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Sample records for one-step pcr sequencing

  1. [One-step PCR sequencing]. Final report, July 1, 1994--August 31, 1997

    Energy Technology Data Exchange (ETDEWEB)

    Shaw, B.R.

    1997-12-31

    The author explored the use of a novel class of boronated nucleic acids, the boranophosphates, as an alternative, but complementary method to dideoxysequencing. Boranophosphates can be used to directly amplify and sequence single- or double-stranded DNA. Fragments are derived not from truncations during polymerase synthesis, but from insertion and digestion back to a boronated marker or delimiter that was incorporated during exponential amplification. The method, which the author calls Boronated One-Step PCR Sequencing, is unique in that it employs a new class of {alpha}-P-boronated 2{prime}-deoxynucleoside 5{prime}-triphosphates first synthesized in the laboratory. These boronated triphosphates exhibit useful properties: (a) they are heat stable, (b) they can be base-specifically incorporated into DNA during the polymerase chain reaction, and (c) once incorporated, the boranophosphate nucleotide (marker) blocks the action of exonuclease. Thus, the positions of the stably-incorporated boronated markers can be revealed by a simple exonuclease digestion, producing a series of fragments--each of which is terminated base-specifically at the boronated markers--and thereby defining the sequence of the PCR product.

  2. One-Step PCR Sequencing. Final Technical Progress Report for February 15, 1997 - November 30, 2001

    Energy Technology Data Exchange (ETDEWEB)

    Shaw, B. R.

    2004-04-16

    We investigated new chemistries and alternate approaches for direct gene sequencing and detection based on the properties of boron-substituted nucleotides as chain delimiters in lieu of conventional chain terminators. Chain terminators, such as the widely used Sanger dideoxynucleotide truncators, stop DNA synthesis during replication and hence are incompatible with further PCR amplification. Chain delimiters, on the other hand, are chemically-modified, ''stealth'' nucleotides that act like normal nucleotides in DNA synthesis and PCR amplification, but can be unmasked following chain extension and exponential amplification. Specifically, chain delimiters give rise to an alternative sequencing strategy based on selective degradation of DNA chains generated by PCR amplification with modified nucleotides. The method as originally devised employed template-directed enzymatic, random incorporation of small amounts of boron-modified nucleotides (e.g., 2'-deoxynucleoside 5'-alpha-[P-borano]- triphosphates) during PCR amplification. Rather than incorporation of dideoxy chain terminators, which are less efficiently incorporated in PCR-based amplification than natural deoxynucleotides, our method is based on selective incorporation and exonuclease degradation of DNA chains generated by efficient PCR amplification of chemically-modified ''stealth'' nucleotides. The stealth nucleotides have a boranophosphate group instead of a normal phosphate, yet behave like normal nucleotides during PCR-amplification. The unique feature of our method is that the position of the stealth nucleotide, and hence DNA sequencing fragments, are revealed at the desired, appropriate moment following PCR amplification. During the current grant period, a variety of new boron-modified nucleotides were synthesized, and new chemistries and enzymatic methods and combinations thereof were explored to improve the method and study the effects of borane modified

  3. Aspergillus PCR: one step closer to standardization.

    NARCIS (Netherlands)

    White, P.L.; Bretagne, S.; Klingspor, L.; Melchers, W.J.G.; McCulloch, E.; Schulz, B.; Finnstrom, N.; Mengoli, C.; Barnes, R.A.; Donnelly, J.P.; Loeffler, J.

    2010-01-01

    PCR has been used as an aid in the diagnosis of invasive aspergillosis for almost 2 decades. A lack of standardization has limited both its acceptance as a diagnostic tool and multicenter clinical evaluations, preventing its inclusion in disease-defining criteria. In 2006, the European Aspergillus

  4. Aspergillus PCR: one step closer to standardization.

    NARCIS (Netherlands)

    White, P.L.; Bretagne, S.; Klingspor, L.; Melchers, W.J.G.; McCulloch, E.; Schulz, B.; Finnstrom, N.; Mengoli, C.; Barnes, R.A.; Donnelly, J.P.; Loeffler, J.

    2010-01-01

    PCR has been used as an aid in the diagnosis of invasive aspergillosis for almost 2 decades. A lack of standardization has limited both its acceptance as a diagnostic tool and multicenter clinical evaluations, preventing its inclusion in disease-defining criteria. In 2006, the European Aspergillus P

  5. One-step generation of error-prone PCR libraries using Gateway® technology

    Directory of Open Access Journals (Sweden)

    Gruet Antoine

    2012-01-01

    Full Text Available Abstract Background Error-prone PCR (epPCR libraries are one of the tools used in directed evolution. The Gateway® technology allows constructing epPCR libraries virtually devoid of any background (i.e., of insert-free plasmid, but requires two steps: the BP and the LR reactions and the associated E. coli cell transformations and plasmid purifications. Results We describe a method for making epPCR libraries in Gateway® plasmids using an LR reaction without intermediate BP reaction. We also describe a BP-free and LR-free sub-cloning method for in-frame transferring the coding sequence of selected clones from the plasmid used to screen the library to another one devoid of tag used for screening (such as the green fluorescent protein. We report preliminary results of a directed evolution program using this method. Conclusions The one-step method enables producing epPCR libraries of as high complexity and quality as does the regular, two-step, protocol for half the amount of work. In addition, it contributes to preserve the original complexity of the epPCR product.

  6. Selective control of primer usage in multiplex one-step reverse transcription PCR

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    Paul Natasha

    2009-12-01

    Full Text Available Abstract Background Multiplex RT-PCR is a valuable technique used for pathogen identification, disease detection and relative quantification of gene expression. The simplification of this protocol into a one-step procedure saves time and reagents. However, intensive PCR optimization is often required to overcome competing undesired PCR primer extension during the RT step. Results Herein, we report multiplex one-step RT-PCR experiments in which the PCR primers contain thermolabile phosphotriester modification groups. The presence of these groups minimizes PCR primer extension during the RT step and allows for control of PCR primer extension until the more stringent, elevated temperatures of PCR are reached. Results reveal that the use of primers whose extension can be controlled in a temperature-mediated way provides improved one-step RT-PCR specificity in both singleplex and multiplex reaction formats. Conclusions The need for an accurate and sensitive technique to quantify mRNA expression levels makes the described modified primer technology a promising tool for use in multiplex one-step RT-PCR. A more accurate representation of the abundances in initial template sample is feasible with modified primers, as artifacts of biased PCR are reduced because of greater improvements in reaction specificity.

  7. Canine distemper virus detection by different methods of One-Step RT-qPCR

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    Claudia de Camargo Tozato

    2016-01-01

    Full Text Available ABSTRACT: Three commercial kits of One-Step RT-qPCR were evaluated for the molecular diagnosis of Canine Distemper Virus. Using the kit that showed better performance, two systems of Real-time RT-PCR (RT-qPCR assays were tested and compared for analytical sensitivity to Canine Distemper Virus RNA detection: a One-Step RT-qPCR (system A and a One-Step RT-qPCR combined with NESTED-qPCR (system B. Limits of detection for both systems were determined using a serial dilution of Canine Distemper Virus synthetic RNA or a positive urine sample. In addition, the same urine sample was tested using samples with prior centrifugation or ultracentrifugation. Commercial kits of One-Step RT-qPCR assays detected canine distemper virus RNA in 10 (100% urine samples from symptomatic animals tested. The One-Step RT-qPCR kit that showed better results was used to evaluate the analytical sensitivity of the A and B systems. Limit of detection using synthetic RNA for the system A was 11 RNA copies µL-1 and 110 RNA copies µl-1 for first round System B. The second round of the NESTED-qPCR for System B had a limit of detection of 11 copies µl-1. Relationship between Ct values and RNA concentration was linear. The RNA extracted from the urine dilutions was detected in dilutions of 10-3 and10-2 by System A and B respectively. Urine centrifugation increased the analytical sensitivity of the test and proved to be useful for routine diagnostics. The One-Step RT-qPCR is a fast, sensitive and specific method for canine distemper routine diagnosis and research projects that require sensitive and quantitative methodology.

  8. Development of a One-Step Multiplex PCR Assay for Differential Detection of Major Mycobacterium Species.

    Science.gov (United States)

    Chae, Hansong; Han, Seung Jung; Kim, Su-Young; Ki, Chang-Seok; Huh, Hee Jae; Yong, Dongeun; Koh, Won-Jung; Shin, Sung Jae

    2017-09-01

    The prevalence of tuberculosis continues to be high, and nontuberculous mycobacterial (NTM) infection has also emerged worldwide. Moreover, differential and accurate identification of mycobacteria to the species or subspecies level is an unmet clinical need. Here, we developed a one-step multiplex PCR assay using whole-genome analysis and bioinformatics to identify novel molecular targets. The aims of this assay were to (i) discriminate between the Mycobacterium tuberculosis complex (MTBC) and NTM using rv0577 or RD750, (ii) differentiate M. tuberculosis (M. tuberculosis) from MTBC using RD9, (iii) selectively identify the widespread M. tuberculosis Beijing genotype by targeting mtbk_20680, and (iv) simultaneously detect five clinically important NTM (M. avium, M. intracellulare, M. abscessus, M. massiliense, and M. kansasii) by targeting IS1311, DT1, mass_3210, and mkan_rs12360 An initial evaluation of the multiplex PCR assay using reference strains demonstrated 100% specificity for the targeted Mycobacterium species. Analytical sensitivity ranged from 1 to 10 pg for extracted DNA and was 10(3) and 10(4) CFU for pure cultures and nonhomogenized artificial sputum cultures, respectively, of the targeted species. The accuracy of the multiplex PCR assay was further evaluated using 55 reference strains and 94 mycobacterial clinical isolates. Spoligotyping, multilocus sequence analysis, and a commercial real-time PCR assay were employed as standard assays to evaluate the multiplex PCR assay with clinical M. tuberculosis and NTM isolates. The PCR assay displayed 100% identification agreement with the standard assays. Our multiplex PCR assay is a simple, convenient, and reliable technique for differential identification of MTBC, M. tuberculosis, M. tuberculosis Beijing genotype, and major NTM species. Copyright © 2017 American Society for Microbiology.

  9. Novel Rotavirus VP7 Typing Assay Using a One-Step Reverse Transcriptase PCR Protocol and Product Sequencing and Utility of the Assay for Epidemiological Studies and Strain Characterization, Including Serotype Subgroup Analysis

    Science.gov (United States)

    DiStefano, Daniel J.; Kraiouchkine, Nikolai; Mallette, Laura; Maliga, Marianne; Kulnis, Gregory; Keller, Paul M.; Clark, H. Fred; Shaw, Alan R.

    2005-01-01

    Rotavirus is the most common cause of severe dehydrating gastroenteritis in infants. To date, 10 different serotypes of rotavirus have been identified in human stools. While four or five serotypes dominate, serotype circulation varies with season and geography. Since our laboratory has been involved in the development of a multivalent rotavirus vaccine, it is important to identify the serotypes of rotavirus encountered during our clinical trials. We have developed methodologies for the molecular identification of rotavirus strains based on VP7 gene segment sequence. A 365-bp reverse transcriptase PCR product was generated from the VP7 gene segment using a pair of novel degenerate primers. All serotypes tested (both animal and human) yielded an identically sized product after amplification. Sequencing of these products is performed using truncated versions of the original primers. The sequence generated is compared against a database of rotavirus VP7 sequences, with the G type determined, based on the sequence homology. Using this assay, we have correctly identified human VP7 strains from a panel of available serotypes, as well as numerous animal strains. The assay was qualified using rotavirus positive stool samples, negative stool samples, and rotavirus-spiked stool samples. In addition, samples from cases of acute gastroenteritis collected at Children's Hospital of Philadelphia have been evaluated and indicate that the assay is able to discriminate subtle differences within serotypes. The assay has been utilized in the testing of >3,000 antigen-positive (enzyme immunoassay) samples collected during clinical trials of a rotavirus vaccine (RotaTeq) and identified a serotype in ∼92% of samples (3, 17, 19). PMID:16333070

  10. Detection of Zika virus by SYBR green one-step real-time RT-PCR.

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    Xu, Ming-Yue; Liu, Si-Qing; Deng, Cheng-Lin; Zhang, Qiu-Yan; Zhang, Bo

    2016-10-01

    The ongoing Zika virus (ZIKV) outbreak has rapidly spread to new areas of Americas, which were the first transmissions outside its traditional endemic areas in Africa and Asia. Due to the link with newborn defects and neurological disorder, numerous infected cases throughout the world and various mosquito vectors, the virus has been considered to be an international public health emergency. In the present study, we developed a SYBR Green based one-step real-time RT-PCR assay for rapid detection of ZIKV. Our results revealed that the real-time assay is highly specific and sensitive in detection of ZIKV in cell samples. Importantly, the replication of ZIKV at different time points in infected cells could be rapidly monitored by the real-time RT-PCR assay. Specifically, the real-time RT-PCR showed acceptable performance in measurement of infectious ZIKV RNA. This assay could detect ZIKV at a titer as low as 1PFU/mL. The real-time RT-PCR assay could be a useful tool for further virology surveillance and diagnosis of ZIKV.

  11. Development and evaluation of a real-time one step Reverse-Transcriptase PCR for quantitation of Chandipura Virus

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    Tandale Babasaheb V

    2008-12-01

    Full Text Available Abstract Background Chandipura virus (CHPV, a member of family Rhabdoviridae was attributed to an explosive outbreak of acute encephalitis in children in Andhra Pradesh, India in 2003 and a small outbreak among tribal children from Gujarat, Western India in 2004. The case-fatality rate ranged from 55–75%. Considering the rapid progression of the disease and high mortality, a highly sensitive method for quantifying CHPV RNA by real-time one step reverse transcriptase PCR (real-time one step RT-PCR using TaqMan technology was developed for rapid diagnosis. Methods Primers and probe for P gene were designed and used to standardize real-time one step RT-PCR assay for CHPV RNA quantitation. Standard RNA was prepared by PCR amplification, TA cloning and run off transcription. The optimized real-time one step RT-PCR assay was compared with the diagnostic nested RT-PCR and different virus isolation systems [in vivo (mice in ovo (eggs, in vitro (Vero E6, PS, RD and Sand fly cell line] for the detection of CHPV. Sensitivity and specificity of real-time one step RT-PCR assay was evaluated with diagnostic nested RT-PCR, which is considered as a gold standard. Results Real-time one step RT-PCR was optimized using in vitro transcribed (IVT RNA. Standard curve showed linear relationship for wide range of 102-1010 (r2 = 0.99 with maximum Coefficient of variation (CV = 5.91% for IVT RNA. The newly developed real-time RT-PCR was at par with nested RT-PCR in sensitivity and superior to cell lines and other living systems (embryonated eggs and infant mice used for the isolation of the virus. Detection limit of real-time one step RT-PCR and nested RT-PCR was found to be 1.2 × 100 PFU/ml. RD cells, sand fly cells, infant mice, and embryonated eggs showed almost equal sensitivity (1.2 × 102 PFU/ml. Vero and PS cell-lines (1.2 × 103 PFU/ml were least sensitive to CHPV infection. Specificity of the assay was found to be 100% when RNA from other viruses or healthy

  12. A One-Step PCR-Based Assay to Evaluate the Efficiency and Precision of Genomic DNA-Editing Tools.

    Science.gov (United States)

    Germini, Diego; Bou Saada, Yara; Tsfasman, Tatiana; Osina, Kristina; Robin, Chloé; Lomov, Nikolay; Rubtsov, Mikhail; Sjakste, Nikolajs; Lipinski, Mar; Vassetzky, Yegor

    2017-06-16

    Despite rapid progress, many problems and limitations persist and limit the applicability of gene-editing techniques. Making use of meganucleases, TALENs, or CRISPR/Cas9-based tools requires an initial step of pre-screening to determine the efficiency and specificity of the designed tools. This step remains time consuming and material consuming. Here we propose a simple, cheap, reliable, time-saving, and highly sensitive method to evaluate a given gene-editing tool based on its capacity to induce chromosomal translocations when combined with a reference engineered nuclease. In the proposed technique, designated engineered nuclease-induced translocations (ENIT), a plasmid coding for the DNA-editing tool to be tested is co-transfected into carefully chosen target cells along with that for an engineered nuclease of known specificity and efficiency. If the new enzyme efficiently cuts within the desired region, then specific chromosomal translocations will be generated between the two targeted genomic regions and be readily detectable by a one-step PCR or qPCR assay. The PCR product thus obtained can be directly sequenced, thereby determining the exact position of the double-strand breaks induced by the gene-editing tools. As a proof of concept, ENIT was successfully tested in different cell types and with different meganucleases, TALENs, and CRISPR/Cas9-based editing tools.

  13. One-Step Multiplex PCR Assay for Differentiating Proposed New Species "Clostridium neonatale" from Closely Related Species.

    Science.gov (United States)

    Ferraris, Laurent; Schönherr, Sophia; Bouvet, Philippe; Dauphin, Brunhilde; Popoff, Michel; Butel, Marie Jose; Aires, Julio

    2015-11-01

    "Clostridium neonatale" sp. nov., previously involved in an outbreak of neonatal necrotizing enterocolitis, was recently proposed as a new species of the Clostridium genus sensu stricto. We developed a one-step multiplex colony PCR for C. neonatale identification and investigated C. neonatale intestinal colonization frequency in healthy preterm neonates. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  14. OPTIMAL DISTRIBUTED FUSION ALGORITHM WITH ONE-STEP OUT-OF-SEQUENCE ESTIMATES

    Institute of Scientific and Technical Information of China (English)

    Ge Quanbo; Wen Chenglin

    2008-01-01

    The transmission modes of multi-hop and broadcasting for Wireless Sensor Networks (WSN) often make random and unknown transmission delays appear, so multisensor data fusion based on delayed systems attracts intense attention from lots of researchers. The existing achievements for the delayed fusion all focus on Out-Of-Sequence Measurements (OOSM) problem which has many dis- advantages such as high communication cost, low computational efficiency, huge computational com- plexity and storage requirement, bad real-time performance and so on. In order to overcome these problems occurred in the OOSM fusion, the Out-Of-Sequence Estimates (OOSE) are considered to solve the delayed fusion for the first time. Different from OOSM which belongs to the centralized fusion, the OOSE scheme transmits local estimates from local sensors to the central processor and is thus the distributed fusion; thereby, the OOSE fusion can not only avoid the problems suffered in the OOSM fusion but also make the design of fusion algorithm highly simple and easy. Accordingly, a novel optimal linear recursive prediction weighted fusion method is proposed for one-step OOSE problem in this letter. As a tradeoff, its fusion accuracy is slightly lower than that of the OOSM method because the current OOSM fusion is a smooth estimate and OOSE gets a prediction estimate. But, the smooth result of the OOSE problem also has good fusion accuracy. Performance analysis and computer simulation show that the total performance of the proposed one-step OOSE fusion algorithm is better than the current one-step OOSM fusion in the practical tracking systems.

  15. Development and evaluation of novel one-step TaqMan realtime RT-PCR assays for the detection and direct genotyping of genogroup I and II noroviruses

    DEFF Research Database (Denmark)

    Schultz, Anna Charlotte; Vega, Everado; Dalsgaard, Anders;

    2011-01-01

    , polioviruses, and rotaviruses. L-RT-qPCR products were typed by sequencing. ResultsThe novel GI and GII L-RT-qPCR assays detected and typed all but one of the NoV positive panel samples. As few as 5–500 RNA copies could be accurately typed by sequencing of amplicons. ConclusionsWe developed novel one-step Taq......BackgroundCurrent detection and genotyping methods of genogroup (G) I and II noroviruses (NoVs) consist of a 2-step approach including detection of viral RNA by TaqMan realtime RT-PCR (RT-qPCR) followed by conventional RT-PCR and sequencing of partial regions of ORF1 or ORF2. ObjectiveTo develop...... novel long-template one-step TaqMan assays (L-RT-qPCR) for the rapid detection and direct genotyping of GI and GII NoVs and to evaluate the sensitivity and specificity of the assays. Study designGI and GII-specific broadly reactive L-RT-qPCR assays were developed by combining existing NoV primers...

  16. A One-Step PCR Method for Detecting the First Base of Splice Donor of Wx Intron 1 in Rice

    Institute of Scientific and Technical Information of China (English)

    MAO Xing-xue; LIU Yan-zhuo; XIAO Xin; CHEN Jian-wei; LUO Wen-yong; LI Xiao-fang

    2004-01-01

    A new method of one-step PGR was devised for detecting the first nucleotide in the splice donor site of Wx intron 1.compared to the regular PCR-Acc I method, the method can produce the same result for detecting +1 nucleotide of Wx intron 1.The reliability of the new method was confirmed with 30 rice varieties. The new technique is more convenient and cheaper than the regular PCR-Acc I method, and could be widely deploded in rice molecular marker assistant selection.

  17. One-Step RT-PCR protocols improve the rate of dengue diagnosis compared to Two-Step RT-PCR approaches.

    Science.gov (United States)

    De Paula, Sérgio Oliveira; de Melo Lima, Cristiane; Torres, Maria Paula; Pereira, Márcia Rodrigues Garbin; Lopes da Fonseca, Benedito Antônio

    2004-08-01

    Dengue is the most important arboviral disease transmitted to humans. In our laboratory, we have been working on the standardization of the polymerase chain reaction (PCR) diagnosis of this disease. In this work, we compared five commercial kits regularly used on reverse-transcription polymerase chain reaction (RT-PCR) protocols: two Two-Step kits (SuperScript II RT/Super Mix kit and reverse transcription system/Taq DNA polymerase) and three One-Step kits (ready-to-go RT-PCR Beads kit, QIAGEN One-Step RT-PCR kit, and AcessQuick RT-PCR system). Thirty-one serum samples of patients with clinical diagnosis of dengue fever (DF) were analyzed by RT-PCR and serology. RNA extraction was done with the QIAamp Viral RNA kit, and cDNA synthesis and PCR done according to the manufacturer's protocol for the five kits. Out of the 31 serum samples collected from patients suspected of having dengue, 27 were IgM-positive, confirming the dengue diagnosis. Out of those, 24 were positive by the ready-to-go RT-PCR Beads kit, 25 were positive by AcessQuick RT-PCR system and 27 were positive by QIAGEN One-Step RT-PCR kit. On the other hand, only six samples were positive by the SuperScript II RT/Super Mix kits and 10 were positive by reverse transcription system/Taq DNA polymerase kit. The best performance observed with the One-Step kits was confirmed in spiked samples with known quantities of dengue-1 virus since they detected up 1 x 10(2) PFU/ml, while the most sensitive Two-Step kit detected up 1 x 10(4) PFU/ml. These data show that One-Step RT-PCR kits yielded a higher rate of dengue virus detection than the Two-Step kits and correlated well with the serological diagnosis.

  18. A method for generating sticky-end PCR products which facilitates unidirectional cloning and the one-step assembly of complex DNA constructs.

    Science.gov (United States)

    Walker, Andrew; Taylor, James; Rowe, Duncan; Summers, David

    2008-05-01

    We have developed and tested a method for the restriction enzyme-independent generation of sticky-end PCR products. The method is suitable for use with a proof-reading polymerase such as pfu, or any other heat-stable polymerase which produces a blunt-end product. The technique can be used to achieve unidirectional cloning of PCR products with an efficiency greater than 90%. Because the sequences of the sticky ends are defined by the user and potentially can be of any length, the method can also be exploited for the one-step construction of recombinant plasmids from multiple functional cassettes, without the use of restriction enzymes.

  19. A novel enterovirus and parechovirus multiplex one-step real-time PCR-validation and clinical experience

    DEFF Research Database (Denmark)

    Nielsen, A. C. Y.; Bottiger, B.; Midgley, S. E.

    2013-01-01

    and human parechovirus type 3 had a similar seasonal pattern with a peak during the summer and autumn. Human parechovirus type 3 was almost invariably found in children less than 4 months of age. In conclusion, a multiplex assay was developed allowing simultaneous detection of 2 viruses, which can cause......As the number of new enteroviruses and human parechoviruses seems ever growing, the necessity for updated diagnostics is relevant. We have updated an enterovirus assay and combined it with a previously published assay for human parechovirus resulting in a multiplex one-step RT-PCR assay....... The multiplex assay was validated by analysing the sensitivity and specificity of the assay compared to the respective monoplex assays, and a good concordance was found. Furthermore, the enterovirus assay was able to detect 42 reference strains from all 4 species, and an additional 9 genotypes during panel...

  20. Novel One-Step Multiplex PCR-Based Method for HLA Typing and Preimplantational Genetic Diagnosis of -Thalassemia

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    Raquel M. Fernández

    2013-01-01

    Full Text Available Preimplantation genetic diagnosis (PGD of single gene disorders, combined with HLA matching (PGD-HLA, has emerged as a tool for couples at risk of transmitting a genetic disease to select unaffected embryos of an HLA tissue type compatible with that of an existing affected child. Here, we present a novel one-step multiplex PCR to genotype a spectrum of STRs to simultaneously perform HLA typing and PGD for -thalassemia. This method is being routinely used for PGD-HLA cycles in our department, with a genotyping success rate of 100%. As an example, we present the first successful PGD-HLA typing in Spain, which resulted in the birth of a boy and subsequent successful HSC transplantation to his affected brother, who is doing well 4 years following transplantation. The advantage of our method is that it involves only a round of single PCR for multiple markers amplification (up to 10 markers within the HLA and 6 markers at the -globin loci. This strategy has allowed us to considerably reduce the optimization of the PCR method for each specific PGD-HLA family as well as the time to obtain molecular results in each cycle.

  1. One-step multiplex quantitative RT-PCR for the simultaneous detection of viroids and phytoplasmas of pome fruit trees.

    Science.gov (United States)

    Malandraki, Ioanna; Varveri, Christina; Olmos, Antonio; Vassilakos, Nikon

    2015-03-01

    A one-step multiplex real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) based on TaqMan chemistry was developed for the simultaneous detection of Pear blister canker viroid and Apple scar skin viroid along with universal detection of phytoplasmas, in pome trees. Total nucleic acids (TNAs) extraction was performed according to a modified CTAB protocol. Primers and TaqMan MGB probes for specific detection of the two viroids were designed in this study, whereas for phytoplasma detection published universal primers and probe were used, with the difference that the later was modified to carry a MGB quencher. The pathogens were detected simultaneously in 10-fold serial dilutions of TNAs from infected plant material into TNAs of healthy plant up to dilutions 10(-5) for viroids and 10(-4) for phytoplasmas. The multiplex real-time assay was at least 10 times more sensitive than conventional protocols for viroid and phytoplasma detection. Simultaneous detection of the three targets was achieved in composite samples at least up to a ratio of 1:100 triple-infected to healthy tissue, demonstrating that the developed assay has the potential to be used for rapid and massive screening of viroids and phytoplasmas of pome fruit trees in the frame of certification schemes and surveys.

  2. Development of a one-step duplex RT-qPCR for the quantification of phocine distemper virus.

    Science.gov (United States)

    Bogomolni, Andrea L; Frasca, Salvatore; Matassa, Keith A; Nielsen, Ole; Rogers, Kara; De Guise, Sylvain

    2015-04-01

    Worldwide, stranded marine mammals and the network personnel who respond to marine mammal mortality have provided much of the information regarding marine morbillivirus infections. An assay to determine the amount of virus present in tissue samples would be useful to assist in routine surveying of animal health and for monitoring large-scale die-off events. False negatives from poor-quality samples prevent determination of the true extent of infection, while only small amounts of tissue samples or archived RNA may be available at the time of collection for future retrospective analysis. We developed a one-step duplex real-time reverse transcriptase-quantitative-PCR assay (RT-qPCR) based on Taqman probe technology to quantify phocine distemper virus (PDV) isolated from an outbreak in harbor (Phoca vitulina concolor) and gray seals (Halichoerus grypus) along the northeast US coast in 2006. The glyceraldehyde-3-phosphate-dehydrogenase (GAPDH) gene was selected to assess RNA quality. This duplex assay is specific for PDV and sensitive through a range of 10(0) to 10(9) copies ds-plasmid DNA. For the GAPDH target, the reaction in duplex amplified 10(0) to 10(9) copies of ds-plasmid DNA and was detectable in multiple seal species. This assay reduced the likelihood of false negative results due to degradation of tissues and well-to-well variability while providing sensitive and specific detection of PDV, which would be applicable in molecular epidemiologic studies and pathogen detection in field and laboratory investigations involving a variety of seal species.

  3. A broad spectrum, one-step reverse-transcription PCR amplification of the neuraminidase gene from multiple subtypes of influenza A virus

    Directory of Open Access Journals (Sweden)

    Chen Wenbin

    2008-07-01

    Full Text Available Abstract Background The emergence of high pathogenicity strains of Influenza A virus in a variety of human and animal hosts, with wide geographic distribution, has highlighted the importance of rapid identification and subtyping of the virus for outbreak management and treatment. Type A virus can be classified into subtypes according to the viral envelope glycoproteins, hemagglutinin and neuraminidase. Here we review the existing specificity and amplification of published primers to subtype neuraminidase genes and describe a new broad spectrum primer pair that can detect all 9 neuraminidase subtypes. Results Bioinformatic analysis of 3,337 full-length influenza A neuraminidase segments in the NCBI database revealed semi-conserved regions not previously targeted by primers. Two degenerate primers with M13 tags, NA8F-M13 and NA10R-M13 were designed from these regions and used to generate a 253 bp cDNA product. One-step RT-PCR testing was successful in 31/32 (97% cases using a touchdown protocol with RNA from over 32 different cultured influenza A virus strains representing the 9 neuraminidase subtypes. Frozen blinded clinical nasopharyngeal aspirates were also assayed and were mostly of subtype N2. The region amplified was direct sequenced and then used in database searches to confirm the identity of the template RNA. The RT-PCR fragment generated includes one of the mutation sites related to oseltamivir resistance, H274Y. Conclusion Our one-step RT-PCR assay followed by sequencing is a rapid, accurate, and specific method for detection and subtyping of different neuraminidase subtypes from a range of host species and from different geographical locations.

  4. Pentaprobe: a comprehensive sequence for the one-step detection of DNA-binding activities.

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    Kwan, Ann H Y; Czolij, Robert; Mackay, Joel P; Crossley, Merlin

    2003-10-15

    The rapid increase in the number of novel proteins identified in genome projects necessitates simple and rapid methods for assigning function. We describe a strategy for determining whether novel proteins possess typical sequence-specific DNA-binding activity. Many proteins bind recognition sequences of 5 bp or less. Given that there are 4(5) possible 5 bp sites, one might expect the length of sequence required to cover all possibilities would be 4(5) x 5 or 5120 nt. But by allowing overlaps, utilising both strands and using a computer algorithm to generate the minimum sequence, we find the length required is only 516 base pairs. We generated this sequence as six overlapping double-stranded oligonucleotides, termed pentaprobe, and used it in gel retardation experiments to assess DNA binding by both known and putative DNA-binding proteins from several protein families. We have confirmed binding by the zinc finger proteins BKLF, Eos and Pegasus, the Ets domain protein PU.1 and the treble clef N- and C-terminal fingers of GATA-1. We also showed that the N-terminal zinc finger domain of FOG-1 does not behave as a typical DNA-binding domain. Our results suggest that pentaprobe, and related sequences such as hexaprobe, represent useful tools for probing protein function.

  5. Quantum dot-enhanced detection of dual short RNA sequences via one-step template-dependent surface hybridization

    Energy Technology Data Exchange (ETDEWEB)

    Song Wenqing; Qiu Xue; Lau Choiwan [School of Pharmacy, Key Laboratory of Smart Drug Delivery, Ministry of Education and PLA, Fudan University, 826 Zhangheng Road, Shanghai 201203 (China); Lu Jianzhong, E-mail: jzlu@shmu.edu.cn [School of Pharmacy, Key Laboratory of Smart Drug Delivery, Ministry of Education and PLA, Fudan University, 826 Zhangheng Road, Shanghai 201203 (China)

    2012-07-20

    Graphical abstract: A novel multiplexed method for short RNA detection is reported that employed a design strategy in which quantum dots functionalized reporter DNA were used to capture a short single-stranded RNA sequence from a target solution and then to specifically adsorb onto a common capture probe-modified 96-well plate via a one-step template-dependent, surface hybridization for simultaneous fluorescence detection. Highlights: Black-Right-Pointing-Pointer A ligase-free sensor was demonstrated for the specific detection of dual short RNA. Black-Right-Pointing-Pointer The method was sensitive and simultaneous. Black-Right-Pointing-Pointer Quantum dots-modified reporter probes could increase the melting temperature. Black-Right-Pointing-Pointer Quantum dots functionalized reporter DNA hybridized with capture DNA and target RNA. Black-Right-Pointing-Pointer Target RNA was captured via a one-step template-dependent hybridization. - Abstract: A novel multiplexed method for short RNA detection is reported that employs a design strategy in which capture and reporter probes anneal to each other in the presence of a short RNA target via the formation of a stable three-component complex. Quantum dots (QDs) functionalized with reporter DNA are thus specifically bound onto a capture probe-modified 96-well plate by one-step hybridization for simple RNA detection. In comparison with conventional organic dye-modified reporter probes, the use of reporter DNA-modified QD conjugates increase the melting temperature and lead to the detection of short RNA without the need for a ligation reaction. Moreover, QD properties allow multiple short RNA sequences to be simultaneously determined via rapid and simple one-step hybridization, as exemplified herein. The present results clearly demonstrate that this new strategy can be used to detect dual-short RNA sequence at concentrations of 10 pM in 100 {mu}L.

  6. Rapid diagnosis of acute hemorrhagic conjunctivitis due to coxsackievirus A24 variant by real-time one-step RT-PCR.

    Science.gov (United States)

    Lévêque, Nicolas; Lahlou Amine, Idriss; Tcheng, Remy; Falcon, Delphine; Rivat, Nathalie; Dussart, Philippe; Muyembe, Jean-Jacques; Chomel, Jean-Jacques; Norder, Helene; Eugene, Maxime; Lina, Bruno

    2007-06-01

    Coxsackievirus A24 variant is, together with enterovirus 70 and adenoviruses, the major etiological agent involved in acute hemorrhagic conjunctivitis outbreaks worldwide. However, the standard virus isolation method followed by serotyping or VP1 region sequencing is time-consuming. A rapid method for the detection of coxsackievirus A24 variant from conjunctival swab specimens would be useful in the context of explosive and extensive outbreaks. A one-step real-time RT-PCR assay based on TaqMan technology was thus developed and assessed on 36 conjunctival swabs from outbreaks of conjunctivitis in Morocco in 2004 due to a coxsackievirus A24 variant and in Corsica in 2006 due to adenovirus type 3, and 83 virus strains including 41 coxsackievirus A24 variant collected in French Guiana and Guadeloupe in 2003, in the Democratic Republic of the Congo in 2003, in Morocco in 2004 and 42 other virus species genetically close or known to be responsible for conjunctivitis. All the conjunctival swabs from coxsackievirus A24 variant related outbreak and the 41 coxsackievirus A24 variant strains were tested positive by the RT-PCR assay within 4h. This novel single-tube real-time RT-PCR assay is sensitive and specific, and consists in a reliable and faster alternative to the viral culture for recent and future acute hemorrhagic conjunctivitis outbreaks caused by coxsackievirus A24 variant.

  7. A sensitive one-step real-time PCR for detection of avian influenza viruses using a MGB probe and an internal positive control

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    Delogu Mauro

    2006-05-01

    Full Text Available Abstract Background Avian influenza viruses (AIVs are endemic in wild birds and their introduction and conversion to highly pathogenic avian influenza virus in domestic poultry is a cause of serious economic losses as well as a risk for potential transmission to humans. The ability to rapidly recognise AIVs in biological specimens is critical for limiting further spread of the disease in poultry. The advent of molecular methods such as real time polymerase chain reaction has allowed improvement of detection methods currently used in laboratories, although not all of these methods include an Internal Positive Control (IPC to monitor for false negative results. Therefore we developed a one-step reverse transcription real time PCR (RRT-PCR with a Minor Groove Binder (MGB probe for the detection of different subtypes of AIVs. This technique also includes an IPC. Methods RRT-PCR was developed using an improved TaqMan technology with a MGB probe to detect AI from reference viruses. Primers and probe were designed based on the matrix gene sequences from most animal and human A influenza virus subtypes. The specificity of RRT-PCR was assessed by detecting influenza A virus isolates belonging to subtypes from H1–H13 isolated in avian, human, swine and equine hosts. The analytical sensitivity of the RRT-PCR assay was determined using serial dilutions of in vitro transcribed matrix gene RNA. The use of a rodent RNA as an IPC in order not to reduce the efficiency of the assay was adopted. Results The RRT-PCR assay is capable to detect all tested influenza A viruses. The detection limit of the assay was shown to be between 5 and 50 RNA copies per reaction and the standard curve demonstrated a linear range from 5 to 5 × 108 copies as well as excellent reproducibility. The analytical sensitivity of the assay is 10–100 times higher than conventional RT-PCR. Conclusion The high sensitivity, rapidity, reproducibility and specificity of the AIV RRT-PCR with

  8. Development of a One-Step Duplex RT-PCR Method for the Simultaneous Detection of VP3/VP1 and VP1/P2B Regions of the Hepatitis A Virus.

    Science.gov (United States)

    Kim, Mi-Ju; Lee, Shin-Young; Kim, Hyun-Joong; Lee, Jeong Su; Joo, In Sun; Kwak, Hyo Sun; Kim, Hae-Yeong

    2016-08-28

    The simultaneous detection and accurate identification of hepatitis A virus (HAV) is critical in food safety and epidemiological studies to prevent the spread of HAV outbreaks. Towards this goal, a one-step duplex reverse-transcription (RT)-PCR method was developed targeting the VP1/P2B and VP3/VP1 regions of the HAV genome for the qualitative detection of HAV. An HAV RT-qPCR standard curve was produced for the quantification of HAV RNA. The detection limit of the duplex RT-PCR method was 2.8 × 10(1) copies of HAV. The PCR products enabled HAV genotyping analysis through DNA sequencing, which can be applied for epidemiological investigations. The ability of this duplex RT-PCR method to detect HAV was evaluated with HAV-spiked samples of fresh lettuce, frozen strawberries, and oysters. The limit of detection of the one-step duplex RT-PCR for each food model was 9.4 × 10(2) copies/20 g fresh lettuce, 9.7 × 10(3) copies/20 g frozen strawberries, and 4.1 × 10(3) copies/1.5 g oysters. Use of a one-step duplex RT-PCR method has advantages such as shorter time, decreased cost, and decreased labor owing to the single amplification reaction instead of four amplifications necessary for nested RT-PCR.

  9. Development of a highly sensitive real-time one step RT-PCR combined complementary locked primer technology and conjugated minor groove binder probe

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    Lee Sunhwa

    2011-06-01

    Full Text Available Abstract Background Enterovirus (EV infections are commonly associated with encephalitis and meningitis. Detection of enteroviral RNA in clinical specimens has been demonstrated to improve the management of patients, by ruling out other causes of disease. Method To develop a sensitive and reliable assay for routine laboratory diagnosis, we developed a real-time one step reverse transcription polymerase chain reaction (RT-PCR assay with minor groove binder probes and primers modified with complementary locked primer technology (TMC-PCR. We checked the sensitivity of the developed assay by comparing it to a previously published TaqMan probe real-time one-step RT-PCR (TTN-PCR procedure using enteroviral isolates, Enterovirus Proficiency panels from Quality Control on Molecular Diagnostics (QCMD-2007, and clinical specimens from patients with suspected EV infections. Results One hundred clinical specimens from 158 suspected viral meningitis cases were determined to be positive by the TMC-PCR assay (63.29%, whereas only 60 were found to be positive by the TTN-PCR assay (37.97%. The positive and negative agreements between the TMC-PCR and TTN-PCR assays were 100% and 59.2%, respectively. Conclusion This data suggest that the TMC-PCR assay may be suitable for routine diagnostic screening from patient suspected EV infection.

  10. Establishment of one-step SYBR green-based real time-PCR assay for rapid detection and quantification of chikungunya virus infection.

    Science.gov (United States)

    Ho, Phui San; Ng, Mary Mah Lee; Chu, Justin Jang Hann

    2010-01-21

    Chikungunya virus (CHIKV) is a mosquito-borne alphavirus and one of the prevalent re-emerging arbovirus in tropical and subtropical regions of Asia, Africa, and Central and South America. It produces a spectrum of illness ranging from inapparent infection to moderate febrile illness as well as severe arthralgia or arthritis affecting multiple joints. In this study, a quantitative, one-step real-time SYBR Green-based RT-PCR system for the non-structural protein 2 (nsP2) of CHIKV that can quantify a wide range of viral RNA concentrations was developed. Comparisons between the conventional semi-quantitative RT-PCR assay, immunofluorescence detection method and the one-step SYBR Green-based RT-PCR assay in the detection of CHIKV infection revealed much rapid and increase sensitivity of the latter method. Furthermore, this newly developed assay was validated by in vitro experiments in which ribavirin, a well-known RNA virus inhibitor, showed a dose-dependent inhibition of virus replication on cells that was assessed by viral infectivity and viral RNA production. Our results demonstrate the potential of this newly developed one-step SYBR Green I-based RT-PCR assay may be a useful tool in rapid detection of CHIKV and monitoring the extent of viral replication possibly in patients' samples.

  11. Establishment of one-step SYBR green-based real time-PCR assay for rapid detection and quantification of chikungunya virus infection

    Directory of Open Access Journals (Sweden)

    Chu Justin

    2010-01-01

    Full Text Available Abstract Chikungunya virus (CHIKV is a mosquito-borne alphavirus and one of the prevalent re-emerging arbovirus in tropical and subtropical regions of Asia, Africa, and Central and South America. It produces a spectrum of illness ranging from inapparent infection to moderate febrile illness as well as severe arthralgia or arthritis affecting multiple joints. In this study, a quantitative, one-step real-time SYBR Green-based RT-PCR system for the non-structural protein 2 (nsP2 of CHIKV that can quantify a wide range of viral RNA concentrations was developed. Comparisons between the conventional semi-quantitative RT-PCR assay, immunofluorescence detection method and the one-step SYBR Green-based RT-PCR assay in the detection of CHIKV infection revealed much rapid and increase sensitivity of the latter method. Furthermore, this newly developed assay was validated by in vitro experiments in which ribavirin, a well-known RNA virus inhibitor, showed a dose-dependent inhibition of virus replication on cells that was assessed by viral infectivity and viral RNA production. Our results demonstrate the potential of this newly developed one-step SYBR Green I-based RT-PCR assay may be a useful tool in rapid detection of CHIKV and monitoring the extent of viral replication possibly in patients' samples.

  12. A one-step multiplex PCR to identify Klebsiella pneumoniae, Klebsiella variicola, and Klebsiella quasipneumoniae in the clinical routine.

    Science.gov (United States)

    Fonseca, Erica Lourenço; Ramos, Nilceia da Veiga; Andrade, Bruno G Nascimento; Morais, Lena L C S; Marin, Michel F Abanto; Vicente, Ana Carolina P

    2017-04-01

    Klebsiella pneumoniae, Klebsiella variicola and Klebsiella quasipneumoniae are difficult to differentiate phenotypically, leading to misinterpretation of their infection prevalence. We propose a multiplex PCR for blaSHV, blaLEN and blaOKP and their flanking gene (deoR). Since this scheme focuses only on chromosomal genes, it will be feasible for Klebsiella identification in the clinical routine.

  13. A one-step real-time multiplex PCR for screening Y-chromosomal microdeletions without downstream amplicon size analysis.

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    Viviana Kozina

    Full Text Available BACKGROUND: Y-chromosomal microdeletions (YCMD are one of the major genetic causes for non-obstructive azoospermia. Genetic testing for YCMD by multiplex polymerase chain reaction (PCR is an established method for quick and robust screening of deletions in the AZF regions of the Y-chromosome. Multiplex PCRs have the advantage of including a control gene in every reaction and significantly reducing the number of reactions needed to screen the relevant genomic markers. PRINCIPAL FINDINGS: The widely established "EAA/EMQN best practice guidelines for molecular diagnosis of Y-chromosomal microdeletions (2004" were used as a basis for designing a real-time multiplex PCR system, in which the YCMD can simply be identified by their melting points. For this reason, some AZF primers were substituted by primers for regions in their genomic proximity, and the ZFX/ZFY control primer was exchanged by the AMELX/AMELY control primer. Furthermore, we substituted the classical SybrGreen I dye by the novel and high-performing DNA-binding dye EvaGreen™ and put substantial effort in titrating the primer combinations in respect to optimal melting peak separation and peak size. SIGNIFICANCE: With these changes, we were able to develop a platform-independent and robust real-time based multiplex PCR, which makes the need for amplicon identification by electrophoretic sizing expendable. By using an open-source system for real-time PCR analysis, we further demonstrate the applicability of automated melting point and YCMD detection.

  14. Selectable one-step PCR-mediated integration of a degron for rapid depletion of endogenous human proteins.

    Science.gov (United States)

    Sheridan, Ryan M; Bentley, David L

    2016-02-01

    Manipulation of protein stability with ligand-regulated degron fusions is a powerful method for investigating gene function. We developed a selectable cassette for easy C-terminal tagging of endogenous human proteins with the E. coli dihydrofolate reductase (eDHFR) degron using CRISPR/Cas9 genome editing. This cassette permits high-efficiency recovery of correct integration events using an in-frame self-cleaving 2A peptide and the puromycin resistance gene. PCR amplified donor eDHFR cassette fragments with 100 bases of homology on each end are integrated by homology-directed repair (HDR) of guide RNA (gRNA)-targeted double-stranded DNA breaks at the 3' ends of open reading frames (ORFs). As proof of principle, we generated cell lines in which three endogenous proteins were tagged with the eDHFR degron. When the antibiotic trimethoprim is removed from the media, each of the eDHFR-tagged proteins was depleted by >90% within 2-4 h, and this depletion was reversed by re-addition of trimethoprim. Since puromycin selection permits recovery of in-frame degron fusions with high efficiency using only 100-bp long regions of homology, this method should be applicable on a genome-wide scale for generating libraries of conditional mutant cell lines.

  15. Development of a thermostabilized, one-step, nested, tetraplex PCR assay for simultaneous identification and differentiation of Entamoeba species, Entamoeba histolytica and Entamoeba dispar from stool samples.

    Science.gov (United States)

    Foo, Phiaw Chong; Chan, Yean Yean; See Too, Wei Cun; Tan, Zi Ning; Wong, Weng Kin; Lalitha, Pattabhiraman; Lim, Boon Huat

    2012-09-01

    Entamoeba histolytica is the only Entamoeba species that causes amoebiasis in humans. Approximately 50 million people are infected, with 100, 000 deaths annually in endemic countries. Molecular diagnosis of Entamoeba histolytica is important to differentiate it from the morphologically identical Entamoeba dispar to avoid unnecessary medication. Conventional molecular diagnostic tests require trained personnel, cold-chain transportation and/or are storage-dependent, which make them user-unfriendly. The aim of this study was to develop a thermostabilized, one-step, nested, tetraplex PCR assay for the detection of Entamoeba histolytica, Entamoeba dispar and Entamoeba species in cold-chain-free and ready-to-use form. The PCR test was designed based on the Entamoeba small subunit rRNA (SSU-rRNA) gene, which detects the presence of any Entamoeba species, and simultaneously can be used to differentiate Entamoeba histolytica from Entamoeba dispar. In addition, a pair of primers was designed to serve as an internal amplification control to help identify inhibitors in the samples. All PCR reagents together with the designed primers were thermostabilized by lyophilization and were stable at 24 °C for at least 6 months. The limit of detection of the tetraplex PCR was found to be 39 pg DNA or 1000 cells for Entamoeba histolytica and 78 pg DNA or 1000 cells for Entamoeba dispar, and the specificity was 100 %. In conclusion, this cold-chain-free, thermostabilized, one-step, nested, multiplex PCR assay was found to be efficacious in differentiating Entamoeba histolytica from other non-pathogenic Entamoeba species.

  16. Establishment and validation of two duplex one-step real-time RT-PCR assays for diagnosis of foot-and-mouth disease.

    Science.gov (United States)

    Gorna, K; Relmy, A; Romey, A; Zientara, S; Blaise-Boisseau, S; Bakkali-Kassimi, L

    2016-09-01

    Two duplex one-step TaqMan-based RT-PCR protocols for detection of foot-and-mouth disease virus (FMDV) were established and validated. Each RT-PCR test consists of a ready-to-use master mix for simultaneous detection of the well established 3D or IRES FMDV targets and incorporates the host β-actin mRNA as an internal control target, in a single-tube assay. The two real-time RT-PCR 3D/β-actin and IRES/β-actin tests are highly sensitive and able to detect up to 7TCID50/ml of FMDV and 10 copies/1μl of viral RNA. In field epithelium samples, the diagnostic sensitivity was 100% (95% CI; 91-100%) for the 3D/β-actin test and 97% (95% CI; 87-100%) for the IRES/β-actin test. The diagnostic specificity was 100% (95% CI; 95-100%) for both RT-PCRs. In addition, the two protocols proved to be robust, showing inter-assay coefficients of variation ranging from 1.94% to 6.73% for the IRES target and from 2.33% to 5.42% for the 3D target for different RNA extractions and different RT-PCR conditions. The internally controlled one-step real-time RT-PCR protocols described in this study provide a rapid, effective and reliable method for the detection of FMDV and thus may improve the routine diagnosis for foot-and-mouth disease.

  17. Diagnosis of Cetacean morbillivirus: A sensitive one step real time RT fast-PCR method based on SYBR(®) Green.

    Science.gov (United States)

    Sacristán, Carlos; Carballo, Matilde; Muñoz, María Jesús; Bellière, Edwige Nina; Neves, Elena; Nogal, Verónica; Esperón, Fernando

    2015-12-15

    Cetacean morbillivirus (CeMV) (family Paramyxoviridae, genus Morbillivirus) is considered the most pathogenic virus of cetaceans. It was first implicated in the bottlenose dolphin (Tursiops truncatus) mass stranding episode along the Northwestern Atlantic coast in the late 1980s, and in several more recent worldwide epizootics in different Odontoceti species. This study describes a new one step real-time reverse transcription fast polymerase chain reaction (real-time RT-fast PCR) method based on SYBR(®) Green to detect a fragment of the CeMV fusion protein gene. This primer set also works for conventional RT-PCR diagnosis. This method detected and identified all three well-characterized strains of CeMV: porpoise morbillivirus (PMV), dolphin morbillivirus (DMV) and pilot whale morbillivirus (PWMV). Relative sensitivity was measured by comparing the results obtained from 10-fold dilution series of PMV and DMV positive controls and a PWMV field sample, to those obtained by the previously described conventional phosphoprotein gene based RT-PCR method. Both the conventional and real-time RT-PCR methods involving the fusion protein gene were 100- to 1000-fold more sensitive than the previously described conventional RT-PCR method.

  18. Development of a rapid DNA extraction method and one-step nested PCR for the detection of Naegleria fowleri from the environment.

    Science.gov (United States)

    Ahmad, Arine Fadzlun; Lonnen, James; Andrew, Peter W; Kilvington, Simon

    2011-10-15

    Naegleria fowleri is a small free-living amoebo-flagellate found in natural and manmade thermal aquatic habitats worldwide. The organism is pathogenic to man causing fatal primary amoebic meningoencephalitis (PAM). Infection typically results from bathing in contaminated water and is usually fatal. It is, therefore, important to identify sites containing N. fowleri in the interests of preventive public health microbiology. Culture of environmental material is the conventional method for the isolation of N. fowleri but requires several days incubation and subsequent biochemical or molecular tests to confirm identification. Here, a nested one-step PCR test, in conjunction with a direct DNA extraction from water or sediment material, was developed for the rapid and reliable detection of N. fowleri from the environment. Here, the assay detected N, fowleri in 18/109 river water samples associated with a nuclear power plant in South West France and 0/10 from a similar site in the UK. Although culture of samples yielded numerous thermophilic free-living amoebae, none were N. fowleri or other thermophilic Naegleria spp. The availability of a rapid, reliable and sensitive one-step nested PCR method for the direct detection of N. fowleri from the environment may aid ecological studies and enable intervention to prevent PAM cases.

  19. Comprehensive multiplex one-step real-time TaqMan qRT-PCR assays for detection and quantification of hemorrhagic fever viruses.

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    Zheng Pang

    Full Text Available BACKGROUND: Viral hemorrhagic fevers (VHFs are a group of animal and human illnesses that are mostly caused by several distinct families of viruses including bunyaviruses, flaviviruses, filoviruses and arenaviruses. Although specific signs and symptoms vary by the type of VHF, initial signs and symptoms are very similar. Therefore rapid immunologic and molecular tools for differential diagnosis of hemorrhagic fever viruses (HFVs are important for effective case management and control of the spread of VHFs. Real-time quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR assay is one of the reliable and desirable methods for specific detection and quantification of virus load. Multiplex PCR assay has the potential to produce considerable savings in time and resources in the laboratory detection. RESULTS: Primers/probe sets were designed based on appropriate specific genes for each of 28 HFVs which nearly covered all the HFVs, and identified with good specificity and sensitivity using monoplex assays. Seven groups of multiplex one-step real-time qRT-PCR assays in a universal experimental system were then developed by combining all primers/probe sets into 4-plex reactions and evaluated with serial dilutions of synthesized viral RNAs. For all the multiplex assays, no cross-reactivity with other HFVs was observed, and the limits of detection were mainly between 45 and 150 copies/PCR. The reproducibility was satisfactory, since the coefficient of variation of Ct values were all less than 5% in each dilution of synthesized viral RNAs for both intra-assays and inter-assays. Evaluation of the method with available clinical serum samples collected from HFRS patients, SFTS patients and Dengue fever patients showed high sensitivity and specificity of the related multiplex assays on the clinical specimens. CONCLUSIONS: Overall, the comprehensive multiplex one-step real-time qRT-PCR assays were established in this study, and proved to be

  20. Development of one-step SYBR Green real-time RT-PCR for quantifying bovine viral diarrhea virus type-1 and its comparison with conventional RT-PCR

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    Lou Sai

    2011-07-01

    Full Text Available Abstract Background Bovine viral diarrhea virus (BVDV is a worldwide pathogen in cattle and acts as a surrogate model for hepatitis C virus (HCV. One-step real-time fluorogenic quantitative reverse transcription polymerase chain reaction (RT-PCR assay based on SYBR Green I dye has not been established for BVDV detection. This study aims to develop a quantitative one-step RT-PCR assay to detect BVDV type-1 in cell culture. Results One-step quantitative SYBR Green I RT-PCR was developed by amplifying cDNA template from viral RNA and using in vitro transcribed BVDV RNA to establish a standard curve. The assay had a detection limit as low as 100 copies/ml of BVDV RNA, a reaction efficiency of 103.2%, a correlation coefficient (R2 of 0.995, and a maximum intra-assay CV of 2.63%. It was 10-fold more sensitive than conventional RT-PCR and can quantitatively detect BVDV RNA levels from 10-fold serial dilutions of titrated viruses containing a titer from 10-1 to 10-5 TCID50, without non-specific amplification. Melting curve analysis showed no primer-dimers and non-specific products. Conclusions The one-step SYBR Green I RT-PCR is specific, sensitive and reproducible for the quantification of BVDV in cell culture. This one-step SYBR Green I RT-PCR strategy may be further optimized as a reliable assay for diagnosing and monitoring BVDV infection in animals. It may also be applied to evaluate candidate agents against HCV using BVDV cell culture model.

  1. Fast-Track, One-Step E. coli Detection: A Miniaturized Hydrogel Array Permits Specific Direct PCR and DNA Hybridization while Amplification.

    Science.gov (United States)

    Beyer, Antje; Pollok, Sibyll; Rudloff, Anne; Cialla-May, Dana; Weber, Karina; Popp, Jürgen

    2016-09-01

    A timesaving and convenient method for bacterial detection based on one-step, one-tube deoxyribonucleic acid (DNA) hybridization on hydrogel array while target gene amplification is described. The hydrogel array is generated by a fast one-pot synthesis, where N,N'-dimethylacrylamide/polyethyleneglycol(PEG1900 )-bisacrylamide mixture polymerizes via radical photoinitiation by visible light within 20 min concomitant with in situ capture probe immobilization. These DNA-functionalized hydrogel droplets arrayed on a planar glass surface are placed in the polymerase chain reaction (PCR) mixture during the thermal amplification cycles. The bacterial cells can be implemented in a direct PCR reaction, omitting the need for prior template DNA extraction. The resulting fluorescence signal is immediately detectable after the end of the PCR (1 h) following one short washing step by microscopy. Therefore a valid signal can be reached within 1.5 h including 10 min for pipetting and placement of the tubes and chips. The performance of this novel hydrogel DNA array was successfully proven with varying cell numbers down to a limit of 10(1) Escherichia coli cells.

  2. A one step real time PCR method for the quantification of hepatitis delta virus RNA using an external armored RNA standard and intrinsic internal control.

    Science.gov (United States)

    Karataylı, Ersin; Altunoğlu, Yasemin Çelik; Karataylı, Senem Ceren; Alagöz, S Gökçe K; Cınar, Kubilay; Yalçın, Kendal; Idilman, Ramazan; Yurdaydın, Cihan; Bozdayı, A Mithat

    2014-05-01

    Hepatitis delta virus (HDV) RNA viral load measurement is critical in diagnosis and monitoring the response to antiviral treatment. Our aim is to design a real time PCR method for accurate quantitation of HDV RNA in clinical specimens using an armored RNA as external standard, and an intrinsic internal control. A plasmid bearing delta antigen region of genotype I HDV genome was used to develop an armored RNA. Serial dilutions of the armored HDV RNA standard with 10(12)copy/mL were used as standards for quantitation. A primer-probe set derived from HDAg region was used in one step EZ RT PCR kit chemistry which uses rTth enzyme allowing reverse transcription and polymerization in the same tube. The kit also uses the advantage of uracil-N-glycosylase (UNG) enzyme treatment to prevent PCR contamination. The established assay has a dynamic range of 10(2)-10(11)copy/mL with a PCR efficiency of 96.9%. Detection limit was 858±32copy/mL with 95% confidence interval. Intra- and inter-assay variabilities were low for high, medium and low levels of viremia. Incorporation of freely circulating GAPDH in serum into the assay as an intrinsic internal control prevented false negative results and failures in PCR amplifications due to inhibitors, inefficient extraction procedures or enzymatic reactions. In conclusion, this study defines a novel assay for sensitive and reliable quantification of HDV RNA using an armored HDV RNA as a standard and GAPDH in plasma or serum as an intrinsic internal control in a single tube. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. Development of a one-step PCR assay with nine primer pairs for the detection of five diarrheagenic Escherichia coli types.

    Science.gov (United States)

    Oh, Kyung-Hwan; Kim, Soo-Bok; Park, Mi-Sun; Cho, Seung-Hak

    2014-06-28

    Certain Escherichia coli (E. coli) strains have the ability to cause diarrheal disease. Five types of diarrheagenic E. coli have been identified, including EHEC, ETEC, EPEC, EAEC, and EIEC. To detect these five diarrheagenic types rapidly, we developed a one-step multiplex PCR (MPPCR) assay using nine primer pairs to amplify nine virulence genes specific to the different virotypes, with each group being represented (i.e., stx1 and stx2 for EHEC, lt, sth, and stp for ETEC, eaeA and bfpA for EPEC, aggR for EAEC, and ipaH for EIEC). The PCR primers were constructed using MultAlin. The sensitivity and specificity of the constructed multiplex PCR primers were measured using DNA isolated from diarrheagenic E. coli strains representing each group. The limits of detection were as follows: 5 × 10(1) CFU/ml for EHEC, 5 × 10(3) CFU/ml for ETEC expressing lt and sth, 5 × 10(4) CFU/ml for ETEC expressing stp, 5 × 102 CFU/ml for EPEC, 5 × 10(4) CFU/ml for EAEC, and 5 × 10(2) CFU/ml for EIEC. To confirm the specificity, C. jejuni, C. perfringens, S. Typhimurium, V. parahaemolyticus, L. monocytogenes, Y. enterocolitica, B. cereus, and S. aureus were used as negative controls, and no amplification was obtained for these. Moreover, this kit was validated using 100 fecal samples from patients with diarrhea and 150 diarrheagenic E. coli strains isolated in Korea. In conclusion, the multiplex PCR assay developed in this study is very useful for the rapid and specific detection of five diarrheagenic E. coli types. This single-step assay will be useful as a rapid and economical method, as it reduces the cost and time required for the identification of diarrheagenic E. coli.

  4. One-step multiplex real time RT-PCR for the detection of bovine respiratory syncytial virus, bovine herpesvirus 1 and bovine parainfluenza virus 3

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    Thonur Leenadevi

    2012-03-01

    Full Text Available Abstract Background Detection of respiratory viruses in veterinary species has traditionally relied on virus detection by isolation or immunofluorescence and/or detection of circulating antibody using ELISA or serum neutralising antibody tests. Multiplex real time PCR is increasingly used to diagnose respiratory viruses in humans and has proved to be superior to traditional methods. Bovine respiratory disease (BRD is one of the most common causes of morbidity and mortality in housed cattle and virus infections can play a major role. We describe here a one step multiplex reverse transcriptase quantitative polymerase chain reaction (mRT-qPCR to detect the viruses commonly implicated in BRD. Results A mRT-qPCR assay was developed and optimised for the simultaneous detection of bovine respiratory syncytial virus (BRSV, bovine herpes virus type 1 (BoHV-1 and bovine parainfluenza virus type 3 (BPI3 i & ii nucleic acids in clinical samples from cattle. The assay targets the highly conserved glycoprotein B gene of BoHV-1, nucleocapsid gene of BRSV and nucleoprotein gene of BPI3. This mRT-qPCR assay was assessed for sensitivity, specificity and repeatability using in vitro transcribed RNA and recent field isolates. For clinical validation, 541 samples from clinically affected animals were tested and mRT-qPCR result compared to those obtained by conventional testing using virus isolation (VI and/or indirect fluorescent antibody test (IFAT. Conclusions The mRT-qPCR assay was rapid, highly repeatable, specific and had a sensitivity of 97% in detecting 102 copies of BRSV, BoHV-1 and BPI3 i & ii. This is the first mRT-qPCR developed to detect the three primary viral agents of BRD and the first multiplex designed using locked nucleic acid (LNA, minor groove binding (MGB and TaqMan probes in one reaction mix. This test was more sensitive than both VI and IFAT and can replace the aforesaid methods for virus detection during outbreaks of BRD.

