowar-Manning, Estelle; Donohue, Kelsey; Cummings, Vanessa; Marzinke, Mark A; Clarke, William; Breaud, Autumn; Fiamma, Agnès; Donnell, Deborah; Kulich, Michal; Mbwambo, Jessie K K; Richter, Linda; Gray, Glenda; Sweat, Michael; Coates, Thomas J; Eshleman, Susan H

2015-08-01

In resource-limited settings, HIV infection is often diagnosed using 2 rapid tests. If the results are discordant, a third tie-breaker test is often used to determine HIV status. This study characterized samples with discordant rapid tests and compared different testing strategies for determining HIV status in these cases. Samples were previously collected from 173 African adults in a population-based survey who had discordant rapid test results. Samples were classified as HIV positive or HIV negative using a rigorous testing algorithm that included two fourth-generation tests, a discriminatory test, and 2 HIV RNA tests. Tie-breaker tests were evaluated, including rapid tests (1 performed in-country), a third-generation enzyme immunoassay, and two fourth-generation tests. Selected samples were further characterized using additional assays. Twenty-nine samples (16.8%) were classified as HIV positive and 24 of those samples (82.8%) had undetectable HIV RNA. Antiretroviral drugs were detected in 1 sample. Sensitivity was 8.3%-43% for the rapid tests; 24.1% for the third-generation enzyme immunoassay; 95.8% and 96.6% for the fourth-generation tests. Specificity was lower for the fourth-generation tests than the other tests. Accuracy ranged from 79.5% to 91.3%. In this population-based survey, most HIV-infected adults with discordant rapid tests were virally suppressed without antiretroviral drugs. Use of individual assays as tie-breaker tests was not a reliable method for determining HIV status in these individuals. More extensive testing algorithms that use a fourth-generation screening test with a discriminatory test and HIV RNA test are preferable for determining HIV status in these cases.
21 CFR 740.18 - Coal tar hair dyes posing a risk of cancer.

Science.gov (United States)

2010-04-01

... 21 Food and Drugs 7 2010-04-01 2010-04-01 false Coal tar hair dyes posing a risk of cancer. 740.18... (CONTINUED) COSMETICS COSMETIC PRODUCT WARNING STATEMENTS Warning Statements § 740.18 Coal tar hair dyes... coal tar hair dye containing any ingredient listed in paragraph (b) of this section shall bear, in...
Gasification of municipal solid waste in a downdraft gasifier: Analysis of tar formation

Directory of Open Access Journals (Sweden)

Tabitha Geoffrey Etutu

2016-04-01

Full Text Available In this study, municipal solid waste (MSW from a dumpsite was converted into refuse derived fuel (RDF and used as feedstock for an air-blown gasification process. The gasification process was conducted in a 10 kg.hr -1 downdraft gasifier at different air flow rates of 300, 350, 400, 450 and 550 NL.min1 at atmospheric pressure in order to investigate the quantity and quality of tar formed. It was shown that the increase in the air flow rate from 300 NL.min1 to 550 NL.min1 led to an increase in the oxidation temperature from 719°C to 870°C and an increase in the reduction temperature from 585°C to 750°C, respectively. Tar was reduced from 15 g.Nm3 to 4.7 g.Nm3 respectively. Heavy tar compounds (>C17 e.g. pyrene and phenathrene, decreased with the increase in the light tar compounds (tar reduction through a tar cracking process.
Recovery of very viscous lubricating oils from shale-tar, etc

Energy Technology Data Exchange (ETDEWEB)

Erdmann, E

1919-09-10

Modification of the process covered by German Patent 335,190 for recovering very viscous lubricating oils, consisting, in place of brown-coal tar, deparafinned peat tar being subjected to the treatment with superheated steam from about 200 to 250/sup 0/C or to heating in vacuum at a temperature below 250/sup 0/C.
Technological changes illustrated by the coal tar and tar dye industry; Die Wandlung der Technik am Beispiel der Steinkohlenteer- und Teerfarben-Chemie

Energy Technology Data Exchange (ETDEWEB)

Collin, G. [Deutsche Gesellschaft fuer Chemisches Apparatewesen, Chemische Technik und Biotechnologie e.V. (DECHEMA), Frankfurt am Main (Germany)

2001-05-01

Coal tar was detected in the 17th century in laboratory experiments based on empirical knowledge. In the 18th century industrial revolution, coal tar was an undesired by-product of iron production and coking plants. It was first used in the 19th century for impregnating railway sleepers. Later developments in atomic theory, new chemical symbols and organic element analysis provided the basis for discovering and chemical characterisation of coal tar constituents. Laboratory experiments with these tar constituents resulted in the first synthetic dyes, the postulation of tetravalent carbon and the resulting structural theory in organic chemistry for systematic synthesis of many tar dyes to substitute natural dyes in the textile industry. The technical application of these syntheses was part 2 of the industrial revolution and the foundation of the chemical industry in Germany, which developed rapidly in the 2nd half of the 19th century. Tar dye chemistry has made a significant contribution to Germany's economic growth and the change from an agricultural to an industrialized country. [German] Die Entdeckung des Steinkohlenteers im 17. Jahrhundert basiert auf durch Erfahrungswissen gepraegten Laboratoriumsexperimenten. Im Verlauf der 'Industriellen Revolution' des 18. Jahrhunderts ist der Steinkohlenteer zunaechst ein laestiges Abfallprodukt der Eisengewinnung im Kokshochofen und der Leuchtgasherstellung durch Kohlenverkokung. Erste technische Applikation finden Steinkohlenteeroele im 19. Jahrhundert durch den Eisenbahnbau zur Langzeit-Konservierung der dafuer benoetigten Holzschwellen. Die wissenschaftlichen Erfkenntnisse zur Atomtheorie, eine neue chemische Zeichensprache und die organische Elementaranalyse werden Voraussetzungen zur Entdeckung und chemischen Charakterisierung der Hauptinhaltsstoffe des Steinkohlenteers. Laboratoriumsexperimente mit den entdeckten Teerinhaltsstoffen fuehren zur Erfindung der ersten synthetischen Farbstoffe, die
Inhaled smoke volume and puff indices with cigarettes of different tar and nicotine levels

International Nuclear Information System (INIS)

Woodman, G.; Newman, S.P.; Pavia, D.; Clarke, S.W.

1987-01-01

Ten asymptomatic smokers each smoked a low, low-to-middle and a middle tar cigarette with approximately the same tar-to-nicotine ratio, in a randomised order. The inhaled smoke volume was measured by tracing the smoke with the inert gas 81 Kr m . Puffing indices were recorded using an electronic smoking analyser and flowhead/cigarette holder. Throughout the study neither the mean inhaled smoke volume per puff nor the total inhaled smoke volume per cigarette changed significantly; however, the mean and total puff volumes were largest with the low tar cigarette and decreased with the higher tar brands. Puff volume was related to puff work (r s =0.83,P s =0.10,P>0.1). It is concluded that when switched between brands with the same tar-to-nicotine ratio, smokers increase their puff volumes with a lower tar cigarette but do not change the volume of smoke inhaled. Puff work and puff resistance were significantly correlated (r s =0.45,P<0.02). (author)
Analysis of low-temperature tar fractions

Energy Technology Data Exchange (ETDEWEB)

Kikkawa, S; Yamada, F

1952-01-01

A preliminary comparative study was made on the applicability of the methods commonly used for the type analysis of petroleum products to the low-temperature tar fractions. The usability of chromatography was also studied.
The effect of HIV infection and HCV viremia on inflammatory mediators and hepatic injury-The Women's Interagency HIV Study.

Directory of Open Access Journals (Sweden)

Sheila M Keating

Full Text Available Hepatitis C virus infection induces inflammation and while it is believed that HIV co-infection enhances this response, HIV control may reduce inflammation and liver fibrosis in resolved or viremic HCV infection. Measurement of systemic biomarkers in co-infection could help define the mechanism of inflammation on fibrosis and determine if HIV control reduces liver pathology. A nested case-control study was performed to explore the relationship of systemic biomarkers of inflammation with liver fibrosis in HCV viremic and/or seropositive women with and without HIV infection. Serum cytokines, chemokines, growth factors and cell adhesion molecules were measured in HIV uninfected (HIV-, n = 18, ART-treated HIV-controlled (ARTc, n = 20, uncontrolled on anti-retroviral therapy (ARTuc, n = 21 and elite HIV controllers (Elite, n = 20. All were HCV seroreactive and had either resolved (HCV RNA-; <50IU/mL or had chronic HCV infection (HCV RNA+. In HCV and HIV groups, aspartate aminotransferase to platelet ratio (APRI was measured and compared to serum cytokines, chemokines, growth factors and cell adhesion molecules. APRI correlated with sVCAM, sICAM, IL-10, and IP-10 levels and inversely correlated with EGF, IL-17, TGF-α and MMP-9 levels. Collectively, all HCV RNA+ subjects had higher sVCAM, sICAM and IP-10 compared to HCV RNA-. In the ART-treated HCV RNA+ groups, TNF-α, GRO, IP-10, MCP-1 and MDC were higher than HIV-, Elite or both. In ARTuc, FGF-2, MPO, soluble E-selectin, MMP-9, IL-17, GM-CSF and TGF-α are lower than HIV-, Elite or both. Differential expression of soluble markers may reveal mechanisms of pathogenesis or possibly reduction of fibrosis in HCV/HIV co-infection.
Acid Tar Lagoons: Management and Recovery

Science.gov (United States)

Bohers, Anna; Hroncová, Emília; Ladomerský, Juraj

2017-04-01

This contribution presents the issue with possibility of definitive removal of dangerous environmental burden in Slovakia - serious historical problem of two acid tar lagoons. In relation to their removal, no technology has been found so far - technologically and economically suitable, what caused problems with its management. Locality Predajná is well known in Slovakia by its character of contrasts: it is situated in the picturesque landscape of National Park buffer zone of Nízke Tatry, on the other site it is contaminated by 229 211m3 of acid tar with its characteristics of toxicity, carcinogenicity, teratogenicity, mutagenicity and toxicity especially for animals and plants. Acid tar in two landfills with depth of 1m in case of the first lagoon and 9,5m in case of the second lagoon is a waste product derived from operation of Petrochema Dubová - refinery and petrochemical plant whose activity was to process the crude oil through processes of sulfonation and adsorption technology for producing lubricating and special oils, synthetic detergents and special white oils for cosmetic and medical purposes. A part of acid tar was incinerated in two incineration plats. Concentration of SO2 in combustion gases was too high and it was not possible to decrease it under the value of 2000 mg.mn-3 [LADOMERSKÝ, J. - SAMEŠOVÁ, D.: Reduction in sulfur dioxide emissions waste gases of incineration plant. Acta facultatis ecologiae. 1999, p. 217-223]. That is why it was necessary to put them out of operation. Later, because of public opposition it was not possible to build a new incineration plat corresponding to the state of the art. Even though actual Slovak and European legislative for protection of environment against such impacts, neither of tried methods - bio or non-biologic treatment methods - was proved as suitable for processing or for recovery in the reason of different factors admission: i.e. strong aggressivity, difficulty with handling because of its sludgy and
Assessment of ground-water contamination by coal-tar derivatives, St. Louis Park area, Minnesota

Science.gov (United States)

Hult, M.F.

1984-01-01

Operation of a coal-tar distillation and wood-preserving facility in St. Louis Park, Minnesota, during 1918-72 contaminated ground water with coal-tar derivatives and inorganic chemicals. Coal-tar derivatives entered the groundwater system through three major paths: (1) Spills and drippings that percolated to the water table, (2) surface runoff and plant process water that was discharged to wetlands south of the former plant site, and (3) movement of coal tar directly into bedrock aquifers through a multiaquifer well on the site.
Simulation of Trajectories of Tar Ball Transport to the Goa Coast

Digital Repository Service at National Institute of Oceanography (India)

Suneel, V.; Vethamony, P.; VinodKumar, K.; Babu, M.T.; Prasad, V.S.R.

Arrival of tar balls to the Goa coast during pre- and southwest monsoon seasons has been a regular phenomenon in the past few years. In one such event, we observed tar ball deposits along the Goa coast during August 2010, April 2011 and May 2011...
The Legend of Hot Tar or Pitch as a Defensive Weapon

DEFF Research Database (Denmark)

Atzbach, Rainer

2015-01-01

research. In reality, this way of fighting can only be seen as a legend, i.e. a story with only a relative truth at its core. This paper will examine the origin of this historical tradition and its archaeological and architectural sources. The chemical and physical properties of tar pitch and its...... production and use during the Middle Ages will be discussed with special focus on the application of tar pitch as an ingredient in medieval and post-medieval thermal weapons (especially Greek Fire, the firebomb and the fire arrow). The punishment of tarring and feathering will also be considered...
Ensamblajes urbanos: la TAR y el examen de la ciudad

Directory of Open Access Journals (Sweden)

Ignacio Farías

2011-03-01

Full Text Available Este artículo presenta nuevas perspectivas de investigación y desafíos analíticos que la teoría del actor-red (TAR abre para los estudios urbanos. En primer lugar, se revisan cómo los principios de relacionalidad híbrida y asociatividad plana de la TAR están siendo adoptados en los estudios urbanos para ampliar simétricamente la ecología urbana a no-humanos e impugnar concepciones escalares del espacio y economías urbanas. A continuación, se propone que la TAR trae consigo un desafío más fundamental relativo a la concepción de la ciudad como objeto de estudio. Mientras su comprensión habitual como objeto espacial, entidad político-económica y/o forma sociocultural subraya su carácter singular, estable y delimitado, la TAR permite pensar la ciudad como un objeto múltiple y decentrado. La noción de ensamblajes urbanos se introduce entonces para dar cuenta de la circulación y devenir de la ciudad en múltiples redes híbridas y translocales. El artículo concluye sopesando algunas de las consecuencias de este exámen de la ciudad, especialmente el reposicionamiento del problema de la complejidad, urbana en este caso, como punto, si no de partida, entonces al menos de llegada para la TAR.
Copyrolysis of coal with coke-oven gas. III. Analysis of tar

Energy Technology Data Exchange (ETDEWEB)

Liao, H.; Sun, C.; Li, B.; Liu, Z. [Chinese Academy of Sciences, Taiyuan (China). State Key Laboratory of Coal Conversion, Institute of Coal Chemistry

1998-02-01

Tars from copyrolysis of Xianfeng lignite with coke-oven gas (COG) at different pressures (0.1-5 MPa) and heating rates (5-25{degree}C/min) to a final temperature of 650{degree}C were analyzed and compared with hydropyrolysis under the same H{sub 2} partial pressure. The results indicated that high contents of BTX, PCX and naphthalene were found in the tar from copyrolysis of Xianfeng lignite with COG. Pressure and heating rate have important effects on tar yields and the contents of BTX, PCX and naphthalene in oil. Increasing pressure and decreasing heating rate enhance the tar yields and result in high yields of BTX and PCX. When compared with hydropyrolysis under the same H{sub 2} partial pressure, the tar yield increases by 1.2 times and the yields of BTX, PCX and naphthalene by about 1.6, 1.3 and 1.6 times, respectively. At the same total pressure (3MPa), the yields of BTX and naphthalene from copyrolysis are equal to those from hydropyrolysis. The results reveal that other components in COG, such as methane, carbon monoxide etc., are of importance for pyrolysis behaviour of coal under COG and improvement of oil qualities. 5 refs., 5 figs., 2 tabs.

Preclinical safety and efficacy of an anti–HIV-1 lentiviral vector containing a short hairpin RNA to CCR5 and the C46 fusion inhibitor

Directory of Open Access Journals (Sweden)

Orit Wolstein

2014-01-01

Full Text Available Gene transfer has therapeutic potential for treating HIV-1 infection by generating cells that are resistant to the virus. We have engineered a novel self-inactivating lentiviral vector, LVsh5/C46, using two viral-entry inhibitors to block early steps of HIV-1 cycle. The LVsh5/C46 vector encodes a short hairpin RNA (shRNA for downregulation of CCR5, in combination with the HIV-1 fusion inhibitor, C46. We demonstrate here the effective delivery of LVsh5/C46 to human T cell lines, peripheral blood mononuclear cells, primary CD4+ T lymphocytes, and CD34+ hematopoietic stem/progenitor cells (HSPC. CCR5-targeted shRNA (sh5 and C46 peptide were stably expressed in the target cells and were able to effectively protect gene-modified cells against infection with CCR5- and CXCR4-tropic strains of HIV-1. LVsh5/C46 treatment was nontoxic as assessed by cell growth and viability, was noninflammatory, and had no adverse effect on HSPC differentiation. LVsh5/C46 could be produced at a scale sufficient for clinical development and resulted in active viral particles with very low mutagenic potential and the absence of replication-competent lentivirus. Based on these in vitro results, plus additional in vivo safety and efficacy data, LVsh5/C46 is now being tested in a phase 1/2 clinical trial for the treatment of HIV-1 disease.
Enrichment of intersubtype HIV-1 recombinants in a dual infection system using HIV-1 strain-specific siRNAs

Science.gov (United States)

2011-01-01

Background Intersubtype HIV-1 recombinants in the form of unique or stable circulating recombinants forms (CRFs) are responsible for over 20% of infections in the worldwide epidemic. Mechanisms controlling the generation, selection, and transmission of these intersubtype HIV-1 recombinants still require further investigation. All intersubtype HIV-1 recombinants are generated and evolve from initial dual infections, but are difficult to identify in the human population. In vitro studies provide the most practical system to study mechanisms, but the recombination rates are usually very low in dual infections with primary HIV-1 isolates. This study describes the use of HIV-1 isolate-specific siRNAs to enrich intersubtype HIV-1 recombinants and inhibit the parental HIV-1 isolates from a dual infection. Results Following a dual infection with subtype A and D primary HIV-1 isolates and two rounds of siRNA treatment, nearly 100% of replicative virus was resistant to a siRNA specific for an upstream target sequence in the subtype A envelope (env) gene as well as a siRNA specific for a downstream target sequence in the subtype D env gene. Only 20% (10/50) of the replicating virus had nucleotide substitutions in the siRNA-target sequence whereas the remaining 78% (39/50) harbored a recombination breakpoint that removed both siRNA target sequences, and rendered the intersubtype D/A recombinant virus resistant to the dual siRNA treatment. Since siRNAs target the newly transcribed HIV-1 mRNA, the siRNAs only enrich intersubtype env recombinants and do not influence the recombination process during reverse transcription. Using this system, a strong bias is selected for recombination breakpoints in the C2 region, whereas other HIV-1 env regions, most notably the hypervariable regions, were nearly devoid of intersubtype recombination breakpoints. Sequence conservation plays an important role in selecting for recombination breakpoints, but the lack of breakpoints in many conserved
Correlates of HIV-1 genital shedding in Tanzanian women.

Directory of Open Access Journals (Sweden)

Clare Tanton

2011-03-01

Full Text Available Understanding the correlates of HIV shedding is important to inform strategies to reduce HIV infectiousness. We examined correlates of genital HIV-1 RNA in women who were seropositive for both herpes simplex virus (HSV-2 and HIV-1 and who were enrolled in a randomised controlled trial of HSV suppressive therapy (aciclovir 400 mg b.i.d vs. placebo in Tanzania.Samples, including a cervico-vaginal lavage, were collected and tested for genital HIV-1 and HSV and reproductive tract infections (RTIs at randomisation and 6, 12 and 24 months follow-up. Data from all women at randomisation and women in the placebo arm during follow-up were analysed using generalised estimating equations to determine the correlates of cervico-vaginal HIV-1 RNA detection and load.Cervico-vaginal HIV-1 RNA was detected at 52.0% of 971 visits among 482 women, and was independently associated with plasma viral load, presence of genital ulcers, pregnancy, bloody cervical or vaginal discharge, abnormal vaginal discharge, cervical ectopy, Neisseria gonorrhoeae, Chlamydia trachomatis, Trichomonas vaginalis, an intermediate bacterial vaginosis score and HSV DNA detection. Similar factors were associated with genital HIV-1 RNA load.RTIs were associated with increased presence and quantity of genital HIV-1 RNA in this population. These results highlight the importance of integrating effective RTI treatment into HIV care services.
Dimerization of human immunodeficiency virus (type 1) RNA: stimulation by cations and possible mechanism.

Science.gov (United States)

Marquet, R; Baudin, F; Gabus, C; Darlix, J L; Mougel, M; Ehresmann, C; Ehresmann, B

1991-05-11

The retroviral genome consists of two identical RNA molecules joined close to their 5' ends by the dimer linkage structure. Recent findings indicated that retroviral RNA dimerization and encapsidation are probably related events during virion assembly. We studied the cation-induced dimerization of HIV-1 RNA and results indicate that all in vitro generated HIV-1 RNAs containing a 100 nucleotide domain downstream from the 5' splice site are able to dimerize. RNA dimerization depends on the concentration of RNA, mono- and multivalent cations, the size of the monovalent cation, temperature, and pH. Up to 75% of HIV-1 RNA is dimeric in the presence of spermidine. HIV-1 RNA dimer is fairly resistant to denaturing agents and unaffected by intercalating drugs. Antisense HIV-1 RNA does not dimerize but heterodimers can be formed between HIV-1 RNA and either MoMuLV or RSV RNA. Therefore retroviral RNA dimerization probably does not simply proceed through mechanisms involving Watson-Crick base-pairing. Neither adenine and cytosine protonation, nor quartets containing only guanines appear to determine the stability of the HIV-1 RNA dimer, while quartets involving both adenine(s) and guanine(s) could account for our results. A consensus sequence PuGGAPuA found in the putative dimerization-encapsidation region of all retroviral genomes examined may participate in the dimerization process.
Relevance of carbon structure to formation of tar and liquid alkane during coal pyrolysis

International Nuclear Information System (INIS)

Liu, Peng; Le, Jiawei; Wang, Lanlan; Pan, Tieying; Lu, Xilan; Zhang, Dexiang

2016-01-01

Highlights: • Curve-fitting method was used to quantify the accurate contents of structural carbon. • Effect of carbon structure in coal with different rank on formation of pyrolysis tar was studied. • Numerical interrelation between carbon types in coal structure and tar yield is elaborated. • Effect of carbon structure on formation of liquid alkane during coal pyrolysis is discussed. - Abstract: The relevance of carbon structure to formation of tar and liquid alkane during coal pyrolysis were discussed extensively. The pyrolysis tests were carried out in a tube reactor at 873 K and keep 15 min. The carbon distribution in coals was investigated by solid state "1"3C nuclear magnetic resonance (N.M.R.). The curve-fitting method was used to quantify the accurate contents of structural carbon. The alkanes in coal tar were analyzed by Gas Chromatograph–Mass Spectrometer (GC–MS). The results show that oxygen-linked aromatic carbon decreases with the increasing of coal rank. The aliphatic carbon contents of Huainan (HN) coal are 44.20%, the highest among the four coals. The carbon types in coal structure have a significant influence on the formation of tar and liquid alkane. The coal tar yields are related to the aliphatic substituted aromatic carbon, CH_2/CH_3 ratio and oxygen-linked carbon in coal so that the increasing order of tar yield is Inner Mongolia lignite (IM, 6.30 wt.%) < Sinkiang coal (SK, 7.55 wt.%) < Shenmu coal (SM, 12.84 wt.%) < HN (16.29 wt.%). The highest contents of oxygen-linked aromatic carbon in IM lead to phenolic compound of 41.06% in IM-tar. The contents of alkane in SM-tar are the highest because the appropriate CH_2/CH_3 ratio and the highest aliphatic side chains on aromatic rings in SM leading to generate aliphatic hydrocarbon with medium molecular weight easily. The mechanism on formation of tar and liquid alkane plays an important role in guiding the industrialization of pyrolysis-based poly-generation producing tar with high
Identification of sources of tar balls deposited along the Goa coast, India, using fingerprinting techniques

International Nuclear Information System (INIS)

Suneel, V.; Vethamony, P.; Zakaria, M.P.; Naik, B.G.; Prasad, K.V.S.R.

2013-01-01

Highlights: ► This is first fingerprinting study in India on identification of source of tar balls. ► Tar balls were formed from tanker-wash spills and they resemble floating tar ball. ► δ 13 C values of Bombay High crude oil and the present tar balls do not match. ► Compound specific stable carbon isotope analysis confirmed the source of tar balls. ► Source is confirmed as the South East Asian Crude Oil and not the Bombay High crude. -- Abstract: Deposition of tar balls along the coast of Goa, India is a common phenomenon during the southwest monsoon. Representative tar ball samples collected from various beaches of Goa and one Bombay High (BH) crude oil sample were subjected to fingerprint analysis based on diagnostic ratios of n-alkane, biomarkers of pentacyclic tri-terpanes and compound specific stable carbon isotope (δ 13 C) analysis to confirm the source. The results were compared with the published data of Middle East Crude Oil (MECO) and South East Asian Crude Oil (SEACO). The results revealed that the tar balls were from tanker-wash derived spills. The study also confirmed that the source is not the BH, but SEACO. The present study suggests that the biomarkers of alkanes and hopanes coupled with stable carbon isotope analysis act as a powerful tool for tracing the source of tar balls, particularly when the source specific biomarkers fail to distinguish the source
2012 HIV Diagnostics Conference: the molecular diagnostics perspective.

Science.gov (United States)

Branson, Bernard M; Pandori, Mark

2013-04-01

2012 HIV Diagnostic Conference Atlanta, GA, USA, 12-14 December 2012. This report highlights the presentations and discussions from the 2012 National HIV Diagnostic Conference held in Atlanta (GA, USA), on 12-14 December 2012. Reflecting changes in the evolving field of HIV diagnostics, the conference provided a forum for evaluating developments in molecular diagnostics and their role in HIV diagnosis. In 2010, the HIV Diagnostics Conference concluded with the proposal of a new diagnostic algorithm which included nucleic acid testing to resolve discordant screening and supplemental antibody test results. The 2012 meeting, picking up where the 2010 meeting left off, focused on scientific presentations that assessed this new algorithm and the role played by RNA testing and new developments in molecular diagnostics, including detection of total and integrated HIV-1 DNA, detection and quantification of HIV-2 RNA, and rapid formats for detection of HIV-1 RNA.
29 CFR 1926.1102 - Coal tar pitch volatiles; interpretation of term.

Science.gov (United States)

2010-07-01

... 29 Labor 8 2010-07-01 2010-07-01 false Coal tar pitch volatiles; interpretation of term. 1926.1102 Section 1926.1102 Labor Regulations Relating to Labor (Continued) OCCUPATIONAL SAFETY AND HEALTH... Hazardous Substances § 1926.1102 Coal tar pitch volatiles; interpretation of term. Note: The requirements...
A review of the primary measures for tar elimination in biomass gasification processes

International Nuclear Information System (INIS)

Devi, Lopamudra; Ptasinski, K.J.; Janssen, F.J.J.G.

2003-01-01

Tar formation is one of the major problems to deal with during biomass gasification. Tar condenses at reduced temperature, thus blocking and fouling process equipments such as engines and turbines. Considerable efforts have been directed on tar removal from fuel gas. Tar removal technologies can broadly be divided into two approaches; hot gas cleaning after the gasifier (secondary methods), and treatments inside the gasifier (primary methods). Although secondary methods are proven to be effective, treatments inside the gasifier are gaining much attention as these may eliminate the need for downstream cleanup. In primary treatment, the gasifier is optimized to produce a fuel gas with minimum tar concentration. The different approaches of primary treatment are (a) proper selection of operating parameters, (b) use of bed additive/catalyst, and (c) gasifier modifications. The operating parameters such as temperature, gasifying agent, equivalence ratio, residence time, etc. play an important role in formation and decomposition of tar. There is a potential of using some active bed additives such as dolomite, olivine, char, etc. inside the gasifier. Ni-based catalyst are reported to be very effective not only for tar reduction, but also for decreasing the amount of nitrogenous compounds such as ammonia. Also, reactor modification can improve the quality of the product gas. The concepts of two-stage gasification and secondary air injection in the gasifier are of prime importance. Some aspects of primary methods and the research and development in this area are reviewed and cited in the present paper
Solid state 13 C NMR quantitative study of wood tar pitches

International Nuclear Information System (INIS)

Prauchner, Marcos Juliano; Pasa, Vanya Marcia Duarte; Menezes, Sonia Maria Cabral de

1999-01-01

In this work, solid-state 13 C NMR is used with other techniques to characterize Eucalyptus tar pitches and to follow their polymerization reactions. The pitches are the residues of distillation (about 50% m;m) of the tar generated in Eucalyptus slow pyrolysis for charcoal production in metal industry
29 CFR 1915.1002 - Coal tar pitch volatiles; interpretation of term.

Science.gov (United States)

2010-07-01

... 29 Labor 7 2010-07-01 2010-07-01 false Coal tar pitch volatiles; interpretation of term. 1915.1002 Section 1915.1002 Labor Regulations Relating to Labor (Continued) OCCUPATIONAL SAFETY AND HEALTH... Toxic and Hazardous Substances § 1915.1002 Coal tar pitch volatiles; interpretation of term. Note: The...
Avoiding tar formation in biocoke production from waste biomass

International Nuclear Information System (INIS)

Adrados, A.; De Marco, I.; Lopez-Urionabarrenechea, A.; Solar, J.; Caballero, B.

2015-01-01

This paper focuses in avoiding tar formation and in optimizing pyrolysis gas (maximizing H 2 and CO) in the production of biocoke from waste lignocellulosic biomass. In order to obtain metallurgical grade biochar (biocoke) slow heating rate and high temperature are required. Under such conditions useless pyrolysis liquids, mainly composed of water together with some heavy-sticky tars, are obtained. In order to make biocoke a cost-effective process it is necessary to optimize pyrolysis vapors avoiding tar formation and maximizing the amount and quality of both coke and gases. With this objective, in this work different heating rates (3–20 °C min −1 ) and catalysts (zeolite, Ni/CeO 2 –Al 2 O 3 ) have been tested in a two step pyrolysis process. Olive tree cuttings have been pyrolyzed in a 3.5 L batch reactor at 750 °C and the vapors generated have been thermally and catalytically treated at 900 °C in a second tubular reactor. About 25 wt.% biocoke useful as reducing agent in certain metallurgical processes, ≈57 wt.% gases with near 50 vol.% H 2 , and no tar production has been achieved when a heating rate of 3 °C min −1 and the homemade Ni/CeO 2 –Al 2 O 3 catalyst were used. - Highlights: • Metallurgical grade biochar was obtained by olive waste pyrolysis. • Low heating rates avoid tar formation and increase gas and biochar yields. • Ni/CeO 2 –Al 2 O 3 was better than HZSM5 zeolite for vapor upgrading in a second step. • Ni/CeO 2 –Al 2 O 3 and 3 °C min −1 gave the maximum H 2 , gas and biochar yields
RNA helicase MOV10 functions as a co-factor of HIV-1 Rev to facilitate Rev/RRE-dependent nuclear export of viral mRNAs

International Nuclear Information System (INIS)

Huang, Feng; Zhang, Junsong; Zhang, Yijun; Geng, Guannan; Liang, Juanran; Li, Yingniang; Chen, Jingliang; Liu, Chao; Zhang, Hui

2015-01-01

Human immunodeficiency virus type 1 (HIV-1) exploits multiple host factors during its replication. The REV/RRE-dependent nuclear export of unspliced/partially spliced viral transcripts needs the assistance of host proteins. Recent studies have shown that MOV10 overexpression inhibited HIV-1 replication at various steps. However, the endogenous MOV10 was required in certain step(s) of HIV-1 replication. In this report, we found that MOV10 potently enhances the nuclear export of viral mRNAs and subsequently increases the expression of Gag protein and other late products through affecting the Rev/RRE axis. The co-immunoprecipitation analysis indicated that MOV10 interacts with Rev in an RNA-independent manner. The DEAG-box of MOV10 was required for the enhancement of Rev/RRE-dependent nuclear export and the DEAG-box mutant showed a dominant-negative activity. Our data propose that HIV-1 utilizes the anti-viral factor MOV10 to function as a co-factor of Rev and demonstrate the complicated effects of MOV10 on HIV-1 life cycle. - Highlights: • MOV10 can function as a co-factor of HIV-1 Rev. • MOV10 facilitates Rev/RRE-dependent transport of viral mRNAs. • MOV10 interacts with Rev in an RNA-independent manner. • The DEAG-box of MOV10 is required for the enhancement of Rev/RRE-dependent export.
RNA helicase MOV10 functions as a co-factor of HIV-1 Rev to facilitate Rev/RRE-dependent nuclear export of viral mRNAs

Energy Technology Data Exchange (ETDEWEB)

Huang, Feng; Zhang, Junsong; Zhang, Yijun; Geng, Guannan; Liang, Juanran; Li, Yingniang; Chen, Jingliang [Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080 (China); Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080 (China); Liu, Chao, E-mail: liuchao9@mail.sysu.edu.cn [Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080 (China); Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080 (China); Zhang, Hui [Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080 (China); Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080 (China)

2015-12-15

Human immunodeficiency virus type 1 (HIV-1) exploits multiple host factors during its replication. The REV/RRE-dependent nuclear export of unspliced/partially spliced viral transcripts needs the assistance of host proteins. Recent studies have shown that MOV10 overexpression inhibited HIV-1 replication at various steps. However, the endogenous MOV10 was required in certain step(s) of HIV-1 replication. In this report, we found that MOV10 potently enhances the nuclear export of viral mRNAs and subsequently increases the expression of Gag protein and other late products through affecting the Rev/RRE axis. The co-immunoprecipitation analysis indicated that MOV10 interacts with Rev in an RNA-independent manner. The DEAG-box of MOV10 was required for the enhancement of Rev/RRE-dependent nuclear export and the DEAG-box mutant showed a dominant-negative activity. Our data propose that HIV-1 utilizes the anti-viral factor MOV10 to function as a co-factor of Rev and demonstrate the complicated effects of MOV10 on HIV-1 life cycle. - Highlights: • MOV10 can function as a co-factor of HIV-1 Rev. • MOV10 facilitates Rev/RRE-dependent transport of viral mRNAs. • MOV10 interacts with Rev in an RNA-independent manner. • The DEAG-box of MOV10 is required for the enhancement of Rev/RRE-dependent export.
Cancer risk estimation for mixtures of coal tars and benzo(a)pyrene

International Nuclear Information System (INIS)

Gaylor, D.W.; Culp, S.J.; Goldstein, L.S.; Beland, F.A.

2000-01-01

Two-year chronic bioassays were conducted by using B6C3F1 female mice fed several concentrations of two different mixtures of coal tars from manufactured gas waste sites or benzo(a)pyrene (BaP). The purpose of the study was to obtain estimates of cancer potency of coal tar mixtures, by using conventional regulatory methods, for use in manufactured gas waste site remediation. A secondary purpose was to investigate the validity of using the concentration of a single potent carcinogen, in this case benzo(a)pyrene, to estimate the relative risk for a coal tar mixture. The study has shown that BaP dominates the cancer risk when its concentration is greater than 6,300 ppm in the coal tar mixture. In this case the most sensitive tissue site is the forestomach. Using low-dose linear extrapolation, the lifetime cancer risk for humans is estimated to be: Risk -4 (ppm coal tar in total diet) + 240 x 10 -4 (ppm BaP in total diet), based on forestomach tumors. If the BaP concentration in the coal tar mixture is less than 6,300 ppm, the more likely case, then lung tumors provide the largest estimated upper limit of risk, Risk -4 (ppm coal tar in total diet), with no contribution of BaP to lung tumors. The upper limit of the cancer potency (slope factor) for lifetime oral exposure to benzo(a)pyrene is 1.2 x 10 -3 per microg per kg body weight per day from this Good Laboratory Practice (GLP) study compared with the current value of 7.3 x 10 -3 per microg per kg body weight per day listed in the US EPA Integrated Risk Information System
Hepatitis B and C Co-Infection in HIV Patients from the TREAT Asia HIV Observational Database: Analysis of Risk Factors and Survival

Science.gov (United States)

Chen, Marcelo; Wong, Wing-Wai; Law, Matthew G.; Kiertiburanakul, Sasisopin; Yunihastuti, Evy; Merati, Tuti Parwati; Lim, Poh Lian; Chaiwarith, Romanee; Phanuphak, Praphan; Lee, Man Po; Kumarasamy, Nagalingeswaran; Saphonn, Vonthanak; Ditangco, Rossana; Sim, Benedict L. H.; Nguyen, Kinh Van; Pujari, Sanjay; Kamarulzaman, Adeeba; Zhang, Fujie; Pham, Thuy Thanh; Choi, Jun Yong; Oka, Shinichi; Kantipong, Pacharee; Mustafa, Mahiran; Ratanasuwan, Winai; Durier, Nicolas; Chen, Yi-Ming Arthur

2016-01-01

Background We assessed the effects of hepatitis B (HBV) or hepatitis C (HCV) co-infection on outcomes of antiretroviral therapy (ART) in HIV-infected patients enrolled in the TREAT Asia HIV Observational Database (TAHOD), a multi-center cohort of HIV-infected patients in the Asia-Pacific region. Methods Patients testing HBs antigen (Ag) or HCV antibody (Ab) positive within enrollment into TAHOD were considered HBV or HCV co-infected. Factors associated with HBV and/or HCV co-infection were assessed by logistic regression models. Factors associated with post-ART HIV immunological response (CD4 change after six months) and virological response (HIV RNA <400 copies/ml after 12 months) were also determined. Survival was assessed by the Kaplan-Meier method and log rank test. Results A total of 7,455 subjects were recruited by December 2012. Of patients tested, 591/5656 (10.4%) were HBsAg positive, 794/5215 (15.2%) were HCVAb positive, and 88/4966 (1.8%) were positive for both markers. In multivariate analysis, HCV co-infection, age, route of HIV infection, baseline CD4 count, baseline HIV RNA, and HIV-1 subtype were associated with immunological recovery. Age, route of HIV infection, baseline CD4 count, baseline HIV RNA, ART regimen, prior ART and HIV-1 subtype, but not HBV or HCV co-infection, affected HIV RNA suppression. Risk factors affecting mortality included HCV co-infection, age, CDC stage, baseline CD4 count, baseline HIV RNA and prior mono/dual ART. Shortest survival was seen in subjects who were both HBV- and HCV-positive. Conclusion In this Asian cohort of HIV-infected patients, HCV co-infection, but not HBV co-infection, was associated with lower CD4 cell recovery after ART and increased mortality. PMID:26933963
Experimental and theoretical evaluation of the performance of a tar solar water heater

International Nuclear Information System (INIS)

Ammari, H.D.; Nimir, Y.L.