  5. One-Step Multiplex RT-qPCR Assay for the Detection of Peste des petits ruminants virus, Capripoxvirus, Pasteurella multocida and Mycoplasma capricolum subspecies (ssp.) capripneumoniae

    Science.gov (United States)

    Lamien, Charles Euloge; Spergser, Joachim; Lelenta, Mamadou; Wade, Abel; Gelaye, Esayas; Loitsch, Angelika; Minoungou, Germaine; Thiaucourt, Francois; Diallo, Adama

    2016-01-01

    Respiratory infections, although showing common clinical symptoms like pneumonia, are caused by bacterial, viral or parasitic agents. These are often reported in sheep and goats populations and cause huge economic losses to the animal owners in developing countries. Detection of these diseases is routinely done using ELISA or microbiological methods which are being reinforced or replaced by molecular based detection methods including multiplex assays, where detection of different pathogens is carried out in a single reaction. In the present study, a one-step multiplex RT-qPCR assay was developed for simultaneous detection of Capripoxvirus (CaPV), Peste de petits ruminants virus (PPRV), Pasteurella multocida (PM) and Mycoplasma capricolum ssp. capripneumonia (Mccp) in pathological samples collected from small ruminants with respiratory disease symptoms. The test performed efficiently without any cross-amplification. The multiplex PCR efficiency was 98.31%, 95.48%, 102.77% and 91.46% whereas the singleplex efficiency was 93.43%, 98.82%, 102.55% and 92.0% for CaPV, PPRV, PM and Mccp, respectively. The correlation coefficient was greater than 0.99 for all the targets in both multiplex and singleplex. Based on cycle threshold values, intra and inter assay variability, ranged between the limits of 2%–4%, except for lower concentrations of Mccp. The detection limits at 95% confidence interval (CI) were 12, 163, 13 and 23 copies/reaction for CaPV, PPRV, PM and Mccp, respectively. The multiplex assay was able to detect CaPVs from all genotypes, PPRV from the four lineages, PM and Mccp without amplifying the other subspecies of mycoplasmas. The discriminating power of the assay was proven by accurate detection of the targeted pathogen (s) by screening 58 viral and bacterial isolates representing all four targeted pathogens. Furthermore, by screening 81 pathological samples collected from small ruminants showing respiratory disease symptoms, CaPV was detected in 17 samples

  6. One-Step Multiplex RT-qPCR Assay for the Detection of Peste des petits ruminants virus, Capripoxvirus, Pasteurella multocida and Mycoplasma capricolum subspecies (ssp. capripneumoniae.

    Directory of Open Access Journals (Sweden)

    Tirumala Bharani Kumar Settypalli

    Full Text Available Respiratory infections, although showing common clinical symptoms like pneumonia, are caused by bacterial, viral or parasitic agents. These are often reported in sheep and goats populations and cause huge economic losses to the animal owners in developing countries. Detection of these diseases is routinely done using ELISA or microbiological methods which are being reinforced or replaced by molecular based detection methods including multiplex assays, where detection of different pathogens is carried out in a single reaction. In the present study, a one-step multiplex RT-qPCR assay was developed for simultaneous detection of Capripoxvirus (CaPV, Peste de petits ruminants virus (PPRV, Pasteurella multocida (PM and Mycoplasma capricolum ssp. capripneumonia (Mccp in pathological samples collected from small ruminants with respiratory disease symptoms. The test performed efficiently without any cross-amplification. The multiplex PCR efficiency was 98.31%, 95.48%, 102.77% and 91.46% whereas the singleplex efficiency was 93.43%, 98.82%, 102.55% and 92.0% for CaPV, PPRV, PM and Mccp, respectively. The correlation coefficient was greater than 0.99 for all the targets in both multiplex and singleplex. Based on cycle threshold values, intra and inter assay variability, ranged between the limits of 2%-4%, except for lower concentrations of Mccp. The detection limits at 95% confidence interval (CI were 12, 163, 13 and 23 copies/reaction for CaPV, PPRV, PM and Mccp, respectively. The multiplex assay was able to detect CaPVs from all genotypes, PPRV from the four lineages, PM and Mccp without amplifying the other subspecies of mycoplasmas. The discriminating power of the assay was proven by accurate detection of the targeted pathogen (s by screening 58 viral and bacterial isolates representing all four targeted pathogens. Furthermore, by screening 81 pathological samples collected from small ruminants showing respiratory disease symptoms, CaPV was detected in

  7. Sensitive Detection of Measles Virus Infection in the Blood and Tissues of Humanized Mouse by One-step Quantitative RT-PCR

    Directory of Open Access Journals (Sweden)

    Shota eIkeno

    2013-10-01

    Full Text Available Live attenuated measles virus (MV has long been recognized as a safe and effective vaccine, and it has served as the basis for development of various MV-based vaccines. However, because MV is a human-tropic virus, the evaluation of MV-based vaccines has been hampered by the lack of a small-animal model. The humanized mouse, a recently developed system in which an immunodeficient mouse is transplanted with human fetal tissues or hematopoietic stem cells, may represent a suitable model. Here, we developed a sensitive one-step quantitative reverse transcription (qRT PCR that simultaneously measures nucleocapsid (N and human RNase P mRNA levels. The results can be used to monitor MV infection in a humanized mouse model. Using this method, we elucidated the replication kinetics of MV expressing EGFP both in vitro and in humanized mice in parallel with flow-cytometric analysis. Because our qRT-PCR system was sensitive enough to detect MV expression using RNA extracted from a small number of cells, it can be used to monitor MV infection in humanized mice by sequential blood sampling.

  8. Specific detection of H5N1 avian influenza A virus in field specimens by a one-step RT-PCR assay

    Directory of Open Access Journals (Sweden)

    Gupta Sanjay

    2006-03-01

    Full Text Available Abstract Background Continuous outbreaks of the highly pathogenic H5N1 avian influenza A in Asia has resulted in an urgent effort to improve current diagnostics to aid containment of the virus and lower the threat of a influenza pandemic. We report here the development of a PCR-based assay that is highly specific for the H5N1 avian influenza A virus. Methods A one-step reverse-transcription PCR assay was developed to detect the H5N1 avian influenza A virus. The specificity of the assay was shown by testing sub-types of influenza A virus and other viral and bacterial pathogens; and on field samples. Results Validation on 145 field specimens from Vietnam and Malaysia showed that the assay was specific without cross reactivity to a number of other infuenza strains as well as human respiratory related pathogens. Detection was 100% from allantoic fluid in H5N1 positive samples, suggesting it to be a reliable sampling source for accurate detection. Conclusion The assay developed from this study indicates that the primers are specific for the H5N1 influenza virus. As shown by the field tested results, this assay would be highly useful as a diagnostic tool to help identify and control influenza epidemics.

  9. Rapid Detection Co-infections of Classical Swine Fever Virus and Porcine Reproductive and Respiratory Syndrome Virus by One-step Multiplex RT-PCR

    Institute of Scientific and Technical Information of China (English)

    TIAN Hong; WU Jinyan; YAN Chen; SHANG Youjun; YIN Shuanghui; LIU Xiangtao

    2011-01-01

    Classical swine fever virus (CSFV) and porcine reproductive and respiratory syndrome virus (PRRSV) have caused immense economic loss in the pig industry and are considered to be the two most important infectious diseases of pigs in the world A multiplex reverse transcription polymerase chain reaction (multiplex RT-PCR) was developed for CSFV and PRRSV co-infections or infections, respectively. A set of two pairs of primer was designed based on the sequence of nonstructural protein NS54B of CSFV and ORF7 gene of PRRSV. The diagnostic accuracy of multiplex RT-PCR assay was evaluated by using 56 field clinical samples by multiplex RT-PCR, single RT-PCR and sequence analysis; and the specificity of multiplex PCR was verified by using constructed plasmids containing the specific viral target fragments of PRRSV and CSFV, respectively. The results indicated that this assay could reliably differentiate PRRSV and CSFV in co-infection samples. The multiplex RT-PCR developed in this study might provide a new avenue to the rapid the detection of CSFV and PRRSV in one reaction.

  10. Development of novel AllGlo-probe-based one-step multiplex qRT-PCR assay for rapid identification of avian influenza virus H7N9.

    Science.gov (United States)

    Zhang, Yanjun; Mao, Haiyan; Yan, Juying; Wang, Xinying; Zhang, Lei; Guus, Koch; Li, Hui; Li, Zhen; Chen, Yin; Gong, Liming; Chen, Zhiping; Xia, Shichang

    2014-07-01

    Recently, human deaths have resulted from infection with low-pathogenicity avian influenza virus H7N9 strains that have emerged recently in China. To strengthen H7N9 surveillance and outbreak control, rapid and reliable diagnostic methods are needed. To develop a sensitive quantitative real-time RT-PCR assay for rapid detection of H7N9 viral RNA, primers and AllGlo probes were designed to target the HA and NA genes of H7N9. Conserved sequences in the HA and NA genes were identified by phylogenic analysis and used as targets for H7N9 virus detection. The similarities of the targeted HA and NA gene sequences from different H7 and N9 influenza virus strains were 93.2-99.9 % and 96.0-99.6 %, respectively The specificity and sensitivity of the new multiplex real-time qRT-PCR was established. The test was used for the detection of viral RNA in human pharyngeal swabs and environmental samples. The detection limit of the multiplex qRT-PCR was estimated to be about 10(-1) TCID50/reaction. Finally, the diagnostic sensitivities of the multiplex qRT-PCR, virus isolation and TaqMan qRT-PCR were compared using pharyngeal swabs and environmental samples. These analyses yielded positive results in 46.7 %, 43.3 % and 20.0 % of the samples, respectively. The novel multiplex AllGlo qRT-PCR is a rapid and sensitive method to identify H7N9 virus in clinical and environmental samples and can be used to facilitate studies on the epidemiology of H7N9 virus.

  11. Cost-effective one-step PCR amplification of cystic fibrosis delta F508 fragment in a single cell for preimplantation genetic diagnosis.

    Science.gov (United States)

    Tsai, Y H

    1999-11-01

    The combination of in vitro fertilization (IVF) with PCR technologies enables diagnosis of single gene defects for preimplantation genetic diagnosis. This has been accomplished by two-step nested PCR, or PEP-PCR followed by nested PCR processes. To improve the detection of single cell genetic defects, the lysate of a single lymphocyte, with or without cystic fibrosis DeltaF508 mutation (CFDeltaF508), was incubated in a higher ionic strength solution containing mercaptoethanol prior to the addition of primers to the denatured cellular DNA. A single cell in 5 microl lysis buffer was incubated at 65 degrees C for 15 min, cooled, and neutralized with an equal volume of neutralizing buffer. A 5 microl aliquot of a solution X containing 50 mM MgCl(2), 1 M NaCl, and 10 mM mercaptoethanol was added to the neutralized cell lysate, followed by incubation at 93 degrees C for 15 min. The step was crucial to the successful amplification of CFDeltaF508 DNA fragment. The incubation of cell lysate in solution with the high level of sulphydryl reducing agent and a high ionic strength of about 0.45, at 93 degrees C for 15 min, might denature many chromatin-binding proteins and also ensure the complete dissociation of dsDNA. After the addition of PCR mix, the resulting reaction mixture still contained a sufficient level of sulphydryl reducing agent and 0.135 total ionic strength. This might reduce significantly the interference of various protein factors with DNA, and favour the primer-template annealing. The efficient initial annealing of the primers to target DNA sequences would facilitate PCR amplification efficacy. In conclusion, in more than 80 single cells tested (apart from one) the CFDeltaF508 defect was successfully demonstrated with the present protocol (>99 per cent), without using fluorescent primers and expensive automatic instrumentation.

  12. Development and Application of One Step RT-PCR Method for Detection of Bovine Viral Diarrhea Virus%牛病毒性腹泻病毒一步法RT-PCR检测方法的建立与应用

    Institute of Scientific and Technical Information of China (English)

    王春庆

    2013-01-01

    To establish a rapid bovine viral diarrhea virus (BVDV) pathogen detection methods, based on BVDV gene sequence in GenBank, we synthesized one pair of primers, established one step RT-PCR for BVDV detection. The method was used for infectious bovine rhinotracheitis virus (IBRV), classical swine fever virus (CSFV), bovine para influenza virus 3 (BPIV3) , all of the PCR results were negative, the sensitivity was 1 ng RNA. The established one step PCR method had good specificity, sensitivity, reproducibility, it could detect very low levels of BVDV quickly and accurately, it provided a kind of rapid, sensitive, specific and precise molecular biology detection method for pathogen detection and molecular epidemiology of material such as BVDV.%为建立一种快速检测牛病毒性腹泻病毒病原的方法,本研究根据GenBank上登录的牛病毒性腹泻病毒(bovine viral diarrhea virus,BVDV)基因组序列,设计1对引物,建立了检测BVDV的一步法RT-PCR方法.该方法对牛传染性鼻气管炎病毒、猪瘟病毒、牛副流感病毒3型的扩增结果均为阴性,检测的敏感性达1 ng RNA.该一步法RT-PCR方法具有良好的特异性、敏感性、重复性,可以准确快速检测出极低含量的BVDV,将为BVDV的病原检测及分子流行病学调查等提供一种快速、灵敏、特异、准确的分子生物学检测方法.

  13. One-step multiplex real-time RT-PCR assay for detecting and genotyping wild-type group A rotavirus strains and vaccine strains (Rotarix® and RotaTeq® in stool samples

    Directory of Open Access Journals (Sweden)

    Rashi Gautam

    2016-01-01

    Full Text Available Background. Group A rotavirus (RVA infection is the major cause of acute gastroenteritis (AGE in young children worldwide. Introduction of two live-attenuated rotavirus vaccines, RotaTeq® and Rotarix®, has dramatically reduced RVA associated AGE and mortality in developed as well as in many developing countries. High-throughput methods are needed to genotype rotavirus wild-type strains and to identify vaccine strains in stool samples. Quantitative RT-PCR assays (qRT-PCR offer several advantages including increased sensitivity, higher throughput, and faster turnaround time. Methods. In this study, a one-step multiplex qRT-PCR assay was developed to detect and genotype wild-type strains and vaccine (Rotarix® and RotaTeq® rotavirus strains along with an internal processing control (Xeno or MS2 RNA. Real-time RT-PCR assays were designed for VP7 (G1, G2, G3, G4, G9, G12 and VP4 (P[4], P[6] and P[8] genotypes. The multiplex qRT-PCR assay also included previously published NSP3 qRT-PCR for rotavirus detection and Rotarix® NSP2 and RotaTeq® VP6 qRT-PCRs for detection of Rotarix® and RotaTeq® vaccine strains respectively. The multiplex qRT-PCR assay was validated using 853 sequence confirmed stool samples and 24 lab cultured strains of different rotavirus genotypes. By using thermostable rTth polymerase enzyme, dsRNA denaturation, reverse transcription (RT and amplification (PCR steps were performed in single tube by uninterrupted thermocycling profile to reduce chances of sample cross contamination and for rapid generation of results. For quantification, standard curves were generated using dsRNA transcripts derived from RVA gene segments. Results. The VP7 qRT-PCRs exhibited 98.8–100% sensitivity, 99.7–100% specificity, 85–95% efficiency and a limit of detection of 4–60 copies per singleplex reaction. The VP7 qRT-PCRs exhibited 81–92% efficiency and limit of detection of 150–600 copies in multiplex reactions. The VP4 q

  14. One-step multiplex real-time RT-PCR assay for detecting and genotyping wild-type group A rotavirus strains and vaccine strains (Rotarix® and RotaTeq®) in stool samples.

    Science.gov (United States)

    Gautam, Rashi; Mijatovic-Rustempasic, Slavica; Esona, Mathew D; Tam, Ka Ian; Quaye, Osbourne; Bowen, Michael D

    2016-01-01

    Background. Group A rotavirus (RVA) infection is the major cause of acute gastroenteritis (AGE) in young children worldwide. Introduction of two live-attenuated rotavirus vaccines, RotaTeq® and Rotarix®, has dramatically reduced RVA associated AGE and mortality in developed as well as in many developing countries. High-throughput methods are needed to genotype rotavirus wild-type strains and to identify vaccine strains in stool samples. Quantitative RT-PCR assays (qRT-PCR) offer several advantages including increased sensitivity, higher throughput, and faster turnaround time. Methods. In this study, a one-step multiplex qRT-PCR assay was developed to detect and genotype wild-type strains and vaccine (Rotarix® and RotaTeq®) rotavirus strains along with an internal processing control (Xeno or MS2 RNA). Real-time RT-PCR assays were designed for VP7 (G1, G2, G3, G4, G9, G12) and VP4 (P[4], P[6] and P[8]) genotypes. The multiplex qRT-PCR assay also included previously published NSP3 qRT-PCR for rotavirus detection and Rotarix® NSP2 and RotaTeq® VP6 qRT-PCRs for detection of Rotarix® and RotaTeq® vaccine strains respectively. The multiplex qRT-PCR assay was validated using 853 sequence confirmed stool samples and 24 lab cultured strains of different rotavirus genotypes. By using thermostable rTth polymerase enzyme, dsRNA denaturation, reverse transcription (RT) and amplification (PCR) steps were performed in single tube by uninterrupted thermocycling profile to reduce chances of sample cross contamination and for rapid generation of results. For quantification, standard curves were generated using dsRNA transcripts derived from RVA gene segments. Results. The VP7 qRT-PCRs exhibited 98.8-100% sensitivity, 99.7-100% specificity, 85-95% efficiency and a limit of detection of 4-60 copies per singleplex reaction. The VP7 qRT-PCRs exhibited 81-92% efficiency and limit of detection of 150-600 copies in multiplex reactions. The VP4 qRT-PCRs exhibited 98

  15. One-step microlithography

    Science.gov (United States)

    Kahlen, Franz-Josef; Sankaranarayanan, Srikanth; Kar, Aravinda

    1997-09-01

    Subject of this investigation is a one-step rapid machining process to create miniaturized 3D parts, using the original sample material. An experimental setup where metal powder is fed to the laser beam-material interaction region has been built. The powder is melted and forms planar, 2D geometries as the substrate is moved under the laser beam in XY- direction. After completing the geometry in the plane, the substrate is displaced in Z-direction, and a new layer of material is placed on top of the just completed deposit. By continuous repetition of this process, 3D parts wee created. In particular, the impact of the focal spot size of the high power laser beam on the smallest achievable structures was investigated. At a translation speed of 51 mm/s a minimum material thickness of 590 micrometers was achieved. Also, it was shown that a small Z-displacement has a negligible influence on the continuity of the material deposition over this power range. A high power CO2 laser was used as energy source, the material powder under investigation was stainless steel SS304L. Helium was used as shield gas at a flow rate of 15 1/min. The incident CO2 laser beam power was varied between 300 W and 400 W, with the laser beam intensity distribute in a donut mode. The laser beam was focused to a focal diameter of 600 (Mu) m.

  16. Development of a One-Step Immunocapture Real-Time RT-PCR Assay for Detection of Tobacco Mosaic Virus in Soil

    Directory of Open Access Journals (Sweden)

    Jin-Guang Yang

    2012-12-01

    Full Text Available Tobacco mosaic virus (TMV causes significant losses in many economically important crops. Contaminated soils may play roles as reservoirs and sources of transmission for TMV. In this study we report the development of an immunocapture real-time RT-PCR (IC-real-time RT-PCR assay for direct detection of TMV in soils without RNA isolation. A series of TMV infected leaf sap dilutions of 1:101, 1:102, 1:103, 1:104, 1:105 and 1:106 (w/v, g/mL were added to one gram of soil. The reactivity of DAS-ELISA and conventional RT-PCR was in the range of 1:102 and 1:103 dilution in TMV-infested soils, respectively. Meanwhile, the detection limit of IC-real-time RT-PCR sensitivity was up to 1:106 dilution. However, in plant sap infected by TMV, both IC-real-time RT-PCR and real-time RT-PCR were up to 1:106 dilution, DAS-ELISA could detect at least 1:103 dilution. IC-real-time RT-PCR method can use either plant sample extracts or cultivated soils, and show higher sensitivity than RT-PCR and DAS-ELISA for detection of TMV in soils. Therefore, the proposed IC-real-time RT-PCR assay provides an alternative for quick and very sensitive detection of TMV in soils, with the advantage of not requiring a concentration or RNA purification steps while still allowing detection of TMV for disease control.

  17. One-step Multiplex RT-PCR Method for Simultaneous Detection of Seed Transmissible Bacteria and Viruses in Pepper and Tomato Seeds

    Directory of Open Access Journals (Sweden)

    Kyusik Jeong

    2011-04-01

    Full Text Available The aim of this study was to develop specific and sensitive PCR-based procedures for simultaneous detection of economically important plant seed infection pathogenic bacteria and virus, Xanthomonns campestris pv. vesicatoria (Xcv, Clavibacter michiganensis subsp. michiganensis (Cmm, Erwinia carotovora subsp. carotovora (Ecc, Pepper mild mottle virus (PMMoV and Tobacco mild green mosaic virus (TMGMV in pepper and tomato seeds. Most of pepper and tomato bacterial and virus diseases are responsible for germination and growth obstruction. PCR with arbitral primers: selection of specific primers, performance of PCR with specific primers and determination of the threshold level for pathogens detection. To detect simultaneously the Xcv, Cmm, Ecc, PMMoV and TMGMV in pepper and tomato seeds, five pairs (Cmm-F/R, Ecc-F/R, Xcv-F/R, PMMoV-F/R, TMGMV-F/R of specific primer were synthesized by primer-blast program. The multiplex PCR for the five pathogens in pepper and tomato seeds could detect specially without interference among primers and/or cDNA of plant seeds and other plant pathogens. The PCR result for pathogen detection using 20 commercial pepper and 10 tomato seed samples, Ecc was detected from 4 pepper and 2 tomato seed samples, PMMoV was detected from 1 pepper seed sample, and PMMoV and TMGMV were simultaneously detected from 1 pepper seed sample.

  18. Development and evaluation of one-step rRT-PCR and immunohistochemical methods for detection of Rift Valley fever virus in biosafety level 2 diagnostic laboratories.

    Science.gov (United States)

    Drolet, Barbara S; Weingartl, Hana M; Jiang, Jieyuan; Neufeld, James; Marszal, Peter; Lindsay, Robbin; Miller, Myrna M; Czub, Markus; Wilson, William C

    2012-02-01

    Rift Valley fever virus (RVFV) is a zoonotic insect transmitted virus endemic to Africa and the Arabian Peninsula. Infection causes abortions and high mortality in newborn ruminants. The overall human infection rate is BSL-4 conditions and require inactivation and safety testing for use outside of containment. In this study, antiserum against recombinant RVFV-nucleocapsid (N) was produced to develop an immunohistochemical (IHC) assay which was subsequently evaluated on formalin fixed lamb and calf tissues at BSL-2 laboratory conditions. Antigen was detected by IHC in 79% of rRT-PCR-positive sheep and 70% of rRT-PCR-positive calf tissues tested. Once validated and approved by national regulatory agencies, these assays can be safely produced and distributed to regional diagnostic laboratories, providing capacity for early detection of RVFV in suspected ruminant samples.

  19. Establishment of thermophilic anaerobic terephthalic acid degradation system through one-step temperature increase startup strategy - Revealed by Illumina Miseq Sequencing.

    Science.gov (United States)

    Ma, Kai-Li; Li, Xiang-Kun; Wang, Ke; Meng, Ling-Wei; Liu, Gai-Ge; Zhang, Jie

    2017-10-01

    Over recent years, thermophilic digestion was constantly focused owing to its various advantage over mesophilic digestion. Notably, the startup approach of thermophilic digester needs to be seriously considered as unsuitable startup ways may result in system inefficiency. In this study, one-step temperature increase startup strategy from 37 °C to 55 °C was applied to establish a thermophilic anaerobic system treating terephthalic acid (TA) contained wastewater, meanwhile, the archaeal and bacterial community compositions at steady periods of 37 °C and 55 °C during the experimental process was also compared using Illumina Miseq Sequencing. The process operation demonstrated that the thermophilic TA degradation system was successfully established at 55 °C with over 95% COD reduction. For archaea community, the elevation of operational temperature from 37 °C to 55 °C accordingly increase the enrichment of hydrogenotrophic methanogens but decrease the abundance of the acetotrophic ones. While for bacterial community, the taxonomic analysis suggested that Syntrophorhabdus (27.40%) was the dominant genus promoting the efficient TA degradation under mesophilic condition, whereas OPB95 (24.99%) and TA06 (14.01%) related populations were largely observed and probably take some crucial role in TA degradation under thermophilic condition. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. 弹回引物鉴定军团菌属与嗜肺军团菌%A snapback primer mediated one-step PCR assay for the identification of Legionella and Legionella pneumophila strains

    Institute of Scientific and Technical Information of China (English)

    柳朔怡; 屈平华; 顾全

    2015-01-01

    目的:设计一种弹回引物荧光PCR方法鉴定军团菌属和嗜肺军团菌。方法通过分析军团菌16S rRNA基因序列,采用生物信息学方法设计引物,优化实验条件,对方法的特异性、灵敏度进行评估,并对186株环境军团菌分离株与15份环境水样进行鉴定。结果经弹回引物检测,军团菌属菌株在85℃~86℃处有扩增子熔解峰,嗜肺军团菌在71℃处有探针结合区熔解峰,非军团菌未检测到熔解峰。弹回引物对标准菌株DNA与模拟水样灵敏度分别为1 ng/μl与(1×103~1×104)/ml。弹回引物对环境分离株验证实验中,成功鉴定了186株军团菌和44株嗜肺军团菌;对15份环境水样直接检测,检出12份军团菌属阳性水样与4份嗜肺军团菌阳性水样。结论弹回引物荧光PCR方法可用于军团菌属和嗜肺军团菌的鉴定,具有较高的特异性与灵敏度。%Objective To test a snapback primer for the identification of Legionella and Legionella pneumophila ( L.pneumophila) strains in a one-step real-time PCR assay.Methods A novel primer was designed with a pair of genus-specific primers of Legionella strains.The species-specific probe sequences of L.pneumophila strains were linked at the 5′end of the reverse primer.The sensitivity and specificity of the novel PCR assay were tested with 43 types of Legionella and non-Legionella strains.The established PCR as-say was used to identify 186 wild Legionella strains isolated from 11 provinces of China and 15 environmental water samples.Results The amplicon melting peak of Legionella strains was detected at 85-86℃.The snapback melting peak of L.pneumophila was detected at 71℃.No melting peak of non-Legionella strains was detected.The sensitivity of the standard strains and simulated water samples were 1 ng/μl DNA tem-plates and (1×103-1×104 )/ml, respectively.186 Legionella strains and 44 L.pneumophila strains isolated from environmental water

  1. Establishment and Application of One-step RT-PCR Assay for BVDV Detection%牛病毒性腹泻病毒一步法.RT-PCR检测方法的建立及应用

    Institute of Scientific and Technical Information of China (English)

    于新友; 李天芝; 沈志强

    2015-01-01

    An one-step RT-PCR assay for detection of BVDV was established using a pair of primers based on the 5'-untranslated region gene of bovine viral diarrhea virus (BVDV), and the speciifcity, sensitivity were studied.This method speciifcally amplify a fragment from BVDV, but not from control virus, with a detection limit of 1pg RNA of BVDV.Therefore the established one-step RT-PCR technique provided a sensitive, speciifc, fast and reliablemethod for diagnosis and epizootic study of the BVDV.%根据牛病毒性腹泻病毒(BVDV)5′端非编码区基因保守序列设计引物,建立了检测BVDV一步法反转录-聚合酶链(RT-PCR)方法,并对其特异性、敏感性进行了研究。结果表明,该方法对BVDV检测的灵敏度达到1pg RNA,特异性强、敏感性高,可用于牛病毒性腹泻病的早期确诊和病毒鉴定。

  2. One step forwards for the routine use of high-throughput DNA sequencing in environmental monitoring. An efficient and standardizable method to maximize the detection of environmental bacteria.

    Science.gov (United States)

    Bruno, Antonia; Sandionigi, Anna; Galimberti, Andrea; Siani, Eleonora; Labra, Massimo; Cocuzza, Clementina; Ferri, Emanuele; Casiraghi, Maurizio

    2017-02-01

    We propose an innovative, repeatable, and reliable experimental workflow to concentrate and detect environmental bacteria in drinking water using molecular techniques. We first concentrated bacteria in water samples using tangential flow filtration and then we evaluated two methods of environmental DNA extraction. We performed tests on both artificially contaminated water samples and real drinking water samples. The efficiency of the experimental workflow was measured through qPCR. The successful applicability of the high-throughput DNA sequencing (HTS) approach was demonstrated on drinking water samples. Our results demonstrate the feasibility of our approach in high-throughput-based studies, and we suggest incorporating it in monitoring strategies to have a better representation of the microbial community. In the recent years, HTS techniques have become key tools in the study of microbial communities. To make the leap from academic laboratories to the routine monitoring (e.g., water treatment plants laboratories), we here propose an experimental workflow suitable for the introduction of HTS as a standard method for detecting environmental bacteria. © 2016 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

  3. Pressure-driven one-step solid phase-based on-chip sample preparation on a microfabricated plastic device and integration with flow-through polymerase chain reaction (PCR).

    Science.gov (United States)

    Tran, Hong Hanh; Trinh, Kieu The Loan; Lee, Nae Yoon

    2013-10-01

    In this study, we fabricate a monolithic poly(methylmethacrylate) (PMMA) microdevice on which solid phase-based DNA preparation and flow-through polymerase chain reaction (PCR) units were functionally integrated for one-step sample preparation and amplification operated by pressure. Chelex resin, which is used as a solid support for DNA preparation, can capture denatured proteins but releases DNA, and the purified DNA can then be used as a template in a subsequent amplification process. Using the PMMA microdevices, DNA was successfully purified from both Escherichia coli and human hair sample, and the plasmid vector inserted in E. coli and the D1S80 locus in human genomic DNA were successfully amplified from on-chip purified E. coli and human hair samples. Furthermore, the integration potential of the proposed sample preparation and flow-through PCR units was successfully demonstrate on a monolithic PMMA microdevice with a seamless flow, which could pave the way for a pressure-driven, simple one-step sample preparation and amplification with greatly decreased manufacture cost and enhanced device disposability.

  4. DNA Isolation from Paraffin Sections by an Adjusted One-Step Protocol and its Qualification Test by PCR%一步法分离石蜡切片DNA的改进与鉴定

    Institute of Scientific and Technical Information of China (English)

    彭剑桥; 雷平; 杨秦; 朱敏

    2015-01-01

    ,by which the DNA content was extracted by one-step digestion with proteinase K lysis buffer;its effectiveness were evidenced by PCR of mitochondrial DNA and nuclear DNA fragments.

  5. A Rapid and Sensitive One Step-SYBR Green Based Semi Quantitative Real Time RT-PCR for the Detection of peste des petits ruminants Virus in the Clinical Samples

    Institute of Scientific and Technical Information of China (English)

    Vinayagamurthy Balamurugan; Arnab Sen; Gnanavel Venkatesan; Vinita Yadav; Vandna Bhanot; Veerakyathappa Bhanuprakash; Raj Kumar Singh

    2012-01-01

    A sensitive and rapid single step real time (rt) RT-PCR was standardized using one-step Brilliant SYBR Green kit(R) for detection and semi-quantitation of peste des petitis ruminants virus (PPRV) using the virus RNA and matrix (M) protein gene-specific primers and compared with established conventional RT-PCR and TaqMan RT-PCR.The assay amplifies a 124 bp fragment of the PPRV M gene with Tm of 78.28 to 78.50.The assay was linear within a range of 50 ng to 0.5 fg total virus RNA with a detection limit (sensitivity) of 0.5 fg.Based on the serial dilution of the live-attenuated PPR vaccine virus,the detection limit was ~0.0001 cell culture infectious dose 50% units (TCID50).Additionally,swab materials spiked with known titre of vaccine virus were equally well detected in the assay.The standardized rt RT-PCR was easily employed for the detection of PPRV nucleic acid directly in the field and experimental clinical samples.The assay detected the PPRV nucleic acid as early as 3 day post infection (dpi) and up to 20 dpi in swab materials from the experimental samples.The assay was rapid and more sensitive than TaqMan and conventional RT-PCR in the detection of PPRV nucleic acid from the PPR suspected clinical samples of sheep and goats.Therefore,the established,simplified SYBR green rt RT-PCR is an alternative test to the already existing various diagnostic assays and could be useful for rapid clinical diagnosis with advantage in reducing risk of contamination.

  6. A one-step, triplex, real-time RT-PCR assay for the simultaneous detection of enterovirus 71, coxsackie A16 and pan-enterovirus in a single tube.

    Directory of Open Access Journals (Sweden)

    Shiyin Zhang

    Full Text Available The recent, ongoing epidemic of hand, foot, and mouth disease (HFMD, which is caused by enterovirus infection, has affected millions of children and resulted in thousands of deaths in China. Enterovirus 71 (EV71 and coxsackie A16 (CA16 are the two major distinct pathogens for HFMD. However, EV71 is more commonly associated with neurologic complications and even fatalities. Therefore, simultaneously detecting and differentiating EV71 and CA16 specifically from other enteroviruses for diagnosing HFMD is important. Here, we developed a one-step, triplex, real-time RT-PCR assay for the simultaneous detection of EV71, CA16, and pan-enterovirus (EVs in a single tube with an internal amplification control. The detection results for the serially diluted viruses indicate that the lower limit of detection for this assay is 0.001-0.04 TCID50/ml, 0.02 TCID50/ml, and 0.001 TCID50/ml for EVs, EV71, and CA16, respectively. After evaluating known HFMD virus stocks of 17 strains of 16 different serotypes, this assay showed a favorable detection spectrum and no obvious cross-reactivity. The results for 141 clinical throat swabs from HFMD-suspected patients demonstrated sensitivities of 98.4%, 98.7%, and 100% for EVs, EV71, and CA16, respectively, and 100% specificity for each virus. The application of this one-step, triplex, real-time RT-PCR assay in clinical units will contribute to HFMD surveillance and help to identify causative pathogen in patients with suspected HFMD.

  7. One-Step Recovery of scFv Clones from High-Throughput Sequencing-Based Screening of Phage Display Libraries Challenged to Cells Expressing Native Claudin-1

    Directory of Open Access Journals (Sweden)

    Emanuele Sasso

    2015-01-01

    Full Text Available Expanding the availability of monoclonal antibodies interfering with hepatitis C virus infection of hepatocytes is an active field of investigation within medical biotechnologies, to prevent graft reinfection in patients subjected to liver transplantation and to overcome resistances elicited by novel antiviral drugs. In this paper, we describe a complete pipeline for screening of phage display libraries of human scFvs against native Claudin-1, a tight-junction protein involved in hepatitis C virus infection, expressed on the cell surface of human hepatocytes. To this aim, we implemented a high-throughput sequencing approach for library screening, followed by a simple and effective strategy to recover active binder clones from enriched sublibraries. The recovered clones were successfully converted to active immunoglobulins, thus demonstrating the effectiveness of the whole procedure. This novel approach can guarantee rapid and cheap isolation of antibodies for virtually any native antigen involved in human diseases, for therapeutic and/or diagnostic applications.

  8. The one step fermionic ladder

    Science.gov (United States)

    Das, Joy Prakash; Setlur, Girish S.

    2017-10-01

    The one step fermionic ladder refers to two parallel Luttinger Liquids (poles of the ladder) placed such that there is a finite probability of electrons hopping between the two poles at a pair of opposing points along each of the poles. The many-body Green function for such a system is calculated in presence of forward scattering interactions using the powerful non-chiral bosonization technique (NCBT). This technique is based on a non-standard harmonic analysis of the rapidly varying parts of the density fields appropriate for the study of strongly inhomogeneous ladder systems. The closed analytical expression for the correlation function obtained from NCBT is nothing but the series involving the RPA (Random Phase Approximation) diagrams in powers of the forward scattering coupling strength resummed to include only the most singular terms with the source of inhomogeneities treated exactly. Finally the correlation functions are used to study physical phenomena such as Friedel oscillations and the conductance of such systems with the potential difference applied across various ends.

  9. Molecular characterization of two Rocio flavivirus strains isolated during the encephalitis epidemic in São Paulo State, Brazil and the development of a one-step RT-PCR assay for diagnosis.

    Science.gov (United States)

    Coimbra, Terezinha Lisieux Moraes; Santos, Raimundo N; Petrella, Selma; Nagasse-Sugahara, Teresa Keico; Castrignano, Silvana Beres; Santos, Cecília L Simões

    2008-01-01

    Rocio virus (ROCV) was responsible for an explosive encephalitis epidemic in the 1970s affecting about 1,000 residents of 20 coastland counties in São Paulo State, Brazil. ROCV was first isolated in 1975 from the cerebellum of a fatal human case of encephalitis. Clinical manifestations of the illness are similar to those described for St. Louis encephalitis. ROCV shows intense antigenic cross-reactivity with Japanese encephalitis complex (JEC) viruses, particularly with Ilheus (ILHV), St. Louis encephalitis, Murray Valley and West Nile viruses. In this study, we report a specific RT-PCR assay for ROCV diagnosis and the molecular characterization of the SPAn37630 and SPH37623 strains. Partial nucleotide sequences of NS5 and E genes determined from both strains were used in phylogenetic analysis. The results indicated that these strains are closely related to JEC viruses, but forming a distinct subclade together with ILHV, in accordance with results recently reported by Medeiros et al. (2007).

  10. Signal to cut-off (S/CO ratio and detection of HCV genotype 1 by real-time PCR one-step method: is there any direct relationship?

    Directory of Open Access Journals (Sweden)

    Guilherme Albertoni

    2010-04-01

    Full Text Available BACKGROUND: Polymerase chain reaction (PCR methods play an essential role in providing data related to diagnosis, monitoring and treatment of hepatitis C virus (HCV infection. EIA results are reported as ''reactive'' or ''non reactive'' and EIA S/CO ratio may also be reported as ''high'' or ''low.'' This study aimed to evaluate the performance of a real-time RT-PCR and assess whether there is relationship between S/CO and PCR results. STUDY DESIGN AND METHODS: Sera from blood donors were analyzed by Enzyme-Linked Immunosorbent Assay (ELISA and RT-PCR assay to detect HCV infection. RESULTS: The RT-PCR assay to genotypes 1a/b showed an acceptable linear response in serial dilutions. The samples were divided into two groups based on their serological results: group A - S/CO ratio 3 (41 samples. Viral loads were confirmed positive in group B samples in 90%, and in group A samples were confirmed positive in only 13% by RT-PCR. CONCLUSION: The methodology used was able to detect the presence of RNA-HCV genotype I in 90% of the samples serologically positive in group B. All negative samples were sent to search for other genotypes of HCV (genotypes 2-6 and were confirmed as negative. These data suggests that these negative samples may have HCV RNA viral load below the detection limit of our test (310 IU/ mL, or a false positive result in serological test, or spontaneous viral clearance occurred.

  11. Signal to cut-off (S/CO ratio and detection of HCV genotype 1 by real-time PCR one-step method: is there any direct relationship?

    Directory of Open Access Journals (Sweden)

    Guilherme Albertoni

    Full Text Available BACKGROUND: Polymerase chain reaction (PCR methods play an essential role in providing data related to diagnosis, monitoring and treatment of hepatitis C virus (HCV infection. EIA results are reported as ''reactive'' or ''non reactive'' and EIA S/CO ratio may also be reported as ''high'' or ''low.'' This study aimed to evaluate the performance of a real-time RT-PCR and assess whether there is relationship between S/CO and PCR results. STUDY DESIGN AND METHODS: Sera from blood donors were analyzed by Enzyme-Linked Immunosorbent Assay (ELISA and RT-PCR assay to detect HCV infection. RESULTS: The RT-PCR assay to genotypes 1a/b showed an acceptable linear response in serial dilutions. The samples were divided into two groups based on their serological results: group A - S/CO ratio 3 (41 samples. Viral loads were confirmed positive in group B samples in 90%, and in group A samples were confirmed positive in only 13% by RT-PCR. CONCLUSION: The methodology used was able to detect the presence of RNA-HCV genotype I in 90% of the samples serologically positive in group B. All negative samples were sent to search for other genotypes of HCV (genotypes 2-6 and were confirmed as negative. These data suggests that these negative samples may have HCV RNA viral load below the detection limit of our test (310 IU/ mL, or a false positive result in serological test, or spontaneous viral clearance occurred.

  12. The use of a one-step real-time reverse transcription polymerase chain reaction (rRT-PCR) for the surveillance of viral hemorrhagic septicemia virus (VHSV) in Minnesota.

    Science.gov (United States)

    Phelps, Nicholas B D; Patnayak, Devi P; Jiang, Yin; Goyal, Sagar M

    2012-12-01

    Viral hemorrhagic septicemia virus (VHSV) is a highly contagious and pathogenic virus of fish. The virus infects more than 70 fish species worldwide, in both fresh and salt water. A new viral strain (VHSV-IVb) has proven both virulent and persistent, spreading throughout the Great Lakes of North America and to inland water bodies in the region. To better understand the geographic distribution of the virus, we used a modified real-time reverse transcription polymerase chain reaction (rRT-PCR) assay for high-throughput testing of fish for VHSV. The assay was shown to be twice as sensitive as the gold standard, virus isolation, and did not cross react with other viruses found in fish. In addition, the diagnostic turnaround time was reduced from 28 to 30 d for virus isolation to 2-4 d for rRT-PCR. To demonstrate the usefulness of the rRT-PCR assay, 115 high-priority water bodies in Minnesota were tested by both methods from April 2010 to June 2011. All survey sites tested negative for VHSV by both methods. The survey results have informed fisheries managers on the absence of VHSV in Minnesota and have better prepared them for the eventual arrival of the disease. In addition, the results demonstrate the value of this rRT-PCR as a surveillance tool to rapidly identify an outbreak so that it can be controlled in a timely manner.

  13. Rapid identification and differentiation of clinical isolates of enteropathogenic Escherichia coli (EPEC), atypical EPEC, and Shiga toxin-producing Escherichia coli by a one-step multiplex PCR method

    NARCIS (Netherlands)

    Müller, Daniel; Hagedorn, Peter; Brast, Sabine; Heusipp, Gerhard; Bielaszewska, Martina; Friedrich, Alexander W; Karch, Helge; Schmidt, M Alexander

    2006-01-01

    Enteropathogenic Escherichia coli (EPEC), atypical enteropathogenic E. coli, and Shiga toxin-producing E. coli differ in their virulence factor profiles, clinical manifestations, and prognosis, and they require different therapeutic measures. We developed and evaluated a robust multiplex PCR to iden

  14. Rapid identification and differentiation of clinical isolates of enteropathogenic Escherichia coli (EPEC), atypical EPEC, and Shiga toxin-producing Escherichia coli by a one-step multiplex PCR method

    NARCIS (Netherlands)

    Müller, Daniel; Hagedorn, Peter; Brast, Sabine; Heusipp, Gerhard; Bielaszewska, Martina; Friedrich, Alexander W; Karch, Helge; Schmidt, M Alexander

    2006-01-01

    Enteropathogenic Escherichia coli (EPEC), atypical enteropathogenic E. coli, and Shiga toxin-producing E. coli differ in their virulence factor profiles, clinical manifestations, and prognosis, and they require different therapeutic measures. We developed and evaluated a robust multiplex PCR to iden

  15. Detection of the Genomic Sequence of Yellow Fever Virus by One-step RT-PCR%黄热病毒的一步RT-PCR法检测

    Institute of Scientific and Technical Information of China (English)

    彭文明; 邓永强; 于曼; 范保昌; 祝庆余; 秦鄂德

    2003-01-01

    自不同稀释度的乳鼠脑病毒悬液中制备总RNA,在自制缓冲液条件下,进行一步RT-PCR法检测.对一步RT-PCR法与常规RT-PCR的敏感性进行比较,并且以基孔肯亚病毒和登革1-4型病毒RNA为模板进行特异性观察.结果表明,本研究建立的一步RT-PCR法可检出2.8×103PFU的病毒,敏感性比常规RT-PCR法高10倍,且与基孔肯亚病毒、登革病毒1-4型无交叉反应,具有良好的特异性和敏感性,适用于黄热病毒的病原学检测.

  16. A rapid, one step molecular identification of Trichoderma citrinoviride and Trichoderma reesei.

    Science.gov (United States)

    Saroj, Dina B; Dengeti, Shrinivas N; Aher, Supriya; Gupta, Anil K

    2015-06-01

    Trichoderma species are widely used as production hosts for industrial enzymes. Identification of Trichoderma species requires a complex molecular biology based identification involving amplification and sequencing of multiple genes. Industrial laboratories are required to run identification tests repeatedly in cell banking procedures and also to prove absence of production host in the product. Such demands can be fulfilled by a brief method which enables confirmation of strain identity. This communication describes one step identification method for two common Trichoderma species; T. citrinoviride and T. reesei, based on identification of polymorphic region in the nucleotide sequence of translation elongation factor 1 alpha. A unique forward primer and common reverse primer resulted in 153 and 139 bp amplicon for T. citrinoviride and T. reesei, respectively. Simplification was further introduced by using mycelium as template for PCR amplification. Method described in this communication allows rapid, one step identification of two Trichoderma species.

  17. One-step construction of mutagenesis libraries via in situ error-prone PCR%通过原位易错PCR一步构建基因突变文库

    Institute of Scientific and Technical Information of China (English)

    王未未; 张永昌; 刘明杰; 邵蔚蓝

    2014-01-01

    主要介绍一种通过原位易错PCR构建随机突变文库的新技术.本实验室最近发表的一项国际专利中,利用来源于海栖热孢菌的极耐热性DNA连接酶,在传统PCR循环中加入一个连接步骤,即变性一退火一延伸一连接的四步循环法PCR,从而实现环状质粒的PCR指数扩增(PPCP).原位易错PCR中所用引物为一段线性双链DNA,它含有与模板质粒不同的筛选标记,产物转化宿主菌后,模板质粒在筛选平板上被直接剔除.筛选到的阳性突变子可用作模板直接进入突变文库的再次构建,通过筛选获得二级或多级累加的正突变.利用这种方法构建了一个木聚糖酶基因和一个纤维素酶基因的随机突变文库,并筛选出具有正向突变的蛋白,证明以PPCP为基础的原位易错PCR技术,为基因定向进化提供了一种快速有效的随机突变文库构建的新方法.

  18. A method for amplification of unknown flanking sequences based on touchdown PCR and suppression-PCR.

    Science.gov (United States)

    Gao, Song; He, Dan; Li, Guangquan; Zhang, Yanhua; Lv, Huiying; Wang, Li

    2016-09-15

    Thermal asymmetric staggered PCR is the most widely used technique to obtain the flanking sequences. However, it has some limitations, including a low rate of positivity, and complex operation. In this study, a improved method of it was made based on suppression-PCR and touchdown PCR. The PCR fragment obtained by the amplification was used directly for sequencing after gel purification. Using this improved method, the positive rate of amplified flanking sequences of the ATMT mutants reached 99%. In addition, the time from DNA extraction to flanking sequence analysis was shortened to 2 days with about 6 dollars each sample.

  19. Sexing Bovine Embryos Using PCR Amplification of Bovine SRY Sequence

    Institute of Scientific and Technical Information of China (English)

    曾溢滔; 张美兰; 陈美珏; 周霞娣; 黄英; 任兆瑞; 黄淑帧; 胡明信; 吴学清; 高建明; 张斌; 徐慧如

    1994-01-01

    This study analyses the bovine SRY DNA sequence by direct sequencing procedure, followed by the designation of the PCR primers specific for bovine SRY. Using PCR amplification of bovine SRY gene, the embryo sex was determined. The results of the embryo sex identification were confirmed after the embryo transfer and pregnancies.

  20. One-step fabrication of multifunctional micromotors

    Science.gov (United States)

    Gao, Wenlong; Liu, Mei; Liu, Limei; Zhang, Hui; Dong, Bin; Li, Christopher Y.

    2015-08-01

    Although artificial micromotors have undergone tremendous progress in recent years, their fabrication normally requires complex steps or expensive equipment. In this paper, we report a facile one-step method based on an emulsion solvent evaporation process to fabricate multifunctional micromotors. By simultaneously incorporating various components into an oil-in-water droplet, upon emulsification and solidification, a sphere-shaped, asymmetric, and multifunctional micromotor is formed. Some of the attractive functions of this model micromotor include autonomous movement in high ionic strength solution, remote control, enzymatic disassembly and sustained release. This one-step, versatile fabrication method can be easily scaled up and therefore may have great potential in mass production of multifunctional micromotors for a wide range of practical applications.Although artificial micromotors have undergone tremendous progress in recent years, their fabrication normally requires complex steps or expensive equipment. In this paper, we report a facile one-step method based on an emulsion solvent evaporation process to fabricate multifunctional micromotors. By simultaneously incorporating various components into an oil-in-water droplet, upon emulsification and solidification, a sphere-shaped, asymmetric, and multifunctional micromotor is formed. Some of the attractive functions of this model micromotor include autonomous movement in high ionic strength solution, remote control, enzymatic disassembly and sustained release. This one-step, versatile fabrication method can be easily scaled up and therefore may have great potential in mass production of multifunctional micromotors for a wide range of practical applications. Electronic supplementary information (ESI) available: Videos S1-S4 and Fig. S1-S3. See DOI: 10.1039/c5nr03574k

  1. One-step lowrank wave extrapolation

    KAUST Repository

    Sindi, Ghada Atif

    2014-01-01

    Wavefield extrapolation is at the heart of modeling, imaging, and Full waveform inversion. Spectral methods gained well deserved attention due to their dispersion free solutions and their natural handling of anisotropic media. We propose a scheme a modified one-step lowrank wave extrapolation using Shanks transform in isotropic, and anisotropic media. Specifically, we utilize a velocity gradient term to add to the accuracy of the phase approximation function in the spectral implementation. With the higher accuracy, we can utilize larger time steps and make the extrapolation more efficient. Applications to models with strong inhomogeneity and considerable anisotropy demonstrates the utility of the approach.

  2. 一步法RT-PCR检测血清混合样品在BVDV清除计划中的应用%The Application of the One-Step RT-PCR Method to Detect the Serum Mixed Samples in BVDV Eradication Programme

    Institute of Scientific and Technical Information of China (English)

    黄凯; 邵晓磊; 马翀

    2011-01-01

    Total 58 of BVDV (Bovine Viral diarrhea virus) antigen positive sera were detected by one-step RT-PCR method. The results revealed that the minimum detection limit was 5μL/per sample, and the standard sera value of OD was 0.3. In addition, the mathematical deduction proved that the test cost of BVDV eradication programme was the lowest, when the number of the serum mixed samples were 10 to 30. Compared with only using ELISA-Ag, the testing cost of RT-PCR and ELISA-Ag conjunctive use reduced 70%. In one words, the one-step RT-PCR which was used in our study has high sensitivity and specificity. When taking ELISA-Ag conjunotive use in BVDV eradication programme, the test cost could be reduced greatly, so this method was worth to use.%利用一步法RT-PCR对58份BVDV抗原阳性血清进行检测.试验证明,对OD450=0.3的标准血清,该方法的最低检出限为5μL/头,血清混合检测时至少可将60份OD450>0.3的阳性血清等量混合.此外,RT-PCR与ELISA-Ag联合使用时,数学推导证明当混合样品为10~30个/份时,BVDV清除计划检测成本最低,相比单独使用ELISA-Ag,成本至少下降70%.综上,本试验确立的一步法RT-PCR灵敏度高,特异性好,联合ELISA-Ag使用,可大幅降低BVDV清除计划的检测成本,故值得推广使用.

  3. 布鲁氏菌种及种内部分生物型快速PCR鉴定方法的建立及应用研究%Development and application of one-step polymerase chain reaction(PCR) for rapid identification of Brucella species and some biovars

    Institute of Scientific and Technical Information of China (English)

    李振军; 侯雪新; 孙渭歌; 贾雪; 田国忠

    2013-01-01

    目的 建立一步法PCR快速鉴定布鲁氏菌种及种内部分生物型.方法 设计6对引物,建立一步法PCR反应,将布鲁氏菌6个种和种内某些生物型进行鉴定,应用该方法检测了27株布鲁氏菌参考菌株和239株临床分离的布鲁氏菌,并与生物学分型方法进行比较.结果 通过一步法PCR能够将待检菌株准确的鉴定到布鲁氏菌种,对于猪种可以定位到生物型和疫苗株;对于牛种可以鉴定到牛种生物型1、3、4 与2、5、6、7、9两组生物型;对于羊种可以鉴定到1与2、3两组生物型和羊种疫苗株.生物学分型方法和PCR方法准确鉴定到种水平的符合率分别为98.33%和100%.结论 一步法PCR是一种快速、特异、简便而低费用的鉴定布鲁氏菌种的分子分型方法.%Objective To develop a one-step PCR assay for rapid discrimination of six Brucella species and some intraspecific biovars.Methods Using 6 pairs of primers in one-step PCR to differentiate six classical Brucella species and some biovar in ordinary PCR instrument.The tested strains including 27 reference strains of six Brucella species and 239 Brucella strains were estimated by the PCR assay and biological identification methods.Results The six Brucella species could be precisely differentiated by the onestep PCR assay from the tested strains.Five biovars and vaccine strain of B.suis species could be determined,and biovars 1,3,4 and biovars 2,5,6,7,9 of B.abortus species could be identified at the level of their biovar,moreover,biovars 1,2 and 3,and vaccine strain Rev 1 of B.melitensis species were also discriminated at the biovar and strain level.The accurate rates of the biological identification method and the PCR assay were 98.33% and 100% respectively.Conclusion One-step PCR assay was a rapid,specific,and low cost method for identification of Brucella species and discriminating biovars in ordinary PCR instrument.

  4. Microbiome profiling by illumina sequencing of combinatorial sequence-tagged PCR products

    NARCIS (Netherlands)

    G.B. Gloor (Gregory); R.B.S. Hummelen (Ruben); J.M. Macklaim (Jean); R.J. Dickson (Russell); A.D. Fernandes (Andrew); R.A. MacPhee (Roderick); G. Reid (Gregor)

    2010-01-01

    textabstractWe developed a low-cost, high-throughput microbiome profiling method that uses combinatorial sequence tags attached to PCR primers that amplify the rRNA V6 region. Amplified PCR products are sequenced using an Illumina paired-end protocol to generate millions of overlapping reads.

  5. One-step real-time fluorescent quantitative PCR assay for mumps virus in clinical saliva specimens%腮腺炎病毒临床口漱液样本的一步法实时荧光定量PCR检测

    Institute of Scientific and Technical Information of China (English)

    施海晶; 王晶晶; 陈俊英; 陈巍; 潘明; 赵钢; 孙强明

    2013-01-01

    Objective To develop an one-step real-time fluorescent quantitative PCR assay for mumps virus (MuV) in clinical saliva specimens and provide a basis for clinical diagnosis,prevention and control of mumps.Methods A total of 101 clinical saliva specimens collected from suspected patients with mumps in Yunnan and Sichuan Province as well as Guangxi Zhuang Autonomous Region,China were determined by cell culture-MuV specific nested PCR and real-time PCR with TaqMan probe respectively,based on which the sensitivities of the two methods were compared.Results Thirty-one MuV-positive specimens were found by cell culture-MuV specific nested PCR,all of which belonged to genotype F as proved by phylogenetic tree.However,41 MuV-positive specimens were found by real-time PCR with TaqMan probe,including the 31 positive specimens proved by cell culture-MuV specific nested PCR,indicating that the positive rate of Muv by real-time RT-PCR with TaqMan probe (40.59%) was higher than that by traditional cell culture-nested PCR (30.69%).Conclusion The sensitivity,specificity and simplicity of real-time PCR with TaqMan probe were higher than those of traditional cell culture-MuV specific nested PCR,which might be used for the clinical diagnosis,prevention and control of mumps.%目的 建立腮腺炎病毒(mumps virus,MuV)临床口漱液样本一步法荧光定量PCR检测方法,为腮腺炎的临床诊断及免疫防控提供依据.方法 对101份采集自中国南部3个省、自治区(云南、四川、广西)的临床疑似腮腺炎患者口漱液样本,分别采用细胞培养-MuV特异的巢式PCR法及TaqMan探针Real-time PCR法进行检测,比较两种方法检测MuV的灵敏性.结果 细胞培养-MuV特异的巢式PCR法共检出31份MuV阳性样本,系统进化分析表明,该31株MuV均属于F基因亚型;TaqMan探针Real-time PCR法共检出41份MuV阳性样本,其中包含了细胞培养-MuV特异的巢式PCR法检出的31份阳性样本,TaqMan探针Real-time RT

  6. Directed PCR-free engineering of highly repetitive DNA sequences

    Directory of Open Access Journals (Sweden)

    Preissler Steffen

    2011-09-01

    Full Text Available Abstract Background Highly repetitive nucleotide sequences are commonly found in nature e.g. in telomeres, microsatellite DNA, polyadenine (poly(A tails of eukaryotic messenger RNA as well as in several inherited human disorders linked to trinucleotide repeat expansions in the genome. Therefore, studying repetitive sequences is of biological, biotechnological and medical relevance. However, cloning of such repetitive DNA sequences is challenging because specific PCR-based amplification is hampered by the lack of unique primer binding sites resulting in unspecific products. Results For the PCR-free generation of repetitive DNA sequences we used antiparallel oligonucleotides flanked by restriction sites of Type IIS endonucleases. The arrangement of recognition sites allowed for stepwise and seamless elongation of repetitive sequences. This facilitated the assembly of repetitive DNA segments and open reading frames encoding polypeptides with periodic amino acid sequences of any desired length. By this strategy we cloned a series of polyglutamine encoding sequences as well as highly repetitive polyadenine tracts. Such repetitive sequences can be used for diverse biotechnological applications. As an example, the polyglutamine sequences were expressed as His6-SUMO fusion proteins in Escherichia coli cells to study their aggregation behavior in vitro. The His6-SUMO moiety enabled affinity purification of the polyglutamine proteins, increased their solubility, and allowed controlled induction of the aggregation process. We successfully purified the fusions proteins and provide an example for their applicability in filter retardation assays. Conclusion Our seamless cloning strategy is PCR-free and allows the directed and efficient generation of highly repetitive DNA sequences of defined lengths by simple standard cloning procedures.

  7. PCR primers for metazoan mitochondrial 12S ribosomal DNA sequences.

    Directory of Open Access Journals (Sweden)

    Ryuji J Machida

    Full Text Available BACKGROUND: Assessment of the biodiversity of communities of small organisms is most readily done using PCR-based analysis of environmental samples consisting of mixtures of individuals. Known as metagenetics, this approach has transformed understanding of microbial communities and is beginning to be applied to metazoans as well. Unlike microbial studies, where analysis of the 16S ribosomal DNA sequence is standard, the best gene for metazoan metagenetics is less clear. In this study we designed a set of PCR primers for the mitochondrial 12S ribosomal DNA sequence based on 64 complete mitochondrial genomes and then tested their efficacy. METHODOLOGY/PRINCIPAL FINDINGS: A total of the 64 complete mitochondrial genome sequences representing all metazoan classes available in GenBank were downloaded using the NCBI Taxonomy Browser. Alignment of sequences was performed for the excised mitochondrial 12S ribosomal DNA sequences, and conserved regions were identified for all 64 mitochondrial genomes. These regions were used to design a primer pair that flanks a more variable region in the gene. Then all of the complete metazoan mitochondrial genomes available in NCBI's Organelle Genome Resources database were used to determine the percentage of taxa that would likely be amplified using these primers. Results suggest that these primers will amplify target sequences for many metazoans. CONCLUSIONS/SIGNIFICANCE: Newly designed 12S ribosomal DNA primers have considerable potential for metazoan metagenetic analysis because of their ability to amplify sequences from many metazoans.

  8. PCR master mixes harbour murine DNA sequences. Caveat emptor!

    Directory of Open Access Journals (Sweden)

    Philip W Tuke

    Full Text Available BACKGROUND: XMRV is the most recently described retrovirus to be found in Man, firstly in patients with prostate cancer (PC and secondly in 67% of patients with chronic fatigue syndrome (CFS and 3.7% of controls. Both disease associations remain contentious. Indeed, a recent publication has concluded that "XMRV is unlikely to be a human pathogen". Subsequently related but different polytropic MLV (pMLV sequences were also reported from the blood of 86.5% of patients with CFS. and 6.8% of controls. Consequently we decided to investigate blood donors for evidence of XMRV/pMLV. METHODOLOGY/PRINCIPAL FINDINGS: Testing of cDNA prepared from the whole blood of 80 random blood donors, generated gag PCR signals from two samples (7C and 9C. These had previously tested negative for XMRV by two other PCR based techniques. To test whether the PCR mix was the source of these sequences 88 replicates of water were amplified using Invitrogen Platinum Taq (IPT and Applied Biosystems Taq Gold LD (ABTG. Four gag sequences (2D, 3F, 7H, 12C were generated with the IPT, a further sequence (12D by ABTG re-amplification of an IPT first round product. Sequence comparisons revealed remarkable similarities between these sequences, endogeous MLVs and the pMLV sequences reported in patients with CFS. CONCLUSIONS/SIGNIFICANCE: Methodologies for the detection of viruses highly homologous to endogenous murine viruses require special caution as the very reagents used in the detection process can be a source of contamination and at a level where it is not immediately apparent. It is suggested that such contamination is likely to explain the apparent presence of pMLV in CFS.

  9. Rapid One-Step Selection Method for Generating Nucleic Acid Aptamers: Development of a DNA Aptamer against alpha-Bungarotoxin

    DEFF Research Database (Denmark)

    Lauridsen, Lasse Holm; Shamaileh, Hadi A.; Edwards, Stacey L.

    2012-01-01

    Background: Nucleic acids based therapeutic approaches have gained significant interest in recent years towards the development of therapeutics against many diseases. Recently, research on aptamers led to the marketing of Macugen (R), an inhibitor of vascular endothelial growth factor (VEGF...... by PCR enrichment of the selected aptamers. One round of selection successfully identified a DNA aptamer sequence with a binding affinity of 7.58 mu M. Conclusion: We have demonstrated a one-step method for rapid production of nucleic acid aptamers. Although the reported binding affinity is in the low...... micromolar range, we believe that this could be further improved by using larger targets, increasing the stringency of selection and also by combining a capillary electrophoresis separation prior to the one-step selection. Furthermore, the method presented here is a user-friendly, cheap and an easy way...