2003-01-01

The paper presents an experimental and theoretical evaluation of the performance of a tar solar water heater and comparison with that of a conventional type collector. The performance of both collectors is assessed under the same conditions. Both of the collectors have the same surface area and are glazed. The conventional type has the water tubes welded to the absorber plate, whereas in the tar type, the tar acts as an absorber plate that covers the water tubes. The theoretical model for each collector type, with the transient effects taken into account, is based on a control volume and a time base in the related energy equations. By considering a small element of the collector in each case, three partial differential equations were developed for each collector and were solved numerically by the Runge-Kutta method of the fifth order. A good agreement was achieved between the numerical and experimental results for both the conventional and tar collectors, indicating the feasibility of employing the theoretical model in the design of flat plate solar collectors. The results also showed that the conventional collector is more efficient than the tar type during most of the daylight, but the tar collector had the added advantage of better conservation of energy in late afternoon and evening
Estimating release of polycyclic aromatic hydrocarbons from coal tar at manufactured-gas plant sites

International Nuclear Information System (INIS)

Loehr, R.C.; Rao, P.S.C.; Lee, L.S.; Okuda, I.

1992-08-01

One component of the EPRI's research on Envirorunental Behavior of Organic Substances (EBOS) consists of developing information and models to predict releases of monocyclic and polycyclic aromatic hydrocarbons (MAHs and PAHs) to groundwater from coal tars and contaminated soils at MGP sites. The results of this report focus primarily on release of PAHs from coal tars. There are at least two approaches to predicting the release of organic chemicals from coal tar to water. The simplest method to estimate aqueous concentrations is to assume that water solubility of a PAH compound released from the tar can be defined by equilibrium precipitation-dissolution reactions. Application of Raoult's law is another method to predict aqueous concentrations, which requires the assumption of ''ideal'' behavior for partitioning of PAHs between the tar and water phases. To evaluate the applicability of these two methods for predicting PAH releases, laboratory experiments were conducted with eight coal tar samples from former MGP sites across the country. Migration of chemicals in the environment and resulting contaminant plumes in groundwater are determined by leachate concentrations of the chemicals. The use of equilibrium precipitation-dissolution reactions will usually result in an overestimation of PAH concentrations in the leachate from a coal tar source, and thus the resulting PAH concentrations in groundwater. Raoult's law appears to be a more accurate approach to predicting the release of several PAHs from coal tars. Furthermore, if nonequilibrium conditions prevail, aqueous-phase PAH concentrations will be even lower than those predicted using Raoult's law
Release of polyaromatic hydrocarbons from coal tar contaminated soils

International Nuclear Information System (INIS)

Priddy, N.D.; Lee, L.S.

1996-01-01

A variety of process wastes generated from manufactured gas production (MGP) have contaminated soils and groundwater at production and disposal sites. Coal tar, consisting of a complex mixture of hydrocarbons present as a nonaqueous phase liquid, makes up a large portion of MGP wastes. Of the compounds in coal tar, polyaromatic hydrocarbons (PAHs) are the major constituents of environmental concern due to their potential mutagenic and carcinogenic hazards. Characterization of the release of PAHs from the waste-soil matrix is essential to quantifying long-term environmental impacts in soils and groundwater. Currently, conservative estimates for the release of PAHs to the groundwater are made assuming equilibrium conditions and using relationships derived from artificially contaminated soils. Preliminary work suggests that aged coal tar contaminated soils have much lower rates of desorption and a greater affinity for retaining organic contaminants. To obtain better estimates of desorption rates, the release of PAHs from a coal tar soil was investigated using a flow-interruption, miscible displacement technique. Methanol/water solutions were employed to enhance PAH concentrations above limits of detection. For each methanol/water solution employed, a series of flow interrupts of varying times was invoked. Release rates from each methanol/water solution were estimated from the increase in concentration with duration of flow interruption. Aqueous-phase release rates were then estimated by extrapolation using a log-linear cosolvency model
Extraction of tar acids with methanol from low-temperature tar

Energy Technology Data Exchange (ETDEWEB)

Funasaka, W; Yokogawa, C; Suga, S

1948-01-01

From 20 grams crude middle oil, boiling at 200/sup 0/ to 250/sup 0/, acid content 40%, tar acids were extracted at 20/sup 0/ to 30/sup 0/ with MeOH for comparison with EtOH, NMe/sub 3/, and ethylene glycol. When 80% MeOH is used, the oil extracted amounts to 61%, including 9% acids, if the ratio of crude oil and solvent is kept at 1:2. EtOH is inferior to MeOH. The properties of the crude oil and the purified oil extracted with 80% MeOH are described.

Markovian negentropies in bioinformatics. 1. A picture of footprints after the interaction of the HIV-1 Psi-RNA packaging region with drugs.

Science.gov (United States)

Díaz, Humberto González; de Armas, Ronal Ramos; Molina, Reinaldo

2003-11-01

Many experts worldwide have highlighted the potential of RNA molecules as drug targets for the chemotherapeutic treatment of a range of diseases. In particular, the molecular pockets of RNA in the HIV-1 packaging region have been postulated as promising sites for antiviral action. The discovery of simpler methods to accurately represent drug-RNA interactions could therefore become an interesting and rapid way to generate models that are complementary to docking-based systems. The entropies of a vibrational Markov chain have been introduced here as physically meaningful descriptors for the local drug-nucleic acid complexes. A study of the interaction of the antibiotic Paromomycin with the packaging region of the RNA present in type-1 HIV has been carried out as an illustrative example of this approach. A linear discriminant function gave rise to excellent discrimination among 80.13% of interacting/non-interacting sites. More specifically, the model classified 36/45 nucleotides (80.0%) that interacted with paromomycin and, in addition, 85/106 (80.2%) footprinted (non-interacting) sites from the RNA viral sequence were recognized. The model showed a high Matthews' regression coefficient (C = 0.64). The Jackknife method was also used to assess the stability and predictability of the model by leaving out adenines, C, G, or U. Matthews' coefficients and overall accuracies for these approaches were between 0.55 and 0.68 and 75.8 and 82.7, respectively. On the other hand, a linear regression model predicted the local binding affinity constants between a specific nucleotide and the aforementioned antibiotic (R2 = 0.83,Q2 = 0.825). These kinds of models may play an important role either in the discovery of new anti-HIV compounds or in the elucidation of their mode of action. On request from the corresponding author (humbertogd@cbq.uclv.edu.cu or humbertogd@navegalia.com).
Tar Removal from Biomass Producer Gas by Using Biochar

DEFF Research Database (Denmark)

Ravenni, Giulia; Henriksen, Ulrik Birk; Ahrenfeldt, Jesper

2017-01-01

The biomass-derived char (biochar) produced in the gasifier as a residue, is a potential solution for removing tars from producer gas. This work investigates the interaction between tar compounds and biochar. Residual biochar from a TwoStage gasifier was tested as bed material in a laboratory setup....... Phenol and naphthalene were chosen as model tars, and entrained in a nitrogen flow. The gaseous stream was sampled before and after the biochar bed to evaluate the extent of conversion. The biochar bed (30g) was tested at 250°C, 500°C and 600°C, with for 3 consecutive hours. The compounds concentration...... in the gas phase was quantified by stable isotope dilution analysis, using Gas Chromatography-Mass Spectrometry (GC-MS). Results showed a significant effect of biochar on the removal of phenol, at all temperatures. Naphthalene was removed less efficiently at higher temperature, and this trend was even more...
Solvent refining of low-temperature tar with liquid ammonia

Energy Technology Data Exchange (ETDEWEB)

Ishida, K

1953-01-01

The middle fractions of low-temperature tar were treated with mixed solutions of H/sub 2/O and liquid NH/sub 3/ at 0/sup 0/ and 20/sup 0/, and with liquid NH/sub 3/ at -10, 0, + 10, and 20/sup 0/, and phase equilibrium between tar acids, neutral oil, and solvents were studied. The distribution ratio ranged from less than 1 to greater than 1 when the solvent contained about 20 percent (by weight) H/sub 2/O. When the solvent contained less than 85 percent (by weight) NH/sub 3/, the yield of extract was small but the purity of phenols in the extracted oil was above 90 percent. Solvent containing about 85 percent NH/sub 3/ (by weight) is considered optimum for separating tar acids from oils. A novel definition is proposed for solvent selectivity as the difference between the concentration of the solute in the extract layer, on a solvent-free basis, and the concentration in the raffinate layer.
Syphilis and HIV-1 co-infection: influence on CD4 T cell count, HIV-1 viral load and treatment response

DEFF Research Database (Denmark)

Kofoed, Kristian; Gerstoft, Jan; Mathiesen, Lars Reinhardt

2006-01-01

OBJECTIVES: To assess the effect of human immunodeficiency virus (HIV)-1 and syphilis coinfection on HIV-ribonucleic acid (RNA) viral load, CD4 cell count, and the response in rapid plasmin reagin (RPR) to treatment of the syphilis infection. STUDY DESIGN: Cases of syphilis diagnosed during 1 year...... in HIV-infected patients in Copenhagen were included. HIV-RNA, CD4 cell counts, and RPR-serology were measured before, during, and after syphilis. RESULTS: Forty-one patients were included. CD4 cell count decreased significantly during infection in patients with primary and secondary stages of syphilis...... (mean 106 cells/mm, P = 0.03). Treatment of syphilis was associated with an increase in the CD4 cell count and a decrease in HIV-RNA in the overall group (mean 66 cells/mm and -0.261 RNA log10 copies/ml, P = 0.02 and 0.04). The serological response rates for 15 patients treated with penicillin and 25...
Influenza vaccination of HIV-1-positive and HIV-1-negative former intravenous drug users.

Science.gov (United States)

Amendola, A; Boschini, A; Colzani, D; Anselmi, G; Oltolina, A; Zucconi, R; Begnini, M; Besana, S; Tanzi, E; Zanetti, A R

2001-12-01

The immunogenicity of an anti-influenza vaccine was assessed in 409 former intravenous drug user volunteers and its effect on the levels of HIV-1 RNA, proviral DNA and on CD4+ lymphocyte counts in a subset HIV-1-positive subjects was measured. HIV-1-positive individuals (n = 72) were divided into three groups on the basis of their CD4+ lymphocyte counts, while the 337 HIV-1-negative participants were allocated into group four. Haemagglutination inhibiting (HI) responses varied from 45.8 to 70% in the HIV-1-positive subjects and were significantly higher in group four (80.7% responses to the H1N1 strain, 81.6% to the H3N2 strain, and 83% to the B strain). The percentage of subjects with HI protective antibody titres (> or = 1:40) increased significantly after vaccination, especially in HIV-1 uninfected subjects. Immunization caused no significant changes in CD4+ counts and in neither plasma HIV-1 RNA nor proviral DNA levels. Therefore, vaccination against influenza may benefit persons infected by HIV-1. Copyright 2001 Wiley-Liss, Inc.
Ukrainian brown-coal tars recovered at low-temperature carbonization with solid heating medium

Energy Technology Data Exchange (ETDEWEB)

Kuznetsov, V I; Govorova, R P; Fadeicheva, A G; Kigel, T B; Chernykh, M K

1955-01-01

Three samples of tar were recovered in the laboratory from brown coals carbonized at 375/sup 0/ to 456/sup 0/ +- 25/sup 0/ in a retort with inner heating by solid circulating medium, namely, semicoke (ratio: 4 or 3:1) first heated to 700/sup 0/. One comparative (parallel) experiment was carried out in a retort with inner heating by inert gases entering the retort at 580/sup 0/ to 600/sup 0/ and leaving it at 115/sup 0/ to 120/sup 0/. The tars that were recovered from the retort with the solid heating medium contained a high percentage of coal dust and moisture, which were separated from the tars in supercentrifuges (15,000 rpm). Four samples of cleaned tars were fractionated in a Cu flask with a 2-ball fractional column. The tars from the retort with the solid-heating medium are characterized by increased yield of the petroleum-ether fraction (16.3 or 19.3%) and decreased yield of the paraffin fraction (15.1 to 21.2%) in comparison with those of tar from the retort with gas heating (5.9% of the petroleum ether fraction and 36.5% of paraffin fraction). The yield of paraffin from the paraffin fraction also decreased from 90.6% to 62.6-74.3%. This result shows that in the first case the carbonized products were cracked to a higher degree than those from the retort with gas heating. In raw phenols recovered from fractions of investigated tars, the yield of the phenol-cresol fraction (182/sup 0/ to 204/sup 0/) decreased from 25.9% to 13.0-18.9%.
Analysis of the environmental control technology for tar sand development

Energy Technology Data Exchange (ETDEWEB)

de Nevers, N.; Glenne, B.; Bryner, C.

1979-06-01

The environmental technology for control of air pollution, water pollution, and for the disposal, stabilization, and vegetation of the waste tar sand were thoroughly investigated. Although some difficulties may be encountered in any of these undertakings, it seems clear that the air and water pollution problems can be solved to meet any applicable standard. Currently there are two large-scale plants producing liquid fuels from tar sands in Alberta, Canada which use similar technology involving surface mining, hot water extraction, and surface disposal of waste sand. These projects all meet the Canadian environmental control regulations in force at the time they began. The largest US deposits of tar sands are much smaller than the Canadian; 95 percent are located in the state of Utah. Their economics do not appear as attractive as the Canadian deposits. The environmental control costs are not large enough to make an otherwise economic project uneconomic. The most serious environmental conflict likely to occur over the recovery of liquid fuels from the US deposits of tar sands is that caused by the proximity of the deposits to national parks, national monuments, and a national recreation area in Utah. These areas have very stringent air pollution requirements; and even if the air pollution control requirements can be met, there may still be adequate opposition to large-scale mining ventures in these areas to prevent their commercial exploitation. Another environmental constraint may be water rights availability.Essentially all of the water running in the Colorado river basin is now legally allocated. Barring new interpretations of the legality of water rights purchase, Utah tar sands developments should be able to obtain water by purchasing existing irrigation water rights.
Catalytic decomposition of tar derived from wood waste pyrolysis using Indonesian low grade iron ore as catalyst

Energy Technology Data Exchange (ETDEWEB)

Wicakso, Doni Rahmat [Chemical Engineering Department, Faculty of Engineering, Lambung Mangkurat University, Jalan A. Yani KM. 36 Banjarbaru, 70714, South Kalimantan (Indonesia); Chemical Engineering Department, Faculty of Engineering, Gadjah Mada University, Jalan Grafika No. 2 Bulaksumur, Yogyakarta, 55281 (Indonesia); Sutijan; Rochmadi [Chemical Engineering Department, Faculty of Engineering, Gadjah Mada University, Jalan Grafika No. 2 Bulaksumur, Yogyakarta, 55281 (Indonesia); Budiman, Arief, E-mail: abudiman@ugm.ac.id [Chemical Engineering Department, Faculty of Engineering, Gadjah Mada University, Jalan Grafika No. 2 Bulaksumur, Yogyakarta, 55281 (Indonesia); Center for Energy Studies, Gadjah Mada University, Sekip K1A, Yogyakarta, 55281 (Indonesia)

2016-06-03

Low grade iron ore can be used as an alternative catalyst for bio-tar decomposition. Compared to other catalysts, such as Ni, Rd, Ru, Pd and Pt, iron ore is cheaper. The objective of this research was to investigate the effect of using low grade iron ore as catalyst for tar catalytic decomposition in fixed bed reactor. Tar used in this experiment was pyrolysis product of wood waste while the catalyst was Indonesian low grade iron ore. The variables studied were temperatures between 500 – 600 °C and catalyst weight between 0 – 40 gram. The first step, tar was evaporated at 450 °C to produce tar vapor. Then, tar vapor was flowed to fixed bed reactor filled low grade iron ore. Gas and tar vapor from reactor was cooled, then the liquid and uncondensable gas were analyzed by GC/MS. The catalyst, after experiment, was weighed to calculate total carbon deposited into catalyst pores. The results showed that the tar components that were heavy and light hydrocarbon were decomposed and cracked within the iron ore pores to from gases, light hydrocarbon (bio-oil) and carbon, thus decreasing content tar in bio-oil and increasing the total gas product. In conclusion, the more low grade iron ore used as catalyst, the tar content in the liquid decrease, the H{sup 2} productivity increased and calorimetric value of bio-oil increased.
Clinical value of determination HIV viral load in the cerebrospinal fluid of HIV-infected patients

Directory of Open Access Journals (Sweden)

V. B. Musatov

2015-01-01

Full Text Available Aim. To analyze the concentration of HIV RNA in the cerebrospinal fluid and to evaluate its significance in the pathology of the central nervous system among HIV infected persons.Materials: We examined 36 patients with HIV infection with signs of pathology of the central nervous system. All patients was done completed a standard investigation of cerebrospinal fluid, cytological examination and detection viral load of HIV in the cerebrospinal fluid and serum.Results. A different of opportunistic and HIV-related disease was diagnosed in 29 patients. The most frequent pathology of the nervous system (12 cases is a diffuse HIV-associated brain damage occurring in 7 patients in the form of aseptic non purulent meningitis and in 5 patients in the form of encephalitis. The average value of the absolute and relative count of CD4-lymphocytes in patients amounted 147,0 cells/μl (40,0; 408,75 and 10.0% (4,00; 18,50. Pathological changes in cellular composition and protein concentration of cerebrospinal fluid detected in 19 cases. Replication of HIV in the cerebrospinal fluid are detected in 31 of 32 patients not receiving antiretroviral therapy, including 17 patients with normal values of cerebrospinal fluid. The average HIV viral load in the cerebrospinal fluid was 15 133,0 copies/ml (2501,0; 30624,0 or 4,18 (3,35; 4,48 lg HIV RNA, average HIV viral load in serum – 62 784,0 copies/ml (6027,5; 173869,0 or 4,80 4,80 (3,7; 5,2 lg HIV RNA. The concentration of HIV in the cerebrospinal fluid was significantly lower than in serum (4,18 and 4,80 lg HIV RNA, p=0.027. 4 patients with severe, multietiology damage of the central nervous system viral, microbial and fungal etiology, there was an inverse relationship between the concentration of HIV in the cerebrospinal fluid and in serum, the concentrations of HIV was higher in the cerebrospinal fluid.Conclusion: Among the majority of HIV-infected patients with signs of the central
Phytotoxicity and Plant Productivity Analysis of Tar-Enriched Biochars

Science.gov (United States)

Keller, M. L.; Masiello, C. A.; Dugan, B.; Rudgers, J. A.; Capareda, S. C.

2008-12-01

Biochar is one of the three by-products obtained by the pyrolysis of organic material, the other two being syngas and bio-oil. The pyrolysis of biomass has generated a great amount of interest in recent years as all three by-products can be put toward beneficial uses. As part of a larger project designed to evaluate the hydrologic impact of biochar soil amendment, we generated a biochar through fast pyrolysis (less than 2 minutes) of sorghum stock at 600°C. In the initial biochar production run, the char bin was not purged with nitrogen. This inadvertent change in pyrolysis conditions produced a fast-pyrolysis biochar enriched with tars. We chose not to discard this batch, however, and instead used it to test the impact of tar-enriched biochars on plants. A suite of phytotoxicity tests were run to assess the effects of tar-rich biochar on plant germination and plant productivity. We designed the experiment to test for negative effects, using an organic carbon and nutrient-rich, greenhouse- optimized potting medium instead of soil. We used Black Seeded Simpson lettuce (Lactuca sativa) as the test organism. We found that even when tars are present within biochar, biochar amendment up to 10% by weight caused increased lettuce germination rates and increased biomass productivity. In this presentation, we will report the statistical significance of our germination and biomass data, as well as present preliminary data on how biochar amendment affects soil hydrologic properties.
Carbon materials for syngas conditioning and tar removal

International Nuclear Information System (INIS)

Romero Millán, Lina María; Sierra Vargas, Fabio Emiro

2017-01-01

Within the framework of worldwide energy context, the development of technologies and processes for energy production form renewable and non-conventional sources is a priority. According to this, gasification is an interesting process that converts different kinds of organic materials in fuel gases. The main issue related with this process is the fact that the producer gas contains also contaminants and tars that are undesirable for the gas usage in internal combustion motors or turbines. The present work aims to analyze the actual state of the existing methods to remove tars form gasification fuel gases, emphasizing the use of different kinds of carbon materials. (author)
Process from removing benzine, toluene, etc. , from petroleum residues, coal tar, and shale tar, etc

Energy Technology Data Exchange (ETDEWEB)

Hlawaty, F

1888-08-11

A process is described for the preparation of ligroin and its homologs as well as naphthalene and anthracene consisting in leading superheated water vapor into a mixture of petroleum residues (or mineral coal tar, etc.) heated to about 400/sup 0/C with cellulosic substances as sage shreds, sea grass, or straw, with addition of caustic alkali.
Bacterial vaginosis, alterations in vaginal flora and HIV genital shedding among HIV-1-infected women in Mozambique

Directory of Open Access Journals (Sweden)

Robert D Kirkcaldy

2011-05-01

Full Text Available Objectives. We investigated whether abnormal vaginal flora, including bacterial vaginosis (BV, are associated with detection of cervical HIV-1 RNA among HIV-infected women in Mozambique. Methods. We obtained clinical data and vaginal specimens from HIV-infected women registering for their first visit at one of two HIV care clinics in Mozambique. We compared women with detectable cervical HIV viral load (≥40 copies/ml with women with undetectable cervical HIV. Results. We enrolled 106 women. Women with abnormal vaginal flora (intermediate Nugent scores, 4 - 6 were more likely to have detectable cervical HIV RNA then women with normal vaginal flora (adjusted odds ratio 7.2 (95% confidence interval 1.8 - 29.1, adjusted for CD4 count. Women with BV had a non-significantly higher likelihood of detectable cervical HIV than women with normal flora. Conclusions. Abnormal vaginal flora were significantly associated with cervical HIV expression. Further research is needed to confirm this relationship.
Trans-activation of the 5' to 3' viral DNA strand transfer by nucleocapsid protein during reverse transcription of HIV1 RNA.

Science.gov (United States)

Darlix, J L; Vincent, A; Gabus, C; de Rocquigny, H; Roques, B

1993-08-01

Two DNA strand transfer reactions take place during reverse transcription of the retroviral genome. The first transfer, that of the minus-strand strong stop DNA from the 5' end of the viral RNA to the 3' end, has been studied in vitro with two RNAs mimicking the 5' and 3' regions of the HIV1 genome and with nucleocapsid protein, NCp7, and reverse transcriptase. The results show that NCp7 strongly activates the 5' to 3' DNA strand transfer during reverse transcription while a basic peptide resembling NCp7 is inactive. Activation of the first transfer by several NCp7 derived peptides and the influence of the terminal redundancies (R) present at the 5' and 3' ends of HIV1 RNA were also examined. The first transfer is optimal in the presence of intact NCp7 and necessitates R on both the 5' and 3' RNAs. Sequencing of full length viral DNA products reveals approximately 40% misincorporations at the first nucleotide beyond the transfer point. If such base misincorporations occur during proviral DNA synthesis with possible homologous recombinations it may well contribute to the high level of genetic variability of HIV.
Carbazole is a naturally occurring inhibitor of angiogenesis and inflammation isolated from antipsoriatic coal tar

Energy Technology Data Exchange (ETDEWEB)

Jack L. Arbiser; Baskaran Govindarajan; Traci E. Battle; Rebecca Lynch; David A. Frank; Masuko Ushio-Fukai; Betsy N. Perry; David F. Stern; G. Tim Bowden; Anquan Liu; Eva Klein; Pawel J. Kolodziejski; N. Tony Eissa; Chowdhury F. Hossain; Dale G. Nagle [Emory University School of Medicine, Atlanta, GA (United States). Department of Dermatology

2006-06-15

Coal tar is one of the oldest and an effective treatment for psoriasis. Coal tar has been directly applied to the skin, or used in combination with UV light as part of the Goeckerman treatment. The use of coal tar has caused long-term remissions in psoriasis, but has fallen out of favor because the treatment requires hospitalization and coal tar is poorly acceptable aesthetically to patients. Thus, determining the active antipsoriatic component of coal tar is of considerable therapeutic interest. We fractionated coal tar into its components, and tested them using the SVR angiogenesis inhibitor assay. Treatment of SVR endothelial cells with coal tar fractions resulted in the isolation of a single fraction with antiangiogenic activity. The active antiangiogenic compound in coal tar is carbazole. In addition to antiangiogenic activity, carbazole inhibited the production of inflammatory IL-15 by human mononuclear cells. IL-15 is elevated in psoriasis and is thought to contribute to psoriatic inflammation. Carbazole treatment also reduced activity of inducible nitric oxide synthase (iNOS), which is proinflammatory and elevated in psoriasis. The effect of carbazole on upstream pathways in human psoriasis was determined, and carbazole was shown to inhibit signal transducer and activator of transcription (stat)3-mediated transcription, which has been shown to be relevant in human psoriasis. IL-15, iNOS, and stat3 activation require the activation of the small GTPase rac for optimal activity. Carbazole was found to inhibit rac activation as a mechanism for its inhibition of downstream inflammatory and angiogenic pathways. Given its antiangiogenic and anti-inflammatory activities, carbazole is likely a major component of the antipsoriatic activity of coal tar. Carbazole and derivatives may be useful in the therapy of human psoriasis.
Comprehensive database of Manufactured Gas Plant tars. Part C. Heterocyclic and hydroxylated polycyclic aromatic hydrocarbons.

Science.gov (United States)

Gallacher, Christopher; Thomas, Russell; Lord, Richard; Kalin, Robert M; Taylor, Chris

2017-08-15

Coal tars are a mixture of organic and inorganic compounds that were by-products from the manufactured gas and coke making industries. The tar compositions varied depending on many factors such as the temperature of production and the type of retort used. For this reason a comprehensive database of the compounds found in different tar types is of value to understand both how their compositions differ and what potential chemical hazards are present. This study focuses on the heterocyclic and hydroxylated compounds present in a database produced from 16 different tars from five different production processes. Samples of coal tar were extracted using accelerated solvent extraction (ASE) and derivatized post-extraction using N,O-bis(trimethylsilyl)trifluoroacetamide (BSTFA) with 1% trimethylchlorosilane (TMCS). The derivatized samples were analysed using two-dimensional gas chromatography combined with time-of-flight mass spectrometry (GCxGC/TOFMS). A total of 865 heterocyclic compounds and 359 hydroxylated polycyclic aromatic hydrocarbons (PAHs) were detected in 16 tar samples produced by five different processes. The contents of both heterocyclic and hydroxylated PAHs varied greatly with the production process used, with the heterocyclic compounds giving information about the feedstock used. Of the 359 hydroxylated PAHs detected the majority would not have been be detected without the use of derivatization. Coal tars produced using different production processes and feedstocks yielded tars with significantly different heterocyclic and hydroxylated contents. The concentrations of the individual heterocyclic compounds varied greatly even within the different production processes and provided information about the feedstock used to produce the tars. The hydroxylated PAH content of the samples provided important analytical information that would otherwise not have been obtained without the use of derivatization and GCxGC/TOFMS. Copyright © 2017 John Wiley & Sons, Ltd.
Elucidating the Burden of HIV in Tissues Using Multiplexed Immunofluorescence and In Situ Hybridization: Methods for the Single-Cell Phenotypic Characterization of Cells Harboring HIV In Situ.

Science.gov (United States)

Vasquez, Joshua J; Hussien, Rajaa; Aguilar-Rodriguez, Brandon; Junger, Henrik; Dobi, Dejan; Henrich, Timothy J; Thanh, Cassandra; Gibson, Erica; Hogan, Louise E; McCune, Joseph; Hunt, Peter W; Stoddart, Cheryl A; Laszik, Zoltan G

2018-02-01

Persistent tissue reservoirs of HIV present a major barrier to cure. Defining subsets of infected cells in tissues is a major focus of HIV cure research. Herein, we describe a novel multiplexed in situ hybridization (ISH) (RNAscope) protocol to detect HIV-DNA (vDNA) and HIV-RNA (vRNA) in formalin-fixed paraffin-embedded (FFPE) human tissues in combination with immunofluorescence (IF) phenotyping of the infected cells. We show that multiplexed IF and ISH (mIFISH) is suitable for quantitative assessment of HIV vRNA and vDNA and that multiparameter IF phenotyping allows precise identification of the cellular source of the ISH signal. We also provide semi-quantitative data on the impact of various tissue fixatives on the detectability of vDNA and vRNA with RNAscope technology. Finally, we describe methods to quantitate the ISH signal on whole-slide digital images and validation of the quantitative ISH data with quantitative real-time PCR for vRNA. It is our hope that this approach will provide insight into the biology of HIV tissue reservoirs and to inform strategies aimed at curing HIV.
Tar removal from biosyngas in the biomass gasification process. (Liquid + liquid) equilibrium {water + solvent (paraxylene and methyl hexadecanoate) + model molecules of tar (benzene, toluene, phenol)}

International Nuclear Information System (INIS)

Bassil, Georgio; Mokbel, Ilham; Abou Naccoul, Ramy; Stephan, Juliette; Jose, Jacques; Goutaudier, Christelle

2012-01-01

Highlights: ► (Liquid + liquid) equilibria at atmospheric pressure. ► Solubility of benzene (or toluene or phenol) in paraxylene at (303 to 343) K. ► Solubility of benzene (or toluene or phenol) in methyl palmitate or methyl hexadecanoate at (303 to 343) K. ► Correlation of LLE using NRTL model. - Abstract: Tar is generated in the process by the condensation of the gas resulting from biomass gasification. The objective of this work is a contribution to the database on thermodynamic quantity which will be useful at the operation of tar removal from aqueous medium. With this aim, (liquid + liquid) equilibrium of {water + solvent (paraxylene and methyl hexadecanoate) + model molecules of tar (benzene, toluene, phenol)} was studied at temperatures (303.2, 323.2, and 343.2) K. The data obtained were correlated with the non-random two-liquid (NRTL) model.
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.
Influence of cigarette filter ventilation on smokers' mouth level exposure to tar and nicotine.

Science.gov (United States)

Caraway, John W; Ashley, Madeleine; Bowman, Sheri A; Chen, Peter; Errington, Graham; Prasad, Krishna; Nelson, Paul R; Shepperd, Christopher J; Fearon, Ian M

2017-12-01

Cigarette filter ventilation allows air to be drawn into the filter, diluting the cigarette smoke. Although machine smoking reveals that toxicant yields are reduced, it does not predict human yields. The objective of this study was to investigate the relationship between cigarette filter ventilation and mouth level exposure (MLE) to tar and nicotine in cigarette smokers. We collated and reviewed data from 11 studies across 9 countries, in studies performed between 2005 and 2013 which contained data on MLE from 156 products with filter ventilation between 0% and 87%. MLE among 7534 participants to tar and nicotine was estimated using the part-filter analysis method from spent filter tips. For each of the countries, MLE to tar and nicotine tended to decrease as filter ventilation increased. Across countries, per-cigarette MLE to tar and nicotine decreased as filter ventilation increased from 0% to 87%. Daily MLE to tar and nicotine also decreased across the range of increasing filter ventilation. These data suggest that on average smokers of highly ventilated cigarettes are exposed to lower amounts of nicotine and tar per cigarette and per day than smokers of cigarettes with lower levels of ventilation. Copyright © 2017 British American Tobacco. Published by Elsevier Inc. All rights reserved.

Creating and maintaining a gas cap in tar sands formations

Science.gov (United States)

Vinegar, Harold J.; Karanikas, John Michael; Dinkoruk, Deniz Sumnu; Wellington, Scott Lee

2010-03-16

Methods for treating a tar sands formation are disclosed herein. Methods for treating a tar sands formation may include providing heat to at least part of a hydrocarbon layer in the formation from one or more heaters located in the formation. Pressure may be allowed to increase in an upper portion of the formation to provide a gas cap in the upper portion. At least some hydrocarbons are produced from a lower portion of the formation.
The documentation of tar balls on oiled shorelines : lessons from the New Carissa, Oregon

International Nuclear Information System (INIS)

Owens, E.H.; Zimlicki-Owens, L.M.; Lamarche, A.; Reimer, P.D.; Martin, C.A.

2000-01-01

The New Carissa, carrying approximately 400,000 gallons of fuel oils ran aground on the outer shore of North Spit, in the vicinity of Coos Bay, Oregon, on February 4, 1999. The oil was released directly into the nearshore surf zone. Following the spill, a stretch of approximately 300 km of the coast of Oregon was surveyed and monitored. The need for the documentation of stranded tar balls in the neighbourhood of the spill site prompted the implementation of a long-term observation program. Initially, Shoreline Clean-up and Assessment Technique (SCAT) reporting procedures were required. Heavy oiling was followed by stranded oil taking the form of tar balls. The amount of oil on the shoreline decreased and the SCAT procedures alone were no longer adequate. They provided estimations of oil quantities that were too high and failed to provide any discrimination between amounts of oil observed on the beaches. A new reporting technique called Beach Assessment Reporting was designed to overcome the difficulties and record adequately the character and frequency of stranded tar balls. Maps, tables and histograms of stranded tar ball volumes and concentrations were discussed. Since the data spanned nine orders of magnitude at times, the semi-logarithmic scale time series plots of the concentration of the tar balls was used in order to identify trends. Conventional histograms only identified large values and camouflaged smaller trends in the time series. A direct method for describing tar ball concentrations geographically proved to be the use of weekly maximum tar ball concentration maps by segment. 10 refs., 2 tabs., 9 figs
Comparative assessment of coal tars obtained from 10 former manufactured gas plant sites in the eastern United States

Energy Technology Data Exchange (ETDEWEB)

Brown, D.G.; Gupta, L.; Kim, T.H.; Moo-Young, H.K.; Coleman, A.J. [Lehigh University, Bethlehem, PA (United States). Dept. of Civil & Environmental Engineering

2006-11-15

A comparative analysis was performed on eleven coal tars obtained from former manufactured gas plant sites in the eastern United States. Bulk properties analyzed included percent ash, Karl Fisher water content, viscosity and average molecular weight. Chemical properties included monocyclic- and polycyclic-aromatic hydrocarbon (PAH) concentrations, alkylated aromatic concentrations, and concentrations of aliphatic and aromatic fractions. It was found that there was at least an order-of-magnitude variation in all properties measured between the eleven coal tars. Additionally, two coal tars obtained from the same manufactured gas plant site had very different properties, highlighting that there can be wide variations in coal tar properties from different samples obtained from the same site. Similarities were also observed between the coal tars. The relative chemical distributions were similar for all coal tars, and the coal tars predominantly consisted of PAHs, with naphthalene being the single-most prevalent compound. The C{sub 9-22} aromatic fraction, an indicator of all PAHs up to a molecular weight of approximately 276 g mole{sup -1}, showed a strong power-law relationship with the coal tar average molecular weight (MWct). And the concentrations of individual PAHs decreased linearly as MWct increased up to ca. 1000 g mole{sup -1}, above which they remained low and variable. Implications of these properties and their variation with MWct on groundwater quality are discussed. Ultimately, while these similarities do allow generalities to be made about coal tars, the wide range of coal tar bulk and chemical properties reported here highlights the complex nature of coal tars.
Intragenic HIV-1 env sequences that enhance gag expression

International Nuclear Information System (INIS)

Suptawiwat, Ornpreya; Sutthent, Ruengpung; Lee, T.-H.; Auewarakul, Prasert

2003-01-01

Expression of HIV-1 genes is regulated at multiple levels including the complex RNA splicing and transport mechanisms. Multiple cis-acting elements involved in these regulations have been previously identified in various regions of HIV-1 genome. Here we show that another cis-acting element was present in HIV-1 env region. This element enhanced the expression of Gag when inserted together with Rev response element (RRE) into a truncated HIV-1 genome in the presence of Rev. The enhancing activity was mapped to a 263-bp fragment in the gp41 region downstream to RRE. RNA analysis showed that it might function by promoting RNA stability and Rev-dependent RNA export. The enhancement was specific to Rev-dependent expression, since it did not enhance Gag expression driven by Sam68, a cellular protein that has been shown to be able to substitute for Rev in RNA export function
Physicochemical Approaches for the Remediation of Former Manufactured Gas Plant Tars

Science.gov (United States)

Hauswirth, S.; Miller, C. T.