  10. Deletion of Efflux Pump Gene acrAB in E. coli with PCR Product One-step Method%利用PCR产物一步法敲除大肠埃希菌的外排泵基因acrAB

    Institute of Scientific and Technical Information of China (English)

    纪芳; 鄢志雄; 李文丹; 祝贺; 梁勇

    2012-01-01

    A PCR fragment including 30nt of flanking DNA homologous to the chromosome in each end and a antibiotic-resistant gene in the middle is introduced into the host cell of BW25113/ pIJ790. The three proteins of h phage---Exo,Bet and Gam, expressed by pIJ790, composing the Red recombination system has the advantage of high one-step recombination rate of linear fragment. The antibiotic-resistant gene replaces the target gene as a result. This research obtaines a derivative of E. coli whose efflux pump gene aerAB is deleted. The mutant strain will help to research of mechanism of antimierobial materials.%通过电转化将一段PCR产物引入宿主菌BW25113/pIJ790细胞内,PCR产物两端有与染色体同源的30个核苷酸序列,中间是抗生素抗性基因。pIJ790上编码λ噬菌体的3个重组蛋白:Exo、Bet和Gam组成Red重组系统,可实现线性片段的一步法高效重组,以PCR产物中的抗生素抗性基因取代靶基因。通过该方法得到了大肠埃希菌的外排泵基因acrAB敲除突变株,该菌株在抗菌物质的抗菌机制研究方面能发挥一定的作用。

  11. Automated degenerate PCR primer design for high-throughput sequencing improves efficiency of viral sequencing

    Directory of Open Access Journals (Sweden)

    Li Kelvin

    2012-11-01

    Full Text Available Abstract Background In a high-throughput environment, to PCR amplify and sequence a large set of viral isolates from populations that are potentially heterogeneous and continuously evolving, the use of degenerate PCR primers is an important strategy. Degenerate primers allow for the PCR amplification of a wider range of viral isolates with only one set of pre-mixed primers, thus increasing amplification success rates and minimizing the necessity for genome finishing activities. To successfully select a large set of degenerate PCR primers necessary to tile across an entire viral genome and maximize their success, this process is best performed computationally. Results We have developed a fully automated degenerate PCR primer design system that plays a key role in the J. Craig Venter Institute’s (JCVI high-throughput viral sequencing pipeline. A consensus viral genome, or a set of consensus segment sequences in the case of a segmented virus, is specified using IUPAC ambiguity codes in the consensus template sequence to represent the allelic diversity of the target population. PCR primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the full length of the specified target region. As part of the tiling process, primer pairs are computationally screened to meet the criteria for successful PCR with one of two described amplification protocols. The actual sequencing success rates for designed primers for measles virus, mumps virus, human parainfluenza virus 1 and 3, human respiratory syncytial virus A and B and human metapneumovirus are described, where >90% of designed primer pairs were able to consistently successfully amplify >75% of the isolates. Conclusions Augmenting our previously developed and published JCVI Primer Design Pipeline, we achieved similarly high sequencing success rates with only minor software modifications. The recommended methodology for the construction of the consensus

  12. Automated degenerate PCR primer design for high-throughput sequencing improves efficiency of viral sequencing.

    Science.gov (United States)

    Li, Kelvin; Shrivastava, Susmita; Brownley, Anushka; Katzel, Dan; Bera, Jayati; Nguyen, Anh Thu; Thovarai, Vishal; Halpin, Rebecca; Stockwell, Timothy B

    2012-11-06

    In a high-throughput environment, to PCR amplify and sequence a large set of viral isolates from populations that are potentially heterogeneous and continuously evolving, the use of degenerate PCR primers is an important strategy. Degenerate primers allow for the PCR amplification of a wider range of viral isolates with only one set of pre-mixed primers, thus increasing amplification success rates and minimizing the necessity for genome finishing activities. To successfully select a large set of degenerate PCR primers necessary to tile across an entire viral genome and maximize their success, this process is best performed computationally. We have developed a fully automated degenerate PCR primer design system that plays a key role in the J. Craig Venter Institute's (JCVI) high-throughput viral sequencing pipeline. A consensus viral genome, or a set of consensus segment sequences in the case of a segmented virus, is specified using IUPAC ambiguity codes in the consensus template sequence to represent the allelic diversity of the target population. PCR primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the full length of the specified target region. As part of the tiling process, primer pairs are computationally screened to meet the criteria for successful PCR with one of two described amplification protocols. The actual sequencing success rates for designed primers for measles virus, mumps virus, human parainfluenza virus 1 and 3, human respiratory syncytial virus A and B and human metapneumovirus are described, where >90% of designed primer pairs were able to consistently successfully amplify >75% of the isolates. Augmenting our previously developed and published JCVI Primer Design Pipeline, we achieved similarly high sequencing success rates with only minor software modifications. The recommended methodology for the construction of the consensus sequence that encapsulates the allelic variation of the targeted

  13. Noncontinuously binding loop-out primers for avoiding problematic DNA sequences in PCR and sanger sequencing.

    Science.gov (United States)

    Sumner, Kelli; Swensen, Jeffrey J; Procter, Melinda; Jama, Mohamed; Wooderchak-Donahue, Whitney; Lewis, Tracey; Fong, Michael; Hubley, Lindsey; Schwarz, Monica; Ha, Youna; Paul, Eleri; Brulotte, Benjamin; Lyon, Elaine; Bayrak-Toydemir, Pinar; Mao, Rong; Pont-Kingdon, Genevieve; Best, D Hunter

    2014-09-01

    We present a method in which noncontinuously binding (loop-out) primers are used to exclude regions of DNA that typically interfere with PCR amplification and/or analysis by Sanger sequencing. Several scenarios were tested using this design principle, including M13-tagged PCR primers, non-M13-tagged PCR primers, and sequencing primers. With this technique, a single oligonucleotide is designed in two segments that flank, but do not include, a short region of problematic DNA sequence. During PCR amplification or sequencing, the problematic region is looped-out from the primer binding site, where it does not interfere with the reaction. Using this method, we successfully excluded regions of up to 46 nucleotides. Loop-out primers were longer than traditional primers (27 to 40 nucleotides) and had higher melting temperatures. This method allows the use of a standardized PCR protocol throughout an assay, keeps the number of PCRs to a minimum, reduces the chance for laboratory error, and, above all, does not interrupt the clinical laboratory workflow.

  14. Nucleic acid sequence detection using multiplexed oligonucleotide PCR

    Science.gov (United States)

    Nolan, John P.; White, P. Scott

    2006-12-26

    Methods for rapidly detecting single or multiple sequence alleles in a sample nucleic acid are described. Provided are all of the oligonucleotide pairs capable of annealing specifically to a target allele and discriminating among possible sequences thereof, and ligating to each other to form an oligonucleotide complex when a particular sequence feature is present (or, alternatively, absent) in the sample nucleic acid. The design of each oligonucleotide pair permits the subsequent high-level PCR amplification of a specific amplicon when the oligonucleotide complex is formed, but not when the oligonucleotide complex is not formed. The presence or absence of the specific amplicon is used to detect the allele. Detection of the specific amplicon may be achieved using a variety of methods well known in the art, including without limitation, oligonucleotide capture onto DNA chips or microarrays, oligonucleotide capture onto beads or microspheres, electrophoresis, and mass spectrometry. Various labels and address-capture tags may be employed in the amplicon detection step of multiplexed assays, as further described herein.

  15. Evaluation of one-step luminescent cyanoacrylate fuming.

    Science.gov (United States)

    Khuu, Alicia; Chadwick, Scott; Spindler, Xanthe; Lam, Rolanda; Moret, Sébastien; Roux, Claude

    2016-06-01

    One-step luminescent cyanoacrylates have recently been introduced as an alternative to the conventional cyanoacrylate fuming methods. These new techniques do not require the application of a luminescent post-treatment in order to enhance cyanoacrylate-developed fingermarks. In this study, three one-step polymer cyanoacrylates: CN Yellow Crystals (Aneval Inc.), PolyCyano UV (Foster+Freeman Ltd.) and PECA Multiband (BVDA), and one monomer cyanoacrylate: Lumikit™ (Crime Scene Technology), were evaluated against a conventional two-step cyanoacrylate fuming method (Cyanobloom (Foster+Freeman Ltd.) with rhodamine 6G stain). The manufacturers' recommended conditions or conditions compatible with the MVC™ 1000/D (Foster+Freeman Ltd.) were assessed with fingermarks aged for up to 8 weeks on non-porous and semi-porous substrates. Under white light, Cyanobloom generally gave better development than the one-step treatments across the substrates. Similarly when viewed under the respective luminescent conditions, Cyanobloom with rhodamine 6G stain resulted in improved contrast against the one-step treatments except on polystyrene, where PolyCyano UV and PECA Multiband gave better visualisation. Rhodamine 6G post-treatment of one-step samples did not significantly enhance the contrast of any of the one-step treatments against Cyanobloom/rhodamine 6G-treated samples.

  16. Rapid one-step selection method for generating nucleic acid aptamers: development of a DNA aptamer against α-bungarotoxin.

    Directory of Open Access Journals (Sweden)

    Lasse H Lauridsen

    Full Text Available BACKGROUND: Nucleic acids based therapeutic approaches have gained significant interest in recent years towards the development of therapeutics against many diseases. Recently, research on aptamers led to the marketing of Macugen®, an inhibitor of vascular endothelial growth factor (VEGF for the treatment of age related macular degeneration (AMD. Aptamer technology may prove useful as a therapeutic alternative against an array of human maladies. Considering the increased interest in aptamer technology globally that rival antibody mediated therapeutic approaches, a simplified selection, possibly in one-step, technique is required for developing aptamers in limited time period. PRINCIPAL FINDINGS: Herein, we present a simple one-step selection of DNA aptamers against α-bungarotoxin. A toxin immobilized glass coverslip was subjected to nucleic acid pool binding and extensive washing followed by PCR enrichment of the selected aptamers. One round of selection successfully identified a DNA aptamer sequence with a binding affinity of 7.58 µM. CONCLUSION: We have demonstrated a one-step method for rapid production of nucleic acid aptamers. Although the reported binding affinity is in the low micromolar range, we believe that this could be further improved by using larger targets, increasing the stringency of selection and also by combining a capillary electrophoresis separation prior to the one-step selection. Furthermore, the method presented here is a user-friendly, cheap and an easy way of deriving an aptamer unlike the time consuming conventional SELEX-based approach. The most important application of this method is that chemically-modified nucleic acid libraries can also be used for aptamer selection as it requires only one enzymatic step. This method could equally be suitable for developing RNA aptamers.

  17. Rapid one-step selection method for generating nucleic acid aptamers: development of a DNA aptamer against α-bungarotoxin.

    Science.gov (United States)

    Lauridsen, Lasse H; Shamaileh, Hadi A; Edwards, Stacey L; Taran, Elena; Veedu, Rakesh N

    2012-01-01

    Nucleic acids based therapeutic approaches have gained significant interest in recent years towards the development of therapeutics against many diseases. Recently, research on aptamers led to the marketing of Macugen®, an inhibitor of vascular endothelial growth factor (VEGF) for the treatment of age related macular degeneration (AMD). Aptamer technology may prove useful as a therapeutic alternative against an array of human maladies. Considering the increased interest in aptamer technology globally that rival antibody mediated therapeutic approaches, a simplified selection, possibly in one-step, technique is required for developing aptamers in limited time period. Herein, we present a simple one-step selection of DNA aptamers against α-bungarotoxin. A toxin immobilized glass coverslip was subjected to nucleic acid pool binding and extensive washing followed by PCR enrichment of the selected aptamers. One round of selection successfully identified a DNA aptamer sequence with a binding affinity of 7.58 µM. We have demonstrated a one-step method for rapid production of nucleic acid aptamers. Although the reported binding affinity is in the low micromolar range, we believe that this could be further improved by using larger targets, increasing the stringency of selection and also by combining a capillary electrophoresis separation prior to the one-step selection. Furthermore, the method presented here is a user-friendly, cheap and an easy way of deriving an aptamer unlike the time consuming conventional SELEX-based approach. The most important application of this method is that chemically-modified nucleic acid libraries can also be used for aptamer selection as it requires only one enzymatic step. This method could equally be suitable for developing RNA aptamers.

  18. Characterization of Theileria species by PCR using specific target sequences.

    Science.gov (United States)

    Maxia, L; Reale, S; Loria, G R; Greco, A; Vitale, F; Glorioso, N S; Sparagano, O

    1999-09-01

    Theileriosis is an infectious disease in tropical countries and in the Mediterranean area. It is caused by Theileria, a haemoprotozoan, transmitted by vectors belonging to the Ixodidae. In Southern Italy and in Sicily the infection is due mainly to T. annulata, but in some cases other species are involved in the disease. The authors describe a method to identify theileriosis in cattle blood samples, using PCR and hybridization techniques. Different primer sets were used to amplify different DNA target sequences, both genus and species specific. Blood samples from cattle were collected in Sicily. The DNA extracted from blood samples was employed first to detect the presence of the 18S ribosomal subunit gene specific for Theileria genus. Successively the positive samples were analysed to identify the species, T. annulata or T. buffeli/orientalis, using as target sequences for amplification respectively a fragment of the TAMS-1 and p33/34 antigens gene. Here the authors describe for the first time the presence of T. buffeli/orientalis infection in Sicilian herds. In fact 66% of positive blood samples were T. buffeli/orientalis infected.

  19. Real-Time PCR Identification of Unique Bacillus anthracis Sequences.

    Science.gov (United States)

    Cieślik, P; Knap, J; Kolodziej, M; Mirski, T; Joniec, J; Graniak, G; Zakowska, D; Winnicka, I; Bielawska-Drózd, A

    2015-01-01

    Bacillus anthracis is a spore-forming, Gram-positive microorganism. It is a causative agent of anthrax, a highly infectious disease. It belongs to the "Bacillus cereus group", which contains other closely related species, including Bacillus cereus, Bacillus thuringiensis, Bacillus mycoides, Bacillus weihenstephanensis, and Bacillus pseudomycoides. B. anthracis naturally occurs in soil environments. The BA5345 genetic marker was used for highly specific detection of B. anthracis with TaqMan probes. The detection limit of a real-time PCR assay was estimated at the level of 16.9 copies (CI95% - 37.4 to 37.86, SD = 0.2; SE = 0.118). Oligonucleotides designed for the targeted sequences (within the tested locus) revealed 100 % homology to B. anthracis strain reference sequences deposited in the database (NCBI) and high specificity to all tested B. anthracis strains. Additional in silico analysis of plasmid markers pag and cap genes with B. anthracis strains included in the database was carried out. Our study clearly indicates that the BA5345 marker can be used with success as a chromosomal marker in routine identification of B. anthracis; moreover, detection of plasmid markers indicates virulence of the examined strains.

  20. Detection of Citrus leprosis virus C using specific primers and TaqMan probe in one-step real-time reverse-transcription polymerase chain reaction assays.

    Science.gov (United States)

    Choudhary, Nandlal; Wei, G; Govindarajulu, A; Roy, Avijit; Li, Wenbin; Picton, Deric D; Nakhla, M K; Levy, L; Brlansky, R H

    2015-11-01

    Citrus leprosis virus C (CiLV-C), a causal agent of the leprosis disease in citrus, is mostly present in the South and Central America and spreading toward the North America. To enable better diagnosis and inhibit the further spread of this re-emerging virus a quantitative (q) real-time reverse transcription polymerase chain reaction (qRT-PCR) assay is needed for early detection of CiLV-C when the virus is present in low titer in citrus leprosis samples. Using the genomic sequence of CiLV-C, specific primers and probe were designed and synthesized to amplify a 73 nt amplicon from the movement protein (MP) gene. A standard curve of the 73 nt amplicon MP gene was developed using known 10(10)-10(1) copies of in vitro synthesized RNA transcript to estimate the copy number of RNA transcript in the citrus leprosis samples. The one-step qRT-PCR detection assays for CiLV-C were determined to be 1000 times more sensitive when compared to the one-step conventional reverse transcription polymerase chain reaction (RT-PCR) CiLV-C detection method. To evaluate the quality of the total RNA extracts, NADH dehydrogenase gene specific primers (nad5) and probe were included in reactions as an internal control. The one-step qRT-PCR specificity was successfully validated by testing for the presence of CiLV-C in the total RNA extracts of the citrus leprosis samples collected from Belize, Costa Rica, Mexico and Panama. Implementation of the one-step qRT-PCR assays for CiLV-C diagnosis should assist regulatory agencies in surveillance activities to monitor the distribution pattern of CiLV-C in countries where it is present and to prevent further dissemination into citrus growing countries where there is no report of CiLV-C presence.

  1. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing

    DEFF Research Database (Denmark)

    Binladen, Jonas; Gilbert, M Thomas P; Bollback, Jonathan P

    2007-01-01

    BACKGROUND: The invention of the Genome Sequence 20 DNA Sequencing System (454 parallel sequencing platform) has enabled the rapid and high-volume production of sequence data. Until now, however, individual emulsion PCR (emPCR) reactions and subsequent sequencing runs have been unable to combine ...... be applied to PCR-based assays of multiple homologous PCR products. The new approach will be of value to a broad range of research areas, such as those of comparative genomics, complete mitochondrial analyses, population genetics, and phylogenetics.......BACKGROUND: The invention of the Genome Sequence 20 DNA Sequencing System (454 parallel sequencing platform) has enabled the rapid and high-volume production of sequence data. Until now, however, individual emulsion PCR (emPCR) reactions and subsequent sequencing runs have been unable to combine...... template DNA from multiple individuals, as homologous sequences cannot be subsequently assigned to their original sources. METHODOLOGY: We use conventional PCR with 5'-nucleotide tagged primers to generate homologous DNA amplification products from multiple specimens, followed by sequencing through...

  2. Data Analysis of Transcriptomic Sequences and qPCR Validations for Microbial Communities during Algal Blooms

    Science.gov (United States)

    A training opportunity is open to a highly microbial-research-motivated student to conduct sequence analysis, explore novel genes and metabolic pathways, validate resultant findings using qPCR/RT-qPCR and summarize the findings

  3. Variable bandwidth and one-step local M-estimator

    Institute of Scientific and Technical Information of China (English)

    范剑青; 蒋建成

    2000-01-01

    A robust version of local linear regression smoothers augmented with variable bandwidth is studied. The proposed method inherits the advantages of local polynomial regression and overcomes the shortcoming of lack of robustness of least-squares techniques. The use of variable bandwidth enhances the flexibility of the resulting local M- estimators and makes them possible to cope well with spatially inho-mogeneous curves, heteroscedastic errors and nonuniform design densities. Under appropriate regularity conditions, it is shown that the proposed estimators exist and are asymptotically normal. Based on the robust estimation equation, one-step local M-estimators are introduced to reduce computational burden. It is demonstrated that the one-step local M-estimators share the same asymptotic distributions as the fully iterative M-estimators, as long as the initial estimators are good enough. In other words, the one-step local M-estimators reduce significantly the computation cost of the fully iterative M-estim

  4. One-step fabrication of supramolecular microcapsules from microfluidic droplets.

    Science.gov (United States)

    Zhang, Jing; Coulston, Roger J; Jones, Samuel T; Geng, Jin; Scherman, Oren A; Abell, Chris

    2012-02-10

    Although many techniques exist for preparing microcapsules, it is still challenging to fabricate them in an efficient and scalable process without compromising functionality and encapsulation efficiency. We demonstrated a simple one-step approach that exploits a versatile host-guest system and uses microfluidic droplets to generate porous microcapsules with easily customizable functionality. The capsules comprise a polymer-gold nanoparticle composite held together by cucurbit[8]uril ternary complexes. The dynamic yet highly stable micrometer-sized structures can be loaded in one step during capsule formation and are amenable to on-demand encapsulant release. The internal chemical environment can be probed with surface enhanced Raman spectroscopy.

  5. Convenient one-step synthesis of 5-carboxy-seminaphthofluoresceins

    DEFF Research Database (Denmark)

    Hammershøj, Peter; Thyhaug, Erling; Harris, Pernille

    2017-01-01

    The one-step synthesis and characterization of a series of regioisomerically pure 5-carboxy-seminaphthofluoresceins (5-carboxy-SNAFLs) is reported. The optical properties were determined in aqueous buffer at around biological pH, and highly pH sensitive, large Stokes-shift fluorophores with emiss......The one-step synthesis and characterization of a series of regioisomerically pure 5-carboxy-seminaphthofluoresceins (5-carboxy-SNAFLs) is reported. The optical properties were determined in aqueous buffer at around biological pH, and highly pH sensitive, large Stokes-shift fluorophores...

  6. Gene expression analysis using strains constructed by NHEJ-mediated one-step promoter cloning in the yeast Kluyveromyces marxianus.

    Science.gov (United States)

    Suzuki, Ayako; Fujii, Hiroshi; Hoshida, Hisashi; Akada, Rinji

    2015-09-01

    Gene expression analysis provides valuable information to evaluate cellular state. Unlike quantitative mRNA analysis techniques like reverse-transcription PCR and microarray, expression analysis using a reporter gene has not been commonly used for multiple-gene analysis, probably due to the difficulty in preparing multiple reporter-gene constructs. To circumvent this problem, we developed a novel one-step reporter-gene construction system mediated by non-homologous end joining (NHEJ) in the yeast Kluyveromyces marxianus. As a selectable reporter gene, the ScURA3 selection marker was fused in frame with a red fluorescent gene yEmRFP (ScURA3:yEmRFP). The N-terminally truncated ScURA3:yEmRFP fragment was prepared by PCR. Promoter sequences were also prepared by PCR using primers containing the sequence of the deleted ScURA3 N-terminus to attach at their 3(') ends. The two DNA fragments were used for the transformation of a ura3(-) strain of K. marxianus, in which two DNA fragments are randomly joined and integrated into the chromosome through NHEJ. Only the correctly aligned fragments produced transformants on uracil-deficient medium and expressed red fluorescence under the control of the introduced promoters. A total of 36 gene promoters involved in glycolysis and other pathways were analyzed. Fluorescence measurements of these strains allowed real-time gene expression analysis in different culture conditions.

  7. Fundamental study of a one-step ambient temperature ferrite ...

    African Journals Online (AJOL)

    Fundamental study of a one-step ambient temperature ferrite process for treatment ... The approach involves the controlled oxidation of ferrous-containing AMD water at ... The resulting oxidation product is the ferrite (M13+2M22+O4) magnetite ...

  8. Convenient one-step synthesis of 5-carboxy-seminaphthofluoresceins

    DEFF Research Database (Denmark)

    Hammershøj, Peter; Thyhaug, Erling; Harris, Pernille

    2017-01-01

    The one-step synthesis and characterization of a series of regioisomerically pure 5-carboxy-seminaphthofluoresceins (5-carboxy-SNAFLs) is reported. The optical properties were determined in aqueous buffer at around biological pH, and highly pH sensitive, large Stokes-shift fluorophores with emiss...

  9. Sources of PCR-induced distortions in high-throughput sequencing data sets

    Science.gov (United States)

    Kebschull, Justus M.; Zador, Anthony M.

    2015-01-01

    PCR permits the exponential and sequence-specific amplification of DNA, even from minute starting quantities. PCR is a fundamental step in preparing DNA samples for high-throughput sequencing. However, there are errors associated with PCR-mediated amplification. Here we examine the effects of four important sources of error—bias, stochasticity, template switches and polymerase errors—on sequence representation in low-input next-generation sequencing libraries. We designed a pool of diverse PCR amplicons with a defined structure, and then used Illumina sequencing to search for signatures of each process. We further developed quantitative models for each process, and compared predictions of these models to our experimental data. We find that PCR stochasticity is the major force skewing sequence representation after amplification of a pool of unique DNA amplicons. Polymerase errors become very common in later cycles of PCR but have little impact on the overall sequence distribution as they are confined to small copy numbers. PCR template switches are rare and confined to low copy numbers. Our results provide a theoretical basis for removing distortions from high-throughput sequencing data. In addition, our findings on PCR stochasticity will have particular relevance to quantification of results from single cell sequencing, in which sequences are represented by only one or a few molecules. PMID:26187991

  10. Oligoribonucleotide (ORN) Interference-PCR (ORNi-PCR): A Simple Method for Suppressing PCR Amplification of Specific DNA Sequences Using ORNs

    OpenAIRE

    Naoki Tanigawa; Toshitsugu Fujita; Hodaka Fujii

    2014-01-01

    Polymerase chain reaction (PCR) amplification of multiple templates using common primers is used in a wide variety of molecular biological techniques. However, abundant templates sometimes obscure the amplification of minor species containing the same primer sequences. To overcome this challenge, we used oligoribonucleotides (ORNs) to inhibit amplification of undesired template sequences without affecting amplification of control sequences lacking complementarity to the ORNs. ORNs were effect...

  11. One-step pickling-activation before magnesium alloy plating

    Institute of Scientific and Technical Information of China (English)

    WANG Xin-juan; YU Gang; OUYANG Yue-jun; HE Xiao-mei; ZHANG Jun; YE Li-yuan

    2009-01-01

    A one-step pickling-activation process was proposed as an environmental friendly pretreatment method in phosphate-permanganate solution before electroplating on magnesium alloys. The effects of pickling-activation on qualities of coating were assessed by adhesion and porosity testing of copper plating. The interfacial reactions between specimen and solution were analyzed with SEM, EDX and XRD. The results show that the developed process of pickling-activation can equalize the potentials on substrate surface. The compacted zinc film can be obtained by zinc immersion after treating magnesium alloy in the pH 4-6 phosphate-permanganate solution for 3-5 min. The adhesion and corrosion resistance of copper plating are enhanced. The one-step pickling-activation can replace the existing two-step process of acid pickling and activation which contains a great deal of chromium and fluorine. The procedure of surface pretreatment is simplified and the production environment is improved.

  12. A novel one-step Helicobacter pylori saliva antigen test

    Directory of Open Access Journals (Sweden)

    Bi-Ling Yang

    2015-02-01

    Conclusion: The one-step HPS test exhibited a high sensitivity and low specificity compared with the other tests, indicating that it is not sufficiently accurate for use in a clinical setting for diagnosing H. pylori infection. However, the test is simple to use (requiring only a saliva sample, inexpensive, and noninvasive in its application, and thus appealing for use in population-based prevalence surveys of the epidemiology of H. pylori infection.

  13. Variable bandwidth and one-step local M-estimator

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A robust version of local linear regression smoothers augmented with variable bandwidth is studied. The proposed method inherits the advantages of local polynomial regression and overcomes the shortcoming of lack of robustness of least-squares techniques. The use of variable bandwidth enhances the flexibility of the resulting local M-estimators and makes them possible to cope well with spatially inhomogeneous curves, heteroscedastic errors and nonuniform design densities. Under appropriate regularity conditions, it is shown that the proposed estimators exist and are asymptotically normal. Based on the robust estimation equation, one-step local M-estimators are introduced to reduce computational burden. It is demonstrated that the one-step local M-estimators share the same asymptotic distributions as the fully iterative M-estimators, as long as the initial estimators are good enough. In other words, the one-step local M-estimators reduce significantly the computation cost of the fully iterative M-estimators without deteriorating their performance. This fact is also illustrated via simulations.

  14. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing.

    Directory of Open Access Journals (Sweden)

    Jonas Binladen

    Full Text Available BACKGROUND: The invention of the Genome Sequence 20 DNA Sequencing System (454 parallel sequencing platform has enabled the rapid and high-volume production of sequence data. Until now, however, individual emulsion PCR (emPCR reactions and subsequent sequencing runs have been unable to combine template DNA from multiple individuals, as homologous sequences cannot be subsequently assigned to their original sources. METHODOLOGY: We use conventional PCR with 5'-nucleotide tagged primers to generate homologous DNA amplification products from multiple specimens, followed by sequencing through the high-throughput Genome Sequence 20 DNA Sequencing System (GS20, Roche/454 Life Sciences. Each DNA sequence is subsequently traced back to its individual source through 5'tag-analysis. CONCLUSIONS: We demonstrate that this new approach enables the assignment of virtually all the generated DNA sequences to the correct source once sequencing anomalies are accounted for (miss-assignment rate<0.4%. Therefore, the method enables accurate sequencing and assignment of homologous DNA sequences from multiple sources in single high-throughput GS20 run. We observe a bias in the distribution of the differently tagged primers that is dependent on the 5' nucleotide of the tag. In particular, primers 5' labelled with a cytosine are heavily overrepresented among the final sequences, while those 5' labelled with a thymine are strongly underrepresented. A weaker bias also exists with regards to the distribution of the sequences as sorted by the second nucleotide of the dinucleotide tags. As the results are based on a single GS20 run, the general applicability of the approach requires confirmation. However, our experiments demonstrate that 5'primer tagging is a useful method in which the sequencing power of the GS20 can be applied to PCR-based assays of multiple homologous PCR products. The new approach will be of value to a broad range of research areas, such as those of

  15. Sequence Optimized Real-Time RT-PCR Assay for Detection of Crimean-Congo Hemorrhagic Fever Virus

    Science.gov (United States)

    2017-03-21

    density macroarrays [15], high density resequencing arrays [16], 55 padlock probes with colorimetric readout [17], LAMP [18], and polymerase chain reaction ...Announcement). Briefly, the S segment of each virus was amplified using the 83 SuperScript III One-Step RT- PCR system with Platinum Taq DNA Polymerase High...Platinum One-Step Quantitative RT- PCR System) # Rxns = Reagents Stock [Final] 1rxn 28 2X Reaction Mix 2 1 10 280 Nuclease-free water 1.7 47.6 100 µM F

  16. PCR amplification of repetitive sequences as a possible approach in relative species quantification

    DEFF Research Database (Denmark)

    Ballin, Nicolai Zederkopff; Vogensen, Finn Kvist; Karlsson, Anders H

    2012-01-01

    in binary mixtures. PCR LUX primers were designed that amplify repetitive and single copy sequences to establish the species dependent number (constants) (SDC) of amplified repetitive sequences per genome. The SDCs and data from amplification of repetitive sequences were tested for their applicability...... to relatively quantify the amount of chicken DNA in a binary mixture of chicken DNA and pig DNA. However, the designed PCR primers lack the specificity required for regulatory species control....

  17. A Class of Multiderivative Hybrid One-step Methods

    Institute of Scientific and Technical Information of China (English)

    Feng-jian Yang; Xin-ming Chen; Ai-guo Zhang

    2002-01-01

    This paper presents a class of hybrid one-step methods that are obtained by using Cramer's rule and rational approximations to function exp (q). The algorithms fall into the catalogue of implicit formula, which involves sth order derivative and s+1 free parameters. The order of the algorithms satisfies s+1≤p≤2s+2. The stability of the methods is also studied, necessary and sufficient conditions for A-stability and L-stability are given. In addition, some examples are also given to demonstrate the method presented.

  18. An enhanced method for sequence walking and paralog mining: TOPO® Vector-Ligation PCR

    Directory of Open Access Journals (Sweden)

    Davis Thomas M

    2010-03-01

    Full Text Available Abstract Background Although technological advances allow for the economical acquisition of whole genome sequences, many organisms' genomes remain unsequenced, and fully sequenced genomes may contain gaps. Researchers reliant upon partial genomic or heterologous sequence information require methods for obtaining unknown sequences from loci of interest. Various PCR based techniques are available for sequence walking - i.e., the acquisition of unknown DNA sequence adjacent to known sequence. Many such methods require rigid, elaborate protocols and/or impose narrowly confined options in the choice of restriction enzymes for necessary genomic digests. We describe a new method, TOPO® Vector-Ligation PCR (or TVL-PCR that innovatively integrates available tools and familiar concepts to offer advantages as a means of both targeted sequence walking and paralog mining. Findings TVL-PCR exploits the ligation efficiency of the pCR®4-TOPO® (Invitrogen, Carlsbad, California vector system to capture fragments of unknown sequence by creating chimeric molecules containing defined priming sites at both ends. Initially, restriction enzyme-digested genomic DNA is end-repaired to create 3' adenosine overhangs and is then ligated to pCR4-TOPO vectors. The ligation product pool is used directly as a template for nested PCR, using specific primers to target orthologous sequences, or degenerate primers to enable capture of paralogous gene family members. We demonstrated the efficacy of this method by capturing entire coding and partial promoter sequences of several strawberry Superman-like genes. Conclusions TVL-PCR is a convenient and efficient method for DNA sequence walking and paralog mining that is applicable to any organism for which relevant DNA sequence is available as a basis for primer design.

  19. One-step 18F labeling of biomolecules using organotrifluoroborates

    Science.gov (United States)

    Liu, Zhibo; Lin, Kuo-Shyan; Bénard, François; Pourghiasian, Maral; Kiesewetter, Dale O; Perrin, David M; Chen, Xiaoyuan

    2017-01-01

    Herein we present a general protocol for the functionalization of biomolecules with an organotrifluoroborate moiety so that they can be radiolabeled with aqueous 18F fluoride (18F−) and used for positron emission tomography (PET) imaging. Among the β+-emitting radionuclides, fluorine-18 (18F) is the isotope of choice for PET, and it is produced, on-demand, in many hospitals worldwide. Organotrifluoroborates can be 18F-labeled in one step in aqueous conditions via 18F–19F isotope exchange. This protocol features a recently designed ammoniomethyltrifluoroborate, and it describes the following: (i) a synthetic strategy that affords modular synthesis of radiolabeling precursors via a copper-catalyzed ‘click’ reaction; and (ii) a one-step 18F-labeling method that obviates the need for HPLC purification. Within 30 min, 18F-labeled PET imaging probes, such as peptides, can be synthesized in good chemical and radiochemical purity (>98%), satisfactory radiochemical yield of 20–35% (n > 20, non-decay corrected) and high specific activity of 40–111 GBq/µmol (1.1–3.0 Ci/µmol). The entire procedure, including the precursor preparation and 18F radiolabeling, takes 7–10 d. PMID:26313478

  20. Genetic analysis of the PKHD1 gene with long-rang PCR sequencing.

    Science.gov (United States)

    Tong, Yong-Qing; Liu, Bei; Fu, Chao-Hong; Zheng, Hong-Yun; Gu, Jian; Liu, Hang; Luo, Hong-Bo; Li, Yan

    2016-10-01

    PKHD1 gene mutations are found responsible for autosomal recessive polycystic kidney disease (ARPKD). However, it is inconvenient to detect the mutations by common polymerase chain reaction (PCR) because the open reading frame of PKHD1 is very long. Recently, long-range (LR) PCR is demonstrated to be a more sensitive mutation screening method for PKHD1 by directly sequencing. In this study, the entire PKHD1 coding region was amplified by 29 reactions to avoid the specific PCR amplification of individual exons, which generated the size of 1 to 7 kb products by LR PCR. This method was compared to the screening method with standard direct sequencing of each individual exon of the gene by a reference laboratory in 15 patients with ARPKD. The results showed that a total of 37 genetic changes were detected with LR PCR sequencing, which included 33 variations identified by the reference laboratory with standard direct sequencing. LR PCR sequencing had 100% sensitivity, 96% specificity, and 97.0% accuracy, which were higher than those with standard direct sequencing method. In conclusion, LR PCR sequencing is a reliable method with high sensitivity, specificity and accuracy for detecting genetic variations. It also has more intronic coverage and lower cost, and is an applicable clinical method for complex genetic analyses.

  1. PCR-Internal Transcribed Spacer (ITS) genes sequencing and ...

    African Journals Online (AJOL)

    2. Department of Pure and Applied Zoology, Federal University of Agriculture, Abeokuta, Nigeria. 3. ... Keywords: Internal transcribed spacer genes, phylogenetic, genetic ... ization of fungi by polymerase chain reaction (PCR) am- .... Basic Local Alignment search Tool (BLAST) to establish ..... Population structure and.

  2. Isolation of laccase gene-specific sequences from white rot and brown rot fungi by PCR

    Energy Technology Data Exchange (ETDEWEB)

    D`Souza, T.M.; Boominathan, K.; Reddy, C.A. [Michigan State Univ., East Lansing, MI (United States)

    1996-10-01

    Degenerate primers corresponding to the consensus sequences of the copper-binding regions in the N-terminal domains of known basidiomycete laccases were used to isolate laccase gene-specific sequences from strains representing nine genera of wood rot fungi. All except three gave the expected PCR product of about 200 bp. Computer searches of the databases identified the sequences of each of the PCR product of about 200 bp. Computer searches of the databases identified the sequence of each of the PCR products analyzed as a laccase gene sequence, suggesting the specificity of the primers. PCR products of the white rot fungi Ganoderma lucidum, Phlebia brevispora, and Trametes versicolor showed 65 to 74% nucleotide sequence similarity to each other; the similarity in deduced amino acid sequences was 83 to 91%. The PCR products of Lentinula edodes and Lentinus tigrinus, on the other hand, showed relatively low nucleotide and amino acid similarities (58 to 64 and 62 to 81%, respectively); however, these similarities were still much higher than when compared with the corresponding regions in the laccases of the ascomycete fungi Aspergillus nidulans and Neurospora crassa. A few of the white rot fungi, as well as Gloeophyllum trabeum, a brown rot fungus, gave a 144-bp PCR fragment which had a nucleotide sequence similarity of 60 to 71%. Demonstration of laccase activity in G. trabeum and several other brown rot fungi was of particular interest because these organisms were not previously shown to produce laccases. 36 refs., 6 figs., 2 tabs.

  3. One-step method for the production of nanofluids

    Energy Technology Data Exchange (ETDEWEB)

    Kostic, Milivoje (Sycamore, IL); Golubovic, Mihajlo (Chicago, IL); Hull, John (Downers Grove, IL); Choi, Stephen U. S. (Naperville, IL)

    2011-08-16

    A one step method and system for producing nanofluids by a nanoparticle-source evaporation and deposition of the evaporant into a base fluid. The base fluid such oil or ethylene glycol is placed in a rotating cylindrical drum having an adjustable heater-boat-evaporator and heat exchanger-cooler apparatus. As the drum rotates, a thin liquid layer is formed on the inside surface of the drum. An insulated heater-boat-evaporator having an evaporant material (nanoparticle-source) placed within its boat evaporator is adjustably positioned near a portion of the rotating thin liquid layer, the evaporant material being heated thereby evaporating a portion of the evaporant material and forming nanoparticles, the nanoparticles absorbed by the liquid film to form nanofluid.

  4. One-step method for the production of nanofluids

    Energy Technology Data Exchange (ETDEWEB)

    Kostic, Milivoje (Chicago, IL); Golubovic, Mihajlo (Chicago, IL); Hull, John R. (Downers Grove, IL); Choi, Stephen U. S. (Napersville, IL)

    2010-05-18

    A one step method and system for producing nanofluids by a particle-source evaporation and deposition of the evaporant into a base fluid. The base fluid such (i.e. ethylene glycol) is placed in a rotating cylindrical drum having an adjustable heater-boat-evaporator and heat exchanger-cooler apparatus. As the drum rotates, a thin liquid layer is formed on the inside surface of the drum. A heater-boat-evaporator having an evaporant material (particle-source) placed within its boat evaporator is adjustably positioned near a portion of the rotating thin liquid layer, the evaporant material being heated thereby evaporating a portion of the evaporant material, the evaporated material absorbed by the liquid film to form nanofluid.

  5. One-step electrodeposition process to fabricate cathodic superhydrophobic surface

    Energy Technology Data Exchange (ETDEWEB)

    Chen Zhi, E-mail: c2002z@nwpu.edu.cn [Department of Applied Physics, Northwestern Polytechnical University, Xi' an 710129 (China); Li Feng [Department of Applied Physics, Northwestern Polytechnical University, Xi' an 710129 (China); Hao Limei [Department of Applied Physics, Xi' an University of Science and Technology, Xi' an 710054 (China); Chen Anqi; Kong Youchao [Department of Applied Physics, Northwestern Polytechnical University, Xi' an 710129 (China)

    2011-12-01

    In this work, a rapid one-step process is developed to fabricate superhydrophobic cathodic surface by electrodepositing copper plate in an electrolyte solution containing manganese chloride (MnCl{sub 2}{center_dot}4H{sub 2}O), myristic acid (CH{sub 3}(CH{sub 2}){sub 12}COOH) and ethanol. The superhydrophobic surfaces were characterized by means of scanning electron microscopy (SEM), and Fourier transform infrared spectroscopy (FTIR) and X-ray diffraction (XRD). The shortest electrolysis time for fabricating a superhydrophobic surface is about 1 min, the measured maximum contact angle is 163 Degree-Sign and rolling angle is less than 3 Degree-Sign . Furthermore, this method can be easily extended to other conductive materials. The approach is time-saving and cheap, and it is supposed to have a promising future in industrial fields.

  6. One-step electrodeposition process to fabricate cathodic superhydrophobic surface

    Science.gov (United States)

    Chen, Zhi; Li, Feng; Hao, Limei; Chen, Anqi; Kong, Youchao

    2011-12-01

    In this work, a rapid one-step process is developed to fabricate superhydrophobic cathodic surface by electrodepositing copper plate in an electrolyte solution containing manganese chloride (MnCl2·4H2O), myristic acid (CH3(CH2)12COOH) and ethanol. The superhydrophobic surfaces were characterized by means of scanning electron microscopy (SEM), and Fourier transform infrared spectroscopy (FTIR) and X-ray diffraction (XRD). The shortest electrolysis time for fabricating a superhydrophobic surface is about 1 min, the measured maximum contact angle is 163° and rolling angle is less than 3°. Furthermore, this method can be easily extended to other conductive materials. The approach is time-saving and cheap, and it is supposed to have a promising future in industrial fields.

  7. Digital PCR provides sensitive and absolute calibration for high throughput sequencing

    Directory of Open Access Journals (Sweden)

    Fan H Christina

    2009-03-01

    Full Text Available Abstract Background Next-generation DNA sequencing on the 454, Solexa, and SOLiD platforms requires absolute calibration of the number of molecules to be sequenced. This requirement has two unfavorable consequences. First, large amounts of sample-typically micrograms-are needed for library preparation, thereby limiting the scope of samples which can be sequenced. For many applications, including metagenomics and the sequencing of ancient, forensic, and clinical samples, the quantity of input DNA can be critically limiting. Second, each library requires a titration sequencing run, thereby increasing the cost and lowering the throughput of sequencing. Results We demonstrate the use of digital PCR to accurately quantify 454 and Solexa sequencing libraries, enabling the preparation of sequencing libraries from nanogram quantities of input material while eliminating costly and time-consuming titration runs of the sequencer. We successfully sequenced low-nanogram scale bacterial and mammalian DNA samples on the 454 FLX and Solexa DNA sequencing platforms. This study is the first to definitively demonstrate the successful sequencing of picogram quantities of input DNA on the 454 platform, reducing the sample requirement more than 1000-fold without pre-amplification and the associated bias and reduction in library depth. Conclusion The digital PCR assay allows absolute quantification of sequencing libraries, eliminates uncertainties associated with the construction and application of standard curves to PCR-based quantification, and with a coefficient of variation close to 10%, is sufficiently precise to enable direct sequencing without titration runs.

  8. Stability of repetitive-sequence PCR patterns with respect to culture age and subculture frequency.

    Science.gov (United States)

    Kang, Hyunseok Peter; Dunne, W Michael

    2003-06-01

    To examine the stability of repetitive-sequence (rep) PCR profiles, six species of bacteria were subcultured to blood agar plates and DNA was extracted from the cultures after 24, 48, and 72 h of incubation at 35 degrees C. In addition, the same species were subcultured to fresh blood plates daily and DNA was extracted from the cultures after growth of 5, 10, and 15 subcultures, respectively. rep PCR analysis demonstrated that all rep PCR fingerprints from a single species were identical.

  9. Ribosomal PCR and DNA sequencing for detection and identification of bacteria

    DEFF Research Database (Denmark)

    Jensen, Kristine Helander; Dargis, Rimtas; Christensen, Jens Jørgen

    2014-01-01

    -haemolytic streptococci, especially within the mitis group. The data show that ribosomal PCR with subsequent DNA sequencing of the PCR product is a most valuable supplement to culture for identifying bacterial agents of both acute and prolonged infections. However, some bacteria, including non-haemolytic streptococci...

  10. Oligonucleotide chip, real-time PCR and sequencing for genotyping of hepatitis B virus

    Institute of Scientific and Technical Information of China (English)

    Yong-Zhong Wang; Guo-Xiang Wu; Li-Bo Luo; Min Chen; Li-Hua Ruan

    2007-01-01

    AIM: To compare the oligonucleotide chip, real-time PCR and sequencing for genotyping of hepatitis B virus in Chinese patients with chronic hepatitis B.METHODS: Mixture of samples with different genotypes and clinical serum samples from 126 chronic hepatitis B patients was tested for hepatitis B virus genotypes by oligonucleotide chip, real-time PCR and sequencing of PCR products, respectively. Clinical performances, time required and costs of the three assays were evaluated.RESULTS: Oligonucleotide chips and real-time PCR detected 1% and 0.1% genotypes, respectively, in mixed samples. Of the 126 clinical samples from patients with chronic hepatitis B, genotype B was detected in 41(33%), 41 (33%) and 45 (36%) samples, and genotype C in 76 (60%), 76 (60%) and 81 (64%) samples, by oligonucleotide chip, real-time PCR and sequencing,respectively. Oligonucleotide chip and real-time PCR detected mixed genotypes B and C in 9 samples. Realtime PCR was the rapidest and cheapest among the three assays.CONCLUSION: Oligonucleotide chip and real-time PCR are able to detect mixed genotypes, while sequencing only detects the dominant genotype in clinical samples.

  11. A-T linker adapter polymerase chain reaction for determining flanking sequences by rescuing inverse PCR or thermal asymmetric interlaced PCR products.

    Science.gov (United States)

    Trinh, Quoclinh; Zhu, Pengyu; Shi, Hui; Xu, Wentao; Hao, Junran; Luo, Yunbo; Huang, Kunlun

    2014-12-01

    The polymerase chain reaction (PCR)-based genome walking method has been extensively used to isolate unknown flanking sequences, whereas nonspecific products are always inevitable. To resolve these problems, we developed a new strategy to isolate the unknown flanking sequences by combining A-T linker adapter PCR with inverse PCR (I-PCR) or thermal asymmetric interlaced PCR (TAIL-PCR). The result showed that this method can be efficiently achieved with the flanking sequence from the Arabidopsis mutant and papain gene. Our study provides researchers with an additional method for determining genomic DNA flanking sequences to identify the target band from bulk of bands and to eliminate the cloning step for sequencing.

  12. One step facile synthesis of ferromagnetic magnetite nanoparticles

    Science.gov (United States)

    Suppiah, Durga Devi; Abd Hamid, Sharifah Bee

    2016-09-01

    The ferromagnetic properties of magnetite (Fe3O4) were influenced by the nanoparticle size, hence importance were given to the synthesis method. This paper clearly shows that magnetite nanoparticles were successfully synthesized by employing one step controlled precipitation method using a single salt (Iron(II) sulfate) iron precursor. The acquired titration curve from this method provides vital information on the possible reaction mechanism leading to the magnetite (Fe3O4) nanoparticles formation. Goethite (α-FeOOH) was obtained at pH 4, while the continuous addition of hydroxyl ions (OH-) forms iron hydroxides (Fe(OH)2). This subsequently reacts with the goethite, producing magnetite (Fe3O4) at pH 10. Spectroscopy studies validate the magnetite phase existence while structural and morphology analysis illustrates cubic shaped magnetite with an average size of 35 nm was obtained. The synthesized magnetite might be superparamagnetic though lower saturation magnetization (67.5 emu/g) measured at room temperature as compared to bulk magnetite. However the nanoparticles surface anisotropy leads to higher remanence (12 emu/g) and coercivity (117.7 G) making the synthesized magnetite an excellent candidate to be utilized in recording devices. The understanding of the magnetite synthesis mechanism can not only be used to achieve even smaller magnetite nanoparticles but also to prepare different types of iron oxides hydroxides using different iron precursor source.

  13. Methanobactin-mediated one-step synthesis of gold nanoparticles.

    Science.gov (United States)

    Xin, Jia-ying; Cheng, Dan-dan; Zhang, Lan-xuan; Lin, Kai; Fan, Hong-chen; Wang, Yan; Xia, Chun-gu

    2013-11-01

    Preparation of gold nanoparticles with a narrow size distribution has enormous importance in nanotechnology. Methanobactin (Mb) is a copper-binding small peptide that appears to function as an agent for copper sequestration and uptake in methanotrophs. Mb can also bind and catalytically reduce Au (III) to Au (0). In this study, we demonstrate a facile Mb-mediated one-step synthetic route to prepare monodispersed gold nanoparticles. Continuous reduction of Au (III) by Mb can be achieved by using hydroquinone as the reducing agent. The gold nanoparticles have been characterized by UV-visible spectroscopy. The formation and the surface plasmon resonance properties of the gold nanoparticles are highly dependent on the ratio of Au (III) to Mb in solution. X-ray photoelectron spectroscopy (XPS), fluorescence spectra and Fourier transform-infrared spectroscopy (FT-IR) spectra suggest that Mb molecules catalytically reduce Au (III) to Au (0) with the concomitant production of gold nanoparticles, and then, Mb statically adsorbed onto the surface of gold nanoparticles to form an Mb-gold nanoparticles assembly. This avoids secondary nucleation. The formed gold nanoparticles have been demonstrated to be monodispersed and uniform by transmission electron microscopy (TEM) images. Analysis of these particles shows an average size of 14.9 nm with a standard deviation of 1.1 nm. The gold nanoparticles are extremely stable and can resist aggregation, even after several months.

  14. One-step electrospinning of cross-linked chitosan fibers.

    Science.gov (United States)

    Schiffman, Jessica D; Schauer, Caroline L

    2007-09-01

    Chitin is a nitrogen-rich polysaccharide that is abundant in crustaceans, mollusks, insects, and fungi and is the second most abundant organic material found in nature next to cellulose. Chitosan, the N-deacetylated derivative of chitin, is environmentally friendly, nontoxic, biodegradable, and antibacterial. Fibrous mats are typically used in industries for filter media, catalysis, and sensors. Decreasing fiber diameters within these mats causes many beneficial effects such as increased specific surface area to volume ratios. When the intrinsically beneficial effects of chitosan are combined with the enhanced properties of nanofibrous mats, applications arise in a wide range of fields, including medical, packaging, agricultural, and automotive. This is particularly important as innovative technologies that focus around bio-based materials are currently of high urgency, as they can decrease dependencies on fossil fuels. We have demonstrated that Schiff base cross-linked chitosan fibrous mats can be produced utilizing a one-step electrospinning process that is 25 times faster and, therefore, more economical than a previously reported two-step vapor-cross-linking method. These fibrous mats are insoluble in acidic, basic, and aqueous solutions for 72 h. Additionally, this improved production method results in a decreased average fiber diameter, which measures 128 +/- 40 nm. Chemical and structural analyses were conducted utilizing Fourier transform infrared spectroscopy, solubility studies, and scanning electron microscopy.

  15. Methanobactin-Mediated One-Step Synthesis of Gold Nanoparticles

    Directory of Open Access Journals (Sweden)

    Yan Wang

    2013-11-01

    Full Text Available Preparation of gold nanoparticles with a narrow size distribution has enormous importance in nanotechnology. Methanobactin (Mb is a copper-binding small peptide that appears to function as an agent for copper sequestration and uptake in methanotrophs. Mb can also bind and catalytically reduce Au (III to Au (0. In this study, we demonstrate a facile Mb-mediated one-step synthetic route to prepare monodispersed gold nanoparticles. Continuous reduction of Au (III by Mb can be achieved by using hydroquinone as the reducing agent. The gold nanoparticles have been characterized by UV-visible spectroscopy. The formation and the surface plasmon resonance properties of the gold nanoparticles are highly dependent on the ratio of Au (III to Mb in solution. X-ray photoelectron spectroscopy (XPS, fluorescence spectra and Fourier transform-infrared spectroscopy (FT-IR spectra suggest that Mb molecules catalytically reduce Au (III to Au (0 with the concomitant production of gold nanoparticles, and then, Mb statically adsorbed onto the surface of gold nanoparticles to form an Mb-gold nanoparticles assembly. This avoids secondary nucleation. The formed gold nanoparticles have been demonstrated to be monodispersed and uniform by transmission electron microscopy (TEM images. Analysis of these particles shows an average size of 14.9 nm with a standard deviation of 1.1 nm. The gold nanoparticles are extremely stable and can resist aggregation, even after several months.

  16. One Step Hydrogen Generation Through Sorption Enhanced Reforming

    Energy Technology Data Exchange (ETDEWEB)

    Mays, Jeff [Gas Technology Inst., Des Plaines, IL (United States)

    2017-08-03

    One-step hydrogen generation, using Sorption Enhanced Reforming (SER) technology, is an innovative means of providing critical energy and environmental improvements to US manufacturing processes. The Gas Technology Institute (GTI) is developing a Compact Hydrogen Generator (CHG) process, based on SER technology, which successfully integrates previously independent process steps, achieves superior energy efficiency by lowering reaction temperatures, and provides pathways to doubling energy productivity with less environmental pollution. GTI’s prior CHG process development efforts have culminated in an operational pilot plant. During the initial pilot testing, GTI identified two operating risks- 1) catalyst coating with calcium aluminate compounds, 2) limited solids handling of the sorbent. Under this contract GTI evaluated alternative materials (one catalyst and two sorbents) to mitigate both risks. The alternate catalyst met performance targets and did not experience coating with calcium aluminate compounds of any kind. The alternate sorbent materials demonstrated viable operation, with one material enabling a three-fold increase in sorbent flow. The testing also demonstrated operation at 90% of its rated capacity. Lastly, a carbon dioxide co-production study was performed to assess the advantage of the solid phase separation of carbon dioxide- inherent in the CHG process. Approximately 70% lower capital cost is achievable compared to SMR-based hydrogen production with CO2 capture, as well as improved operating costs.

  17. PCR-DGGE Analysis: Unravelling Complex Mixtures of Badnavirus Sequences Present in Yam Germplasm.

    Science.gov (United States)

    Turaki, Aliyu A; Bömer, Moritz; Silva, Gonçalo; Kumar, P Lava; Seal, Susan E

    2017-07-11

    Badnaviruses (family Caulimoviridae, genus Badnavirus) have emerged as serious pathogens especially affecting the cultivation of tropical crops. Badnavirus sequences can be integrated in host genomes, complicating the detection of episomal infections and the assessment of viral genetic diversity in samples containing a complex mixture of sequences. Yam (Dioscorea spp.) plants are hosts to a diverse range of badnavirus species, and recent findings have suggested that mixed infections occur frequently in West African yam germplasm. Historically, the determination of the diversity of badnaviruses present in yam breeding lines has been achieved by cloning and sequencing of polymerase chain reaction (PCR) products. In this study, the molecular diversity of partial reverse transcriptase (RT)-ribonuclease H (RNaseH) sequences from yam badnaviruses was analysed using PCR-dependent denaturing gradient gel electrophoresis (PCR-DGGE). This resulted in the identification of complex 'fingerprints' composed of multiple sequences of Dioscorea bacilliform viruses (DBVs). Many of these sequences show high nucleotide identities to endogenous DBV (eDBV) sequences deposited in GenBank, and fall into six monophyletic species groups. Our findings highlight PCR-DGGE as a powerful tool in badnavirus diversity studies enabling a rapid indication of sequence diversity as well as potential candidate integrated sequences revealed by their conserved nature across germplasm.

  18. One-step continuous synthesis of functionalized magnetite nanoflowers

    Science.gov (United States)

    Thomas, G.; Demoisson, F.; Chassagnon, R.; Popova, E.; Millot, N.

    2016-04-01

    For the first time, functionalized magnetite nanoparticles (Fe3O4 NPs) that form aggregates with a nanoflower morphology were synthesized using a rapid (11 s) one-step continuous hydrothermal process, which was recently modified, and their application as a T 2 magnetic resonance imaging (MRI) contrast agent was evaluated. The nanoparticles functionalized with 3,4-dihydroxy-L-phenylalanine (LDOPA) or 3,4-dihydroxyhydrocinnamic acid (DHCA) consisted of small crystallites of approximately 15 nm of diameter that assembled to form flower-shaped aggregate structures. The Fe3O4-LDOPA nanoflowers exhibited a high transverse relaxivity, r 2 of 418 ± 10 l mmolFe -1 s-1 at 3 T owing to magnetic dipolar interactions, which is twice as that of the commercial Feridex®/Endorem®. The prepared nanostructures were compared with bare Fe3O4 NPs and citrated Fe3O4 NPs. DHCA, LDOPA, and citric acid (CA) were found to have an anti-oxidizing effect and to influence the crystallite size and the lattice parameter of the NPs. DHCA and LDOPA increased the crystallite size, whereas CA decreased it. Surface modification increased the colloidal stability of NPs as compared to bare NPs. Nanoflower suspensions of Fe3O4-LDOPA NPs were found to be stable in the phosphate-buffered saline, saline medium, and minimal essential medium and formed aggregates of sizes smaller than 120 nm. All samples were found to be superparamagnetic in nature and the highest saturation magnetization was obtained for the Fe3O4-LDOPA samples. These NPs can bind to polymers such as PEG, and to fluorescent and chelating agents owing to the presence of free -NH2 or -COOH groups on the surface of NPs, allowing their use in dual imaging applications.

  19. Molecular Properties of Poliovirus Isolates: Nucleotide Sequence Analysis, Typing by PCR and Real-Time RT-PCR.

    Science.gov (United States)

    Burns, Cara C; Kilpatrick, David R; Iber, Jane C; Chen, Qi; Kew, Olen M

    2016-01-01

    Virologic surveillance is essential to the success of the World Health Organization initiative to eradicate poliomyelitis. Molecular methods have been used to detect polioviruses in tissue culture isolates derived from stool samples obtained through surveillance for acute flaccid paralysis. This chapter describes the use of realtime PCR assays to identify and serotype polioviruses. In particular, a degenerate, inosine-containing, panpoliovirus (panPV) PCR primer set is used to distinguish polioviruses from NPEVs. The high degree of nucleotide sequence diversity among polioviruses presents a challenge to the systematic design of nucleic acid-based reagents. To accommodate the wide variability and rapid evolution of poliovirus genomes, degenerate codon positions on the template were matched to mixed-base or deoxyinosine residues on both the primers and the TaqMan™ probes. Additional assays distinguish between Sabin vaccine strains and non-Sabin strains. This chapter also describes the use of generic poliovirus specific primers, along with degenerate and inosine-containing primers, for routine VP1 sequencing of poliovirus isolates. These primers, along with nondegenerate serotype-specific Sabin primers, can also be used to sequence individual polioviruses in mixtures.

  20. Screening PCR Versus Sanger Sequencing: Detection of CALR Mutations in Patients With Thrombocytosis.

    Science.gov (United States)

    Jeong, Ji Hun; Lee, Hwan Tae; Seo, Ja Young; Seo, Yiel Hea; Kim, Kyung Hee; Kim, Moon Jin; Lee, Jae Hoon; Park, Jinny; Hong, Jun Shik; Park, Pil Whan; Ahn, Jeong Yeal

    2016-07-01

    Mutations in calreticulin (CALR) have been reported to be key markers in the molecular diagnosis of myeloid proliferative neoplasms. In most previous reports, CALR mutations were analyzed by using Sanger sequencing. Here, we report a new, rapid, and convenient system for screening CALR mutations without sequencing. Eighty-three bone marrow samples were obtained from 81 patients with thrombocytosis. PCR primers were designed to detect wild-type CALR (product: 357 bp) and CALR with type 1 (product: 302 bp) and type 2 mutations (product: 272 bp) in one reaction. The results were confirmed by Sanger sequencing and compared with results from fragment analysis. The minimum detection limit of the screening PCR was 10 ng for type 1, 1 ng for type 2, and 0.1 ng for cases with both mutations. CALR type 1 and type 2 mutants were detected with screening PCR with a maximal analytical sensitivity of 3.2% and <0.8%, respectively. The screening PCR detected 94.1% (16/17) of mutation cases and showed concordant results with sequencing in the cases of type 1 and type 2 mutations. Sanger sequencing identified one novel mutation (c.1123_1132delinsTGC). Compared with sequencing, the screening PCR showed 94.1% sensitivity, 100.0% specificity, 100.0% positive predictive value, and 98.5% negative predictive value. Compared with fragment analysis, the screening PCR presented 88.9% sensitivity and 100.0% specificity. This screening PCR is a rapid, sensitive, and cost-effective method for the detection of major CALR mutations.

  1. Exponential megapriming PCR (EMP) cloning--seamless DNA insertion into any target plasmid without sequence constraints.

    Science.gov (United States)

    Ulrich, Alexander; Andersen, Kasper R; Schwartz, Thomas U

    2012-01-01

    We present a fast, reliable and inexpensive restriction-free cloning method for seamless DNA insertion into any plasmid without sequence limitation. Exponential megapriming PCR (EMP) cloning requires two consecutive PCR steps and can be carried out in one day. We show that EMP cloning has a higher efficiency than restriction-free (RF) cloning, especially for long inserts above 2.5 kb. EMP further enables simultaneous cloning of multiple inserts.

  2. Exponential megapriming PCR (EMP cloning--seamless DNA insertion into any target plasmid without sequence constraints.

    Directory of Open Access Journals (Sweden)

    Alexander Ulrich

    Full Text Available We present a fast, reliable and inexpensive restriction-free cloning method for seamless DNA insertion into any plasmid without sequence limitation. Exponential megapriming PCR (EMP cloning requires two consecutive PCR steps and can be carried out in one day. We show that EMP cloning has a higher efficiency than restriction-free (RF cloning, especially for long inserts above 2.5 kb. EMP further enables simultaneous cloning of multiple inserts.

  3. A Novel Universal Primer-Multiplex-PCR Method with Sequencing Gel Electrophoresis Analysis

    Science.gov (United States)

    Huang, Kunlun; Zhang, Nan; Yuan, Yanfang; Shang, Ying; Luo, Yunbo

    2012-01-01

    In this study, a novel universal primer-multiplex-PCR (UP-M-PCR) method adding a universal primer (UP) in the multiplex PCR reaction system was described. A universal adapter was designed in the 5′-end of each specific primer pairs which matched with the specific DNA sequences for each template and also used as the universal primer (UP). PCR products were analyzed on sequencing gel electrophoresis (SGE) which had the advantage of exhibiting extraordinary resolution. This method overcame the disadvantages rooted deeply in conventional multiplex PCR such as complex manipulation, lower sensitivity, self-inhibition and amplification disparity resulting from different primers, and it got a high specificity and had a low detection limit of 0.1 ng for single kind of crops when screening the presence of genetically modified (GM) crops in mixture samples. The novel developed multiplex PCR assay with sequencing gel electrophoresis analysis will be useful in many fields, such as verifying the GM status of a sample irrespective of the crop and GM trait and so on. PMID:22272223

  4. A Simple Multiplex PCR Approach for Target Enrichment in Next-Gen Sequencing

    Science.gov (United States)

    Zhu, Qi; Hebel, Chris; Zhou, Xiaochun

    2014-01-01

    Multiplexing PCR is a simple way to extract genomic regions of interest for various medical and genetic tests. Somatic mutations lead to various diseases including cancer. These mutations are unlikely to be best detected using regular whole genome sequencing. Clinical samples often consist of disease cells, e.g. cancer cells, surrounded by normal cells. Thus, deep sequencing of hundreds to thousands fold coverage is required to detect the mutations. In clinical research many doctors are interested in specific genes or genomic regions and they want to extract the regions from genomic DNA or RNA before sequencing. Many current clinical, forensic, and heretical genetic test workflows start with multiplexing PCR to extract genetic marker carrying regions from whole genomes before running hybridization, sequencing, or electrophoresis tests to identify the markers. Personal medicine and prognosis mostly involve examining sequence variations of a number of targeted genes and metabolic pathway genes so as to predict drug efficacies and drug toxicities. We have developed a new multiplexing PCR approach with a significantly simplified workflow and significantly improved robustness. When applied to sequencing target enrichment application, the workflow for producing amplified targets involves only one hands-on step and one PCR run. The approach is designed to require low sample input and to produce superior amplicon uniformity and sequence specificity. The approach involves a novel primer design and a proprietary reaction composition. A PCR run consists of two functionally separated reaction phases, namely target capture and library amplification, without any hands-on step in between. The performance of the new approach will be demonstrated by a caner panel data.

  5. Polymerase chain reaction (PCR) amplification of a nucleoprotein gene sequence of infectious hematopoietic necrosis virus

    Science.gov (United States)

    Arakawa, C.K.; Deering, R.E.; Higman, K.H.; Oshima, K.H.; O'Hara, P.J.; Winton, J.R.

    1990-01-01

    The polymerase chain reaction [PCR) was used to amplify a portion of the nucleoprotein [NI gene of infectious hematopoietic necrosis virus (IHNV). Using a published sequence for the Round Butte isolate of IHNV, a pair of PCR pnmers was synthesized that spanned a 252 nucleotide region of the N gene from residue 319 to residue 570 of the open reading frame. This region included a 30 nucleotide target sequence for a synthetic oligonucleotide probe developed for detection of IHNV N gene messenger RNA. After 25 cycles of amplification of either messenger or genomic RNA, the PCR product (DNA) of the expected size was easily visible on agarose gels stained with ethidium bromide. The specificity of the amplified DNA was confirmed by Southern and dot-blot analysis using the biotinylated oligonucleotide probe. The PCR was able to amplify the N gene sequence of purified genomic RNA from isolates of IHNV representing 5 different electropherotypes. Using the IHNV primer set, no PCR product was obtained from viral hemorrhagic septicemia virus RNA, but 2 higher molecular weight products were synthesized from hirame rhabdovirus RNA that did not hybridize with the biotinylated probe. The PCR could be efficiently performed with all IHNV genomic RNA template concentrations tested (1 ng to 1 pg). The lowest level of sensitivity was not determined. The PCR was used to amplify RNA extracted from infected cell cultures and selected tissues of Infected rainbow trout. The combination of PCR and nucleic acid probe promises to provide a detection method for IHNV that is rapid, h~ghly specific, and sensitive.

  6. Novel computational methods for increasing PCR primer design effectiveness in directed sequencing

    Directory of Open Access Journals (Sweden)

    Busam Dana

    2008-04-01

    Full Text Available Abstract Background Polymerase chain reaction (PCR is used in directed sequencing for the discovery of novel polymorphisms. As the first step in PCR directed sequencing, effective PCR primer design is crucial for obtaining high-quality sequence data for target regions. Since current computational primer design tools are not fully tuned with stable underlying laboratory protocols, researchers may still be forced to iteratively optimize protocols for failed amplifications after the primers have been ordered. Furthermore, potentially identifiable factors which contribute to PCR failures have yet to be elucidated. This inefficient approach to primer design is further intensified in a high-throughput laboratory, where hundreds of genes may be targeted in one experiment. Results We have developed a fully integrated computational PCR primer design pipeline that plays a key role in our high-throughput directed sequencing pipeline. Investigators may specify target regions defined through a rich set of descriptors, such as Ensembl accessions and arbitrary genomic coordinates. Primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the specified target regions. As part of the tiling process, primer pairs are computationally screened to meet the criteria for success with one of two PCR amplification protocols. In the process of improving our sequencing success rate, which currently exceeds 95% for exons, we have discovered novel and accurate computational methods capable of identifying primers that may lead to PCR failures. We reveal the laboratory protocols and their associated, empirically determined computational parameters, as well as describe the novel computational methods which may benefit others in future primer design research. Conclusion The high-throughput PCR primer design pipeline has been very successful in providing the basis for high-quality directed sequencing results and for minimizing

  7. A Bac Library and Paired-PCR Approach to Mapping and Completing the Genome Sequence of Sulfolobus Solfataricus P2

    DEFF Research Database (Denmark)

    She, Qunxin; Confalonieri, F.; Zivanovic, Y.;

    2000-01-01

    -productive because there was a high sequence bias in the cosmid and lambda libraries. Therefore, a new approach was devised for linking the sequenced regions which may be generally applicable. BAC libraries were constructed and terminal sequences of the clones were determined and used for both end mapping and PCR...... screening. The PCR approaches included a novel chromosome walking method termed “paired-PCR”. 21 gaps were filled by BAC end sequence analyses and 6 gaps were filled by PCR including three large ones by paired-PCR. The complete map revealed that 0.9 Mb remained to be sequenced and 34 BAC clones were...... selected for walking over small gaps and preparing template libraries for larger ones. It is concluded that an optimal strategy for sequencing microorganism genomes involves construction of a high-resolution physical map by BAC end analyses, PCR screening and paired-PCR chromosome walking after about half...

  8. One-step selection of Vaccinia virus-binding DNA aptamers by MonoLEX

    Directory of Open Access Journals (Sweden)

    Stöcklein Walter

    2007-08-01

    Full Text Available Abstract Background As a new class of therapeutic and diagnostic reagents, more than fifteen years ago RNA and DNA aptamers were identified as binding molecules to numerous small compounds, proteins and rarely even to complete pathogen particles. Most aptamers were isolated from complex libraries of synthetic nucleic acids by a process termed SELEX based on several selection and amplification steps. Here we report the application of a new one-step selection method (MonoLEX to acquire high-affinity DNA aptamers binding Vaccinia virus used as a model organism for complex target structures. Results The selection against complete Vaccinia virus particles resulted in a 64-base DNA aptamer specifically binding to orthopoxviruses as validated by dot blot analysis, Surface Plasmon Resonance, Fluorescence Correlation Spectroscopy and real-time PCR, following an aptamer blotting assay. The same oligonucleotide showed the ability to inhibit in vitro infection of Vaccinia virus and other orthopoxviruses in a concentration-dependent manner. Conclusion The MonoLEX method is a straightforward procedure as demonstrated here for the identification of a high-affinity DNA aptamer binding Vaccinia virus. MonoLEX comprises a single affinity chromatography step, followed by subsequent physical segmentation of the affinity resin and a single final PCR amplification step of bound aptamers. Therefore, this procedure improves the selection of high affinity aptamers by reducing the competition between aptamers of different affinities during the PCR step, indicating an advantage for the single-round MonoLEX method.

  9. External and semi-internal controls for PCR amplification of homologous sequences in mixed templates.

    Science.gov (United States)

    Kalle, Elena; Gulevich, Alexander; Rensing, Christopher

    2013-11-01

    In a mixed template, the presence of homologous target DNA sequences creates environments that almost inevitably give rise to artifacts and biases during PCR. Heteroduplexes, chimeras, and skewed template-to-product ratios are the exclusive attributes of mixed template PCR and never occur in a single template assay. Yet, multi-template PCR has been used without appropriate attention to quality control and assay validation, in spite of the fact that such practice diminishes the reliability of results. External and internal amplification controls became obligatory elements of good laboratory practice in different PCR assays. We propose the inclusion of an analogous approach as a quality control system for multi-template PCR applications. The amplification controls must take into account the characteristics of multi-template PCR and be able to effectively monitor particular assay performance. This study demonstrated the efficiency of a model mixed template as an adequate external amplification control for a particular PCR application. The conditions of multi-template PCR do not allow implementation of a classic internal control; therefore we developed a convenient semi-internal control as an acceptable alternative. In order to evaluate the effects of inhibitors, a model multi-template mix was amplified in a mixture with DNAse-treated sample. Semi-internal control allowed establishment of intervals for robust PCR performance for different samples, thus enabling correct comparison of the samples. The complexity of the external and semi-internal amplification controls must be comparable with the assumed complexity of the samples. We also emphasize that amplification controls should be applied in multi-template PCR regardless of the post-assay method used to analyze products.

  10. A new trilocus sequence-based multiplex-PCR to detect major Acinetobacter baumannii clones.

    Science.gov (United States)

    Martins, Natacha; Picão, Renata Cristina; Cerqueira-Alves, Morgana; Uehara, Aline; Barbosa, Lívia Carvalho; Riley, Lee W; Moreira, Beatriz Meurer

    2016-08-01

    A collection of 163 Acinetobacter baumannii isolates detected in a large Brazilian hospital, was potentially related with the dissemination of four clonal complexes (CC): 113/79, 103/15, 109/1 and 110/25, defined by University of Oxford/Institut Pasteur multilocus sequence typing (MLST) schemes. The urge of a simple multiplex-PCR scheme to specify these clones has motivated the present study. The established trilocus sequence-based typing (3LST, for ompA, csuE and blaOXA-51-like genes) multiplex-PCR rapidly identifies international clones I (CC109/1), II (CC118/2) and III (CC187/3). Thus, the system detects only one (CC109/1) out of four main CC in Brazil. We aimed to develop an alternative multiplex-PCR scheme to detect these clones, known to be present additionally in Africa, Asia, Europe, USA and South America. MLST, performed in the present study to complement typing our whole collection of isolates, confirmed that all isolates belonged to the same four CC detected previously. When typed by 3LST-based multiplex-PCR, only 12% of the 163 isolates were classified into groups. By comparative sequence analysis of ompA, csuE and blaOXA-51-like genes, a set of eight primers was designed for an alternative multiplex-PCR to distinguish the five CC 113/79, 103/15, 109/1, 110/25 and 118/2. Study isolates and one CC118/2 isolate were blind-tested with the new alternative PCR scheme; all were correctly clustered in groups of the corresponding CC. The new multiplex-PCR, with the advantage of fitting in a single reaction, detects five leading A. baumannii clones and could help preventing the spread in healthcare settings.

  11. Examining Sources of Error in PCR by Single-Molecule Sequencing

    Science.gov (United States)

    Potapov, Vladimir

    2017-01-01

    Next-generation sequencing technology has enabled the detection of rare genetic or somatic mutations and contributed to our understanding of disease progression and evolution. However, many next-generation sequencing technologies first rely on DNA amplification, via the Polymerase Chain Reaction (PCR), as part of sample preparation workflows. Mistakes made during PCR appear in sequencing data and contribute to false mutations that can ultimately confound genetic analysis. In this report, a single-molecule sequencing assay was used to comprehensively catalog the different types of errors introduced during PCR, including polymerase misincorporation, structure-induced template-switching, PCR-mediated recombination and DNA damage. In addition to well-characterized polymerase base substitution errors, other sources of error were found to be equally prevalent. PCR-mediated recombination by Taq polymerase was observed at the single-molecule level, and surprisingly found to occur as frequently as polymerase base substitution errors, suggesting it may be an underappreciated source of error for multiplex amplification reactions. Inverted repeat structural elements in lacZ caused polymerase template-switching between the top and bottom strands during replication and the frequency of these events were measured for different polymerases. For very accurate polymerases, DNA damage introduced during temperature cycling, and not polymerase base substitution errors, appeared to be the major contributor toward mutations occurring in amplification products. In total, we analyzed PCR products at the single-molecule level and present here a more complete picture of the types of mistakes that occur during DNA amplification. PMID:28060945

  12. PRISE (PRImer SElector): software for designing sequence-selective PCR primers.

    Science.gov (United States)

    Fu, Qi; Ruegger, Paul; Bent, Elizabeth; Chrobak, Marek; Borneman, James

    2008-03-01

    This report presents PRImer Selector (PRISE), a new software package that implements several features that improve and streamline the design of sequence-selective PCR primers. The PRISE design process involves two main steps. In the first step, target and non-target DNA sequences are identified. In the second step, primers are designed to amplify target (but not non-target) sequences. One important feature of PRISE is that it automates the task of placing primer-template mismatches at the 3' end of the primers - a property that is crucial for sequence selectivity. Once a list of candidate primers has been produced, sorting tools in PRISE speed up the selection process by allowing a user to sort the primers by properties such as amplicon length, GC content and sequence selectivity. PRISE can be used to design primers with a range of specificities, targeting individual sequences as well as diverse assemblages of genes. PRISE also allows user-defined primers to be analyzed, enabling their properties to be examined in relation to target and non-target sequences. The utility of PRISE was demonstrated by using it to design sequence-selective PCR primers for an rRNA gene from the fungus Pochonia chlamydosporia.

  13. Estimating Digital Inter-Symbol Interference Channel Blindly Based on the One-Step Branch Transition Rules in Trellises

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A novel discrete-time digital inter-symbol interference (ISI) channel blind estimation sub-optimal algorithm is proposed. This algorithm reduces the complexity of the optimal maximum likelihood sequence estimation(MLSE) considerably based on the one-step branch transition rules in trellises, and is suitable for the estimation of the channels with small lengths of ISI.

  14. Fusion primer and nested integrated PCR (FPNI-PCR: a new high-efficiency strategy for rapid chromosome walking or flanking sequence cloning

    Directory of Open Access Journals (Sweden)

    Wang Zhen

    2011-11-01

    Full Text Available Abstract Background The advent of genomics-based technologies has revolutionized many fields of biological enquiry. However, chromosome walking or flanking sequence cloning is still a necessary and important procedure to determining gene structure. Such methods are used to identify T-DNA insertion sites and so are especially relevant for organisms where large T-DNA insertion libraries have been created, such as rice and Arabidopsis. The currently available methods for flanking sequence cloning, including the popular TAIL-PCR technique, are relatively laborious and slow. Results Here, we report a simple and effective fusion primer and nested integrated PCR method (FPNI-PCR for the identification and cloning of unknown genomic regions flanked known sequences. In brief, a set of universal primers was designed that consisted of various 15-16 base arbitrary degenerate oligonucleotides. These arbitrary degenerate primers were fused to the 3' end of an adaptor oligonucleotide which provided a known sequence without degenerate nucleotides, thereby forming the fusion primers (FPs. These fusion primers are employed in the first step of an integrated nested PCR strategy which defines the overall FPNI-PCR protocol. In order to demonstrate the efficacy of this novel strategy, we have successfully used it to isolate multiple genomic sequences namely, 21 orthologs of genes in various species of Rosaceace, 4 MYB genes of Rosa rugosa, 3 promoters of transcription factors of Petunia hybrida, and 4 flanking sequences of T-DNA insertion sites in transgenic tobacco lines and 6 specific genes from sequenced genome of rice and Arabidopsis. Conclusions The successful amplification of target products through FPNI-PCR verified that this novel strategy is an effective, low cost and simple procedure. Furthermore, FPNI-PCR represents a more sensitive, rapid and accurate technique than the established TAIL-PCR and hiTAIL-PCR procedures.

  15. Identification of rat genes by TWINSCAN gene prediction, RT-PCR, and direct sequencing

    DEFF Research Database (Denmark)

    Wu, Jia Qian; Shteynberg, David; Arumugam, Manimozhiyan

    2004-01-01

    The publication of a draft sequence of a third mammalian genome--that of the rat--suggests a need to rethink genome annotation. New mammalian sequences will not receive the kind of labor-intensive annotation efforts that are currently being devoted to human. In this paper, we demonstrate...... an alternative approach: reverse transcription-polymerase chain reaction (RT-PCR) and direct sequencing based on dual-genome de novo predictions from TWINSCAN. We tested 444 TWINSCAN-predicted rat genes that showed significant homology to known human genes implicated in disease but that were partially...

  16. A primer design strategy for PCR amplification of GC-rich DNA sequences.

    Science.gov (United States)

    Li, Li-Yan; Li, Qiang; Yu, Yan-Hong; Zhong, Mei; Yang, Lei; Wu, Qing-Hong; Qiu, Yu-Rong; Luo, Shen-Qiu

    2011-06-01

    To establish a primer design method for amplification of GC-rich DNA sequences. A group of 15 pairs of primers with higher T(m) (>79.7°C) and lower level ΔT(m) (designed to amplify GC-rich sequences (66.0%-84.0%). The statistical analysis of primer parameters and GC content of PCR products was performed and compared with literatures. Other control experiments were conducted using shortened primers for GC-rich PCR amplifications in this study, and the statistical analysis of shortened primer parameters and GC content of PCR products was performed compared with primers not shortened. A group of 26 pairs of primers were designed to test the applicability of this primer designing strategy in amplifications of non-GC-rich sequences (35.2%-53.5%). All the DNA sequences in this study were successfully amplified. Statistical analyses show that the T(m) and ΔT(m) were the main factors influencing amplifications. This primer designing strategy offered a perfect tool for amplification of GC-rich sequences. It proves that the secondary structures cannot be formed at higher annealing temperature conditions (>65°C), and we can overcome this difficulty easily by designing primers and using higher annealing temperature. Crown Copyright © 2011. Published by Elsevier Inc. All rights reserved.

  17. A diagnostic one-step real-time reverse transcription polymerase chain reaction method for accurate detection of influenza virus type A

    Science.gov (United States)

    Behzadi, Mohammad Amin; Alborzi, Abdolvahab

    2016-01-01

    Introduction Influenza A is known as a public health concern worldwide. In this study, a novel one-step real-time reverse transcription polymerase chain reaction (rtRT-PCR) assay was designed and optimized for the detection of influenza A viruses. Material and methods The primers and probe were designed based on the analysis of 90 matrix nucleotide sequence data of influenza type A subtypes from the GenBank database of the National Center for Biotechnology Information (NCBI). The influenza virus A/Tehran/5652/2010 (H1N1 pdm09) was used as a reference. The rtRT-PCR assay was optimized, compared with that of the World Health Organization (WHO), and its analytical sensitivity, specificity and reproducibility were evaluated. In total, 64 nasopharyngeal swabs from patients with influenza-like illness (ILI) and 41 samples without ILI symptoms were tested for the virus, using conventional cell culture, direct immunofluorescence antibody (DFA) methods, and one-step rtRT-PCR with the designed primer set and probe and the WHO’s. Results The optimized assay results were similar to the WHO’s. The optimized assay results were similar to WHO’s, with non-significant differences for 10–103 copies of viral RNA/reaction (p > 0.05). It detected 10 copies of viral RNA/reaction with high reproducibility and no cross reactivity with other respiratory viruses. A specific cytopathic effect was observed in 6/64 (9.37%) of the ILI group using conventional culture and DFA staining methods; however, it was not seen in non-ILI. Also, the results of our assay and the WHO’s were similar to those of viral isolation and DFA staining. Conclusions Given the high specificity, sensitivity and reproducibility of this novel assay, it can serve as a reliable diagnostic tool for the detection of influenza A viruses in clinical specimens and lab experiments. PMID:27904520

  18. A one-step miniprep for the isolation of plasmid DNA and lambda phage particles.

    Directory of Open Access Journals (Sweden)

    George Lezin

    Full Text Available Plasmid DNA minipreps are fundamental techniques in molecular biology. Current plasmid DNA minipreps use alkali and the anionic detergent SDS in a three-solution format. In addition, alkali minipreps usually require additional column-based purification steps and cannot isolate other extra-chromosomal elements, such as bacteriophages. Non-ionic detergents (NIDs have been used occasionally as components of multiple-solution plasmid DNA minipreps, but a one-step approach has not been developed. Here, we have established a one-tube, one-solution NID plasmid DNA miniprep, and we show that this approach also isolates bacteriophage lambda particles. NID minipreps are more time-efficient than alkali minipreps, and NID plasmid DNA performs better than alkali DNA in many downstream applications. In fact, NID crude lysate DNA is sufficiently pure to be used in digestion and sequencing reactions. Microscopic analysis showed that the NID procedure fragments E. coli cells into small protoplast-like components, which may, at least in part, explain the effectiveness of this approach. This work demonstrates that one-step NID minipreps are a robust method to generate high quality plasmid DNA, and NID approaches can also isolate bacteriophage lambda particles, outperforming current standard alkali-based minipreps.

  19. Routine ribosomal PCR and DNA sequencing for detection and identification of bacteria

    DEFF Research Database (Denmark)

    Kemp, Michael; Jensen, Kristine H; Dargis, Rimtas

    2010-01-01

    Detection and identification of bacteria by PCR and DNA sequencing from clinical sample material has been introduced as a diagnostic routine analysis during the last 5-10 years. Assays analyzing ribosomal genes have been found to be particularly useful. The technique has identified unusual bacteria...... as well as well-known bacteria in unusual infectious foci. Thereby, it has proven its value both in diagnosing infections in individual patients and as a tool to establish the pathogenic potential of bacteria not previously associated with disease. To be of clinical relevance, results from ribosomal PCR...

  20. A practical method for barcoding and size-trimming PCR templates for amplicon sequencing.

    Science.gov (United States)

    Mäki, Anita; Rissanen, Antti J; Tiirola, Marja

    2016-02-01

    Sample barcoding facilitates the analysis of tens or even hundreds of samples in a single next-generation sequencing (NGS) run, but more efficient methods are needed for high-throughput barcoding and size-trimming of long PCR products. Here we present a two-step PCR approach for barcoding followed by pool shearing, adapter ligation, and 5' end selection for trimming sets of DNA templates of any size. Our new trimming method offers clear benefits for phylogenetic studies, since targeting exactly the same region maximizes the alignment and enables the use of operational taxonomic unit (OTU)-based algorithms.

  1. A Comparison of Molecular Typing Methods Applied to Enterobacter cloacae complex: hsp60 Sequencing, Rep-PCR, and MLST

    Directory of Open Access Journals (Sweden)

    Roberto Viau

    2017-02-01

    Full Text Available Molecular typing using repetitive sequenced-based PCR (rep-PCR and hsp60 sequencing were applied to a collection of diverse Enterobacter cloacae complex isolates. To determine the most practical method for reference laboratories, we analyzed 71 E. cloacae complex isolates from sporadic and outbreak occurrences originating from 4 geographic areas. While rep-PCR was more discriminating, hsp60 sequencing provided a broader and a more objective geographical tracking method similar to multilocus sequence typing (MLST. In addition, we suggest that MLST may have higher discriminative power compared to hsp60 sequencing, although rep-PCR remains the most discriminative method for local outbreak investigations. In addition, rep-PCR can be an effective and inexpensive method for local outbreak investigation.

  2. Rapid identification and mapping of insertion sequences in Escherichia coli genomes using vectorette PCR

    Directory of Open Access Journals (Sweden)

    Dean Antony M

    2004-07-01

    Full Text Available Abstract Background Insertion sequences (IS are small DNA segments capable of transposing within and between prokaryotic genomes, often causing insertional mutations and chromosomal rearrangements. Although several methods are available for locating ISs in microbial genomes, they are either labor-intensive or inefficient. Here, we use vectorette PCR to identify and map the genomic positions of the eight insertion sequences (IS1, 2, 3, 4, 5, 30, 150, and 186 found in E. coli strain CGSC6300, a close relative of MG1655 whose genome has been sequenced. Results Genomic DNA from strain CGSC6300 was digested with a four-base cutter Rsa I and the resulting restriction fragments ligated onto vectorette units. Using IS-specific primers directed outward from the extreme ends of each IS and a vectorette primer, flanking DNA fragments were amplified from all but one of the 37 IS elements identified in the genomic sequence of MG1655. Purification and sequencing of the PCR products confirmed that they are IS-associated flanking DNA fragments corresponding to the known IS locations in the MG1655 genome. Seven additional insertions were found in strain CGSC6300 indicating that very closely related isolates of the same laboratory strain (the K12 isolate may differ in their IS complement. Two other E. coli K12 derivatives, TD2 and TD10, were also analyzed by vectorette PCR. They share 36 of the MG1655 IS sites as well as having 16 and 18 additional insertions, respectively. Conclusion This study shows that vectorette PCR is a swift, efficient, reliable method for typing microbial strains and identifying and mapping IS insertion sites present in microbial genomes. Unlike Southern hybridization and inverse PCR, our approach involves only one genomic digest and one ligation step. Vectorette PCR is then used to simultaneously amplify all IS elements of a given type, making it a rapid and sensitive means to survey IS elements in genomes. The ability to rapidly

  3. Real Time PCR to detect hazelnut allergen coding sequences in processed foods.

    Science.gov (United States)

    Iniesto, Elisa; Jiménez, Ana; Prieto, Nuria; Cabanillas, Beatriz; Burbano, Carmen; Pedrosa, Mercedes M; Rodríguez, Julia; Muzquiz, Mercedes; Crespo, Jesús F; Cuadrado, Carmen; Linacero, Rosario

    2013-06-01

    A quantitative RT-PCR method, employing novel primer sets designed on Cor a 9, Cor a 11 and Cor a 13 allergen-coding sequences has been setup and validated. Its specificity, sensitivity and applicability have been compared. The effect of processing on detectability of these hazelnut targets in complex food matrices was also studied. The DNA extraction method based on CTAB-phenol-chloroform was the best for hazelnut. RT-PCR using primers for Cor a 9, 11 and 13 allowed a specific and accurate amplification of these sequences. The limit of detection was 1 ppm of raw hazelnut. The method sensitivity and robustness were confirmed with spiked samples. Thermal treatments (roasting and autoclaving) reduced yield and amplificability of hazelnut DNA, however, high-hydrostatic pressure did not affect. Compared with an ELISA assay, this RT-PCR showed higher sensitivity to detected hazelnut traces in commercial foodstuffs. The RT-PCR method described is the most sensitive of those reported for the detection of hazelnut traces in processed foods.

  4. Detection by real time PCR of walnut allergen coding sequences in processed foods.

    Science.gov (United States)

    Linacero, Rosario; Ballesteros, Isabel; Sanchiz, Africa; Prieto, Nuria; Iniesto, Elisa; Martinez, Yolanda; Pedrosa, Mercedes M; Muzquiz, Mercedes; Cabanillas, Beatriz; Rovira, Mercè; Burbano, Carmen; Cuadrado, Carmen

    2016-07-01

    A quantitative real-time PCR (RT-PCR) method, employing novel primer sets designed on Jug r 1, Jug r 3, and Jug r 4 allergen-coding sequences, was set up and validated. Its specificity, sensitivity, and applicability were evaluated. The DNA extraction method based on CTAB-phenol-chloroform was best for walnut. RT-PCR allowed a specific and accurate amplification of allergen sequence, and the limit of detection was 2.5pg of walnut DNA. The method sensitivity and robustness were confirmed with spiked samples, and Jug r 3 primers detected up to 100mg/kg of raw walnut (LOD 0.01%, LOQ 0.05%). Thermal treatment combined with pressure (autoclaving) reduced yield and amplification (integrity and quality) of walnut DNA. High hydrostatic pressure (HHP) did not produce any effect on the walnut DNA amplification. This RT-PCR method showed greater sensitivity and reliability in the detection of walnut traces in commercial foodstuffs compared with ELISA assays.

  5. DNA TYPING FOR HLA - DR ALLELES BY PCR - AMPLIFICATION WITH SEQUENCE- SPECIFIC PRIMERS

    Institute of Scientific and Technical Information of China (English)

    谭建明; 谢桐; 徐琴君

    1999-01-01

    Ohjective To establish a rapid genetyping for HLA- DR alleles by polymerase chain reaction wiht sequence - specifie primers (PCR - SSP) for clinical application. Material and Methods The subjects of study included 69 recipients, 43 unrelated donors and 5 cell lines, Genomic DNA was prepared from peripheral blood leukoeytes by a salting- out method, Thirty primers designed according to the HLA- DRB nucleotide sequences, and synthesized on a 391 DNN synthesizer,Twenty separate PCR reactions were perfomed for each sample, The amplification was accomplished by 34 cycles consisting of denaturation at 94℃ for 30 seconds, annealing at 60℃ for 50 seconds and extension at 72℃ for 40 seconds The specificity of matching was determined by standard DNAs and Southem hybeidization using DIG labeling probes. Results All 112 samples and 5 cell lines were able to be typed by PCR-SSP,No false positive or false negative typing results were obtained. The reproducibility was 100 %,The size of the .specific product was in cnoccrdance with the size of the designed primers. The overall time for genotyping was 4 bours. The typing results were confirned by Southem hybridization.Conelusions Genotyping for HLA- DR by PCR- SSP is a rapid and accurate matching technique suited for clinical application.

  6. Sequence-Specific Biosensing of DNA Target through Relay PCR with Small-Molecule Fluorophore.

    Science.gov (United States)

    Yasmeen, Afshan; Du, Feng; Zhao, Yongyun; Dong, Juan; Chen, Haodong; Huang, Xin; Cui, Xin; Tang, Zhuo

    2016-07-15

    Polymerase chain reaction coupled with signal generation offers sensitive recognition of target DNA sequence; however, these procedures require fluorophore-labeled oligonucleotide probes and high-tech equipment to achieve high specificity. Therefore, intensive research has been conducted to develop reliable, convenient, and economical DNA detection methods. The relay PCR described here is the first sequence-specific detection method using a small-molecule fluorophore as a sensor and combines the classic 5'-3' exonuclease activity of Taq polymerase with an RNA mimic of GFP to build a label-free DNA detection platform. Primarily, Taq polymerase cleaves the 5' noncomplementary overhang of the target specific probe during extension of the leading primer to release a relay oligo to initiate tandem PCR of the reporting template, which encodes the sequence of RNA aptamer. Afterward, the PCR product is transcribed to mRNA, which could generate a fluorescent signal in the presence of corresponding fluorophore. In addition to high sensitivity and specificity, the flexibility of choosing different fluorescent reporting signals makes this method versatile in either single or multiple target detection.

  7. Simple and comprehensive SLA-DQB1 genotyping using genomic PCR and direct sequencing.

    Science.gov (United States)

    Park, K; Choi, H; Thong, L M; Kwon, O-J; Kim, J-H; Lee, H-T; Kim, Y-B; Park, S-B; Park, C

    2010-10-01

    To enable the efficient analysis of a highly polymorphic swine major histocompatibility complex (MHC) class II gene, swine leukocyte antigen (SLA)-DQB1, we developed a simple and comprehensive high-resolution genotyping protocol. To obtain sufficient sequence information to design a set of common genotyping primers for SLA-DQB1, we cloned SLA-DQB1 introns 1 and 2 from 11 alleles with official four-digit allelic designations and sequenced the regions directly surrounding the SLA-DQB1 exon 2. Significant intronic nucleotide variations, including several deletions, were identified. Based on 733-bp assembled genomic sequences including introns 1 and 2 and exon 2 from 11 different alleles, a primer set was identified that allowed the ubiquitous amplification and analysis of the complete SLA-DQB1 exon 2 sequence. We then developed a method to directly sequence the amplified polymerase chain reaction (PCR) products without further experimental steps. We especially focused on avoiding superimposed peaks, which arose from the presence of allelic deletions, in the sequencing electropherogram of SLA-DQB1 heterozygous animals. The genotyping accuracy was evaluated by comparing the results of genomic sequence-based typing (GSBT) with those of other available methods, including cDNA sequence-based typing (SBT), low-resolution PCR typing with sequence-specific primers, allelic segregation analysis, and heterozygote simulation typing. In all cases, the results were consistent between SLA-DQB1 GSBT and previously reported methods or expected results. We applied it to genotype 350 animals from seven pig breeds. The observed level of heterozygosity from our genotyping was ∼51%, reflecting that a large portion of the animals were inbred miniature pigs. Among the seven pig breeds tested, the allelic diversity of SLA-DQB1 was highest in Berkshire pigs. In conclusion, we have developed a simple and effective SLA-DQB1 GSBT method by combining simple genomic DNA PCR and direct sequencing

  8. A one pot, one step, precision cloning method with high throughput capability.

    Directory of Open Access Journals (Sweden)

    Carola Engler

    Full Text Available Current cloning technologies based on site-specific recombination are efficient, simple to use, and flexible, but have the drawback of leaving recombination site sequences in the final construct, adding an extra 8 to 13 amino acids to the expressed protein. We have devised a simple and rapid subcloning strategy to transfer any DNA fragment of interest from an entry clone into an expression vector, without this shortcoming. The strategy is based on the use of type IIs restriction enzymes, which cut outside of their recognition sequence. With proper design of the cleavage sites, two fragments cut by type IIs restriction enzymes can be ligated into a product lacking the original restriction site. Based on this property, a cloning strategy called 'Golden Gate' cloning was devised that allows to obtain in one tube and one step close to one hundred percent correct recombinant plasmids after just a 5 minute restriction-ligation. This method is therefore as efficient as currently used recombination-based cloning technologies but yields recombinant plasmids that do not contain unwanted sequences in the final construct, thus providing precision for this fundamental process of genetic manipulation.

  9. High throughput sequencing analysis of RNA libraries reveals the influences of initial library and PCR methods on SELEX efficiency.

    Science.gov (United States)

    Takahashi, Mayumi; Wu, Xiwei; Ho, Michelle; Chomchan, Pritsana; Rossi, John J; Burnett, John C; Zhou, Jiehua

    2016-09-22

    The systemic evolution of ligands by exponential enrichment (SELEX) technique is a powerful and effective aptamer-selection procedure. However, modifications to the process can dramatically improve selection efficiency and aptamer performance. For example, droplet digital PCR (ddPCR) has been recently incorporated into SELEX selection protocols to putatively reduce the propagation of byproducts and avoid selection bias that result from differences in PCR efficiency of sequences within the random library. However, a detailed, parallel comparison of the efficacy of conventional solution PCR versus the ddPCR modification in the RNA aptamer-selection process is needed to understand effects on overall SELEX performance. In the present study, we took advantage of powerful high throughput sequencing technology and bioinformatics analysis coupled with SELEX (HT-SELEX) to thoroughly investigate the effects of initial library and PCR methods in the RNA aptamer identification. Our analysis revealed that distinct "biased sequences" and nucleotide composition existed in the initial, unselected libraries purchased from two different manufacturers and that the fate of the "biased sequences" was target-dependent during selection. Our comparison of solution PCR- and ddPCR-driven HT-SELEX demonstrated that PCR method affected not only the nucleotide composition of the enriched sequences, but also the overall SELEX efficiency and aptamer efficacy.

  10. Molecular Detection of Verticillium albo-atrum by PCR Based on Its Sequences

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    We developed one species-specific PCR assays for rapid and accurate detection of the pathogenic fungi Verticilliumalbo-atrum in diseased plant tissues and soil. Based on differences in internal transcribed spacer (ITS) sequences ofVerticilliun spp., a pair of species-specific primers, Vaa1/Vaa2, was synthesized. After screening 17 isolates of V. albo-atrum, 121 isolates from the Ascomycota, Basidiomycota, Deuteromycota, and Oomycota, the Vaa1/Vaa2 primers amplifiedonly a single PCR band of approximately 330 bp from V. albo-atrum. The detection sensitivity with primers Vaa1/Vaa2 was10 fg of genomic DNA. Using ITS1/ITS4 as the first-round primers, combined with Vaa1/Vaa2, the nested PCR procedureswere developed, and the detection sensitivity increased 1 000-fold to 10 ag. The detection sensitivity for the soil pathogenswas 100-conidiag-1 soil. The PCR-based methods developed here could simplify both plant disease diagnosis and pathogen monitoring as well as guide plant disease management.

  11. [Rapid construction of full-length MnSOD cDNA of chickens by one-step 3'RACE].

    Science.gov (United States)

    Bu, You-Quan; Luo, Xu-Gang; Liu, Bin; Li, Su-Fen

    2004-07-01

    RACE (rapid amplification of cDNA ends) is a popular technique to rapidly obtain the full-length cDNA. After obtaining the 3' cDNA and 5' cDNA fragments with a overlapped region by 3' RACE and 5' RACE, the full-length cDNA could be generated by end-to-end PCR or subcloning. In this study, 3' RACE combined with touch-down PCR was successfully used for the rapid construction of full-length MnSOD cDNA of chickens. Compared with the conventional end-to-end PCR or subcloning, this method, called one-step 3' RACE, is fast, economical and highly specific. It especially fits the rapid construction of full-length cDNA by RACE method.

  12. BatchPrimer3: a high throughput web application for PCR and sequencing primer design.

    Science.gov (United States)

    You, Frank M; Huo, Naxin; Gu, Yong Qiang; Luo, Ming-Cheng; Ma, Yaqin; Hane, Dave; Lazo, Gerard R; Dvorak, Jan; Anderson, Olin D

    2008-05-29

    Microsatellite (simple sequence repeat - SSR) and single nucleotide polymorphism (SNP) markers are two types of important genetic markers useful in genetic mapping and genotyping. Often, large-scale genomic research projects require high-throughput computer-assisted primer design. Numerous such web-based or standard-alone programs for PCR primer design are available but vary in quality and functionality. In particular, most programs lack batch primer design capability. Such a high-throughput software tool for designing SSR flanking primers and SNP genotyping primers is increasingly demanded. A new web primer design program, BatchPrimer3, is developed based on Primer3. BatchPrimer3 adopted the Primer3 core program as a major primer design engine to choose the best primer pairs. A new score-based primer picking module is incorporated into BatchPrimer3 and used to pick position-restricted primers. BatchPrimer3 v1.0 implements several types of primer designs including generic primers, SSR primers together with SSR detection, and SNP genotyping primers (including single-base extension primers, allele-specific primers, and tetra-primers for tetra-primer ARMS PCR), as well as DNA sequencing primers. DNA sequences in FASTA format can be batch read into the program. The basic information of input sequences, as a reference of parameter setting of primer design, can be obtained by pre-analysis of sequences. The input sequences can be pre-processed and masked to exclude and/or include specific regions, or set targets for different primer design purposes as in Primer3Web and primer3Plus. A tab-delimited or Excel-formatted primer output also greatly facilitates the subsequent primer-ordering process. Thousands of primers, including wheat conserved intron-flanking primers, wheat genome-specific SNP genotyping primers, and Brachypodium SSR flanking primers in several genome projects have been designed using the program and validated in several laboratories. BatchPrimer3 is a

  13. PCR Strategies for Complete Allele Calling in Multigene Families Using High-Throughput Sequencing Approaches.

    Directory of Open Access Journals (Sweden)

    Elena Marmesat

    Full Text Available The characterization of multigene families with high copy number variation is often approached through PCR amplification with highly degenerate primers to account for all expected variants flanking the region of interest. Such an approach often introduces PCR biases that result in an unbalanced representation of targets in high-throughput sequencing libraries that eventually results in incomplete detection of the targeted alleles. Here we confirm this result and propose two different amplification strategies to alleviate this problem. The first strategy (called pooled-PCRs targets different subsets of alleles in multiple independent PCRs using different moderately degenerate primer pairs, whereas the second approach (called pooled-primers uses a custom-made pool of non-degenerate primers in a single PCR. We compare their performance to the common use of a single PCR with highly degenerate primers using the MHC class I of the Iberian lynx as a model. We found both novel approaches to work similarly well and better than the conventional approach. They significantly scored more alleles per individual (11.33 ± 1.38 and 11.72 ± 0.89 vs 7.94 ± 1.95, yielded more complete allelic profiles (96.28 ± 8.46 and 99.50 ± 2.12 vs 63.76 ± 15.43, and revealed more alleles at a population level (13 vs 12. Finally, we could link each allele's amplification efficiency with the primer-mismatches in its flanking sequences and show that ultra-deep coverage offered by high-throughput technologies does not fully compensate for such biases, especially as real alleles may reach lower coverage than artefacts. Adopting either of the proposed amplification methods provides the opportunity to attain more complete allelic profiles at lower coverages, improving confidence over the downstream analyses and subsequent applications.

  14. Detection of methylation in promoter sequences by melting curve analysis-based semiquantitative real time PCR

    Directory of Open Access Journals (Sweden)

    Lázcoz Paula

    2008-02-01

    Full Text Available Abstract Background We present two melting curve analysis (MCA-based semiquantitative real time PCR techniques to detect the promoter methylation status of genes. The first, MCA-MSP, follows the same principle as standard MSP but it is performed in a real time thermalcycler with results being visualized in a melting curve. The second, MCA-Meth, uses a single pair of primers designed with no CpGs in its sequence. These primers amplify both unmethylated and methylated sequences. In clinical applications the MSP technique has revolutionized methylation detection by simplifying the analysis to a PCR-based protocol. MCA-analysis based techniques may be able to further improve and simplify methylation analyses by reducing starting DNA amounts, by introducing an all-in-one tube reaction and by eliminating a final gel stage for visualization of the result. The current study aimed at investigating the feasibility of both MCA-MSP and MCA-Meth in the analysis of promoter methylation, and at defining potential advantages and shortcomings in comparison to currently implemented techniques, i.e. bisulfite sequencing and standard MSP. Methods The promoters of the RASSF1A (3p21.3, BLU (3p21.3 and MGMT (10q26 genes were analyzed by MCA-MSP and MCA-Meth in 13 astrocytoma samples, 6 high grade glioma cell lines and 4 neuroblastoma cell lines. The data were compared with standard MSP and validated by bisulfite sequencing. Results Both, MCA-MSP and MCA-Meth, successfully determined promoter methylation. MCA-MSP provided information similar to standard MSP analyses. However the analysis was possible in a single tube and avoided the gel stage. MCA-Meth proved to be useful in samples with intermediate methylation status, reflected by a melting curve position shift in dependence on methylation extent. Conclusion We propose MCA-MSP and MCA-Meth as alternative or supplementary techniques to MSP or bisulfite sequencing.

  15. PRISE2: software for designing sequence-selective PCR primers and probes.

    Science.gov (United States)

    Huang, Yu-Ting; Yang, Jiue-in; Chrobak, Marek; Borneman, James

    2014-09-25

    PRISE2 is a new software tool for designing sequence-selective PCR primers and probes. To achieve high level of selectivity, PRISE2 allows the user to specify a collection of target sequences that the primers are supposed to amplify, as well as non-target sequences that should not be amplified. The program emphasizes primer selectivity on the 3' end, which is crucial for selective amplification of conserved sequences such as rRNA genes. In PRISE2, users can specify desired properties of primers, including length, GC content, and others. They can interactively manipulate the list of candidate primers, to choose primer pairs that are best suited for their needs. A similar process is used to add probes to selected primer pairs. More advanced features include, for example, the capability to define a custom mismatch penalty function. PRISE2 is equipped with a graphical, user-friendly interface, and it runs on Windows, Macintosh or Linux machines. PRISE2 has been tested on two very similar strains of the fungus Dactylella oviparasitica, and it was able to create highly selective primers and probes for each of them, demonstrating the ability to create useful sequence-selective assays. PRISE2 is a user-friendly, interactive software package that can be used to design high-quality selective primers for PCR experiments. In addition to choosing primers, users have an option to add a probe to any selected primer pair, enabling design of Taqman and other primer-probe based assays. PRISE2 can also be used to design probes for FISH and other hybridization-based assays.

  16. PCR-activated cell sorting for cultivation-free enrichment and sequencing of rare microbes.

    Directory of Open Access Journals (Sweden)

    Shaun W Lim

    Full Text Available Microbial systems often exhibit staggering diversity, making the study of rare, interesting species challenging. For example, metagenomic analyses of mixed-cell populations are often dominated by the sequences of the most abundant organisms, while those of rare microbes are detected only at low levels, if at all. To overcome this, selective cultivation or fluorescence-activated cell sorting (FACS can be used to enrich for the target species prior to sequence analysis; however, since most microbes cannot be grown in the lab, cultivation strategies often fail, while cell sorting requires techniques to uniquely label the cell type of interest, which is often not possible with uncultivable microbes. Here, we introduce a culture-independent strategy for sorting microbial cells based on genomic content, which we term PCR-activated cell sorting (PACS. This technology, which utilizes the power of droplet-based microfluidics, is similar to FACS in that it uses a fluorescent signal to uniquely identify and sort target species. However, PACS differs importantly from FACS in that the signal is generated by performing PCR assays on the cells in microfluidic droplets, allowing target cells to be identified with high specificity with suitable design of PCR primers and TaqMan probes. The PACS assay is general, requires minimal optimization and, unlike antibody methods, can be developed without access to microbial antigens. Compared to non-specific methods in which cells are sorted based on size, granularity, or the ability to take up dye, PACS enables genetic sequence-specific sorting and recovery of the cell genomes. In addition to sorting microbes, PACS can be applied to eukaryotic cells, viruses, and naked nucleic acids.

  17. Infectious hypodermal and hematopoietic necrosis virus from Brazil: Sequencing, comparative analysis and PCR detection.

    Science.gov (United States)

    Silva, Douglas C D; Nunes, Allan R D; Teixeira, Dárlio I A; Lima, João Paulo M S; Lanza, Daniel C F

    2014-08-30

    A 3739 nucleotide fragment of Infectious hypodermal and hematopoietic necrosis virus (IHHNV) from Brazil was amplified and sequenced. This fragment contains the entire coding sequences of viral proteins, the full 3' untranslated region (3'UTR) and a partial sequence of 5' untranslated region (5'UTR). The genome organization of IHHNV revealed the three typical major coding domains: a left ORF1 of 2001 bp that codes NS1, a left ORF2 (NS2) of 1091 bp that codes NS2 and a right ORF3 of 990 bp that codes VP. Nucleotide and amino acid sequences of the three viral proteins were compared with putative amino acid sequences of viruses reported from different regions. Comparisons among genomes from different geographic locations reveal 31 nucleotide regions that are 100% similar, distributed throughout the genome. An analysis of secondary structure of UTR regions, revealed regions with high probability to form hairpins, that may be involved in mechanisms of viral replication. Additionally, a maximum likelihood analysis indicates that Brazilian IHHNV belongs to lineage III, in the infectious IHHNV group, and is clustered with IHHNV isolates from Hawaii, China, Taiwan, Vietnam and South Korea. A new nested PCR targeting conserved nucleotide regions is proposed to detect IHHNV.

  18. [High efficiency genome walking method for flanking sequences of cotton mitochondrial double-copy atpA gene based on optimized inverse PCR and TAIL-PCR].

    Science.gov (United States)

    Zhang, Xiao; Zhang, Rui; Sun, Guoqing; Shi, Ji; Meng, Zhigang; Zhou, Tao; Hou, Siyu; Liang, Chengzhen; Yu, Yuanhua; Guo, Sandui

    2012-01-01

    Cloning of flanking sequences of double-copy gene is a challenge in molecular biology. We developed a method to solve this problem by combining an optimized inverse PCR (iPCR) with TAIL-PCR. First, Southern blotting analysis was used to determine a proper restriction enzyme that could obtain proper-length restriction fragments that contained the target gene. Then optimized iPCR was performed to amplify the restriction fragments that contained the separated copies of the gene. Based on the obtained sequences, TAIL-PCR was performed to amplify further flanking regions of the gene. With this method, we obtained all of the EcoR I restriction fragments (2.2-5.1 kb) and Hind III restriction fragments (8.5-11.7 kb) of mitochondrial atpA gene in cytoplasmic male sterile (CMS) line and maintainer line of Upland cotton. The results showed that this method was an efficient approach to clone flanking sequences of double-copy gene.

  19. Effect of evaporation of solvents from one-step, self-etching adhesives

    DEFF Research Database (Denmark)

    Furuse, Adilson Yoshio; Peutzfeldt, Anne; Asmussen, Erik

    2008-01-01

    PURPOSE: To investigate whether and to what extent the bonding capacity of one-step, self-etching adhesives is influenced by the degree to which solvent is evaporated. MATERIALS AND METHODS: Seven one-step, self-etching adhesives were tested (Adper Prompt L-Pop, Clearfil S3 Bond, Futurabond NR, G...

  20. Qualitative and quantitative event-specific PCR detection methods for oxy-235 canola based on the 3' integration flanking sequence.

    Science.gov (United States)

    Yang, Litao; Guo, Jinchao; Zhang, Haibo; Liu, Jia; Zhang, Dabing

    2008-03-26

    As more genetically modified plant events are approved for commercialization worldwide, the event-specific PCR method has become the key method for genetically modified organism (GMO) identification and quantification. This study reveals the 3' flanking sequence of the exogenous integration of Oxy-235 canola employing thermal asymmetric interlaced PCR (TAIL-PCR). On the basis of the revealed 3' flanking sequence, PCR primers and TaqMan probe were designed and qualitative and quantitative PCR assays were established for Oxy-235 canola. The specificity and limits of detection (LOD) and quantification (LOQ) of these two PCR assays were validated to as low as 0.1% for the relative LOD of qualitative PCR assay; the absolute LOD and LOQ were low to 10 and 20 copies of canola genomic DNA in quantitative PCR assay, respectively. Furthermore, ideal quantified results were obtained in the practical canola sample detection. All of the results indicate that the developed qualitative and quantitative PCR methods based on the revealed 3' integration flanking sequence are suitable for GM canola Oxy-235 identification and quantification.

  1. Identification of Sinorhizobium (Ensifer) medicae based on a specific genomic sequence unveiled by M13-PCR fingerprinting.

    Science.gov (United States)

    Dourado, Ana Catarina; Alves, Paula I L; Tenreiro, Tania; Ferreira, Eugénio M; Tenreiro, Rogério; Fareleira, Paula; Crespo, M Teresa Barreto

    2009-12-01

    A collection of nodule isolates from Medicago polymorpha obtained from southern and central Portugal was evaluated by M13-PCR fingerprinting and hierarchical cluster analysis. Several genomic clusters were obtained which, by 16S rRNA gene sequencing of selected representatives, were shown to be associated with particular taxonomic groups of rhizobia and other soil bacteria. The method provided a clear separation between rhizobia and co-isolated non-symbiotic soil contaminants. Ten M13-PCR groups were assigned to Sinorhizobium (Ensifer) medicae and included all isolates responsible for the formation of nitrogen-fixing nodules upon re-inoculation of M. polymorpha test-plants. In addition, enterobacterial repetitive intergenic consensus (ERIC)-PCR fingerprinting indicated a high genomic heterogeneity within the major M13- PCR clusters of S. medicae isolates. Based on nucleotide sequence data of an M13-PCR amplicon of ca. 1500 bp, observed only in S. medicae isolates and spanning locus Smed_3707 to Smed_3709 from the pSMED01 plasmid sequence of S. medicae WSM419 genome's sequence, a pair of PCR primers was designed and used for direct PCR amplification of a 1399-bp sequence within this fragment. Additional in silico and in vitro experiments, as well as phylogenetic analysis, confirmed the specificity of this primer combination and therefore the reliability of this approach in the prompt identification of S. medicae isolates and their distinction from other soil bacteria.

  2. A One-Step System for Convenient and Flexible Assembly of Transcription Activator-Like Effector Nucleases (TALENs).

    Science.gov (United States)

    Zhao, Jinlong; Sun, Wenye; Liang, Jing; Jiang, Jing; Wu, Zhao

    2016-09-01

    Transcription activator-like effector nucleases (TALENs) are powerful tools for targeted genome editing in diverse cell types and organisms. However, the highly identical TALE repeat sequences make it challenging to assemble TALEs using conventional cloning approaches, and multiple repeats in one plasmid are easily catalyzed for homologous recombination in bacteria. Although the methods for TALE assembly are constantly improving, these methods are not convenient because of laborious assembly steps or large module libraries, limiting their broad utility. To overcome the barrier of multiple assembly steps, we report a one-step system for the convenient and flexible assembly of a 180 TALE module library. This study is the first demonstration to ligate 9 mono-/dimer modules and one circular TALEN backbone vector in a one step process, generating 9.5 to 18.5 repeat sequences with an overall assembly rate higher than 50%. This system makes TALEN assembly much simpler than the conventional cloning of two DNA fragments because this strategy combines digestion and ligation into one step using circular vectors and different modules to avoid gel extraction. Therefore, this system provides a convenient tool for the application of TALEN-mediated genome editing in scientific studies and clinical trials.

  3. Optimality analysis of one-step OOSM filtering algorithms in target tracking

    Institute of Scientific and Technical Information of China (English)

    ZHOU WenHui; LI Lin; CHEN GuoHai; YU AnXi

    2007-01-01

    In centralized multisensor tracking systems, there are out-of-sequence measurements (OOSMs) frequently arising due to different time delays in communication links and varying pre-processing times at the sensor. Such OOSM arrival can induce the "negative-time measurement update" problem, which is quite common in real multisensor tracking systems. The A1 optimal update algorithm with OOSM is presented by Bar-Shalom for one-step case. However, this paper proves that the optimality of A1 algorithm is lost in direct discrete-time model (DDM) of the process noise, it holds true only in discretized continuous-time model (DCM). One better OOSM filtering algorithm for DDM case is presented. Also, another new optimal OOSM filtering algorithm, which is independent of the discrete time model of the process noise, is presented here. The performance of the two new algorithms is compared with that of A1 algorithm by Monte Carlo simulations. The effectiveness and correctness of the two proposed algorithms are validated by analysis and simulation results.

  4. One-step discrimination scheme on N-particle Greenberger-Horne-Zeilinger bases

    Institute of Scientific and Technical Information of China (English)

    Wang Xin-Wen; Liu Xiang; Fang Mao-Fa

    2007-01-01

    We present an experimentally feasible one-step discrimination scheme on Bell bases with trapped ions, and then generalize it to the case of N-ion Greenberger-Horne-Zeilinger (GHZ) bases. In the scheme, all the orthogonal and complete N-ion GHZ internal states can be exactly discriminated only by one step, and thus it takes very short time. Moreover, the scheme is insensitive to thermal motion and dose not require the individual addressing of the ions. The Bell-state and GHZ-state one-step discrimination scheme can be widely used in quantum information processing based on ion-trap set-up.

  5. The gut microbiotassay – a high-throughput real-time PCR chip combined with next generation sequencing

    DEFF Research Database (Denmark)

    Hermann-Bank, Marie Louise; Skovgaard, Kerstin; Mølbak, Lars

    this assay with the high-throughput real-time PCR chip “Access Array 48.48” from Fluidigm. The chip executes 2304 individual reactions in parallel and afterwards it is possible to harvest the amplicons for next-generation sequencing. This approach gives a taxonomical overview of the gut microbiota, hence...... generation sequencing both provides a quantitative measure in terms of Cq-values achieved from the real-time PCR, as well as the deeper information obtained from next-generation sequencing of the amplicons. It is quick to perform and offers a high-throughput at a relatively low cost. These features make...

  6. Are one-step adhesives easier to use and better performing? Multifactorial assessment of contemporary one-step self-etching adhesives.

    Science.gov (United States)

    Van Landuyt, Kirsten L; Mine, Atsushi; De Munck, Jan; Jaecques, Siegfried; Peumans, Marleen; Lambrechts, Paul; Van Meerbeek, Bart

    2009-06-01

    The objective of this study was to examine whether one-step self-etching adhesives (1-SEAs) really have an advantage over multistep systems. Nine one-step self-etching adhesives (Absolute, Adper Prompt L-Pop, Clearfil S3 Bond, G-Bond, Hybrid Bond, iBond, One-up Bond F Plus, Optibond All-in-one and Xeno III) were included in this study. One two-step self-etching adhesive (Clearfil SE Bond) and one three-step etch-and-rinse adhesive (Optibond FL) served as controls. Their microtensile bond strength to bur-cut enamel and dentin was determined using a standardized protocol and the respective adhesive/dentin interface of these adhesives was characterized by transmission electron microscopy. Statistical analysis was performed with the Kruskal-Wallis nonparametric test. Regarding bond strength, the control adhesives tended to perform superior to the one-step adhesives. However, a significant difference between the control adhesives and some one-step adhesives could not always be demonstrated, partly due to the statistical setup of this study. Interface analysis by electron microscopy showed wide variation among the one-step adhesives, depending on their composition and their acidity. 1-SEAs also exhibited two different kinds of droplets, depending on their hydrophilicity. Hydrophobic HEMA-free 1-SEAs such as G-Bond were prone to phase separation, while especially HEMA-containing hydrophilic 1-SEAs, such as Clearfil S3 Bond and Xeno III were predisposed to forming osmosis-induced droplets. Hybrid bond, Absolute, and iBond featured both phase separation as well as osmosis. Optibond All-in-one exhibited a clustering reaction of the filler particles upon solvent evaporation. All adhesives including the control adhesives showed signs of nanoleakage, indicating that all adhesives are to some extent permeable to water. A definitive conclusion with regard to quantitative assessment of nanoleakage was much hindered by inconsistencies in the silver deposition. The application

  7. One-step apexification using platelet rich fibrin matrix and mineral trioxide aggregate apical barrier

    Directory of Open Access Journals (Sweden)

    Anisha Kumar

    2014-01-01

    In one-step apexification using MTA, the technical problem encountered is controlling the overfill or underfill of MTA. The use of a matrix material helps to overcome this shortcoming. Platelet rich fibrin (PRF is an immune platelet concentrate, which can be used as a matrix, it also promotes wound healing and repair. This case report presents a case of one step apexification using MTA as an apical barrier and autologous PRF as an internal matrix.

  8. Automated purification of Borrelia burgdorferi s.l. PCR products with KingFisher{sup TM} magnetic particle processor prior to genome sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Maekinen, Johanna E-mail: johanna.makinen@utu.fi; Marttila, Harri; Viljanen, Matti K

    2001-07-01

    Borrelia burgdorferi sensu lato genospecies were differentiated by PCR-based sequencing of the borrelial flagellin gene. To evaluate the usefulness of KingFisher{sup TM} magnetic particle processor in PCR product purification, borrelia PCR products were purified with KingFisher{sup TM} magnetic particle processor prior to cycle sequencing and the quality of the sequence data received was analyzed. KingFisher was found to offer a rapid and reliable alternative for borrelial PCR product purification.

  9. HAPCAD: An open-source tool to detect PCR crossovers in next-generation sequencing generated HLA data.

    Science.gov (United States)

    McDevitt, Shana L; Bredeson, Jessen V; Roy, Scott W; Lane, Julie A; Noble, Janelle A

    2016-03-01

    Next-generation sequencing (NGS) based HLA genotyping can generate PCR artifacts corresponding to IMGT/HLA Database alleles, for which multiple examples have been observed, including sequence corresponding to the HLA-DRB1(∗)03:42 allele. Repeat genotyping of 131 samples, previously genotyped as DRB1(∗)03:01 homozygotes using probe-based methods, resulted in the heterozygous call DRB1(∗)03:01+DRB1(∗)03:42. The apparent rare DRB1(∗)03:42 allele is hypothesized to be a "hybrid amplicon" generated by PCR crossover, a process in which a partial PCR product denatures from its template, anneals to a different allele template, and extends to completion. Unlike most PCR crossover products, "hybrid amplicons" always corresponds to an IMGT/HLA Database allele, necessitating a case-by-case analysis of whether its occurrence reflects the actual allele or is simply the result of PCR crossover. The Hybrid Amplicon/PCR Crossover Artifact Detector (HAPCAD) program mimics jumping PCR in silico and flags allele sequences that may also be generated as hybrid amplicon.

  10. PCR-based VNTR core sequence analysis for inferring genetic diversity in the shrimp Litopenaeus vannamei

    Directory of Open Access Journals (Sweden)

    Freitas Patrícia Domingues de

    2002-01-01

    Full Text Available The genetic variation in two farmed strains (F3-Panama and F17-Venezuela of the shrimp Litopenaeus vannamei was examined based on DNA multiloci analyses. Eighteen adults of each strain were analyzed by PCR using a set of VNTR core sequence primers. Genetic similarity, mean allele frequency, mean heterozygosity and the frequency of polymorphic loci were determined for both strains. A dendrogram of genetic similarity was produced by UPGMA clustering. The results for three primers (INS, M13, YN73 revealed different levels of genetic variation within the strains. The higher genetic similarity seen within strain F17 was apparently related to inbreeding, although a bottleneck effect could not be discarded. The low level of genetic variability of this strain could account for the reduced adaptive advantage of these animals and their inability to adjust to breeding conditions in Brazil.

  11. A general method for nested RT-PCR amplification and sequencing the complete HCV genotype 1 open reading frame

    Directory of Open Access Journals (Sweden)

    Tavis John E

    2005-12-01

    Full Text Available Abstract Background Hepatitis C virus (HCV is a pathogenic hepatic flavivirus with a single stranded RNA genome. It has a high genetic variability and is classified into six major genotypes. Genotype 1a and 1b cause the majority of infections in the USA. Viral genomic sequence information is needed to correlate viral variation with pathology or response to therapy. However, reverse transcription-polymerase chain reaction (RT-PCR of the HCV genome must overcome low template concentration and high target sequence diversity. Amplification conditions must hence have both high sensitivity and specificity yet recognize a heterogeneous target population to permit general amplification with minimal bias. This places divergent demands of the amplification conditions that can be very difficult to reconcile. Results RT and nested PCR conditions were optimized independently and systematically for amplifying the complete open reading frame (ORF from HCV genotype 1a and 1b using several overlapping amplicons. For each amplicon, multiple pairs of nested PCR primers were optimized. Using these primers, the success rate (defined as the rate of production of sufficient DNA for sequencing with any one of the primer pairs for a given amplicon for amplification of 72 genotype 1a and 1b patient plasma samples averaged over 95% for all amplicons. In addition, two sets of sequencing primers were optimized for each genotype 1a and 1b. Viral consensus sequences were determined by directly sequencing the amplicons. HCV ORFs from 72 patients have been sequenced using these primers. Sequencing errors were negligible because sequencing depth was over 4-fold and both strands were sequenced. Primer bias was controlled and monitored through careful primer design and control experiments. Conclusion Optimized RT-PCR and sequencing conditions are useful for rapid and reliable amplification and sequencing of HCV genotype 1a and 1b ORFs.

  12. Plant or fungal sequences? An alternative optimized PCR protocol to avoid ITS (nrDNA misamplification

    Directory of Open Access Journals (Sweden)

    Vitor Fernandes Oliveira de Miranda

    2010-02-01

    Full Text Available The nuclear ribosomal DNA internal transcribed spacers (ITS1 and ITS2 from leaves of Drosera (Droseraceae were amplified using "universal" primers. The analysis of the products demonstrated most samples were a molecular mixture as a result of unsuccessful and non-specific amplifications. Among the obtained sequences, two were from Basidiomycota fungi. Homologous sequences of Basidiomycota were obtained from GenBank database and added to a data set with sequences from Drosera leaves. Parsimony analysis demonstrated that one sequence was amplified from an Ustilaginomycetes fungus, and another from a Heterobasidiomycetes. Possibly these fungi were associated to leaves of Drosera, and not because of samples contamination. In order to provide optimization and a better specificity of PCR (polymerase chain reaction, a very successful method was demonstrated using dimethyl sulfoxide (DMSO and bovine serum albumin (BSA in reactions.Os espaçadores internos transcritos do DNA nuclear ribossomal (ITS1 e ITS2 de folhas de Drosera (Droseraceae foram amplificados com o emprego de iniciadores "universais". A análise demonstrou que a maior parte das amostras continha uma mistura resultante de amplificações não-específicas. Dentre as sequências de DNA obtidas, duas delas foram de fungos basidiomicetos. Sequências homólogas foram obtidas do GenBank e analisadas junto às sequências obtidas de folhas de Drosera. Através das análises filogenéticas de máxima parcimônia foi possível identificar uma seqüência como sendo de um Ustilaginomycetes e outra de Heterobasidiomycetes (Basidiomycota. Possivelmente esses organismos estavam associados às folhas de Drosera e assim não sejam resultantes de contaminação. Com o objetivo de otimizar e buscar uma melhor especificidade das reações de PCR, um protocolo bem sucedido foi demonstrado com o uso de dimetilsulfóxido (DMSO e soroalbumina bovina (BSA.