2014-12-01

Former manufactured gas plant (FMGP) tars are one of the most challenging non-aqueous phase liquid (NAPL) contaminants to remediate due to their complex chemical composition, high viscosities, and ability to alter wettability. In this work, we investigate several in situ remediation techniques for the removal of tar from porous media. Batch and column experiments were conducted to test the effectiveness of mobilization, solubilization, and chemical oxidation remediation approaches. Alkaline (NaOH), surfactant (Triton X-100), and polymer (xanthan gum) agents were used in various combinations to reduce tar-water interfacial tension, increase flushing solution viscosity, and increase the solubilities of tar components. Base-activated sodium persulfate was used alone and in combination with surfactant to chemically oxidized tar components. The effectiveness of each method was assessed in terms of both removal of PAHs from the system and reduction of dissolved-phase effluent polycyclic aromatic hydrocarbon (PAH) concentrations. In column studies, alkaline-polymer (AP) and alkaline-surfactant-polymer (ASP) solutions efficiently mobilized 81-93% and 95-96% of residual PAHs, respectively, within two pore volumes. The impact of AP flushing on dissolved-phase PAH concentrations was relatively low; however, the concentrations of several low molar mass PAHs were significantly reduced after ASP flushing. Surfactant-polymer (SP) solutions removed over 99% of residual PAHs through a combination of mobilization and solubilization, and reduced the post-remediation, dissolved-phase total PAH concentration by 98.4-99.1%. Degradation of residual PAHs by base-activated sodium persulfate was relatively low (30-50%), and had little impact on dissolved-phase PAH concentrations.
Nevirapine, sodium concentration and HIV-1 RNA in breast milk and plasma among HIV-infected women receiving short-course antiretroviral prophylaxis

DEFF Research Database (Denmark)

Salado-Rasmussen, Kirsten; Theilgaard, Zahra Persson; Chiduo, Mercy G.

2015-01-01

and breast milk after intrapartum single-dose nevirapine combined with either 1-week tail of Combivir (zidovudine/lamivudine) or single-dose Truvada (tenofovir/emtricitabine). Methods Maternal plasma and bilateral breast milk samples were collected between April 2008 and April 2011 at 1, 4 and 6 weeks...... postpartum from HIV-infected Tanzanian women. Moreover, plasma samples were collected at delivery from mother and infant. Results HIV-1 RNA was quantified in 1,212 breast milk samples from 273 women. At delivery, 96% of the women and 99% of the infants had detectable nevirapine in plasma with a median...... (interquartile range, IQR) of 1.5 μg/mL (0.75–2.20 μg/mL) and 1.04 μg/mL (0.39–1.71 μg/mL), respectively (P women had detectable nevirapine in plasma and breast milk, with a median (IQR) of 0.13 μg/mL (0.13–0.39 μg/mL) and 0.22 μg/mL (0.13–0.34 μg...
Acute HIV Infection in Pregnancy: The Case for Third Trimester Rescreening

Directory of Open Access Journals (Sweden)

Jocelyn Wertz

2011-01-01

Full Text Available Combination testing with anti-HIV Elisa and Western blot is both sensitive and specific for diagnosis of established HIV-1 infection but could not detect acute HIV infection (AHI. AHI is a time of extremely high viral load, which may correlate to increased risk of horizontal or vertical transmission. Thus, early identification of AHI could allow for interventions to decrease transmission. However, recognition of AHI can be challenging as symptoms could be absent or nonspecific, therefore, AHI is often not detected, particularly in pregnancy. We present a case report of AHI in a pregnant woman who presented with headache and fever. She tested negative for HIV in the first trimester and at time of AHI at 26 3/7 weeks by anti-HIV Elisa, but was diagnosed with AHI based on an HIV RNA viral load of 434,000 copies/mL. This report presents a case for improved awareness of AHI in pregnancy, and the need for repeat HIV testing in late pregnancy, and highlighted that early detection of AHI might be possible with adding HIV RNA testing at time of standard anti-HIV Elisa screening test in pregnancy. Novel laboratory approaches including pooling of sera for HIV RNA could reduce the cost of HIV RNA testing.
The purification of coal tar by the addition of quinoline and Zn(oh)/sub 2/

International Nuclear Information System (INIS)

Zhou, P.; Chen, Q.L.; Ao, X.Q.; Kang, C

2017-01-01

The coal tar was purified by the addition of quinoline and Zn(OH)2, in order to decrease the content of carbon and inorganic oxide particles. The effect on the viscosity and ash content of the coal tar were investigated by altering temperature, time, and the amount of quinolone and Zn(OH)2 . When the volume ratio between quinolone and coal tar was 20:1 and the static time was 24 h. The viscosity of three layers decreased with rising temperature. When the static temperature and time was 45 °C and 24 h, respectively. The viscosity of three layers decreased with the arising amount of quinoline. And when the volume ratio between quinolone and coal tar was 20:1 and the temperature was 45 °C. The viscosity of three layers decreased first and then increased with the prolonging of static time. And when the static time of coal tar was 24 h, the viscosity of coal tar is the lowest. Because of the lower viscosity of coal tar, decreasing the content of carbon and ash particles in upper and middle layer, the ash content decreased from 0.168% to 0.092%. The addition of Zn(OH)2 can lead ash content in middle layer decrease to 0.058%. Zn2SiO4 and ZnAl2O4 may be produced due to the reaction between Zn (OH) 2 and SiO2 or Al2O3, which can settle down easily. The results show that the content of carbon and inorganic oxide particles in upper-middle-class (the middle 4/5 of the whole volume) decreased with the addition of quinolone and Zn(OH)2 . When the volume ratio between quinolone and coal tar was 50:2, quality ratio between coal tar and Zn(OH)2 was 20000:1, the mixture were heated up to 45 °C at atmospheric pressure and keeping this constant temperature for 24 h, the ash content in upper-middle-class can decreased to 0.058%. (author)
Acute HIV Discovered During Routine HIV Screening With HIV Antigen-Antibody Combination Tests in 9 US Emergency Departments.

Science.gov (United States)

White, Douglas A E; Giordano, Thomas P; Pasalar, Siavash; Jacobson, Kathleen R; Glick, Nancy R; Sha, Beverly E; Mammen, Priya E; Hunt, Bijou R; Todorovic, Tamara; Moreno-Walton, Lisa; Adomolga, Vincent; Feaster, Daniel J; Branson, Bernard M

2018-01-05

Newer combination HIV antigen-antibody tests allow detection of HIV sooner after infection than previous antibody-only immunoassays because, in addition to HIV-1 and -2 antibodies, they detect the HIV-1 p24 antigen, which appears before antibodies develop. We determine the yield of screening with HIV antigen-antibody tests and clinical presentations for new diagnoses of acute and established HIV infection across US emergency departments (EDs). This was a retrospective study of 9 EDs in 6 cities with HIV screening programs that integrated laboratory-based antigen-antibody tests between November 1, 2012, and December 31, 2015. Unique patients with newly diagnosed HIV infection were identified and classified as having either acute HIV infection or established HIV infection. Acute HIV infection was defined as a repeatedly reactive antigen-antibody test result, a negative HIV-1/HIV-2 antibody differentiation assay, or Western blot result, but detectable HIV ribonucleic acid (RNA); established HIV infection was defined as a repeatedly reactive antigen-antibody test result and a positive HIV-1/HIV-2 antibody differentiation assay or Western blot result. The primary outcomes were the number of new HIV diagnoses and proportion of patients with laboratory-defined acute HIV infection. Secondary outcomes compared reason for visit and the clinical presentation of acute HIV infection. In total, 214,524 patients were screened for HIV and 839 (0.4%) received a new diagnosis, of which 122 (14.5%) were acute HIV infection and 717 (85.5%) were established HIV infection. Compared with patients with established HIV infection, those with acute HIV infection were younger, had higher RNA and CD4 counts, and were more likely to have viral syndrome (41.8% versus 6.5%) or fever (14.3% versus 3.4%) as their reason for visit. Most patients with acute HIV infection displayed symptoms attributable to acute infection (median symptom count 5 [interquartile range 3 to 6]), with fever often
RT-PCR Detection of HIV in Republic of Macedonia

Directory of Open Access Journals (Sweden)

Golubinka Bosevska

2008-11-01

Full Text Available The aim of the study was to detect HIV RNA in seropositive patients using RT-PCR method and thus, to establish PCR methodology in the routine laboratory works.The total of 33 examined persons were divided in two groups: 1 13 persons seropositive for HIV; and 2 20 healthy persons - randomly selected blood donors that made the case control group. The subjects age was between 25 and 52 years (average 38,5.ELFA test for combined detection of HIV p24 antigen and anti HIV-1 + 2 IgG and ELISA test for detection of antibodies against HIV-1 and HIV-2, were performed for each examined person. RNA from the whole blood was extracted using a commercial kit based on salt precipitation. Detection of HIV RNA was performed using RT-PCR kit. Following nested PCR, the product was separated by electrophoresis in 1,5 % agarose gel. The result was scored positive if the band of 210bp was visible regardless of intensity Measures of precaution were taken during all the steps of the work and HIV infected materials were disposed of accordingly.In the group of blood donors ELFA, ELISA and RT-PCR were negative. Assuming that prevalence of HIV infection is zero, the clinical specificity of RT-PCR is 100 %. The analytical specificity of RT-PCR method was tested against Hepatitis C and B, Human Papiloma Virus, Cytomegalovirus, Herpes Simplex Virus, Rubella Virus, Mycobacterium tuberculosis, Chlamydia trachomatis. None of these templates yielded amplicon. In the group of 13 seropositive persons, 33 samples were analyzed. HIV RNA was detected in 15 samples. ELISA and ELFA test were positive in all samples. Different aliquots of the samples were tested independently and showed the same results. After different periods of storing the RNA samples at -70°C, RT-PCR reaction was identical to the one performed initially. The obtained amplicons were maintained frozen at -20°C for a week and the subsequently performed electrophoresis was identical to the previous one. The reaction is
Material Properties and Characteristics for Development of an Expert System for Coal-Tar Sealers

National Research Council Canada - National Science Library

Shoenberger, James

2001-01-01

.... Several coal-tar mixtures that varied with source of the coal-tar emulsion, amount of aggregate, and amount of polymer used in the mixtures were evaluated for their field performance and material properties...
Paleontological overview of oil shale and tar sands areas in Colorado, Utah, and Wyoming.

Energy Technology Data Exchange (ETDEWEB)

Murphey, P. C.; Daitch, D.; Environmental Science Division

2009-02-11

In August 2005, the U.S. Congress enacted the Energy Policy Act of 2005, Public Law 109-58. In Section 369 of this Act, also known as the ''Oil Shale, Tar Sands, and Other Strategic Unconventional Fuels Act of 2005,'' Congress declared that oil shale and tar sands (and other unconventional fuels) are strategically important domestic energy resources that should be developed to reduce the nation's growing dependence on oil from politically and economically unstable foreign sources. In addition, Congress declared that both research- and commercial-scale development of oil shale and tar sands should (1) be conducted in an environmentally sound manner using management practices that will minimize potential impacts, (2) occur with an emphasis on sustainability, and (3) benefit the United States while taking into account concerns of the affected states and communities. To support this declaration of policy, Congress directed the Secretary of the Interior to undertake a series of steps, several of which are directly related to the development of a commercial leasing program for oil shale and tar sands. One of these steps was the completion of a programmatic environmental impact statement (PEIS) to analyze the impacts of a commercial leasing program for oil shale and tar sands resources on public lands, with an emphasis on the most geologically prospective lands in Colorado, Utah, and Wyoming. For oil shale, the scope of the PEIS analysis includes public lands within the Green River, Washakie, Uinta, and Piceance Creek Basins. For tar sands, the scope includes Special Tar Sand Areas (STSAs) located in Utah. This paleontological resources overview report was prepared in support of the Oil Shale and Tar Sands Resource Management Plan Amendments to Address Land Use Allocations in Colorado, Utah, and Wyoming and PEIS, and it is intended to be used by Bureau of Land Management (BLM) regional paleontologists and field office staff to support future
Biomass Gasifier ''Tars'': Their Nature, Formation, and Conversion

Energy Technology Data Exchange (ETDEWEB)

Milne, T. A.; Evans, R. J. (National Renewable Energy Laboratory); Abatzaglou, N. (Kemestrie, Inc.)

1998-11-01

The main purpose of this review is to update the information on gasification tar, the most cumbersome and problematic parameter in any gasification commercialization effort. The work aims to present to the community the scientific and practical aspects of tar formation and conversion (removal) during gasification as a function of the various technological and technical parameters and variables.
Evolutionary rate variation and RNA secondary structure prediction

DEFF Research Database (Denmark)

Knudsen, B.; Andersen, E.S.; Damgaard, C.

2004-01-01

Predicting RNA secondary structure using evolutionary history can be carried out by using an alignment of related RNA sequences with conserved structure. Accurately determining evolutionary substitution rates for base pairs and single stranded nucleotides is a concern for methods based on this type...... by applying rates derived from tRNA and rRNA to the prediction of the much more rapidly evolving 5'-region of HIV-1. We find that the HIV-1 prediction is in agreement with experimental data, even though the relative evolutionary rate between A and G is significantly increased, both in stem and loop regions...
Dual vapor extraction on acidic sludge tar at a former refinery

International Nuclear Information System (INIS)

Lear, P.R.; Beall, P.; Townsend, S.

1996-01-01

OHM Remediation Services Corp conducted a pilot-scale demonstration for a novel application of dual vapor extraction technology for the pretreatment of the acid tar sludge material. The acid tar sludge comprised of approximately 60% asphaltene hydrocarbon material, 20% clay, and up to 20% sulfuric acid (H 2 SO 4 ). The liquid layer in the bottom of the pits has a low pH ( 2 ) gas which is released with the sludge material is excavated or handled. The objective of the dual vapor extraction was to remove the SO 2 vapors and liquid layer containing sulfuric acid prior to any further treatment. The dual vapor extraction would reduce the amount of alkaline reagent required for neutralization while eliminating the health and safety concerns. Overall, the DVE pilot demonstration successfully showed that both liquids and vapors could be removed from the acid tar sludge material. The liquid present in the lower portions of the pits will have pH values of 1.0 or less and acidities on the order of 5% H 2 SO 4 . The liquid removed from the acid tar sludge material by a DVE system will have slightly higher pH (∼1.5) and lower alkalinities (∼3% H 2 SO 4 ). The SO 2 concentration in the vapors removed by the DVE system will be variable with initial levels approaching 1,200 ppmv SO 2 . The SO 2 concentration in the vapor phase should decrease with time. A caustic scrubber solution will remove any SO 2 from the vapor phase. After DVE treatment, the acid tar sludge material would have a slightly increased pH and a decreased SO 2 concentration
Toxicity of coal-tar and asphalt sealants to eastern newts, Notophthalmus viridescens

Energy Technology Data Exchange (ETDEWEB)

Bommarito, T.; Sparling, D.W.; Halbrook, R.S. [South Illinois University, Carbondale, IL (United States). Cooperative Wildlife Research Laboratory

2010-09-15

Between 1970 and 2000 the concentration of total polycyclic aromatic hydrocarbons (TPAH) in several lakes across the country increased whereas those of other persistent organic pollutants (POPs) tended to remain stable or declined. Urbanized watersheds experienced greater rises in TPAH concentration compared to non-urban lakes. Sources for urban PAHs include industrial wastes, vehicular exhausts and oil leaks and sealants from pavement surfaces. Both coal-tar and asphalt sealants are used to protect surfaces but runoff from surfaces coated with coal-tar can have mean concentrations of 3500 mg TPAHs kg{sup -1}, much higher than runoff from asphalt-sealed or cement surfaces. Unaltered parent compounds of PAHs can have many lethal and sublethal toxic effects, but oxidation and UV radiation can alter the toxicity of these compounds, sometimes creating degradates that are many times more toxic than parent compounds. The purposes of this study were to determine if coal-tar sealants can be toxic to adult eastern newts (Notophthalmus viridescens) and to compare the toxicity of coal-tar sealant to that of asphalt sealant. Newts were exposed to sediments containing dried sealants ranging from 0 mg kg{sup -1} to 1500 mg kg{sup -1} under simultaneous exposure to UV radiation and visible light to determine concentration/response relationships. No significant mortality occurred with any treatment. Significant effects due to sealants included decreased righting ability and diminished liver enzyme activities. Coal-tar sealant was more effective in inducing these changes than was asphalt sealant.
Tar analysis from biomass gasification by means of online fluorescence spectroscopy

Science.gov (United States)

Baumhakl, Christoph; Karellas, Sotirios

2011-07-01

Optical methods in gas analysis are very valuable mainly due to their non-intrusive character. That gives the possibility to use them for in-situ or online measurements with only optical intervention in the measurement volume. In processes like the gasification of biomass, it is of high importance to monitor the gas quality in order to use the product gas in proper machines for energy production following the restrictions in the gas composition but also improving its quality, which leads to high efficient systems. One of the main problems in the biomass gasification process is the formation of tars. These higher hydrocarbons can lead to problems in the operation of the energy system. Up to date, the state of the art method used widely for the determination of tars is a standardized offline measurement system, the so-called "Tar Protocol". The aim of this work is to describe an innovative, online, optical method for determining the tar content of the product gas by means of fluorescence spectroscopy. This method uses optical sources and detectors that can be found in the market at low cost and therefore it is very attractive, especially for industrial applications where cost efficiency followed by medium to high precision are of high importance.
Changes in HIV-1 subtypes B and C genital tract RNA in women and men after initiation of antiretroviral therapy.

Science.gov (United States)

Fiscus, Susan A; Cu-Uvin, Susan; Eshete, Abel Tilahun; Hughes, Michael D; Bao, Yajing; Hosseinipour, Mina; Grinsztejn, Beatriz; Badal-Faesen, Sharlaa; Dragavon, Joan; Coombs, Robert W; Braun, Ken; Moran, Laura; Hakim, James; Flanigan, Timothy; Kumarasamy, N; Campbell, Thomas B

2013-07-01

Combination antiretroviral therapy (cART) reduces genital tract human immunodeficiency virus type 1 (HIV-1) load and reduces the risk of sexual transmission, but little is known about the efficacy of cART for decreasing genital tract viral load (GTVL) and differences in sex or HIV-1 subtype. HIV-1 RNA from blood plasma, seminal plasma, or cervical wicks was quantified at baseline and at weeks 48 and 96 after entry in a randomized clinical trial of 3 cART regimens. One hundred fifty-eight men and 170 women from 7 countries were studied (men: 55% subtype B and 45% subtype C; women: 24% subtype B and 76% subtype C). Despite similar baseline CD4(+) cell counts and blood plasma viral loads, women with subtype C had the highest GTVL (median, 5.1 log10 copies/mL) compared to women with subtype B and men with subtype C or B (4.0, 4.0, and 3.8 log10 copies/mL, respectively; P female genital tract may serve as a reservoir of persistent HIV-1 replication during cART and affect the use of cART to prevent sexual and perinatal transmission of HIV-1.
Tar ball concentrations in the ocean around the Cape of Good Hope before and after a major oil spill

Energy Technology Data Exchange (ETDEWEB)

Eagle, G A; Green, A; Williams, J

1979-11-01

From August 1977 to August 1978, tar ball concentrations around the southwestern coast of South Africa were sampled. Prior to a tanker collision on December 16, 1977, the area was relatively free of floating tar. Following the collision, tar ball concentrations increased; tar was transported by wind and currents, at average speeds of about 1 km/hr. In areas of slack currents, tar was observed for as long as 8 months after the spill. Results provided information about surface current trends.
Skin cancer in patients with psoriasis treated with coal tar. A 25-year follow-up study

International Nuclear Information System (INIS)

Pittelkow, M.R.; Perry, H.O.; Muller, S.A.; Maughan, W.Z.; O'Brien, P.C.

1981-01-01

For many years, crude coal tar has been used for the treatment of psoriasis. The possible carcinogenic effect of crude coal tar and ultraviolet (UV) radiation (Goeckerman regimen), considered individually or in combination, has been of some concern to physicians. A 25-year follow-up study was completed on 280 patients with psoriasis who were hospitalized and treated with crude coal tar and UV radiation at the Mayo Clinic, Rochester, Minn, during the years 1950 through 1954. The results of this study suggest that the incidence of skin cancer is not appreciably increased above the expected incidence for the general population when patients are treated with coal tar ointments. It seems that the Goeckerman regimen (topical crude coal tar combined with UV radiation) can be used with minimal risk for skin cancer in the treatment of psoriasis

Volatilization of polycyclic aromatic hydrocarbons from coal-tar-sealed pavement

Science.gov (United States)

Van Metre, Peter C.; Majewski, Michael S.; Mahler, Barbara J.; Foreman, William T.; Braun, Christopher L.; Wilson, Jennifer T.; Burbank, Teresa L.

2012-01-01

Coal-tar-based pavement sealants, a major source of PAHs to urban water bodies, are a potential source of volatile PAHs to the atmosphere. An initial assessment of volatilization of PAHs from coal-tar-sealed pavement is presented here in which we measured summertime gas-phase PAH concentrations 0.03 m and 1.28 m above the pavement surface of seven sealed (six with coal-tar-based sealant and one with asphalt-based sealant) and three unsealed (two asphalt and one concrete) parking lots in central Texas. PAHs also were measured in parking lot dust. The geometric mean concentration of the sum of eight frequently detected PAHs (ΣPAH8) in the 0.03-m samples above sealed lots (1320 ng m-3) during the hottest part of the day was 20 times greater than that above unsealed lots (66.5 ng m-3). The geometric mean concentration in the 1.28-m samples above sealed lots (138 ng m-3) was five times greater than above unsealed lots (26.0 ng m-3). Estimated PAH flux from the sealed lots was 60 times greater than that from unsealed lots (geometric means of 88 and 1.4 μg m-2 h-1, respectively). Although the data set presented here is small, the much higher estimated fluxes from sealed pavement than from unsealed pavement indicate that coal-tar-based sealants are emitting PAHs to urban air at high rates compared to other paved surfaces.
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.
Detailed grouping and functional composition of neutral substances in low-temperature tar

Energy Technology Data Exchange (ETDEWEB)

Kalechits, I V; Salimgareeva, F G; Popova, N I; Kurbangaleeva, D K; Klykova, G G

1955-01-01

The grouping and the functional composition of the neutral substances in coal tar were characterized by means of adsorption on silica gel with subsequent chemical analysis of each fraction. The neutral materials were obtained by consecutive treatment of a C/sub 6/H/sub 6/ solution of coal tar with 10 percent alkali and 5 percent H/sub 2/SO/sub 4/ to remove the phenols and the bases. The data show that of the neutral substances (only 75% were identified) 40.5% were aromatic hydrocarbons. Based on a study of all of the data, it was proposed that 90% of the composition of coal tars is aromatic. The physical constants of the separated fractions were determined and are presented in tabular form.
Research and information needs for management of tar sands development. Interim report Apr-May 83

Energy Technology Data Exchange (ETDEWEB)

1983-05-01

The report discusses important research and information needs for federal lease management of lands with tar sands resources. Short-term needs include more complete definition and characterization of deposits, hydrology, and regions downwind from tar sands areas. Longer-term needs include demonstration-scale operations to resolve production, waste management, and reclamation problems and to provide opportunities for measurement, analysis, and assessment of mining and processing wastes and emissions. Most of the known federal tar sands resource is in eastern Utah and contains about 25 billion barrels of bitumen. Recent legislation provides that existing mining claims and oil and gas leases may be converted to combined hydrocarbon leases including tar sands. Federal approval, which must be applied for by November 1983, is a condition for conversion.
Investigation of sulfur-polycyclic aromatic hydrocarbon in coal derived tars of pyrolysis and hydropyrolysis

Energy Technology Data Exchange (ETDEWEB)

Chen, H.; Li, B.; Zhang, B. [Chinese Academy of Sciences, Taiyuan (China). State Key Laboratory of Coal Conversion

1999-07-01

A study was undertaken to characterize sulphur forms in coal derived tars from pyrolysis and hydropyrolysis of bituminous coal and lignite. The pyrolysis tars were analyzed for content of polycyclic aromatic sulfur hydrocarbons (PASH). 5 refs., 3 figs., 3 tabs.
Crystallization and preliminary X-ray diffraction analysis of the periplasmic domain of the Escherichia coli aspartate receptor Tar and its complex with aspartate

Energy Technology Data Exchange (ETDEWEB)

Mise, Takeshi; Matsunami, Hideyuki; Samatey, Fadel A.; Maruyama, Ichiro N., E-mail: ichi@oist.jp [Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami, Okinawa 904-0495 (Japan)

2014-08-27

The periplasmic domain of the E. coli aspartate receptor Tar was cloned, expressed, purified and crystallized with and without bound ligand. The crystals obtained diffracted to resolutions of 1.58 and 1.95 Å, respectively. The cell-surface receptor Tar mediates bacterial chemotaxis toward an attractant, aspartate (Asp), and away from a repellent, Ni{sup 2+}. To understand the molecular mechanisms underlying the induction of Tar activity by its ligands, the Escherichia coli Tar periplasmic domain with and without bound aspartate (Asp-Tar and apo-Tar, respectively) were each crystallized in two different forms. Using ammonium sulfate as a precipitant, crystals of apo-Tar1 and Asp-Tar1 were grown and diffracted to resolutions of 2.10 and 2.40 Å, respectively. Alternatively, using sodium chloride as a precipitant, crystals of apo-Tar2 and Asp-Tar2 were grown and diffracted to resolutions of 1.95 and 1.58 Å, respectively. Crystals of apo-Tar1 and Asp-Tar1 adopted space group P4{sub 1}2{sub 1}2, while those of apo-Tar2 and Asp-Tar2 adopted space groups P2{sub 1}2{sub 1}2{sub 1} and C2, respectively.
Performance of the BioPlex 2200 HIV Ag-Ab assay for identifying acute HIV infection.

Science.gov (United States)

Eshleman, Susan H; Piwowar-Manning, Estelle; Sivay, Mariya V; Debevec, Barbara; Veater, Stephanie; McKinstry, Laura; Bekker, Linda-Gail; Mannheimer, Sharon; Grant, Robert M; Chesney, Margaret A; Coates, Thomas J; Koblin, Beryl A; Fogel, Jessica M

Assays that detect HIV antigen (Ag) and antibody (Ab) can be used to screen for HIV infection. To compare the performance of the BioPlex 2200 HIV Ag-Ab assay and two other Ag/Ab combination assays for detection of acute HIV infection. Samples were obtained from 24 individuals (18 from the US, 6 from South Africa); these individuals were classified as having acute infection based on the following criteria: positive qualitative RNA assay; two negative rapid tests; negative discriminatory test. The samples were tested with the BioPlex assay, the ARCHITECT HIV Ag/Ab Combo test, the Bio-Rad GS HIV Combo Ag-Ab EIA test, and a viral load assay. Twelve (50.0%) of 24 samples had RNA detected only ( > 40 to 13,476 copies/mL). Ten (43.5%) samples had reactive results with all three Ag/Ab assays, one sample was reactive with the ARCHITECT and Bio-Rad assays, and one sample was reactive with the Bio-Rad and BioPlex assays. The 11 samples that were reactive with the BioPlex assay had viral loads from 83,010 to >750,000 copies/mL; 9/11 samples were classified as Ag positive/Ab negative by the BioPlex assay. Detection of acute HIV infection was similar for the BioPlex assay and two other Ag/Ab assays. All three tests were less sensitive than a qualitative RNA assay and only detected HIV Ag when the viral load was high. The BioPlex assay detected acute infection in about half of the cases, and identified most of those infections as Ag positive/Ab negative. Copyright © 2018 Elsevier B.V. All rights reserved.
The role of char and tar in determining the gas-phase partitioning of nitrogen during biomass gasification

International Nuclear Information System (INIS)

Broer, Karl M.; Brown, Robert C.

2015-01-01

Highlights: • Switchgrass was gasified at an equivalence ratio of zero and 650–850 °C. • Short residence times were employed to minimize secondary reactions. • Char- and tar-bound nitrogen, NH_3, HCN, and N_2 were all significant products. • Increasing temperature leads to increased release of gaseous nitrogen compounds. • Kinetic models of gasification should include nitrogen release from char and tar. - Abstract: Gasification is an attractive option for converting biomass into fuels and chemicals. Most biomass contains significant amounts of fuel-bound nitrogen (FBN), which partially converts into ammonia (NH_3) and hydrogen cyanide (HCN) during gasification. These nitrogen compounds are problematic as they can lead to NO_X emissions or catalyst poisoning in downstream applications of syngas. FBN can convert to other products as well, including diatomic nitrogen (N_2), char-bound nitrogen (char-N), and tar-bound nitrogen (tar-N). Efforts to predict concentrations of NH_3 and HCN have been hindered by a lack of accurate, comprehensive measurements of nitrogen partitioning among gasification products. The present study gasified switchgrass under allothermal, short residence time conditions and measured NH_3, HCN, char-N, and tar-N as a function of temperature in the range of 650–850 °C with diatomic nitrogen determined by difference. It was found that a major portion of FBN was retained in the char and tar products. As temperature was increased, char and tar were consumed, releasing nitrogen as gaseous NH_3 and HCN. This increase in undesirable nitrogen compounds is contrary to the predictions of most gasification models, which overlook the presence of significant nitrogen in char and tar even if they include tar cracking and char gasification reactions. The results of this study demonstrate that gas-phase reactions alone are not sufficient to predict the fate of nitrogen during gasification. In order for modeling efforts to obtain more accurate
Systemic Immune Activation and HIV Shedding in the Female Genital Tract.

Science.gov (United States)

Spencer, LaShonda Y; Christiansen, Shawna; Wang, Chia-Hao H; Mack, Wendy J; Young, Mary; Strickler, Howard D; Anastos, Kathryn; Minkoff, Howard; Cohen, Mardge; Geenblatt, Ruth M; Karim, Roksana; Operskalski, Eva; Frederick, Toni; Homans, James D; Landay, Alan; Kovacs, Andrea

2016-02-01

Plasma HIV RNA is the most significant determinant of cervical HIV shedding. However, shedding is also associated with sexually transmitted infections (STIs) and cervical inflammation. The mechanism by which this occurs is poorly understood. There is evidence that systemic immune activation promotes viral entry, replication, and HIV disease progression. We hypothesized that systemic immune activation would be associated with an increase in HIV genital shedding. Clinical assessments, HIV RNA in plasma and genital secretions, and markers of immune activation (CD38(+)DR(+) and CD38(-)DR(-)) on CD4(+) and CD8(+) T cells in blood were evaluated in 226 HIV+ women enrolled in the Women's Interagency HIV Study. There were 569 genital evaluations of which 159 (28%) exhibited HIV RNA shedding, defined as HIV viral load >80 copies per milliliter. We tested associations between immune activation and shedding using generalized estimating equations with logit link function. In the univariate model, higher levels of CD4(+) and CD8(+) T-cell activation in blood were significantly associated with genital tract shedding. However, in the multivariate model adjusting for plasma HIV RNA, STIs, and genital tract infections, only higher levels of resting CD8(+) T cells (CD38(-)DR(-)) were significantly inversely associated with HIV shedding in the genital tract (odds ratios = 0.44, 95% confidence interval: 0.21 to 0.9, P = 0.02). The association of systemic immune activation with genital HIV shedding is multifactorial. Systemic T-cell activation is associated with genital tract shedding in univariate analysis but not when adjusting for plasma HIV RNA, STIs, and genital tract infections. In addition, women with high percentage of resting T cells are less likely to have HIV shedding compared with those with lower percentages. These findings suggest that a higher percentage of resting cells, as a result of maximal viral suppression with treatment, may decrease local genital activation, HIV
CCR5 Gene Disruption via Lentiviral Vectors Expressing Cas9 and Single Guided RNA Renders Cells Resistant to HIV-1 Infection

Science.gov (United States)

Liu, Jingjing; Zhang, Di; Kimata, Jason T.; Zhou, Paul

2014-01-01

CCR5, a coreceptor for HIV-1 entry, is a major target for drug and genetic intervention against HIV-1. Genetic intervention strategies have knocked down CCR5 expression levels by shRNA or disrupted the CCR5 gene using zinc finger nucleases (ZFN) or Transcription activator-like effector nuclease (TALEN). In the present study, we silenced CCR5 via CRISPR associated protein 9 (Cas9) and single guided RNAs (sgRNAs). We constructed lentiviral vectors expressing Cas9 and CCR5 sgRNAs. We show that a single round transduction of lentiviral vectors expressing Cas9 and CCR5 sgRNAs into HIV-1 susceptible human CD4+ cells yields high frequencies of CCR5 gene disruption. CCR5 gene-disrupted cells are not only resistant to R5-tropic HIV-1, including transmitted/founder (T/F) HIV-1 isolates, but also have selective advantage over CCR5 gene-undisrupted cells during R5-tropic HIV-1 infection. Importantly, using T7 endonuclease I assay we did not detect genome mutations at potential off-target sites that are highly homologous to these CCR5 sgRNAs in stably transduced cells even at 84 days post transduction. Thus we conclude that silencing of CCR5 via Cas9 and CCR5-specific sgRNAs could be a viable alternative strategy for engineering resistance against HIV-1. PMID:25541967
Potential contributions of asphalt and coal tar to black carbon quantification in urban dust, soils, and sediments

Energy Technology Data Exchange (ETDEWEB)

Yang, Y.; Mahler, B.J.; Van Metre, P.C.; Ligouis, B.; Werth, C.J. [University of Illinois Urbana Champaign, Urbana, IL (USA). Dept. of Civil & Environmental Engineering

2010-12-01

Measurements of black carbon (BC) using either chemical or thermal oxidation methods are generally thought to indicate the amount of char and/or soot present in a sample. In urban environments, however, asphalt and coal-tar particles worn from pavement are ubiquitous and, because of their pyrogenic origin, could contribute to measurements of BC. Here we explored the effect of the presence of asphalt and coal-tar particles on the quantification of BC in a range of urban environmental sample types, and evaluated biases in the different methods used for quantifying BC. Samples evaluated were pavement dust, residential and commercial area soils, lake sediments from a small urban watershed, and reference materials of asphalt and coal tar. Total BC was quantified using chemical treatment through acid dichromate (Cr{sub 2}O{sub 7}) oxidation and chemo-thermal oxidation at 375{sup o}C (CTO-375). BC species, including soot and char/charcoal, asphalt, and coal tar, were quantified with organic petrographic analysis. Comparison of results by the two oxidation methods and organic petrography indicates that both coal tar and asphalt contribute to BC quantified by Cr{sub 2}O{sub 7} oxidation, and that coal tar contributes to BC quantified by CTO-375. These results are supported by treatment of asphalt and coal-tar reference samples with Cr2O7 oxidation and CTO-375. The reference asphalt is resistant to Cr{sub 2}O{sub 7} oxidation but not to CTO-375, and the reference coal tar is resistant to both Cr2O7 oxidation and CTO-375. These results indicate that coal tar and/or asphalt can contribute to BC measurements in samples from urban areas using Cr{sub 2}O{sub 7} oxidation or CTO-375, and caution is advised when interpreting BC measurements made with these methods.
A prospective study of vaginal trichomoniasis and HIV-1 shedding in women on antiretroviral therapy

Directory of Open Access Journals (Sweden)

Masese Linnet N

2011-11-01

Full Text Available Abstract Background Trichomonas vaginalis has been associated with increased vaginal HIV-1 RNA shedding in antiretroviral therapy (ART-naïve women. The effect of trichomoniasis on vaginal HIV-1 shedding in ART-treated women has not been characterized. We tested the hypothesis that T. vaginalis infection would increase vaginal HIV-1 RNA shedding in women on ART, and that successful treatment would reduce vaginal HIV-1 RNA levels. Methods We conducted a prospective cohort study including monthly follow-up of 147 women receiving ART in Mombasa, Kenya. Those with T. vaginalis infection, defined by the presence of motile trichomonads on vaginal saline wet mount, received treatment with single dose metronidazole (2 g. Test of cure was performed at the next monthly visit. Using the pre-infection visit as the reference category, we compared detection of vaginal HIV-1 RNA before versus during and after infection using generalized estimating equations. A cut-off of 100 HIV-1 RNA copies/swab was used as the lower limit for linear quantitation. Results Among 31 women treated for trichomoniasis, the concentration of vaginal HIV-1 RNA was above the limit for quantitation before, during, and after T. vaginalis infection in 4 (13% [95% CI 4% - 30%], 4 (13% [95% CI 4% - 30%], and 5 (16% [95% confidence interval {CI} 5% - 34%] women respectively. After adjusting for potential confounding factors, we could detect no difference in the likelihood of detecting vaginal HIV-1 RNA before versus during infection (odds ratio [OR] 1.41, 95% CI 0.23 - 8.79, p = 0.7. In addition, detection of HIV-1 RNA was similar before infection versus after successful treatment (OR 0.68, 95% CI (0.13 - 3.45, p = 0.6. Conclusion Detection of vaginal HIV-1 RNA during ART was uncommon at visits before, during and after T. vaginalis infection.
Different patterns of HIV-1 DNA after therapy discontinuation

Directory of Open Access Journals (Sweden)

Ghinelli Florio

2005-09-01

Full Text Available Abstract Background By persisting in infected cells for a long period of time, proviral HIV-1 DNA can represent an alternative viral marker to RNA viral load during the follow-up of HIV-1 infected individuals. In the present study sequential blood samples of 10 patients under antiretroviral treatment from 1997 with two NRTIs, who refused to continue any antiviral regimen, were analyzed for 16 – 24 weeks to study the possible relationship between DNA and RNA viral load. Methods The amount of proviral DNA was quantified by SYBR green real-time PCR in peripheral blood mononuclear cells from a selected group of ten patients with different levels of plasmatic viremia (RNA viral load. Results Variable levels of proviral DNA were found without any significant correlation between proviral load and plasma HIV-1 RNA levels. Results obtained showed an increase or a rebound in viral DNA in most patients, suggesting that the absence of therapy reflects an increase and/or a persistence of cells containing viral DNA. Conclusion Even though plasma HIV RNA levels remain the basic parameter to monitor the intensity of viral replication, the results obtained seem to indicate that DNA levels could represent an adjunct prognostic marker in monitoring HIV-1 infected subjects.
Volatilization of polycyclic aromatic hydrocarbons from coal-tar-sealed pavement.

Science.gov (United States)

Van Metre, Peter C; Majewski, Michael S; Mahler, Barbara J; Foreman, William T; Braun, Christopher L; Wilson, Jennifer T; Burbank, Teresa L

2012-06-01

Coal-tar-based pavement sealants, a major source of PAHs to urban water bodies, are a potential source of volatile PAHs to the atmosphere. An initial assessment of volatilization of PAHs from coal-tar-sealed pavement is presented here in which we measured summertime gas-phase PAH concentrations 0.03 m and 1.28 m above the pavement surface of seven sealed (six with coal-tar-based sealant and one with asphalt-based sealant) and three unsealed (two asphalt and one concrete) parking lots in central Texas. PAHs also were measured in parking lot dust. The geometric mean concentration of the sum of eight frequently detected PAHs (ΣPAH(8)) in the 0.03-m samples above sealed lots (1320 ng m(-3)) during the hottest part of the day was 20 times greater than that above unsealed lots (66.5 ng m(-3)). The geometric mean concentration in the 1.28-m samples above sealed lots (138 ng m(-3)) was five times greater than above unsealed lots (26.0 ng m(-3)). Estimated PAH flux from the sealed lots was 60 times greater than that from unsealed lots (geometric means of 88 and 1.4 μg m(-2) h(-1), respectively). Although the data set presented here is small, the much higher estimated fluxes from sealed pavement than from unsealed pavement indicate that coal-tar-based sealants are emitting PAHs to urban air at high rates compared to other paved surfaces. Published by Elsevier Ltd.
UTILIZATION OF ACTIVATED ZEOLITE AS MOLECULAR SIEVE IN CHROMATOGRAPHIC COLUMN FOR SEPARATION OF COAL TAR COMPOUNDS

Directory of Open Access Journals (Sweden)

Dwi Retno Nurotul Wahidiyah

2010-06-01

Full Text Available Application of activated zeolite (ZAA as molecular sieve to separate compounds of coal tar from vaccum fractional distillation, have been done. The size of zeolite was 10-20 mesh and used as solid phase in column chromatography with length of 30 cm. The first step of the research was coal pyrolisis and the product (tar was distillated by fractional column and vaccum system at reduced pressure 44 cmHg and maximum temperature at 200 oC. The distillate from this procedure was flowed to the column chromatography of zeolite (ZAA. The compound absorbed by zeolite was eluted with varying solvents, i.e: CCl4, acetone and ethanol. Each fraction was then analyzed by gas chromatography. The results showed, zeolite have a capability to separate the compounds of tar and it tends to absorb medium hydrocarbon. The nonpolar eluent [CCl4] gives the better result in eluting tar compound than polar (ethanol or medium polar eluents (acetone. Keywords: zeolite, coal tar, column chromatography
Development of secondary chamber for tar cracking-improvement of wood pyrolysis performance in pre-vacuum chamber

Science.gov (United States)

Siahaan, S.; Homma, H.; Homma, H.

2018-02-01

Energy crisis and global warming, in other words, climate change are critical topics discussed in various parts of the world. Global warming primarily result from too much emission of carbon dioxide (CO2) in the atmosphere. To mitigate global warming, or climate change and improve electrification in rural areas, wood pyrolysis technology is developed in a laboratory scale, of which gases are directly applicable to the gas engine generator. Our laboratory has developed a prototype of wood pyrolysis plant with a pre-vacuum chamber. However, tar yield was around 40 wt% of feedstock. This research aims to reduce tar yield by secondary tar cracking. For the secondary tar cracking, a secondary pre-vacuum chamber is installed after primary pre-vacuum chamber. Gases generated in the primary pre-vacuum chamber are lead into the secondary chamber that is heated up to 1000 K. This paper reports performance of the secondary chamber for secondary tar cracking in homogeneous mode and heterogeneous mode with char.
IDENTIFICATION OF SOME CARCINOGENIC POLYCYCLIC AROMATIC HYDROCARBONS IN BANGLADESHI VEHICLES EXHAUST TAR BY GAS CHROMATOGRAPHY-MASS SPECTROPHOTOMETER

Directory of Open Access Journals (Sweden)

M. Amzad Hossain

2010-06-01

Full Text Available A more sensitive GC-MS method has been established for the determination of some carcinogenic polycyclic aromatic hydrocarbons (PAHs in vehicles exhaust tar samples. The tar samples were extracted using dichloromethane (DMC: n-hexane solvent mixture. A multi-layer clean-up (silica gel/sodium sulphate column was used, followed by glass fiber filter (GFF paper. The method was successfully applied to determine a number of PAHs present in exhaust tar sample of different vehicles of the Atomic Energy Centre, Dhaka, Bangladesh. Keywords: Carcinogenic polycyclic aromatic hydrocarbons, vehicles tar samples, identification, GC-MS/MS
Coal-tar based pavement sealant toxicity to freshwater macroinvertebrates.

Science.gov (United States)

Bryer, Pamela J; Scoggins, Mateo; McClintock, Nancy L

2010-05-01

Non-point-source pollution is a major source of ecological impairment in urban stream systems. Recent work suggests that coal-tar pavement sealants, used extensively to protect parking areas, may be contributing a large portion of the polycyclic aromatic hydrocarbon (PAH) loading seen in urban stream sediments. The hypothesis that dried coal-tar pavement sealant flake could alter the macroinvertebrate communities native to streams in Austin, TX was tested using a controlled outdoor laboratory type approach. The treatment groups were: control, low, medium, and high with total PAH concentrations (TPAH = sum of 16 EPA priority pollutant PAHs) of 0.1, 7.5, 18.4, & 300 mg/kg respectively. The low, medium, and high treatments were created via the addition of dried coal-tar pavement sealant to a sterile soil. At the start of the 24-day exposure, sediment from a minimally impacted local reference site containing a community of live sediment-dwelling benthic macroinvertebrates was added to each replicate. An exposure-dependent response was found for several stream health measures and for several individual taxa. There were community differences in abundance (P = 0.0004) and richness (P pavement sealants contain bioavailable PAHs that may harm aquatic environments. Copyright 2009 Elsevier Ltd. All rights reserved.
Solvent extraction of Southern US tar sands

Energy Technology Data Exchange (ETDEWEB)

Penney, W.R.

1990-01-01

The Department of Chemical Engineering at the University of Arkansas, in association with Diversified Petroleum Recovery, Inc. (DPR) of Little Rock, Arkansas, has been developing a solvent extraction process for the recovery of bitumen from tar sands for the past five years. The unique feature of the process is that the bitumen is recovered from the solvent by contacting with a co-solvent, which causes the bitumen to precipitate. The overall purpose of this project is to study both the technical and economic feasibility of applying this technology for recovery of bitumen from tar sands by (1) investigating the socioeconmic factors which affect (a) plant siting and (b) the market value of recovered bitumen; (2) operating a process demonstration unit at the rate of 1 lb/hr recovered bitumen while producing clean sand and recyclable solvents; and (3) determine the economic conditions which will make a bitumen recovery project economical. DPR has analyzed the historical trends of domestic production, consumption, discoveries and reserves of crude oil. They have started an investigation of the volatility in the price of crude oil and of gasoline prices and of the differential between gasoline and crude oil. DPR continues to analyze the geographical movement and demand for asphalt products. Utah does not appear economically attractive as a site for a bitumen from tar sands asphalt plant. Oklahoma sites are now being studied. This report also contains the quarterly progress report from a University of Nevada study to determine bitumen composition, oxygen uptake rates, and viscosities of Alabama and Utah bitumens. Both reports have been indexed separately for inclusion on the data base.
Pelagic tar, dissolved/dispersed petroleum hydrocarbons and plastic distribution in the Cretan Sea, Greece

Energy Technology Data Exchange (ETDEWEB)

Kornilios, S.; Drakopoulos, P.G.; Dounas, C. [Institute of Marine Biology of Crete, Iraklio (Greece). Environmental Dept.

1998-12-01

During the first cruise of R/V `Philia` in July 1997 within the framework of the TALOS programme supported by the Greek Ministry of Physical Planning and Public Works, the sampling of floating tar, litter and sea water for dissolved/dispersed petroleum hydrocarbons (DDPH) was carried out in the Cretan Sea. Analysis of these data has allowed a first assessment of the status of floating marine pollution in the region. DDPH measurements showed a mean concentration of 0.145 {mu}g/l of chrysene equivalents (n = 24). Tar and plastics concentrations were in the range of 1-4280 and 0-1160 {mu}g/m{sup 2}, respectively. Mean pelagic tar concentration was 318 {mu}g/m{sup 2}, more than two times higher than what was reported for the area in previous studies. Based on in situ hydrographic observations there is strong evidence that most of the floating tar enters the Cretan Sea through the Ionian Sea. (author)

Pelagic tar, dissolved/dispersed petroleum hydrocarbons and plastic distribution in the Cretan Sea, Greece

Energy Technology Data Exchange (ETDEWEB)

Kornilios, S.; Drakopoulos, P.G.; Dounas, C. [Institute of Marine Biology of Crete, Iraklio (Greece). Environmental Dept.

1998-12-01

During the first cruise of R/V 'Philia' in July 1997 within the framework of the TALOS programme supported by the Greek Ministry of Physical Planning and Public Works, the sampling of floating tar, litter and sea water for dissolved/dispersed petroleum hydrocarbons (DDPH) was carried out in the Cretan Sea. Analysis of these data has allowed a first assessment of the status of floating marine pollution in the region. DDPH measurements showed a mean concentration of 0.145 {mu}g/l of chrysene equivalents (n = 24). Tar and plastics concentrations were in the range of 1-4280 and 0-1160 {mu}g/m{sup 2}, respectively. Mean pelagic tar concentration was 318 {mu}g/m{sup 2}, more than two times higher than what was reported for the area in previous studies. Based on in situ hydrographic observations there is strong evidence that most of the floating tar enters the Cretan Sea through the Ionian Sea. (author)
Pelagic tar, dissolved/dispersed petroleum hydrocarbons and plastic distribution in the Cretan Sea, Greece

International Nuclear Information System (INIS)

Kornilios, S.; Drakopoulos, P.G.; Dounas, C.

1998-01-01

During the first cruise of R/V 'Philia' in July 1997 within the framework of the TALOS programme supported by the Greek Ministry of Physical Planning and Public Works, the sampling of floating tar, litter and sea water for dissolved/dispersed petroleum hydrocarbons (DDPH) was carried out in the Cretan Sea. Analysis of these data has allowed a first assessment of the status of floating marine pollution in the region. DDPH measurements showed a mean concentration of 0.145 μg/l of chrysene equivalents (n = 24). Tar and plastics concentrations were in the range of 1-4280 and 0-1160 μg/m 2 , respectively. Mean pelagic tar concentration was 318 μg/m 2 , more than two times higher than what was reported for the area in previous studies. Based on in situ hydrographic observations there is strong evidence that most of the floating tar enters the Cretan Sea through the Ionian Sea. (author)
77 FR 48431 - Safety Zone for Fireworks Display, Pamlico and Tar Rivers; Washington, NC

Science.gov (United States)

2012-08-14

... near the Pamlico and Tar Rivers to commemorate Beaufort County's 300th anniversary. The temporary... 1625-AA00 Safety Zone for Fireworks Display, Pamlico and Tar Rivers; Washington, NC AGENCY: Coast Guard, DHS. ACTION: Temporary final rule. SUMMARY: The Coast Guard is establishing a temporary safety zone on...
Nuclear Export Signal Masking Regulates HIV-1 Rev Trafficking and Viral RNA Nuclear Export.

Science.gov (United States)

Behrens, Ryan T; Aligeti, Mounavya; Pocock, Ginger M; Higgins, Christina A; Sherer, Nathan M

2017-02-01

HIV-1's Rev protein forms a homo-oligomeric adaptor complex linking viral RNAs to the cellular CRM1/Ran-GTP nuclear export machinery through the activity of Rev's prototypical leucine-rich nuclear export signal (NES). In this study, we used a functional fluorescently tagged Rev fusion protein as a platform to study the effects of modulating Rev NES identity, number, position, or strength on Rev subcellular trafficking, viral RNA nuclear export, and infectious virion production. We found that Rev activity was remarkably tolerant of diverse NES sequences, including supraphysiological NES (SNES) peptides that otherwise arrest CRM1 transport complexes at nuclear pores. Rev's ability to tolerate a SNES was both position and multimerization dependent, an observation consistent with a model wherein Rev self-association acts to transiently mask the NES peptide(s), thereby biasing Rev's trafficking into the nucleus. Combined imaging and functional assays also indicated that NES masking underpins Rev's well-known tendency to accumulate at the nucleolus, as well as Rev's capacity to activate optimal levels of late viral gene expression. We propose that Rev multimerization and NES masking regulates Rev's trafficking to and retention within the nucleus even prior to RNA binding. HIV-1 infects more than 34 million people worldwide causing >1 million deaths per year. Infectious virion production is activated by the essential viral Rev protein that mediates nuclear export of intron-bearing late-stage viral mRNAs. Rev's shuttling into and out of the nucleus is regulated by the antagonistic activities of both a peptide-encoded N-terminal nuclear localization signal and C-terminal nuclear export signal (NES). How Rev and related viral proteins balance strong import and export activities in order to achieve optimal levels of viral gene expression is incompletely understood. We provide evidence that multimerization provides a mechanism by which Rev transiently masks its NES peptide
Longer duration of homelessness is associated with a lower likelihood of non-detectable plasma HIV-1 RNA viral load among people who use illicit drugs in a Canadian setting.

Science.gov (United States)

Loh, Jane; Kennedy, Mary Clare; Wood, Evan; Kerr, Thomas; Marshall, Brandon; Parashar, Surita; Montaner, Julio; Milloy, M-J

2016-11-01

Homelessness is common among people who use drugs (PWUD) and, for those living with HIV/AIDS, an important contributor to sub-optimal HIV treatment outcomes. This study aims to investigate the relationship between the duration of homelessness and the likelihood of plasma HIV-1 RNA viral load (VL) non-detectability among a cohort of HIV-positive PWUD. We used data from the ACCESS study, a long-running prospective cohort study of HIV-positive PWUD linked to comprehensive HIV clinical records including systematic plasma HIV-1 RNA VL monitoring. We estimated the longitudinal relationship between the duration of homelessness and the likelihood of exhibiting a non-detectable VL (i.e., effects modelling. Between May 1996 and June 2014, 922 highly active antiretroviral therapy-exposed participants were recruited and contributed 8188 observations. Of these, 4800 (59%) were characterized by non-detectable VL. Participants reported they were homeless in 910 (11%) interviews (median: six months, interquartile range: 6-12 months). A longer duration of homelessness was associated with lower odds of VL non-detectability (adjusted odds ratio = 0.71 per six-month period of homelessness, 95% confidence interval: 0.60-0.83) after adjustment for age, ancestry, drug use patterns, engagement in addiction treatment, and other potential confounders. Longer durations of episodes of homelessness in this cohort of HIV-positive illicit drug users were associated with a lower likelihood of plasma VL non-detectability. Our findings suggest that interventions that seek to promptly house homeless individuals, such as Housing First approaches, might assist in maximizing the clinical and public health benefits of antiretroviral therapy among people living with HIV/AIDS.
The extraction of bitumen from western tar sands. Annual report, July 1990--July 1991

Energy Technology Data Exchange (ETDEWEB)

Oblad, A.G.; Bunger, J.W.; Deo, M.D.; Hanson, F.V.; Miller, J.D.; Seader, J.D.

1992-04-01

Contents of this report include the following: executive summary; characterization of the native bitumen from the Whiterocks oil sand deposit; influence of carboxylic acid content on bitumen viscosity; water based oil sand separation technology; extraction of bitumen from western oil sands by an energy-efficient thermal method; large- diameter fluidized bed reactor studies; rotary kiln pyrolysis of oil sand; catalytic upgrading of bitumen and bitumen derived liquids; ebullieted bed hydrotreating and hydrocracking; super critical fluid extraction; bitumen upgrading; 232 references; Appendix A--Whiterocks tar sand deposit bibliography; Appendix B--Asphalt Ridge tar sand deposit bibliography; and Appendix C--University of Utah tar sands bibliography.
Selected constituents in the smokes of U. S. commercial cigaretts: tar, nicotine, carbon monoxide and carbon dioxide

Energy Technology Data Exchange (ETDEWEB)

Jenkins, R.A.; Quincy, R.B.; Guerin, M.R.

1979-05-01

One hundred twenty-one brands of United States commercial cigarettes were analyzed for their deliveries of tar, nicotine, carbon monoxide, and carbon dioxide under standard analytical smoking conditions. The sample included both filter and nonfilter cigarettes. Comparisons of carbon monoxide deliveries over the range of observed tar deliveries indicated a very high correlation between CO and tar for filter cigarettes, but nonfilter cigarettes tended to produce much less CO than would have been predicted from their tar deliveries. Comparison of ORNL nicotine values for specific brands with those determined by the Federal Trade Commission yield no statistically significant differences between laboratories. 4 figures, 6 tables.
Some studies on tar pillets at Veraval coast (Gujarat)

Digital Repository Service at National Institute of Oceanography (India)

Kadam, A.N.

Infrared spectroscopic (IR) analysis indicated that the tar pillets contain saturated hydrocarbons particularly higher homologues of n-paraffins, unsaturated and carbonyl type of polar compounds. Gas chromatographic (GLC) fingerprint pattern...
Hydrogen production from biomass tar by catalytic steam reforming

International Nuclear Information System (INIS)

Yoon, Sang Jun; Choi, Young-Chan; Lee, Jae-Goo

2010-01-01

The catalytic steam reforming of model biomass tar, toluene being a major component, was performed at various conditions of temperature, steam injection rate, catalyst size, and space time. Two kinds of nickel-based commercial catalyst, the Katalco 46-3Q and the Katalco 46-6Q, were evaluated and compared with dolomite catalyst. Production of hydrogen generally increased with reaction temperature, steam injection rate and space time and decreased with catalyst size. In particular, zirconia-promoted nickel-based catalyst, Katalco 46-6Q, showed a higher tar conversion efficiency and shows 100% conversion even relatively lower temperature conditions of 600 deg. C. Apparent activation energy was estimated to 94 and 57 kJ/mol for dolomite and nickel-based catalyst respectively.
SL1 revisited: functional analysis of the structure and conformation of HIV-1 genome RNA.

Science.gov (United States)

Sakuragi, Sayuri; Yokoyama, Masaru; Shioda, Tatsuo; Sato, Hironori; Sakuragi, Jun-Ichi

2016-11-11

The dimer initiation site/dimer linkage sequence (DIS/DLS) region of HIV is located on the 5' end of the viral genome and suggested to form complex secondary/tertiary structures. Within this structure, stem-loop 1 (SL1) is believed to be most important and an essential key to dimerization, since the sequence and predicted secondary structure of SL1 are highly stable and conserved among various virus subtypes. In particular, a six-base palindromic sequence is always present at the hairpin loop of SL1 and the formation of kissing-loop structure at this position between the two strands of genomic RNA is suggested to trigger dimerization. Although the higher-order structure model of SL1 is well accepted and perhaps even undoubted lately, there could be stillroom for consideration to depict the functional SL1 structure while in vivo (in virion or cell). In this study, we performed several analyses to identify the nucleotides and/or basepairing within SL1 which are necessary for HIV-1 genome dimerization, encapsidation, recombination and infectivity. We unexpectedly found that some nucleotides that are believed to contribute the formation of the stem do not impact dimerization or infectivity. On the other hand, we found that one G-C basepair involved in stem formation may serve as an alternative dimer interactive site. We also report on our further investigation of the roles of the palindromic sequences on viral replication. Collectively, we aim to assemble a more-comprehensive functional map of SL1 on the HIV-1 viral life cycle. We discovered several possibilities for a novel structure of SL1 in HIV-1 DLS. The newly proposed structure model suggested that the hairpin loop of SL1 appeared larger, and genome dimerization process might consist of more complicated mechanism than previously understood. Further investigations would be still required to fully understand the genome packaging and dimerization of HIV.
Any impact of blips and low-level viraemia episodes among HIV-infected patients with sustained virological suppression on ART?

Science.gov (United States)

Pernas, Berta; Grandal, Marta; Pertega, Sonia; Cañizares, Angelina; Castro-Iglesias, Ángeles; Mena, Álvaro; Rodriguez-Osorio, Iria; Tabernilla, Andrés; Pedreira, José D; Poveda, Eva

2016-04-01

The objective of this study was to evaluate the prevalence of blips and risk of virological failure (VF) among HIV-infected patients with sustained virological suppression (HIV-RNA ART. Newly diagnosed (2004-13) HIV-infected patients with sustained virological suppression on ART (minimum follow-up of 3 months) were identified. Risk of VF was evaluated according to different plasma HIV-RNA quantification values based on the limits of quantification/detection of current commercial assays (20 copies/mL). Kaplan-Meier and Cox proportional hazards models were used to compare the cumulative incidence of VF. A total of 565 newly diagnosed HIV-infected patients were identified: 453 started ART and 354 achieved virological suppression. Prevalence of blips (isolated HIV-RNA ranging from 50 to 200 copies/mL) and VF (HIV-RNA ≥50 copies/mL) was 22.7% and 8.8%, respectively (mean follow-up of 42 months). Multivariate analysis identified differences between HIV-RNA values as an independent predictor of VF (P = 0.008); risk of VF was higher for patients with blips [HR 2.500 (95% CI 0.524-11.926)] and for those with at least three consecutive detected, but not quantified, HIV-RNA determinations (HIV-RNA 200 copies/mL [33.7% at 24 and 60 months versus ART. HIV patients with blips and at least three consecutive detected, but not quantified, HIV-RNA determinations (<20 copies/mL) had a higher risk of VF. These findings highlight the relevance of maintaining HIV-RNA levels below the limits of quantification of current assays (<20 copies/mL). © The Author 2015. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
Methamphetamine inhibits HIV-1 replication in CD4+ T cells by modulating anti-HIV-1 miRNA expression.

Science.gov (United States)

Mantri, Chinmay K; Mantri, Jyoti V; Pandhare, Jui; Dash, Chandravanu

2014-01-01

Methamphetamine is the second most frequently used illicit drug in the United States. Methamphetamine abuse is associated with increased risk of HIV-1 acquisition, higher viral loads, and enhanced HIV-1 pathogenesis. Although a direct link between methamphetamine abuse and HIV-1 pathogenesis remains to be established in patients, methamphetamine has been shown to increase HIV-1 replication in macrophages, dendritic cells, and cells of HIV transgenic mice. Intriguingly, the effects of methamphetamine on HIV-1 replication in human CD4(+) T cells that serve as the primary targets of infection in vivo are not clearly understood. Therefore, we examined HIV-1 replication in primary CD4(+) T cells in the presence of methamphetamine in a dose-dependent manner. Our results demonstrate that methamphetamine had a minimal effect on HIV-1 replication at concentrations of 1 to 50 μmol/L. However, at concentrations >100 μmol/L, it inhibited HIV-1 replication in a dose-dependent manner. We also discovered that methamphetamine up-regulated the cellular anti-HIV-1 microRNAs (miR-125b, miR-150, and miR-28-5p) in CD4(+) T cells. Knockdown experiments illustrated that up-regulation of the anti-HIV miRNAs inhibited HIV-1 replication. These results are contrary to the paradigm that methamphetamine accentuates HIV-1 pathogenesis by increasing HIV-1 replication. Therefore, our findings underline the complex interaction between drug use and HIV-1 and necessitate comprehensive understanding of the effects of methamphetamine on HIV-1 pathogenesis. Copyright © 2014 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.
Luminescence monitoring of oil or tar contamination for industrial hygiene

International Nuclear Information System (INIS)

Gammage, R.B.; Vo-Dinh, T.

1980-01-01

Synfuel plants produce potentially carcinogenic oils and tars. Exposure of workers to these tars and oils is difficult to avoid completely and occurs via direct contact with dirty surfaces or condensation of escaped fumes onto or within the body. Surface skin, measurements are made directly with a near-ultraviolet luminoscope employing a fiber optics lightguide and a stethoscopic cap pressed against the skin. This instrument is especially suitable for measuring ng to μg/cm 2 amounts of residual contamination remaining on the surface of the skin after washing. To minimize the potential for carcinogenicity, the excitating ultraviolet light intensity is only 1/100th that of sunlight. (orig.)
Heavy crude and tar sands - the long-term oil reserve

Energy Technology Data Exchange (ETDEWEB)

Barnea, J

1984-10-01

It appears that heavy crude and tar sands occur in many sedimentary areas, and estimates of known world-wide quantities exceed those known for conventional light crude resources. Although there are not precise figures available, production could be as high as three million barrels per day, with Venezuela, the US, and Canada the largest producers. There are different scales to measure the costs of production because of differences in the quality of various types of heavy crude and tar sands. Economic development of these resources should banish fears of oil scarcity in the foreseeable future. A center for information exchange through international meetings and publications is under development.
Effects of electric current upon catalytic steam reforming of biomass gasification tar model compounds to syngas

International Nuclear Information System (INIS)

Tao, Jun; Lu, Qiang; Dong, Changqing; Du, Xiaoze; Dahlquist, Erik

2015-01-01

Highlights: • ECR technique was proposed to convert biomass gasification tar model compounds. • Electric current enhanced the reforming efficiency remarkably. • The highest toluene conversion reached 99.9%. • Ni–CeO 2 /γ-Al 2 O 3 exhibited good stability during the ECR performance. - Abstract: Electrochemical catalytic reforming (ECR) technique, known as electric current enhanced catalytic reforming technique, was proposed to convert the biomass gasification tar into syngas. In this study, Ni–CeO 2 /γ-Al 2 O 3 catalyst was prepared, and toluene was employed as the major feedstock for ECR experiments using a fixed-bed lab-scale setup where thermal electrons could be generated and provided to the catalyst. Several factors, including the electric current intensity, reaction temperature and steam/carbon (S/C) ratio, were investigated to reveal their effects on the conversion of toluene as well as the composition of the gas products. Moreover, toluene, two other tar model compounds (benzene and 1-methylnaphthalene) and real tar (tar-containing wastewater) were subjected to the long period catalytic stability tests. All the used catalysts were analyzed to determine their carbon contents. The results indicated that the presence of electric current enhanced the catalytic performance remarkably. The toluene conversion reached 99.9% under the electric current of 4 A, catalytic temperature of 800 °C and S/C ratio of 3. Stable conversion performances of benzene, 1-methylnaphthalene and tar-containing wastewater were also observed in the ECR process. H 2 and CO were the major gas products, while CO 2 and CH 4 were the minor ones. Due to the promising capability, the ECR technique deserves further investigation and application for efficient tar conversion
Pyrolysis kinetics of phenols from lignite semicoking tar

Energy Technology Data Exchange (ETDEWEB)

Platonov, V.V.; Polovetskaya, O.S.; Proskuryakov, V.A.; Shavyrina, O.A. [Leo Tolstoy Tula State Pedag University, Tula (Russian Federation)

2002-11-01

The features of pyrolysis of phenols from lignite semicoking tar were studied. The activation energy and order of the reactions of accumulation of methane, hydrogen, carbon monoxide and dioxide, naphthalene and its methyl homologs, phenols, and isomeric cresols and dimethylphenols were determined.
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.
Pyrolysis of aseptic packages (tetrapak) in a laboratory screw type reactor and secondary thermal/catalytic tar decomposition

Energy Technology Data Exchange (ETDEWEB)

Haydary, J., E-mail: juma.haydary@stuba.sk [Institute of Chemical and Environmental Engineering, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava (Slovakia); Susa, D.; Dudáš, J. [Institute of Chemical and Environmental Engineering, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava (Slovakia)

2013-05-15

Highlights: ► Pyrolysis of aseptic packages was carried out in a laboratory flow reactor. ► Distribution of tetrapak into the product yields was obtained. ► Composition of the pyrolysis products was estimated. ► Secondary thermal and catalytic decomposition of tars was studied. ► Two types of catalysts (dolomite and red clay marked AFRC) were used. - Abstract: Pyrolysis of aseptic packages (tetrapak cartons) in a laboratory apparatus using a flow screw type reactor and a secondary catalytic reactor for tar cracking was studied. The pyrolysis experiments were realized at temperatures ranging from 650 °C to 850 °C aimed at maximizing of the amount of the gas product and reducing its tar content. Distribution of tetrapak into the product yields at different conditions was obtained. The presence of H{sub 2}, CO, CH{sub 4}, CO{sub 2} and light hydrocarbons, HCx, in the gas product was observed. The Aluminum foil was easily separated from the solid product. The rest part of char was characterized by proximate and elemental analysis and calorimetric measurements. The total organic carbon in the tar product was estimated by elemental analysis of tars. Two types of catalysts (dolomite and red clay marked AFRC) were used for catalytic thermal tar decomposition. Three series of experiments (without catalyst in a secondary cracking reactor, with dolomite and with AFRC) at temperatures of 650, 700, 750, 800 and 850 °C were carried out. Both types of catalysts have significantly affected the content of tars and other components in pyrolytic gases. The effect of catalyst on the tetrapack distribution into the product yield on the composition of gas and on the total organic carbon in the tar product is presented in this work.
Machine-smoking studies of cigarette filter color to estimate tar yield by visual assessment and through the use of a colorimeter.

Science.gov (United States)

Morton, Michael J; Williams, David L; Hjorth, Heather B; Smith, Jennifer H

2010-04-01

This paper explores using the intensity of the stain on the end of the filter ("filter color") as a vehicle for estimating cigarette tar yield, both by instrument reading of the filter color and by visual comparison to a template. The correlation of machine-measured tar yield to filter color measured with a colorimeter was reasonably strong and was relatively unaffected by different puff volumes or different tobacco moistures. However, the correlation of filter color to machine-measured nicotine yield was affected by the moisture content of the cigarette. Filter color, as measured by a colorimeter, was generally comparable to filter extraction of either nicotine or solanesol in its correlation to machine-smoked tar yields. It was found that the color of the tar stain changes over time. Panelists could generally correctly order the filters from machine-smoked cigarettes by tar yield using the intensity of the tar stain. However, there was considerable variation in the panelist-to-panelist tar yield estimates. The wide person-to-person variation in tar yield estimates, and other factors discussed in the text could severely limit the usefulness and practicality of this approach for visually estimating the tar yield of machine-smoked cigarettes. Copyright 2009 Elsevier Inc. All rights reserved.
Fungal cultures of tar bush and creosote bush for production of two phenolic antioxidants (pyrocatechol and gallic acid).

Science.gov (United States)

Ventura, J; Gutiérrez-Sanchez, G; Rodríguez-Herrera, R; Aguilar, C N

2009-01-01

'Tar bush' and 'creosote bush' were substrates of fungal cultivation for tannase production and gallic acid and pyrocatechol accumulation. Aspergillus niger GH1 grew similarly on both plant materials under solid state culture conditions, reaching maximal levels after 4 d. Fungal strain degraded all tannin content of creosote bush after 4 d of fermentation and >75 % of tar bush after 5 d. Higher level of tannase activity was detected in tar bush fermentation. Biotransformation of tannins to gallic acid was high (93 % in creosote bush and 89 % in tar bush). Pyrocatechol was released poorly. Kinetic parameters of tannin conversion were calculated.

Family physicians and youth tobacco-free education: outcomes of the Colorado Tar Wars program.

Science.gov (United States)

Cain, Jeffrey J; Dickinson, W Perry; Fernald, Douglas; Bublitz, Caroline; Dickinson, L Miriam; West, David

2006-01-01

Tar Wars is a national school-based tobacco-free education program operated by the American Academy of Family Physicians. The Tar Wars lesson uses an interactive 45-min session taught by volunteer family physicians in 4th- and 5th-grade classrooms and focuses on the short-term image-based consequences of tobacco use. In this study, we evaluated the effectiveness of the Tar Wars program in Colorado with both quantitative and qualitative measures. Students participating in the quantitative evaluation were tested before and after a Tar Wars teaching session using a 14-question test covering the short-term and image-based consequences of tobacco use, cost of smoking, tobacco advertising, and social norms of tobacco use. Qualitative evaluation of the program included guided telephone interviews and focus groups with participating students, teachers, and presenters. Quantitative evaluation showed statistically significant improvement in correct responses for the 14 questions measured with an average increase in correct responses from 8.95 to 10.23. Three areas recommended by the Centers for Disease Control (CDC) for youth tobacco prevention showed greater change in correct responses, including cost of smoking, truth of tobacco advertising, and peer norms of tobacco use. Qualitative evaluation found that the overall message of the session was well received, that previously known tobacco information was reinforced by its presentation in a novel format, and that new information learned included cost of smoking, truth of tobacco advertising, and peer norms of tobacco use. The Tar Wars lesson plan is effective in increasing students' understanding about the short-term consequences of tobacco use, cost of tobacco use, truth of tobacco advertising, and peer norms. Tar Wars meets the CDC guidelines as one component of effective comprehensive youth tobacco prevention.
No Increased Risk of Cancer after Coal Tar Treatment in Patients with Psoriasis or Eczema

NARCIS (Netherlands)

Roelofzen, Judith H. J.; Aben, Katja K. H.; Oldenhof, Ursula T. H.; Coenraads, Pieter-Jan; Alkemade, Hans A.; van de Kerkhof, Peter C. M.; van der Valk, Pieter G. M.; Kiemeney, Lambertus A. L. M.

Coal tar is an effective treatment for psoriasis and eczema, but it contains several carcinogenic compounds. Occupational and animal studies have shown an increased risk of cancer after exposure to coal tar. Many dermatologists have abandoned this treatment for safety reasons, although the risk of
Tar removal from biomass derived fuel gas by pulsed corona discharges: chemical kinetic study II

NARCIS (Netherlands)

Nair, S.A.; Yan, K.; Pemen, A.J.M.; Heesch, van E.J.M.; Ptasinski, K.J.; Drinkenburg, A.A.H.

2005-01-01

Tar (heavy hydrocarbon or poly aromatic hydrocarbon (PAH)) removal from biomass derived fuel gas is one of the biggest obstacles in its utilization for power generation. We have investigated pulsed corona as a method for tar removal. Our previous experimental results indicate the energy consumption
Impact of viral hepatitis co-infection on response to antiretroviral therapy and HIV disease progression in the HIV-NAT cohort

NARCIS (Netherlands)

Law, W. Phillip; Duncombe, Chris J.; Mahanontharit, Apicha; Boyd, Mark A.; Ruxrungtham, Kiat; Lange, Joep M. A.; Phanuphak, Praphan; Cooper, David A.; Dore, Gregory J.

2004-01-01

OBJECTIVE: To examine the impact of viral hepatitis co-infection on HIV disease outcomes following commencement of combination antiretroviral therapy in a developing country setting. METHODS: HIV RNA suppression, CD4 cell count recovery, and HIV disease progression were examined within a cohort of
Yeast tRNAPhe expressed in human cells can be selected by HIV-1 for use as a reverse transcription primer

International Nuclear Information System (INIS)

Kelly, Nathan J.; Morrow, Casey D.

2003-01-01

All naturally occurring human immune deficiency viruses (HIV-1) select and use tRNA Lys,3 as the primer for reverse transcription. Studies to elucidate the mechanism of tRNA selection from the intracellular milieu have been hampered due to the difficulties in manipulating the endogenous levels of tRNA Lys,3 . We have previously described a mutant HIV-1 with a primer binding site (PBS) complementary to yeast tRNA Phe (psHIV-Phe) that relies on transfection of yeast tRNA Phe for infectivity. To more accurately recapitulate the selection process, a cDNA was designed for the intracellular expression of the yeast tRNA Phe . Increasing amounts of the plasmid encoding tRNA Phe resulted in a corresponding increase in levels of yeast tRNA Phe in the cell. The yeast tRNA Phe isolated from cells transfected with the cDNA for yeast tRNA Phe , or in the cell lines expressing yeast tRNA Phe , were aminoacylated, indicating that the expressed yeast tRNA Phe was incorporated into tRNA biogenesis pathways and translation. Increasing the cytoplasmic levels of tRNA Phe resulted in increased encapsidation of tRNA Phe in viruses with a PBS complementary to tRNA Phe (psHIV-Phe) or tRNA Lys,3 (wild-type HIV-1). Production of infectious psHIV-Phe was dependent on the amount of cotransfected tRNA Phe cDNA. Increasing amounts of plasmids encoding yeast tRNA Phe produced an increase of infectious psHIV-Phe that plateaued at a level lower than that from the transfection of the wild-type genome, which uses tRNA Lys,3 as the primer for reverse transcription. Cell lines were generated that expressed yeast tRNA Phe at levels approximately 0.1% of that for tRNA Lys,3 . Even with this reduced level of yeast tRNA Phe , the cell lines complemented psHIV-Phe over background levels. The results of these studies demonstrate that intracellular levels of primer tRNA can have a direct effect on HIV-1 infectivity and further support the role for PBS-tRNA complementarity in the primer selection process
Abating coal tar seepage into surface water bodies using sheet piles with sealed interlocks

International Nuclear Information System (INIS)

Collingwood, B.I.; Boscardin, M.D.; Murdock, R.F.