  13. PCR primers for metazoan nuclear 18S and 28S ribosomal DNA sequences.

    Directory of Open Access Journals (Sweden)

    Ryuji J Machida

    Full Text Available BACKGROUND: Metagenetic analyses, which amplify and sequence target marker DNA regions from environmental samples, are increasingly employed to assess the biodiversity of communities of small organisms. Using this approach, our understanding of microbial diversity has expanded greatly. In contrast, only a few studies using this approach to characterize metazoan diversity have been reported, despite the fact that many metazoan species are small and difficult to identify or are undescribed. One of the reasons for this discrepancy is the availability of universal primers for the target taxa. In microbial studies, analysis of the 16S ribosomal DNA is standard. In contrast, the best gene for metazoan metagenetics is less clear. In the present study, we have designed primers that amplify the nuclear 18S and 28S ribosomal DNA sequences of most metazoan species with the goal of providing effective approaches for metagenetic analyses of metazoan diversity in environmental samples, with a particular emphasis on marine biodiversity. METHODOLOGY/PRINCIPAL FINDINGS: Conserved regions suitable for designing PCR primers were identified using 14,503 and 1,072 metazoan sequences of the nuclear 18S and 28S rDNA regions, respectively. The sequence similarity of both these newly designed and the previously reported primers to the target regions of these primers were compared for each phylum to determine the expected amplification efficacy. The nucleotide diversity of the flanking regions of the primers was also estimated for genera or higher taxonomic groups of 11 phyla to determine the variable regions within the genes. CONCLUSIONS/SIGNIFICANCE: The identified nuclear ribosomal DNA primers (five primer pairs for 18S and eleven for 28S and the results of the nucleotide diversity analyses provide options for primer combinations for metazoan metagenetic analyses. Additionally, advantages and disadvantages of not only the 18S and 28S ribosomal DNA, but also other

  14. Application of PCR amplicon sequencing using a single primer pair in PCR amplification to assess variations in Helicobacter pylori CagA EPIYA tyrosine phosphorylation motifs

    OpenAIRE

    Karlsson Anneli; Monstein Hans-Jürg; Ryberg Anna; Borch Kurt

    2010-01-01

    Background The presence of various EPIYA tyrosine phosphorylation motifs in the CagA protein of Helicobacter pylori has been suggested to contribute to pathogenesis in adults. In this study, a unique PCR assay and sequencing strategy was developed to establish the number and variation of cagA EPIYA motifs. Findings MDA-DNA derived from gastric biopsy specimens from eleven subjects with gastritis was used with M13- and T7- sequence-tagged primers for amplification of the cagA EPIYA motif regio...

  15. One-step production of immobilized alpha-amylase in recombinant Escherichia coli.

    Science.gov (United States)

    Rasiah, Indira A; Rehm, Bernd H A

    2009-04-01

    Industrial enzymes are often immobilized via chemical cross-linking onto solid supports to enhance stability and facilitate repeated use in bioreactors. For starch-degrading enzymes, immobilization usually places constraints on enzymatic conversion due to the limited diffusion of the macromolecular substrate through available supports. This study describes the one-step immobilization of a highly thermostable alpha-amylase (BLA) from Bacillus licheniformis and its functional display on the surface of polyester beads inside engineered Escherichia coli. An optimized BLA variant (Termamyl) was N-terminally fused to the polyester granule-forming enzyme PhaC of Cupriavidus necator. The fusion protein lacking the signal sequence mediated formation of stable polyester beads exhibiting alpha-amylase activity. The alpha-amylase beads were assessed with respect to alpha-amylase activity, which was demonstrated qualitatively and quantitatively. The immobilized alpha-amylase showed Michaelis-Menten enzyme kinetics exerting a V(max) of about 506 mU/mg of bead protein with a K(m) of about 5 microM, consistent with that of free alpha-amylase. The stability of the enzyme at 85 degrees C and the capacity for repeated usage in a starch liquefaction process were also demonstrated. In addition, structural integrity and functionality of the beads at extremes of pH and temperature, demonstrating their suitability for industrial use, were confirmed by electron microscopy and protein/enzyme analysis. This study proposes a novel, cost-effective method for the production of immobilized alpha-amylase in a single step by using the polyester granules forming protein PhaC as a fusion partner in engineered E. coli.

  16. 454 next generation-sequencing outperforms allele-specific PCR, Sanger sequencing, and pyrosequencing for routine KRAS mutation analysis of formalin-fixed, paraffin-embedded samples.

    Science.gov (United States)

    Altimari, Annalisa; de Biase, Dario; De Maglio, Giovanna; Gruppioni, Elisa; Capizzi, Elisa; Degiovanni, Alessio; D'Errico, Antonia; Pession, Annalisa; Pizzolitto, Stefano; Fiorentino, Michelangelo; Tallini, Giovanni

    2013-01-01

    Detection of KRAS mutations in archival pathology samples is critical for therapeutic appropriateness of anti-EGFR monoclonal antibodies in colorectal cancer. We compared the sensitivity, specificity, and accuracy of Sanger sequencing, ARMS-Scorpion (TheraScreen®) real-time polymerase chain reaction (PCR), pyrosequencing, chip array hybridization, and 454 next-generation sequencing to assess KRAS codon 12 and 13 mutations in 60 nonconsecutive selected cases of colorectal cancer. Twenty of the 60 cases were detected as wild-type KRAS by all methods with 100% specificity. Among the 40 mutated cases, 13 were discrepant with at least one method. The sensitivity was 85%, 90%, 93%, and 92%, and the accuracy was 90%, 93%, 95%, and 95% for Sanger sequencing, TheraScreen real-time PCR, pyrosequencing, and chip array hybridization, respectively. The main limitation of Sanger sequencing was its low analytical sensitivity, whereas TheraScreen real-time PCR, pyrosequencing, and chip array hybridization showed higher sensitivity but suffered from the limitations of predesigned assays. Concordance between the methods was k = 0.79 for Sanger sequencing and k > 0.85 for the other techniques. Tumor cell enrichment correlated significantly with the abundance of KRAS-mutated deoxyribonucleic acid (DNA), evaluated as ΔCt for TheraScreen real-time PCR (P = 0.03), percentage of mutation for pyrosequencing (P = 0.001), ratio for chip array hybridization (P = 0.003), and percentage of mutation for 454 next-generation sequencing (P = 0.004). Also, 454 next-generation sequencing showed the best cross correlation for quantification of mutation abundance compared with all the other methods (P < 0.001). Our comparison showed the superiority of next-generation sequencing over the other techniques in terms of sensitivity and specificity. Next-generation sequencing will replace Sanger sequencing as the reference technique for diagnostic detection of KRAS mutation in archival tumor tissues.

  17. Assessment of 'one-step' versus 'sequential' embryo culture conditions through embryonic genome methylation and hydroxymethylation changes.

    Science.gov (United States)

    Salvaing, J; Peynot, N; Bedhane, M N; Veniel, S; Pellier, E; Boulesteix, C; Beaujean, N; Daniel, N; Duranthon, V

    2016-11-01

    In comparison to in vivo development, how do different conditions of in vitro culture ('one step' versus 'sequential medium') impact DNA methylation and hydroxymethylation in preimplantation embryos? Using rabbit as a model, we show that DNA methylation and hydroxymethylation are both affected by in vitro culture of preimplantation embryos and the effect observed depends on the culture medium used. Correct regulation of DNA methylation is essential for embryonic development and DNA hydroxymethylation appears more and more to be a key player. Modifications of the environment of early embryos are known to have long term effects on adult phenotypes and health; these probably rely on epigenetic alterations. The study design we used is both cross sectional (control versus treatment) and longitudinal (time-course). Each individual in vivo experiment used embryos flushed from the donor at the 2-, 4-, 8-, 16- or morula stage. Each stage was analyzed in at least two independent experiments. Each individual in vitro experiment used embryos flushed from donors at the 1-cell stage (19 h post-coïtum) which were then cultured in parallel in the two tested media until the 2-, 4-, 8- 16-cell or morula stages. Each stage was analyzed in at least three independent experiments. In both the in vivo and in vitro experiments, 4-cell stage embryos were always included as an internal reference. Immunofluorescence with antibodies specific for 5-methylcytosine (5meC) and 5-hydroxymethylcytosine (5hmeC) was used to quantify DNA methylation and hydroxymethylation levels in preimplantation embryos. We assessed the expression of DNA methyltransferases (DNMT), of ten eleven translocation (TET) dioxigenases and of two endogenous retroviral sequences (ERV) using RT-qPCR, since the expression of endogenous retroviral sequences is known to be regulated by DNA methylation. Three repeats were first done for all stages; then three additional repetitions were performed for those stages showing

  18. Effect of One-Step and Multi-Steps Polishing System on Enamel Roughness

    Directory of Open Access Journals (Sweden)

    Cynthia Sumali

    2013-07-01

    Full Text Available Normal 0 false false false MicrosoftInternetExplorer4 The final procedures of orthodontic treatment are bracket debonding and cleaning the remaining adhesive. Multi-step polishing system is the most common method used. The disadvantage of that system is long working time, because of the stages that should be done. Therefore, dental material manufacturer make an improvement to the system, to reduce several stages into one stage only. This new system is known as one-step polishing system. Objective: To compare the effect of one-step and multi-step polishing system on enamel roughness after orthodontic bracket debonding. Methods: Randomized control trial was conducted included twenty-eight maxillary premolar randomized into two polishing system; one-step OptraPol (Ivoclar, Vivadent and multi-step AstroPol (Ivoclar, Vivadent. After bracket debonding, the remaining adhesive on each group was cleaned by subjective polishing system for ninety seconds using low speed handpiece. The enamel roughness was subjected to profilometer, registering two roughness parameters (Ra, Rz. Independent t-test was used to analyze the mean score of enamel roughness in each group. Results: There was no significant difference of enamel roughness between one-step and multi-step polishing system (p>0.005. Conclusion: One-step polishing system can produce a similar enamel roughness to multi-step polishing system after bracket debonding and adhesive cleaning.DOI: 10.14693/jdi.v19i3.136

  19. Evaluation of one-step micro polishers for residual resin removal after debonding on fluorosed teeth

    Directory of Open Access Journals (Sweden)

    Padmalatha Challa

    2014-01-01

    Full Text Available Aim and objectives: To evaluate the effectiveness of one step micro polishers for residual resin removal on fluorosed teeth using scanning electron microscope (SEM. Methods and Material: 55 teeth with mild to moderate fluorosis were selected with five teeth as control. Metal brackets were bonded onto 50 teeth which were divided into 5 groups. The finishing and polishing methods which were tested include tungsten carbide burs (TCB, multistep finishing system (Sof-Lex, one step polishers (PoGo and combination of TCB with multistep and one step polishing systems. After resin removal, all the samples were examined under SEM for assessment of the enamel surface. Results: The enamel surface was closest to untouched enamel in samples finished with the PoGo one step polishers followed by Sof-Lex multistep finishing system. However, they took the longest time to finish. TCB required the shortest time for residual resin removal. Conclusions: All polishing systems produce a certain degree of damage to the enamel surface with the smoothest surface being produced by one step polishers on fluorosed teeth.

  20. Simple Detection of the IS6110 Sequence of Mycobacterium tuberculosis Complex in Sputum, Based on PCR with Graphene Oxide.

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    Sang-Hyun Hwang

    Full Text Available Graphene oxide (GO has proven to be a satisfactory DNA-sensor platform for applications in enzyme-free signal amplification, fluorescence-based amplification, and nanoparticle-based platforms because of its excellent electrical, thermal, and optical properties. In this study, we designed a novel platform for the fluorescence detection of biomolecules, using a fluorescent dye-labeled primer and GO. We applied this system for the detection of the IS6110 insertion sequence of the Mycobacterium tuberculosis complex (MTB and evaluated its feasibility for use in molecular diagnostics. Fifty-four sputum specimens were collected at our institution from October 2010 to March 2012. To detect MTB in the samples, we performed PCR amplification of the IS6110 DNA sequence using FAM-labeled primers, after which the PCR amplicon was incubated with GO and the fluorescence was measured. The results were compared with those obtained by conventional real-time quantitative PCR (RQ-PCR. The fluorescence intensity observed increased in a concentration-dependent manner with the FAM-labeled IS6110 amplicon. The results of the PCR-GO system for detecting IS6110 DNA were in good agreement with those obtained with conventional RQ-PCR (kappa statistic = 0.925. The PCR-GO system detected MTB DNA in 23 of 25 RQ-PCR-positive sputum samples (92.0%; 95% CI, 75.0-98.0%, but not in 29 of 29 RQ-PCR-negative sputum samples (100%; 95% CI, 88.1-100.0%. These results indicate the utility of the PCR-GO system in molecular diagnostics.

  1. Simple Detection of the IS6110 Sequence of Mycobacterium tuberculosis Complex in Sputum, Based on PCR with Graphene Oxide.

    Science.gov (United States)

    Hwang, Sang-Hyun; Kim, Dong-Eun; Sung, Heungsup; Park, Byeong-Min; Cho, Mi-Jeong; Yoon, Ok-Jin; Lee, Do-Hoon

    2015-01-01

    Graphene oxide (GO) has proven to be a satisfactory DNA-sensor platform for applications in enzyme-free signal amplification, fluorescence-based amplification, and nanoparticle-based platforms because of its excellent electrical, thermal, and optical properties. In this study, we designed a novel platform for the fluorescence detection of biomolecules, using a fluorescent dye-labeled primer and GO. We applied this system for the detection of the IS6110 insertion sequence of the Mycobacterium tuberculosis complex (MTB) and evaluated its feasibility for use in molecular diagnostics. Fifty-four sputum specimens were collected at our institution from October 2010 to March 2012. To detect MTB in the samples, we performed PCR amplification of the IS6110 DNA sequence using FAM-labeled primers, after which the PCR amplicon was incubated with GO and the fluorescence was measured. The results were compared with those obtained by conventional real-time quantitative PCR (RQ-PCR). The fluorescence intensity observed increased in a concentration-dependent manner with the FAM-labeled IS6110 amplicon. The results of the PCR-GO system for detecting IS6110 DNA were in good agreement with those obtained with conventional RQ-PCR (kappa statistic = 0.925). The PCR-GO system detected MTB DNA in 23 of 25 RQ-PCR-positive sputum samples (92.0%; 95% CI, 75.0-98.0%), but not in 29 of 29 RQ-PCR-negative sputum samples (100%; 95% CI, 88.1-100.0%). These results indicate the utility of the PCR-GO system in molecular diagnostics.

  2. Improved diagnostic PCR assay for Actinobacillus pleuropneumoniae based on the nucleotide sequence of an outer membrane lipoprotein

    DEFF Research Database (Denmark)

    Gram, Trine; Ahrens, Peter

    1998-01-01

    The gene (omlA) coding for an outer membrane protein of Actinobacillus pleuropneumoniae serotypes 1 and 5 has been described earlier and has formed the basis for development of a specific PCR assay, The corresponding regions of all 12 A. pleuropneumoniae reference strains of biovar 1 were sequenc...... and sensitivity of this PCR compared to those of culture suggest the use of this PCR for routine identification of A. pleuropneumoniae.......The gene (omlA) coding for an outer membrane protein of Actinobacillus pleuropneumoniae serotypes 1 and 5 has been described earlier and has formed the basis for development of a specific PCR assay, The corresponding regions of all 12 A. pleuropneumoniae reference strains of biovar 1 were sequenced...... species related to A. pleuropneumoniae or isolated from pigs were assayed. They were all found negative in the PCR, as were tonsil cultures from 50 pigs of an A. pleuropneumoniae-negative herd. The sensitivity assessed by agarose gel analysis of the PCR product was 10(2) CFU/PCR test tube. The specificity...

  3. Non PCR-amplified Transcripts and AFLP fragments as reduced representations of the quail genome for 454 Titanium sequencing

    Directory of Open Access Journals (Sweden)

    Leterrier Christine

    2010-07-01

    Full Text Available Abstract Background SNP (Single Nucleotide Polymorphism discovery is now routinely performed using high-throughput sequencing of reduced representation libraries. Our objective was to adapt 454 GS FLX based sequencing methodologies in order to obtain the largest possible dataset from two reduced representations libraries, produced by AFLP (Amplified Fragment Length Polymorphism for genomic DNA, and EST (Expressed Sequence Tag for the transcribed fraction of the genome. Findings The expressed fraction was obtained by preparing cDNA libraries without PCR amplification from quail embryo and brain. To optimize the information content for SNP analyses, libraries were prepared from individuals selected in three quail lines and each individual in the AFLP library was tagged. Sequencing runs produced 399,189 sequence reads from cDNA and 373,484 from genomic fragments, covering close to 250 Mb of sequence in total. Conclusions Both methods used to obtain reduced representations for high-throughput sequencing were successful after several improvements. The protocols may be used for several sequencing applications, such as de novo sequencing, tagged PCR fragments or long fragment sequencing of cDNA.

  4. HIGH ORDER ONE-STEP A-STABLE EXPONENTIALLY FITTED METHODS

    Institute of Scientific and Technical Information of China (English)

    YangFengiian; ChenXinming; LuoYiping

    1999-01-01

    In this paper,the necessary and sutlicient conditions for general one-step methoos to be exponentially fitted at q0∈C are given, A class of multtderivative hybrid one-step methods of order at least s+1 is constructed with s+1 parameters,where s is the order of derivative. The necessary and sufficient conditions for these methods to be A-stable and exponentially fitted is proved, Furthermore,a class of A-stable 2 parameters hybrid one-step methods of order at least 8 are constructed,which use 4th order derivative,These methods are exponentially fitted at q0 if and only its fitted function f(q) satisfies f(q0)= 0, Finally,an A-stable exponentlally fitted method of order 8 is obtained.

  5. Multiplex PCR and Next Generation Sequencing for the Non-Invasive Detection of Bladder Cancer.

    Directory of Open Access Journals (Sweden)

    Douglas G Ward

    Full Text Available Highly sensitive and specific urine-based tests to detect either primary or recurrent bladder cancer have proved elusive to date. Our ever increasing knowledge of the genomic aberrations in bladder cancer should enable the development of such tests based on urinary DNA.DNA was extracted from urine cell pellets and PCR used to amplify the regions of the TERT promoter and coding regions of FGFR3, PIK3CA, TP53, HRAS, KDM6A and RXRA which are frequently mutated in bladder cancer. The PCR products were barcoded, pooled and paired-end 2 x 250 bp sequencing performed on an Illumina MiSeq. Urinary DNA was analysed from 20 non-cancer controls, 120 primary bladder cancer patients (41 pTa, 40 pT1, 39 pT2+ and 91 bladder cancer patients post-TURBT (89 cancer-free.Despite the small quantities of DNA extracted from some urine cell pellets, 96% of the samples yielded mean read depths >500. Analysing only previously reported point mutations, TERT mutations were found in 55% of patients with bladder cancer (independent of stage, FGFR3 mutations in 30% of patients with bladder cancer, PIK3CA in 14% and TP53 mutations in 12% of patients with bladder cancer. Overall, these previously reported bladder cancer mutations were detected in 86 out of 122 bladder cancer patients (70% sensitivity and in only 3 out of 109 patients with no detectable bladder cancer (97% specificity.This simple, cost-effective approach could be used for the non-invasive surveillance of patients with non-muscle-invasive bladder cancers harbouring these mutations. The method has a low DNA input requirement and can detect low levels of mutant DNA in a large excess of normal DNA. These genes represent a minimal biomarker panel to which extra markers could be added to develop a highly sensitive diagnostic test for bladder cancer.

  6. A new method for typing bovine major histocompatibility complex class II DRB3 alleles by combining two established PCR sequence-based techniques.

    Science.gov (United States)

    Takeshima, S-N; Matsumoto, Y; Miyasaka, T; Arainga-Ramirez, M; Saito, H; Onuma, M; Aida, Y

    2011-09-01

    Recently, two polymerase chain reaction sequence-based typing (PCR-SBT) methods were reported for the genotyping of the bovine leukocyte antigen (BoLA)-DRB3. One technique is a single PCR-SBT (sPCR-SBT) method that generates heterozygous sequences that are subsequently analyzed by the haplofinder program, while the other technique is a nested PCR-SBT (nPCR-SBT) method that allows the analysis of heterozygous sequences using the assign 400ATF software. In this study, these techniques were compared and then integrated to produce an improved genotyping method. The primer set used for sPCR-SBT was more accurate than those used for nPCR-SBT. Combining sPCR-SBT with the assign 400ATF software previously reported for nPCR-SBT enables rapid and accurate genotyping of a large number of DNA samples.

  7. Simple One-Step Method to Synthesize Polypyrrole-Indigo Carmine-Silver Nanocomposite

    Directory of Open Access Journals (Sweden)

    Lara Fernandes Loguercio

    2016-01-01

    Full Text Available A nanocomposite of indigo carmine doped polypyrrole/silver nanoparticles was obtained by a one-step electrochemical process. The nanocomposite was characterized by scanning electron microscopy, infrared spectroscopy, ultraviolet-visible-near infrared spectroscopy, and cyclic voltammetry. The simple one-step process allowed the growth of silver nanoparticles during the polymerization of polypyrrole, resulting in films with electrochromic behavior and improved electroactivity. In addition, polypyrrole chains in the nanocomposite were found to present longer conjugation length than pristine polypyrrole films.

  8. The symmetric MSD encoder for one-step adder of ternary optical computer

    Science.gov (United States)

    Kai, Song; LiPing, Yan

    2016-08-01

    The symmetric Modified Signed-Digit (MSD) encoding is important for achieving the one-step MSD adder of Ternary Optical Computer (TOC). The paper described the symmetric MSD encoding algorithm in detail, and developed its truth table which has nine rows and nine columns. According to the truth table, the state table was developed, and the optical-path structure and circuit-implementation scheme of the symmetric MSD encoder (SME) for one-step adder of TOC were proposed. Finally, a series of experiments were designed and performed. The observed results of the experiments showed that the scheme to implement SME was correct, feasible and efficient.

  9. One-step Conversion of Furfural into 2-Methyltetrahydrofuran under Mild Conditions.

    Science.gov (United States)

    Dong, Fang; Zhu, Yulei; Ding, Guoqiang; Cui, Jinglei; Li, Xianqing; Li, Yongwang

    2015-05-11

    One-step direct conversion of biomass-derived furfural to 2-methyltetrahydrofuran was realized under atmospheric pressure over a dual solid catalyst based on two-stage-packed Cu-Pd in a reactor; this is the first report that one-step conversion of furfural resulted in high yield of 2-methyltetrahydrofuran (97.1 %) under atmospheric pressure. This strategy provided a successive hydrogenation process, which avoids high H2 pressure, uses the reactor efficiently, and eliminates the product-separation step. Therefore, it could enhance the overall efficiency as a result of low cost and high yield.

  10. Parallel tagged amplicon sequencing of relatively long PCR products using the Illumina HiSeq platform and transcriptome assembly.

    Science.gov (United States)

    Feng, Yan-Jie; Liu, Qing-Feng; Chen, Meng-Yun; Liang, Dan; Zhang, Peng

    2016-01-01

    In phylogenetics and population genetics, a large number of loci are often needed to accurately resolve species relationships. Normally, loci are enriched by PCR and sequenced by Sanger sequencing, which is expensive when the number of amplicons is large. Next-generation sequencing (NGS) techniques are increasingly used for parallel amplicon sequencing, which reduces sequencing costs tremendously, but has not reduced preparation costs very much. Moreover, for most current NGS methods, amplicons need to be purified and quantified before sequencing and their lengths are also restricted (normally HiSeq paired-end 90-bp data. Overall, we validate a rapid, cost-effective and scalable approach to sequence a large number of targeted loci from a large number of samples that is particularly suitable for both phylogenetics and population genetics studies that require a modest scale of data.

  11. Comparison of PCR-RFLP pattern with sequencing analysis of the ITS region of Hyrcanain\\'s Tilia

    Directory of Open Access Journals (Sweden)

    Hamed Yousefzadeh

    2014-01-01

    T. hyrcana and T. rubra from Hyrcanian's origin, but it could not separate T. begonifloia from the other hyrcanian species. In this respect, derived results were similar to sequencing one. In conclusion, with regard to less expensive and less time consuming PCR-RFLP technique and high similarity between its result with sequencing, we recommend this method as a simple and economical method with relatively high efficiency studding plant phylogeny.

  12. Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Charles K Lee

    Full Text Available Analysis of microbial communities by high-throughput pyrosequencing of SSU rRNA gene PCR amplicons has transformed microbial ecology research and led to the observation that many communities contain a diverse assortment of rare taxa-a phenomenon termed the Rare Biosphere. Multiple studies have investigated the effect of pyrosequencing read quality on operational taxonomic unit (OTU richness for contrived communities, yet there is limited information on the fidelity of community structure estimates obtained through this approach. Given that PCR biases are widely recognized, and further unknown biases may arise from the sequencing process itself, a priori assumptions about the neutrality of the data generation process are at best unvalidated. Furthermore, post-sequencing quality control algorithms have not been explicitly evaluated for the accuracy of recovered representative sequences and its impact on downstream analyses, reducing useful discussion on pyrosequencing reads to their diversity and abundances. Here we report on community structures and sequences recovered for in vitro-simulated communities consisting of twenty 16S rRNA gene clones tiered at known proportions. PCR amplicon libraries of the V3-V4 and V6 hypervariable regions from the in vitro-simulated communities were sequenced using the Roche 454 GS FLX Titanium platform. Commonly used quality control protocols resulted in the formation of OTUs with >1% abundance composed entirely of erroneous sequences, while over-aggressive clustering approaches obfuscated real, expected OTUs. The pyrosequencing process itself did not appear to impose significant biases on overall community structure estimates, although the detection limit for rare taxa may be affected by PCR amplicon size and quality control approach employed. Meanwhile, PCR biases associated with the initial amplicon generation may impose greater distortions in the observed community structure.

  13. Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing.

    Science.gov (United States)

    Lee, Charles K; Herbold, Craig W; Polson, Shawn W; Wommack, K Eric; Williamson, Shannon J; McDonald, Ian R; Cary, S Craig

    2012-01-01

    Analysis of microbial communities by high-throughput pyrosequencing of SSU rRNA gene PCR amplicons has transformed microbial ecology research and led to the observation that many communities contain a diverse assortment of rare taxa-a phenomenon termed the Rare Biosphere. Multiple studies have investigated the effect of pyrosequencing read quality on operational taxonomic unit (OTU) richness for contrived communities, yet there is limited information on the fidelity of community structure estimates obtained through this approach. Given that PCR biases are widely recognized, and further unknown biases may arise from the sequencing process itself, a priori assumptions about the neutrality of the data generation process are at best unvalidated. Furthermore, post-sequencing quality control algorithms have not been explicitly evaluated for the accuracy of recovered representative sequences and its impact on downstream analyses, reducing useful discussion on pyrosequencing reads to their diversity and abundances. Here we report on community structures and sequences recovered for in vitro-simulated communities consisting of twenty 16S rRNA gene clones tiered at known proportions. PCR amplicon libraries of the V3-V4 and V6 hypervariable regions from the in vitro-simulated communities were sequenced using the Roche 454 GS FLX Titanium platform. Commonly used quality control protocols resulted in the formation of OTUs with >1% abundance composed entirely of erroneous sequences, while over-aggressive clustering approaches obfuscated real, expected OTUs. The pyrosequencing process itself did not appear to impose significant biases on overall community structure estimates, although the detection limit for rare taxa may be affected by PCR amplicon size and quality control approach employed. Meanwhile, PCR biases associated with the initial amplicon generation may impose greater distortions in the observed community structure.

  14. Improved PCR-Based Detection of Soil Transmitted Helminth Infections Using a Next-Generation Sequencing Approach to Assay Design

    Science.gov (United States)

    Pilotte, Nils; Papaiakovou, Marina; Grant, Jessica R.; Bierwert, Lou Ann; Llewellyn, Stacey; McCarthy, James S.; Williams, Steven A.

    2016-01-01

    Background The soil transmitted helminths are a group of parasitic worms responsible for extensive morbidity in many of the world’s most economically depressed locations. With growing emphasis on disease mapping and eradication, the availability of accurate and cost-effective diagnostic measures is of paramount importance to global control and elimination efforts. While real-time PCR-based molecular detection assays have shown great promise, to date, these assays have utilized sub-optimal targets. By performing next-generation sequencing-based repeat analyses, we have identified high copy-number, non-coding DNA sequences from a series of soil transmitted pathogens. We have used these repetitive DNA elements as targets in the development of novel, multi-parallel, PCR-based diagnostic assays. Methodology/Principal Findings Utilizing next-generation sequencing and the Galaxy-based RepeatExplorer web server, we performed repeat DNA analysis on five species of soil transmitted helminths (Necator americanus, Ancylostoma duodenale, Trichuris trichiura, Ascaris lumbricoides, and Strongyloides stercoralis). Employing high copy-number, non-coding repeat DNA sequences as targets, novel real-time PCR assays were designed, and assays were tested against established molecular detection methods. Each assay provided consistent detection of genomic DNA at quantities of 2 fg or less, demonstrated species-specificity, and showed an improved limit of detection over the existing, proven PCR-based assay. Conclusions/Significance The utilization of next-generation sequencing-based repeat DNA analysis methodologies for the identification of molecular diagnostic targets has the ability to improve assay species-specificity and limits of detection. By exploiting such high copy-number repeat sequences, the assays described here will facilitate soil transmitted helminth diagnostic efforts. We recommend similar analyses when designing PCR-based diagnostic tests for the detection of other

  15. Polymorphism Analysis on Partial Sequence of Pig Obese Gene of Different Breeds by PCR-SSCP

    Institute of Scientific and Technical Information of China (English)

    SONG Yuefen; YU Hao; YANG Xiuqin; LIU Di

    2006-01-01

    Polymorphisms of porcine ob exon 1 and exon 2 among different breeds including Landrace, Duroc, Min pig, Yorkshire pig, double-muscled Yorkshire, Sanjiang pig, wild boar and cross bred pig were analyzed by PCR-SSCP in the current study. Three pairs of primers according to the ob cDNA sequence obtained from GenBank database were designed to amplify the first two exons, which were then genotyped by SSCP. The T to C transversion was found in exon 2, which resulted in 3 genotypes named AA, AB and BB, respectively in these different porcine breeds. There was only genotype of BB in the Min pig, while no allele B was detected in double-muscled Yorkshire, and the 3genotypes all existed in other breeds. There was significant difference on the genotype frequencies in various breeds.There was a trend that the frequency of allele A was positively associated with muscle ratio distribution on the one hand, and on the other hand, it was linked to the selected direction. So the allele A could be used as a selective marker of high muscle ratio in pig breeding.

  16. One-step Multiplex Transgenesis via Sleeping Beauty Transposition in Cattle.

    Science.gov (United States)

    Garrels, Wiebke; Talluri, Thirumala R; Apfelbaum, Ronja; Carratalá, Yanet P; Bosch, Pablo; Pötzsch, Kerstin; Grueso, Esther; Ivics, Zoltán; Kues, Wilfried A

    2016-02-24

    Genetically modified cattle are important for developing new biomedical models and for an improved understanding of the pathophysiology of zoonotic diseases. However, genome editing and genetic engineering based on somatic cell nuclear transfer suffer from a low overall efficiency. Here, we established a highly efficient one-step multiplex gene transfer system into the bovine genome.

  17. Atomic GHZ States Prepared in Two Directly Coupled Cavities with Virtual Excitations in One Step

    Institute of Scientific and Technical Information of China (English)

    杨榕灿; 黄志平; 郭强; 张鹏飞; 钟纯勇; 张天才

    2011-01-01

    A scheme for one-step preparation of atomic GHZ states in two directly coupled cavities via virtual excitations is proposed. In the whole procedure, the information is carried only in two ground states of A-type atoms, while the excited states of atoms and cavity modes are virtually excited, leading the system to be insensitive to atomic spontaneous emission and photon loss.

  18. Fast-ion energy resolution by one-step reaction gamma-ray spectrometry

    DEFF Research Database (Denmark)

    Salewski, Mirko; Nocente, M.; Gorini, G.

    2016-01-01

    The spectral broadening of γ-rays from fusion plasmas can be measured in high-resolution gamma-ray spectrometry (GRS). We derive weight functions that determine the observable velocity space and quantify the velocity-space sensitivity of one-step reaction high-resolution GRS measurements in magne...

  19. One-step synthesis of silver nanoparticle-filled Nylon 6 nanofibers and their antibacterial properties

    Science.gov (United States)

    A novel and facile one-step approach to in situ synthesize silver nanoparticle-filled nylon 6 nanofibers by electrospinning is reported. The method does not need post-treatments and can be carried out at ambient conditions without using additional chemicals. It employs the electrospinning solvent as...

  20. Noether's theorem and one-step corrections method for holonomic system

    Institute of Scientific and Technical Information of China (English)

    Shang Mei; Chen Xiang-Wei

    2006-01-01

    In this paper, a new computational method for improving the accuracy of numerically computed solutions is introduced. The computational method is based on the one-step method and conserved quantities of holonomic systems are considered as kinematical constraints in this method.

  1. One-step synthesis of three-dimensional Pd polyhedron networks with enhanced electrocatalytic performance.

    Science.gov (United States)

    Xu, You; Xu, Rui; Cui, Jianhua; Liu, Yang; Zhang, Bin

    2012-04-21

    Three-dimensional Pd polyhedron networks (Pd PNs) have been fabricated for the first time through a one-step, Cu(2+)-assisted, solution-chemical approach. These as-prepared 3D Pd PNs exhibit high stability and remarkably improved electrocatalytic activity toward formic acid oxidation over commercially available Pd black. This journal is © The Royal Society of Chemistry 2012

  2. Constraint Stabilization and One-Step Correction Method for Dynamical Systems

    Institute of Scientific and Technical Information of China (English)

    SHANG Mei; CHEN Xiang-wei; MEI Feng-xiang

    2007-01-01

    A computational method of constraint stabilization and correction is introduced.The method is based on the Baumgart's one-step method.Constraint conditions are addressed to stabilize and correct the solution.Two examples are given to illustrate the results of the method.

  3. One-step polymer surface modification for minimizing drug, protein, and DNA adsorption in microanalytical systems

    DEFF Research Database (Denmark)

    Larsen, Esben Kjær Unmack; Larsen, Niels Bent

    2013-01-01

    The non-specific adsorption of dissolved analytes strongly reduces the sensitivity and reliability in polymer microanalytical systems. Here, a one-step aqueous phase procedure modifies polymer material surfaces to strongly reduce their non-specific adsorption of a broad range of organic analytes ...... systems, including polystyrene (PS), cyclic olefin copolymer (COC), liquid crystalline polymer (LCP), and polyimide (PI)....

  4. Two Steps Forward, One Step Backward: Must This Be the Future of Diversity?

    Science.gov (United States)

    Butler, Johnnella E.

    2013-01-01

    Johnnella Butler writes here that the title of this article "Two Steps Forward, One Step Backward," expresses the "wicked problem" of diversity as a concrete goal in higher education. The concept of the "wicked problem," is a term coined in the late 1960s by social planners. Consulting Wikipedia, as so many of our…

  5. Development of a one step strip test for the detection of sulfadimidine residues

    NARCIS (Netherlands)

    Verheijen, R.; Stouten, P.; Cazemier, G.; Haasnoot, W.

    1998-01-01

    The one step strip test described is a competitive immunoassay in which the detector reagent consists of colloidal gold particles coated with affinity purified polyclonal anti-sulfadimidine (SDD) antibodies. The capture reagent in the assay is an SDD–ovalbumin conjugate which is immobilised on the l

  6. One step to generate quantum controlled phase-shift gate using a trapped ion

    Institute of Scientific and Technical Information of China (English)

    Zhang Shi-Jun; Ma Chi; Zhang Wen-Hai; Ye Liu

    2008-01-01

    This paper presents a very simple scheme for generating quantum controlled phase-shift gate with only one step by using the two vibrational modes of a trapped ion as the two qubits.The scheme couples two vibration degrees of freedom coupled with a suitable chosen laser excitation via the ionic states.

  7. One-step isolation of plasma membrane proteins using magnetic beads with immobilized concanavalin A

    DEFF Research Database (Denmark)

    Lee, Yu-Chen; Block, Gregory; Chen, Huiwen;

    2008-01-01

    We have developed a simple method for isolating and purifying plasma membrane proteins from various cell types. This one-step affinity-chromatography method uses the property of the lectin concanavalin A (ConA) and the technique of magnetic bead separation to obtain highly purified plasma membran...

  8. Rapid in vitro splicing of coding sequences from genomic DNA by isothermal recombination reaction-based PCR

    Directory of Open Access Journals (Sweden)

    Wenxuan Chen

    2016-09-01

    Full Text Available Cloning of coding sequence (CDS is an important step for gene function research. Here, we reported a simple and efficient strategy for assembling multiple-exon into an intron-free CDS from genomic DNA (gDNA by an isothermal recombination reaction-based PCR (IRR-PCR method. As an example, a 2067-bp full-length CDS of the anther-specific expression gene OsABCG15, which is composed of seven exons and six introns, was generated by IRR-PCR using genomic DNA of rice leaf as the template. Actually, this approach can be wildly applied to any DNA sequences assembly to achieve CDS cloning, gene fusion and multiple site-directed mutagenesis in functional genomics studies in vitro.

  9. Unexpected Diagnosis of Cerebral Toxoplasmosis by 16S and D2 Large-Subunit Ribosomal DNA PCR and Sequencing

    DEFF Research Database (Denmark)

    Kruse, Alexandra Yasmin Collin; Kvich, Lasse Andersson; Eickhardt-Dalbøge, Steffen Robert;

    2015-01-01

    The protozoan parasite Toxoplasma gondii causes severe opportunistic infections. Here, we report an unexpected diagnosis of cerebral toxoplasmosis. T. gondii was diagnosed by 16S and D2 large-subunit (LSU) ribosomal DNA (rDNA) sequencing of a cerebral biopsy specimen and confirmed by T. gondii......-specific PCR and immunohistochemistry. The patient was later diagnosed with HIV/AIDS....

  10. Identification of Meloidogyne incognita, M. javanica and M. arenaria using sequence characterised amplified region (SCAR) based PCR assays

    NARCIS (Netherlands)

    Zijlstra, C.; Donkers-Venne, T.H.M.; Fargette, M.

    2000-01-01

    Three randomly amplified polymorphic DNA (RAPD) markers, OPA-l2420,OPB-061200 and OPA-OI700. species specific to the root-knot nematode species Meloidogyrie arenaria, M. incogriita and M,ja vanica respectively, were identified. After sequencing these RAPD-PCR products, longer primers of 1s to 23 nuc

  11. Microvariation artifacts introduced by PCR and cloning of closely related 16S rRNA gene sequences

    NARCIS (Netherlands)

    Speksnijder, A.G.C.L.; Kowalchuk, G.A.; Jong, S. de; Kline, E.; Stephen, J.R.; Laanbroek, H.J.

    2001-01-01

    A defined template mixture of seven closely related 16S-rDNA clones was used in a PCR-cloning experiment to assess and track sources of artifactual sequence variation in 16S rDNA clone libraries. At least 14% of the recovered clones contained aberrations. Artifact sources were polymerase errors, a m

  12. Microvariation Artifacts Introduced by PCR and Cloning of Closely Related 16S rRNA Gene Sequences

    NARCIS (Netherlands)

    Speksnijder, A.G.C.L.; Kowalchuk, G.A.; Jong, de S.; Kline, E.; Stephen, J.R.; Laanbroek, H.J.

    2001-01-01

    A defined template mixture of seven closely related 16S-rDNA clones was used in a PCR-cloning experiment to assess and track sources of artifactual sequence variation in 16S rDNA clone libraries. At least 14% of the recovered clones contained aberrations. Artifact sources were polymerase errors, a m

  13. EGFR Mutations Detection in Non-small Cell Lung Cancer Tissues by Real-time PCR and DNA Sequencing

    Directory of Open Access Journals (Sweden)

    Qinghua ZHOU

    2009-12-01

    Full Text Available Background and objective Small molecule tyrosine kinase inhibitors (TKIs, such as gefitinib and erlotinib that target the kinase domain of epidermal growth factor receptor (EGFR are making successful progression for advanced non-small cell lung cancer patients treatment. The growing evidences revealed that EGFR exon 19 and 21 mutation status in NSCLC patients was correlated with the outcome for EGFR-TKI treatment. In this study, two methods of Real-time PCR and DNA sequencing were compared to detected EGFR exon 19 and 21 mutations. Methods EGFR exon19 mutation del-E746-A750 and exon 21mutation L858R were detected by Real-time PCR and DNA sequencing in 103 NSCLC patients. Chi-square test was used to analyze the consistance. Results There was no significant difference between the two methods. However, Real-time PCR was more convenient and sensitive compared to DNA sequencing. Conclusion Real-time PCR was more suitable for clinical testing than DNA sequencing.

  14. PCR-based study of the presence of Y-chromosome sequences in patients with Ullrich-Turner syndrome

    Energy Technology Data Exchange (ETDEWEB)

    Coto, E.; Menendez, M.J.; Lopez-Larrea, C. [Universidad Complutense, Madrid (Spain)] [and others

    1995-07-03

    The presence of Y chromosome sequences in Ullrich-Turner syndrome (UTS) patients has been suggested in previous work. Karyotype analysis estimated at about 60% of patients with a 45, X constitution and molecular analysis (Southern blot analysis with several Y chromosome probes and PCR of specific sequences) identified the presence of Y chromosome material in about 40% of 45, X patients. We have developed a very sensitive, PCR-based method to detect Y specific sequences in DNA from UTS patients. This protocol permits the detection of a single cell carrying a Y sequence among 10{sup 5} Y-negative cells. We studied 18 UTS patients with 4 Y-specific sequences. In 11 patients we detected a positive amplification for at least one Y sequence. The existence of a simple and sensitive method for the detection of Y sequences has important implications for UTS patients, in view of the risk for some of the females carrying Y chromosome material of developing gonadoblastoma and virilization. Additionally, some of the UTS-associated phenotypes, such as renal anomalies, could be correlated with the presence of Y chromosome-specific sequences. 27 refs., 2 figs., 1 tab.

  15. Multiplex PCR for Identification of Two Capsular Types in Epidemic KPC-Producing Klebsiella pneumoniae Sequence Type 258 Strains

    Science.gov (United States)

    Chen, Liang; Chavda, Kalyan D.; Findlay, Jacqueline; Peirano, Gisele; Hopkins, Katie; Pitout, Johann D. D.; Bonomo, Robert A.; Woodford, Neil; DeLeo, Frank R.

    2014-01-01

    We developed a multiplex PCR assay capable of identifying two capsular polysaccharide synthesis sequence types (sequence type 258 [ST258] cps-1 and cps-2) in epidemic Klebsiella pneumoniae ST258 strains. The assay performed with excellent sensitivity (100%) and specificity (100%) for identifying cps types in 60 ST258 K. pneumoniae sequenced isolates. The screening of 419 ST258 clonal isolates revealed a significant association between cps type and K. pneumoniae carbapenemase (KPC) variant: cps-1 is largely associated with KPC-2, while cps-2 is primarily associated with KPC-3. PMID:24733470

  16. A Lab on a chip device for rapid identification of Avian Influenza virus by on-chip sample preparation and solid phase PCR

    DEFF Research Database (Denmark)

    Yi, Sun; Dhumpa, Raghuram; Bang, Dang Duong

    2009-01-01

    In this paper, we describe a novel lab-on-a-chip device for fast AIV screening by integrating DNA microarray-based solid phase PCR on microchip. The device can handle viral samples in an automatic way. Moreover, multiplex PCR and sequence detection are done in one-step, which greatly simplifies...

  17. A Lab on a chip device for rapid identification of Avian Influenza virus by on-chip sample preparation and solid phase PCR

    DEFF Research Database (Denmark)

    Yi, Sun; Dhumpa, Raghuram; Bang, Dang Duong

    2009-01-01

    In this paper, we describe a novel lab-on-a-chip device for fast AIV screening by integrating DNA microarray-based solid phase PCR on microchip. The device can handle viral samples in an automatic way. Moreover, multiplex PCR and sequence detection are done in one-step, which greatly simplifies t...

  18. Information theory-based algorithm for in silico prediction of PCR products with whole genomic sequences as templates

    Directory of Open Access Journals (Sweden)

    He Junjian

    2005-07-01

    Full Text Available Abstract Background A new algorithm for assessing similarity between primer and template has been developed based on the hypothesis that annealing of primer to template is an information transfer process. Results Primer sequence is converted to a vector of the full potential hydrogen numbers (3 for G or C, 2 for A or T, while template sequence is converted to a vector of the actual hydrogen bond numbers formed after primer annealing. The former is considered as source information and the latter destination information. An information coefficient is calculated as a measure for fidelity of this information transfer process and thus a measure of similarity between primer and potential annealing site on template. Conclusion Successful prediction of PCR products from whole genomic sequences with a computer program based on the algorithm demonstrated the potential of this new algorithm in areas like in silico PCR and gene finding.

  19. External and semi-internal controls for PCR amplification of homologous sequences in mixed templates

    DEFF Research Database (Denmark)

    Kalle, Elena; Gulevich, Alexander; Rensing, Christopher Günther T

    2013-01-01

    in a single template assay. Yet, multi-template PCR has been used without appropriate attention to quality control and assay validation, in spite of the fact that such practice diminishes the reliability of results. External and internal amplification controls became obligatory elements of good laboratory...... practice in different PCR assays. We propose the inclusion of an analogous approach as a quality control system for multi-template PCR applications. The amplification controls must take into account the characteristics of multi-template PCR and be able to effectively monitor particular assay performance...

  20. Sex determination by SRY PCR and sequencing of Tasmanian devil facial tumour cell lines reveals non-allograft transmission.

    Science.gov (United States)

    Cui, Xianlan; Wang, Yunfeng; Hua, Bobby; Miller, Webb; Zhao, Yan; Cui, Hongyu; Kong, Xiangang

    2016-05-20

    Devil facial tumour disease (DFTD) is an infectious tumour disease and was hypothesised to be transmitted by allograft during biting based on two cytogenetic findings of DFTD tumours in 2006. It was then believed that DFTD tumours were originally from a female devil. In this study the devil sex-determining region Y (SRY) gene was PCR amplified and sequenced, and six pairs of devil SRY PCR primers were used for detection of devil SRY gene fragments in purified DFTD tumour cell lines. Using three pairs of devil SRY PCR primers, devil SRY gene sequence was detected by PCR and sequencing in genomic DNA of DFTD tumour cell lines from six male devils, but not from six female devils. Four out of six DFTD tumour cell lines from male devils contained nucleotides 288-482 of the devil SRY gene, and another two DFTD tumour cell lines contained nucleotides 381-577 and 493-708 of the gene, respectively. These results indicate that the different portions of the SRY gene in the DFTD tumours of the male devils were originally from the male hosts, rejecting the currently believed DFTD allograft transmission theory. The reasons why DFTD transmission was incorrectly defined as allograft are discussed.

  1. FastPCR: An in silico tool for fast primer and probe design and advanced sequence analysis.

    Science.gov (United States)

    Kalendar, Ruslan; Khassenov, Bekbolat; Ramankulov, Yerlan; Samuilova, Olga; Ivanov, Konstantin I

    2017-07-01

    Polymerase chain reaction (PCR) is one of the most important laboratory techniques used in molecular biology, genetics and molecular diagnostics. The success of a PCR-based method largely depends on the correct nucleic acid sequence analysis in silico prior to a wet-bench experiment. Here, we report the development of an online Java-based software for virtual PCR on linear or circular DNA templates and multiple primer or probe search from large or small databases. Primer or probe sensitivity and specificity are predicted by searching a database to find sequences with an optimal number of mismatches, similarity and stability. The software determines primer location, orientation, efficiency of binding and calculates primer melting temperatures for standard and degenerate oligonucleotides. The software is suitable for batch file processing, which is essential for automation when working with large amounts of data. The online Java software is available for download at http://primerdigital.com/tools/pcr.html. Accession numbers for the sequences resulting from this study: EU140956 EU177767 EU867815 EU882730 FJ975775-FJ975780 HM481419 HM481420 KC686837-KC686839 KM262797. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Hybridization Capture Using Short PCR Products Enriches Small Genomes by Capturing Flanking Sequences (CapFlank)

    DEFF Research Database (Denmark)

    Tsangaras, Kyriakos; Wales, Nathan; Sicheritz-Pontén, Thomas;

    2014-01-01

    Solution hybridization capture methods utilize biotinylated oligonucleotides as baits to enrich homologous sequences from next generation sequencing (NGS) libraries. Coupled with NGS, the method generates kilo to gigabases of high confidence consensus targeted sequence. However, in many experimen...

  3. One-Step Dynamic Classifier Ensemble Model for Customer Value Segmentation with Missing Values

    Directory of Open Access Journals (Sweden)

    Jin Xiao

    2014-01-01

    Full Text Available Scientific customer value segmentation (CVS is the base of efficient customer relationship management, and customer credit scoring, fraud detection, and churn prediction all belong to CVS. In real CVS, the customer data usually include lots of missing values, which may affect the performance of CVS model greatly. This study proposes a one-step dynamic classifier ensemble model for missing values (ODCEM model. On the one hand, ODCEM integrates the preprocess of missing values and the classification modeling into one step; on the other hand, it utilizes multiple classifiers ensemble technology in constructing the classification models. The empirical results in credit scoring dataset “German” from UCI and the real customer churn prediction dataset “China churn” show that the ODCEM outperforms four commonly used “two-step” models and the ensemble based model LMF and can provide better decision support for market managers.

  4. THE CRITICAL LOAD PARAMETER OF A TIMOSHENKO BEAM WITH ONE-STEP CHANGE IN CROSS SECTION

    Directory of Open Access Journals (Sweden)

    Goran Janevski

    2014-12-01

    Full Text Available The paper analyzes the transverse vibration of a Timoshenko beam with one-step change in cross-section when subjected to an axial force. The axial force is equal in both of the beam portions. Three types of beam which occur commonly in engineering application are considered. The frequency equation of the Timoshenko beam with one-step change in cross-section is expressed as the fourth order determinant equated to zero. The critical compressive axial force is expressed as a function of the critical load parameter which is tabulated for four classical boundary conditions. Apart from the results presented in Tables, the paper also provides calculated values of the critical load parameter for other values of system parameters along with the graphic representation of their dependence on the step position parameter.

  5. One Step Combustion Synthesis Of YAG:Ce Phosphor For Solid State Lighting

    Science.gov (United States)

    Yadav, Pooja; Gupta, K. Vijay Kumar; Muley, Aarti; Joshi, C. P.; Moharil, S. V.

    2011-10-01

    YAG:Ce is an important phosphor having applications in various fields ranging from solid state lighting to scintillation detectors. YAG phosphors doped with activators are mainly synthesized by solid state reaction techniques that require high sintering temperatures (above 1500°C) to eliminate YAM and YAP phases. Though several soft chemical routes have been explored for synthesis of YAG, most of these methods are complex and phase pure materials are not obtained in one step, but prolonged annealing at temperatures around 1000 C or above becomes necessary. One step combustion synthesis of YAG:Ce3+ and related phosphors carried out at 500 C furnace temperature is reported here. Activation with Ce3+ could be achieved during the synthesis without taking recourse to any post-combustion thermal treatment. LEDs prepared from the combustion synthesized YAG:Ce3+, exhibited properties comparable to those produced from the commercial phosphor.

  6. One-Step Implementation of Single Spin Measurement in Spin Star Network

    Institute of Scientific and Technical Information of China (English)

    DENG Hong-Liang; FANG Xi-Ming

    2008-01-01

    We present an efficient one-step scheme for a single spin measurement based on nuclear magnetic resonance (NMR)techniques.This scheme considerably reduces the time of operation using a spin star network where a target spin and an ancillary spin are coupled to a ring of N spins.As opposed to the proposal in [Phys.Rev.Lett.97(2006)100501]using a cubic lattice crystal to achieve a cubic speedup,the distinct advantage of this scheme is that under ideal conditions it requires the application of only one step to create a system of N correlated spins.In the process of single spin measurement,the total macroscopic magnetization,the individual magnetization and the transfer fideity are calculated analytically as simple cosine functions of time and the amplitude of irradiation.

  7. One-step purification of metallothionein extracted from two different sources.

    Science.gov (United States)

    Honda, Rubens T; Araújo, Roziete Mendes; Horta, Bruno Brasil; Val, Adalberto L; Demasi, Marilene

    2005-06-25

    We describe a one-step purification of hepatic metallothionein from the Amazon fish Colossoma macropomum injected with cadmium and from the copper-loaded metallothionein from the yeast Saccharomyces cerevisiae, performed by affinity chromatography through metal-chelating columns. Yeast metallothionein was purified from Cu2+-loaded resin and eluted by a continuous EDTA gradient whereas hepatic metallothionein extracted from fishes was purified by Ni2+-loaded resin and eluted by a continuous imidazol gradient. Purified metallothioneins were evaluated by SDS-PAGE and characterized by UV spectra of the apo- and Cd2+-loaded protein. This method allowed high purity and yield as well as rapid one-step extraction of both metal-loaded and apoprotein.

  8. One-step solution combustion synthesis of pure Ni nanopowders with enhanced coercivity: The fuel effect

    Science.gov (United States)

    Khort, Alexander; Podbolotov, Kirill; Serrano-García, Raquel; Gun'ko, Yurii K.

    2017-09-01

    In this paper, we report a new modified one-step combustion synthesis technique for production of Ni metal nanoparticles. The main unique feature of our approach is the use of microwave assisted foam preparation. Also, the effect of different types of fuels (urea, citric acid, glycine and hexamethylenetetramine) on the combustion process and characteristics of resultant solid products were investigated. It is observed that the combination of microwave assisted foam preparation and using of hexamethylenetetramine as a fuel allows producing pure ferromagnetic Ni metal nanoparticles with enhanced coercivity (78 Oe) and high value of saturation magnetization (52 emu/g) by one-step solution combustion synthesis under normal air atmosphere without any post-reduction processing.

  9. Fast-ion energy resolution by one-step reaction gamma-ray spectrometry

    DEFF Research Database (Denmark)

    Salewski, Mirko; Nocente, M.; Gorini, G.;

    2016-01-01

    The spectral broadening of γ-rays from fusion plasmas can be measured in high-resolution gamma-ray spectrometry (GRS). We derive weight functions that determine the observable velocity space and quantify the velocity-space sensitivity of one-step reaction high-resolution GRS measurements in magne...... general formalism using reactions with and without intrinsic broadening of the γ-rays for the GRS diagnostic at JET....

  10. Ethanol Manufacture through One-step Cellulose Liquefaction Developed by Zhongren Bioenergy Company

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    @@ The pilot scale tests of one-step direct liquefaction of cel-lulose biomass developed by a Sino-US joint venture, the Huaibei Zhongren Bioenergy Technical Development Company, Ltd. in Anhui province, have made great success. This method aiming to produce fuel and chemical feedstocks from cellulose biomass requires mild reaction conditions and all organic substances contained in the cellulose biom-ass can be completely converted without losses (without carbonization and gasification).

  11. Explicit One-Step P-Stable Methods for Second Order Periodic Initial Value Problems

    Institute of Scientific and Technical Information of China (English)

    Qinghong Li; Yongzhong Song

    2006-01-01

    In this paper, we present an explicit one-step method for solving periodic initial value problems of second order ordinary differential equations. The method is P-stable, and of first algebraic order and high phase-lag order. To improve the algebraic order, we give a composition second order scheme with the proposed method and its adjoint. We report some numerical results to illustrate the efficiency of our methods.

  12. Profilometry with Grating Projection Based on One-step Phase Shift

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    An optical technique for 3-D shape measurement is presented. This technique, based on a deformed projected grating pattern which carries 3-D information of the measured object, can automatically and accurately obtain the phase map of a measured object by using one-step phase shift algorithm.In comparison with traditional phase-shift technique, the technique is much faster, with the equivalent accuracy. Only one frame image is sufficient for measuring. Experimental result of typical object is presented.

  13. Genomic prediction for Nordic Red Cattle using one-step and selection index blending

    DEFF Research Database (Denmark)

    Guosheng, Su; Madsen, Per; Nielsen, Ulrik Sander

    2012-01-01

    This study investigated the accuracy of direct genomic breeding values (DGV) using a genomic BLUP model, genomic enhanced breeding values (GEBV) using a one-step blending approach, and GEBV using a selection index blending approach for 15 traits of Nordic Red Cattle. The data comprised 6,631 bull......-step blending approach is a good alternative to predict GEBV in practical genetic evaluation program....

  14. Simple Scheme for Directly Measuring Concurrence of Two-Qubit Pure States in One Step

    Institute of Scientific and Technical Information of China (English)

    YANG Rong-Can; LIN Xiu; HUANG Zhi-Ping; LI Hong-Cai

    2009-01-01

    In the present work, a simple scheme for the direct measurement of the concurrence of two-qubit pure states is proposed.The scheme is based on trapped ions and only needs one step when the two identical pure states are given.The vibrational mode in our proposal is only virtually excited, which is important in view of decoherence.Furthermore, the scheme is feasible based on current technologies.

  15. One-Step Dynamic Classifier Ensemble Model for Customer Value Segmentation with Missing Values

    OpenAIRE

    Jin Xiao; Bing Zhu; Geer Teng; Changzheng He; Dunhu Liu

    2014-01-01

    Scientific customer value segmentation (CVS) is the base of efficient customer relationship management, and customer credit scoring, fraud detection, and churn prediction all belong to CVS. In real CVS, the customer data usually include lots of missing values, which may affect the performance of CVS model greatly. This study proposes a one-step dynamic classifier ensemble model for missing values (ODCEM) model. On the one hand, ODCEM integrates the preprocess of missing values and the classif...

  16. One-step synthesis of silver nanoparticles, nanorods, and nanowires on the surface of DNA network.

    Science.gov (United States)

    Wei, Gang; Zhou, Hualan; Liu, Zhiguo; Song, Yonghai; Wang, Li; Sun, Lanlan; Li, Zhuang

    2005-05-12

    Here, we describe a one-step synthesis of silver nanoparticles, nanorods, and nanowires on DNA network surface in the absence of surfactant. Silver ions were first adsorbed onto the DNA network and then reduced in sodium borohydride solution. Silver nanoparticles, nanorods, and nanowires were formed by controlling the size of pores of the DNA network. The diameter of the silver nanoparticles and the aspect ratio of the silver nanorods and nanowires can be controlled by adjusting the DNA concentration and reduction time.

  17. One-step synthesis of 1-chloro-3-arylacetone derivatives from arylacetic acids.

    Science.gov (United States)

    Zacuto, Michael J; Dunn, Robert F; Figus, Margaret

    2014-09-19

    A practical one-step method has been developed to prepare α-chloroketones from readily available, inexpensive phenylacetic acid derivatives. The method utilizes the unique reactivity of an intermediate Mg-enolate dianion, which displays selectivity for the carbonyl carbon of chloromethyl carbonyl electrophiles. Decarboxylation of the intermediate occurs spontaneously during the reaction quench. The utility of the reaction products has been demonstrated through the total synthesis of the natural product cimiracemate B.

  18. One Step Preparation of Controlled Drug Release Systems in Supercritical Carbon Dioxide

    Institute of Scientific and Technical Information of China (English)

    CAO Liqin; WANG Chengwei; CHEN Liuping

    2009-01-01

    Drug delivery systems based on copolymers of N-isopropylacrylamide were fn-st prepared by a one step method, in which supercritical carbon dioxide was simultaneously used as a polymerization medium and an impregnation agent. The obtained microspheres were characterized by scanning electronic microscopy (SEM), differential scan-ning calorimetry (DSC), transmission electron microscopy (TEM) and X-ray diffraction (XRD). The release effect of the in situ prepared microgels impregnated with ibuprofen was presented through in vitro release simulation.

  19. Sequence polymorphism can produce serious artifacts in real-time PCR assays: lessons from Pacific oysters

    Science.gov (United States)

    Since it was first described in the mid-1990s, quantitative real time PCR (Q-PCR) has been widely used in many fields of biomedical research and molecular diagnostics. This method is routinely used to validate whole transcriptome analyses such as DNA microarrays, suppressive subtractive hybridizati...

  20. Evaluating formability of LCP plate for sacral fractures with one step inverse forming finite element analysis.

    Science.gov (United States)

    Li, Xiaoda; Zhang, Xiangkui; Hu, Ping; Liu, Weijie; Shen, Guozhe; Zhan, Xianghui

    2015-01-01

    The locking compression plate fixation treatment for the unstable sacral fractures is simple and effective, with less trauma and complications. Some locking compression plate parts have been made of high-strength Plate manufactured by hot stamping process since the demand for lightweight biomedical materials. Finite Element (FE) method of One-Step inverse forming based on deformation theory is the tool to evaluate the formability of locking compression plate panel quickly in initial design for reducing costs and development cycle of Plate. But current one-step inverse forming methods are all suitable for cold stamping, not hot-stamping. This paper proposed one-step inverse forming method and workflow for hot-stamping of locking compression Plate. And the B pillar of a sacral bone was simulated and its computing result was compared with experimental value. The result shows that the proposed method in this paper can quickly evaluate high temperature formability of high-strength Plate. And the method is proposed to be used in initial design.

  1. One-step graphene coating of heteroepitaxial GaN films.

    Science.gov (United States)

    Choi, Jae-Kyung; Huh, Jae-Hoon; Kim, Sung-Dae; Moon, Daeyoung; Yoon, Duhee; Joo, Kisu; Kwak, Jinsung; Chu, Jae Hwan; Kim, Sung Youb; Park, Kibog; Kim, Young-Woon; Yoon, Euijoon; Cheong, Hyeonsik; Kwon, Soon-Yong

    2012-11-02

    Today, state-of-the-art III-Ns technology has been focused on the growth of c-plane nitrides by metal-organic chemical vapor deposition (MOCVD) using a conventional two-step growth process. Here we show that the use of graphene as a coating layer allows the one-step growth of heteroepitaxial GaN films on sapphire in a MOCVD reactor, simplifying the GaN growth process. It is found that the graphene coating improves the wetting between GaN and sapphire, and, with as little as ~0.6 nm of graphene coating, the overgrown GaN layer on sapphire becomes continuous and flat. With increasing thickness of the graphene coating, the structural and optical properties of one-step grown GaN films gradually transition towards those of GaN films grown by a conventional two-step growth method. The InGaN/GaN multiple quantum well structure grown on a GaN/graphene/sapphire heterosystem shows a high internal quantum efficiency, allowing the use of one-step grown GaN films as 'pseudo-substrates' in optoelectronic devices. The introduction of graphene as a coating layer provides an atomic playground for metal adatoms and simplifies the III-Ns growth process, making it potentially very useful as a means to grow other heteroepitaxial films on arbitrary substrates with lattice and thermal mismatch.

  2. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.