1995-01-01

A former coal tar processing facility processed crude coal tar supplied from manufactured gas plants in the area. Coal-tar-contaminated ground water from the site was observed seeping through an existing timber bulkhead along a tidal river and producing a multicolored sheen on the surface of the river. As part of a short-term measure to abate the seepage into the river, 64-m long anchored sheet pile wall with sheet pile wing walls at each end was constructed inland of the of the timber bulkhead. The sheet piles extended to low-permeability soils at depth and the interlocks of the sheet piles were provided with polyurethane rubber seals. Based on postconstruction observations for leakage and sheens related to leakage, the steel sheet piles with polyurethane rubber interlock seals appeared to provide a successful seal and abate coal-tar-contaminated ground water seepage into the river. The tie rod penetration sealing proved to be a more problematic detail, but through several postconstruction grouting episodes, an effective seal was produced
[HIV encephalopathy due to drug resistance despite 2-year suppression of HIV viremia by cART].

Science.gov (United States)

Sekiya, Hiroaki; Kawamoto, Michi; Togo, Masaya; Yoshimura, Hajime; Imai, Yukihiro; Kohara, Nobuo

2014-01-01

A 57-year-old man presented with subacute progression of cognitive impairment (MMSE 22/30). He had been diagnosed as AIDS two years before and taking atazanavir, abacavir, and lamivudine. HIV RNA of plasma had been negative. On admission, HIV RNA was 4,700 copy/ml and 5,200 copy/ml in plasma and in cerebrospinal fluid respectively, suggesting treatment failure of cART. The brain magnetic resonance imaging showed high intensity areas in the white matter of the both frontal lobes and brain stem. The drug-resistance test revealed the resistance of lamivudine and abacavir. We introduced the CNS penetration effectiveness (CPE) score to evaluate the drug penetration of HIV drugs. As the former regimen had low points (7 points), we optimized the regimen to raltegravir, zidovudine, and darunavir/ritonavir (scoring 10 points). His cognitive function improved as normal (MMSE 30/30) in 2 weeks and HIV-RNA became undetectable both in plasma and CSF in a month. In spite of the cognitive improvement, the white matter hyperintensity expanded. To rule out malignant lymphoma or glioblastoma, the brain biopsy was performed from the right frontal lobe. It revealed microglial hyperplasia and diffuse perivascular infiltration by CD8+/CD4-lymphocytes. No malignant cells were found and the polymerase chain reaction analyses excluded other viruses. Considering the drug penetration to the central nervous system is important for treating HIV encephalopathy.
Human microRNA target analysis and gene ontology clustering by GOmir, a novel stand-alone application.

Science.gov (United States)

Roubelakis, Maria G; Zotos, Pantelis; Papachristoudis, Georgios; Michalopoulos, Ioannis; Pappa, Kalliopi I; Anagnou, Nicholas P; Kossida, Sophia

2009-06-16

microRNAs (miRNAs) are single-stranded RNA molecules of about 20-23 nucleotides length found in a wide variety of organisms. miRNAs regulate gene expression, by interacting with target mRNAs at specific sites in order to induce cleavage of the message or inhibit translation. Predicting or verifying mRNA targets of specific miRNAs is a difficult process of great importance. GOmir is a novel stand-alone application consisting of two separate tools: JTarget and TAGGO. JTarget integrates miRNA target prediction and functional analysis by combining the predicted target genes from TargetScan, miRanda, RNAhybrid and PicTar computational tools as well as the experimentally supported targets from TarBase and also providing a full gene description and functional analysis for each target gene. On the other hand, TAGGO application is designed to automatically group gene ontology annotations, taking advantage of the Gene Ontology (GO), in order to extract the main attributes of sets of proteins. GOmir represents a new tool incorporating two separate Java applications integrated into one stand-alone Java application. GOmir (by using up to five different databases) introduces miRNA predicted targets accompanied by (a) full gene description, (b) functional analysis and (c) detailed gene ontology clustering. Additionally, a reverse search initiated by a potential target can also be conducted. GOmir can freely be downloaded BRFAA.
Effect of the rate of heating on the quality of the primary tar in low-temperature coal-carbonization process

Energy Technology Data Exchange (ETDEWEB)

Turskii, Y I

1956-01-01

Two stages are observed. The first stage yields products of the primary and partial decomposition of coal, mainly water, CO/sub 2/, and CO as decomposition products of functional groups (-COOH, > CO, - OH, and so forth). No tar is formed in this stage. The structural decomposition and tar formation occur in the second stage. The rate of heating is important for the quality of the tar obtained. The slow rate of heating with both stages following each other yields a good-quality tar, richer in C and H, with lower O content. In case of high rate of heating both stages overlap. The tar is of poorer quality with higher specific gravity, and contains more O and asphaltenes. The complete experimental data are given in detail.
{sup 13}C relaxation in an RNA hairpin

Energy Technology Data Exchange (ETDEWEB)

King, G.C. [Univ. of South Wales, Kensington (Australia)]|[Rice Univ., Houston, TX (United States); Akratos, C. [Univ. of South Wales, Kensington (Australia); Xi, Z.; Michnica, M.J. [Rice Univ., Houston, TX (United States)

1994-12-01

This initial survey of {sup 13}C relaxation in the {triangle}TAR RNA element has generated a number of interesting results that should prove generally useful for future studies. The most readily comparable study in the literature monitored {sup 13}C relaxation of the methyl groups from unusual bases in tRNA{sup Phe}. The study, which used T{sub 1} and NOE data only, reported order parameters for the methyl group axis that ranged between 0.51 and 0.97-a range similar to that observed here. However, they reported a breakdown of the standard order parameter analysis at higher (118-MHz {sup 13}C) frequencies, which should serve to emphasize the need for a thorough exploration of suitable motional models.
BTX production by in-situ contact reforming of low-temperature tar from coal with zeolite-derived catalysts; Zeolite kei shokubai wo mochiita sekitan teion tar no sesshoku kaishitsu ni yoru BTX no seisei

Energy Technology Data Exchange (ETDEWEB)

Matsunaga, T.; Fuda, K.; Murakami, K.; Kyo, M.; Hosoya, S.; Kobayashi, S. [Akita University, Akita (Japan). Mining College

1996-10-28

On BTX production process from low-temperature tar obtained by pyrolysis of coal, the effect of exchanged metallic species and reaction temperature were studied using metallic ion-exchanged Y-zeolite as catalyst. In experiment, three kinds of coals with different produced tar structures such as Taiheiyo and PSOC-830 sub-bituminous coals and Loy Yang brown coal were used. Y-zeolite ion-exchanged with metal chloride aqueous solution was used as catalyst. Zn{sup 2+}, Ni{sup 2+} and In{sup 3+} were used as metal ions to be exchanged. The experiment was conducted by heating a pyrolysis section up to 600{degree}C for one hour after preheating a contact reforming section up to a certain proper temperature. As a result, the Ni system catalyst was effective for BTX production from aromatic-abundant tar, while the Zn system one from lower aromatic tar. In general, relatively high yields of toluene and xylene were obtained at lower temperature, while those of benzene at higher temperature. 4 figs., 1 tab.
Coliquefaction of coal, tar sand bitumen and plastic (interaction among coal, bitumen and plastic); Sekitan/tar sand bitumen/plastic no kyoekika ni okeru kyozon busshitsu no eikyo

Energy Technology Data Exchange (ETDEWEB)

Yamaguchi, H.; Okuyama, Y.; Matsubara, K. [NKK Corp., Tokyo (Japan); Kamo, T.; Sato, Y. [National Institute for Resources and Environment, Tsukuba (Japan)

1996-10-28

For the improvement of economy, coliquefaction of coal, tar sand bitumen and plastic was performed under low hydrogen pressure, to investigate the influence of interaction among these on the liquefaction characteristics. For comparison, coliquefaction was also performed under the hydrogen pressure same as the NEDOL process. In addition, for clarifying its reaction mechanism, coliquefaction of dibenzyl and plastic was performed as a model experiment, to illustrate the distribution of products and composition of oil, and to discuss the interaction between dibenzyl and various plastics, and between various plastics. Under direct coal liquefaction conditions, coprocessing of Tanito Harum coal, Athabasca tar sand and plastic was carried out under low hydrogen pressure with an autoclave. The observed value of oil yield was higher than the calculated value based on the values from separate liquefaction of coal and plastic, which suggested the interaction between coal and the mixed plastic. The results of coliquefaction of coal, tar sand bitumen and plastic could be explained from the obtained oil yield and its composition by the coliquefaction of dibenzyl and plastic. 2 refs., 3 tabs.
Integrated and Total HIV-1 DNA Predict Ex Vivo Viral Outgrowth.

Directory of Open Access Journals (Sweden)

Maja Kiselinova

2016-03-01

Full Text Available The persistence of a reservoir of latently infected CD4 T cells remains one of the major obstacles to cure HIV. Numerous strategies are being explored to eliminate this reservoir. To translate these efforts into clinical trials, there is a strong need for validated biomarkers that can monitor the reservoir over time in vivo. A comprehensive study was designed to evaluate and compare potential HIV-1 reservoir biomarkers. A cohort of 25 patients, treated with suppressive antiretroviral therapy was sampled at three time points, with median of 2.5 years (IQR: 2.4-2.6 between time point 1 and 2; and median of 31 days (IQR: 28-36 between time point 2 and 3. Patients were median of 6 years (IQR: 3-12 on ART, and plasma viral load (<50 copies/ml was suppressed for median of 4 years (IQR: 2-8. Total HIV-1 DNA, unspliced (us and multiply spliced HIV-1 RNA, and 2LTR circles were quantified by digital PCR in peripheral blood, at 3 time points. At the second time point, a viral outgrowth assay (VOA was performed, and integrated HIV-1 DNA and relative mRNA expression levels of HIV-1 restriction factors were quantified. No significant change was found for long- and short-term dynamics of all HIV-1 markers tested in peripheral blood. Integrated HIV-1 DNA was associated with total HIV-1 DNA (p<0.001, R² = 0.85, us HIV-1 RNA (p = 0.029, R² = 0.40, and VOA (p = 0.041, R2 = 0.44. Replication-competent virus was detected in 80% of patients by the VOA and it correlated with total HIV-1 DNA (p = 0.039, R² = 0.54. The mean quantification difference between Alu-PCR and VOA was 2.88 log10, and 2.23 log10 between total HIV-1 DNA and VOA. The levels of usHIV-1 RNA were inversely correlated with mRNA levels of several HIV-1 restriction factors (TRIM5α, SAMHD1, MX2, SLFN11, pSIP1. Our study reveals important correlations between the viral outgrowth and total and integrated HIV-1 DNA measures, suggesting that the total pool of HIV-1 DNA may predict the size of the
Numerical simulation of vortex pyrolysis reactors for condensable tar production from biomass

Energy Technology Data Exchange (ETDEWEB)

Miller, R.S.; Bellan, J. [California Inst. of Tech., Pasadena, CA (United States). Jet Propulsion Lab.

1998-08-01

A numerical study is performed in order to evaluate the performance and optimal operating conditions of vortex pyrolysis reactors used for condensable tar production from biomass. A detailed mathematical model of porous biomass particle pyrolysis is coupled with a compressible Reynolds stress transport model for the turbulent reactor swirling flow. An initial evaluation of particle dimensionality effects is made through comparisons of single- (1D) and multi-dimensional particle simulations and reveals that the 1D particle model results in conservative estimates for total pyrolysis conversion times and tar collection. The observed deviations are due predominantly to geometry effects while directional effects from thermal conductivity and permeability variations are relatively small. Rapid ablative particle heating rates are attributed to a mechanical fragmentation of the biomass particles that is modeled using a critical porosity for matrix breakup. Optimal thermal conditions for tar production are observed for 900 K. Effects of biomass identity, particle size distribution, and reactor geometry and scale are discussed.
Analysis of the use of coal tar as a binder in bituminous mixtures, using Marshall and Ramcodes methodologies

International Nuclear Information System (INIS)

Ochoa-Díaz, R

2013-01-01

This paper presents an alternative use of coal tar, a by-product of the steel industry, given the problems of accumulation and negative environmental impact. Therefore, it is necessary to analyze the incorporation of coal tar as a binder in paving mixtures. First, this paper presents the origin, description of the main characteristics, and properties of tar. Then, this paper evaluates the mix of coal tar by means of the RAMCODES and Marshall methodologies to determine its resistance. The results of the tests explain the physical and mechanical properties of the mix. Taking into account the results of both methods, this paper makes a comparison to determine the suitability of the RAMCODES methodology in the mix design. Finally, it analyzes the alternatives to coal tar that can be used as binders in bituminous mixes for pavement and the advantages of their uses under some specific conditions
Quantitative analysis of phenol and alkylphenols in Brazilian coal tar

Directory of Open Access Journals (Sweden)

Elina Bastos Caramão

2004-04-01

Full Text Available The main purpose of this work is the identification and quantification of phenolic compounds in coal tar samples from a ceramics factory in Cocal (SC, Brazil. The samples were subjected to preparative scale liquid chromatography, using Amberlyst A-27TM ion-exchange resin as stationary phase. The fractions obtained were classified as "acids" and "BN" (bases and neutrals. The identification and quantification of phenols, in the acid fraction, was made by gas chromatography coupled to mass spectrometry (GC/MS. Nearly twenty-five phenols were identified in the samples and nine of them were also quantified. The results showed that coal tar has large quantities of phenolic compounds of industrial interest.
Inferior clinical outcome of the CD4+ cell count-guided antiretroviral treatment interruption strategy in the SMART study: role of CD4+ Cell counts and HIV RNA levels during follow-up

DEFF Research Database (Denmark)

Lundgren, Jens; Babiker, Abdel; El-Sadr, Wafaa

2008-01-01

BACKGROUND AND METHODS: The SMART study compared 2 strategies for using antiretroviral therapy-drug conservation (DC) and viral suppression (VS)-in 5,472 human immunodeficiency virus (HIV)-infected patients with CD4+ cell counts >350 cells/microL. Rates and predictors of opportunistic disease...... or death (OD/death) and the relative risk (RR) in DC versus VS groups according to the latest CD4+ cell count and HIV RNA level are reported. RESULTS: During a mean of 16 months of follow-up, DC patients spent more time with a latest CD4+ cell count ...%) and with a latest HIV RNA level >400 copies/mL (71% vs. 28%) and had a higher rate of OD/death (3.4 vs. 1.3/100 person-years) than VS patients. For periods of follow- up with a CD4+ cell count
Understanding the fate and transport of petroleum hydrocarbons from coal tar within gasholders.

Science.gov (United States)

Coulon, Frédéric; Orsi, Roberto; Turner, Claire; Walton, Chris; Daly, Paddy; Pollard, Simon J T

2009-02-01

Coal tars have been identified as posing a threat to human health due to their toxic, mutagenic and carcinogenic characteristics. Workers involved in former gasholders decommissioning are potentially exposed to relevant concentrations of volatile and semi-volatile hydrocarbons upon opening up derelict tanks and during tar excavation/removal. While information on contaminated sites air-quality and its implications on medium-long term exposure is available, acute exposure issues associated with the execution of critical tasks are less understood. Calculations indicated that the concentration of a given contaminant in the gasholder vapour phase only depends on the coal tar composition, being only barely affected by the presence of water in the gasholder and the tar volume/void space ratio. Fugacity modelling suggested that risk-critical compounds such as benzene, naphthalene and other monocyclic and polycyclic aromatic hydrocarbons may gather in the gasholder air phase at significant concentrations. Gasholder emissions were measured on-site and compared with the workplace exposure limits (WELs) currently in use in UK. While levels for most of the toxic compounds were far lower than WELs, benzene air-concentrations where found to be above the accepted threshold. In addition due to the long exposure periods involved in gasholder decommissioning and the significant contribution given by naphthalene to the total coal tar vapour concentration, the adoption of a WEL for naphthalene may need to be considered to support operators in preventing human health risk at the workplace. The Level I fugacity approach used in this study demonstrated its suitability for applications to sealed environments such as gasholders and its further refining could provide a useful tool for land remediation risk assessors.
Effect of genital herpes on cervicovaginal HIV shedding in women co-infected with HIV AND HSV-2 in Tanzania.

Science.gov (United States)

Todd, Jim; Riedner, Gabriele; Maboko, Leonard; Hoelscher, Michael; Weiss, Helen A; Lyamuya, Eligius; Mabey, David; Rusizoka, Mary; Belec, Laurent; Hayes, Richard

2013-01-01

To compare the presence and quantity of cervicovaginal HIV among HIV seropositive women with clinical herpes, subclinical HSV-2 infection and without HSV-2 infection respectively; to evaluate the association between cervicovaginal HIV and HSV shedding; and identify factors associated with quantity of cervicovaginal HIV. Four groups of HIV seropositive adult female barworkers were identified and examined at three-monthly intervals between October 2000 and March 2003 in Mbeya, Tanzania: (1) 57 women at 70 clinic visits with clinical genital herpes; (2) 39 of the same women at 46 clinic visits when asymptomatic; (3) 55 HSV-2 seropositive women at 60 clinic visits who were never observed with herpetic lesions; (4) 18 HSV-2 seronegative women at 45 clinic visits. Associations of genital HIV shedding with HIV plasma viral load (PVL), herpetic lesions, HSV shedding and other factors were examined. Prevalence of detectable genital HIV RNA varied from 73% in HSV-2 seronegative women to 94% in women with herpetic lesions (geometric means 1634 vs 3339 copies/ml, p = 0.03). In paired specimens from HSV-2 positive women, genital HIV viral shedding was similar during symptomatic and asymptomatic visits. On multivariate regression, genital HIV RNA (log10 copies/mL) was closely associated with HIV PVL (β = 0.51 per log10 copies/ml increase, 95%CI:0.41-0.60, pgenital HIV than the presence of herpetic lesions. These data support a role of HSV-2 infection in enhancing HIV transmissibility.
Effectiveness of etravirine-based therapy for treatment-experienced HIV-infected patients.

Science.gov (United States)

Huerta García, Gloria; Mata-Marín, José Antonio; Domínguez-Hermosillo, Juan Carlos; Chavez-García, Marcelino; Banda-Lara, Marco Issac; Nuñez-Rodríguez, Nohemi; Cruz-Herrera, Javier Enrique; Sandoval-Ramírez, Jorge Luis; Villagómez-Ruiz, Alfredo; Manjarrez-Tellez, Bulmaro; Gaytan-Martínez, Jesús Enrique

2016-06-30

Treatment options are limited for HIV-1-infected individuals who have received extensive previous antiretroviral therapy. ETV has shown significant clinical benefits in treatment-experienced HIV-1+ patients with antiretroviral resistance. The aim of this study was to evaluate the effectiveness of ETV plus optimized background regimen in real-life conditions in a cohort of highly HIV-1 antiretroviral-experienced patients. Retrospective cohort of treatment-experienced HIV-1-infected adults with virological failure who started therapy with an ETV-containing regimen. The effectiveness was evaluated using HIV-1 RNA viral load and changes in CD4+ cell count after 48 weeks of treatment. Forty-two patients ≥ 16 years of age were included; 74% were men, and the median age was 45 years (IQR 41-53). All participants had prior non-nucleoside reverse transcriptase inhibitor use (55% nevirapine, 83%, efavirenz, and 28% both). Baseline median HIV-1 RNA viral load was 15,598 copies/mL (IQR 2651-84,175) and CD4+ cell count was 276 cells/mL (IQR 155-436). After 48 weeks of treatment, 90.5% (95% CI 78-96) of patients had HIV-1 RNA viral load treatment to a median of 407 cells/mL (IQR 242-579); p HIV-1 RNA viral load ≥ 100,000 copies/mL (OR 7.6; 95% CI 1.2-44.80; p = 0.025). Our study provides clinically important evidence of the effectiveness and safety of ETV in highly antiretroviral-experienced HIV-1-infected patients.

Therapeutic doses of irradiation activate viral transcription and induce apoptosis in HIV-1 infected cells

International Nuclear Information System (INIS)

Iordanskiy, Sergey; Van Duyne, Rachel; Sampey, Gavin C; Woodson, Caitlin M; Fry, Kelsi; Saifuddin, Mohammed; Guo, Jia; Wu, Yuntao; Romerio, Fabio; Kashanchi, Fatah

2015-01-01

The highly active antiretroviral therapy reduces HIV-1 RNA in plasma to undetectable levels. However, the virus continues to persist in the long-lived resting CD4"+ T cells, macrophages and astrocytes which form a viral reservoir in infected individuals. Reactivation of viral transcription is critical since the host immune response in combination with antiretroviral therapy may eradicate the virus. Using the chronically HIV-1 infected T lymphoblastoid and monocytic cell lines, primary quiescent CD4"+ T cells and humanized mice infected with dual-tropic HIV-1 89.6, we examined the effect of various X-ray irradiation (IR) doses (used for HIV-related lymphoma treatment and lower doses) on HIV-1 transcription and viability of infected cells. Treatment of both T cells and monocytes with IR, a well-defined stress signal, led to increase of HIV-1 transcription, as evidenced by the presence of RNA polymerase II and reduction of HDAC1 and methyl transferase SUV39H1 on the HIV-1 promoter. This correlated with the increased GFP signal and elevated level of intracellular HIV-1 RNA in the IR-treated quiescent CD4"+ T cells infected with GFP-encoding HIV-1. Exposition of latently HIV-1infected monocytes treated with PKC agonist bryostatin 1 to IR enhanced transcription activation effect of this latency-reversing agent. Increased HIV-1 replication after IR correlated with higher cell death: the level of phosphorylated Ser46 in p53, responsible for apoptosis induction, was markedly higher in the HIV-1 infected cells following IR treatment. Exposure of HIV-1 infected humanized mice with undetectable viral RNA level to IR resulted in a significant increase of HIV-1 RNA in plasma, lung and brain tissues. Collectively, these data point to the use of low to moderate dose of IR alone or in combination with HIV-1 transcription activators as a potential application for the “Shock and Kill” strategy for latently HIV-1 infected cells. - Highlights: • X-ray irradiation (IR) increases
Therapeutic doses of irradiation activate viral transcription and induce apoptosis in HIV-1 infected cells

Energy Technology Data Exchange (ETDEWEB)

Iordanskiy, Sergey [School of Systems Biology, Laboratory of Molecular Virology, George Mason University, Manassas, VA 20110 (United States); Van Duyne, Rachel [School of Systems Biology, Laboratory of Molecular Virology, George Mason University, Manassas, VA 20110 (United States); Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702 (United States); Sampey, Gavin C; Woodson, Caitlin M; Fry, Kelsi; Saifuddin, Mohammed; Guo, Jia; Wu, Yuntao [School of Systems Biology, Laboratory of Molecular Virology, George Mason University, Manassas, VA 20110 (United States); Romerio, Fabio [Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201 (United States); Kashanchi, Fatah, E-mail: fkashanc@gmu.edu [School of Systems Biology, Laboratory of Molecular Virology, George Mason University, Manassas, VA 20110 (United States)

2015-11-15

The highly active antiretroviral therapy reduces HIV-1 RNA in plasma to undetectable levels. However, the virus continues to persist in the long-lived resting CD4{sup +} T cells, macrophages and astrocytes which form a viral reservoir in infected individuals. Reactivation of viral transcription is critical since the host immune response in combination with antiretroviral therapy may eradicate the virus. Using the chronically HIV-1 infected T lymphoblastoid and monocytic cell lines, primary quiescent CD4{sup +} T cells and humanized mice infected with dual-tropic HIV-1 89.6, we examined the effect of various X-ray irradiation (IR) doses (used for HIV-related lymphoma treatment and lower doses) on HIV-1 transcription and viability of infected cells. Treatment of both T cells and monocytes with IR, a well-defined stress signal, led to increase of HIV-1 transcription, as evidenced by the presence of RNA polymerase II and reduction of HDAC1 and methyl transferase SUV39H1 on the HIV-1 promoter. This correlated with the increased GFP signal and elevated level of intracellular HIV-1 RNA in the IR-treated quiescent CD4{sup +} T cells infected with GFP-encoding HIV-1. Exposition of latently HIV-1infected monocytes treated with PKC agonist bryostatin 1 to IR enhanced transcription activation effect of this latency-reversing agent. Increased HIV-1 replication after IR correlated with higher cell death: the level of phosphorylated Ser46 in p53, responsible for apoptosis induction, was markedly higher in the HIV-1 infected cells following IR treatment. Exposure of HIV-1 infected humanized mice with undetectable viral RNA level to IR resulted in a significant increase of HIV-1 RNA in plasma, lung and brain tissues. Collectively, these data point to the use of low to moderate dose of IR alone or in combination with HIV-1 transcription activators as a potential application for the “Shock and Kill” strategy for latently HIV-1 infected cells. - Highlights: • X-ray irradiation
Association of mitochondrial lysyl-tRNA synthetase with HIV-1 GagPol involves catalytic domain of the synthetase and transframe and integrase domains of Pol

Directory of Open Access Journals (Sweden)

Shalak V. F.

2011-10-01

Full Text Available Aim. Analyze the interaction between Lysyl-tRNA synthetase (LysRS and HIV-1 GagPol to know whether a particular N-terminal sequence of mitochondrial LysRS triggers a specific recognition with GagPol. Methods. Yeast two-hybrid analysis, immunoprecipitation. Results. We have shown that LysRS associates with the Pol domain of GagPol. Conclusions. A model of the assembly of the LysRS:tRNA3Lys:GagPol packaging complex is proposed.
Source identification of a tar residue from Mumbai Beach

Digital Repository Service at National Institute of Oceanography (India)

Kadam, A; Rokade, M.A

A tar residue from Mumbai Beach, Maharashtra, India was matched with the suspected source sample from a tanker using UV, IR and GLC techniques. Negligible differences in several ratios of UV absorbances and ratios of infrared transmittances...
Anomalous capillary flow of coal tar pitches

Energy Technology Data Exchange (ETDEWEB)

Saint Romain, J.L.; Lahaye, J.; Ehrburger, P.; Couderc, P.

1986-06-01

Capillary flow of liquid coal tar pitch into a coke bed was studied. Anomalies in the flow could not be attributed to a plugging effect for mesophase content lower than 20 wt%. The flow behaviour of small pitch droplets can be correlated with the change in physicochemical properties, as measured by the glass transition temperature, on penetration into the coke bed. 4 references.
Retrovirus-specific differences in matrix and nucleocapsid protein-nucleic acid interactions: implications for genomic RNA packaging.

Science.gov (United States)

Sun, Meng; Grigsby, Iwen F; Gorelick, Robert J; Mansky, Louis M; Musier-Forsyth, Karin

2014-01-01

Retroviral RNA encapsidation involves a recognition event between genomic RNA (gRNA) and one or more domains in Gag. In HIV-1, the nucleocapsid (NC) domain is involved in gRNA packaging and displays robust nucleic acid (NA) binding and chaperone functions. In comparison, NC of human T-cell leukemia virus type 1 (HTLV-1), a deltaretrovirus, displays weaker NA binding and chaperone activity. Mutation of conserved charged residues in the deltaretrovirus bovine leukemia virus (BLV) matrix (MA) and NC domains affects virus replication and gRNA packaging efficiency. Based on these observations, we hypothesized that the MA domain may generally contribute to NA binding and genome encapsidation in deltaretroviruses. Here, we examined the interaction between HTLV-2 and HIV-1 MA proteins and various NAs in vitro. HTLV-2 MA displays higher NA binding affinity and better chaperone activity than HIV-1 MA. HTLV-2 MA also binds NAs with higher affinity than HTLV-2 NC and displays more robust chaperone function. Mutation of two basic residues in HTLV-2 MA α-helix II, previously implicated in BLV gRNA packaging, reduces NA binding affinity. HTLV-2 MA binds with high affinity and specificity to RNA derived from the putative packaging signal of HTLV-2 relative to nonspecific NA. Furthermore, an HIV-1 MA triple mutant designed to mimic the basic character of HTLV-2 MA α-helix II dramatically improves binding affinity and chaperone activity of HIV-1 MA in vitro and restores RNA packaging to a ΔNC HIV-1 variant in cell-based assays. Taken together, these results are consistent with a role for deltaretrovirus MA proteins in viral RNA packaging.
HIV-1 persistence following extremely early initiation of antiretroviral therapy (ART during acute HIV-1 infection: An observational study.

Directory of Open Access Journals (Sweden)

Timothy J Henrich

2017-11-01

Full Text Available It is unknown if extremely early initiation of antiretroviral therapy (ART may lead to long-term ART-free HIV remission or cure. As a result, we studied 2 individuals recruited from a pre-exposure prophylaxis (PrEP program who started prophylactic ART an estimated 10 days (Participant A; 54-year-old male and 12 days (Participant B; 31-year-old male after infection with peak plasma HIV RNA of 220 copies/mL and 3,343 copies/mL, respectively. Extensive testing of blood and tissue for HIV persistence was performed, and PrEP Participant A underwent analytical treatment interruption (ATI following 32 weeks of continuous ART.Colorectal and lymph node tissues, bone marrow, cerebral spinal fluid (CSF, plasma, and very large numbers of peripheral blood mononuclear cells (PBMCs were obtained longitudinally from both participants and were studied for HIV persistence in several laboratories using molecular and culture-based detection methods, including a murine viral outgrowth assay (mVOA. Both participants initiated PrEP with tenofovir/emtricitabine during very early Fiebig stage I (detectable plasma HIV-1 RNA, antibody negative followed by 4-drug ART intensification. Following peak viral loads, both participants experienced full suppression of HIV-1 plasma viremia. Over the following 2 years, no further HIV could be detected in blood or tissue from PrEP Participant A despite extensive sampling from ileum, rectum, lymph nodes, bone marrow, CSF, circulating CD4+ T cell subsets, and plasma. No HIV was detected from tissues obtained from PrEP Participant B, but low-level HIV RNA or DNA was intermittently detected from various CD4+ T cell subsets. Over 500 million CD4+ T cells were assayed from both participants in a humanized mouse outgrowth assay. Three of 8 mice infused with CD4+ T cells from PrEP Participant B developed viremia (50 million input cells/surviving mouse, but only 1 of 10 mice infused with CD4+ T cells from PrEP Participant A (53 million input
Control of HIV-1 env RNA splicing and transport: investigating the role of hnRNP A1 in exon splicing silencer (ESS3a) function

International Nuclear Information System (INIS)

Asai, Kengo; Platt, Craig; Cochrane, Alan

2003-01-01

The control of HIV-1 viral RNA splicing and transport plays an important role in the successful replication of the virus. Previous studies have identified both an exon splicing enhancer (ESE) and a bipartite exon splicing silencer (ESS3a and ESS3b) within the terminal exon of HIV-1 that are involved in modulating both splicing and Rev-mediated export of viral RNA. To define the mechanism of ESS3a function, experiments were carried out to better define the cis and trans components required for ESS3a activity. Mutations throughout the 30-nt element resulted in partial loss of ESS function. Combining mutations was found to have an additive effect, suggesting the presence of multiple binding sites. Analysis of interacting factors identified hnRNP A1 as one component of the complex that modulates ESS3a activity. However, subsequent binding analyses determined that hnRNP A1 interacts with only one portion of ESS3a, suggesting the involvement of another host factor. Parallel analysis of the effect of the mutations on Rev-mediated export determined that there is not a direct correlation between the effect of the mutations on splicing and RNA transport. Consistent with this hypothesis, replacement of ESS3a with consensus hnRNP A1 binding sites was found to be insufficient to block Rev-mediated RNA export
Probiotics Differently Affect Gut-Associated Lymphoid Tissue Indolamine-2,3-Dioxygenase mRNA and Cerebrospinal Fluid Neopterin Levels in Antiretroviral-Treated HIV-1 Infected Patients: A Pilot Study.

Science.gov (United States)

Scagnolari, Carolina; Corano Scheri, Giuseppe; Selvaggi, Carla; Schietroma, Ivan; Najafi Fard, Saeid; Mastrangelo, Andrea; Giustini, Noemi; Serafino, Sara; Pinacchio, Claudia; Pavone, Paolo; Fanello, Gianfranco; Ceccarelli, Giancarlo; Vullo, Vincenzo; d'Ettorre, Gabriella

2016-09-27

Recently the tryptophan pathway has been considered an important determinant of HIV-1 infected patients' quality of life, due to the toxic effects of its metabolites on the central nervous system (CNS). Since the dysbiosis described in HIV-1 patients might be responsible for the microbial translocation, the chronic immune activation, and the altered utilization of tryptophan observed in these individuals, we speculated a correlation between high levels of immune activation markers in the cerebrospinal fluid (CSF) of HIV-1 infected patients and the over-expression of indolamine-2,3-dioxygenase (IDO) at the gut mucosal surface. In order to evaluate this issue, we measured the levels of neopterin in CSF, and the expression of IDO mRNA in gut-associated lymphoid tissue (GALT), in HIV-1-infected patients on effective combined antiretroviral therapy (cART), at baseline and after six months of probiotic dietary management. We found a significant reduction of neopterin and IDO mRNA levels after the supplementation with probiotic. Since the results for the use of adjunctive therapies to reduce the levels of immune activation markers in CSF have been disappointing so far, our pilot study showing the efficacy of this specific probiotic product should be followed by a larger confirmatory trial.
A role for nuclear energy in the recovery of oil from the tar sands of Alberta

International Nuclear Information System (INIS)

Puttagunta, V.R.; Sochaski, R.O.; Robertson, R.F.S.

1976-12-01

Techniques of oil recovery from the tar sands and the energy requirements of this operation are described. Fossil fuels, and CANDU reactors are examined as competitive sources of energy for the tar sands plants. The CANDU-OCR reactor appears to have the necessary flexibility to fit into many of the possible methods of recovering oil from the tar sands. Cost comparisons of fossil and nuclear sources show that, for the supply of process steam, the nuclear source is competitive under the criteria of debt financing or low discount rates on capital, continued escalation, and long plant capital write-off period. (author)
CD32 is expressed on cells with transcriptionally active HIV but does not enrich for HIV DNA in resting T cells.

Science.gov (United States)

Abdel-Mohsen, Mohamed; Kuri-Cervantes, Leticia; Grau-Exposito, Judith; Spivak, Adam M; Nell, Racheal A; Tomescu, Costin; Vadrevu, Surya Kumari; Giron, Leila B; Serra-Peinado, Carla; Genescà, Meritxell; Castellví, Josep; Wu, Guoxin; Del Rio Estrada, Perla M; González-Navarro, Mauricio; Lynn, Kenneth; King, Colin T; Vemula, Sai; Cox, Kara; Wan, Yanmin; Li, Qingsheng; Mounzer, Karam; Kostman, Jay; Frank, Ian; Paiardini, Mirko; Hazuda, Daria; Reyes-Terán, Gustavo; Richman, Douglas; Howell, Bonnie; Tebas, Pablo; Martinez-Picado, Javier; Planelles, Vicente; Buzon, Maria J; Betts, Michael R; Montaner, Luis J

2018-04-18

The persistence of HIV reservoirs, including latently infected, resting CD4 + T cells, is the major obstacle to cure HIV infection. CD32a expression was recently reported to mark CD4 + T cells harboring a replication-competent HIV reservoir during antiretroviral therapy (ART) suppression. We aimed to determine whether CD32 expression marks HIV latently or transcriptionally active infected CD4 + T cells. Using peripheral blood and lymphoid tissue of ART-treated HIV + or SIV + subjects, we found that most of the circulating memory CD32 + CD4 + T cells expressed markers of activation, including CD69, HLA-DR, CD25, CD38, and Ki67, and bore a T H 2 phenotype as defined by CXCR3, CCR4, and CCR6. CD32 expression did not selectively enrich for HIV- or SIV-infected CD4 + T cells in peripheral blood or lymphoid tissue; isolated CD32 + resting CD4 + T cells accounted for less than 3% of the total HIV DNA in CD4 + T cells. Cell-associated HIV DNA and RNA loads in CD4 + T cells positively correlated with the frequency of CD32 + CD69 + CD4 + T cells but not with CD32 expression on resting CD4 + T cells. Using RNA fluorescence in situ hybridization, CD32 coexpression with HIV RNA or p24 was detected after in vitro HIV infection (peripheral blood mononuclear cell and tissue) and in vivo within lymph node tissue from HIV-infected individuals. Together, these results indicate that CD32 is not a marker of resting CD4 + T cells or of enriched HIV DNA-positive cells after ART; rather, CD32 is predominately expressed on a subset of activated CD4 + T cells enriched for transcriptionally active HIV after long-term ART. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.
Effect of menstrual cycle on HIV-1 levels in the peripheral blood and genital tract. WHS 001 Study Team.

Science.gov (United States)

Reichelderfer, P S; Coombs, R W; Wright, D J; Cohn, J; Burns, D N; Cu-Uvin, S; Baron, P A; Coheng, M H; Landay, A L; Beckner, S K; Lewis, S R; Kovacs, A A

2000-09-29

To assess the variation in HIV-1 over the menstrual cycle, including RNA levels in the female genital tract, plasma HIV-1-RNA levels, CD4 cell counts, and culturable virus. A prospective analysis of 55 HIV-1-infected women. Blood and genital tract specimens were collected weekly over 8 weeks, spanning two complete menstrual cycles. Applying repeated-measures models that used menses as the reference level, the variation in viral RNA levels was compared in endocervical canal fluid and cells (collected by Sno-strips and cytobrush, respectively) and ectocervicovaginal lavage (CVL) fluid. Repeated-measures models were also used to assess the variation in plasma CD4 cell counts and viral load. Shedding patterns differed among the three sampling methods, independent of genital tract co-infections. Genital tract HIV-1-RNA levels from CVL fluid and endocervical canal cytobrush specimens were highest during menses and lowest immediately thereafter (P = 0.001 and P = 0.04). The HIV-1-RNA level in endocervical canal fluid was highest in the week preceding menses (P = 0.003). The menstrual cycle had no effect on blood levels of RNA (P = 0.62), culturable virus (P = 0.34), or CD4 cell counts (P = 0.55). HIV-1-RNA levels were higher in endocervical canal fluid than in peripheral blood plasma during the late luteal phase (P = 0.03). HIV-1-RNA levels vary with the menstrual cycle in the female genital tract but not the blood compartment. HIV-1-RNA levels are higher in endocervical canal fluid than in blood plasma. These findings may have important implications for sex-specific pathogenesis, heterosexual transmission, and contraceptive hormone interventions in HIV-1-infected women.
Stuck in the tar sands : how the federal government's proposed climate change strategy lets oil companies off the hook

International Nuclear Information System (INIS)

2008-10-01

The credibility of any federal climate change strategy must be measured against its ability to reduce emissions from the tar sands. However, the federal government has proposed a climate change strategy that would allow tar sands producers to double their total emissions over the next decade. This report discussed how the federal government's proposed climate change strategy lets oil companies off the hook. The report discussed the problems and harmful effects associated with tar sands development, including greenhouse gas emissions; water depletion and pollution; toxic air emissions; destruction of the boreal forest; violation of native rights; threat to energy security; and negative socio-economic spin-off from an overheated economy. The federal government's proposed strategy was also assessed in terms of its weak greenhouse gas targets; ignoring the recent growth in tar sands emissions; adopting intensity-based targets instead of hard caps on greenhouse gas pollution, allowing total emissions from the tar sands to keep climbing; putting off critical measures until 2018; awarding oil companies hundreds of millions of dollars in credits for meeting targets they have already adopted voluntarily; lowballing the price of oil and downplaying future growth in tar sands emissions; ignoring huge portions of the oil industry's greenhouse gas pollution; letting oil companies buy their way out at rockbottom prices instead of forcing them to reduce their own emissions; and subsidizing increased tar sands production. It was concluded that the federal government's proposed plan to reduce greenhouse gas emissions was inadequate, because it failed to crack down on rising greenhouse gas emissions from the tar sands, one of Canada's most carbon intensive and fastest growing industries. 29 refs., 1 appendix
Formation of stable and functional HIV-1 nucleoprotein complexes in vitro.

Science.gov (United States)

Tanchou, V; Gabus, C; Rogemond, V; Darlix, J L

1995-10-06

HIV genomic RNA resides within the nucleocapsid, in the interior of the virus, which serves to protect the RNA against nuclease degradation and to promote its reverse transcription. To investigate the role of nucleocapsid protein (NCp7) in the stability and replication of genomic RNA within the nucleocapsid, we used NCp7, reverse transcriptase (RT) and RNAs representing the 5' and 3' regions of the genome to reconstitute functional HIV-1 nucleocapsids. The nucleoprotein complexes generated in vitro were found to be stable, which, according to biochemical and genetic data, probably results from the tight binding of NCp7 molecules to the RNA and strong NCp7/NCp7 interactions. The nucleoprotein complexes efficiently protected viral RNA against RNase degradation and, at the same time, promoted viral DNA synthesis by RT. DNA strand transfer from the 5' to the 3' RNA template was very efficient in nucleoprotein complexes formed in the presence of both RNAs, but not when the RNAs were in separate complexes. These results indicate that the in vitro reconstituted HIV-1 nucleoprotein complexes function like virion nucleocapsids and thus provide a way to study at the molecular level this viral substructure and the synthesis of proviral DNA, and to search for new anti-HIV agents.
Recovery of naphthalene, anthracene, etc. , from tar

Energy Technology Data Exchange (ETDEWEB)

1920-12-25

A process is described for the recovery of naphthalene, anthracene, and the like from tar oils and similar liquors, characterized in that the oil is treated in a rapidly rotating hammer mill, such as a colloid mill, with water sufficient, in the presence or absence of suitable solvents, for the only portion preferably in the presence of emulsifiers; and is filtered through a filter with fine pores.
Lab-scale pyrolysis of the Automotive Shredder Residue light fraction and characterization of tar and solid products.

Science.gov (United States)

Anzano, Manuela; Collina, Elena; Piccinelli, Elsa; Lasagni, Marina

2017-06-01

The general aim of this study is the recovery of Automotive Shredder Residue (ASR). The ASR light fraction, or car fluff, that was collected at an Italian shredding plant was pyrolysed at various temperatures (500-800°C) in a lab-scale reactor. The condensable gases (tar) and solid residue yields increased with decreasing temperature, and these products were characterized to suggest a potential use to reclaim them. The higher heating value (HHV) of tar was 34-37MJ/kg, which is comparable with those of fossil fuels. Furthermore, the ash content was low (0.06-4.98%). Thus, tar can be used as an alternative fuel. With this prospect, the concentrations of polychlorinated dibenzodioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) in tar were determined. The toxicity of tar changes with temperature (1-5ng I-TEQ/g), and the PCDFs significantly contribute to tar toxicity, which was 75-100% with a maximum of 99.6% at 700°C. Regarding the characterization of the solid residue, the low HHV (2.4-3.3MJ/kg) does not make it suitable for energy recovery. Regarding material recovery, we considered its use as a filler in construction materials or a secondary source for metals. It shows a high metal concentration (280,000-395,000mg/kg), which is similar at different pyrolysis temperatures. At 500°C, polycyclic aromatic hydrocarbons (PAHs) were not detected in the solid residue, whereas the maximum total PAH concentration (19.41ng/g, 700°C) was lower than that in fly ash from MSWI. In conclusion, 500°C is a suitable pyrolysis temperature to obtain valuable tar and solid residue. Copyright © 2017 Elsevier Ltd. All rights reserved.
Concentrations of polycyclic aromatic hydrocarbons (PAHs) and azaarenes in runoff from coal-tar- and asphalt-sealcoated pavement

International Nuclear Information System (INIS)

Mahler, Barbara J.; Van Metre, Peter C.; Foreman, William T.

2014-01-01

Coal-tar-based sealcoat, used extensively on parking lots and driveways in North America, is a potent source of PAHs. We investigated how concentrations and assemblages of PAHs and azaarenes in runoff from pavement newly sealed with coal-tar-based (CT) or asphalt-based (AS) sealcoat changed over time. Samples of simulated runoff were collected from pavement 5 h to 111 d following application of AS or CT sealcoat. Concentrations of the sum of 16 PAHs (median concentrations of 328 and 35 μg/L for CT and AS runoff, respectively) in runoff varied relatively little, but rapid decreases in concentrations of azaarenes and low molecular weight PAHs were offset by increases in high molecular weight PAHs. The results demonstrate that runoff from CT-sealcoated pavement, in particular, continues to contain elevated concentrations of PAHs long after a 24-h curing time, with implications for the fate, transport, and ecotoxicological effects of contaminants in runoff from CT-sealcoated pavement. - Highlights: • We compare PAH and azaarene concentrations in runoff from coal-tar- and asphalt-sealed pavement. • Concentrations in coal-tar-sealcoat runoff greatly exceeded those in asphalt-sealcoat runoff. • Decreases in azaarenes and LMW PAHs were offset by increases in HMW PAHs. • PAH concentrations in coal-tar-sealcoat runoff remained high for months after application. - Concentrations of PAHs in runoff from pavement with coal-tar-based sealcoat continue to be elevated for at least 3 months following sealcoat application
A riboswitch regulates RNA dimerization and packaging in human immunodeficiency virus type 1 virions

NARCIS (Netherlands)

Ooms, Marcel; Huthoff, Hendrik; Russell, Rodney; Liang, Chen; Berkhout, Ben

2004-01-01

The genome of retroviruses, including human immunodeficiency virus type I (HIV-1), consists of two identical RNA strands that are packaged as noncovalently linked dimers. The core packaging and dimerization signals are located in the downstream part of the untranslated leader of HIV-1 RNA-the Psi
Role of uncontrolled HIV RNA level and immunodeficiency in the occurrence of malignancy in HIV-infected patients during the combination antiretroviral therapy era: Agence Nationale de Recherche sur le Sida (ANRS) CO3 Aquitaine Cohort.

Science.gov (United States)

Bruyand, Mathias; Thiébaut, Rodolphe; Lawson-Ayayi, Sylvie; Joly, Pierre; Sasco, Annie Jeanne; Mercié, Patrick; Pellegrin, Jean Luc; Neau, Didier; Dabis, François; Morlat, Philippe; Chêne, Geneviève; Bonnet, Fabrice

2009-10-01

Human immunodeficiency virus (HIV)-infected patients are at higher risk of malignancies. In addition to traditional determinants, a specific deleterious effect of HIV and immunodeficiency is speculated. We aimed at studying the association between immunological and virological characteristics of HIV-infected patients in care and the risk of acquired immunodeficiency syndrome (AIDS)-defining and non-AIDS-defining malignancies. Patients consecutively enrolled in the hospital-based Agence Nationale de Recherche sur le Sida (ANRS) CO3 Aquitaine Cohort were included if the duration of follow-up was >3 months during the period 1998-2006. Multivariate modeling used an extended Cox proportional hazards model for time-dependent covariates and delayed entry. The 4194 patients included in the study developed 251 first malignancies during 22,389 person-years. A higher incidence of AIDS-defining malignancies (107 cases) was independently associated with (1) both longer and current exposures to a plasma HIV RNA level >500 copies/mL (hazard ratio [HR], 1.27 per year [P500 cells/mm(3) to prevent the occurrence of malignancy, this should be integrated to malignancy-prevention policies.
The Depsipeptide Romidepsin Reverses HIV-1 Latency In Vivo.

Directory of Open Access Journals (Sweden)

Ole S Søgaard

2015-09-01

Full Text Available Pharmacologically-induced activation of replication competent proviruses from latency in the presence of antiretroviral treatment (ART has been proposed as a step towards curing HIV-1 infection. However, until now, approaches to reverse HIV-1 latency in humans have yielded mixed results. Here, we report a proof-of-concept phase Ib/IIa trial where 6 aviremic HIV-1 infected adults received intravenous 5 mg/m2 romidepsin (Celgene once weekly for 3 weeks while maintaining ART. Lymphocyte histone H3 acetylation, a cellular measure of the pharmacodynamic response to romidepsin, increased rapidly (maximum fold range: 3.7–7.7 relative to baseline within the first hours following each romidepsin administration. Concurrently, HIV-1 transcription quantified as copies of cell-associated un-spliced HIV-1 RNA increased significantly from baseline during treatment (range of fold-increase: 2.4–5.0; p = 0.03. Plasma HIV-1 RNA increased from <20 copies/mL at baseline to readily quantifiable levels at multiple post-infusion time-points in 5 of 6 patients (range 46–103 copies/mL following the second infusion, p = 0.04. Importantly, romidepsin did not decrease the number of HIV-specific T cells or inhibit T cell cytokine production. Adverse events (all grade 1–2 were consistent with the known side effects of romidepsin. In conclusion, romidepsin safely induced HIV-1 transcription resulting in plasma HIV-1 RNA that was readily detected with standard commercial assays demonstrating that significant reversal of HIV-1 latency in vivo is possible without blunting T cell-mediated immune responses. These finding have major implications for future trials aiming to eradicate the HIV-1 reservoir.clinicaltrials.gov NTC02092116.

Plasma HIV-1 tropism and risk of short-term clinical progression to AIDS or death

DEFF Research Database (Denmark)

Fontdevila, Maria Casadellà; Cozzi-Lepri, Alessandro; Phillips, Andrew

2014-01-01

INTRODUCTION: It is uncertain if plasma HIV-1 tropism is an independent predictor of short-term risk of clinical progression / death, in addition to the CD4 count and HIV RNA level. We conducted a nested case-control study within EuroSIDA to assess this question amongst people with current HIV RNA...
PAH volatilization following application of coal-tar-based pavement sealant

Science.gov (United States)

Van Metre, Peter C.; Majewski, Michael S.; Mahler, Barbara J.; Foreman, William T.; Braun, Christopher L.; Wilson, Jennifer T.; Burbank, Teresa L.

2012-01-01

Coal-tar-based pavement sealants, a major source of PAHs to urban water bodies, have recently been identified as a source of volatile PAHs to the atmosphere. We tracked the volatilization of PAHs for 1 year after application of a coal-tar-based pavement sealant by measuring gas-phase PAH concentrations above the pavement surface and solid-phase PAH concentrations in sealant scraped from the surface. Gas-phase concentrations at two heights (0.03 and 1.28 m) and wind speed were used to estimate volatilization flux. The sum of the concentrations of eight frequently detected PAHs (ΣPAH8) in the 0.03-m sample 1.6 h after application (297,000 ng m-3) was about 5000 times greater than that previously reported for the same height above unsealed parking lots (66 ng m-3). Flux at 1.6 h after application was estimated at 45,000 μg m-2 h-1 and decreased rapidly during the 45 days after application to 160 μg m-2 h-1. Loss of PAHs from the adhered sealant also was rapid, with about a 50% decrease in solid-phase ΣPAH8 concentration over the 45 days after application. There was general agreement, given the uncertainties, in the estimated mass of ΣPAH8 lost to the atmosphere on the basis of air sampling (2–3 g m-2) and adhered sealant sampling (6 g m-2) during the first 16 days after application, translating to a loss to the atmosphere of one-quarter to one-half of the PAHs in the sealcoat product. Combining the estimated mass of ΣPAH8 released to the atmosphere with a national-use estimate of coal-tar-based sealant suggests that PAH emissions from new coal-tar-based sealcoat applications each year (~1000 Mg) are larger than annual vehicle emissions of PAHs for the United States.
An anti-HIV-1 compound that increases steady-state expression of apoplipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3G.

Science.gov (United States)

Ejima, Tomohiko; Hirota, Mayuko; Mizukami, Tamio; Otsuka, Masami; Fujita, Mikako

2011-10-01

Human apoplipoprotein B mRNA-editing enzyme-catalytic polypeptide-like (APOBEC) 3G (A3G) is an antiviral protein that blocks HIV-1 replication. However, the antiviral activity of A3G is overcome by the HIV-1 protein Vif. This inhibitory function of Vif is related to its ability to degrade A3G in the proteasome. This finding prompted us to examine the activities of 4-(dimethylamino)-2,6-bis[(N-(2-[(2-nitrophenyl)dithio]ethyl)amino)methyl]pyridine (SN-2) and SN-3. We found that 5 µM SN-2 increases the expression of A3G to a level much higher than that observed in the absence of Vif, without affecting the level of Vif expression. The proteasome inhibitor MG-132 increased the level of both A3G and Vif expression. These results demonstrate that A3G is ubiquitinated and degraded in the proteasome by a factor other than Vif, and that SN-2 selectively inhibits these processes. Furthermore, 5 µM SN-2 significantly inhibited the MAGI cell infectivity of wild-type HIV-1. These findings may contribute to the development of a novel anti-HIV-1 drug.
Increasing rates of obesity among HIV-infected persons during the HIV epidemic.

Directory of Open Access Journals (Sweden)

Nancy Crum-Cianflone

2010-04-01

Full Text Available The prevalence and factors associated with overweight/obesity among human immunodeficiency virus (HIV-infected persons are unknown.We evaluated prospective data from a U.S. Military HIV Natural History Study (1985-2004 consisting of early diagnosed patients. Statistics included multivariate linear regression and longitudinal linear mixed effects models.Of 1682 patients, 2% were underweight, 37% were overweight, and 9% were obese at HIV diagnosis. Multivariate predictors of a higher body mass index (BMI at diagnosis included more recent year of HIV diagnosis, older age, African American race, and earlier HIV stage (all p<0.05. The majority of patients (62% gained weight during HIV infection. Multivariate factors associated with a greater increase in BMI during HIV infection included more recent year of diagnosis, lower BMI at diagnosis, higher CD4 count, lower HIV RNA level, lack of AIDS diagnosis, and longer HIV duration (all p<0.05. Nucleoside agents were associated with less weight gain; other drug classes had no significant impact on weight change in the HAART era.HIV-infected patients are increasingly overweight/obese at diagnosis and during HIV infection. Weight gain appears to reflect improved health status and mirror trends in the general population. Weight management programs may be important components of HIV care.
The search for a source rock for the giant Tar Sand triangle accumulation, southeastern Utah

Science.gov (United States)

Huntoon, J.E.; Hansley, P.L.; Naeser, N.D.

1999-01-01

A large proportion (about 36%) of the world's oil resource is contained in accumulations of heavy oil or tar. In these large deposits of degraded oil, the oil in place represents only a fraction of what was present at the time of accumulation. In many of these deposits, the source of the oil is unknown, and the oil is thought to have migrated over long distances to the reservoirs. The Tar Sand triangle in southeastern Utah contains the largest tar sand accumulation in the United States, with 6.3 billion bbl of heavy oil estimated to be in place. The deposit is thought to have originally contained 13-16 billion bbl prior to the biodegradation, water washing, and erosion that have taken place since the middle - late Tertiary. The source of the oil is unknown. The tar is primarily contained within the Lower Permian White Rim Sandstone, but extends into permeable parts of overlying and underlying beds. Oil is interpreted to have migrated into the White Rim sometime during the Tertiary when the formation was at a depth of approximately 3500 m. This conclusion is based on integration of fluid inclusion analysis, time-temperature reconstruction, and apatite fission-track modeling for the White Rim Sandstone. Homogenization temperatures cluster around 85-90??C for primary fluid inclusions in authigenic, nonferroan dolomite in the White Rim. The fluid inclusions are associated with fluorescent oil-bearing inclusions, indicating that dolomite precipitation was coeval with oil migration. Burial reconstruction suggests that the White Rim Sandstone reached its maximum burial depth from 60 to 24 Ma, and that maximum burial was followed by unroofing from 24 to 0 Ma. Time-temperature modeling indicates that the formation experienced temperatures of 85-90??C from about 35 to 40 Ma during maximum burial. Maximum formation temperatures of about 105-110??C were reached at about 24 Ma, just prior to unroofing. Thermal modeling is used to examine the history of potential source rocks
HIV-1 Reservoir Association with Immune Activation

Directory of Open Access Journals (Sweden)

Alejandro Vallejo

2015-09-01

Full Text Available In this issue of EBioMedicine, Ruggiero and colleagues describe immune activation biomarkers associated with the size of the HIV reservoir in a carefully designed cross-sectional study. The cohort consists of a homogeneous sample of HIV-1-infected patients with long-term plasma HIV-1 RNA suppression under antiretroviral treatment (ART. It is crucial to explore the potential utility of biomarkers that are easier (less labor intensive, less expensive to measure than integrated HIV DNA load, in order to quickly and accurately quantify cellular reservoirs of HIV.
Marketing 'less harmful, low-tar' cigarettes is a key strategy of the industry to counter tobacco control in China.

Science.gov (United States)

Yang, Gonghuan

2014-03-01

While the 'low-tar' scheme has been widely recognised as a misleading tactic used by the tobacco industry to deceive the public about the true risks of cigarette smoking, a similar campaign using the slogan of 'less harmful, low tar' was launched by the Chinese tobacco industry, that is, State Tobacco Monopoly Administration/China National Tobacco Corporation and began to gain traction during the last decade. Despite the fact that no sufficient research evidence supports the claims made by the industry that these cigarettes are safer, the Chinese tobacco industry has continued to promote them using various health claims. As a result, the production and sales of 'less harmful, low-tar' cigarettes have increased dramatically since 2000. Recently, a tobacco industry senior researcher, whose main research area is 'less harmful, low-tar' cigarettes, was elected as an Academician to the prestigious Chinese Academy of Engineering for his contribution to developing 'less harmful, low-tar' cigarettes. The tobacco researcher's election caused an outcry from the tobacco control community and the general public in China. This paper discusses the Chinese tobacco industry's 'less harmful, low-tar' initiatives and calls for the Chinese government to stop the execution of this deceptive strategy for tobacco marketing.
Quantitative determination of acid oils in low-temperature coal tar by means of fractional distillation

Energy Technology Data Exchange (ETDEWEB)

Jaeger, A

1950-01-01

The aromatic hydroxy compounds in low-temperature tar were separated, and 75 compounds in the boiling range 180/sup 0/ to 320/sup 0/ isolated by means of fractional distillation in packed columns of at least 45 theoretical plates. Mixtures not separable by fractionation were separated by means of other physicochemical or chemical methods. Hydroxy compounds with boiling point up to 230/sup 0/C were detemined quantitatively, as were the phenols present in low-temperature carbonization liquors. With the Krupp-Lurgi process of low-temperature carbonization, 1.8% phenol, 1.8% o-cresol, and 3.6% m-p-cresols were formed. The tar contained up to 1.3% 1:3:5-xylenol and up to 0.9% 1:2:4-xylenol. Of the 12.1% v/v of phenol, cresols, and xylenols present in tar, 11.2% were determined quantitatively, and 9 hydroxy compounds were identified in the remaining 0.9%. On the basis of these investigations, a technical plant that permitted the recovery of pure low-temperature tar phenols and the preparation of a number of different phenol resins from the mixtures was erected.
Studies estimating the dermal bioavailability of polynuclear aromatic hydrocarbons from manufactured plant tar-contaminated soils

International Nuclear Information System (INIS)

Roy, T.A.; Krueger, A.J.; Taylor, B.B.; Mauro, D.M.; Goldstein, L.S.

1998-01-01

In vitro percutaneous absorption studies were performed with contaminated soils or organic extracts of contaminated soils collected at manufactured gas plant (MGP) sites. The MGP tar contaminated soils were found to contain a group of targeted polynuclear aromatic hydrocarbons (PAH) at levels ranging from 10 to 2400 mg/kg. The soil extracts contained target PAH at levels ranging from 12 000 - 34 000 mg/kg. Dermal penetration rates of target PAH from the MGP tar-contaminated soils/soil extracts were determined experimentally through human skin using 3 H-benzo(a)pyrene (BaP) as a surrogate. Results from three MGP sites showed reductions of 2-3 orders of magnitude in PAH absorption through human skin from the most contaminated soils in comparison to the soil extracts. Reduction in PAH penetration can be attributed to PAH concentration and (soil) matrix properties. PAH dermal flux values are used to determine site-specific dermally absorbed dose (DAD) and chronic daily intake (CDI) which are essential terms required to estimate risk associated with human exposure to MGP tar and MGP tar-contaminated soils. 21 refs., 4 figs., 3 tabs
The expression of cholesterol metabolism genes in monocytes from HIV-infected subjects suggests intracellular cholesterol accumulation.

Science.gov (United States)

Feeney, Eoin R; McAuley, Nuala; O'Halloran, Jane A; Rock, Clare; Low, Justin; Satchell, Claudette S; Lambert, John S; Sheehan, Gerald J; Mallon, Patrick W G

2013-02-15

Human immunodeficiency virus (HIV) infection is associated with increased cardiovascular risk and reduced high-density lipoprotein cholesterol (HDL-c). In vitro, HIV impairs monocyte-macrophage cholesterol efflux, a major determinant of circulating HDL-c, by increasing ABCA1 degradation, with compensatory upregulation of ABCA1 messenger RNA (mRNA). We examined expression of genes involved in cholesterol uptake, metabolism, and efflux in monocytes from 22 HIV-positive subjects on antiretroviral therapy (ART-Treated), 30 untreated HIV-positive subjects (ART-Naive), and 22 HIV-negative controls (HIV-Neg). HDL-c was lower and expression of ABCA1 mRNA was higher in ART-Naive subjects than in both ART-Treated and HIV-Neg subjects (both P ART-Treated and ART-Naive subjects than in HIV-Neg controls. In vivo, increased monocyte ABCA1 expression in untreated HIV-infected patients and normalization of ABCA1 expression with virological suppression by ART supports direct HIV-induced impairment of cholesterol efflux previously demonstrated in vitro. However, decreased expression of cholesterol sensing, uptake, and synthesis genes in both untreated and treated HIV infection suggests that both HIV and ART affect monocyte cholesterol metabolism in a pattern consistent with accumulation of intramonocyte cholesterol.
Tar removal from biomass gasification streams: processes and catalysts; Remocao do alcatrao de correntes de gaseificacao de biomassa: processos e catalisadores

Energy Technology Data Exchange (ETDEWEB)

Quitete, Cristina P.B. [Centro de Pesquisa e Desenvolvimento Leopoldo Americo Miguez de Mello (CENPES/PETROBRAS), Rio de Janeiro, RJ (Brazil). Processos de Conversao de Biomassa; Souza, Mariana M.V.M., E-mail: mmattos@eq.ufrj.br [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Centro de Tecnologia. Escola de Quimica

2014-07-01

Biomass gasification is a technology that has attracted great interest in synthesis of biofuels and oxo alcohols. However, this gas contains several contaminants, including tar, which need to be removed. Removal of tar is particularly critical because it can lead to operational problems. This review discusses the major pathways to remove tar, with a particular focus on the catalytic steam reforming of tar. Few catalysts have shown promising results; however, long-term studies in the context of real biomass gasification streams are required to realize their potential. (author)
Human papillomavirus and tar hypothesis for squamous cell cervical ...

Indian Academy of Sciences (India)

2010-08-09

Aug 9, 2010 ... Keywords. Cervical cancer; co-factors; human papillomavirus; tar-based vaginal douche; tobacco smoke; wood smoke. Author Affiliations. Christina Bennett1 Allen E Kuhn2 Harry W Haverkos3. Indiana University School of Medicine, Indianapolis, Indiana 46202-5149, USA; Suite 300, Hamilton Mason Road ...
Coal-tar-based sealcoated pavement: A major PAH source to urban stream sediments

International Nuclear Information System (INIS)

Witter, Amy E.; Nguyen, Minh H.; Baidar, Sunil; Sak, Peter B.

2014-01-01

We used land-use analysis, PAH concentrations and assemblages, and multivariate statistics to identify sediment PAH sources in a small (∼1303 km 2 ) urbanizing watershed located in South-Central, Pennsylvania, USA. A geographic information system (GIS) was employed to quantify land-use features that may serve as PAH sources. Urban PAH concentrations were three times higher than rural levels, and were significantly and highly correlated with combined residential/commercial/industrial land use. Principal components analysis (PCA) was used to group sediments with similar PAH assemblages, and correlation analysis compared PAH sediment assemblages to common PAH sources. The strongest correlations were observed between rural sediments (n = 7) and coke-oven emissions sources (r = 0.69–0.78, n = 5), and between urban sediments (n = 22) and coal-tar-based sealcoat dust (r = 0.94, n = 47) suggesting that coal-tar-based sealcoat is an important urban PAH source in this watershed linked to residential and commercial/industrial land use. -- Highlights: • Total PAH concentrations were measured at 35 sites along an urbanizing land-use gradient. • PAH concentrations increased with increasing urban land-use. • Urban land-use metrics were measured at three spatial scales using GIS. • PAH assemblages indicate coal-tar-based sealcoat is a major urban PAH source. • PAH assemblages indicate coke-oven emissions are an important rural PAH source. -- Coal-tar-based sealcoated pavement is a major PAH source to urban freshwater stream sediments in south-central Pennsylvania, USA
Social-cognitive remediation in schizophrenia: generalization of effects of the Training of Affect Recognition (TAR).

Science.gov (United States)

Wölwer, Wolfgang; Frommann, Nicole

2011-09-01

In the last decade, several social cognitive remediation programs have been developed for use in schizophrenia. Though existing evidence indicates that such programs can improve social cognition, which is essential for successful social functioning, it remains unclear whether the improvements generalize to social cognitive domains not primarily addressed by the intervention and whether the improved test performance transfers into everyday social functioning. The present study investigated whether, beyond its known effects on facial affect recognition, the Training of Affect Recognition (TAR) has effects on prosodic affect recognition, theory of mind (ToM) performance, social competence in a role-play task, and more general social and occupational functioning. Thirty-eight inpatients with a diagnosis of schizophrenia or schizoaffective disorder were randomly assigned to 6 weeks of treatment with the TAR--primarily targeted at facial affect recognition-or Cognitive Remediation Training (CRT)--primarily targeted at neurocognition. Intention-to-treat analyses found significantly larger pre-post improvements with TAR than with CRT in prosodic affect recognition, ToM, and social competence and a trend effect in global social functioning. However, the effects on ToM and social competence were no longer significant in the smaller group of patients who completed treatment according to protocol. Results suggest that TAR effects generalize to other social cognitive domains not primarily addressed. TAR may also enhance social skills and social functioning, although this has to be confirmed. Results are discussed with regard to the need to improve functional outcome in schizophrenia against the background of current evidence from other social cognitive remediation approaches.
Tar sands showdown : Canada and the new politics of oil in an age of climate change

International Nuclear Information System (INIS)

Clarke, T.

2009-01-01

This book outlined the social and environmental issues facing the oil sands industry in Canada, including economic sovereignty, energy security, water rights and free trade. The tar sands have become vital to the Canadian economy, as they have the potential to increase Canada's foreign oil output by 4 to 5 times in the next 15 years. The author discussed the ecological and social impact of the Alberta tar sands and the real cost of development to Albertans and Canadians. Tar sands oil production generates more than 3 times the amount of greenhouse gas emissions than conventional oil production. The industry is also becoming a prime example of the abuse of water sources. The author emphasized the need to build an alternative energy future in an age of global warming. The main objective of this book was to help stimulate a nation-wide public debate about the tar sands and the critical issues at stake regarding Canada's energy future and an environmental strategy for more sustainable development. refs., tabs., figs.
Gc/ms analysis of coal tar composition produced from coal

African Journals Online (AJOL)

Coal pyrolysis is one of the significant approaches for the comprehensive utilization ... planigraphy-GC/MS; therefore a satisfactory analytical result obtained, which .... Among the aliphatic group of the coal tar, the proportion of alkene is larger ...
Optimization of the doxycycline-dependent simian immunodeficiency virus through in vitro evolution

Directory of Open Access Journals (Sweden)

Piatak Mike

2008-06-01

Full Text Available Abstract Background Vaccination of macaques with live attenuated simian immunodeficiency virus (SIV provides significant protection against the wild-type virus. The use of a live attenuated human immunodeficiency virus (HIV as AIDS vaccine in humans is however considered unsafe because of the risk that the attenuated virus may accumulate genetic changes during persistence and evolve to a pathogenic variant. We earlier presented a conditionally live HIV-1 variant that replicates exclusively in the presence of doxycycline (dox. Replication of this vaccine strain can be limited to the time that is needed to provide full protection through transient dox administration. Since the effectiveness and safety of such a conditionally live virus vaccine should be tested in macaques, we constructed a similar dox-dependent SIV variant. The Tat-TAR transcription control mechanism in this virus was inactivated through mutation and functionally replaced by the dox-inducible Tet-On regulatory system. This SIV-rtTA variant replicated in a dox-dependent manner in T cell lines, but not as efficiently as the parental SIVmac239 strain. Since macaque studies will likely require an efficiently replicating variant, we set out to optimize SIV-rtTA through in vitro viral evolution. Results Upon long-term culturing of SIV-rtTA, additional nucleotide substitutions were observed in TAR that affect the structure of this RNA element but that do not restore Tat binding. We demonstrate that the bulge and loop mutations that we had introduced in the TAR element of SIV-rtTA to inactivate the Tat-TAR mechanism, shifted the equilibrium between two alternative conformations of TAR. The additional TAR mutations observed in the evolved variants partially or completely restored this equilibrium, which suggests that the balance between the two TAR conformations is important for efficient viral replication. Moreover, SIV-rtTA acquired mutations in the U3 promoter region. We demonstrate
In situ heat treatment of a tar sands formation after drive process treatment

Science.gov (United States)

Vinegar, Harold J.; Stanecki, John

2010-09-21

A method for treating a tar sands formation includes providing a drive fluid to a hydrocarbon containing layer of the tar sands formation to mobilize at least some hydrocarbons in the layer. At least some first hydrocarbons from the layer are produced. Heat is provided to the layer from one or more heaters located in the formation. At least some second hydrocarbons are produced from the layer of the formation. The second hydrocarbons include at least some hydrocarbons that are upgraded compared to the first hydrocarbons produced by using the drive fluid.
Cigarettes, lung cancer, and coronary heart disease: the effects of inhalation and tar yield.

Science.gov (United States)

Higenbottam, T; Shipley, M J; Rose, G

1982-06-01

Ten-year mortality rates for lung cancer and coronary heart disease have been related to cigarette smoking habits in 17 475 male civil servants aged 40-64 and in sample of 8089 male British residents aged 35-69. Both diseases were more frequent in smokers. Lung cancer rates were higher overall for "non-inhalers", particularly in heavy smokers. Tar yield correlated with the risk of lung cancer in non-inhalers but less so in inhalers. Conversely, coronary deaths were more common among inhalers, and the effect of tar/nicotine yield (such as it was) was confined to inhalers. It appears that there are subtle interactions between the amount smoked, the tar/nicotine yield of the cigarette, and the style of smoking. Thus the effects of a change in cigarette characteristics are hard to predict, and they may be different for respiratory and cardiovascular disease.
Properties of gasification-derived char and its utilization for catalytic tar reforming

Science.gov (United States)

Qian, Kezhen

Char is a low-value byproduct of biomass gasification and pyrolysis with many potential applications, such as soil amendment and the synthesis of activated carbon. The overall goal of the proposed research was to develop novel methods to use char derived from gasification for high-value applications in syngas conditioning. The first objective was to investigate effects of gasification condition and feedstock on properties of char derived from fluidized bed gasification. Results show that the surface areas of most of the char were 1--10 m 2/g and increased as the equivalence ratio increased. Char moisture and fixed carbon contents decreased while ash content increased as equivalence ratio increased. The next objective was to study the properties of sorghum and red cedar char derived from downdraft gasifier. Red cedar char contained more aliphatic carbon and o-alkyl carbon than sorghum char. Char derived from downdraft gasification had higher heating values and lower ash contents than char derived from fluidized bed gasification. The gasification reactivity of red cedar char was higher than that of sorghum char. Then, red cedar char based catalysts were developed with different preparation method to reform toluene and naphthalene as model tars. The catalyst prepared with nickel nitrate was found to be better than that with nickel acetate. The nickel particle size of catalyst impregnated with nickel nitrate was smaller than that of catalyst impregnated with nickel acetate. The particle size of catalyst impregnated with nickel acetate decreased by hydrazine reduction. The catalyst impregnated with nickel nitrate had the highest toluene removal efficiency, which was 70%--100% at 600--800 °C. The presence of naphthalene in tar reduced the catalyst efficiency. The toluene conversion was 36--99% and the naphthalene conversion was 37%--93% at 700--900 °C. Finally, effects of atmosphere and pressure on catalytic reforming of lignin-derived tars over the developed catalyst

Characterization of alkanes, hopanes, and polycyclic aromatic hydrocarbons (PAHs) in tar-balls collected from the East Coast of Peninsular Malaysia.

Science.gov (United States)

Chandru, Kuhan; Zakaria, Mohamad Pauzi; Anita, Sofia; Shahbazi, Azadeh; Sakari, Mahyar; Bahry, Pourya Shahpoury; Mohamed, Che Abd Rahim

2008-05-01

The East Coast of Peninsular Malaysia faces the South China Sea and is vulnerable to oil pollution because of intense petroleum production activities in the area. The South China Sea is also a favored route for supertankers carrying crude oil to the Far East. Consequently, oil spills can occur, causing pollution and contamination in the surrounding areas. Residual oil spills stranded on coastal beaches usually end up as tar-balls. Elucidating the sources of tar-balls using a molecular marker approach is essential in assessing environmental impacts and perhaps settling legal liabilities for affected parties. This study utilizes a multimodal molecular marker approach through the use of diagnostic ratios of alkanes, hopanes, and polycyclic aromatic hydrocarbons (PAHs) to determine the source, distribution and weathering of tar-balls. Hopane ratios (e.g., C29/C30, and summation C31-C35/C30 ratios) were used to identify the sources of tar-balls. The weathering effects were distinguished by using alkanes, namely the unresolved complex mixture (UCM) and low molecular weight/high molecular weight (L/H) ratios. Similarly, PAHs were also used for the determination of weathering processes undergone by the tar-balls. This multimodal molecular marker gave a very strong indication of the sources of tar-balls in this study. For example, 16 out of 17 samples originated from South East Asian Crude Oil (SEACO) with one sample from Merang, Terengganu originating from North Sea Oil (Troll). The TRME-2 sample may have come from a supertanker's ballast water discharge. The second possibility is that the tar-ball may have been transported via oceanographic currents. All 'weathered' sample characterizations were based on the presence of UCM and other ratios. The multimodal molecular marker approach applied in this study has enabled us to partially understand the transport behavior of tar-balls in the marine environment and has revealed insights into the weathering process of tar-balls.
Effect of genital herpes on cervicovaginal HIV shedding in women co-infected with HIV AND HSV-2 in Tanzania.