    Directory of Open Access Journals (Sweden)

    Patrick D Schloss

    Full Text Available The advent of next generation sequencing has coincided with a growth in interest in using these approaches to better understand the role of the structure and function of the microbial communities in human, animal, and environmental health. Yet, use of next generation sequencing to perform 16S rRNA gene sequence surveys has resulted in considerable controversy surrounding the effects of sequencing errors on downstream analyses. We analyzed 2.7×10(6 reads distributed among 90 identical mock community samples, which were collections of genomic DNA from 21 different species with known 16S rRNA gene sequences; we observed an average error rate of 0.0060. To improve this error rate, we evaluated numerous methods of identifying bad sequence reads, identifying regions within reads of poor quality, and correcting base calls and were able to reduce the overall error rate to 0.0002. Implementation of the PyroNoise algorithm provided the best combination of error rate, sequence length, and number of sequences. Perhaps more problematic than sequencing errors was the presence of chimeras generated during PCR. Because we knew the true sequences within the mock community and the chimeras they could form, we identified 8% of the raw sequence reads as chimeric. After quality filtering the raw sequences and using the Uchime chimera detection program, the overall chimera rate decreased to 1%. The chimeras that could not be detected were largely responsible for the identification of spurious operational taxonomic units (OTUs and genus-level phylotypes. The number of spurious OTUs and phylotypes increased with sequencing effort indicating that comparison of communities should be made using an equal number of sequences. Finally, we applied our improved quality-filtering pipeline to several benchmarking studies and observed that even with our stringent data curation pipeline, biases in the data generation pipeline and batch effects were observed that could potentially

  3. Multilocus sequence typing of Mycoplasma hyorhinis strains identified by a real-time TaqMan PCR assay.

    Science.gov (United States)

    Tocqueville, Véronique; Ferré, Séverine; Nguyen, Ngoc Hong Phuc; Kempf, Isabelle; Marois-Créhan, Corinne

    2014-05-01

    A real-time TaqMan PCR assay based on the gene encoding the protein p37 was developed to detect Mycoplasma hyorhinis. Its specificity was validated with 29 epidemiologically unrelated M. hyorhinis strains (28 field strains and one reference strain) and other mycoplasma species or with other microorganisms commonly found in pigs. The estimated detection limit of this qPCR assay was 125 microorganism equivalents/μl. The same 29 epidemiologically unrelated M. hyorhinis strains and four previously fully sequenced strains were typed by two portable typing methods, the sequencing of the p37 gene and a multilocus sequence typing (MLST) scheme. The first method revealed 18 distinct nucleotide sequences and insufficient discriminatory power (0.934). The MLST scheme was developed with the sequenced genomes of the M. hyorhinis strains HUB-1, GDL-1, MCLD, and SK76 and based on the genes dnaA, rpoB, gyrB, gltX, adk, and gmk. In total, 2,304 bp of sequence was analyzed for each strain. MLST was capable of subdividing the 33 strains into 29 distinct sequence types. The discriminatory power of the method was >0.95, which is the threshold value for interpreting typing results with confidence (D=0.989). Population analysis showed that recombination in M. hyorhinis occurs and that strains are diverse but with a certain clonality (one unique clonal complex was identified). The new qPCR assay and the robust MLST scheme are available for the acquisition of new knowledge on M. hyorhinis epidemiology. A web-accessible database has been set up for the M. hyorhinis MLST scheme at http://pubmlst.org/mhyorhinis/.

  4. High Throughput Sample Preparation and Analysis for DNA Sequencing, PCR and Combinatorial Screening of Catalysis Based on Capillary Array Technique

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yonghua [Iowa State Univ., Ames, IA (United States)

    2000-01-01

    Sample preparation has been one of the major bottlenecks for many high throughput analyses. The purpose of this research was to develop new sample preparation and integration approach for DNA sequencing, PCR based DNA analysis and combinatorial screening of homogeneous catalysis based on multiplexed capillary electrophoresis with laser induced fluorescence or imaging UV absorption detection. The author first introduced a method to integrate the front-end tasks to DNA capillary-array sequencers. protocols for directly sequencing the plasmids from a single bacterial colony in fused-silica capillaries were developed. After the colony was picked, lysis was accomplished in situ in the plastic sample tube using either a thermocycler or heating block. Upon heating, the plasmids were released while chromsomal DNA and membrane proteins were denatured and precipitated to the bottom of the tube. After adding enzyme and Sanger reagents, the resulting solution was aspirated into the reaction capillaries by a syringe pump, and cycle sequencing was initiated. No deleterious effect upon the reaction efficiency, the on-line purification system, or the capillary electrophoresis separation was observed, even though the crude lysate was used as the template. Multiplexed on-line DNA sequencing data from 8 parallel channels allowed base calling up to 620 bp with an accuracy of 98%. The entire system can be automatically regenerated for repeated operation. For PCR based DNA analysis, they demonstrated that capillary electrophoresis with UV detection can be used for DNA analysis starting from clinical sample without purification. After PCR reaction using cheek cell, blood or HIV-1 gag DNA, the reaction mixtures was injected into the capillary either on-line or off-line by base stacking. The protocol was also applied to capillary array electrophoresis. The use of cheaper detection, and the elimination of purification of DNA sample before or after PCR reaction, will make this approach an

  5. High Throughput Sample Preparation and Analysis for DNA Sequencing, PCR and Combinatorial Screening of Catalysis Based on Capillary Array Technique

    Energy Technology Data Exchange (ETDEWEB)

    Yonghua Zhang

    2002-05-27

    Sample preparation has been one of the major bottlenecks for many high throughput analyses. The purpose of this research was to develop new sample preparation and integration approach for DNA sequencing, PCR based DNA analysis and combinatorial screening of homogeneous catalysis based on multiplexed capillary electrophoresis with laser induced fluorescence or imaging UV absorption detection. The author first introduced a method to integrate the front-end tasks to DNA capillary-array sequencers. protocols for directly sequencing the plasmids from a single bacterial colony in fused-silica capillaries were developed. After the colony was picked, lysis was accomplished in situ in the plastic sample tube using either a thermocycler or heating block. Upon heating, the plasmids were released while chromsomal DNA and membrane proteins were denatured and precipitated to the bottom of the tube. After adding enzyme and Sanger reagents, the resulting solution was aspirated into the reaction capillaries by a syringe pump, and cycle sequencing was initiated. No deleterious effect upon the reaction efficiency, the on-line purification system, or the capillary electrophoresis separation was observed, even though the crude lysate was used as the template. Multiplexed on-line DNA sequencing data from 8 parallel channels allowed base calling up to 620 bp with an accuracy of 98%. The entire system can be automatically regenerated for repeated operation. For PCR based DNA analysis, they demonstrated that capillary electrophoresis with UV detection can be used for DNA analysis starting from clinical sample without purification. After PCR reaction using cheek cell, blood or HIV-1 gag DNA, the reaction mixtures was injected into the capillary either on-line or off-line by base stacking. The protocol was also applied to capillary array electrophoresis. The use of cheaper detection, and the elimination of purification of DNA sample before or after PCR reaction, will make this approach an

  6. One-step purification and characterization of alginate lyase from a clinical Pseudomonas aeruginosa with destructive activity on bacterial biofilm

    Directory of Open Access Journals (Sweden)

    Parinaz Ghadam

    2017-05-01

    Full Text Available Objective(s: Pseudomonas aeruginosais a Gram-negative and aerobic rod bacterium that displays mucoid and non-mucoid phenotype. Mucoid strains secrete alginate, which is the main agent of biofilms in chronic P. aeruginosa infections, show high resistance to antibiotics; consequently, the biological disruption of mucoid P. aeruginosa biofilms is an attractive area of study for researchers. Alginate lyase gene (algl is a member of alginate producing operon which by glycosidase activity produces primer for other enzymes in this cluster. Also this activity can destroy the extracellular alginate; therefore this enzyme participates in alginate production and destruction pathway. Alginate lyase causes detachment of a biofilm by reducing its adhesion to the surfaces, and increases phagocytosis and antibiotic susceptibility. In this study, alginate lyase was purified in just one step and its properties were investigated. Materials and Methods: The purification was done by affinity chromatography, analysed by SDS-PAGE, and its effect on P. aeruginosa biofilms was surveyed by micro titer plate assay and SEM. The substrate specificity of the enzyme was determined by PCR. Results: Alginate lyase from isolate 48 was purified in one step. It is more thermally resistant than alginate lyase from Pseudomonas aeruginosa PAO1 and poly M, poly G and poly MG alginate were the substrate of this enzyme. Moreover, it has an eradication effect on biofilms from P. aeruginosa 48 and PAO1. Conclusion: In this study an alginate lyase with many characteristics suitable in medicine such as thermal stability, effective on poly M alginate, and bacterial biofilm destructive was introduced and purified.

  7. Comparison of Three Different Hepatitis C Virus Genotyping Methods: 5'NCR PCR-RFLP, Core Type-Specific PCR, and NS5b Sequencing in a Tertiary Care Hospital in South India.

    Science.gov (United States)

    Daniel, Hubert D-J; David, Joel; Raghuraman, Sukanya; Gnanamony, Manu; Chandy, George M; Sridharan, Gopalan; Abraham, Priya

    2017-05-01

    Based on genetic heterogeneity, hepatitis C virus (HCV) is classified into seven major genotypes and 64 subtypes. In spite of the sequence heterogeneity, all genotypes share an identical complement of colinear genes within the large open reading frame. The genetic interrelationships between these genes are consistent among genotypes. Due to this property, complete sequencing of the HCV genome is not required. HCV genotypes along with subtypes are critical for planning antiviral therapy. Certain genotypes are also associated with higher progression to liver cirrhosis. In this study, 100 blood samples were collected from individuals who came for routine HCV genotype identification. These samples were used for the comparison of two different genotyping methods (5'NCR PCR-RFLP and HCV core type-specific PCR) with NS5b sequencing. Of the 100 samples genotyped using 5'NCR PCR-RFLP and HCV core type-specific PCR, 90% (κ = 0.913, P PCR-RFLP and HCV core type-specific PCR, respectively, belonged to genotype 6. All the HCV genotype 1 subtypes were classified accurately by both the methods. This study shows that the 5'NCR-based PCR-RFLP and the HCV core type-specific PCR-based assays correctly identified HCV genotypes except genotype 6 from this region. Direct sequencing of the HCV core region was able to identify all the genotype 6 from this region and serves as an alternative to NS5b sequencing. © 2016 Wiley Periodicals, Inc.

  8. Identification of Mycobacterium ulcerans in the Environment from Regions in Southeast Australia in Which It Is Endemic with Sequence Capture-PCR

    OpenAIRE

    Stinear, Timothy; Davies, John K.; Jenkin, Grant A.; John A Hayman; Oppedisano, Frances; Johnson, Paul D. R.

    2000-01-01

    We recently described the use of PCR to identify the environmental source of Mycobacterium ulcerans during an outbreak of ulcerative disease that occurred in a localized region of southeast Australia. The PCR used was based on amplification of the M. ulcerans-specific insertion sequence, IS2404. In this study we developed a new test that is a substantial improvement over the original PCR method in terms of sensitivity, reliability, and ease of use. In the new method magnetic bead sequence cap...

  9. Simple Real-Time PCR and Amplicon Sequencing Method for Identification of Plasmodium Species in Human Whole Blood.

    Science.gov (United States)

    Lefterova, Martina I; Budvytiene, Indre; Sandlund, Johanna; Färnert, Anna; Banaei, Niaz

    2015-07-01

    Malaria is the leading identifiable cause of fever in returning travelers. Accurate Plasmodium species identification has therapy implications for P. vivax and P. ovale, which have dormant liver stages requiring primaquine. Compared to microscopy, nucleic acid tests have improved specificity for species identification and higher sensitivity for mixed infections. Here, we describe a SYBR green-based real-time PCR assay for Plasmodium species identification from whole blood, which uses a panel of reactions to detect species-specific non-18S rRNA gene targets. A pan-Plasmodium 18S rRNA target is also amplified to allow species identification or confirmation by sequencing if necessary. An evaluation of assay accuracy, performed on 76 clinical samples (56 positives using thin smear microscopy as the reference method and 20 negatives), demonstrated clinical sensitivities of 95.2% for P. falciparum (20/21 positives detected) and 100% for the Plasmodium genus (52/52), P. vivax (20/20), P. ovale (9/9), and P. malariae (6/6). The sensitivity of the P. knowlesi-specific PCR was evaluated using spiked whole blood samples (100% [10/10 detected]). The specificities of the real-time PCR primers were 94.2% for P. vivax (49/52) and 100% for P. falciparum (51/51), P. ovale (62/62), P. malariae (69/69), and P. knowlesi (52/52). Thirty-three specimens were used to test species identification by sequencing the pan-Plasmodium 18S rRNA PCR product, with correct identification in all cases. The real-time PCR assay also identified two samples with mixed P. falciparum and P. ovale infection, which was confirmed by sequencing. The assay described here can be integrated into a malaria testing algorithm in low-prevalence areas, allowing definitive Plasmodium species identification shortly after malaria diagnosis by microscopy. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  10. Integration of PCR-Sequencing Analysis with Multiplex Ligation-Dependent Probe Amplification for Diagnosis of Hereditary Fructose Intolerance.

    Science.gov (United States)

    Ferri, Lorenzo; Caciotti, Anna; Cavicchi, Catia; Rigoldi, Miriam; Parini, Rossella; Caserta, Marina; Chibbaro, Guido; Gasperini, Serena; Procopio, Elena; Donati, Maria Alice; Guerrini, Renzo; Morrone, Amelia

    2012-01-01

    Mutations in the ALDOB gene impair the activity of the hepatic aldolase B enzyme, causing hereditary fructose intolerance (HFI), an inherited autosomic recessive disease of carbohydrate metabolism, that can result in hypoglycemia, liver and kidney failure, coma, and death. Noninvasive diagnosis is possible by identifying mutant ALDOB alleles in suspected patients. We report the genetic characterization of a cohort of 18 HFI Caucasian patients, based on PCR-sequencing and Multiplex Ligation-dependent Probe Amplification (MLPA), with the identification of two novel genetic lesions: a small duplication c.940_941dupT (p.Trp314fsX22) and a large deletion encompassing the promoter region and exon 1. MLPA and long range-PCR (LR-PCR) also identified the recently reported g.7840_14288del6448 allele with a surprisingly high frequency (11%) within our patients' cohort. The most common p.Ala150Pro (44%), p.Ala175Asp (19%), p.Asn335Lys (8%), and/or the known c.360-363del4 (5%), p.Tyr204X (2.8%), IVS6 -2A>G (2.8%) mutant alleles were identified in 14 patients at a homozygous or compound-heterozygous level. The integration of PCR-sequencing analysis with exon-dosage tools [MLPA and quantitative fluorescent multiplex-PCR (QFM-PCR)] led to the full genotyping of patients within our cohort and to the identification of the new deletion encompassing the promoter region and exon 1.

  11. Determination of DQB1 alleles using PCR amplification and allele-specific primers.

    Science.gov (United States)

    Lepage, V; Ivanova, R; Loste, M N; Mallet, C; Douay, C; Naoumova, E; Charron, D

    1995-10-01

    Molecular genotyping of HLA class II genes is commonly carried out using polymerase chain reaction (PCR) in combination with sequence-specific oligotyping (PCR-SSO) or a combination of the PCR and restriction fragment length polymorphism methods (PCR-RFLP). However, the identification of the DQB1 type by PCR-SSO and PCR-RFLP is very time-consuming which is disadvantageous for the typing of cadaveric organ donors. We have developed a DQB1 typing method using PCR in combination with allele-specific amplification (PCR-ASA), which allows the identification of the 17 most frequent alleles in one step using seven amplification mixtures. PCR allele-specific amplification HLA-DQB1 typing is easy to perform, and the results are easy to interpret in routine clinical practice. The PCR-ASA method is therefore better suited to DQB1 typing for organ transplantation than other methods.

  12. Combined use of real-time PCR and nested sequence-based typing in survey of human Legionella infection.

    Science.gov (United States)

    Qin, T; Zhou, H; Ren, H; Shi, W; Jin, H; Jiang, X; Xu, Y; Zhou, M; Li, J; Wang, J; Shao, Z; Xu, X

    2016-07-01

    Legionnaires' disease (LD) is a globally distributed systemic infectious disease. The burden of LD in many regions is still unclear, especially in Asian countries including China. A survey of Legionella infection using real-time PCR and nested sequence-based typing (SBT) was performed in two hospitals in Shanghai, China. A total of 265 bronchoalveolar lavage fluid (BALF) specimens were collected from hospital A between January 2012 and December 2013, and 359 sputum specimens were collected from hospital B throughout 2012. A total of 71 specimens were positive for Legionella according to real-time PCR focusing on the 5S rRNA gene. Seventy of these specimens were identified as Legionella pneumophila as a result of real-time PCR amplification of the dotA gene. Results of nested SBT revealed high genetic polymorphism in these L. pneumophila and ST1 was the predominant sequence type. These data revealed that the burden of LD in China is much greater than that recognized previously, and real-time PCR may be a suitable monitoring technology for LD in large sample surveys in regions lacking the economic and technical resources to perform other methods, such as urinary antigen tests and culture methods.

  13. Ultrasensitive quantitation of human papillomavirus type 16 E6 oncogene sequences by nested real time PCR

    Directory of Open Access Journals (Sweden)

    López-Revilla Rubén

    2010-05-01

    Full Text Available Abstract Background We have developed an ultrasensitive method based on conventional PCR preamplification followed by nested amplification through real time PCR (qPCR in the presence of the DNA intercalating agent EvaGreen. Results Amplification mixtures calibrated with a known number of pHV101 copies carrying a 645 base pair (bp-long insert of the human papillomavirus type 16 (HPV16 E6 oncogene were used to generate the E6-1 amplicon of 645 bp by conventional PCR and then the E6-2 amplicon of 237 bp by nested qPCR. Direct and nested qPCR mixtures for E6-2 amplification corresponding to 2.5 × 102-2.5 × 106 initial pHV101 copies had threshold cycle (Ct values in the ranges of 18.7-29.0 and 10.0-25.0, respectively. The Ct of qPCR mixtures prepared with 1/50 volumes of preamplified mixtures containing 50 ng of DNA of the SiHa cell line (derived from an invasive cervical cancer with one HPV16 genome per cell was 19.9. Thermal fluorescence extinction profiles of E6-2 amplicons generated from pHV101 and SiHa DNA were identical, with a peak at 85.5°C. Conclusions Our method based on conventional preamplification for 15 cycles increased 10,750 times the sensitivity of nested qPCR for the quantitation of the E6 viral oncogene and confirmed that the SiHa cell line contains one E6-HPV16 copy per cell.

  14. PCR mutagenesis identifies a polymerase-binding sequence of sigma 54 that includes a sigma 70 homology region.

    OpenAIRE

    Tintut, Y; Gralla, J D

    1995-01-01

    Sigma 54 is a minor bacterial sigma factor that is not a member of the sigma 70 family of proteins but binds the same core RNA polymerase. Previously, we identified a region of sigma 54 that is important for binding core polymerase. In this work, PCR mutagenesis was used to identify specific amino acids important for this binding. The results show that important residues are clustered most closely in a short sequence that was previously speculated to be potentially homologous to a sequence in...

  15. Polymorphism in the bovine BOLA-DRB3 upstream regulatory regions detected through PCR-SSCP and DNA sequencing.

    Science.gov (United States)

    Ripoli, M V; Peral-García, P; Dulout, F N; Giovambattista, G

    2004-09-15

    In the present work, we describe through polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) and DNA sequencing the polymorphism within the URR-BoLA-DRB3 in 15 cattle breeds. In total, seven PCR-SSCP defined alleles were detected. The alignment of studied sequences showed six polymorphic sites (four transitions, one transversion and one deletion) in the interconsensus regions of the BoLA-DRB3 upstream regulatory region (URR), while the consensus boxes were invariant. Five out of six detected polymorphic sites were of one nucleotide substitution in the interconsensus regions. It is expected that these mutations do not affect significantly the level of expression. In contrast, the deletion observed in the sequence between CCAAT and TATA boxes could have some effect on affinity interactions between the promoter region and the transcription factors. The URR-BoLA-DRB3 DNA analyzed sequences showed moderate level of nucleotide diversity, high level of identity among them and were grouped in the same clade in the phylogenetic tree. In addition, the phylogenetic tree, the similarity analysis and the sequence structure confirmed that the fragment analyzed in this study corresponds to the URR-BoLA-DRB3. The functional role of the observed polymorphic sites among the regulatory motifs in bovine needs to be analyzed and confirmed by means of gene expression assays.

  16. Monitoring transmission routes of Listeria spp. in smoked salmon production with repetitive element sequence-based PCR techniques.

    Science.gov (United States)

    Zunabovic, M; Domig, K J; Pichler, I; Kneifel, W

    2012-03-01

    Various techniques have been used for tracing the transmission routes of Listeria species and for the assessment of hygiene standards in food processing plants. The potential of repetitive element sequence-based PCR (Rep-PCR) methods (GTG₅ and REPI + II) for the typing of Listeria isolates (n = 116), including Listeria monocytogenes (n = 46), was evaluated in a particular situation arising from the relocation of a company producing cold-smoked salmon. Pulsed-field gel electrophoresis (PFGE) using three restriction enzymes (ApaI, AscI, and SmaI) was used for comparison. Identical transmission scenarios among two companies could be identified by cluster analysis of L. monocytogenes isolates that were indistinguishable by both Rep-PCR and PFGE. The calculated diversity index (DI) indicates that Rep-PCR subtyping of Listeria species with primer sets GTG₅ and REPI + II has a lower discrimination power than does PFGE. When concatenated Rep-PCR cluster analysis was used, the DI increased from 0.934 (REPI + II) and 0.923 (GTG₅) to 0.956. The discrimination power of this method was similar to that of PFGE typing based on restriction enzyme Apa I (DI = 0.955). Listeria welshimeri may be useful as an indicator for monitoring smoked salmon processing environments. Rep-PCR meets the expectations of a reasonable, fast, and low-cost molecular subtyping method for the routine monitoring of Listeria species. The discriminatory power as characterized by the DI sufficiently quantifies the probability of unrelated isolates being characterized as different subtypes. Therefore, Rep-PCR typing based on two primer systems (GTG₅ and REPI + II) may be a useful tool for monitoring industrial hygiene.

  17. A dissociative fluorescence enhancement technique for one-step time-resolved immunoassays

    Energy Technology Data Exchange (ETDEWEB)

    Blomberg, Kaj R.; Mukkala, Veli-Matti; Hakala, Harri H.O.; Maekinen, Pauliina H.; Suonpaeae, Mikko U.; Hemmilae, Ilkka A. [PerkinElmer Inc, Wallac Oy, P.O. Box 10, Turku (Finland)

    2011-02-15

    The limitation of current dissociative fluorescence enhancement techniques is that the lanthanide chelate structures used as molecular probes are not stable enough in one-step assays with high concentrations of complexones or metal ions in the reaction mixture since these substances interfere with lanthanide chelate conjugated to the detector molecule. Lanthanide chelates of diethylenetriaminepentaacetic acid (DTPA) are extremely stable, and we used EuDTPA derivatives conjugated to antibodies as tracers in one-step immunoassays containing high concentrations of complexones or metal ions. Enhancement solutions based on different {beta}-diketones were developed and tested for their fluorescence-enhancing capability in immunoassays with EuDTPA-labelled antibodies. Characteristics tested were fluorescence intensity, analytical sensitivity, kinetics of complex formation and signal stability. Formation of fluorescent complexes is fast (5 min) in the presented enhancement solution with EuDTPA probes withstanding strong complexones (ethylenediaminetetra acetate (EDTA) up to 100 mM) or metal ions (up to 200 {mu}M) in the reaction mixture, the signal is intensive, stable for 4 h and the analytical sensitivity with Eu is 40 fmol/L, Tb 130 fmol/L, Sm 2.1 pmol/L and Dy 8.5 pmol/L. With the improved fluorescence enhancement technique, EDTA and citrate plasma samples as well as samples containing relatively high concentrations of metal ions can be analysed using a one-step immunoassay format also at elevated temperatures. It facilitates four-plexing, is based on one chelate structure for detector molecule labelling and is suitable for immunoassays due to the wide dynamic range and the analytical sensitivity. (orig.)

  18. One step synthesis of 6-oxo-cholestan-3β,5α-diol

    Energy Technology Data Exchange (ETDEWEB)

    Voisin, Maud; Silvente-Poirot, Sandrine; Poirot, Marc, E-mail: marc.poirot@inserm.fr

    2014-04-11

    Highlights: • Cholesterol-5,6-epoxides are metabolized into cholestane-3β,5α,6β-triol (CT) in cancer cells. • 6-Oxo-cholestan-3β,5α-diol (OCDO) is a putative metabolite of CT. • The one step syntheses of CT and OCDO from cholesterol are reported. • The one step syntheses of labelled CT and OCDO are reported. - Abstract: Cholesterol metabolism has been recently linked to cancer, highlighting the importance of the characterization of new metabolic pathways in the sterol series. One of these pathways is centered on cholesterol-5,6-epoxides (5,6-ECs). 5,6-ECs can either generate dendrogenin A, a tumor suppressor present in healthy mammalian tissues, or the carcinogenic cholestane-3β,5α,6β-triol (CT) and its putative metabolite 6-oxo-cholestan-3β,5α-diol (OCDO) in tumor cells. We are currently investigating the identification of the enzyme involved in OCDO biosynthesis, which would be highly facilitated by the use of commercially unavailable [{sup 14}C]-cholestane-3β,5α,6β-triol and [{sup 14}C]-6-oxo-cholestan-3β,5α-diol. In the present study we report the one-step synthesis of [{sup 14}C]-cholestane-3β,5α,6β-triol and [{sup 14}C]-6-oxo-cholestan-3β,5α-diol by oxidation of [{sup 14}C]-cholesterol with iodide metaperiodate (HIO{sub 4})

  19. Influence of ageing on self-etch adhesives: one-step vs. two-step systems.

    Science.gov (United States)

    Marchesi, Giulio; Frassetto, Andrea; Visintini, Erika; Diolosà, Marina; Turco, Gianluca; Salgarello, Stefano; Di Lenarda, Roberto; Cadenaro, Milena; Breschi, Lorenzo

    2013-02-01

    The aim of this study was to evaluate microtensile bond strength (μTBS) to dentine, interfacial nanoleakage expression, and stability after ageing, of two-step vs. one-step self-etch adhesives. Human molars were cut to expose middle/deep dentine, assigned to groups (n = 15), and treated with the following bonding systems: (i) Optibond XTR (a two-step self-etch adhesive; Kerr), (ii) Clearfil SE Bond (a two-step self-etch adhesive; Kuraray), (iii) Adper Easy Bond (a one-step self-etch adhesive; 3M ESPE), and (iv) Bond Force (a one-step self-etch adhesive; Tokuyama). Specimens were processed for μTBS testing after 24 h, 6 months, or 1 yr of storage in artificial saliva at 37°C. Nanoleakage expression was examined in similarly processed additional specimens. At baseline the μTBS results ranked in the following order: Adper Easy Bond = Optibond XTR ≥Clearfil SE = Bond Force, and interfacial nanoleakage analysis showed Clearfil SE Bond = Adper Easy Bond = Optibond XTR> Bond Force. After 1 yr of storage, Optibond XTR, Clearfil SE Bond, and Adper Easy Bond showed higher μTBS and lower interfacial nanoleakage expression compared with Bond Force. In conclusion, immediate bond strength, nanoleakage expression, and stability over time were not related to the number of steps of the bonding systems, but to their chemical formulations. © 2012 Eur J Oral Sci.

  20. Long-term durability of one-step adhesive-composite systems to enamel and dentin.

    Science.gov (United States)

    Foxton, Richard M; Melo, Luciana; Stone, David G; Pilecki, Peter; Sherriff, Martin; Watson, Timothy F

    2008-01-01

    This study evaluated the long-term durability of three one-step adhesive-composite systems to ground enamel and dentin. Twenty-seven teeth were randomly divided into three groups of nine. The first group had its crowns sectioned to expose superficial dentin, which was then ground with 600 grit SiC paper. One of three one-step adhesives: a trial bonding agent, OBF-2; i Bond or Adper Prompt L-Pop was applied to the dentin of three teeth and built-up with the corresponding resin composite (Estelite sigma, Venus or Filtek Supreme). The second group of nine teeth had their enamel approximal surfaces ground with wet 600-grit SiC paper, then one of the three one-step adhesives was applied and built-up with resin composite. The bonded specimens were sliced into 0.7 mm-thick slabs. After 24 hours and one year of water storage at 37 degrees C, the slabs were sectioned into beams for the microtensile bond strength test. Failure modes were observed using optical and electron scanning microscopy. The third group of nine teeth had approximal wedge-shaped cavities prepared above the CEJ into dentin. Two-to-three grains of rhodamine B were added to each of the three adhesives prior to restoring the cavities with resin composite. After 24 hours storage, the teeth were sectioned and their interfaces examined with a laser scanning confocal microscope. The bond strengths of the three adhesive-composite systems to both enamel and dentin significantly lessened after one year of water storage, however, there was no significant difference between the materials.

  1. SVM with Quadratic Polynomial Kernel Function Based Nonlinear Model One-step-ahead Predictive Control

    Institute of Scientific and Technical Information of China (English)

    钟伟民; 何国龙; 皮道映; 孙优贤

    2005-01-01

    A support vector machine (SVM) with quadratic polynomial kernel function based nonlinear model one-step-ahead predictive controller is presented. The SVM based predictive model is established with black-box identification method. By solving a cubic equation in the feature space, an explicit predictive control law is obtained through the predictive control mechanism. The effect of controller is demonstrated on a recognized benchmark problem and on the control of continuous-stirred tank reactor (CSTR). Simulation results show that SVM with quadratic polynomial kernel function based predictive controller can be well applied to nonlinear systems, with good performance in following reference trajectory as well as in disturbance-rejection.

  2. One-step iterative reconstruction of conductivity inclusion via the concept of topological derivative

    CERN Document Server

    Park, Won-Kwang

    2013-01-01

    We consider an inverse problem of location identification of small conductivity inhomogeneity inside a conductor via boundary measurements which occurs in the EIT (Electrical Impedance Tomography). For this purpose, we derive topological derivative by applying the asymptotic formula for steady state voltage potentials in the existence of conductivity inclusion of small diameter. Using this derivative, we design only one-step iterative location search algorithm of small conductivity inhomogeneity completely embedded in the homogeneous domain by solving an adjoint problem. Numerical experiments presented for showing the feasibility of proposed algorithm.

  3. Fiber inline Michelson interferometer fabricated by one-step femtosecond laser micromachining for sensing applications

    Science.gov (United States)

    Yuan, Lei; Wu, Hongbin; Wang, Cong; Yu, Yingyu; Wang, Sumei; Xiao, Hai

    2013-12-01

    A fiber inline Michelson interferometer fiber optic sensor was presented for sensing applications, including high temperature performance and refractive index change. The sensor was fabricated using one-step femtosecond (fs) laser micromachining technique. A step structure at the tip of a single mode optical fiber was formed during the micromachining process. The device had a loss of 16 dB and an interference visibility exceeding 18 dB. The capability of this device for temperature sensing up to 1000 °C and refractive index sensing application in various concentrations of ethanol solution were all demonstrated.

  4. One-step synthesis of samarium-doped ceria and its CO catalysis

    Indian Academy of Sciences (India)

    Tian Deng; Chongrong Zhang; Yuyuan Xiao; Anran Xie; Yue Pang; Yanzhao Yang

    2015-09-01

    The samarium-doped ceria (SDC) nanospheres were prepared by the one-step hydrothermal method and characterized by transmission electron microscope, scanning electron microscope, powder X-ray diffraction, X-ray photoelectron spectroscopy, energy-dispersive spectrometer and Raman spectra. According to the results, samarium was doped into the lattice successfully. The as-prepared samples were dispersed well and the average diameter was 60 nm. It showed better catalytic performance than pure ceria and the most appropriate concentration of doping was found.

  5. Polymer Adsorption on Iron Oxide Nanoparticles for One-Step Amino-Functionalized Silica Encapsulation

    Directory of Open Access Journals (Sweden)

    Lionel Maurizi

    2015-01-01

    Full Text Available This paper presents an original method to obtain, in one step, core/shell nanoparticles grafted covalently with polymer and functionalized with amino groups. By combining polyvinyl alcohol (PVA and silica precursors, we were able to obtain silica-coated and amino-functionalized iron oxide nanoparticles (SPIONs cross-linked with PVA. We also showed that using silica and amino-silica precursors together significantly increased the amount of PVA covalently bonded to the SPION surface compared to using only silica precursors. This original and interesting method has high potential for the industrial development of biocompatible functionalized nanoparticles for targeting nanomedicine.

  6. One-step block method for solving Volterra integro-differential equations

    Science.gov (United States)

    Mohamed, Nurul Atikah binti; Majid, Zanariah Abdul

    2015-10-01

    One-step block method for solving linear Volterra integro-differential equations (VIDEs) is presented in this paper. In VIDEs, the unknown function appears in the form of derivative and under the integral sign. The popular methods for solving VIDEs are the method of quadrature or quadrature method combined with numerical method. The proposed block method will solve the ordinary differential equations (ODEs) part and Newton-Cotes quadrature rule is applied to calculate the integral part of VIDEs. Numerical problems are presented to illustrate the performance of the proposed method.

  7. One-step green synthesis of gold nanoparticles by mesophilic filamentous fungi

    Science.gov (United States)

    Vágó, Adél; Szakacs, George; Sáfrán, György; Horvath, Robert; Pécz, Béla; Lagzi, István

    2016-02-01

    We report a one-step and green method for the synthesis of gold nanoparticles by randomly selected 21 types of microscopic fungi. Depending on the exact type of microorganisms and experimental parameters (such as fermentation conditions) highly stable particles with various shapes and sizes were obtained from the cell-free extracts of fungi, as revealed by spectroscopic and electron microscopic measurements. The active compound in the fungal extracellular supernatants which is responsible for the bioreduction was found to be less than 3000 Da in molecular weight determined by molecular sieves.

  8. A ONE-STEP SURFACE MODIFICATION PROCEDURE TO PEG-GRAFTED NANO-TITANIA

    Institute of Scientific and Technical Information of China (English)

    Yong-liang Zhu; Bin Wang; Jian Yu; Zhao-xia Guo

    2007-01-01

    PEG (Polyethylene Glycol)-grafted nano-titania has been obtained in a one-step procedure using hexamethylene diisocyanate as the coupling agent and dibutyltin dilaurate as the catalyst in toluene at 80℃ and characterized qualitatively by FTIR and quantitatively by elemental analysis and thermogravimetric analysis. A comparison of nano-titania with two other commonly used inorganic nanoparticles, nano-silica and nano-alumina, is made, revealing that reactivity order is nanosilica > nano-alumina > nano-titania in view of PEG grafting. Possible mechanism of PEG grafting is also discussed.

  9. One-step Entanglement Generation Between Separated Nitrogen-vacancy Centers Embedded in Photonic Crystal Cavities

    Science.gov (United States)

    Santos, A. F.; Khanna, Faqir C.

    2016-09-01

    We propose a one-step scheme for creating entanglement between two distant nitrogen-vacancy (NV) centers, which are placed in separate single-mode nanocavities in a planar photonic crystal (PC). With a laser-driven, the decoherence from the excited states of the NV centers can be effectively suppressed by virtue of the Raman transition in the dispersive regime. With the assistant of a strong classical field, fast operation can be achieved. The experimental feasibility of the scheme is discussed based on currently available technology.

  10. Template-directed synthesis of flexible porphyrin nanocage and nanorings via one-step olefin metathesis.

    Science.gov (United States)

    Zhu, Bin; Chen, Huanxin; Lin, Wei; Ye, Yang; Wu, Jing; Li, Shijun

    2014-10-29

    We describe the fabrication of a suite of flexible porphyrin cages and nanorings from a simple tetraalkene-derived zinc porphyrin monomer via a highly efficient template-directed strategy. The zinc porphyrin monomers were preorganized together by coordination with N atoms of multidentate ligands. Subsequent one-step olefin metathesis furnished a bisporphyrin cage, a triporphyrin nanoring, and a hexaporphyrin nanoring. In the case of the hexaporphyrin nanoring, 24 terminal olefins from six porphyrin monomers reacted with each other to form 12 new double bonds, delivering the final product. The triporphyrin and hexaporphyrin nanorings were further employed as hosts to encapsulate C60 and C70.

  11. Optimized spray drying process for preparation of one-step calcium-alginate gel microspheres

    Energy Technology Data Exchange (ETDEWEB)

    Popeski-Dimovski, Riste [Department of physic, Faculty of Natural Sciences and Mathematics, “ss. Cyril and Methodius” University, Arhimedova 3, 1000 Skopje, R. Macedonia (Macedonia, The Former Yugoslav Republic of)

    2016-03-25

    Calcium-alginate micro particles have been used extensively in drug delivery systems. Therefore we establish a one-step method for preparation of internally gelated micro particles with spherical shape and narrow size distribution. We use four types of alginate with different G/M ratio and molar weight. The size of the particles is measured using light diffraction and scanning electron microscopy. Measurements showed that with this method, micro particles with size distribution around 4 micrometers can be prepared, and SEM imaging showed that those particles are spherical in shape.

  12. One-step generation of qutrit entanglement via adiabatic passage in cavity quantum electrodynamics

    Institute of Scientific and Technical Information of China (English)

    Ma Song-She; Chen Mei-Feng; Jiang Xia-Ping

    2011-01-01

    A scheme is proposed for generating a three-dimensional entangled state for two atoms trapped in a cavity by one step via adiabatic passage.In the scheme,the two atoms are always in ground states and the field mode of the cavity excited is negligible under a certain condition.Therefore,the scheme is very robust against decoherence.Furthermore,it needs neither the exact control of all parameters nor the accurate control of the interaction time.It is shown that qutrit entanglement can be generated with a high fidelity.

  13. Template-activated strategy toward one-step coating silica colloidal microspheres with sliver.

    Science.gov (United States)

    Wang, Ke; Zhang, Xiaoli; Niu, Chunyu; Wang, Yongqiang

    2014-01-22

    Template-activated strategy was developed to coat silica (SiO2) colloidal microspheres with silver in one step, based on one-pot hydrothermal treatment of silver nitrate, PVP (poly(vinyl pyrrolidone)), and SiO2 colloidal microspheres in ammonia solution. In our reaction system, the surface of SiO2 colloidal microspheres was continually activated with negative-charged SiO(-) groups in ammonia solution, which accumulated [Ag(NH3)2](+) or Ag(+) ions around the SiO2 colloidal microspheres through electrostatic attraction; thereafter these ions could be reduced into Ag nanoparticles in situ by the weak reducer PVP in the solution, and then acted as seeds for the subsequent complete silver coating with the reaction proceeding. Therefore, the traditional three steps for complete silver coating, including prior surface modification, seeding, and subsequent growing, were effectively integrated into one step. The experimental results exhibited that perfect SiO2/Ag core/shell composite microspheres were successfully synthesized through optimizing the reaction parameters like the solvent ingredient, reducer, and the reaction temperature. Additionally, these obtained uniform composite microspheres were further used as SERS substrate by using R6G and thiram as probe molecules, and showed excellent trace detection of these organic chemicals in solution.

  14. Operator Approach to the Master Equation for the One-Step Process

    Science.gov (United States)

    Hnatič, M.; Eferina, E. G.; Korolkova, A. V.; Kulyabov, D. S.; Sevastyanov, L. A.

    2016-02-01

    Background. Presentation of the probability as an intrinsic property of the nature leads researchers to switch from deterministic to stochastic description of the phenomena. The kinetics of the interaction has recently attracted attention because it often occurs in the physical, chemical, technical, biological, environmental, economic, and sociological systems. However, there are no general methods for the direct study of this equation. The expansion of the equation in a formal Taylor series (the so called Kramers-Moyal's expansion) is used in the procedure of stochastization of one-step processes. Purpose. However, this does not eliminate the need for the study of the master equation. Method. It is proposed to use quantum field perturbation theory for the statistical systems (the so-called Doi method). Results: This work is a methodological material that describes the principles of master equation solution based on quantum field perturbation theory methods. The characteristic property of the work is that it is intelligible for non-specialists in quantum field theory. Conclusions: We show the full equivalence of the operator and combinatorial methods of obtaining and study of the one-step process master equation.

  15. One-step synthesis of magnetic chitosan for controlled release of 5-hydroxytryptophan

    Energy Technology Data Exchange (ETDEWEB)

    Santos Menegucci, Jucély dos; Santos, Mac-Kedson Medeiros Salviano; Dias, Diego Juscelino Santos; Chaker, Juliano Alexandre; Sousa, Marcelo Henrique, E-mail: mhsqui@gmail.com

    2015-04-15

    In this work, nanoparticles of chitosan embedded with 25% (w/w) of iron oxide magnetic nanoparticles (magnetite/maghemite) with narrow size-distribution and with a loading efficiency of about 80% for 5-hydroxytryptophan (5-HTP), which is a chemical precursor in the biosynthesis of important neurotransmitters as serotonin, were synthesized with an initial mass ratio of 5-HTP/magnetic chitosan=1.2, using homogeneous precipitation by urea decomposition, in an efficient one-step procedure. Characterization of morphology, structure and surface were performed by XRD, TEM, FTIR, TGA, magnetization and zeta potential measurements, while drug loading and drug releasing were investigated using UV–vis spectroscopy. Kinetic drug release experiments under different pH conditions revealed a pH-sensitivecontrolled-release system, ruled by polymer swelling and/or particle dissolution. - Highlights: • One-step synthesis and incorporation of drug in magnetic chitosan. • Synthesis utilizes a cost-effective and environmentally friendly procedure. • Narrow size distribution of magnetic nanoparticles in the composite. • Composite is a basis for a magnetic pH triggered drug release system.

  16. One-step isolation of plasma membrane proteins using magnetic beads with immobilized concanavalin A1

    Science.gov (United States)

    Lee, Yu-Chen; Block, Gregory; Chen, Huiwen; Folch-Puy, Emma; Foronjy, Robert; Jalili, Roxana; Jendresen, Christian Bille; Kimura, Masashi; Kraft, Edward; Lindemose, Søren; Lu, Jin; McLain, Teri; Nutt, Leta; Ramon-Garcia, Santiago; Smith, Joseph; Spivak, Aaron; Wang, Michael L.; Zanic, Marija; Lin, Sue-Hwa

    2008-01-01

    We have developed a simple method for isolating and purifying plasma membrane proteins from various cell types. This one-step affinity-chromatography method uses the property of the lectin concanavalin A (ConA) and the technique of magnetic-bead separation to obtain highly purified plasma membrane proteins from crude membrane preparations or cell lines. ConA is immobilized onto magnetic beads by binding biotinylated ConA to streptavidin magnetic beads. When these ConA magnetic beads were used to enrich plasma membranes from a crude membrane preparation, this procedure resulted in 3.7-fold enrichment of plasma membrane marker 5′-nucleotidase activity with 70% recovery of the activity in the crude membrane fraction of rat liver. In agreement with the results of 5′-nucleotidase activity, immunoblotting with antibodies specific for a rat liver plasma membrane protein, CEACAM1, indicated that CEACAM1 was enriched about threefold relative to that of the original membranes. In similar experiments, this method produced 13-fold enrichment of 5′-nucleotidase activity with 45% recovery of the activity from a total cell lysate of PC-3 cells and 7.1-fold enrichment of 5′-nucleotidase activity with 33% recovery of the activity from a total cell lysate of HeLa cells. These results suggest that this one-step purification method can be used to isolate total plasma membrane proteins from tissue or cells for the identification of membrane biomarkers. PMID:18765283

  17. One-step ahead prediction of foF2 using time series forecasting techniques

    Directory of Open Access Journals (Sweden)

    A. Belehaki

    2005-11-01

    Full Text Available In this paper the problem of one-step ahead prediction of the critical frequency (foF2 of the middle-latitude ionosphere, using time series forecasting methods, is considered. The whole study is based on a sample of about 58000 observations of foF2 with 15-min time resolution, derived from the Athens digisonde ionograms taken from the Digisonde Portable Sounder (DPS4 located at Palaia Penteli (38° N, 23.5° E, for the period from October 2002 to May 2004. First, the embedding dimension of the dynamical system that generates the above sample is estimated using the false nearest neighbor method. This information is then utilized for the training of the predictors employed in this study, which are the linear predictor, the neural network predictor, the persistence predictor and the k-nearest neighbor predictor. The results obtained by the above predictors suggest that, as far as the mean square error is considered as performance criterion, the first two predictors are significantly better than the latter two predictors. In addition, the results obtained by the linear and the neural network predictors are not significantly different from each other. This may be taken as an indication that a linear model suffices for one step ahead prediction of foF2.

  18. A simple one-step chemistry model for partially premixed hydrocarbon combustion

    Energy Technology Data Exchange (ETDEWEB)

    Fernandez-Tarrazo, Eduardo [Instituto Nacional de Tecnica Aeroespacial, Madrid (Spain); Sanchez, Antonio L. [Area de Mecanica de Fluidos, Universidad Carlos III de Madrid, Leganes 28911 (Spain); Linan, Amable [ETSI Aeronauticos, Pl. Cardenal Cisneros 3, Madrid 28040 (Spain); Williams, Forman A. [Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA 92093-0411 (United States)

    2006-10-15

    This work explores the applicability of one-step irreversible Arrhenius kinetics with unity reaction order to the numerical description of partially premixed hydrocarbon combustion. Computations of planar premixed flames are used in the selection of the three model parameters: the heat of reaction q, the activation temperature T{sub a}, and the preexponential factor B. It is seen that changes in q with equivalence ratio f need to be introduced in fuel-rich combustion to describe the effect of partial fuel oxidation on the amount of heat released, leading to a universal linear variation q(f) for f>1 for all hydrocarbons. The model also employs a variable activation temperature T{sub a}(f) to mimic changes in the underlying chemistry in rich and very lean flames. The resulting chemistry description is able to reproduce propagation velocities of diluted and undiluted flames accurately over the whole flammability limit. Furthermore, computations of methane-air counterflow diffusion flames are used to test the proposed chemistry under nonpremixed conditions. The model not only predicts the critical strain rate at extinction accurately but also gives near-extinction flames with oxygen leakage, thereby overcoming known predictive limitations of one-step Arrhenius kinetics. (author)

  19. Copper nano-clusters prepared by one-step electrodeposition and its application on nitrate sensing

    Directory of Open Access Journals (Sweden)

    Y. Li

    2015-04-01

    Full Text Available This paper describes the fabrication and characterization of copper nano-clusters prepared by a simple one-step electrodeposition process on platinum microelectrode, and the application for nitrate determination. The one-step electrodepostion process was performed by chronoamperometry scan in acidic copper sulphate electrolyte directly. The SEM and electrochemical examination showed that the morphologies and microstructures of deposited copper layers can be precisely controlled by using different deposition voltages. It was found that the copper layer is porous when the deposition voltage is higher than -500 mV, and this porous layer has a larger effective surface area compared with the corresponding smooth flat copper layer deposited under voltage less than -300 mV. Under the optimized deposition voltage, copper clusters constructed by uniform nanoparticles with an average diameter of about 100 nm can be obtained. The mechanism of electrodeposition process for this method was also speculated. The copper layers deposited under different voltages are used in a series of tests in order to evaluate their performance for nitrate sensing. The experimental results reveal that the microelectrode modified by fixed potential deposition under -700 mV had a higher sensitivity of 39.31 μA/mmolL−1 for nitrate detection within the concentration ranging from 0.1 mmolL−1 to 4.0 mmolL−1.

  20. One-Step Printable Perovskite Films Fabricated under Ambient Conditions for Efficient and Reproducible Solar Cells.

    Science.gov (United States)

    Jung, Yen-Sook; Hwang, Kyeongil; Heo, Youn-Jung; Kim, Jueng-Eun; Lee, Donmin; Lee, Cheol-Ho; Joh, Han-Ik; Yeo, Jun-Seok; Kim, Dong-Yu

    2017-08-23

    Despite the potential of roll-to-roll processing for the fabrication of perovskite films, the realization of highly efficient and reproducible perovskite solar cells (PeSCs) through continuous coating techniques and low-temperature processing is still challenging. Here, we demonstrate that efficient and reliable CH3NH3PbI3 (MAPbI3) films fabricated by a printing process can be achieved through synergetic effects of binary processing additives, N-cyclohexyl-2-pyrrolidone (CHP) and dimethyl sulfoxide (DMSO). Notably, these perovskite films are deposited from premixed perovskite solutions for facile one-step processing under a room-temperature and ambient atmosphere. The CHP molecules result in the uniform and homogeneous perovskite films even in the one-step slot-die system, which originate from the high boiling point and low vapor pressure of CHP. Meanwhile, the DMSO molecules facilitate the growth of perovskite grains by forming intermediate states with the perovskite precursor molecules. Consequently, fully printed PeSC based on the binary additive system exhibits a high PCE of 12.56% with a high reproducibility.

  1. One step 'dip' and 'use' Ag nanostructured thin films for ultrahigh sensitive SERS Detection.

    Science.gov (United States)

    Rajkumar, Kanakaraj; Jayram, Naidu Dhanpal; Mangalaraj, Devanesan; Rajendra Kumar, Ramasamy Thangavelu

    2016-11-01

    A simple one step galvanic displacement method which involves dipping of the silicon substrate in the AgNO3/HF solution and using it for SERS application without any further process is demonstrated. The size and shape of the Ag nanoparticles changes as the deposition time is increased. Initially the shape of the particles was nearly spherical and as it grows, becomes oblong and then coalesce to form a discontinuous film with vertically grown hierarchical Ag nanostructures. The sizes of the deposited particles were in the ranges from 30nm to a discontinuous film. It also demonstrated a highly sensitive chemical detection by surface-enhanced Raman scattering of rhodamine 6G dye, down to 10(-16)M concentration. Prepared samples were able to detect lower concentrations of Melamine. Discontinuous thin films with hierarchical Ag nanostructures were obtained for 5min Ag deposition. The formation of Hot spots between the discontinuous islands and also along the hierarchical structures is responsible for the high SERS enhancement. This simple one step, fast, non-lithographic and cost effective method can be applied for various label free detection of analytes of importance.

  2. One-step electrodeposition of graphene loaded nickel oxides nanoparticles for acetaminophen detection.

    Science.gov (United States)

    Liu, Gui-Ting; Chen, Hui-Fen; Lin, Guo-Ming; Ye, Ping-ping; Wang, Xiao-Ping; Jiao, Ying-Zhi; Guo, Xiao-Yu; Wen, Ying; Yang, Hai-Feng

    2014-06-15

    An electrochemical sensor of acetaminophen (AP) based on electrochemically reduced graphene (ERG) loaded nickel oxides (Ni2O3-NiO) nanoparticles coated onto glassy carbon electrode (ERG/Ni2O3-NiO/GCE) was prepared by a one-step electrodeposition process. The as-prepared electrode was characterized by scanning electron microscopy, X-ray photoelectron spectroscopy and Raman spectroscopy. The electrocatalytic properties of ERG/Ni2O3-NiO modified glassy carbon electrode toward the oxidation of acetaminophen were analyzed via cyclic voltammetry (CV) and differential pulse voltammetry (DPV). The electrodes of Ni2O3-NiO/GCE, ERG/GCE, and Ni2O3-NiO deposited ERG/GCE were fabricated for the comparison and the catalytic mechanism understanding. The studies showed that the one-step prepared ERG/Ni2O3-NiO/GCE displayed the highest electro-catalytic activity, attributing to the synergetic effect derived from the unique composite structure and physical properties of nickel oxides nanoparticles and graphene. The low detection limit of 0.02 μM (S/N=3) with the wide linear detection range from 0.04 μM to 100 μM (R=0.998) was obtained. The resulting sensor was successfully used to detect acetaminophen in commercial pharmaceutical tablets and urine samples.

  3. General fabrication of ordered nanocone arrays by one-step selective plasma etching.

    Science.gov (United States)

    Wang, Qiang; Tian, Zhaoshuo; Li, Yunlong; Tian, Shibing; Li, Yunming; Ren, Shoutian; Gu, Changzhi; Li, Junjie

    2014-03-21

    One-step selective direct current (DC) plasma etching technology is employed to fabricate large-area well-aligned nanocone arrays on various functional materials including semiconductor, insulator and metal. The cones have nanoscale apexes (∼2 nm) with high aspect ratios, which were achieved by a selective plasma etching process using only CH4 and H2 in a bias-assisted hot filament chemical vapor deposition (HFCVD) system without any masked process. The CH(3)(+) ions play a major role to etch the roughened surface into a conical structure under the auxiliary of H(+) ions. Randomly formed nano-carbon may act as an original mask on the smooth surface to initiate the following selective ions sputtering. Physical impinging of energetic ions onto the concave regions is predominant in comparison with the etching of convex parts on the surface, which is identified as the key mechanism for the formation of conical nanostructures. This one-step maskless plasma etching technology enables the universal formation of uniform nanocone structures on versatile substrates for many promising applications.

  4. Transparent, superhydrophobic surfaces from one-step spin coating of hydrophobic nanoparticles.

    Science.gov (United States)

    Xu, Lebo; Karunakaran, Raghuraman G; Guo, Jia; Yang, Shu

    2012-02-01

    We study the nonwettability and transparency from the assembly of fluorosilane modified silica nanoparticles (F-SiO(2) NPs) via one-step spin-coating and dip-coating without any surface postpassivation steps. When spin-coating the hydrophobic NPs (100 nm in diameter) at a concentration ≥ 0.8 wt % in a fluorinated solvent, the surface exhibited superhydrophobicity with an advancing water contact angle greater than 150° and a water droplet (5 μL) roll-off angle less than 5°. In comparison, superhydrophobicity was not achieved by dip-coating the same hydrophobic NPs. Scanning electron microscopy (SEM) and atomic force microscopy (AFM) images revealed that NPs formed a nearly close-packed assembly in the superhydrophobic films, which effectively minimized the exposure of the underlying substrate while offering sufficiently trapped air pockets. In the dip-coated films, however, the surface coverage was rather random and incomplete. Therefore, the underlying substrate was exposed and water was able to impregnate between the NPs, leading to smaller water contact angle and larger water contact angle hysteresis. The spin-coated superhydrophobic film was also highly transparent with greater than 95% transmittance in the visible region. Further, we demonstrated that the one-step coating strategy could be extended to different polymeric substrates, including poly(methyl methacrylate) and polyester fabrics, to achieve superhydrophobicity.

  5. One-step synthesis of hierarchically porous carbons for high-performance electric double layer supercapacitors

    Science.gov (United States)

    Zhang, Haitao; Zhang, Lei; Chen, Jun; Su, Hai; Liu, Fangyan; Yang, Weiqing

    2016-05-01

    With plenty of unique porous structure at micro-/nano scale, hierarchically porous carbons (HPCs) are promising for usage in advanced electric double layer supercapacitors (EDLCs) as the electrode materials. However, wide-range adoption of HPC for practical application is largely shadowed by its extremely complex synthesis process with considerably low production efficiency. Herein we reported a simple template-free, one-step sintering method, to massively produce the HPCs for high-performance EDLCs. Resorting to the 3D structure modification of the wide pore size distribution, high surface area of HPCs (up to 3000 m2 g-1) was achieved. By using 1 M Na2SO4 as electrolyte, the as-fabricated HPCs based EDLCs can be operated reversibly over a wide voltage window of 1.6 V with superior specific capacitance of 240 F g-1 under a current density of 0.5 A g-1. In the meanwhile, the EDLCs exhibit excellent rate capability (high power density of 16 kW kg-1 at 10.2 Wh kg-1) and long-term cycling stability with 9% loss of its initial capacitance after 2000 cycles. This output performance distinguished itself among most of the carbon-based EDLCs with neutral aqueous electrolyte. Thus, the template-free one-step sintering method produced HPCs for EDLCs represents a new approach for high-performance energy storage.

  6. One-step fabrication of near superhydrophobic aluminum surface by nanosecond laser ablation

    Science.gov (United States)

    Jagdheesh, R.; García-Ballesteros, J. J.; Ocaña, J. L.

    2016-06-01

    Inspired by the micro and nano structures of biological surface such as lotus leaf, rice leaves, etc. a functional near superhydrophobic surface of pure aluminum has been fabricated using one-step nanosecond laser processing. Thin aluminum sheets are micro-patterned with ultraviolet laser pulses to create near superhydrophobic surface in one-step direct laser writing technique. The impact of number of pulses/microhole with respect to the geometry and static contact angle measurements has been investigated. The microstructure shows the formation of blind microholes along with the micro-wall by laser processing, which improves the composite interface between the three phases such as water, air and solid, thus enhance the wetting property of the surface. The geometrical changes are supported by the chemical changes induced on the surface for improving the degree of hydrophobicity. Laser processed microholes exhibited near superhydrophobic surface with SCA measurement of 148 ± 3°. The static contact angle values are very consistent for repeated measurement at same area and across the laser patterned surface.

  7. Shape-control and characterization of iron nanocrystals prepared via a one-step solvothermal method

    Energy Technology Data Exchange (ETDEWEB)

    Fan, Junmei, E-mail: jmfan@home.ipe.ac.cn [State Key Laboratory of Multi-phase Complex System, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190 (China); Cao, Yuebin [Key Laboratory for Advanced Technology in Environmental Protection of Jiangsu Province, Yancheng Institute of Technology, Yancheng 224051 (China); Yuan, Fangli [State Key Laboratory of Multi-phase Complex System, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190 (China)

    2015-12-01

    In the present work, iron nanocubes, nanorods and nanowires are successfully synthesized by one-step reduction approach in a solvothermal environment. It is analyzed that the iron nanocubes, nanorods and nanowires belong to the pure body-centered cubic structure of α-Fe. Effects of additive sort and the amount of Anionic Gemini surfactant 12-4-12 on the morphology evolution of Fe are discussed based on SEM and TEM images. The possible formation mechanisms of iron nanocubes, nanorods and nanowires are proposed. The Anionic Gemini surfactant 12-4-12 regarded as template plays an important role in the formation of iron nanocrystals. The microwave electromagnetic (EM) (80 wt% Fe) and calculated microwave-absorbing (0.5 mm thickness) properties in 2–18 GHz of the iron nanocubes, nanorods and nanowires are studied systematically. Results show that iron nanowires are superior to nanorods and nanocubes, which indicates the potential to be a super-thin microwave absorber. - Highlights: • Iron nanocubes, nanorods and nanowires were synthesized by one-step reduction. • The Anionic Gemini played a vital role in the formation of iron nanocrystals. • The microwave-absorbing properties in 2–18 GHz of iron nanowires were tiptop. • Iron nanowires have the potential to be a super-thin microwave absorber.

  8. One-step synthesis of nitrogen-iron coordinated carbon nanotube catalysts for oxygen reduction reaction

    Science.gov (United States)

    Choi, Woongchul; Yang, Gang; Kim, Suk Lae; Liu, Peng; Sue, Hung-Jue; Yu, Choongho

    2016-05-01

    Prohibitively expensive precious metal catalysts for oxygen reduction reaction (ORR) have been one of the major hurdles in a wide use of electrochemical cells. Recent significant efforts to develop precious metal free catalysts have resulted in excellent catalytic activities. However, complicated and time-consuming synthesis processes have negated the cost benefit. Moreover, detailed analysis about catalytically active sites and the role of each element in these high-performance catalysts containing nanomaterials for large surface areas are often lacking. Here we report a facile one-step synthesis method of nitrogen-iron coordinated carbon nanotube (CNT) catalysts without precious metals. Our catalysts show excellent long-term stability and onset ORR potential comparable to those of other precious metal free catalysts, and the maximum limiting current density from our catalysts is larger than that of the Pt-based catalysts. We carry out a series of synthesis and characterization experiments with/without iron and nitrogen in CNT, and identify that the coordination of nitrogen and iron in CNT plays a key role in achieving the excellent catalytic performances. We anticipate our one-step process could be used for mass production of precious metal free electrocatalysts for a wide range of electrochemical cells including fuel cells and metal-air batteries.

  9. One-step preparation of antimicrobial silver nanoparticles in polymer matrix

    Energy Technology Data Exchange (ETDEWEB)

    Lyutakov, O., E-mail: lyutakoo@vscht.cz; Kalachyova, Y. [Institute of Chemical Technology, Department of Solid State Engineering (Czech Republic); Solovyev, A. [Institute of Chemical Process Fundamentals of the ASCR (Czech Republic); Vytykacova, S. [Institute of Chemical Technology, Department of Glass and Ceramics (Czech Republic); Svanda, J.; Siegel, J. [Institute of Chemical Technology, Department of Solid State Engineering (Czech Republic); Ulbrich, P. [Institute of Chemical Technology, Department of Biochemistry and Microbiology (Czech Republic); Svorcik, V. [Institute of Chemical Technology, Department of Solid State Engineering (Czech Republic)

    2015-03-15

    Simple one-step procedure for in situ preparation of silver nanoparticles (AgNPs) in the polymer thin films is described. Nanoparticles (NPs) were prepared by reaction of N-methyl pyrrolidone with silver salt in semi-dry polymer film and characterized by transmission electron microscopy, XPS, and UV–Vis spectroscopy techniques. Direct synthesis of NPs in polymer has several advantages; even though it avoids time-consuming NPs mixing with polymer matrix, uniform silver distribution in polymethylmethacrylate (PMMA) films is achieved without necessity of additional stabilization. The influence of the silver concentration, reaction temperature and time on reaction conversion rate, and the size and size-distribution of the AgNPs was investigated. Polymer films doped with AgNPs were tested for their antibacterial activity on Gram-negative bacteria. Antimicrobial properties of AgNPs/PMMA films were found to be depended on NPs concentration, their size and distribution. Proposed one-step synthesis of functional polymer containing AgNPs is environmentally friendly, experimentally simple and extremely quick. It opens up new possibilities in development of antimicrobial coatings with medical and sanitation applications.

  10. One-step disposal of Cr (Ⅵ)-bearing wastewater by natural pyrrhotite

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Cr(Ⅵ)-bearing wastewater can be treated by natural pyrrhotite which is used for reductant to reduce Cr(Ⅵ) and precipitant to precipitate Cr(Ⅲ) simultaneously. The disposal products can be divided into three parts in the beakers,namely supernatant in the upper part,the yellowish colloidal precipitates in the middle part and the pyrrhotite in the lower part. The content of total Cr=Cr(Ⅵ)+Cr(Ⅲ) in the supernatant liquid is 0.06 mg/L,which is lower than 1.5 mg/L of the discharge standard of China and near to 0.05 mg/L of the standard of potable water. This one-step disposal composing of both reduction and precipitation which is traditionally divided into two independent steps called reducing technology and precipitating technology respectively. The new method is of obvious economic advantage and favourable to decreasing surplus mud derived from adding Ca(OH)2 to precipitate Cr(Ⅲ) traditionally so as to avoid recontamination. In fact,sodium sulfite (Na2SO3) used in disposal of Cr(Ⅵ) was traditionally produced from natural mineral of pyrrhotite (FeS). One molecule of FeS is 4 times more than that of Na2SO3 from a view point of rational use of mineral resources. Therefore the prospective of application of the one-step disposal of Cr(Ⅵ) method is full of promise.

  11. Influence of application methods of one-step self-etching adhesives on microtensile bond strength

    Directory of Open Access Journals (Sweden)

    Chul-Kyu Choi,

    2011-05-01

    Full Text Available Objectives The purpose of this study was to evaluate the effect of various application methods of one-step self-etch adhesives to microtensile resin-dentin bond strength. Materials and Methods Thirty-six extracted human molars were used. The teeth were assigned randomly to twelve groups (n = 15, according to the three different adhesive systems (Clearfil Tri-S Bond, Adper Prompt L-Pop, G-Bond and application methods. The adhesive systems were applied on the dentin as follows: 1 The single coating, 2 The double coating, 3 Manual agitation, 4 Ultrasonic agitation. Following the adhesive application, light-cure composite resin was constructed. The restored teeth were stored in distilled water at room temperature for 24 hours, and prepared 15 specimens per groups. Then microtensile bond strength was measured and the failure mode was examined. Results Manual agitation and ultrasonic agitation of adhesive significantly increased the microtensile bond strength than single coating and double coating did. Double coating of adhesive significantly increased the microtensile bond strength than single coating did and there was no significant difference between the manual agitation and ultrasonic agitation group. There was significant difference in microtensile bonding strength among all adhesives and Clearfil Tri-S Bond showed the highest bond strength. Conclusions In one-step self-etching adhesives, there was significant difference according to application methods and type of adhesives. No matter of the material, the manual or ultrasonic agitation of the adhesive showed significantly higher microtensile bond strength.