Directory of Open Access Journals (Sweden)

Jim Todd

Full Text Available To compare the presence and quantity of cervicovaginal HIV among HIV seropositive women with clinical herpes, subclinical HSV-2 infection and without HSV-2 infection respectively; to evaluate the association between cervicovaginal HIV and HSV shedding; and identify factors associated with quantity of cervicovaginal HIV.Four groups of HIV seropositive adult female barworkers were identified and examined at three-monthly intervals between October 2000 and March 2003 in Mbeya, Tanzania: (1 57 women at 70 clinic visits with clinical genital herpes; (2 39 of the same women at 46 clinic visits when asymptomatic; (3 55 HSV-2 seropositive women at 60 clinic visits who were never observed with herpetic lesions; (4 18 HSV-2 seronegative women at 45 clinic visits. Associations of genital HIV shedding with HIV plasma viral load (PVL, herpetic lesions, HSV shedding and other factors were examined.Prevalence of detectable genital HIV RNA varied from 73% in HSV-2 seronegative women to 94% in women with herpetic lesions (geometric means 1634 vs 3339 copies/ml, p = 0.03. In paired specimens from HSV-2 positive women, genital HIV viral shedding was similar during symptomatic and asymptomatic visits. On multivariate regression, genital HIV RNA (log10 copies/mL was closely associated with HIV PVL (β = 0.51 per log10 copies/ml increase, 95%CI:0.41-0.60, p<0.001 and HSV shedding (β = 0.24 per log10 copies/ml increase, 95% CI:0.16-0.32, p<0.001 but not the presence of herpetic lesions (β = -0.10, 95%CI:-0.28-0.08, p = 0.27.HIV PVL and HSV shedding were more important determinants of genital HIV than the presence of herpetic lesions. These data support a role of HSV-2 infection in enhancing HIV transmissibility.
Characterisation and catalytic upgrading of tars from coal-tyre hydropyrolysis

Energy Technology Data Exchange (ETDEWEB)

Mastral, A.M.; Murillo, R.; Callen, M.S.; Garcia, T. [Instituto de Carboquimica, Zaragoza (Spain)

1999-07-01

Tars from coal-tyre hydropyrolysis obtained in a swept fixed bed reactor were upgraded with catalysts. Upgraded oils were characterized, and naphtha, kerosene, gas oil, heavy gas oil and vacuum residue percentages were quantified. 7 refs., 3 tabs.
Class I cultural resource overview for oil shale and tar sands areas in Colorado, Utah and Wyoming.

Energy Technology Data Exchange (ETDEWEB)

O' Rourke, D.; Kullen, D.; Gierek, L.; Wescott, K.; Greby, M.; Anast, G.; Nesta, M.; Walston, L.; Tate, R.; Azzarello, A.; Vinikour, B.; Van Lonkhuyzen, B.; Quinn, J.; Yuen, R.; Environmental Science Division

2007-11-01

In August 2005, the U.S. Congress enacted the Energy Policy Act of 2005, Public Law 109-58. In Section 369 of this Act, also known as the 'Oil Shale, Tar Sands, and Other Strategic Unconventional Fuels Act of 2005', Congress declared that oil shale and tar sands (and other unconventional fuels) are strategically important domestic energy resources that should be developed to reduce the nation's growing dependence on oil from politically and economically unstable foreign sources. The Bureau of Land Management (BLM) is developing a Programmatic Environmental Impact Statement (PEIS) to evaluate alternatives for establishing commercial oil shale and tar sands leasing programs in Colorado, Wyoming, and Utah. This PEIS evaluates the potential impacts of alternatives identifying BLM-administered lands as available for application for commercial leasing of oil shale resources within the three states and of tar sands resources within Utah. The scope of the analysis of the PEIS also includes an assessment of the potential effects of future commercial leasing. This Class I cultural resources study is in support of the Draft Oil Shale and Tar Sands Resource Management Plan Amendments to Address Land Use Allocations in Colorado, Utah, and Wyoming and Programmatic Environmental Impact Statement and is an attempt to synthesize archaeological data covering the most geologically prospective lands for oil shale and tar sands in Colorado, Utah, and Wyoming. This report is based solely on geographic information system (GIS) data held by the Colorado, Utah, and Wyoming State Historic Preservation Offices (SHPOs). The GIS data include the information that the BLM has provided to the SHPOs. The primary purpose of the Class I cultural resources overview is to provide information on the affected environment for the PEIS. Furthermore, this report provides recommendations to support planning decisions and the management of cultural resources that could be impacted by future
Guideline for Sampling and Analysis of Tar and Particles in Biomass Producer Gases. Version 3.3

Energy Technology Data Exchange (ETDEWEB)

Neeft, J.P.A.; Knoef, H.A.M.; Zielke, U.; Sjoestroem, K.; Hasler, P.; Simell, P.A.; Dorrington, M.A.; Thomas, L.; Abatzoglou, N.; Deutch, S.; Greil, C.; Buffinga, G.J.; Brage, C.; Suomalainen, M.

2002-07-01

This Guideline provides a set of procedures for the measurement of organic contaminants and particles in producer gases from biomass gasifiers. The procedures are designed to cover different gasifier types (updraft or downdraft fixed bed or fluidised bed gasifiers), operating conditions (0 - 900C and 0.6-60 bars) and concentration ranges (1 mg/m{sub n}{sup 3} to 300 g/m{sub n}{sup 3}). The Guideline describes a modular sampling train, and a set of procedures, which include: planning and preparation of the sampling, sampling and post-sampling, analysis, calculations, error analysis and reporting. The modular sampling train consists of 4 modules. Module 1 is a preconditioning module for isokinetic sampling and gas cooling. Module 2 is a particle collection module including a heated filter. Module 3 is a tar collection module with a gas quench (optionally by circulating a liquid), impinger bottles and a backup adsorber. Module 4 is a volume-sampling module consisting of a pump, a rotameter, a gas flow meter and pressure and temperature indicators. The equipment and materials that are required for procuring this modular sampling train are given in the Guideline. The sampling procedures consist of a description for isokinetic sampling, a leakage test prior to sampling, the actual sampling and its duration, how the equipment is cleaned after the sampling, and how the samples are prepared and stored. Analysis of the samples is performed via three procedures. Prior to these procedures, the sample is prepared by Soxhlet extraction of the tars on the particle filter and by collection of all tars in one bulk solution. The first procedure describes the weighing of the particle filter to obtain the concentration of particles in the biomass producer gas. The bulk tar solution is used for two purposes: for determination of gravimetric tar and for analysis of individual compounds. The second procedure describes how to determine the gravimetric tar mass from the bulk solution. The
Treatment of low-temperature tar-gas mixtures

Energy Technology Data Exchange (ETDEWEB)

Schick, F

1928-07-04

Process for the treating and conversion of low-temperature tar-vapor and gas mixtures in the presence of metals or metal oxides as well as bodies of large surface, without previous condensation of the liquid material to be treated, characterized by the treatment taking place with a mixture of desulfurizing metals and metal oxides which, if necessary, are precipitated on carriers and large surface nonmetal cracking catalysts, such as active carbon and silica gel.
Receiving demulsifying agent from the acid tar

Energy Technology Data Exchange (ETDEWEB)

Nikitina, A.A.; Belyaeva, A.S.; Kunakova, R.V. [FGBIHE ' Ufa State Academy of Economics and Services' , Ufa (Russian Federation); Movsumzade, E.M. [FGBIHE ' Ufa State Petroleum Technological Univ.' , Ufa (Russian Federation); Lapidus, A.L. [Russian Academy of Sciences, Moscow (Russian Federation). N.D. Zelinsky Institute of Organic Chemistry

2012-07-01

The processing of wastes of petrochemical production makes it possible to reduce the price of produced commodity of petroleum products substantially. Bitumen, fuel oils, tars and other mixture of heavy organic compounds are widely used in road construction, in paint and cable industries, manufacture of roofing materials, are used as boiler and furnace fuel, fuel for marine diesel engines, raw material for the production of modifying additives, fillers, surfaceactive substances, etc. (orig.)
Tar DNA binding protein-43 (TDP-43 associates with stress granules: analysis of cultured cells and pathological brain tissue.

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Liqun Liu-Yesucevitz

2010-10-01

Full Text Available Tar DNA Binding Protein-43 (TDP-43 is a principle component of inclusions in many cases of frontotemporal lobar degeneration (FTLD-U and amyotrophic lateral sclerosis (ALS. TDP-43 resides predominantly in the nucleus, but in affected areas of ALS and FTLD-U central nervous system, TDP-43 is aberrantly processed and forms cytoplasmic inclusions. The mechanisms governing TDP-43 inclusion formation are poorly understood. Increasing evidence indicates that TDP-43 regulates mRNA metabolism by interacting with mRNA binding proteins that are known to associate with RNA granules. Here we show that TDP-43 can be induced to form inclusions in cell culture and that most TDP-43 inclusions co-localize with SGs. SGs are cytoplasmic RNA granules that consist of mixed protein-RNA complexes. Under stressful conditions SGs are generated by the reversible aggregation of prion-like proteins, such as TIA-1, to regulate mRNA metabolism and protein translation. We also show that disease-linked mutations in TDP-43 increased TDP-43 inclusion formation in response to stressful stimuli. Biochemical studies demonstrated that the increased TDP-43 inclusion formation is associated with accumulation of TDP-43 detergent insoluble complexes. TDP-43 associates with SG by interacting with SG proteins, such as TIA-1, via direct protein-protein interactions, as well as RNA-dependent interactions. The signaling pathway that regulates SGs formation also modulates TDP-43 inclusion formation. We observed that inclusion formation mediated by WT or mutant TDP-43 can be suppressed by treatment with translational inhibitors that suppress or reverse SG formation. Finally, using Sudan black to quench endogenous autofluorescence, we also demonstrate that TDP-43 positive-inclusions in pathological CNS tissue co-localize with multiple protein markers of stress granules, including TIA-1 and eIF3. These data provide support for accumulating evidence that TDP-43 participates in the SG pathway.
Brown carbon in tar balls from smoldering biomass combustion

Science.gov (United States)

R. K. Chakrabarty; H. Moosmuller; L.-W. A. Chen; K. Lewis; W. P. Arnott; C. Mazzoleni; M. K. Dubey; C. E. Wold; W. M. Hao; S. M. Kreidenweis

2010-01-01

We report the direct observation of laboratory production of spherical, carbonaceous particles - "tar balls" - from smoldering combustion of two commonly occurring dry mid-latitude fuels. Real-time measurements of spectrally varying absorption Angstrom coefficients (AAC) indicate that a class of light absorbing organic carbon (OC) with wavelength dependent...
Interleukin-9 receptor α chain mRNA formation in CD8+ T cells producing anti-human immunodeficiency virus type 1 substance(s)

International Nuclear Information System (INIS)

Hossain, M.M.; Tsuchie, H.; Detorio, M.A.; Shirono, H.; Hara, C.; Nishimoto, A.; Saji, A.; Koga, J.; Takata, N.; Maniar, J.K.; Saple, D.G.; Taniguchi, K.; Kageyama, S.; Ichimura, H.; Kurimura, T.

1998-01-01

A search for gene(s) associated with anti-human immunodeficiency virus type 1 (HIV-l) activity of CD8 + T cells was attempted using molecular cloning and the relation between the anti-HIV activity of CD8 + T cells and the interleukin-9 receptor a chain (IL-9R-α) mRNA expression from the cDNA clones obtained was examined. The anti-HIV-l activity of CD8 + T cell culture supernatants was assessed by measuring the level of HIV-l replication in a CD4 + T cell line transfected with an infectious HIV-l DNA clone. IL-9R-a mRNA was assayed by reverse transcriptase-polymerase chain reaction (RT-PCR). Of 5 cases showing high level of anti-HIV-l activity (more than 80% suppression of HIV-l replication), the mRNA was detected in 4 cases. Of 10 cases showing low level of anti-HIV-l activity (less than 80% suppression of HIV-l replication), the mRNA was detected in one case. Soluble recombinant human IL-9 receptor (rhIL-9sR) did not suppress HIV-l replication at a concentration of 1 μg/ml. These data suggest that the IL-9R-a mRNA formation in CD8 + T cells may correlate with and play some role in the anti-HIV-l activity of CD8+ T cells from HIV-l-infected individuals. Key words: CD8+ T cells; anti-HIV-l activity; cytokines; interleukin-9 receptor (authors)
Radiocarbon dating of extinct fauna in the Americas recovered from tar pits

International Nuclear Information System (INIS)

Jull, A.J.T.; Iturralde-Vinent, M.; O'Malley, J.M.; MacPhee, R.D.E.; McDonald, H.G.; Martin, P.S.; Moody, J.; Rincon, A.

2004-01-01

We have obtained radiocarbon dates by accelerator mass spectrometry on bones of extinct large mammals from tar pits. Results on some samples of Glyptodon and Holmesina (extinct large mammals similar to armadillos) yielded ages of >25 and >21 ka, respectively. We also studied the radiocarbon ages of three different samples of bones from the extinct Cuban ground sloth, Parocnus bownii, which yielded dates ranging from 4960 ± 280 to 11 880 ± 420 yr BP. In order to remove the tar component pretreat the samples sufficiently to obtain reliable dates, we cleaned the samples by Soxhlet extraction in benzene. Resulting samples of collagenous material were often small
Comparación de los métodos de cuantificación de carga viral de VIH: COBAS® AmpliPrep/COBAS® TaqMan HIV-1 test, v 2.0, y VERSANT HIV-1 RNA 1.0 Assay (kPCR Comparison of COBAS® AmpliPrep/COBAS® TaqMan HIV-1 test, v 2.0 and VERSANT HIV-1 RNA 1.0 (kPCR assays for HIV-1 plasma viral load

Directory of Open Access Journals (Sweden)

María Isabel Múnera-Jaramillo

2012-03-01

Full Text Available Objetivo. El propósito del estudio fue evaluar el desempeño del método VERSANTHIV-1RNA 1.0 Assay® (kPCR (Siemens, para la cuantificación de la carga viral en pacientes con VIH-1, en comparación con el método COBAS® AmpliPrep/COBAS TaqMan HIV-1 test®, v2.0 (Roche Diagnostics (CAP/CTM. Métodos. Las muestras fueron tomadas en dos tubos con EDTA, de 60 pacientes remitidos por el médico tratante para pruebas de carga viral como parte de su control de rutina de VIH/sida, y fueron procesadas para la cuantificación del ARN del VIH-1 por ambas técnicas. Se hizo análisis de regresión y se calcularon los coeficientes de correlación de Pearson, y los de correlación y concordancia de Lin. Se evalúo la concordancia entre las dos técnicas mediante el método de Bland-Altman. Resultados. El promedio de la carga viral por el método CAP/CTM fue 3,2±1,4 long10 copias/ml y, por el método kPCR, 3,0±1,3 long10 copias/ml. El 86,7 % de muestras presentó diferencias entre los dos métodos, menores de 0,5 long10 copias/ml, y el 13,3 % presentó diferencias mayores. El coeficiente de correlación de Pearson entre los dos métodos fue de 0,97 (IC95% 0,95-0,99 y el índice kappa ponderado entre los dos métodos en diferentes rangos de concentración, fue de 0,91 (IC95% 0,87-0,96. El promedio de las diferencias entre las mediciones fue 0,22 long10 copias/ml (IC95% -0,45 a 0,89. Conclusión. Las dos técnicas evaluadas fueron comparables, con el método kPCR se observaron resultados más bajos.Objective: The purpose of this study was to evaluate the performance of the kPCR VERSANT (™ 440 HIV-1RNA 3.0 Assay® (Siemens method for the quantification of viral load in HIV-1 patients, compared to the COBAS AmpliPrep/COBASTaqMan HIV-1 test®, v. 2.0 (Roche Diagnostics (CAP/CTM. Methods: Samples were taken in 2 tubes with EDTA, in 60 patients referred by the attending physician for viral load tests as part of their routine control of HIV/AIDS, and were
Structure-based design of ligands for protein basic domains: Application to the HIV-1 Tat protein

Science.gov (United States)

Filikov, Anton V.; James, Thomas L.

1998-05-01

A methodology has been developed for designing ligands to bind a flexible basic protein domain where the structure of the domain is essentially known. It is based on an empirical binding free energy function developed for highly charged complexes and on Monte Carlo simulations in internal coordinates with both the ligand and the receptor being flexible. HIV-1 encodes a transactivating regulatory protein called Tat. Binding of the basic domain of Tat to TAR RNA is required for efficient transcription of the viral genome. The structure of a biologically active peptide containing the Tat basic RNA-binding domain is available from NMR studies. The goal of the current project is to design a ligand which will bind to that basic domain and potentially inhibit the TAR-Tat interaction. The basic domain contains six arginine and two lysine residues. Our strategy was to design a ligand for arginine first and then a superligand for the basic domain by joining arginine ligands with a linker. Several possible arginine ligands were obtained by searching the Available Chemicals Directory with DOCK 3.5 software. Phytic acid, which can potentially bind multiple arginines, was chosen as a building block for the superligand. Calorimetric binding studies of several compounds to methylguanidine and Arg-/Lys-containing peptides were performed. The data were used to develop an empirical binding free energy function for prediction of affinity of the ligands for the Tat basic domain. Modeling of the conformations of the complexes with both the superligand and the basic domain being flexible has been carried out via Biased Probability Monte Carlo (BPMC) simulations in internal coordinates (ICM 2.6 suite of programs). The simulations used parameters to ensure correct folding, i.e., consistent with the experimental NMR structure of a 25-residue Tat peptide, from a random starting conformation. Superligands for the basic domain were designed by joining together two molecules of phytic acid with
Comparison of the Abbott m2000 HIV-1 Real-Time and Roche AMPLICOR Monitor v1.5 HIV-1 assays on plasma specimens from Rakai, Uganda.

Science.gov (United States)

Ssebugenyi, I; Kizza, A; Mpoza, B; Aluma, G; Boaz, I; Newell, K; Laeyendecker, O; Shott, J P; Serwadda, D; Reynolds, S J

2011-07-01

The need for viral load (VL) monitoring of HIV patients receiving antiretroviral therapy (ART) in resource-limited settings (RLS) has become apparent with studies showing the limitations of immunological monitoring. We compared the Abbott m2000 Real-Time (Abbott) HIV-1 assay with the Roche AMPLICOR Monitor v1.5 (Roche) HIV-1 assay over a range of VL concentrations. Three hundred and eleven plasma samples were tested, including 164 samples from patients on ART ≥ six months and 147 from ART-naïve patients. The Roche assay detected ≥400 copies/mL in 158 (50.8%) samples. Of these, Abbott produced 145 (91.8%) detectable results ≥400 copies/mL; 13 (8.2%) samples produced discrepant results. Concordance between the assays for detecting HIV-1 RNA ≥400 copies/mL was 95.8% (298/311). The sensitivity, specificity, positive predictive value and negative predictive value of Abbott to detect HIV-1 RNA ≥400 copies/mL were 91.8%, 100%, 100% and 92.2%, respectively. For the 151 samples with HIV-1 RNA ≥400 copies/mL for both assays, a good linear correlation was found (r = 0.81, P Abbott assay performed well in our setting, offering an alternative methodology for HIV-1 VL for laboratories with realtime polymerase chain reaction (PCR) capacity.
A whole genome screen for HIV restriction factors

Directory of Open Access Journals (Sweden)

Liu Li

2011-11-01

Full Text Available Abstract Background Upon cellular entry retroviruses must avoid innate restriction factors produced by the host cell. For human immunodeficiency virus (HIV human restriction factors, APOBEC3 (apolipoprotein-B-mRNA-editing-enzyme, p21 and tetherin are well characterised. Results To identify intrinsic resistance factors to HIV-1 replication we screened 19,121 human genes and identified 114 factors with significant inhibition of infection. Those with a known function are involved in a broad spectrum of cellular processes including receptor signalling, vesicle trafficking, transcription, apoptosis, cross-nuclear membrane transport, meiosis, DNA damage repair, ubiquitination and RNA processing. We focused on the PAF1 complex which has been previously implicated in gene transcription, cell cycle control and mRNA surveillance. Knockdown of all members of the PAF1 family of proteins enhanced HIV-1 reverse transcription and integration of provirus. Over-expression of PAF1 in host cells renders them refractory to HIV-1. Simian Immunodeficiency Viruses and HIV-2 are also restricted in PAF1 expressing cells. PAF1 is expressed in primary monocytes, macrophages and T-lymphocytes and we demonstrate strong activity in MonoMac1, a monocyte cell line. Conclusions We propose that the PAF1c establishes an anti-viral state to prevent infection by incoming retroviruses. This previously unrecognised mechanism of restriction could have implications for invasion of cells by any pathogen.
Hairpin-induced tRNA-mediated (HITME) recombination in HIV-1

NARCIS (Netherlands)

Konstantinova, Pavlina; de Haan, Peter; Das, Atze T.; Berkhout, Ben

2006-01-01

Recombination due to template switching during reverse transcription is a major source of genetic variability in retroviruses. In the present study we forced a recombination event in human immunodeficiency virus type 1 (HIV-1) by electroporation of T cells with DNA from a molecular HIV-1 clone that
CRISPR-Cas9 Can Inhibit HIV-1 Replication but NHEJ Repair Facilitates Virus Escape

NARCIS (Netherlands)

Wang, Gang; Zhao, Na; Berkhout, Ben; Das, Atze T.

2016-01-01

Several recent studies demonstrated that the clustered regularly interspaced short palindromic repeats (CRISPR)-associated endonuclease Cas9 can be used for guide RNA (gRNA)-directed, sequence-specific cleavage of HIV proviral DNA in infected cells. We here demonstrate profound inhibition of HIV-1
ANALYSIS OF MEASURED AND MODELED SOLAR RADIATION AT THE TARS SOLAR HEATING PLANT IN DENMARK

DEFF Research Database (Denmark)

Tian, Zhiyong; Perers, Bengt; Furbo, Simon

2017-01-01

, such as solar radiation, inlet and outlet temperature for the solar collector field, flow rate and pressure, ambient temperature, Wind speed and wind direction were measured. Global horizontal radiation, direct normal irradiation (DNI) and total radiation on the tilted collector plane of the flat plate...... collector field have been measured in Tars solar heating plant. To determine the accuracy of modeled and measured solar radiation in Tars solar heating plant, monthly comparisons of measured and calculated radiation using 6 empirical models have been carried out. Comparisons of measured and modeled total......A novel combined solar heating plant with tracking parabolic trough collectors (PTC) and flat plate collectors (FPC) has been constructed and put into operation in Tars, 30 km north of Aalborg, Denmark in August 2015. To assess the operation performance of the plant, detailed parameters...
Parallels between playbacks and Pleistocene tar seeps suggest sociality in an extinct sabretooth cat, Smilodon

OpenAIRE

Carbone, Chris; Maddox, Tom; Funston, Paul J.; Mills, Michael G.L.; Grether, Gregory F.; Van Valkenburgh, Blaire

2008-01-01

Inferences concerning the lives of extinct animals are difficult to obtain from the fossil record. Here we present a novel approach to the study of extinct carnivores, using a comparison between fossil records (n=3324) found in Late Pleistocene tar seeps at Rancho La Brea in North America and counts (n=4491) from playback experiments used to estimate carnivore abundance in Africa. Playbacks and tar seep deposits represent competitive, potentially dangerous encounters where multiple predators ...
Raltegravir versus lopinavir/ritonavir for treatment of HIV-infected late-presenting pregnant women.

Science.gov (United States)

Brites, Carlos; Nóbrega, Isabella; Luz, Estela; Travassos, Ana Gabriela; Lorenzo, Cynthia; Netto, Eduardo M

2018-06-01

Background Late-presenting pregnant women pose a challenge in the prevention of HIV-1 mother-to-child-transmission. We compared the safety and efficacy of raltegravir and lopinavir/ritonavir for this population. Methods We did a single-center, pilot, open-label, randomized trial in Brazil (N = 44). We randomly allocated late-presenting HIV-infected pregnant women (older than 18 years with a plasma HIV-1 RNA >1000 copies/mL) to receive raltegravir 400 mg twice a day or lopinavir/ritonavir 400/100 mg twice a day plus zidovudine and lamivudine (1:1). The primary endpoint was virological suppression at delivery (HIV-1 RNA HIV-infected late-presenting pregnant women.

Coal-tar-based pavement sealcoat and PAHs: implications for the environment, human health, and stormwater management.

Science.gov (United States)

Mahler, Barbara J; Metre, Peter C Van; Crane, Judy L; Watts, Alison W; Scoggins, Mateo; Williams, E Spencer

2012-03-20

Coal-tar-based sealcoat products, widely used in the central and eastern U.S. on parking lots, driveways, and even playgrounds, are typically 20-35% coal-tar pitch, a known human carcinogen that contains about 200 polycyclic aromatic hydrocarbon (PAH) compounds. Research continues to identify environmental compartments-including stormwater runoff, lake sediment, soil, house dust, and most recently, air-contaminated by PAHs from coal-tar-based sealcoat and to demonstrate potential risks to biological communities and human health. In many cases, the levels of contamination associated with sealed pavement are striking relative to levels near unsealed pavement: PAH concentrations in air over pavement with freshly applied coal-tar-based sealcoat, for example, were hundreds to thousands of times higher than those in air over unsealed pavement. Even a small amount of sealcoated pavement can be the dominant source of PAHs to sediment in stormwater-retention ponds; proper disposal of such PAH-contaminated sediment can be extremely costly. Several local governments, the District of Columbia, and the State of Washington have banned use of these products, and several national and regional hardware and home-improvement retailers have voluntarily ceased selling them.
Coal-tar-based pavement sealcoat and PAHs: implications for the environment, human health, and stormwater management

Science.gov (United States)

Mahler, Barbara J.; Van Metre, Peter C.; Crane, Judy L.; Watts, Alison W.; Scoggins, Mateo; Williams, E. Spencer

2012-01-01

Coal-tar-based sealcoat products, widely used in the central and eastern U.S. on parking lots, driveways, and even playgrounds, are typically 20-35% coal-tar pitch, a known human carcinogen that contains about 200 polycyclic aromatic hydrocarbon (PAH) compounds. Research continues to identify environmental compartments—including stormwater runoff, lake sediment, soil, house dust, and most recently, air—contaminated by PAHs from coal-tar-based sealcoat and to demonstrate potential risks to biological communities and human health. In many cases, the levels of contamination associated with sealed pavement are striking relative to levels near unsealed pavement: PAH concentrations in air over pavement with freshly applied coal-tar-based sealcoat, for example, were hundreds to thousands of times higher than those in air over unsealed pavement. Even a small amount of sealcoated pavement can be the dominant source of PAHs to sediment in stormwater-retention ponds; proper disposal of such PAH-contaminated sediment can be extremely costly. Several local governments, the District of Columbia, and the State of Washington have banned use of these products, and several national and regional hardware and home-improvement retailers have voluntarily ceased selling them.
Coal-tar pavement sealants might substantially increase children's PAH exposures

Science.gov (United States)

Williams, E. Spencer; Mahler, Barbara J.; Van Metre, Peter C.

2012-01-01

Dietary ingestion has been identified repeatedly as the primary route of human exposure to polycyclic aromatic hydrocarbons (PAHs), seven of which are classified as probable human carcinogens (B2 PAHs) by the U.S. EPA. Humans are exposed to PAHs through ingestion of cooked and uncooked foods, incidental ingestion of soil and dust, inhalation of ambient air, and absorption through skin. Although PAH sources are ubiquitous in the environment, one recently identified PAH source stands out: Coal-tar-based pavement sealant—a product applied to many parking lots, driveways, and even playgrounds primarily in the central, southern, and eastern U.S.—has PAH concentrations 100–1000 times greater than most other PAH sources. It was reported recently that PAH concentrations in house dust in residences adjacent to parking lots with coal-tar-based sealant were 25 times higher than in residences adjacent to unsealed asphalt parking lots.
How do different cigarette design features influence the standard tar yields of popular cigarette brands sold in different countries?

Science.gov (United States)

O'Connor, R J; Hammond, D; McNeill, A; King, B; Kozlowski, L T; Giovino, G A; Cummings, K M

2008-09-01

To examine the associations among cigarette design features and tar yields of leading cigarette brands sold in the United States, Canada, Australia and the United Kingdom. Government reports and numbers listed on packs were used to obtain data on International Organization for Standardization (ISO)/Federal Trade Commission (FTC) yields for the tar of 172 cigarette varieties sold in the United States, Canada, Australia and the United Kingdom. We used standardised methods to measure the following 11 cigarette design parameters: filter ventilation, cigarette pressure drop, filter pressure drop, tobacco rod length, filter length, cigarette diameter, tipping paper length, tobacco weight, filter weight, rod density and filter density. Filter ventilation was found to be the predominant design feature accounting for the variations between brands in ISO/FTC tar yields in each of the four countries. After accounting for filter ventilation, design parameters such as overwrap length, tobacco weight and rod density played comparatively minor roles in determining tar yields. Variation in ISO/FTC tar yields are predicted by a limited set of cigarette design features, especially filter ventilation, suggesting that governments should consider mandatory disclosure of cigarette design parameters as part of comprehensive tobacco product regulations.
Tenofovir treatment in an unselected cohort of highly antiretroviral experienced HIV positive patients

DEFF Research Database (Denmark)

Lerbaek, A; Kristiansen, Thomas Birk; Katzenstein, TL

2004-01-01

Tenofovir treatment in an unselected cohort of highly antiretroviral experienced HIV positive patients.Lerbaek A, Kristiansen TB, Katzenstein TL, Mathiesen L, Gerstoft J, Nielsen C, Larsen K, Nielsen JO, Obel N, Laursen AL, Nielsen SD. Department of Infectious Diseases, Hvidovre Hospital......, HIV-RNA levels and genotypic resistance were determined at baseline and after 3 and 6 months. After initiation of tenofovir treatment, a mean decrease in HIV-RNA for all 34 patients was observed (-0.43 log1o copies/ml (+/- 1.22) and -0.49 log10 copies/ml (+/- 1.36) after 3 and 6 months, respectively......, respectively). After initiation of tenofovir treatment, no significant increases in CD4 count were observed. All new NRTI-associated mutations could be explained by the background treatment. In conclusion, we observed a significant decrease in HIV-RNA only when tenofovir was prescribed, in conjunction...
Packaging of HCV-RNA into lentiviral vector

International Nuclear Information System (INIS)

Caval, Vincent; Piver, Eric; Ivanyi-Nagy, Roland; Darlix, Jean-Luc; Pagès, Jean-Christophe

2011-01-01

Highlights: ► Description of HCV-RNA Core-D1 interactions. ► In vivo evaluation of the packaging of HCV genome. ► Determination of the role of the three basic sub-domains of D1. ► Heterologous system involving HIV-1 vector particles to mobilise HCV genome. ► Full length mobilisation of HCV genome and HCV-receptor-independent entry. -- Abstract: The advent of infectious molecular clones of Hepatitis C virus (HCV) has unlocked the understanding of HCV life cycle. However, packaging of the genomic RNA, which is crucial to generate infectious viral particles, remains poorly understood. Molecular interactions of the domain 1 (D1) of HCV Core protein and HCV RNA have been described in vitro. Since compaction of genetic information within HCV genome has hampered conventional mutational approach to study packaging in vivo, we developed a novel heterologous system to evaluate the interactions between HCV RNA and Core D1. For this, we took advantage of the recruitment of Vpr fusion-proteins into HIV-1 particles. By fusing HCV Core D1 to Vpr we were able to package and transfer a HCV subgenomic replicon into a HIV-1 based lentiviral vector. We next examined how deletion mutants of basic sub-domains of Core D1 influenced HCV RNA recruitment. The results emphasized the crucial role of the first and third basic regions of D1 in packaging. Interestingly, the system described here allowed us to mobilise full-length JFH1 genome in CD81 defective cells, which are normally refractory to HCV infection. This finding paves the way to an evaluation of the replication capability of HCV in various cell types.
Detection of HIV-1 and Human Proteins in Urinary Extracellular Vesicles from HIV+ Patients

Directory of Open Access Journals (Sweden)

Samuel I. Anyanwu

2018-01-01

Full Text Available Background. Extracellular vesicles (EVs are membrane bound, secreted by cells, and detected in bodily fluids, including urine, and contain proteins, RNA, and DNA. Our goal was to identify HIV and human proteins (HPs in urinary EVs from HIV+ patients and compare them to HIV− samples. Methods. Urine samples were collected from HIV+ (n=35 and HIV− (n=12 individuals. EVs were isolated by ultrafiltration and characterized using transmission electron microscopy, tandem mass spectrometry (LC/MS/MS, and nanoparticle tracking analysis (NTA. Western blots confirmed the presence of HIV proteins. Gene ontology (GO analysis was performed using FunRich and HIV Human Interaction database (HHID. Results. EVs from urine were 30–400 nm in size. More EVs were in HIV+ patients, P<0.05, by NTA. HIV+ samples had 14,475 HPs using LC/MS/MS, while only 111 were in HIV−. HPs in the EVs were of exosomal origin. LC/MS/MS showed all HIV+ samples contained at least one HIV protein. GO analysis showed differences in proteins between HIV+ and HIV− samples and more than 50% of the published HPs in the HHID interacted with EV HIV proteins. Conclusion. Differences in the proteomic profile of EVs from HIV+ versus HIV− samples were found. HIV and HPs in EVs could be used to detect infection and/or diagnose HIV disease syndromes.
The B-Cell Follicle in HIV Infection: Barrier to a Cure.

Science.gov (United States)

Bronnimann, Matthew P; Skinner, Pamela J; Connick, Elizabeth

2018-01-01

The majority of HIV replication occurs in secondary lymphoid organs (SLOs) such as the spleen, lymph nodes, and gut-associated lymphoid tissue. Within SLOs, HIV RNA + cells are concentrated in the B-cell follicle during chronic untreated infection, and emerging data suggest that they are a major source of replication in treated disease as well. The concentration of HIV RNA + cells in the B-cell follicle is mediated by several factors. Follicular CD4 + T-cell subsets including T-follicular helper cells and T-follicular regulatory cells are significantly more permissive to HIV than extrafollicular subsets. The B cell follicle also contains a large reservoir of extracellular HIV virions, which accumulate on the surface of follicular dendritic cells (FDCs) in germinal centers. FDC-bound HIV virions remain infectious even in the presence of neutralizing antibodies and can persist for months or even years. Moreover, the B-cell follicle is semi-immune privileged from CTL control. Frequencies of HIV- and SIV-specific CTL are lower in B-cell follicles compared to extrafollicular regions as the majority of CTL do not express the follicular homing receptor CXCR5. Additionally, CTL in the B-cell follicle may be less functional than extrafollicular CTL as many exhibit the recently described CD8 T follicular regulatory phenotype. Other factors may also contribute to the follicular concentration of HIV RNA + cells. Notably, the contribution of NK cells and γδ T cells to control and/or persistence of HIV RNA + cells in secondary lymphoid tissue remains poorly characterized. As HIV research moves increasingly toward the development of cure strategies, a greater understanding of the barriers to control of HIV infection in B-cell follicles is critical. Although no strategy has as of yet proven to be effective, a range of novel therapies to address these barriers are currently being investigated including genetically engineered CTL or chimeric antigen receptor T cells that express
The B-Cell Follicle in HIV Infection: Barrier to a Cure

Directory of Open Access Journals (Sweden)

Matthew P. Bronnimann

2018-01-01

Full Text Available The majority of HIV replication occurs in secondary lymphoid organs (SLOs such as the spleen, lymph nodes, and gut-associated lymphoid tissue. Within SLOs, HIV RNA+ cells are concentrated in the B-cell follicle during chronic untreated infection, and emerging data suggest that they are a major source of replication in treated disease as well. The concentration of HIV RNA+ cells in the B-cell follicle is mediated by several factors. Follicular CD4+ T-cell subsets including T-follicular helper cells and T-follicular regulatory cells are significantly more permissive to HIV than extrafollicular subsets. The B cell follicle also contains a large reservoir of extracellular HIV virions, which accumulate on the surface of follicular dendritic cells (FDCs in germinal centers. FDC-bound HIV virions remain infectious even in the presence of neutralizing antibodies and can persist for months or even years. Moreover, the B-cell follicle is semi-immune privileged from CTL control. Frequencies of HIV- and SIV-specific CTL are lower in B-cell follicles compared to extrafollicular regions as the majority of CTL do not express the follicular homing receptor CXCR5. Additionally, CTL in the B-cell follicle may be less functional than extrafollicular CTL as many exhibit the recently described CD8 T follicular regulatory phenotype. Other factors may also contribute to the follicular concentration of HIV RNA+ cells. Notably, the contribution of NK cells and γδ T cells to control and/or persistence of HIV RNA+ cells in secondary lymphoid tissue remains poorly characterized. As HIV research moves increasingly toward the development of cure strategies, a greater understanding of the barriers to control of HIV infection in B-cell follicles is critical. Although no strategy has as of yet proven to be effective, a range of novel therapies to address these barriers are currently being investigated including genetically engineered CTL or chimeric antigen receptor T cells
Fresh tar (from biomass gasification) destruction with downstream catalysts: comparison of their intrinsic activity with a realistic kinetic model

Energy Technology Data Exchange (ETDEWEB)

Corella, J.; Narvaez, I.; Orio, A. [Complutense Univ. of Madrid (Spain). Dept. of Chemical Engineering

1996-12-31

A model for fresh tar destruction over catalysts placed downstream a biomass gasifier is presented. It includes the stoichio-metry and the calculation of the kinetic constants for the tar destruction. Catalysts studied include commercial Ni steam reforming catalysts and calcinated dolomites. Kinetic constants for tar destruction are calculated for several particle sizes, times- on-stream and temperatures of the catalyst and equivalence ratios in the gasifier. Such intrinsic kinetic constants allow a rigorous or scientific comparison of solids and conditions to be used in an advanced gasification process. (orig.) 4 refs.
Fresh tar (from biomass gasification) destruction with downstream catalysts: comparison of their intrinsic activity with a realistic kinetic model

Energy Technology Data Exchange (ETDEWEB)

Corella, J; Narvaez, I; Orio, A [Complutense Univ. of Madrid (Spain). Dept. of Chemical Engineering

1997-12-31

A model for fresh tar destruction over catalysts placed downstream a biomass gasifier is presented. It includes the stoichio-metry and the calculation of the kinetic constants for the tar destruction. Catalysts studied include commercial Ni steam reforming catalysts and calcinated dolomites. Kinetic constants for tar destruction are calculated for several particle sizes, times- on-stream and temperatures of the catalyst and equivalence ratios in the gasifier. Such intrinsic kinetic constants allow a rigorous or scientific comparison of solids and conditions to be used in an advanced gasification process. (orig.) 4 refs.
The impact of nevirapine- versus protease inhibitor-based regimens on virological markers of HIV-1 persistence during seemingly suppressive ART.