  12. FastCloning: a highly simplified, purification-free, sequence- and ligation-independent PCR cloning method

    Directory of Open Access Journals (Sweden)

    Lu Jia

    2011-10-01

    Full Text Available Abstract Background Although a variety of methods and expensive kits are available, molecular cloning can be a time-consuming and frustrating process. Results Here we report a highly simplified, reliable, and efficient PCR-based cloning technique to insert any DNA fragment into a plasmid vector or into a gene (cDNA in a vector at any desired position. With this method, the vector and insert are PCR amplified separately, with only 18 cycles, using a high fidelity DNA polymerase. The amplified insert has the ends with ~16-base overlapping with the ends of the amplified vector. After DpnI digestion of the mixture of the amplified vector and insert to eliminate the DNA templates used in PCR reactions, the mixture is directly transformed into competent E. coli cells to obtain the desired clones. This technique has many advantages over other cloning methods. First, it does not need gel purification of the PCR product or linearized vector. Second, there is no need of any cloning kit or specialized enzyme for cloning. Furthermore, with reduced number of PCR cycles, it also decreases the chance of random mutations. In addition, this method is highly effective and reproducible. Finally, since this cloning method is also sequence independent, we demonstrated that it can be used for chimera construction, insertion, and multiple mutations spanning a stretch of DNA up to 120 bp. Conclusion Our FastCloning technique provides a very simple, effective, reliable, and versatile tool for molecular cloning, chimera construction, insertion of any DNA sequences of interest and also for multiple mutations in a short stretch of a cDNA.

  13. PCR Cloning of Partial "nbs" Sequences from Grape ("Vitis aestivalis" Michx)

    Science.gov (United States)

    Chang, Ming-Mei; DiGennaro, Peter; Macula, Anthony

    2009-01-01

    Plants defend themselves against pathogens via the expressions of disease resistance (R) genes. Many plant R gene products contain the characteristic nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains. There are highly conserved motifs within the NBS domain which could be targeted for polymerase chain reaction (PCR) cloning of R…

  14. PCR Cloning of Partial "nbs" Sequences from Grape ("Vitis aestivalis" Michx)

    Science.gov (United States)

    Chang, Ming-Mei; DiGennaro, Peter; Macula, Anthony

    2009-01-01

    Plants defend themselves against pathogens via the expressions of disease resistance (R) genes. Many plant R gene products contain the characteristic nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains. There are highly conserved motifs within the NBS domain which could be targeted for polymerase chain reaction (PCR) cloning of R…

  15. PCR mutagenesis identifies a polymerase-binding sequence of sigma 54 that includes a sigma 70 homology region.

    Science.gov (United States)

    Tintut, Y; Gralla, J D

    1995-10-01

    Sigma 54 is a minor bacterial sigma factor that is not a member of the sigma 70 family of proteins but binds the same core RNA polymerase. Previously, we identified a region of sigma 54 that is important for binding core polymerase. In this work, PCR mutagenesis was used to identify specific amino acids important for this binding. The results show that important residues are clustered most closely in a short sequence that was previously speculated to be potentially homologous to a sequence in sigma 70. The mutagenesis also identifies important residues in the flanking hydrophobic-acidic region of sigma 54, which is absent in sigma 70. Overall, the data indicate that sigma 54 binds core polymerase through a sequence homologous to that of sigma 70 but in addition uses unique motifs to modify this interaction.

  16. One-step reverse transcription loop-mediated isothermal amplification for the rapid detection of cucumber green mottle mosaic virus.

    Science.gov (United States)

    Li, Jin-yu; Wei, Qi-wei; Liu, Yong; Tan, Xin-qiu; Zhang, Wen-na; Wu, Jian-yan; Charimbu, Miriam Karwitha; Hu, Bai-shi; Cheng, Zhao-bang; Yu, Cui; Tao, Xiao-rong

    2013-11-01

    Cucumber green mottle mosaic virus (CGMMV) has caused serious damage to Cucurbitaceae crops worldwide. The virus is considered one of the most serious Cucurbitaceae quarantine causes in many countries. In this study, a highly efficient and practical one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) was developed for the detection of CGMMV. The total RNA or crude RNA extracted from watermelon plants or seeds could be detected easily by this RT-LAMP assay. The RT-LAMP assay was conducted in isothermal (63°C) conditions within 1h. The amplified products of CGMMV could be detected as ladder-like bands using agarose gel electrophoresis or visualized in-tube under UV light with the addition of a fluorescent dye. The RT-LAMP amplification was specific to CGMMV, as no cross-reaction was observed with other viruses. The RT-LAMP assay was 100-fold more sensitive than that of reverse-transcription polymerase chain reaction (RT-PCR). This is the first report of the application of the RT-LAMP assay to detect CGMMV. The sensitive, specific and rapid RT-LAMP assay developed in this study can be applied widely in laboratories, the field and quarantine surveillance of CGMMV.

  17. Identification of a novel Plasmopara halstedii elicitor protein combining de novo peptide sequencing algorithms and RACE-PCR

    Directory of Open Access Journals (Sweden)

    Madlung Johannes

    2010-05-01

    Full Text Available Abstract Background Often high-quality MS/MS spectra of tryptic peptides do not match to any database entry because of only partially sequenced genomes and therefore, protein identification requires de novo peptide sequencing. To achieve protein identification of the economically important but still unsequenced plant pathogenic oomycete Plasmopara halstedii, we first evaluated the performance of three different de novo peptide sequencing algorithms applied to a protein digests of standard proteins using a quadrupole TOF (QStar Pulsar i. Results The performance order of the algorithms was PEAKS online > PepNovo > CompNovo. In summary, PEAKS online correctly predicted 45% of measured peptides for a protein test data set. All three de novo peptide sequencing algorithms were used to identify MS/MS spectra of tryptic peptides of an unknown 57 kDa protein of P. halstedii. We found ten de novo sequenced peptides that showed homology to a Phytophthora infestans protein, a closely related organism of P. halstedii. Employing a second complementary approach, verification of peptide prediction and protein identification was performed by creation of degenerate primers for RACE-PCR and led to an ORF of 1,589 bp for a hypothetical phosphoenolpyruvate carboxykinase. Conclusions Our study demonstrated that identification of proteins within minute amounts of sample material improved significantly by combining sensitive LC-MS methods with different de novo peptide sequencing algorithms. In addition, this is the first study that verified protein prediction from MS data by also employing a second complementary approach, in which RACE-PCR led to identification of a novel elicitor protein in P. halstedii.

  18. Supported PCR : an efficient procedure to amplify sequences flanking a known DNA segment

    NARCIS (Netherlands)

    Rudenko, George N.; Rommens, Caius M.T.; Nijkamp, H. John J.; Hille, Jacques

    1993-01-01

    We describe a novel modification of the polymerase chain reaction for efficient in vitro amplification of genomic DNA sequences flanking short stretches of known sequence. The technique utilizes a target enrichment step, based on the selective isolation of biotinylated fragments from the bulk of gen

  19. PCR detection of ansA from marine bacteria and its sequence characteristics from Bacillus tequilensis NIOS4.

    Science.gov (United States)

    Nayak, Sagar; Porob, Seema; Fernandes, Areena; Meena, Ram Murti; Ramaiah, Nagappa

    2014-02-01

    As many as 71 marine bacterial DNA extracts were PCR screened for L-asparaginase (ansA), a key gene in anti-cancer molecular-searches. Over 62% (44) of them were positive for ansA gene. The positive cultures were from genera Bacillus and Staphylococcus. The ansA gene cloned from isolate NIOS4 belonging to recently described Bacillus tequilensis is 1099 bp in length with a 990 bp ORF coding for 329 amino acids. BLASTx analysis revealed this sequence to be 98% similar to earlier reported ansA sequence from B. subtilis (Accession no. NP390239.1). By comparing its deduced amino acid sequence with other bacterial asparaginase sequences six substitutions at positions 305(Thr), 313(Lys), 314(Leu), 315(Asp), 318(Arg), and 320(Gln) are observed. Key residues like Thr(12), Thr(85), Asp(86), Lys(156), and Phe(165) taking part in active-site formation and imparting catalytic properties are conserved. The phylogenetic tree based of the ansA amino acid sequences revealed close relatedness of the NIOS4 ansA sequence with B. subtilis (Accession no. NP 390239.1). It's very close genetic resemblance to B. subtilis and conservation of certain key amino acid residues suggest it as a prospective candidate for evaluation and, production of L-asparaginases.

  20. Error rates, PCR recombination, and sampling depth in HIV-1 whole genome deep sequencing.

    Science.gov (United States)

    Zanini, Fabio; Brodin, Johanna; Albert, Jan; Neher, Richard A

    2016-12-27

    Deep sequencing is a powerful and cost-effective tool to characterize the genetic diversity and evolution of virus populations. While modern sequencing instruments readily cover viral genomes many thousand fold and very rare variants can in principle be detected, sequencing errors, amplification biases, and other artifacts can limit sensitivity and complicate data interpretation. For this reason, the number of studies using whole genome deep sequencing to characterize viral quasi-species in clinical samples is still limited. We have previously undertaken a large scale whole genome deep sequencing study of HIV-1 populations. Here we discuss the challenges, error profiles, control experiments, and computational test we developed to quantify the accuracy of variant frequency estimation.

  1. Using 454 technology for long-PCR based sequencing of the complete mitochondrial genome from single Haemonchus contortus (Nematoda

    Directory of Open Access Journals (Sweden)

    Waeschenbach Andrea

    2008-01-01

    Full Text Available Abstract Background Mitochondrial (mt genomes represent a rich source of molecular markers for a range of applications, including population genetics, systematics, epidemiology and ecology. In the present study, we used 454 technology (or the GS20, massively parallel picolitre reactor platform to determine the complete mt genome of Haemonchus contortus (Nematoda: Trichostrongylidae, a parasite of substantial agricultural, veterinary and economic significance. We validate this approach by comparison with mt sequences from publicly available expressed sequence tag (EST and genomic survey sequence (GSS data sets. Results The complete mt genome of Haemonchus contortus was sequenced directly from long-PCR amplified template utilizing genomic DNA (~20–40 ng from a single adult male using 454 technology. A single contig was assembled and compared against mt sequences mined from publicly available EST (NemBLAST and GSS datasets. The comparison demonstrated that the 454 technology platform is reliable for the sequencing of AT-rich mt genomes from nematodes. The mt genome sequenced for Haemonchus contortus was 14,055 bp in length and was highly AT-rich (78.1%. In accordance with other chromadorean nematodes studied to date, the mt genome of H. contortus contained 36 genes (12 protein coding, 22 tRNAs, rrnL and rrnS and was similar in structure, size and gene arrangement to those characterized previously for members of the Strongylida. Conclusion The present study demonstrates the utility of 454 technology for the rapid determination of mt genome sequences from tiny amounts of DNA and reveals a wealth of mt genomic data in current databases available for mining. This approach provides a novel platform for high-throughput sequencing of mt genomes from nematodes and other organisms.

  2. One-Step Electrochemical Polymerization of Polyaniline Flexible Counter Electrode Doped by Graphene

    Directory of Open Access Journals (Sweden)

    Qi Qin

    2016-01-01

    Full Text Available To improve the photoelectric property of polyaniline (PANI counter electrode using for flexible dye-sensitized solar cell (DSSC, graphene (GN was doped in PANI films covered on flexible conducting substrate by one-step electrochemical method, and then GN/PANI composites are characterized by scanning electron microscope (SEM, fourier transform infrared spectroscopy (FTIR, four probe instrument, and so on. The results show that PANI particles can be electrodeposited on the surface of GN sheets as the potential rising to 2.0 V. This formed unique PANI-GN-PANI lamellar structure owing to the strong interaction of conjugated π electron between GN and PANI results in the superior conductivity and catalytic performance of GN/PANI electrode. The maximum conversion efficiency of dye-sensitized solar cell with this counter electrode reaches 4.31%, which is much higher than that of GN-free PANI counter electrode.

  3. Properties and Microstructure of One-Step Cold Rolled Steel Strip for Shadow Mask

    Institute of Scientific and Technical Information of China (English)

    LIANG Xuan; LI Jun; PENG Ying-hong

    2008-01-01

    The effect of recrystallization annealing temperature on the properties and microstructure of one-step cold rolled steel strip for shadow mask was studied.The results showed that there was no yield point elongation when the tensile tests were performed on the samples for annealing temperatures ranging from 750℃ to 810 ℃.Moreover,increasing annealing temperature resulted in large grains,which was beneficial to the formability and magnetic property of steel strips.On the other hand,when the sample was annealed at 840 ℃,its microstructure showed ununifortuity with 0.04% yield point elongation,which was not good for the function of the shadow mask.Therefore,the proper recrystallization annealing temperature was about 810 ℃ for the present steel strip for shadow mask.

  4. One-step synthesis of magnetic chitosan for controlled release of 5-hydroxytryptophan

    Science.gov (United States)

    Santos Menegucci, Jucély dos; Santos, Mac-Kedson Medeiros Salviano; Dias, Diego Juscelino Santos; Chaker, Juliano Alexandre; Sousa, Marcelo Henrique

    2015-04-01

    In this work, nanoparticles of chitosan embedded with 25% (w/w) of iron oxide magnetic nanoparticles (magnetite/maghemite) with narrow size-distribution and with a loading efficiency of about 80% for 5-hydroxytryptophan (5-HTP), which is a chemical precursor in the biosynthesis of important neurotransmitters as serotonin, were synthesized with an initial mass ratio of 5-HTP/magnetic chitosan=1.2, using homogeneous precipitation by urea decomposition, in an efficient one-step procedure. Characterization of morphology, structure and surface were performed by XRD, TEM, FTIR, TGA, magnetization and zeta potential measurements, while drug loading and drug releasing were investigated using UV-vis spectroscopy. Kinetic drug release experiments under different pH conditions revealed a pH-sensitivecontrolled-release system, ruled by polymer swelling and/or particle dissolution.

  5. ABS polymer electroless plating through a one-step poly(acrylic acid) covalent grafting.

    Science.gov (United States)

    Garcia, Alexandre; Berthelot, Thomas; Viel, Pascal; Mesnage, Alice; Jégou, Pascale; Nekelson, Fabien; Roussel, Sébastien; Palacin, Serge

    2010-04-01

    A new, efficient, palladium- and chromium-free process for the electroless plating of acrylonitrile-butadiene-styrene (ABS) polymers has been developed. The process is based on the ion-exchange properties of poly(acrylic acid) (PAA) chemically grafted onto ABS via a simple and one-step method that prevents using classical surface conditioning. Hence, ABS electroless plating can be obtained in three steps, namely: (i) the grafting of PAA onto ABS, (ii) the copper Cu(0) seeding of the ABS surface, and (iii) the nickel or copper metallization using commercial-like electroless plating bath. IR, XPS, and SEM were used to characterize each step of the process, and the Cu loading was quantified by atomic absorption spectroscopy. This process successfully compares with the commercial one based on chromic acid etching and palladium-based seed layer, because the final metallic layer showed excellent adhesion with the ABS substrate.

  6. One step paired electrochemical synthesis of iron and iron oxide nanoparticles

    Directory of Open Access Journals (Sweden)

    Ordoukhanian Juliet

    2016-09-01

    Full Text Available In this study, a new one step paired electrochemical method is developed for simultaneous synthesis of iron and iron oxide nanoparticles. iron and iron oxide are prepared as cathodic and anodic products from iron (ii sulfate aqueous solution in a membrane divided electrolytic cell by the pulsed current electrosynthesis. Because of organic solvent-free and electrochemical nature of the synthesis, the process could be considered as green and environmentally friendly. The reduction of energy consumption and low cost are the other significant advantages of this new method that would have a great application potential in the chemical industry. The nanostructure of prepared samples was characterized by Fourier transform infrared spectroscopy (FT-IR, X-ray diffraction (XRD, scanning electron microscopy (SEM and transmission electron microscopy (TEM. The magnetic properties were studied by vibrating sample magnetometer (VsM.

  7. One-step Double-layer Thermal Evaporation Method for Organic Light Emitting Diodes

    Science.gov (United States)

    Kee, Y. Y.; Yong, T. K.; Ong, D. S.; Tou, T. Y.

    2011-03-01

    A new one-step double-layer thermal evaporation method was used to fabricate organic light emitting diodes (OLEDs) with device structure of: ITO (anode)/N,N_-diphenyl-N,N_-bis(3-methylphenyl)-1,1_-diphenyl-4,4_-diamine (TPD) /tris-(8-hydroxyquinoline)aluminum(3) (Alq3)/Al (cathode). These OLEDs were fabricated in cleanroom on the ITO-coated glass with a sheet resistivity of 20Ω/sq and an optical transmittance of 90%. The I-V and brightness characteristic showed that the new method could produce better performance achieving lower turn-on voltage (-2V), higher peak current efficiency (+29%) and higher brightness (+36%).

  8. Superlinear/Quadratic One-step Smoothing Newton Method for P0-NCP

    Institute of Scientific and Technical Information of China (English)

    Li Ping ZHANG; Ji Ye HAN; Zheng Hai HUANG

    2005-01-01

    We propose a one-step smoothing Newton method for solving the non-linear complementarity problem with P0-function (P0-NCP) based on the smoothing symmetric perturbed Fisher function (for short, denoted as the SSPF-function). The proposed algorithm has to solve only one linear system of equations and performs only one line search per iteration. Without requiring any strict complementarity assumption at the P0-NCP solution, we show that the proposed algorithm converges globally and superlinearly under mild conditions. Furthermore, the algorithm has local quadratic convergence under suitable conditions. The main feature of our global convergence results is that we do not assume a priori the existence of an accumulation point. Compared to the previous literatures, our algorithm has stronger convergence results under weaker conditions.

  9. One-step preparation of nitrogen-doped graphene nanosheets for high-performance supercapacitors

    Science.gov (United States)

    Gao, Biaofeng; Zhou, Haitao; Yang, Jianhong

    2017-07-01

    Graphene nanosheets (GNs) have been successfully synthesized by one-step carbonization and simultaneous chemical activation of polyaniline (PANI) nanofibers, with large surface area (1759.5 m2 g-1), high pore volume (1.16 cm3 g-1) and a mesopore rich structure (volume in micropore/total ratio, 2.16%). The vital (NDs) become entrapped within a carbon lattice (to form GNs). GNs could be used as an outstanding electrode material for supercapacitors in EMIMBF4 with high cycling stability (more than 73% retention of the initial capacitance after 10,000 cycles). The symmetric supercapacitor has an excellent energy density of 170.2 Wh kg-1 (25 °C) at 0.5 A g-1, with an operating cell voltage of 4.0 V. Meanwhile, oriented activation with polymers of anisotropic geometry might be regarded as a novel process to prepare GNs.

  10. One-Step Facile Synthesis of a Simple Hole Transport Material for Efficient Perovskite Solar Cells

    KAUST Repository

    Chen, Hu

    2016-04-04

    A hole transporting material was designed for use in perovskite solar cells, with a facile one-step synthesis from inexpensive, com-mercially available reagents. The molecule comprises a central fluorinated phenyl core with pendant aryl amines, namely, 3,6-difluoro-N1,N1,N2,N2,N4,N4,N5,N5-octakis(4-methoxyphenyl)benzene-1,2,4,5-tetraamine (DFTAB). A power conversion efficiency of up to 10.4% was achieved in a mesoporous perovskite device architecture. The merits of a simple and potentially low cost syn-thetic route as well as promising performance in perovskite devices, encourages further development of this materials class as new low-cost hole transporting materials for the scale up of perovskite solar cells.

  11. One-Step Fabrication of Microchannels with Integrated Three Dimensional Features by Hot Intrusion Embossing

    Directory of Open Access Journals (Sweden)

    Mike Debono

    2016-11-01

    Full Text Available We build on the concept of hot intrusion embossing to develop a one-step fabrication method for thermoplastic microfluidic channels containing integrated three-dimensional features. This was accomplished with simple, rapid-to-fabricate imprint templates containing microcavities that locally control the intrusion of heated thermoplastic based on their cross-sectional geometries. The use of circular, rectangular and triangular cavity geometries was demonstrated for the purposes of forming posts, multi-focal length microlense arrays, walls, steps, tapered features and three-dimensional serpentine microchannels. Process variables, such as temperature and pressure, controlled feature dimensions without affecting the overall microchannel geometry. The approach was demonstrated for polycarbonate, cycloolefin copolymer and polystyrene, but in principle is applicable to any thermoplastic. The approach is a step forward towards rapid fabrication of complex, robust, microfluidic platforms with integrated multi-functional elements.

  12. Cellulose acetate from oil palm empty fruit bunch via a one step heterogeneous acetylation.

    Science.gov (United States)

    Wan Daud, Wan Rosli; Djuned, Fauzi Muhammad

    2015-11-05

    Acetone soluble oil palm empty fruit bunch cellulose acetate (OPEFB-CA) of DS 2.52 has been successfully synthesized in a one-step heterogeneous acetylation of OPEFB cellulose without necessitating the hydrolysis stage. This has only been made possible by the mathematical modeling of the acetylation process by manipulating the variables of reaction time and acetic anhydride/cellulose ratio (RR). The obtained model was verified by experimental data with an error of less than 2.5%. NMR analysis showed that the distribution of the acetyl moiety among the three OH groups of cellulose indicates a preference at the C6 position, followed by C3 and C2. XRD revealed that OPEFB-CA is highly amorphous with a degree of crystallinity estimated to be ca. 6.41% as determined from DSC. The OPEFB-CA films exhibited good mechanical properties being their tensile strength and Young's modulus higher than those of the commercial CA.

  13. One-step preparation of zeolite silicalite-1 microspheres with adjustable macroporosity

    KAUST Repository

    Hua, Jia

    2009-06-23

    A facile one-step method was developed for the preparation of zeolite silicalite-1 (or ZSM-5) microspheres without the need of pre-synthesizing zeolite nanocrystals. In this method, Pluronic triblock copolymer F127 was added into a homogeneous silicalite-1 synthesis solution. During the hydrothermal synthesis, zeolite nanocrystals (∼ 100 nm) were formed and spontaneously assembled into uniform micrometer-sized (3-5 μm) spheres due to the presence of F127. The obtained microspheres possess significant textual porosity (up to 0.24 cm 3/g), which can be adjusted by simply adding different amounts of styrene in the synthesis. The zeolite microspheres are useful for enzyme immobilization, and the enzyme loading is proportional to the textual porosity. © 2009 American Chemical Society.

  14. One-Step Synthesis and Photoluminescence Eva-luation of Cadmium-containing Quantum Dots

    Institute of Scientific and Technical Information of China (English)

    Nisha Shukla; Michael M Nigra; Abigail D Ondeck

    2012-01-01

    We have developed a simple one-step process for synthesis of ternary quantum dots (ZnCdSe, MgCdSe) with photoluminescence wavelengths ranging from the red to the blue region of the visible spectrum. The primary aim of this work was to develop a synthesis for the preparation of Cd-containing quantum dots using a Cd precursor with lower toxicity than those used in common syntheses. This synthesis makes use of Cd(acac)2 which is significantly less toxic than precursors such as CdO and CdCl2 . We have studied the effect of solvent boiling point, precursors and reaction time on the photoluminescence properties of the ternary quantum dots. Ternary quantum dots synthesized from Cd(acac)2 in low boiling point solvents have photoluminescence wavelengths in the blue region, while those synthesized in high boiling point solvents have photoluminescence wavelengths in the red region.

  15. One-Step Method for Preparation of Magnetic Nanoparticles Coated with Chitosan

    Directory of Open Access Journals (Sweden)

    Karla M. Gregorio-Jauregui

    2012-01-01

    Full Text Available Preparation of magnetic nanoparticles coated with chitosan in one step by the coprecipitation method in the presence of different chitosan concentrations is reported here. Obtaining of magnetic superparamagnetic nanoparticles was confirmed by X-ray diffraction and magnetic measurements. Scanning transmission electron microscopy allowed to identify spheroidal nanoparticles with around 10-11 nm in average diameter. Characterization of the products by Fourier transform infrared spectroscopy demonstrated that composite chitosan-magnetic nanoparticles were obtained. Chitosan content in obtained nanocomposites was estimated by thermogravimetric analysis. The nanocomposites were tested in Pb2+ removal from a PbCl2 aqueous solution, showing a removal efficacy up to 53.6%. This work provides a simple method for chitosan-coated nanoparticles obtaining, which could be useful for heavy metal ions removal from water.

  16. One step effective removal of Congo Red in chitosan nanoparticles by encapsulation

    Science.gov (United States)

    Alver, Erol; Bulut, Mehmet; Metin, Ayşegül Ülkü; Çiftçi, Hakan

    2017-01-01

    Chitosan nanoparticles (CNPs) were prepared with ionotropic gelation between chitosan and tripolyphosphate for the removal of Congo Red. The production of chitosan nanoparticles and the dye removal process was carried out in one-step. The removal efficiency of Congo Red by encapsulation within chitosan from the aqueous solution and its storage stability are examined at different pH values. The influence of some parameters such as the initial dye concentration, pH value of the dye solution, electrolyte concentration, tripolyphosphate concentration, mixing time and speed on the encapsulation is examined. Congo Red removal efficiency and encapsulation capacity of chitosan nanoparticles were determined as above 98% and 5107 mg Congo Red/g chitosan, respectively.

  17. One-step synthesis of highly reduced graphene hydrogels for high power supercapacitor applications

    Science.gov (United States)

    Banda, Harish; Aradilla, David; Benayad, Anass; Chenavier, Yves; Daffos, Barbara; Dubois, Lionel; Duclairoir, Florence

    2017-08-01

    Graphene hydrogels with high electrical conductivity were prepared by a one-step process using hydrazine hydrate as gel assembly agent (GH-HD). Conventional two-step process of gel formation and further reduction to prepare highly conducting gels was replaced by a single step involving equivalent amount of hydrazine. Optimized graphene oxide concentration was established to facilitate such monolith formation. Extensive characterization and control studies enabled understanding of the material properties and gel formation mechanism. The synthesized gel shows a high electrical conductivity of 1141 S/m. The supercapacitor based on GH-HD delivers a high specific capacitance of 190 F/g at a current density of 0.5 A/g and 123 F/g at very high current density of 100 A/g. Furthermore, excellent power capability and cyclic stability were also observed. 3D macroporous morphology of GH-HD makes it ideal for high rate supercapacitor applications.

  18. Centrifuge modeling of one-step outflow tests for unsaturated parameter estimations

    Directory of Open Access Journals (Sweden)

    H. Nakajima

    2006-05-01

    Full Text Available Centrifuge modeling of one-step outflow tests were carried out using a 2-m radius geotechnical centrifuge, and the cumulative outflow and transient pore pressure were measured during the tests at multiple gravity levels. Based on the scaling law of centrifuge modeling, the measurements generally showed reasonable agreement with prototype data calculated from forward simulations with input parameters determined from standard laboratory tests. The parameter optimizations were examined for three different combinations of input data sets using the test measurements. Within the gravity level examined in this study up to 40 g, the optimized unsaturated parameters compared well when accurate pore pressure measurements were included along with cumulative outflow as input data. The centrifuge modeling technique with its capability to implement variety of instrumentations under well controlled initial and boundary conditions, shortens testing time and can provide significant information for the parameter estimation procedure.

  19. Efficient hydrogen evolution in transition metal dichalcogenides via a simple one-step hydrazine reaction

    Science.gov (United States)

    Cummins, Dustin R.; Martinez, Ulises; Sherehiy, Andriy; Kappera, Rajesh; Martinez-Garcia, Alejandro; Schulze, Roland K.; Jasinski, Jacek; Zhang, Jing; Gupta, Ram K.; Lou, Jun; Chhowalla, Manish; Sumanasekera, Gamini; Mohite, Aditya D.; Sunkara, Mahendra K.; Gupta, Gautam

    2016-01-01

    Hydrogen evolution reaction is catalysed efficiently with precious metals, such as platinum; however, transition metal dichalcogenides have recently emerged as a promising class of materials for electrocatalysis, but these materials still have low activity and durability when compared with precious metals. Here we report a simple one-step scalable approach, where MoOx/MoS2 core-shell nanowires and molybdenum disulfide sheets are exposed to dilute aqueous hydrazine at room temperature, which results in marked improvement in electrocatalytic performance. The nanowires exhibit ∼100 mV improvement in overpotential following exposure to dilute hydrazine, while also showing a 10-fold increase in current density and a significant change in Tafel slope. In situ electrical, gate-dependent measurements and spectroscopic investigations reveal that hydrazine acts as an electron dopant in molybdenum disulfide, increasing its conductivity, while also reducing the MoOx core in the core-shell nanowires, which leads to improved electrocatalytic performance. PMID:27282871

  20. Chitosan-Coated Magnetic Nanoparticles with Low Chitosan Content Prepared in One-Step

    Directory of Open Access Journals (Sweden)

    Yolanda Osuna

    2012-01-01

    Full Text Available Chitosan-coated magnetic nanoparticles (CMNP were obtained at 50°C in a one-step method comprising coprecipitation in the presence of low chitosan content. CMNP showed high magnetization and superparamagnetism. They were composed of a core of 9.5 nm in average diameter and a very thin chitosan layer in accordance with electron microscopy measurements. The results from Fourier transform infrared spectrometry demonstrated that CMNP were obtained and those from thermogravimetric analysis allowed to determine that they were composed of 95 wt% of magnetic nanoparticles and 5 wt% of chitosan. 67% efficacy in the Pb+2 removal test indicated that only 60% of amino groups on CMNP surface bound to Pb, probably due to some degree of nanoparticle flocculation during the redispersion. The very low weight ratio chitosan to magnetic nanoparticles obtained in this study, 0.053, and the high yield of the precipitation reactions (≈97% are noticeable.

  1. Ionic liquid-stabilized non-spherical gold nanofluids synthesized using a one-step method.

    Science.gov (United States)

    Zhang, Hao; Cui, Hua; Yao, Shiwei; Zhang, Kelong; Tao, Haikun; Meng, Haibo

    2012-10-23

    Ionic liquid (IL)-stabilized non-spherical gold nanofluids have been synthesized by a one-step method in aqueous solution. The whole reaction proceeded in room temperature. In the presence of amino-functionalized ionic liquids, gold nanofluids with long-wave surface plasmon resonance (SPR) absorption (>600 nm) could be obtained by adopting tannic acid as the reductant. The specific SPR absorption was related to the non-spherical gold nanoparticles including gold triangle, decahedra, and icosahedra nanocrystals. All the nanocrystals were observed by transmission electron microscopy. It was deduced that the formation of non-spherical gold nanofluids was related to the hydroxyls in tannic acid while IL acted as the synthesis template.

  2. One-step GPS for the estimation of temperature-dependent thermal conductivity

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Chein-Shan [Department of Mechanical and Mechatronic Engineering, Taiwan Ocean University, Keelung 202-24 (China)

    2006-08-15

    In this paper we are concerned with the estimation of temperature-dependent thermal conductivity of a one-dimensional inverse heat conduction problem. First, we construct a one-step group-preserving scheme (GPS) for the semi-discretization of quasilinear heat conduction equation, and then derive a quasilinear algebraic equation to determine the unknown thermal conductivity under a given initial temperature and a measured temperature perturbed by noise at time T. The new method does not require any prior information on the functional form of thermal conductivity. Several examples are examined to show that the new approach has high accuracy and efficiency, and the number of iterations spent in solving the quasilinear algebraic equation is smaller than five even in a large temperature range. (author)

  3. One-Step Fabrication of Microchannels with Integrated Three Dimensional Features by Hot Intrusion Embossing

    Science.gov (United States)

    Debono, Mike; Voicu, Dan; Pousti, Mohammad; Safdar, Muhammad; Young, Robert; Kumacheva, Eugenia; Greener, Jesse

    2016-01-01

    We build on the concept of hot intrusion embossing to develop a one-step fabrication method for thermoplastic microfluidic channels containing integrated three-dimensional features. This was accomplished with simple, rapid-to-fabricate imprint templates containing microcavities that locally control the intrusion of heated thermoplastic based on their cross-sectional geometries. The use of circular, rectangular and triangular cavity geometries was demonstrated for the purposes of forming posts, multi-focal length microlense arrays, walls, steps, tapered features and three-dimensional serpentine microchannels. Process variables, such as temperature and pressure, controlled feature dimensions without affecting the overall microchannel geometry. The approach was demonstrated for polycarbonate, cycloolefin copolymer and polystyrene, but in principle is applicable to any thermoplastic. The approach is a step forward towards rapid fabrication of complex, robust, microfluidic platforms with integrated multi-functional elements. PMID:27916849

  4. New one step functionalization of polycrystalline diamond films using amine derivatives

    Energy Technology Data Exchange (ETDEWEB)

    Agnes, Charles; Ruffinatto, Sebastien; Delbarre, Emma; Roget, Andre; Arnault, Jean-Charles; Omnes, Franck; Mailley, Pascal, E-mail: pascal.mailley@cea.fr, E-mail: franck.omnes@grenoble.cnrs.fr

    2010-11-15

    Diamond received tremendous interest for analytical sciences due to its intrinsic properties. However, the analytical perception of chemical environment requires surface functionalization that brings selectivity to the detection event. Thereby, many works focused on diamond modification using chemical or biochemical entities. We proposed here, a new and straightforward methodology for diamond (bio)functionalization. This method involves the chemical reaction between (bio)chemical entities presenting a primary amine moiety, used as grafting site, and hydrogenated diamond surface. This reaction allows in one step to modify diamond surface whatever its doping level and its crystalline quality. The effectiveness of this new method is exposed here through the grafting of one redox species, ferrocene, and of one biochemical, biotin. The impacts of both functionalization duration and pH are investigated and the robustness of the formed bond is demonstrated owing to biotin-avidin coupling.

  5. Centrifuge modeling of one-step outflow tests for unsaturated parameter estimations

    Directory of Open Access Journals (Sweden)

    H. Nakajima

    2006-01-01

    Full Text Available Centrifuge modeling of one-step outflow tests were carried out using a 2-m radius geotechnical centrifuge, and the cumulative outflow and transient pore water pressure were measured during the tests at multiple gravity levels. Based on the scaling laws of centrifuge modeling, the measurements generally showed reasonable agreement with prototype data calculated from forward simulations with input parameters determined from standard laboratory tests. The parameter optimizations were examined for three different combinations of input data sets using the test measurements. Within the gravity level examined in this study up to 40g, the optimized unsaturated parameters compared well when accurate pore water pressure measurements were included along with cumulative outflow as input data. With its capability to implement variety of instrumentations under well controlled initial and boundary conditions and to shorten testing time, the centrifuge modeling technique is attractive as an alternative experimental method that provides more freedom to set inverse problem conditions for the parameter estimation.

  6. One-Step Synthesis of Monodisperse In-Doped ZnO Nanocrystals

    Directory of Open Access Journals (Sweden)

    Wang QingLing

    2010-01-01

    Full Text Available Abstract A method for the synthesis of high quality indium-doped zinc oxide (In-doped ZnO nanocrystals was developed using a one-step ester elimination reaction based on alcoholysis of metal carboxylate salts. The resulting nearly monodisperse nanocrystals are well-crystallized with typically crystal structure identical to that of wurtzite type of ZnO. Structural, optical, and elemental analyses on the products indicate the incorporation of indium into the host ZnO lattices. The individual nanocrystals with cubic structures were observed in the 5% In–ZnO reaction, due to the relatively high reactivity of indium precursors. Our study would provide further insights for the growth of doped oxide nanocrystals, and deepen the understanding of doping process in colloidal nanocrystal syntheses.

  7. Fluorinated alkyne-derived monolayers on oxide-free silicon nanowires via one-step hydrosilylation

    Science.gov (United States)

    Nguyen Minh, Quyen; Pujari, Sidharam P.; Wang, Bin; Wang, Zhanhua; Haick, Hossam; Zuilhof, Han; van Rijn, Cees J. M.

    2016-11-01

    Passivation of oxide-free silicon nanowires (Si NWs) by the formation of high-quality fluorinated 1-hexadecyne-derived monolayers with varying fluorine content has been investigated. Alkyl chain monolayers (C16H30-xFx) with a varying number of fluorine substituents (x = 0, 1, 3, 9, 17) were attached onto hydrogen-terminated silicon (Sisbnd H) surfaces with an effective one-step hydrosilylation. This surface chemistry gives well-defined monolayers on nanowires that have a cylindrical core-shell structure, as characterized by X-ray photoelectron spectroscopy (XPS), Fourier transform infrared spectroscopy (FT-IR) and static contact angle (SCA) analysis. The monolayers were stable under acidic and basic conditions, as well as under extreme conditions (such as UV exposure), and provide excellent surface passivation, which opens up applications in the fields of field effect transistors, optoelectronics and especially for disease diagnosis.

  8. Corrosion Properties of Polydopamine Coatings Formed in One-Step Immersion Process on Magnesium.

    Science.gov (United States)

    Singer, Ferdinand; Schlesak, Magdalena; Mebert, Caroline; Höhn, Sarah; Virtanen, Sannakaisa

    2015-12-09

    Polydopamine layers were polymerized directly from Tris(hydroxymethyl)aminomethane-buffered solution in a one-step immersion process onto magnesium surface. Scanning electron microscopy showed successful formation of a ∼1 μm thick layer. ASTM D3359-09 "Tape test" revealed excellent adhesion of the layer. X-ray induced photoelectron spectroscopy and Fourier transform infrared spectroscopy verified the presence of polydopamine on the surface. Corrosion measurements were performed in 0.1 M NaCl solution investigating the influence of coating parameters: dopamine concentration, immersion time, solution pH, and immersion angle. Tafel analysis revealed strong improvement of corrosion behavior compared to bare magnesium. Polydopamine layers prepared with optimized coating procedure showed promising corrosion properties in Dulbecco's modified Eagle medium. In summary, polydopamine coatings offer a simple treatment for magnesium to improve the corrosion behavior and could further act as intermediate layer for further surface functionalization.

  9. One-step electro-spinning/netting technique for controllably preparing polyurethane nano-fiber/net.

    Science.gov (United States)

    Hu, Juanping; Wang, Xianfeng; Ding, Bin; Lin, Jinyou; Yu, Jianyong; Sun, Gang

    2011-11-01

    Electro-spinning/netting (ESN) as a cutting-edge technique evokes much interest because of its ability in the one-step preparation of versatile nano-fiber/net (NFN) membranes. Here, a controllable fabrication of polyurethane (PU) NFN membranes with attractive structures, consisting of common electrospun nanofibers and two-dimensional (2D) soap bubble-like structured nano-nets via an ESN process is reported. The unique nanoscaled NFN architecture can be finely controlled by regulating the solution properties and several ESN process parameters. The versatile PU nano-nets comprising interlinked nanowires with ultrathin diameters (5-40 nm) mean that the NFN structured membranes possess several excellent characteristics, such as an extremely large specific surface area, high porosity and large stacking density, which would be particularly useful for applications in ultrafiltration, special protective clothing, ultrasensitive sensors, catalyst support and so on.

  10. Shape-control and characterization of iron nanocrystals prepared via a one-step solvothermal method

    Science.gov (United States)

    Fan, Junmei; Cao, Yuebin; Yuan, Fangli

    2015-12-01

    In the present work, iron nanocubes, nanorods and nanowires are successfully synthesized by one-step reduction approach in a solvothermal environment. It is analyzed that the iron nanocubes, nanorods and nanowires belong to the pure body-centered cubic structure of α-Fe. Effects of additive sort and the amount of Anionic Gemini surfactant 12-4-12 on the morphology evolution of Fe are discussed based on SEM and TEM images. The possible formation mechanisms of iron nanocubes, nanorods and nanowires are proposed. The Anionic Gemini surfactant 12-4-12 regarded as template plays an important role in the formation of iron nanocrystals. The microwave electromagnetic (EM) (80 wt% Fe) and calculated microwave-absorbing (0.5 mm thickness) properties in 2-18 GHz of the iron nanocubes, nanorods and nanowires are studied systematically. Results show that iron nanowires are superior to nanorods and nanocubes, which indicates the potential to be a super-thin microwave absorber.

  11. One-step Patterning of Sub-wavelength Plasmonic Gratings in Metal-Polymer Composites

    CERN Document Server

    Chaudhary, Raghvendra P; Jaiswal, Arun; Hawal, Suyog R; Saxena, Sumit; Shukla, Shobha

    2016-01-01

    2D and 3D micro/nano fabrication based on two-photon polymerization (TPP) has emerged as a strong contender for additive manufacturing for wide variety of applications. In this manuscript we report one step patterning of structurally stable, subwavelength 2D and 3D gold nanostructures using femto-second laser by incorporating single photon photoinitiator only in pure and metal precursor doped polymers. The metal polymer composite nanostructures are written directly by in-situ reduction of gold precursor within the photoresist using femto-second laser irradiation. The photo-initiator triggers the reduction of gold precursor and induces simultaneous polymerization of the photoresist based on two-photon absorption phenomenon. Diffraction gratings with varied loading of gold precursors in photoresist have been fabricated and characterized by measuring their diffraction efficiencies in the infrared region. Minimum line width of 390 nm has been achieved for 5 wt% gold loaded polymers. Systematic studies of the effe...

  12. One-step reduced kinetics for lean hydrogen-air deflagration

    Energy Technology Data Exchange (ETDEWEB)

    Fernandez-Galisteo, D.; Sanchez, A.L. [Area de Mecanica de Fluidos, Univ. Carlos III de Madrid, Leganes 28911 (Spain); Linan, A. [ETSI Aeronauticos, Pl. Cardenal Cisneros 3, Madrid 28040 (Spain); Williams, F.A. [Dept. of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA 92093-0411 (United States)

    2009-05-15

    A short mechanism consisting of seven elementary reactions, of which only three are reversible, is shown to provide good predictions of hydrogen-air lean-flame burning velocities. This mechanism is further simplified by noting that over a range of conditions of practical interest, near the lean flammability limit all reaction intermediaries have small concentrations in the important thin reaction zone that controls the hydrogen-air laminar burning velocity and therefore follow a steady state approximation, while the main species react according to the global irreversible reaction 2H{sub 2} + O{sub 2} {yields} 2H{sub 2}O. An explicit expression for the non-Arrhenius rate of this one-step overall reaction for hydrogen oxidation is derived from the seven-step detailed mechanism, for application near the flammability limit. The one-step results are used to calculate flammability limits and burning velocities of planar deflagrations. Furthermore, implications concerning radical profiles in the deflagration and reasons for the success of the approximations are clarified. It is also demonstrated that adding only two irreversible direct recombination steps to the seven-step mechanism accurately reproduces burning velocities of the full detailed mechanism for all equivalence ratios at normal atmospheric conditions and that an eight-step detailed mechanism, constructed from the seven-step mechanism by adding to it the fourth reversible shuffle reaction, improves predictions of O and OH profiles. The new reduced-chemistry descriptions can be useful for both analytical and computational studies of lean hydrogen-air flames, decreasing required computation times. (author)

  13. Nanotexturing of Conjugated Polymers via One-Step Maskless Oxygen Plasma Etching for Enhanced Tunable Wettability.

    Science.gov (United States)

    Jiang, Youhua; Xu, Jian; Lee, Junghoon; Du, Ke; Yang, Eui-Hyeok; Moon, Myoung-Woon; Choi, Chang-Hwan

    2017-07-11

    A one-step maskless oxygen plasma etching process is investigated to nanopattern conjugated polymer dodecylbenzenesulfonate doped polypyrrole (PPy(DBS)) and to examine the effects of nanostructures on the inherent tunable wettability of the surface and the droplet mobility. Etching characteristics such as the geometry and dimensions of the nanostructures are systematically examined for the etching power and duration. The mechanism of self-formation of vertically aligned dense-array pillared nanostructures in the one-step maskless oxygen plasma etching process is also investigated. Results show that lateral dimensions such as the periodicity and diameter of the pillared nanostructures are insensitive to the etching power and duration, whereas the length and aspect ratio of the nanostructures increase with them. X-ray photoelectron spectroscopy analysis and thermal treatment of the polymer reveal that the codeposition of impurities on the surface resulting from the holding substrate is the primary reason for the self-formation of nanostructures during the oxygen plasma etching, whereas the local crystallinity subject to thermal treatment has a minor effect on the lateral dimensions. Retaining the tunable wettability (oleophobicity) for organic droplets during the electrochemical redox (i.e., reduction and oxidization) process, the nanotextured PPy(DBS) surface shows significant enhancement of droplet mobility compared to that of the flat PPy(DBS) surface with no nanotexture by making the surface superoleophobic (i.e., in a Cassie-Baxter wetting state). Such enhancement of the tunable oleophobicity and droplet mobility of the conjugated polymer will be of great significance in many applications such as microfluidics, lab-on-a-chip devices, and water/oil treatment.

  14. One-step green synthesis of bimetallic Fe/Pd nanoparticles used to degrade Orange II

    Energy Technology Data Exchange (ETDEWEB)

    Luo, Fang; Yang, Die; Chen, Zuliang, E-mail: zuliang.chen@newcastle.edu.au; Megharaj, Mallavarapu; Naidu, Ravendra

    2016-02-13

    Highlights: • Green synthesis of bimetallic Fe/Pd NPs was firstly reported using the one-step method. • 98.0% of Orange II was removed by Fe/Pd NPs, but only 16.0% by Fe NPs. • Fe/Pd NPs with a diameter ranging from 10 to 100 nm were observed. • Removing Orange II using Fe/Pd NPs involved both adsorption and catalytic degradation. - Abstract: To reduce cost and enhance reactivity, bimetallic Fe/Pd nanoparticles (NPs) were firstly synthesized using grape leaf aqueous extract to remove Orange II. Green synthesized bimetallic Fe/Pd NPs (98.0%) demonstrated a far higher ability to remove Orange II in 12 h compared to Fe NPs (16.0%). Meanwhile, all precursors, e.g., grape leaf extract, Fe{sup 2+} and Pd{sup 2+}, had no obvious effect on removing Orange II since less than 2.0% was removed. Kinetics study revealed that the removal rate fitted well to the pseudo-first-order reduction and pseudo-second-order adsorption model, meaning that removing Orange II via Fe/Pd NPs involved both adsorption and catalytic reduction. The remarkable stability of Fe/Pd NPs showed the potential application for removing azo dyes. Furthermore, Scanning Electron Microscopy (SEM) and Fourier Transform Infrared Spectroscopy (FTIR) confirmed the changes in Fe/Pd NPs before and after reaction with Orange II. High Performance Liquid Chromatography–Mass Spectrum (HPLC–MS) identified the degraded products in the removal of Orange II, and finally a removal mechanism was proposed. This one-step strategy using grape leaf aqueous extract to synthesize Fe/Pd NPs is simple, cost-effective and environmentally benign, making possible the large-scale production of Fe/Pd NPs for field remediation.

  15. Facile one-step fabrication of magnetite particles under mild hydrothermal conditions

    Energy Technology Data Exchange (ETDEWEB)

    Keerthana, D. Shanthini; Namratha, K. [Centre for Materials Science and Technology, Vijnana Bhavan, University of Mysore, Manasagangothri, Mysore 6 (India); Byrappa, K., E-mail: kbyrappa@gmail.com [Centre for Materials Science and Technology, Vijnana Bhavan, University of Mysore, Manasagangothri, Mysore 6 (India); Yathirajan, H.S. [Centre for Materials Science and Technology, Vijnana Bhavan, University of Mysore, Manasagangothri, Mysore 6 (India); DOS in Chemistry, University of Mysore, Manasagangothri, Mysore 6 (India)

    2015-03-15

    Hydrophilic magnetite particles for biological applications were synthesized by hydrothermal method in the presence of D-Glucose as both reducing and capping agent in a facile, one-step, low energy and environmentally friendly route. The role of D-Glucose as a reducing agent in the formation of magnetite particles under mild hydrothermal conditions has been investigated. The absence of D-Glucose results in the formation of hematite. The magnetite particles synthesized were characterized using powder X-ray Diffraction (XRD), Fourier Transform Infrared (FTIR) Spectroscopy, High Resolution Scanning Electron Microscopy (HR-SEM), Dynamic Light Scattering (DLS) and Vibrating Sample Magnetometery (VSM). The influence of the quantity of D-Glucose used and the reaction duration on the formation of magnetite were studied. DLS and HR-SEM results show that the size of the particles was in nano- to micron range. The antioxidant potency of the particles was confirmed using DPPH assay, where 2,2- Diphenyl-1-picrylhydrazyl was used as a source of free radicals. Hence the magnetite particles obtained could be considered for the use in various biological applications. - Highlights: • Magnetite and hematite particles were synthesized using hydrothermal route. • The reactants and experimental parameters were optimized to get single phase magnetite particles. • The role of D-Glucose as a reducing and capping agent is discussed. • The magnetite particles showed very good free radical scavenging ability. • The authors report a simple, facile, one-step method using hydrated ferric salt as a single iron precursor.

  16. Recombinant Passenger Proteins Can Be Conveniently Purified by One-Step Affinity Chromatography.

    Directory of Open Access Journals (Sweden)

    Hua-zhen Wang

    Full Text Available Fusion tag is one of the best available tools to date for enhancement of the solubility or improvement of the expression level of recombinant proteins in Escherichia coli. Typically, two consecutive affinity purification steps are often necessitated for the purification of passenger proteins. As a fusion tag, acyl carrier protein (ACP could greatly increase the soluble expression level of Glucokinase (GlcK, α-Amylase (Amy and GFP. When fusion protein ACP-G2-GlcK-Histag and ACP-G2-Amy-Histag, in which a protease TEV recognition site was inserted between the fusion tag and passenger protein, were coexpressed with protease TEV respectively in E. coli, the efficient intracellular processing of fusion proteins was achieved. The resulting passenger protein GlcK-Histag and Amy-Histag accumulated predominantly in a soluble form, and could be conveniently purified by one-step Ni-chelating chromatography. However, the fusion protein ACP-GFP-Histag was processed incompletely by the protease TEV coexpressed in vivo, and a large portion of the resulting target protein GFP-Histag aggregated in insoluble form, indicating that the intracellular processing may affect the solubility of cleaved passenger protein. In this context, the soluble fusion protein ACP-GFP-Histag, contained in the supernatant of E. coli cell lysate, was directly subjected to cleavage in vitro by mixing it with the clarified cell lysate of E. coli overexpressing protease TEV. Consequently, the resulting target protein GFP-Histag could accumulate predominantly in a soluble form, and be purified conveniently by one-step Ni-chelating chromatography. The approaches presented here greatly simplify the purification process of passenger proteins, and eliminate the use of large amounts of pure site-specific proteases.

  17. Recombinant Passenger Proteins Can Be Conveniently Purified by One-Step Affinity Chromatography.

    Science.gov (United States)

    Wang, Hua-zhen; Chu, Zhi-zhan; Chen, Chang-chao; Cao, Ao-cheng; Tong, Xin; Ouyang, Can-bin; Yuan, Qi-hang; Wang, Mi-nan; Wu, Zhong-kun; Wang, Hai-hong; Wang, Sheng-bin

    2015-01-01

    Fusion tag is one of the best available tools to date for enhancement of the solubility or improvement of the expression level of recombinant proteins in Escherichia coli. Typically, two consecutive affinity purification steps are often necessitated for the purification of passenger proteins. As a fusion tag, acyl carrier protein (ACP) could greatly increase the soluble expression level of Glucokinase (GlcK), α-Amylase (Amy) and GFP. When fusion protein ACP-G2-GlcK-Histag and ACP-G2-Amy-Histag, in which a protease TEV recognition site was inserted between the fusion tag and passenger protein, were coexpressed with protease TEV respectively in E. coli, the efficient intracellular processing of fusion proteins was achieved. The resulting passenger protein GlcK-Histag and Amy-Histag accumulated predominantly in a soluble form, and could be conveniently purified by one-step Ni-chelating chromatography. However, the fusion protein ACP-GFP-Histag was processed incompletely by the protease TEV coexpressed in vivo, and a large portion of the resulting target protein GFP-Histag aggregated in insoluble form, indicating that the intracellular processing may affect the solubility of cleaved passenger protein. In this context, the soluble fusion protein ACP-GFP-Histag, contained in the supernatant of E. coli cell lysate, was directly subjected to cleavage in vitro by mixing it with the clarified cell lysate of E. coli overexpressing protease TEV. Consequently, the resulting target protein GFP-Histag could accumulate predominantly in a soluble form, and be purified conveniently by one-step Ni-chelating chromatography. The approaches presented here greatly simplify the purification process of passenger proteins, and eliminate the use of large amounts of pure site-specific proteases.

  18. One-step chromatographic purification of Helicobacter pylori neutrophil-activating protein expressed in Bacillus subtilis.

    Directory of Open Access Journals (Sweden)

    Kuo-Shun Shih

    Full Text Available Helicobacter pylori neutrophil-activating protein (HP-NAP, a major virulence factor of Helicobacter pylori (H. pylori, is capable of activating human neutrophils to produce reactive oxygen species (ROS and secrete inammatory mediators. HP-NAP is a vaccine candidate, a possible drug target, and a potential in vitro diagnostic marker for H. pylori infection. HP-NAP has also been shown to be a novel therapeutic agent for the treatment of allergic asthma and bladder cancer. Hence, an efficient way to obtain pure HP-NAP needs to be developed. In this study, one-step anion-exchange chromatography in negative mode was applied to purify the recombinant HP-NAP expressed in Bacillus subtilis (B. subtilis. This purification technique was based on the binding of host cell proteins and/or impurities other than HP-NAP to DEAE Sephadex resins. At pH 8.0, almost no other proteins except HP-NAP passed through the DEAE Sephadex column. More than 60% of the total HP-NAP with purity higher than 91% was recovered in the flow-through fraction from this single-step DEAE Sephadex chromatography. The purified recombinant HP-NAP was further demonstrated to be a multimeric protein with a secondary structure of α-helix and capable of activating human neutrophils to stimulate ROS production. Thus, this one-step negative chromatography using DEAE Sephadex resin can efficiently yield functional HP-NAP from B. subtilis in its native form with high purity. HP-NAP purified by this method could be further utilized for the development of new drugs, vaccines, and diagnostics for H. pylori infection.

  19. One-step surgical placement of Brånemark implants: a prospective multicenter clinical study.

    Science.gov (United States)

    Becker, W; Becker, B E; Israelson, H; Lucchini, J P; Handelsman, M; Ammons, W; Rosenberg, E; Rose, L; Tucker, L M; Lekholm, U

    1997-01-01

    This prospective longitudinal multicenter study evaluated the clinical outcomes after placement and restoration of one-step Brånemark implants into the maxillae and mandibles of completely and partially edentulous patients. Six surgical treatment centers participated in this study, in which 135 implants were placed into 63 adult patients. All implants were stable after placement. The majority of implants were placed into type B bone with minimal jaw resorption and type 2 bone quality. After implant placement, standard transmucosal healing abutments were firmly placed. The average amount of time between implant placement and prosthetic abutment connection was 170 days in the maxillae and 147 days in the mandibles. To evaluate crestal bone changes caused by implant placement, a periodontal probe was used to measure midbuccally from the top of the implant cylinder to the alveolar crest; in 29 patients, 54 midbuccal bone crest sites were remeasured following prosthetic abutment connection. Crestal bone changes in mandibles and maxillae were statistically and clinically insignificant. Six implants were lost prior to loading and one implant has not been restored. No implants or restorations were lost after loading. At 1 year, the implant success rate was 95.6%. Mesiodistal radiographic measurements from 34 patients were averaged, and changes from prosthetic abutment connection to, on average, 12 months follow-up were compared. The radiographs, which were digitalized, measured from the bottom of the implant cylinder to the most coronal bone in contact with implant thread. For mandibular implants, the mean radiographic bone level at prosthetic abutment connection was 1.07 mm; after loading, it was 1.35 mm. For maxillary implants, the mean radiographic bone height at prosthetic abutment connection was 1.16 mm; after loading, it was 1.36 mm. These changes were not statistically significant. The 1-year outcomes from this patient series indicate that one-step Br

  20. Development of a rapid, one-step screening method for the isolation of presumptive proteolytic enterococci.

    Science.gov (United States)

    Graham, Ken; Rea, Rosemary; Simpson, Paul; Stack, Helena

    2017-01-01

    Enterococci show higher proteolytic activities than other lactic acid bacteria and thus have received considerable attention in scientific literature in recent years. Proteolytic enzymes of enterococci have warranted the use of some species as starter, adjuncts or protective cultures and as probiotics, while in some strains they have also been linked with virulence. Consequently, the isolation and identification of proteolytic enterococci is becoming of increasing interest and importance. However, current screening methods for proteolytic enterococci can be time consuming, requiring a two-step procedure which may take up to 96h. This study describes a method, utilising Kanamycin Skim Milk Aesculin Azide (KSMEA) agar, for the isolation of proteolytic enterococci in one-step, thereby significantly reducing screening time. KSMEA combines the selective properties of Kanamycin Aesculin Azide Agar (KAA) with skim milk powder for the detection of proteolytic enterococci. Enterococci produced colonies with a black halo on KSMEA which were accompanied by a zone of clearing in the media when enterococci were proteolytic. KSMEA medium retained the selectivity of KAA, while proteolytic enterococci were easily distinguished from non-proteolytic enterococci when two known strains were propagated on KSMEA. KSMEA also proved effective at isolating and detecting enterococci in raw milk, faeces and soil. Isolates recovered from the screen were confirmed as enterococci using genus-specific primers. Proteolytic enterococci were present in the raw milk sample only and were easily distinguishable from non-proteolytic enterococci and other microorganisms. Therefore, KSMEA provides a rapid, one-step screening method for the isolation of presumptive proteolytic enterococci.

  1. Simple, multiplexed, PCR-based barcoding of DNA enables sensitive mutation detection in liquid biopsies using sequencing.

    Science.gov (United States)

    Ståhlberg, Anders; Krzyzanowski, Paul M; Jackson, Jennifer B; Egyud, Matthew; Stein, Lincoln; Godfrey, Tony E

    2016-06-20

    Detection of cell-free DNA in liquid biopsies offers great potential for use in non-invasive prenatal testing and as a cancer biomarker. Fetal and tumor DNA fractions however can be extremely low in these samples and ultra-sensitive methods are required for their detection. Here, we report an extremely simple and fast method for introduction of barcodes into DNA libraries made from 5 ng of DNA. Barcoded adapter primers are designed with an oligonucleotide hairpin structure to protect the molecular barcodes during the first rounds of polymerase chain reaction (PCR) and prevent them from participating in mis-priming events. Our approach enables high-level multiplexing and next-generation sequencing library construction with flexible library content. We show that uniform libraries of 1-, 5-, 13- and 31-plex can be generated. Utilizing the barcodes to generate consensus reads for each original DNA molecule reduces background sequencing noise and allows detection of variant alleles below 0.1% frequency in clonal cell line DNA and in cell-free plasma DNA. Thus, our approach bridges the gap between the highly sensitive but specific capabilities of digital PCR, which only allows a limited number of variants to be analyzed, with the broad target capability of next-generation sequencing which traditionally lacks the sensitivity to detect rare variants.

  2. Differential diagnosis of Trichostrongylus and hookworm eggs via PCR using ITS-1 sequence

    OpenAIRE

    Yong, Tai-Soon; Lee, Jong-Ho; Sim, Seobo; Lee, Jongweon; Min, Duk-Young; Chai, Jong-Yil; Eom, Keeseon S.; Sohn, Woon-Mok; Lee, Soon-Hyung; Rim, Han-Jong

    2007-01-01

    Trichostrongylus eggs observed in cellophane-thick smears are difficult, in practice, to distinguish from hookworm eggs. In order to overcome these limitations, a molecular approach was conducted. A Trichostrongylus colubriformis adult worm was obtained from a human in Laos, which was identified morphologically. ITS-1 sequence of this worm was determined, and found to be most similar with that of T. colubriformis among the Trichostrongylus spp. reported so far. Then, this sequence was compare...

  3. Supported PCR: an efficient procedure to amplify sequences flanking a known DNA segment

    OpenAIRE

    Rudenko, George N.; Rommens, Caius M.T.; Nijkamp, H. John J.; Hille, Jacques

    1993-01-01

    We describe a novel modification of the polymerase chain reaction for efficient in vitro amplification of genomic DNA sequences flanking short stretches of known sequence. The technique utilizes a target enrichment step, based on the selective isolation of biotinylated fragments from the bulk of genomic DNA on streptavidin-containing support. Subsequently, following ligation with a second universal linker primer, the selected fragments can be amplified to amounts suitable for further molecula...

  4. Island rescue PCR: a rapid and efficient method for isolating transcribed sequences from yeast artificial chromosomes and cosmids.

    Science.gov (United States)

    Valdes, J M; Tagle, D A; Collins, F S

    1994-06-07

    The identification of transcripts from large genomic regions cloned in yeast artificial chromosomes (YACs) or cosmids continues to be a critical and often rate-limiting step in positional cloning of human disease genes. We have developed a PCR-based method for rapid and efficient generation of probes from YACs or cosmids that can be used for cDNA library screening. The method, which we call island rescue PCR (IRP), is based upon the observation that the 5' ends of many genes are associated with (G+C)-rich regions called CpG islands. In IRP, the YAC of interest is digested with a restriction enzyme that recognizes sequences of high CpG content, and vectorette linkers are ligated to the cleaved ends. The PCR is used to amplify the region extending from the cleaved restriction enzyme site to the nearest SINE (Alu) repeat. In many cases this product contains sequences from the 5' end of the associated gene. cDNA clones isolated with these products are then verified by mapping them back to the original YAC. The method allows rapid screening of > 500 kb of human genomic insert in one experiment, is tolerant of contaminating yeast sequences, and can also be applied to cosmid pools. In a control experiment, the method was able to identify cDNA clones for the neurofibromatosis type 1 (NF1) gene using a probe generated from a YAC in the region. Application of IRP has yielded nine other genes from YACs isolated from chromosome locations 4p16.3 and 17q21.

  5. 应用一步PCR法检测并鉴定马疱疹病毒1型和4型%Detection and Identification of Equine Herpesvirus-1 and -4 by One-step Polymerase Chain Reaction

    Institute of Scientific and Technical Information of China (English)

    易新萍; 单文鲁; 冉多良; 王宁; 岳城; 恩特马克

    2001-01-01

    A rapid method for detection and identification of equineherpesvirus-1 (EHV-1) and equine herpesvirus-4 (EHV-4) was developed using polymerase chain reaction (PCR). Primers for PCR were designed based on nucleotide sequences of glycoprotein B genes of EHV-1 and EHV-4 to amplify specific regions for EHV-1 or EHV-4 or a common region of both viruses. By using type specific primers, amplified fragments were identified as EHV-1 or EHV-4 in a one-step reaction. We have applied this technique to specimens from abortive fetuses of Przewalskii horse in Xinjiang. The results indicate that PCR can be used for rapid, sensitive and specific detection and identification of EHV-1 and EHV-4. Furthermore, EHV-1 and EHV-4 can be clearly distiguished in a one-step PCR reaction. It provides a new apporach for the diagnosis of the two virus types in future.%聚合酶链反应(PCR)可作为一种快速检测并鉴别马疱疹病毒1型(EHV-1)和马疱疹病毒4型(EHV-4)的诊断方法。PCR引物是根据编码EHV-1和EHV-4的糖蛋白B(gB)基因上的共有的核苷酸序列或型特有的核苷酸序列设计的。利用这两种病毒的型特异性混合引物,在一步PCR反应中检测并鉴别EHV-1和EHV-4,而同一疱疹病毒科的单纯疱疹病毒1型(HSV-1)、伪狂犬病毒(PRV)、马立克氏病病毒(MDV)均无特异性扩增。应用建立的PCR方法检测了普氏野马流产胎儿病料,实验结果表明,这种PCR方法是一种直接检测并鉴定EHV-1和EHV-4的快速、敏感的诊断方法,同时,它可在一步PCR反应中直接鉴别这两种病毒,可用于病料中EHV-1和EHV-4检测的初步筛选。

  6. Development of a One-Step Probe Based Molecular Assay for Rapid Immunodiagnosis of Infection with M. tuberculosis Using Dried Blood Spots

    DEFF Research Database (Denmark)

    Blauenfeldt, Thomas; Heyckendorf, Jan; Graff Jensen, Sidse

    2014-01-01

    %, p = ns.). CONCLUSION: We developed a rapid, robust and accurate molecular immunodiagnostic test for M. tuberculosis infection. By combining DBS based sample acquisition, mail or currier based sample transport with centralized molecular detection, this immunodiagnostic test concept can reduce...... detection. AIM: To develop a robust IP-10 based molecular assay for the diagnosis of infection with M. tubercuolsis from whole blood and DBS. METHOD: We developed a one-step probe based multiplex RT-qPCR assay for detecting IP-10 and IFN-γ mRNA expression from whole blood and DBS samples. The assay...