Science.gov (United States)

Kiselinova, Maja; Anna, Maria; Malatinkova, Eva; Vervish, Karen; Beloukas, Apostolos; Messiaen, Peter; Bonczkowski, Pawel; Trypsteen, Wim; Callens, Steven; Verhofstede, Chris; De Spiegelaere, Ward; Vandekerckhove, Linos

2014-01-01

The source and significance of residual plasma HIV-1 RNA detection during suppressive ART remain controversial. It has been proposed that nevirapine (NVP)-based regimens achieve a greater HIV-1 RNA suppression than regimens containing a protease inhibitor (PI). The aim of this study was to compare the effect of receiving NVP- vs PI-based ART on the virological markers of HIV persistence in peripheral blood. The study population comprised 161 HIV-1 infected patients receiving either NVP-based (n=81) or PI-based (n=80) ART and showing a HIV-1 RNA load stably suppressed ART, with median (IQR) levels of 5 (3-6) and 5 (3-8) copies/mL, respectively. HIV-1 RNA detection was associated with shorter duration of suppressive ART regardless of treatment arm (p=0.007), and lower CD4 nadir (p=0.015). HIV-1 DNA levels were median 282 (120-484) and 213 (87-494) copies/106 PBMCs in the two groups respectively, and were lowest (ART HIV-1 RNA load (p=0.0001). In this comprehensive characterization of patients on long-term suppressive ART, we did not observe evidence for a greater suppressive activity of NVP-based over PI-based therapy on plasma and intracellular markers of virus persistence. Overall excellent correlation was observed between the markers, allowing the identification of a subset of treated patients with low HIV-1 expression as an important cohort for future HIV cure studies.
Changes in tar yields and cigarette design in samples of Chinese cigarettes, 2009 and 2012.

Science.gov (United States)

Schneller, Liane M; Zwierzchowski, Benjamin A; Caruso, Rosalie V; Li, Qiang; Yuan, Jiang; Fong, Geoffrey T; O'Connor, Richard J

2015-11-01

China is home to the greatest number of smokers as well as the greatest number of smoking-related deaths. An active and growing market of cigarettes marketed as 'light' or 'low tar' may keep health-concerned smokers from quitting, wrongly believing that such brands are less harmful. This study sought to observe changes in cigarette design characteristics and reported tar, nicotine and carbon monoxide (TNCO) levels in a sample of cigarette brands obtained in seven Chinese cities from 2009 to 2012. Cigarettes were purchased and shipped to Roswell Park Cancer Institute, where 91 pairs of packs were selected for physical cigarette design characteristic testing and recording of TNCO values. Data analysis was conducted using SPSS, and was initially characterised using descriptive statistics, correlations and generalised estimating equations to observe changes in brand varieties over time. Reported TNCO values on packs saw mean tar, nicotine and CO levels decrease from 2009 to 2012 by 7.9%, 4.5% and 6.0%, respectively. Ventilation was the only cigarette design feature that significantly changed over time (p<0.001), with an increase of 31.7%. Significant predictors of tar and CO yield overall were ventilation and per-cigarette tobacco weight, while for nicotine tobacco moisture was also an independent predictor of yield. The use of ventilation to decrease TNCO emissions is misleading smokers to believe that they are smoking a 'light/low' tar cigarette that is healthier, and is potentially forestalling the quitting behaviours that would begin to reduce the health burden of tobacco in China, and so should be prohibited. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/
mirPub: a database for searching microRNA publications.

Science.gov (United States)

Vergoulis, Thanasis; Kanellos, Ilias; Kostoulas, Nikos; Georgakilas, Georgios; Sellis, Timos; Hatzigeorgiou, Artemis; Dalamagas, Theodore

2015-05-01

Identifying, amongst millions of publications available in MEDLINE, those that are relevant to specific microRNAs (miRNAs) of interest based on keyword search faces major obstacles. References to miRNA names in the literature often deviate from standard nomenclature for various reasons, since even the official nomenclature evolves. For instance, a single miRNA name may identify two completely different molecules or two different names may refer to the same molecule. mirPub is a database with a powerful and intuitive interface, which facilitates searching for miRNA literature, addressing the aforementioned issues. To provide effective search services, mirPub applies text mining techniques on MEDLINE, integrates data from several curated databases and exploits data from its user community following a crowdsourcing approach. Other key features include an interactive visualization service that illustrates intuitively the evolution of miRNA data, tag clouds summarizing the relevance of publications to particular diseases, cell types or tissues and access to TarBase 6.0 data to oversee genes related to miRNA publications. mirPub is freely available at http://www.microrna.gr/mirpub/. vergoulis@imis.athena-innovation.gr or dalamag@imis.athena-innovation.gr Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.
Role of immune activation in CD4+ T-cell depletion in HIV-1 infected Indian patients.

Science.gov (United States)

Vajpayee, M; Kaushik, S; Sreenivas, V; Mojumdar, K; Mendiratta, S; Chauhan, N K

2009-01-01

The correlation of immune activation with CD4(+) depletion and HIV-1 disease progression has been evidenced by several studies involving mainly clade B virus. However, this needs to be investigated in developing countries such as India predominately infected with clade C virus. In a cross-sectional study of 68 antiretroviral treatment naïve, HIV-1 infected Indian patients, we studied the association between CD4(+) T cells, plasma HIV-1 RNA levels, and immune activation markers using unadjusted and adjusted correlative analyses. Significant negative correlations of higher magnitude were observed between the CD4(+) T cell percentages and plasma HIV-1 RNA levels in the study population when adjusted for the effects of immune activation markers. However, the negative association of CD4(+) T cells with immune activation markers remained unaffected when controlled for the effects of plasma HIV-1 RNA levels. Our results support the important role of immune activation in CD4(+) T cell depletion and disease progression during untreated HIV-1 infection.
Perversities of Extreme Dependence and Unequal Growth in the TAR

NARCIS (Netherlands)

A.M. Fischer (Andrew Martín)

2007-01-01

textabstractThe official Chinese press recently came out with a series of articles reporting the latest statistics on the phenomenally rapid economic growth that has been taking place in the Tibet Autonomous Region (TAR) since the mid-1990s through sheer force of Central Government subsidies.
PAHs underfoot: Contaminated dust from coal-tar sealcoated pavement is widespread in the United States

Science.gov (United States)

Van Metre, P.C.; Mahler, B.J.; Wilson, J.T.

2009-01-01

We reported in 2005 that runoff from parking lots treated with coal-tar-based sealcoat was a major source of polycyclic aromatic hydrocarbons (PAHs) to streams in Austin, Texas. Here we present new data from nine U. S. cities that show nationwide patterns in concentrations of PAHs associated with sealcoat Dust was swept from parking lots in six cities in the central and eastern U. S., where coal-tar-based sealcoat dominates use, and three cities in the western U. S., where asphalt-based sealcoat dominates use. For six central and eastern cities, median ?? PAH concentrations in dust from sealcoated and unsealcoated pavement are 2200 and 27 mg/kg, respectively. For three western cities, median ?? PAH concentrations in dust from sealcoated and unsealcoated pavement are similar and very low (2. 1 and 0. 8 mg/kg, respectively). Lakes in the central and eastern cities where pavement was sampled have bottom sediments with higher PAH concentrations than do those in the western cities relative to degree of urbanization. Bottom-sediment PAH assemblages are similar to those of sealcoated pavement dust regionally, implicating coal-tar-based sealcoat as a PAH source to the central and eastern lakes. Concentrations of benzo[a]pyrene in dust from coal-tar sealcoated pavement and adjacent soils greatly exceed generic soil screening levels, suggesting that research on human-health risk is warranted.
Quality control assessment of human immunodeficiency virus type 2 (HIV-2) viral load quantification assays: results from an international collaboration on HIV-2 infection in 2006

NARCIS (Netherlands)

Damond, Florence; Benard, Antoine; Ruelle, Jean; Alabi, Abraham; Kupfer, Bernd; Gomes, Perpetua; Rodes, Berta; Albert, Jan; Böni, Jürg; Garson, Jeremy; Ferns, Bridget; Matheron, Sophie; Chene, Geneviève; Brun-Vezinet, Françoise; Goubau, Patrick; Campa, Pauline; Descamps, Diane; Simon, François; Taieb, Audrey; Autran, Brigitte; Cotten, Matt; Jaye, Assan; Peterson, Kevin; Rowland-Jones, Sarah; Rockstroh, Jürgen; Schwarze-Zander, Carolynne; de Wolf, Frank; van Sighem, Ard; Reiss, Peter; van der Loeff, Maarten Schim; Schutten, Martin; Camacho, Ricardo; Mansinho, Kamal; Antunes, Francisco; Luis, Franca; Valadas, Emilia; Toro, Carlos; Soriano, Vicente; Gyllensten, Katarina; Sonnerborg, Anders; Yilmaz, Aylin; Gisslén, Magnus; Calmy, Alexandra; Rickenbach, Martin; Pillay, Deenan; Tosswill, Jennifer; Anderson, Jane; Chadwick, David

2008-01-01

Human immunodeficiency virus type 2 (HIV-2) RNA quantification assays used in nine laboratories of the ACHI(E)V(2E) (A Collaboration on HIV-2 Infection) study group were evaluated. In a blinded experimental design, laboratories quantified three series of aliquots of an HIV-2 subtype A strain, each
Geology and resources of the Tar Sand Triangle, southeastern Utah

Energy Technology Data Exchange (ETDEWEB)

Dana, G.F.; Oliver, R.L.; Elliott, J.R.

1984-05-01

The Tar Sand Triangle is located in southeastern Utah between the Dirty Devil and Colorado Rivers and covers an area of about 200 square miles. The geology of the area consists of gently northwest dipping strata exposed in the box canyons and slopes of the canyonlands morphology. Strata in the area range in age from Jurassic to Permian. The majority of tar sand saturation is found in the Permian White Rim Sandstone Member of the Cutler Formation. The White Rim Sandstone Member consists of a clean, well-sorted sandstone which was deposited in a shallow marine environment. Resources were calculated from analytical data from the three coreholes drilled by the Laramie Energy Technology Center and other available data. The total in-place resources, determined from this study, are 6.3 billion barels. Previous estimates ranged from 2.9 to 16 million barrels. More coring and analyses will be necessary before a more accurate determination of resources can be attempted. 8 references, 11 figures, 7 tables.
Prophylaxis and treatment of HIV-1 infection in pregnancy - Swedish Recommendations 2017.

Science.gov (United States)

Navér, Lars; Albert, Jan; Carlander, Christina; Flamholc, Leo; Gisslén, Magnus; Karlström, Olof; Svedhem-Johansson, Veronica; Sönnerborg, Anders; Westling, Katarina; Yilmaz, Aylin; Pettersson, Karin

2018-01-24

Prophylaxis and treatment with antiretroviral drugs have resulted in a very low rate of mother-to-child transmission (MTCT) of HIV during recent years. Registration of new antiretroviral drugs, modification of clinical praxis, updated general treatment guidelines and increasing knowledge about MTCT have necessitated regular revisions of the recommendations for 'Prophylaxis and treatment of HIV-1 infection in pregnancy'. The Swedish Reference Group for Antiviral Therapy (RAV) has updated the recommendations from 2013 at an expert meeting 19 September 2017. In the new text, current treatment guidelines for non-pregnant are considered. The most important revisions are that: (1) Caesarean section and infant prophylaxis with three drugs are recommended when maternal HIV RNA >150 copies/mL (previously >50 copies/mL). The treatment target of undetectable HIV RNA remains unchanged <50 copies/mL; (2) Obstetric management and mode of delivery at premature rupture of the membranes and rupture of the membranes at full term follow the same procedures as in HIV negative women; (3) Vaginal delivery is recommended to a well-treated woman with HIV RNA <150 copies/mL regardless of gestational age, if no obstetric contraindications are present; (4) Treatment during pregnancy should begin as soon as possible and should continue after delivery; (5) Ongoing well-functioning HIV treatment at pregnancy start should usually be retained; (6) Recommended drugs and drug combinations have been updated.

Potent inhibition of HIV-1 replication by a Tat mutant.

Directory of Open Access Journals (Sweden)

Luke W Meredith

Full Text Available Herein we describe a mutant of the two-exon HIV-1 Tat protein, termed Nullbasic, that potently inhibits multiple steps of the HIV-1 replication cycle. Nullbasic was created by replacing the entire arginine-rich basic domain of wild type Tat with glycine/alanine residues. Like similarly mutated one-exon Tat mutants, Nullbasic exhibited transdominant negative effects on Tat-dependent transactivation. However, unlike previously reported mutants, we discovered that Nullbasic also strongly suppressed the expression of unspliced and singly-spliced viral mRNA, an activity likely caused by redistribution and thus functional inhibition of HIV-1 Rev. Furthermore, HIV-1 virion particles produced by cells expressing Nullbasic had severely reduced infectivity, a defect attributable to a reduced ability of the virions to undergo reverse transcription. Combination of these inhibitory effects on transactivation, Rev-dependent mRNA transport and reverse transcription meant that permissive cells constitutively expressing Nullbasic were highly resistant to a spreading infection by HIV-1. Nullbasic and its activities thus provide potential insights into the development of potent antiviral therapeutics that target multiple stages of HIV-1 infection.
Differentially-Expressed Pseudogenes in HIV-1 Infection

Directory of Open Access Journals (Sweden)

Aditi Gupta

2015-09-01

Full Text Available Not all pseudogenes are transcriptionally silent as previously thought. Pseudogene transcripts, although not translated, contribute to the non-coding RNA pool of the cell that regulates the expression of other genes. Pseudogene transcripts can also directly compete with the parent gene transcripts for mRNA stability and other cell factors, modulating their expression levels. Tissue-specific and cancer-specific differential expression of these “functional” pseudogenes has been reported. To ascertain potential pseudogene:gene interactions in HIV-1 infection, we analyzed transcriptomes from infected and uninfected T-cells and found that 21 pseudogenes are differentially expressed in HIV-1 infection. This is interesting because parent genes of one-third of these differentially-expressed pseudogenes are implicated in HIV-1 life cycle, and parent genes of half of these pseudogenes are involved in different viral infections. Our bioinformatics analysis identifies candidate pseudogene:gene interactions that may be of significance in HIV-1 infection. Experimental validation of these interactions would establish that retroviruses exploit this newly-discovered layer of host gene expression regulation for their own benefit.
Differentially-Expressed Pseudogenes in HIV-1 Infection.

Science.gov (United States)

Gupta, Aditi; Brown, C Titus; Zheng, Yong-Hui; Adami, Christoph

2015-09-29

Not all pseudogenes are transcriptionally silent as previously thought. Pseudogene transcripts, although not translated, contribute to the non-coding RNA pool of the cell that regulates the expression of other genes. Pseudogene transcripts can also directly compete with the parent gene transcripts for mRNA stability and other cell factors, modulating their expression levels. Tissue-specific and cancer-specific differential expression of these "functional" pseudogenes has been reported. To ascertain potential pseudogene:gene interactions in HIV-1 infection, we analyzed transcriptomes from infected and uninfected T-cells and found that 21 pseudogenes are differentially expressed in HIV-1 infection. This is interesting because parent genes of one-third of these differentially-expressed pseudogenes are implicated in HIV-1 life cycle, and parent genes of half of these pseudogenes are involved in different viral infections. Our bioinformatics analysis identifies candidate pseudogene:gene interactions that may be of significance in HIV-1 infection. Experimental validation of these interactions would establish that retroviruses exploit this newly-discovered layer of host gene expression regulation for their own benefit.
PeaTAR1B: Characterization of a Second Type 1 Tyramine Receptor of the American Cockroach, Periplaneta americana.

Science.gov (United States)

Blenau, Wolfgang; Balfanz, Sabine; Baumann, Arnd

2017-10-30

The catecholamines norepinephrine and epinephrine regulate important physiological functions in vertebrates. In insects; these neuroactive substances are functionally replaced by the phenolamines octopamine and tyramine. Phenolamines activate specific guanine nucleotide-binding (G) protein-coupled receptors (GPCRs). Type 1 tyramine receptors are better activated by tyramine than by octopamine. In contrast; type 2 tyramine receptors are almost exclusively activated by tyramine. Functionally; activation of type 1 tyramine receptors leads to a decrease in the intracellular concentration of cAMP ([cAMP] i ) whereas type 2 tyramine receptors can mediate Ca 2+ signals or both Ca 2+ signals and effects on [cAMP] i . Here; we report that the American cockroach ( Periplaneta americana ) expresses a second type 1 tyramine receptor (PeaTAR1B) in addition to PeaTAR1A (previously called PeaTYR1). When heterologously expressed in flpTM cells; activation of PeaTAR1B by tyramine leads to a concentration-dependent decrease in [cAMP] i . Its activity can be blocked by a series of established antagonists. The functional characterization of two type 1 tyramine receptors from P. americana ; PeaTAR1A and PeaTAR1B; which respond to tyramine by changing cAMP levels; is a major step towards understanding the actions of tyramine in cockroach physiology and behavior; particularly in comparison to the effects of octopamine.
PeaTAR1B: Characterization of a Second Type 1 Tyramine Receptor of the American Cockroach, Periplaneta americana

Directory of Open Access Journals (Sweden)

Wolfgang Blenau

2017-10-01

Full Text Available The catecholamines norepinephrine and epinephrine regulate important physiological functions in vertebrates. In insects; these neuroactive substances are functionally replaced by the phenolamines octopamine and tyramine. Phenolamines activate specific guanine nucleotide-binding (G protein-coupled receptors (GPCRs. Type 1 tyramine receptors are better activated by tyramine than by octopamine. In contrast; type 2 tyramine receptors are almost exclusively activated by tyramine. Functionally; activation of type 1 tyramine receptors leads to a decrease in the intracellular concentration of cAMP ([cAMP]i whereas type 2 tyramine receptors can mediate Ca2+ signals or both Ca2+ signals and effects on [cAMP]i. Here; we report that the American cockroach (Periplaneta americana expresses a second type 1 tyramine receptor (PeaTAR1B in addition to PeaTAR1A (previously called PeaTYR1. When heterologously expressed in flpTM cells; activation of PeaTAR1B by tyramine leads to a concentration-dependent decrease in [cAMP]i. Its activity can be blocked by a series of established antagonists. The functional characterization of two type 1 tyramine receptors from P. americana; PeaTAR1A and PeaTAR1B; which respond to tyramine by changing cAMP levels; is a major step towards understanding the actions of tyramine in cockroach physiology and behavior; particularly in comparison to the effects of octopamine.
Wrapping up the bad news – HIV assembly and release

Directory of Open Access Journals (Sweden)

Meng Bo

2013-01-01

Full Text Available Abstract The late Nobel Laureate Sir Peter Medawar once memorably described viruses as ‘bad news wrapped in protein’. Virus assembly in HIV is a remarkably well coordinated process in which the virus achieves extracellular budding using primarily intracellular budding machinery and also the unusual phenomenon of export from the cell of an RNA. Recruitment of the ESCRT system by HIV is one of the best documented examples of the comprehensive way in which a virus hijacks a normal cellular process. This review is a summary of our current understanding of the budding process of HIV, from genomic RNA capture through budding and on to viral maturation, but centering on the proteins of the ESCRT pathway and highlighting some recent advances in our understanding of the cellular components involved and the complex interplay between the Gag protein and the genomic RNA.
Cost effectiveness of screening strategies for early identification of HIV and HCV infection in injection drug users.

Directory of Open Access Journals (Sweden)

Lauren E Cipriano

Full Text Available To estimate the cost, effectiveness, and cost effectiveness of HIV and HCV screening of injection drug users (IDUs in opioid replacement therapy (ORT.Dynamic compartmental model of HIV and HCV in a population of IDUs and non-IDUs for a representative U.S. urban center with 2.5 million adults (age 15-59.We considered strategies of screening individuals in ORT for HIV, HCV, or both infections by antibody or antibody and viral RNA testing. We evaluated one-time and repeat screening at intervals from annually to once every 3 months. We calculated the number of HIV and HCV infections, quality-adjusted life years (QALYs, costs, and incremental cost-effectiveness ratios (ICERs.Adding HIV and HCV viral RNA testing to antibody testing averts 14.8-30.3 HIV and 3.7-7.7 HCV infections in a screened population of 26,100 IDUs entering ORT over 20 years, depending on screening frequency. Screening for HIV antibodies every 6 months costs $30,700/QALY gained. Screening for HIV antibodies and viral RNA every 6 months has an ICER of $65,900/QALY gained. Strategies including HCV testing have ICERs exceeding $100,000/QALY gained unless awareness of HCV-infection status results in a substantial reduction in needle-sharing behavior.Although annual screening for antibodies to HIV and HCV is modestly cost effective compared to no screening, more frequent screening for HIV provides additional benefit at less cost. Screening individuals in ORT every 3-6 months for HIV infection using both antibody and viral RNA technologies and initiating ART for acute HIV infection appears cost effective.
Herpes simplex virus type 2 (HSV-2) genital shedding in HSV-2-/HIV-1-co-infected women receiving effective combination antiretroviral therapy.

Science.gov (United States)

Péré, Héléne; Rascanu, Aida; LeGoff, Jérome; Matta, Mathieu; Bois, Frédéric; Lortholary, Olivier; Leroy, Valériane; Launay, Odile; Bélec, Laurent

2016-03-01

The dynamics of genital shedding of HSV-2 DNA was assessed in HIV-1-infected women taking combination antiretroviral therapy (cART). HIV-1 RNA, HIV-1 DNA and HSV DNA loads were measured during 12-18 months using frozen plasma, PBMC and cervicovaginal lavage samples from 22 HIV-1-infected women, including 17 women naive for antiretroviral therapy initiating cART and 5 women with virological failure switching to a new regimen. Nineteen (86%) women were HSV-2-seropositive. Among HSV-2-/HIV-1-co-infected women, HIV-1 RNA loads showed a rapid fall from baseline after one month of cART, in parallel in paired plasma and cervicovaginal secretions. In contrast, HIV-1 DNA loads did not show significant variations from baseline up to 18 months of treatment in both systemic and genital compartments. HSV DNA was detected at least once in 12 (63%) of 19 women during follow up: HSV-2 shedding in the genital compartment was observed in 11% of cervicovaginal samples at baseline and in 16% after initiating or switching cART. Cervicovaginal HIV-1 RNA loads were strongly associated with plasma HIV-1 RNA loads over time, but not with cervicovaginal HSV DNA loads. Reactivation of genital HSV-2 replication frequently occurred despite effective cART in HSV-2-/HIV-1-co-infected women. Genital HSV-2 replication under cART does not influence cervicovaginal HIV-1 RNA or DNA shedding. © The Author(s) 2015.
HIV-infected individuals with the CCR delta32/CCR5 genotype have lower HIV RNA levels and higher CD4 cell counts in the early years of the infection than do patients with the wild type. Copenhagen AIDS Cohort Study Group

DEFF Research Database (Denmark)

Katzenstein, T L; Eugen-Olsen, J; Hofmann, B

1997-01-01

The relations among serum HIV RNA levels, CD4 cell counts, presence of the mutant CCR5-allele in heterozygous form, and clinical outcome was analyzed in 96 patients from the Copenhagen AIDS Cohort. In the early years of the infection, patients with the CCR5 delta32/CCR5 genotype had significantly...
Calcipotriol versus coal tar: a prospective randomized study in stable plaque psoriasis

Energy Technology Data Exchange (ETDEWEB)

Sharma, V.; Kaur, I.; Kumar, B. [Postgraduate Institute of Medicinal Education & Research, Chandigarh (India)

2003-10-01

Topical therapies are the first line of treatment for patients with stable plaque psoriasis (SPP) affecting a limited body surface area. Very few trials comparing newer agents, such as 0.005% topical calcipotriol, with conventional modes of therapy, such as coal tar ointment, have been reported. A prospective, right-left randomized, investigator-blinded study with a 12-week treatment period and an 8-week follow-up period was performed. It was found that 0.005% calcipotriol ointment produced a faster initial response and had better cosmetic acceptability in patients, although after a long period of treatment, i.e. 12 weeks, 5% coal tar ointment had comparable efficacy. There was no statistically significant difference in the relapse rates between the two modalities.
p24 as a predictor of mortality in a cohort of HIV-1-infected adults in rural Africa

DEFF Research Database (Denmark)

Erikstrup, C.; Kallestrup, P.; Zinyama-Gutsire, R.B.

2008-01-01

in a cohort of HIV-1-infected individuals in Zimbabwe. METHODS: Treatment-naive HIV-1-infected individuals (n=198) from the Mupfure Schistosomiasis and HIV Cohort were followed until death or censoring (3-4.3 years). At baseline, p24, HIV-RNA, CD4 cell counts, and clinical staging (Centers for Disease Control...... and Prevention classification) were assessed. RESULTS: p24 correlated with HIV-RNA (PDisease Control and Prevention category (P... regression. p24 predicted mortality in univariate Cox analysis (Pstudy to evaluate the prognostic strength of p24 in an area with a predominance of HIV subtype C infections. p24 correlated...
Heating tar sands formations to visbreaking temperatures

Science.gov (United States)

Karanikas, John Michael [Houston, TX; Colmenares, Tulio Rafael [Houston, TX; Zhang, Etuan [Houston, TX; Marino, Marian [Houston, TX; Roes, Augustinus Wilhelmus Maria [Houston, TX; Ryan, Robert Charles [Houston, TX; Beer, Gary Lee [Houston, TX; Dombrowski, Robert James [Houston, TX; Jaiswal, Namit [Houston, TX

2009-12-22

Methods for treating a tar sands formation are described herein. Methods may include heating at least a section of a hydrocarbon layer in the formation from a plurality of heaters located in the formation. The heat may be controlled so that at least a majority of the section reaches an average temperature of between 200.degree. C. and 240.degree. C., which results in visbreaking of at least some hydrocarbons in the section. At least some visbroken hydrocarbon fluids may be produced from the formation.
Functional Equivalence of Retroviral MA Domains in Facilitating Psi RNA Binding Specificity by Gag

Directory of Open Access Journals (Sweden)

Tiffiny Rye-McCurdy

2016-09-01

Full Text Available Retroviruses specifically package full-length, dimeric genomic RNA (gRNA even in the presence of a vast excess of cellular RNA. The “psi” (Ψ element within the 5′-untranslated region (5′UTR of gRNA is critical for packaging through interaction with the nucleocapsid (NC domain of Gag. However, in vitro Gag binding affinity for Ψ versus non-Ψ RNAs is not significantly different. Previous salt-titration binding assays revealed that human immunodeficiency virus type 1 (HIV-1 Gag bound to Ψ RNA with high specificity and relatively few charge interactions, whereas binding to non-Ψ RNA was less specific and involved more electrostatic interactions. The NC domain was critical for specific Ψ binding, but surprisingly, a Gag mutant lacking the matrix (MA domain was less effective at discriminating Ψ from non-Ψ RNA. We now find that Rous sarcoma virus (RSV Gag also effectively discriminates RSV Ψ from non-Ψ RNA in a MA-dependent manner. Interestingly, Gag chimeras, wherein the HIV-1 and RSV MA domains were swapped, maintained high binding specificity to cognate Ψ RNAs. Using Ψ RNA mutant constructs, determinants responsible for promoting high Gag binding specificity were identified in both systems. Taken together, these studies reveal the functional equivalence of HIV-1 and RSV MA domains in facilitating Ψ RNA selectivity by Gag, as well as Ψ elements that promote this selectivity.
Hepatitis C virus infection in HIV-infected patients.

Science.gov (United States)

Sulkowski, Mark S

2007-10-01

The hepatitis C virus (HCV) is a spherical enveloped RNA virus of the Flaviviridae family, classified within the Hepacivirus genus. Since its discovery in 1989, HCV has been recognized as a major cause of chronic hepatitis and hepatic fibrosis that progresses in some patients to cirrhosis and hepatocellular carcinoma. In the United States, approximately 4 million people have been infected with HCV, and 10,000 HCVrelated deaths occur each year. Due to shared routes of transmission, HCV and HIV co-infection are common, affecting approximately one third of all HIV-infected persons in the United States. In addition, HIV co-infection is associated with higher HCV RNA viral load and a more rapid progression of HCV-related liver disease, leading to an increased risk of cirrhosis. HCV infection may also impact the course and management of HIV disease, particularly by increasing the risk of antiretroviral drug-induced hepatotoxicity. Thus, chronic HCV infection acts as an opportunistic disease in HIV-infected persons because the incidence of infection is increased and the natural history of HCV infection is accelerated in co-infected persons. Strategies to prevent primary HCV infection and to modify the progression of HCV-related liver disease are urgently needed among HIV/HCV co-infected individuals.
Viruses & kidney disease: beyond HIV

Science.gov (United States)

Waldman, Meryl; Marshall, Vickie; Whitby, Denise; Kopp, Jeffrey B.

2008-01-01

HIV-infected patients may acquire new viral co-infections; they may also experience the reactivation or worsening of existing viral infections, including active, smoldering, or latent infections. HIV-infected patients may be predisposed to these viral infections due to immunodeficiency or to risk factors common to HIV and other viruses. A number of these affect the kidney, either by direct infection or by deposition of immune complexes. In this review we discuss the renal manifestations and treatment of hepatitis C virus, BK virus, adenovirus, cytomegalovirus, and parvovirus B19 in patients with HIV disease. We also discuss an approach to the identification of new viral renal pathogens, using a viral gene chip to identify viral DNA or RNA. PMID:19013331
HIV and schistosomiasis in rural Zimbabwe

DEFF Research Database (Denmark)

Kotzé, Sebastian Ranzi; Zinyama-Gutsire, Rutendo; Kallestrup, Per

2015-01-01

BACKGROUND: Vitamin A has widespread effects on immune function and is therefore interesting in HIV-infection. Retinol-binding protein (RBP or RBP4) is a negative acute-phase protein and a marker of vitamin A status. Our aim was to investigate the association of RBP with HIV progression, infection...... with schistosomiasis, inflammatory cytokines, and mortality. METHODS: The study included 192 HIV-infected and 177 HIV-uninfected individuals from Mupfure in rural Zimbabwe. Of these, 208 were infected with Schistosoma haematobium, 27 with S. mansoni and 48 with both. Plasma RBP, HIV-RNA, CD4 cell count, haemoglobin......, cytokines, clinical staging (CDC category), self-reported level of function (Karnoffsky Performance Score, KPS) and schistosomiasis status were assessed at baseline. Participants were followed up for survival 3-4 years post-enrolment. RESULTS: RBP levels were lower in HIV-infected individuals(p
Proteomic analysis of PBMCs: characterization of potential HIV-associated proteins

Directory of Open Access Journals (Sweden)

Yin Lin

2010-03-01

Full Text Available Abstract Background The human immunodeficiency virus type 1 (HIV-1 pandemic has continued unabated for nearly 30 years. To better understand the influence of virus on host cells, we performed the differential proteome research of peripheral blood mononuclear cells (PBMCs from HIV-positive patients and healthy controls. Results 26 protein spots with more than 1.5-fold difference were detected in two dimensional electrophoresis (2DE gels. 12 unique up-regulated and one down-regulated proteins were identified in HIV-positive patients compared with healthy donors. The mRNA expression of 10 genes was analyzed by real time RT-PCR. It shows that the mRNA expression of talin-1, vinculin and coronin-1C were up-regulated in HIV positive patients and consistent with protein expression. Western blotting analysis confirmed the induction of fragments of vinculin, talin-1 and filamin-A in pooled and most part of individual HIV-positive clinical samples. Bioinformatic analysis showed that a wide host protein network was disrupted in HIV-positive patients. Conclusions Together, this work provided useful information to facilitate further investigation of the underlying mechanism of HIV and host cell protein interactions, and discovered novel potential biomarkers such as fragment of vinculin, filamin-A and talin-1 for anti-HIV research.
Herpes viruses and HIV-1 drug resistance mutations influence the virologic and immunologic milieu of the male genital tract.

Science.gov (United States)

Gianella, Sara; Morris, Sheldon R; Anderson, Christy; Spina, Celsa A; Vargas, Milenka V; Young, Jason A; Richman, Douglas D; Little, Susan J; Smith, Davey M

2013-01-02

To further understand the role that chronic viral infections of the male genital tract play on HIV-1 dynamics and replication. Retrospective, observational study including 236 paired semen and blood samples collected from 115 recently HIV-1 infected antiretroviral naive men who have sex with men. In this study, we evaluated the association of seminal HIV-1 shedding to coinfections with seven herpes viruses, blood plasma HIV-1 RNA levels, CD4 T-cell counts, presence of transmitted drug resistance mutations (DRMs) in HIV-1 pol, participants' age and stage of HIV-infection using multivariate generalized estimating equation methods. Associations between herpes virus shedding, seminal HIV-1 levels, number and immune activation of seminal T-cells was also investigated (Mann-Whitney). Seminal herpes virus shedding was observed in 75.7% of individuals. Blood HIV-1 RNA levels (P herpes virus (HHV)-8 levels (P herpes viruses seminal shedding in our cohort. Shedding of CMV, EBV and HHV-8 and absence of DRM were associated with increased frequency of HIV-1 shedding and/or higher levels of HIV-1 RNA in semen, which are likely important cofactors for HIV-1 transmission.
Use of advanced chemical fingerprinting in PAH source identification and allocation at a coal tar processing site

International Nuclear Information System (INIS)

Brown, J.S.; Boehm, P.D.; Douglas, G.S.

1995-01-01

Advanced chemical fingerprinting analyses were used to determine source allocation at a former coal tar processing facility which had been converted to a petroleum recycling site. Soil samples from the site had high petroleum hydrocarbon concentrations and elevated levels of polynuclear aromatic hydrocarbons (PAH). Comparisons of PAH distributions were used to differentiate the coal tar hydrocarbons from the petroleum hydrocarbons in soil samples. A more specific technique was needed to accurately allocate the contribution of the two sources to the observed PAH contamination in the soil. Petroleum biomarkers (steranes and triterpanes) which are present in crude oils and many refined petroleum products but are absent in coal tar were used to quantitatively allocate the source of the PAH contamination based on the relative ratio of the PAH to the biomarkers in soil samples. Using the resulting coal tar/petroleum source ratio the contribution of petroleum to the overall PAH contamination at the site was calculated. A multivariate statistical technique (principal component analysis or PCA) was used to provide an independent validation of the source allocation. The results of the source allocation provided a foundation for the site clean-up and remediation costs
Sexual Activity Without Condoms and Risk of HIV Transmission in Serodifferent Couples When the HIV-Positive Partner Is Using Suppressive Antiretroviral Therapy

DEFF Research Database (Denmark)

Rodger, Alison J; Cambiano, Valentina; Bruun, Tina

2016-01-01

IMPORTANCE: A key factor in assessing the effectiveness and cost-effectiveness of antiretroviral therapy (ART) as a prevention strategy is the absolute risk of HIV transmission through condomless sex with suppressed HIV-1 RNA viral load for both anal and vaginal sex. OBJECTIVE: To evaluate the ra...

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