  7. An efficient and more sustainable one-step continuous-flow multicomponent synthesis approach to chromene derivatives

    Science.gov (United States)

    A simple and rapid one-step continuous-flow synthesis route has been developed for the preparation of chromene derivatives from the reaction of aromatic aldehydes, α-cyanomethylene compounds and naphthols. In this contribution, a one-step continuous-flow protocol in a continuous ...

  8. Simple and reliable procedure for PCR amplification of genomic DNA from yeast cells using short sequencing primers

    DEFF Research Database (Denmark)

    Haaning, J; Oxvig, C; Overgaard, Michael Toft;

    1997-01-01

    Yeast is widely used in molecular biology. Heterologous expression of recombinant proteins in yeast involves screening of a large number of recombinants. We present an easy and reliable procedure for amplifying genomic DNA from freshly grown cells of the methylotrophic yeast Pichia pastoris...... by means of PCR without any prior DNA purification steps. This method involves a simple boiling step of whole yeast cells in the presence of detergent, and subsequent amplification of genomic DNA using short sequencing primers in a polymerase chain reaction assay with a decreasing annealing temperature...

  9. One-step cell lysis suitable for quantitative bacteria detection in inhibitor-laden sands

    Science.gov (United States)

    Lim, Hyun Jeong; Choi, Jung-Hyun; Son, Ahjeong

    2015-04-01

    Complexity and heterogeneity of soils often hinder effective DNA extraction from the soil matrix. In particular, conventional DNA extraction techniques require extensive purification which makes DNA extraction time-consuming and labor-intensive. Other drawbacks include lower recovery yield, degradation, and damage of DNA, which are also caused by intensive purifications during DNA extraction. Therefore a rapid and simple and yet effective DNA pretreatment method is preferred for environmental monitoring and screening. This study has evaluated the feasibility of simple physical pretreatment for effective cell lysis of bacteria in sands. Bead beating method was selected as an effective physical cell lysis method in this study. We examined the capability of this physical lysis for Pseudomonas putida seeded sands without additional chemical purification steps. The lysate from the method was analysed by the quantitative polymerase chain reaction (qPCR) assay and subsequently compared to that by commercial DNA extraction kit. The best lysis condition (treatment with 0.1 mm glass beads at 3000 rpm for 3 minutes) was selected. The qPCR results of bead beating treated samples showed the better performance than that of conventional DNA extraction kit. Moreover, the qPCR assay was performed to the sands laden with qPCR inhibitors (humic acids, clay, and magnesium), which generally present in environmental samples. Further experiments with the sands containing less than 10 μg/g of humic acids and 70% of clay showed successful quantification results of qPCR assay. In conclusion, the bead beating method is useful for simplified DNA extraction prior to qPCR analysis for sand samples of particular composition. It is expected that this approach will be beneficial for environmental in-situ analysis or immediate pre-screening. It also provides the groundwork for future studies with real soil samples that have various physico-chemical properties.

  10. An isothermal, label-free, and rapid one-step RNA amplification/detection assay for diagnosis of respiratory viral infections.

    Science.gov (United States)

    Koo, Bonhan; Jin, Choong Eun; Lee, Tae Yoon; Lee, Jeong Hoon; Park, Mi Kyoung; Sung, Heungsup; Park, Se Yoon; Lee, Hyun Jung; Kim, Sun Mi; Kim, Ji Yeun; Kim, Sung-Han; Shin, Yong

    2017-04-15

    Recently, RNA viral infections caused by respiratory viruses, such as influenza, parainfluenza, respiratory syncytial virus, coronavirus, and Middle East respiratory syndrome-coronavirus (MERS-CoV), and Zika virus, are a major public health threats in the world. Although myriads of diagnostic methods based on RNA amplification have been developed in the last decades, they continue to lack speed, sensitivity, and specificity for clinical use. A rapid and accurate diagnostic method is needed for appropriate control, including isolation and treatment of the patients. Here, we report an isothermal, label-free, one-step RNA amplification and detection system, termed as iROAD, for the diagnosis of respiratory diseases. It couples a one-step isothermal RNA amplification method and a bio-optical sensor for simultaneous viral RNA amplification/detection in a label-free and real-time manner. The iROAD assay offers a one-step viral RNA amplification/detection example to rapid analysis (<20min). The detection limit of iROAD assay was found to be 10-times more sensitive than that of real-time reverse transcription-PCR method. We confirmed the clinical utility of the iROAD assay by detecting viral RNAs obtained from 63 human respiratory samples. We envision that the iROAD assay will be useful and potentially adaptable for better diagnosis of emerging infectious diseases including respiratory diseases.

  11. Sequence variations in C9orf72 downstream of the hexanucleotide repeat region and its effect on repeat-primed PCR interpretation

    DEFF Research Database (Denmark)

    Nordin, Angelica; Akimoto, Chizuru; Wuolikainen, Anna

    2017-01-01

    -PCR data. Our objective was to determine the properties of these sequence variations with regard to prevalence, the range of variation, and effect on disease prognosis. We screened a multi-national cohort (n = 6981) for the HREM and samples with deviant RP-PCR curves were identified. The deviant samples...

  12. Comparison of amplicon-sequencing, pyrosequencing and real-time PCR for detection of YMDD mutants in patients with chronic hepatitis B

    Institute of Scientific and Technical Information of China (English)

    Zhi-Jun Yang; Mei-Zeng Tu; Jian Liu; Xiao-Ling Wang; Hong-Zhi Jin

    2006-01-01

    AIM: To compare the sequencing of PCR products, pyrosequencing, and real-time PCR for detection of Tyrosinemethionine-aspartate-aspartate (YMDD) mutants in patients with chronic hepatitis B.METHODS: Mixtures of plasmids and serum samples from 69 chronic hepatitis B patients treated with lamivudine were tested for YMDD mutations by sequencing of PCR products, pyrosequencing, and real-time PCR, respectively. Time required and reagent costs of the three assays were evaluated.RESULTS: Real-time PCR detected 100%, 50%, 10%,1% and 0.1% of YVDD plasmid in mixtures with 106 copies/mL of YMDD plasmid, whereas sequencing and pyrosequencing only detected 100% and 50% of YVDD plasmid in aliquots of the corresponding mixtures. Completely concordant results were obtained from 60 (87%)out of the 69 clinical serum samples by the three assays.Mutants were detected by real-time PCR in less than 20% of the total virus population, but no mutant was detected by sequencing and pyrosequencing. In addition,real-time PCR required less time and was more cost-effective than the other two assays. However, throughput of pyrosequencing was the highest.CONCLUSION: Among the three assays compared,real-time PCR is the most sensitive, cost-effective, and time saving for monitoring YMDD mutants in patients with chronic hepatitis B on lamivudine therapy.

  13. Changes in human fecal microbiota due to chemotherapy analyzed by TaqMan-PCR, 454 sequencing and PCR-DGGE fingerprinting.

    Directory of Open Access Journals (Sweden)

    Jutta Zwielehner

    Full Text Available BACKGROUND: We investigated whether chemotherapy with the presence or absence of antibiotics against different kinds of cancer changed the gastrointestinal microbiota. METHODOLOGY/PRINCIPAL FINDINGS: Feces of 17 ambulant patients receiving chemotherapy with or without concomitant antibiotics were analyzed before and after the chemotherapy cycle at four time points in comparison to 17 gender-, age- and lifestyle-matched healthy controls. We targeted 16S rRNA genes of all bacteria, Bacteroides, bifidobacteria, Clostridium cluster IV and XIVa as well as C. difficile with TaqMan qPCR, denaturing gradient gel electrophoresis (DGGE fingerprinting and high-throughput sequencing. After a significant drop in the abundance of microbiota (p = 0.037 following a single treatment the microbiota recovered within a few days. The chemotherapeutical treatment marginally affected the Bacteroides while the Clostridium cluster IV and XIVa were significantly more sensitive to chemotherapy and antibiotic treatment. DGGE fingerprinting showed decreased diversity of Clostridium cluster IV and XIVa in response to chemotherapy with cluster IV diversity being particularly affected by antibiotics. The occurrence of C. difficile in three out of seventeen subjects was accompanied by a decrease in the genera Bifidobacterium, Lactobacillus, Veillonella and Faecalibacterium prausnitzii. Enterococcus faecium increased following chemotherapy. CONCLUSIONS/SIGNIFICANCE: Despite high individual variations, these results suggest that the observed changes in the human gut microbiota may favor colonization with C. difficile and Enterococcus faecium. Perturbed microbiota may be a target for specific mitigation with safe pre- and probiotics.

  14. One-step detection of circulating tumor cells in ovarian cancer using enhanced fluorescent silica nanoparticles

    Directory of Open Access Journals (Sweden)

    Kim JH

    2013-06-01

    Full Text Available Jin Hyun Kim,1,* Hyun Hoon Chung,2,* Min Sook Jeong,1 Mi Ryoung Song,1 Keon Wook Kang,3,4 Jun Sung Kim1 1R&D Center, Biterials Co, Ltd, Seoul, Republic of Korea; 2Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Republic of Korea; 3Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea; 4Cancer Research Institute, Seoul National University, Seoul, Republic of Korea *These authors contributed equally to this work Abstract: Ovarian cancer is the fifth-leading cause of cancer-related deaths among women as a result of late diagnosis. For survival rates to improve, more sensitive and specific methods for earlier detection of ovarian cancer are needed. This study presents the development of rapid and specific one-step circulating tumor cell (CTC detection using flow cytometry in a whole-blood sample with fluorescent silica nanoparticles. We prepared magnetic nanoparticle (MNP-SiO2(rhodamine B isothiocyanate [RITC] (MNP-SiO2[RITC] incorporating organic dyes [RITC, λmax(ex/em = 543/580 nm] in the silica shell. We then controlled the amount of organic dye in the silica shell of MNP-SiO2(RITC for increased fluorescence intensity to overcome the autofluorescence of whole blood and increase the sensitivity of CTC detection in whole blood. Next, we modified the surface function group of MNP-SiO2(RITC from –OH to polyethylene glycol (PEG/COOH and conjugated a mucin 1 cell surface-associated (MUC1 antibody on the surface of MNP-SiO2(RITC for CTC detection. To study the specific targeting efficiency of MUC1-MNP-SiO2(RITC, we used immunocytochemistry with a MUC1-positive human ovarian cancer cell line and a negative human embryonic kidney cell line. This technology was capable of detecting 100 ovarian cancer cells in 50 µL of whole blood. In conclusion, we developed a one-step CTC detection technology in ovarian cancer based on multifunctional silica nanoparticles

  15. One-step preparation and photocatalytic performance of vanadium doped TiO{sub 2} coatings

    Energy Technology Data Exchange (ETDEWEB)

    Vasilić, R., E-mail: rastko.vasilic@ff.bg.ac.rs [University of Belgrade, Faculty of Physics, Studentski trg 12-16, 11000 Belgrade (Serbia); Stojadinović, S. [University of Belgrade, Faculty of Physics, Studentski trg 12-16, 11000 Belgrade (Serbia); Radić, N. [University of Belgrade, Institute of Chemistry, Technology and Metallurgy, Department of Catalysis and Chemical Engineering, Njegoševa 12, 11000 Belgrade (Serbia); Stefanov, P. [Institute of General and Inorganic Chemistry, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 11, Sofia 1113 (Bulgaria); Dohčević-Mitrović, Z. [University of Belgrade, Institute of Physics, Pregrevica 118, 11080 Belgrade (Serbia); Grbić, B. [University of Belgrade, Institute of Chemistry, Technology and Metallurgy, Department of Catalysis and Chemical Engineering, Njegoševa 12, 11000 Belgrade (Serbia)

    2015-02-01

    In this paper, we have investigated one-step preparation of vanadium doped TiO{sub 2} coatings formed by plasma electrolytic oxidation (PEO) of titanium in electrolyte containing 10 g/L Na{sub 3}PO{sub 4}·12H{sub 2}O + 0.5 g/L NH{sub 4}VO{sub 3}. The morphology, phase structure, and elemental composition of the formed coatings were characterized by atomic force microscopy (AFM), x-ray diffraction (XRD), and x-ray photoelectron spectroscopy (XPS) techniques. Ultraviolet–visible diffuse reflectance spectroscopy (UV–Vis DRS) was employed to evaluate the band gap energy of obtained coatings. Vanadium doped TiO{sub 2} coatings are partly crystallized and mainly composed of anatase phase TiO{sub 2}, with up to about 2 wt% of vanadium present in the surface layer of the oxide. The valence band photoelectron spectra and UV–Vis DRS showed that vanadium doped TiO{sub 2} coatings exhibit notable red shift with respect to the pure TiO{sub 2} coatings. The photocatalytic activity was evaluated by monitoring the degradation of methyl orange under simulated sunlight conditions. Photocatalytic activity of vanadium doped TiO{sub 2} coatings increases with PEO time. Prolonged PEO times result in higher roughness of obtained coatings, thus increasing surface area available for methyl orange degradation. Vanadium doped TiO{sub 2} coatings obtained after 180 s of PEO time exhibit the best photocatalytic activity and about 67% of methyl orange is degraded after 12 h of irradiation under simulated sunlight. - Highlights: • One-step preparation of V-doped TiO{sub 2} coatings in 10 g/L Na{sub 3}PO{sub 4}·12H{sub 2}O + 0.5 g/L NH{sub 4}VO{sub 3}. • Properties of obtained coatings strongly depend on microdischarge characteristics. • Band gap of V-doped TiO{sub 2} coatings is shifted towards red side of the spectrum. • V-doped TiO{sub 2} coatings have better photocatalytic activity than pure TiO{sub 2}. • After 12 h of simulated sunlight irradiation, 67% of

  16. H2-Assistance One-Step Growth of Si Nanowires and Their Growth Mechanism

    Institute of Scientific and Technical Information of China (English)

    QIU Ming-Xia; RUAN Shuang-Chen; GAO Biao; HUO Kai-Fu; ZHAI Jian-Pang; LI Ling; LIAO Hui; XU Xin-Tong

    2011-01-01

    Large-scale nanowires are grown on Si wafers by the catalyst-free one-step thermal reaction method in Ar/H2 mixture atmosphere at 1000℃. The x-ray diffraction and energy dispersive x-ray spectroscopy results reveal that the final nanowires are of silicon nanostructures. The Held emission scanning electron microscopy shows that these self-organized Si nanowires (SiNWs) possess curly crowns with diameters varying from 10 to 300 nm and lengths of up to several hundreds of micrometers. The transmission electron microscopy indicates that the nanowires are pure Si with amorphous structures. All the measurement results show that no silicon oxide is generated in our products. The growth mechanism is proposed tentatively. Silicon oxide is reduced into Si nanoparticles under the Ar/H2 mixture, which is the main reason for the formation of such SiNWs. Our experiments offer a method of preparing Si nanostructures by simply reducing silicon oxide at high temperature.%Large-scale nanowires are grown on Si wafers by the catalyst-free one-step thermal reaction method in Ar/H2 mixture atmosphere at 1000℃.The x-ray diffraction and energy dispersive x-ray spectroscopy results reveal that the final nanowires are of silicon nanostructures.The field emission scanning electron microscopy shows that these self-organized Si nanowires (SiNWs) possess curly crowns with diameters varying from 10 to 300nm and lengths of up to several hundreds of micrometers.The transmission electron microscopy indicates that the nanowires are pure Si with amorphous structures.All the measurement results show that no silicon oxide is generated in our products.The growth mechanism is proposed tentatively.Silicon oxide is reduced into Si nanoparticles under the Ar/H2 mixture,which is the main reason for the formation of such SiNWs.Our experiments offer a method of preparing Si nanostructures by simply reducing silicon oxide at high temperature.Silicon nanowires (SiNWs) have higher carrier mobility,a larger

  17. Relationship between mechanical properties of one-step self-etch adhesives and water sorption.

    Science.gov (United States)

    Hosaka, Keiichi; Nakajima, Masatoshi; Takahashi, Masahiro; Itoh, Shima; Ikeda, Masaomi; Tagami, Junji; Pashley, David H

    2010-04-01

    The purpose of this study was to evaluate the relationship between changes in the modulus of elasticity and ultimate tensile strength of one-step self-etch adhesives, and their degree of water sorption. Five one-step self-etch adhesives, Xeno IV (Dentsply Caulk), G Bond (GC Corp.), Clearfil S3 Bond (Kuraray Medical Inc.), Bond Force (Tokuyama Dental Corp.), and One-Up Bond F Plus (Tokuyama Dental Corp.) were used. Ten dumbelled-shaped polymers of each adhesive were used to obtain the modulus of elasticity by the three-point flexural bending test and the ultimate tensile strength by microtensile testing. The modulus of elasticity and the ultimate tensile strength were measured in both dry and wet conditions before/after immersion in water for 24h. Water sorption was measured, using a modification of the ISO-4049 standard. Each result of the modulus of elasticity and ultimate tensile strength was statistically analyzed using a two-way ANOVA and the result of water sorption was statistically analyzed using a one-way ANOVA. Regression analyses were used to determine the correlations between the modulus of elasticity and the ultimate tensile strength in dry or wet states, and also the percent decrease in these properties before/after immersion of water vs. water sorption. In the dry state, the moduli of elasticity of the five adhesive polymers varied from 948 to 1530 MPa, while the ultimate tensile strengths varied from 24.4 to 61.5 MPa. The wet specimens gave much lower moduli of elasticity (from 584 to 1073 MPa) and ultimate tensile strengths (from 16.5 to 35.0 MPa). Water sorption varied from 32.1 to 105.8 g mm(-3). The moduli of elasticity and ultimate tensile strengths of the adhesives fell significantly after water-storage. Water sorption depended on the constituents of the adhesive systems. The percent decreases in the ultimate tensile strengths of the adhesives were related to water sorption, while the percent reductions in the moduli of elasticity of the

  18. In silico and in vitro evaluation of PCR-based assays for the detection of Bacillus anthracis chromosomal signature sequences

    DEFF Research Database (Denmark)

    Ågren, Joakim; Hamidjaja, Raditijo A.; Hansen, Trine

    2013-01-01

    on unique markers present on virulence plasmids pXO1 and pXO2, relatively few assays incorporate chromosomal DNA markers due to the close relatedness of B. anthracis to the B. cereus group strains. For the detection of chromosomal DNA, different genes have been used, such as BA813, rpoB, gyrA, plcR, S......Bacillus anthracis, the causative agent of anthrax, is a zoonotic pathogen that is relatively common throughout the world and may cause life threatening diseases in animals and humans. There are many PCR-based assays in use for the detection of B. anthracis. While most of the developed assays rely......-layer, and prophage-lambda. Following a review of the literature, an in silico analysis of all signature sequences reported for identification of B. anthracis was conducted. Published primer and probe sequences were compared for specificity against 134 available Bacillus spp. genomes. Although many of the chromosomal...

  19. Subtyping of type A influenza by sequencing the variable regions of HA gene specifically amplified with RT-PCR

    Institute of Scientific and Technical Information of China (English)

    YAN An; DING GuoHui; ZHOU ZhenFeng; DONG Hui; ZHANG YaKun; ZHU Lei; HE YunGang; ZHANG GuoQing; LI YiXue; SUN Bing; HUANG Zhong; LAN Ke; JIN Li; WANG HongYan; WANG XiaoNing; YANG Zhong; ZHONG Yang; DAI JianXin; GUO YaJun; WANG Hao; CHE XiaoYan; WU Fan; YUAN ZhenGan; ZHANG Xi; CAO ZhiWei; ZHOU XiaoNong; ZHOU JiaHai; MA ZhiYong; TONG GuangZhi; ZHAO GuoPing; JIN WeiRong; XIONG Hui

    2009-01-01

    The outbreak of a novel influenza A (H1N1) virus across the globe poses a threat to human health.It is of paramount importance to develop a rapid,reliable and inexpensive diagnostic procedure.Based on the bioinformatic information from public database,primers specific for influenza A virus surface protein haemagglutinin (HA) of several subtypes (including H1,H2,H3,H5,H7 and H9) were designed.Primer-specific PCR products were subjected to sequencing for accurately distinguishing H1 and H3 subtypes from others.This sequencing-based detection method will not only be applied to rapid detection and simultaneous subtype identification of new influenza A virus H1N1,but also provide the strategies to monitor other new types of influenza virus with explosive potential.

  20. Rapid Amplification of Flanking Sequences of a Known DNA Region by Partial Restriction Digestion and Hot Start PCR

    Institute of Scientific and Technical Information of China (English)

    LOU Qun-feng; LIU Qiang; YANG Yin-gui; CHEN Jin-feng

    2008-01-01

    A simple and efficient method for cloning the flanking genomic sequences of a known DNA region is reported in this study. This method combined partial restriction endonuclease digestion, adaptor ligation, and a single round polymerase chain reaction. Total genomic DNA was partially digested with the frequent-cutting restriction enzyme Mse Ⅰ. The partially digested products were ligated to an unphosphorylated adaptor. A hot start PCR amplification with Taq polymerase and dNTP was performed with a DNA-specific primer and the adaptor primer complementary to the adaptor and the Mse Ⅰ recognition site. The amplified products were fractionated, cloned and sequenced. By this method, we cloned the downstream region of a gynoecious marker TG/CAC234 from cucumber (Cucumis sativus L.).

  1. Comparison of two commercial broadrange PCR and sequencing assays for identification of bacteria in culture-negative clinical samples

    DEFF Research Database (Denmark)

    Stavnsbjerg, Camilla; Frimodt-Moller, Niels; Moser, Claus Ernst

    2017-01-01

    Background Culturing has long been the gold standard for detecting aetiologic agents in bacterial infections. In some cases, however, culturing fails to detect the infection. To further investigate culture-negative samples, amplification and subsequent sequencing of the 16S rRNA gene is often...... applied. The aim of the present study was to compare the current method used at our Department of Clinical Microbiology, based on the MicroSeq ID system (Applied Biosystems, USA) with the Universal Microbe Detection (UMD) SelectNA kit (Molzym, Germany). Methods 76 culture-negative samples were first...... in a real-time PCR and sequenced. Results 22 of 76 samples (28.9%) were positive for bacteria with the UMD SelectNA, which was significantly more (p = 0.0055) than the MicroSeq ID where 11 of 76 samples (14.5%) were positive. The UMD SelectNA assay identified more relevant bacterial pathogens than the Micro...

  2. Verification of Frequency in Species of Nontuberculous Mycobacteria in Kermanshah Drinking Water Supplies Using the PCR-Sequencing Method.

    Science.gov (United States)

    Mohajeri, Parviz; Yazdani, Laya; Shahraki, Abdolrazagh Hashemi; Alvandi, Amirhoshang; Atashi, Sara; Farahani, Abbas; Almasi, Ali; Rezaei, Mansour

    2017-04-01

    Nontuberculous mycobacteria are habitants of environment, especially in aquatic systems. Some of them cause problems in immunodeficient patients. Over the last decade, 16S rRNA gene sequencing was established in 45 novel species of nontuberculous mycobacteria. Experiences revealed that this method underestimates the diversity, but does not distinguish between some of mycobacterium subsp. To recognize emerging rapidly growing mycobacteria and identify their subsp, rpoB gene sequencing has been developed. To better understand the transmission of nontuberculous mycobacterial species from drinking water and preventing the spread of illness with these bacteria, the aim of this study was to detect the presence of bacteria by PCR-sequencing techniques. Drinking water samples were collected from different areas of Kermanshah city in west of IRAN. After decontamination with cetylpyridinium chloride, samples were filtered with 0.45-micron filters, the filter transferred directly on growth medium waiting to appear in colonies, then DNA extraction and PCR were performed, and products were sent to sequencing. We found 35/110 (32%) nontuberculous mycobacterial species in drinking water samples, isolates included Mycobacterium goodii, Mycobacterium aurum, and Mycobacterium gastri with the most abundance (11.5%), followed by Mycobacterium smegmatis, Mycobacterium porcinum, Mycobacterium peregrinum, Mycobacterium mucogenicum, and Mycobacterium chelonae (8%). In this study, we recognized the evidence of contamination by nontuberculous mycobacteria in corroded water pipes. As a result of the high prevalence of these bacteria in drinking water in Kermanshah, this is important evidence of transmission through drinking water. This finding can also help public health policy makers control these isolates in drinking water supplies in Kermanshah.

  3. Recent sequence variation in probe binding site affected detection of respiratory syncytial virus group B by real-time RT-PCR.

    Science.gov (United States)

    Kamau, Everlyn; Agoti, Charles N; Lewa, Clement S; Oketch, John; Owor, Betty E; Otieno, Grieven P; Bett, Anne; Cane, Patricia A; Nokes, D James

    2017-03-01

    Direct immuno-fluorescence test (IFAT) and multiplex real-time RT-PCR have been central to RSV diagnosis in Kilifi, Kenya. Recently, these two methods showed discrepancies with an increasing number of PCR undetectable RSV-B viruses. Establish if mismatches in the primer and probe binding sites could have reduced real-time RT-PCR sensitivity. Nucleoprotein (N) and glycoprotein (G) genes were sequenced for real-time RT-PCR positive and negative samples. Primer and probe binding regions in N gene were checked for mismatches and phylogenetic analyses done to determine molecular epidemiology of these viruses. New primers and probe were designed and tested on the previously real-time RT-PCR negative samples. N gene sequences revealed 3 different mismatches in the probe target site of PCR negative, IFAT positive viruses. The primers target sites had no mismatches. Phylogenetic analysis of N and G genes showed that real-time RT-PCR positive and negative samples fell into distinct clades. Newly designed primers-probe pair improved detection and recovered previous PCR undetectable viruses. An emerging RSV-B variant is undetectable by a quite widely used real-time RT-PCR assay due to polymorphisms that influence probe hybridization affecting PCR accuracy. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  4. On-demand one-step synthesis of monodisperse functional polymeric microspheres with droplet microfluidics.

    Science.gov (United States)

    Yu, Xu; Cheng, Gong; Zhou, Ming-Da; Zheng, Si-Yang

    2015-04-07

    A simple and robust method for one-step synthesis of monodisperse functional polymeric microspheres was established by generation of reversed microemulsion droplets in aqueous phase inside microfluidic chips and controlled evaporation of the organic solvent. Using this method, water-soluble nanomaterials can be easily encapsulated into biodegradable Poly(D,L-lactic-co-glycolic acid) (PLGA) to form functional microspheres. By controlling the flow rate of microemulsion phase, PLGA polymeric microspheres with narrow size distribution and diameters in the range of ∼50-100 μm were obtained. As a demonstration of the versatility of the approach, high-quality fluorescent CdTe:Zn(2+) quantum dots (QDs) of various emission spectra, superparamagnetic Fe3O4 nanoparticles, and water-soluble carbon nanotubes (CNTs) were used to synthesize fluorescent PLGA@QDs, magnetic PLGA@Fe3O4, and PLGA@CNTs polymeric microspheres, respectively. In order to show specific applications, the PLGA@Fe3O4 were modified with polydopamine (PDA), and then the silver nanoparticles grew on the surfaces of the PLGA@Fe3O4@PDA polymeric microspheres by reducting the Ag(+) to Ag(0). The as-prepared PLGA@Fe3O4@PDA-Ag microspheres showed a highly efficient catalytic reduction of the 4-nitrophenol, a highly toxic substance. The monodisperse uniform functional PLGA polymeric microspheres can potentially be critically important for multiple biomedical applications.

  5. Rapid one-step assays for on-site monitoring of mouse and rat urinary allergens.

    Science.gov (United States)

    Koets, Marjo; Renström, Anne; Zahradnik, Eva; Bogdanovic, Jelena; Wouters, Inge M; van Amerongen, Aart

    2011-12-01

    Allergy to rodent proteins is common among laboratory animal workers. Sensitive methods to measure exposure to these allergens have been developed. These assays are, however, expensive, time-consuming, and require a laboratory facility and methodological expertise. A simple method to screen for allergen spread, or to test whether hygiene standards are maintained, would be useful. Lateral flow immunoassays (LFIAs) are especially suited for field settings; the tests are simple and results are visible within minutes. LFIAs were developed for detection of the rodent urinary allergens Mus m 1 and Rat n 1. Pilot studies were performed in animal facilities in three countries using both extracts from airborne dust samples and samples collected by wiping surfaces. For comparison and determination of sensitivity, the concentrations of rodent urinary allergens in the samples were also measured using enzyme immunoassays (EIAs). The LFIAs for rat and mouse urinary allergens had a detection limit of 31 pg allergen per mL in a buffer system with purified allergen standards. Results of environmental dust extracts tested in LFIAs correlated well with levels obtained using EIAs. Spread of rodent allergens, or non-adherence to hygiene around laboratory animal facilities, may aggravate rodent allergy. Using a simple, sensitive one-step assay, allergens can be detected to prevent allergen exposure. The results reveal that the rapid assays are suited for on-site demonstration of exposure to rodent allergens, and thus, useful in occupational hygiene practice.

  6. A one-step-ahead pseudo-DIC for comparison of Bayesian state-space models.

    Science.gov (United States)

    Millar, R B; McKechnie, S

    2014-12-01

    In the context of state-space modeling, conventional usage of the deviance information criterion (DIC) evaluates the ability of the model to predict an observation at time t given the underlying state at time t. Motivated by the failure of conventional DIC to clearly choose between competing multivariate nonlinear Bayesian state-space models for coho salmon population dynamics, and the computational challenge of alternatives, this work proposes a one-step-ahead DIC, DICp, where prediction is conditional on the state at the previous time point. Simulations revealed that DICp worked well for choosing between state-space models with different process or observation equations. In contrast, conventional DIC could be grossly misleading, with a strong preference for the wrong model. This can be explained by its failure to account for inflated estimates of process error arising from the model mis-specification. DICp is not based on a true conditional likelihood, but is shown to have interpretation as a pseudo-DIC in which the compensatory behavior of the inflated process errors is eliminated. It can be easily calculated using the DIC monitors within popular BUGS software when the process and observation equations are conjugate. The improved performance of DICp is demonstrated by application to the multi-stage modeling of coho salmon abundance in Lobster Creek, Oregon. © 2014, The International Biometric Society.

  7. One-Step Electrodeposited Nickel Cobalt Sulfide Nanosheet Arrays for High-Performance Asymmetric Supercapacitors

    KAUST Repository

    Chen, Wei

    2014-09-23

    A facile one-step electrodeposition method is developed to prepare ternary nickel cobalt sulfide interconnected nanosheet arrays on conductive carbon substrates as electrodes for supercapacitors, resulting in exceptional energy storage performance. Taking advantages of the highly conductive, mesoporous nature of the nanosheets and open framework of the three-dimensional nanoarchitectures, the ternary sulfide electrodes exhibit high specific capacitance (1418 F g(-1) at 5 A g(-1) and 1285 F g(-1) at 100 A g(-1)) with excellent rate capability. An asymmetric supercapacitor fabricated by the ternary sulfide nanosheet arrays as positive electrode and porous graphene film as negative electrode demonstrates outstanding electrochemical performance for practical energy storage applications. Our asymmetric supercapacitors show a high energy density of 60 Wh kg(-1) at a power density of 1.8 kW kg(-1). Even when charging the cell within 4.5 s, the energy density is still as high as 33 Wh kg(-1) at an outstanding power density of 28.8 kW kg(-1) with robust long-term cycling stability up to 50 000 cycles.

  8. One-step large-scale deposition of salt-free DNA origami nanostructures

    Science.gov (United States)

    Linko, Veikko; Shen, Boxuan; Tapio, Kosti; Toppari, J. Jussi; Kostiainen, Mauri A.; Tuukkanen, Sampo

    2015-10-01

    DNA origami nanostructures have tremendous potential to serve as versatile platforms in self-assembly -based nanofabrication and in highly parallel nanoscale patterning. However, uniform deposition and reliable anchoring of DNA nanostructures often requires specific conditions, such as pre-treatment of the chosen substrate or a fine-tuned salt concentration for the deposition buffer. In addition, currently available deposition techniques are suitable merely for small scales. In this article, we exploit a spray-coating technique in order to resolve the aforementioned issues in the deposition of different 2D and 3D DNA origami nanostructures. We show that purified DNA origamis can be controllably deposited on silicon and glass substrates by the proposed method. The results are verified using either atomic force microscopy or fluorescence microscopy depending on the shape of the DNA origami. DNA origamis are successfully deposited onto untreated substrates with surface coverage of about 4 objects/mm2. Further, the DNA nanostructures maintain their shape even if the salt residues are removed from the DNA origami fabrication buffer after the folding procedure. We believe that the presented one-step spray-coating method will find use in various fields of material sciences, especially in the development of DNA biochips and in the fabrication of metamaterials and plasmonic devices through DNA metallisation.

  9. One-step uniform growth of magnesium hydride nanoparticles on graphene

    Directory of Open Access Journals (Sweden)

    Yuqin Huang

    2017-02-01

    Full Text Available A simple solvent-free method to synthesize MgH2 nanoparticles (MgH2 NPs uniformly grown on graphene nanosheets (GNs has been reported in this paper. Based on the formation of MgH2 by di-n-butylmagnesium ((C4H92Mg thermal decomposition under hydrogen pressure, the GNs were added as matrix to hinder the agglomeration and growing of MgH2 NPs. The fabricated MgH2/GNs nanocomposites, in which MgH2 NPs were homogenously growing in the graphene matrix, have been synthesized by the favorable adsorption energy between (C4H92Mg and GNs. Resulting from the one-step solvent-free route, the generated MgH2 NPs shows high hydrogen capacity and steady hydriding and dehydriding properties, without the interference of the synthetic medium. At the same time, the size of the fabricated MgH2 NPs can be controlled by adjusting the mass ratio of MgH2 to graphene, the various hydrogen pressure and temperature. Attributed to smaller size effect, well uniform distribution of high density MgH2 NPs, and the agglomeration blocking ability of graphene, the MgH2/GNs-40 wt% exhibits the favorite hydrogen storage performance.

  10. Perovskite Hollow Fibers with Precisely Controlled Cation Stoichiometry via One-Step Thermal Processing.

    Science.gov (United States)

    Zhu, Jiawei; Zhang, Guangru; Liu, Gongping; Liu, Zhengkun; Jin, Wanqin; Xu, Nanping

    2017-05-01

    The practical applications of perovskite hollow fibers (HFs) are limited by challenges in producing these easily, cheaply, and reliably. Here, a one-step thermal processing approach is reported for the efficient production of high performance perovskite HFs, with precise control over their cation stoichiometry. In contrast to traditional production methods, this approach directly uses earth-abundant raw chemicals in a single thermal process. This approach can control cation stoichiometry by avoiding interactions between the perovskites and polar solvents/nonsolvents, optimizes sintering, and results in high performance HFs. Furthermore, this method saves much time and energy (≈ 50%), therefore pollutant emissions are greatly reduced. One successful example is Ba0.5Sr0.5Co0.8Fe0.2O3-δ HFs, which are used in an oxygen-permeable membrane. This exhibits high oxygen permeation flux values that exceed desired commercial targets and compares favorably with previously reported oxygen-permeable membranes. Studies on other perovskites have produced similarly successful results. Overall, this approach could lead to energy efficient, solid-state devices for industrial application in energy and environmental fields. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Self-Stratified Antimicrobial Acrylic Coatings via One-Step UV Curing.

    Science.gov (United States)

    Zhao, Jie; Millians, William; Tang, Saide; Wu, Tiehang; Zhu, Lei; Ming, Weihua

    2015-08-26

    We designed and synthesized a novel quaternary ammonium methacrylate compound (QAC-2) bearing a perfluoroalkyl tail on one end and an acrylic moiety on the other. Via one-step UV curing of QAC-2 and methyl methacrylate (MMA) with ethylene glycol dimethacrylate (EGDMA) as the cross-linker, we obtained cross-linked coatings with excellent antimicrobial property, as demonstrated by the total kill against both Gram-negative Escherichia coli (E. coli) and Gram-positive Staphylococcus epidermidis (S. epidermidis) at a QAC-2 concentration as low as ∼0.06 mol % (∼0.4 wt %) relative to MMA, which was substantially lower than the QAC amount needed in the coatings containing QACs with a hydrocarbon tail. A zone of inhibition test confirmed that the antimicrobial effect was on the basis of contact killing and there was no leaching of antimicrobial species from the cross-linked coating. The high antimicrobial potency in QAC-2-containing films was the consequence of strong surface enrichment of the fluorinated QAC, as confirmed by X-ray photoelectron spectroscopy (XPS).

  12. Preparation of native cellulose-AgCl fiber with antimicrobial activity through one-step electrospinning.

    Science.gov (United States)

    Wang, Shaojun; Zhang, Xiaomin; Luo, Ting; Zhu, Jin; Su, Shengpei

    2017-02-01

    The native Cellulose-AgCl fiber have been firstly fabricated by one-step electrospinning of cellulose solution with poly(vinyl pyrrolidone) (PVP) and AgNO3. X-ray diffraction, Scanning electron microscopy (SEM), Energy dispersive spectrometer, Thermo-gravimetric analysis and Fourier transform infrared are used to characterize the crystal structure, morphology and composition of cellulose-AgCl nanocomposites. The results of SEM indicate that the size of AgCl in cellulose fiber matrix is able to be adjusted by the addition of Polyvinylpyrrolidone (PVP). The antimicrobial activity of the nanocomposites fiber is also tested against the model microbes E. coli (Gram-negative) and S. aureus (Gram-positive). The results indicate that cellulose-AgCl nanocomposites have a good antimicrobial activity, which is improving with the decrease of AgCl size in fiber matrix. This work provides a novel and simple way to adjust the AgCl size in electrospinning cellulose matrix which can be applied as functional biomaterials.

  13. One-step synthesis of boronic acid functionalized gold nanoclusters for photoluminescence sensing of dopamine

    Science.gov (United States)

    Chen, Huide; Liu, Chunxiu; Xia, Yunsheng

    2017-03-01

    This study is the first to report one-step synthesis of boronic acid functionalized gold nanoclusters (AuNCs) using mixed ligands of 4-mercaptophenylboronic acid (MPBA) and glutathione. Furthermore, the emission color of the products can be fancily tuned from green to near-infrared by simply changing the proportion of the two stabilizers. In basic media, dopamine (DA) molecules themselves polymerize each other and form polydopamine with large amounts of cis-diol groups, which then react with boronic acid groups on the AuNC’s surface based on the formation of boronate esters. As a result, the photoluminescence of the AuNCs is well quenched by the electron transfer effect. Accordingly, DA molecules are assayed from 0.5 to 9 μM, and the detection limit is as low as 0.1 μM. The as-prepared AuNCs exhibit high selectivity; the existing biomolecules including various amino acids, ascorbic acid, uric acid, glucose, etc, do not interfere with the assay. The proposed method is successfully applied to the assay of DA in human serum, indicating its practical potential.

  14. One-Step Green Synthesis of Metallic Nanoparticles Using Sodium Alginate

    Directory of Open Access Journals (Sweden)

    Jesus Valdez

    2016-01-01

    Full Text Available Metallic nanoparticles have been focus of research because of their characteristic properties, specifically the LSPR which can have wide applications in biomedical sciences and engineering. Currently, traditional physical and chemical methods can synthesize these nanoparticles but their disadvantages such as costs, time, effectiveness, and toxicity of precursors provide a wide range of problems for the synthesis of these nanoparticles. Recently, some natural polymers and organic compounds have been used for the synthesis of nanoparticles by green methods. In this study, we synthesize copper, silver, and gold nanoparticles using sodium alginate as reducing and stabilizing agent under microwave irradiation. The LSPR for each system was observed by UV-vis spectroscopy. Particle size distribution and zeta potential demonstrate the size and stability for these nanoparticles. FESEM and TEM microscopies have shown the size and morphology of these systems correlated with UV-vis, particle size distribution, and zeta potential analyses. The study demonstrates a rapid, facile, cheaper, and one-step green method of synthesis for these metallic nanoparticles being an alternative to the conventional methods used for synthesis of metallic nanoparticles.

  15. One-step femtosecond laser welding and internal machining of three glass substrates

    Science.gov (United States)

    Tan, Hua; Duan, Ji'an

    2017-05-01

    In this paper, it demonstrated one-step femtosecond laser welding and internal machining of three fused silica substrates in the optical- and non-optical-contact regimes by focusing 1030-nm laser pulses at the middle of the second substrate. Focusing laser pulses within the second glass in optical-contact and non-optical-contact samples induces permanent internal structural modification, leading to the three glass substrates bonding together simultaneously. The bonding mechanism is based on the internal modification of glass, and this mechanism is different from that of ordinary glass welding at the interface. Welding-spot size is affected by not only the gap distance (ablation effect) and heat transmission, but also by gravity through examining the sizes of the welding spots on the four contact welding surfaces. The maximum bonding strength of the lower interface (56.2 MPa) in the optical-contact regime is more than double that (27.6 MPa) in the non-optical-contact regime.

  16. One-step Fabrication of Nanoporous Black Silicon Surfaces for Solar Cells using Modified Etching Solution

    Institute of Scientific and Technical Information of China (English)

    Ye-hua Tang; Chun-lan Zhou; Su Zhou; Yan Zhao; Wen-jing Wang; Jian-ming Fei; Hong-bin Cao

    2013-01-01

    Currently,a conventional two-step method has been used to generate black silicon (BS)surfaces on silicon substrates for solar cell manufacturing.However,the performances of the solar cell made with such surface generation method are poor,because of the high surface recombination caused by deep etching in the conventional surface generation method for BS.In this work,a modified wet chemical etching solution with additives was developed.A zhomogeneous BS layer with random porous structure was obtained from the modified solution in only one step at room temperature.The BS layer had low reflectivity and shallow etching depth.The additive in the etch solution performs the function of pH-modulation.After 16-min etching,the etching depth in the samples was approximately 200 nm,and the spectrum-weighted-reflectivity in the range from 300 nm to 1200 nm was below 5%,BS solar cells were fabricated in the production line.The decreased etching depth can improve the electrical performance of solar cells because of the decrease in surface recombination.An efficiency of 15,63% for the modified etching BS solar cells was achieved on a large area,ptype single crystalline silicon substrate with a 624.32-mV open circuit voltage and a 77.88%fill factor.

  17. Adsorption of phosphate in water using one-step synthesized zirconium-loaded reduced graphene oxide

    Science.gov (United States)

    Luo, Xin; Wang, Xiurong; Bao, Shaopan; Liu, Xiawei; Zhang, Weicheng; Fang, Tao

    2016-12-01

    In this account, a one-step green hydrothermal method for zirconium-loaded reduced graphene oxide (RGO-Zr) adsorbent was developed in pure water. It is based on the formation of initially strong-coupling RGO-Zr nanocomposites followed by in situ reduction of GO to RGO during the hydrothermal treatment. The phosphate adsorption performance of the as-prepared nanocomposites was investigated in aqueous environment under various conditions. The characterization results of RGO-Zr nanocomposites showed that ZrO2 was successfully integrated onto the RGO sheets in amorphous. The data from equilibrium phosphate adsorption on RGO-Zr revealed that the adsorption kinetics followed a pseudo-second-order kinetic model, where the adsorption isotherm fitted the Langmuir isotherm model with a maximum adsorption capacity of 27.71 mg P/g at pH 5 and 298 K. The improved phosphate adsorption on RGO-Zr was caused by the dispersion of ZrO2 on the RGO surface. Furthermore, the phosphate adsorption was found insensitive to the increase in pH while it was sensitive to the increase in temperature. The coexisting anions of SO42-, F-, Cl-, NO3- and CO32- affected the phosphate adsorption in a different way. Results suggest that the present RGO-Zr adsorbent has the potential for controlling phosphorus pollution in water.

  18. One-step electrochemical synthesis of graphene/polyaniline composite film and its applications

    Energy Technology Data Exchange (ETDEWEB)

    Feng, Xiao-Miao; Li, Rui-Mei; Ma, Yan-Wen; Chen, Run-Feng; Shi, Nai-En; Fan, Qu-Li; Huang, Wei [Key Laboratory for Organic Electronics and Information Displays (KLOEID) and Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications (NUPT), Nanjing 210046 (China)

    2011-08-09

    This work describes a new one-step large-scale electrochemical synthesis of graphene/polyaniline (PANI) composite films using graphite oxide (GO) and aniline as the starting materials. The size of the film could be controlled by the area of indium tin oxide (ITO). Scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS), Fourier transform infrared spectroscopy (FTIR), and ultraviolet-visible absorption spectrum (UV-vis) results demonstrated that the graphene/PANI composite film was successfully synthesized. The obtained graphene/PANI composite film showed large specific area, high conductivity, good biocompatibility, and fast redox properties and had perfect layered and encapsulated structures. Electrochemical experiments indicated that the composite film had high performances and could be widely used in applied electrochemical fields. As a model, horseradish peroxidase (HRP) was entrapped onto the film-modified glassy carbon electrode (GCE) and used to construct a biosensor. The immobilized HRP showed a pair of well-defined redox peaks and high catalytic activity for the reduction of H{sub 2}O{sub 2}. Furthermore, the graphene/PANI composite film could be directly used as the supercapacitor electrode. The supercapacitor showed a high specific capacitance of 640 F g{sup -1} with a retention life of 90% after 1000 charge/discharge cycles. (Copyright copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  19. One-step process for superhydrophobic metallic surfaces by wire electrical discharge machining.

    Science.gov (United States)

    Bae, Won Gyu; Song, Ki Young; Rahmawan, Yudi; Chu, Chong Nam; Kim, Dookon; Chung, Do Kwan; Suh, Kahp Y

    2012-07-25

    We present a direct one-step method to fabricate dual-scale superhydrophobic metallic surfaces using wire electrical discharge machining (WEDM). A dual-scale structure was spontaneously formed by the nature of exfoliation characteristic of Al 7075 alloy surface during WEDM process. A primary microscale sinusoidal pattern was formed via a programmed WEDM process, with the wavelength in the range of 200 to 500 μm. Notably, a secondary roughness in the form of microcraters (average roughness, Ra: 4.16 to 0.41 μm) was generated during the exfoliation process without additional chemical treatment. The low surface energy of Al 7075 alloy (γ = 30.65 mJ/m(2)) together with the presence of dual-scale structures appears to contribute to the observed superhydrophobicity with a static contact angle of 156° and a hysteresis less than 3°. To explain the wetting characteristics on dual-scale structures, we used a simple theoretical model. It was found that Cassie state is likely to present on the secondary roughness in all fabricated surfaces. On the other hand, either Wenzel or Cassie state can present on the primary roughness depending on the characteristic length of sinusoidal pattern. In an optimal condition of the serial cutting steps with applied powers of ∼30 and ∼8 kW, respectively, a stable, superhydrophobic metallic surface was created with a sinusoidal pattern of 500 μm wavelength.

  20. One-Step Electrochemical Preparation of Multilayer Graphene Functionalized with Nitrogen

    Science.gov (United States)

    Ustavytska, Olena; Kurys, Yaroslav; Koshechko, Vyacheslav; Pokhodenko, Vitaly

    2017-03-01

    A new environmentally friendly one-step method for producing multilayer (preferably 7-9 layers) nitrogen-doped graphene (N-MLG) with a slight amount of oxygen-containing defects was developed. The approach is based on the electrochemical exfoliation of graphite electrode in the presence of azide ions under the conditions of electrolysis with pulse changing of the electrode polarization potential. It was found that usage of azide anions lead not only to the exfoliation of graphite but also to the simultaneous functionalization of graphene sheets by nitrogen atoms (as a result of electrochemical decomposition of azide anions with ammonia evolution). Composition, morphology, structure, and electrochemical properties of N-MLG were characterized by C,H,N analysis, transmission electron microscopy, atomic force microscopy, FTIR, UV-Vis, and Raman spectroscopy, as well as cyclic voltammetry. The perspective of using N-MLG as oxygen reduction reaction electrocatalyst and for the electrochemical analysis of biomarkers (dopamine, ascorbic acid, and uric acid) in their mixtures was shown.

  1. One-step solid state synthesis of capped γ-Fe(2)O(3) nanocrystallites.

    Science.gov (United States)

    Zboril, R; Bakandritsos, A; Mashlan, M; Tzitzios, V; Dallas, P; Trapalis, Ch; Petridis, D

    2008-03-05

    The thermally induced solid state synthesis of soluble organophilic maghemite (γ-Fe(2)O(3)) nanocrystallites is described. The solvent-free one-step synthesis involves the reaction in the melt state of Fe(NO)(3)·9H(2)O and RCOOH (R = C(11)H(23), C(15)H(31)) at 240 °C. The method yields well-crystallized nanoparticles of γ-Fe(2)O(3) functionalized with the corresponding aliphatic acid. Transmission electron microscopy (TEM) and atomic force microscopy (AFM) observations reveal composite particles with faceted magnetic cores and average size of 20 nm, which are well capped with the surrounding organic sheath. The Fourier transform infrared (FT-IR) spectra and thermal analysis suggest a bimodal configuration of the organic shell including chemically coordinated and physisorbed molecules of aliphatic acid. The chemical bonding of the carboxylate groups to the surface iron atoms is also indicated by a paramagnetic doublet with unchanged area in the variable temperature Mössbauer spectra. The spinel γ-Fe(2)O(3) particles exhibit perfect structural and magnetic ordering, including the almost ideal ratio of octahedral to tetrahedral positions (5/3) and very low degree of spin canting, as confirmed by in-field Mössbauer spectroscopy. Magnetic measurements demonstrate the suitable properties required in various (bio)magnetic applications like superparamagnetic behavior at room temperature, high saturation magnetization achievable at low applied fields and suppressed magnetic interactions.

  2. A rapid one-step electrodeposition process for fabrication of superhydrobic surfaces on anode and cathode

    Institute of Scientific and Technical Information of China (English)

    郝丽梅; 闫小乐; 解忧; 张涛; 陈志

    2016-01-01

    This work presents a method to solve the weak solubility of zinc chloride (ZnCl2) in the ethanol by adding some reasonable water into an ethanol electrolyte containing ZnCl2and myristic acid (CH3(CH2)12COOH). A rapid one-step electrodeposition process was developed to fabricate anodic (2.5 min) and cathodic (40 s) superhydrophobic surfaces of copper substrate (contact angle more than 150°) in an aqueous ethanol electrolyte. Morphology, composition, chemical structure and superhydrophobicity of these superhydrophobic surfaces were investigated by SEM, FTIR, XRD, and contact angle measurement, respectively. The results indicate that water ratio of the electrolyte can reduce the required deposition time, superhydrophobic surface needs over 30 min with anhydrous electrolyte, while it needs only 2.5 min with electrolyte including 10 mL water, and the maximum contact angle of anodic surface is 166° and that of the cathodic surface is 168°. Two copper electrode surfaces have different reactions in the process of electrodeposition time, and the anodic copper surface covers copper myristate (Cu[CH3(CH2)12COO]2) and cupric chloride (CuCl); while, zinc myristate (Zn[CH3(CH2)12COO]2) and pure zinc (Zn) appear on the cathodic surface.

  3. A novel oromucosal prolonged release mucoadhesive suspension by one step spray coagulation method.

    Science.gov (United States)

    Cilurzo, Francesco; Gennari, Chiara G M; Selmin, Francesca; Musazzi, Umberto M; Rumio, Cristiano; Minghetti, Paola

    2013-06-01

    An oromucosal mucoadhesive suspension (OMS) able to combine the peculiarities of prolonged release mucoadhesive microparticles with those of an immediate release oromucosal solution is described. Microparticles were obtained by ionotropic gelation of alginate blended with another mucoadhesive material in a one step process where the cross-linking bath constituted the suspension vehicle. The effects of formulation and processing conditions on OMS performances were measured in-vitro determining the enhancement of drug penetration in buccal porcine mucosa and inhibition of tooth plaque formation using flurbiprofen and delmopinol as model drugs, respectively. Well-formed and spherical microparticles were obtained combining alginate with carbomer; linear dependence of particle size from the feed composition, viscosity and atomization pressure was found. As demonstrated by using FITC-labelled microparticles, the system remained onto the buccal mucosa at least for a six hour period. As a consequence, 0.1% flurbiprofen OMS guaranteed a concentration of flurbiprofen into buccal porcine mucosa over 6 hours comparable to 0.25% flurbiprofen reference solution, allowing a potential reduction of the 60% administered dose. The use of in-house made artificial mouth revealed that the once-a-day administration of 0.1% delmopinol OMS was as effective in plaque inhibition as the 0.2% delmopinol reference solution product given twice-a-day. These results suggested that the development of bioadhesive oromucosal suspensions, localizing the drug into buccal cavity, can reduce regimen and administrated dose.

  4. One-Step Synthesis of PEGylated Gold Nanoparticles with Tunable Surface Charge

    Directory of Open Access Journals (Sweden)

    Rares Stiufiuc

    2013-01-01

    Full Text Available The present work reports a rapid, simple and efficient one-step synthesis and detailed characterisation of stable aqueous colloids of gold nanoparticles (AuNPs coated with unmodified poly(ethyleneglycol (PEG molecules of different molecular weights and surface charges. By mixing and heating aqueous solutions of PEG with variable molecular chain and gold(III chloride hydrate (HAuCl4 in the presence of NaOH, we have successfully produced uniform colloidal 5 nm PEG coated AuNPs of spherical shape with tunable surface charge and an average diameter of 30 nm within a few minutes. It has been found out that PEGylated AuNPs provide optical enhancement of the characteristic vibrational bands of PEG molecules attached to the gold surface when they are excited with both visible (532 nm and NIR (785 nm laser lines. The surface enhanced Raman scattering (SERS signal does not depend on the length of the PEG molecular chain enveloping the AuNPs, and the stability of the colloid is not affected by the addition of concentrated salt solution (0.1 M NaCl, thus suggesting their potential use for in vitro and in vivo applications. Moreover, by gradually changing the chain length of the biopolymer, we were able to control nanoparticles’ surface charge from −28 to −2 mV, without any modification of the Raman enhancement properties and of the colloidal stability.

  5. One-step purification of soluble recombinant human 6-phosphogluconate dehydrogenase from Escherichia coli.

    Science.gov (United States)

    Chan, Barden; Sukhatme, Vikas P

    2013-11-01

    6-Phosphogluconate dehydrogenase (6PGD), the third enzyme in the pentose phosphate pathway, was recently identified as a novel target in human lung cancer. In this report, we present an expression and purification scheme of recombinant human 6PGD from Escherichia coli. Using a DE3 derivative strain expressing tRNAs for seven rare codons in E. coli called Rosetta2 (DE3), a large quantity of soluble human 6PGD can be expressed with an N-terminal histidine tag and purified by a one-step purification procedure to near homogeneity without denaturants or refolding. Three to seven milligrams of purified protein could be obtained from 100 ml of culture. This recombinant human 6PGD follows classic Michaelis-Menton saturation kinetics with respect to both substrates NADP(+) and 6-phosphogluconate. The respective k(cat) and K(m) were comparable to those of 6PGDs purified from mammalian tissues. Using this purified 6PGD enzyme, we devised an endpoint colorimetric assay suitable for high-throughput screening for human 6PGD inhibitors.

  6. Improved adhesion of superhydrophobic layer on metal surfaces via one step spraying method

    Directory of Open Access Journals (Sweden)

    Wael I. El Dessouky

    2017-03-01

    Full Text Available Superhydrophobic metal substrates have been fabricated by a simple spraying method. The processes of decreasing surface free energy and increasing surface roughness have been accomplished in one step via the addition of functionalized silica (silica nano particles with octyltriethoxysilane to adhesive polymer. The method is simple, cost-effective and can be applied on the large industrial scale. Scanning electron microscopy (SEM was used for surface morphology analysis, showing the roughness produced by surface treatment. The wettability of the micro-nano silica film varied from hydrophilicity (water contact angle 88° to superhydrophobicity (water contact angle 156.9°, while sliding contact angles dramatically decreased (<5° by adding Functionalized silica and/or adhesive polymer. Roughness increased with silica increment which improves the wettability. The coatings were electrochemically characterized by electrochemical impedance spectroscopy (EIS and Tafel polarization curves; it was found that both systems had good performance against corrosion in 3.5% sodium chloride solution. Furthermore, the stability of the coated layer on copper substrate was investigated.

  7. One-step electrodeposition process to fabricate corrosion-resistant superhydrophobic surface on magnesium alloy.

    Science.gov (United States)

    Liu, Qin; Chen, Dexin; Kang, Zhixin

    2015-01-28

    A simple, one-step method has been developed to construct a superhydrophobic surface by electrodepositing Mg-Mn-Ce magnesium plate in an ethanol solution containing cerium nitrate hexahydrate and myristic acid. Scanning electron microscopy, energy-dispersive X-ray spectroscopy, X-ray photoelectron spectroscopy, and Fourier transform infrared spectroscopy were employed to characterize the surfaces. The shortest electrodeposition time to obtain a superhydrophobic surface was about 1 min, and the as-prepared superhydrophobic surfaces had a maximum contact angle of 159.8° and a sliding angle of less than 2°. Potentiodynamic polarization and electrochemical impedance spectroscopy measurements demonstrated that the superhydrophobic surface greatly improved the corrosion properties of magnesium alloy in 3.5 wt % aqueous solutions of NaCl, Na2SO4, NaClO3, and NaNO3. Besides, the chemical stability and mechanical durability of the as-prepared superhydrophobic surface were also examined. The presented method is rapid, low-cost, and environmentally friendly and thus should be of significant value for the industrial fabrication of anticorrosive superhydrophobic surfaces and should have a promising future in expanding the applications of magnesium alloys.

  8. Nearly Perfect Durable Superhydrophobic Surfaces Fabricated by a Simple One-Step Plasma Treatment.

    Science.gov (United States)

    Ryu, Jeongeun; Kim, Kiwoong; Park, JooYoung; Hwang, Bae Geun; Ko, YoungChul; Kim, HyunJoo; Han, JeongSu; Seo, EungRyeol; Park, YongJong; Lee, Sang Joon

    2017-05-16

    Fabrication of superhydrophobic surfaces is an area of great interest because it can be applicable to various engineering fields. A simple, safe and inexpensive fabrication process is required to fabricate applicable superhydrophobic surfaces. In this study, we developed a facile fabrication method of nearly perfect superhydrophobic surfaces through plasma treatment with argon and oxygen gases. A polytetrafluoroethylene (PTFE) sheet was selected as a substrate material. We optimized the fabrication parameters to produce superhydrophobic surfaces of superior performance using the Taguchi method. The contact angle of the pristine PTFE surface is approximately 111.0° ± 2.4°, with a sliding angle of 12.3° ± 6.4°. After the plasma treatment, nano-sized spherical tips, which looked like crown-structures, were created. This PTFE sheet exhibits the maximum contact angle of 178.9°, with a sliding angle less than 1°. As a result, this superhydrophobic surface requires a small external force to detach water droplets dripped on the surface. The contact angle of the fabricated superhydrophobic surface is almost retained, even after performing an air-aging test for 80 days and a droplet impacting test for 6 h. This fabrication method can provide superb superhydrophobic surface using simple one-step plasma etching.

  9. One-step green synthesis of bimetallic Fe/Pd nanoparticles used to degrade Orange II.

    Science.gov (United States)

    Luo, Fang; Yang, Die; Chen, Zuliang; Megharaj, Mallavarapu; Naidu, Ravendra

    2016-02-13

    To reduce cost and enhance reactivity, bimetallic Fe/Pd nanoparticles (NPs) were firstly synthesized using grape leaf aqueous extract to remove Orange II. Green synthesized bimetallic Fe/Pd NPs (98.0%) demonstrated a far higher ability to remove Orange II in 12h compared to Fe NPs (16.0%). Meanwhile, all precursors, e.g., grape leaf extract, Fe(2+) and Pd(2+), had no obvious effect on removing Orange II since less than 2.0% was removed. Kinetics study revealed that the removal rate fitted well to the pseudo-first-order reduction and pseudo-second-order adsorption model, meaning that removing Orange II via Fe/Pd NPs involved both adsorption and catalytic reduction. The remarkable stability of Fe/Pd NPs showed the potential application for removing azo dyes. Furthermore, Scanning Electron Microscopy (SEM) and Fourier Transform Infrared Spectroscopy (FTIR) confirmed the changes in Fe/Pd NPs before and after reaction with Orange II. High Performance Liquid Chromatography-Mass Spectrum (HPLC-MS) identified the degraded products in the removal of Orange II, and finally a removal mechanism was proposed. This one-step strategy using grape leaf aqueous extract to synthesize Fe/Pd NPs is simple, cost-effective and environmentally benign, making possible the large-scale production of Fe/Pd NPs for field remediation. Copyright © 2015 Elsevier B.V. All rights reserved.

  10. Chitosan-coated magnetic nanoparticles prepared in one step by reverse microemulsion precipitation.

    Science.gov (United States)

    López, Raúl G; Pineda, María G; Hurtado, Gilberto; León, Ramón Díaz de; Fernández, Salvador; Saade, Hened; Bueno, Darío

    2013-09-27

    Chitosan-coated magnetic nanoparticles (CMNP) were obtained at 70 °C and 80 °C in a one-step method, which comprises precipitation in reverse microemulsion in the presence of low chitosan concentration in the aqueous phase. X-ray diffractometry showed that CMNP obtained at both temperatures contain a mixture of magnetite and maghemite nanoparticles with ≈4.5 nm in average diameter, determined by electron microscopy, which suggests that precipitation temperature does not affect the particle size. The chitosan coating on nanoparticles was inferred from Fourier transform infrared spectrometry measurements; furthermore, the carbon concentration in the nanoparticles allowed an estimation of chitosan content in CMNP of 6%-7%. CMNP exhibit a superparamagnetic behavior with relatively high final magnetization values (≈49-53 emu/g) at 20 kOe and room temperature, probably due to a higher magnetite content in the mixture of magnetic nanoparticles. In addition, a slight direct effect of precipitation temperature on magnetization was identified, which was ascribed to a possible higher degree of nanoparticles crystallinity as temperature at which they are obtained increases. Tested for Pb2+ removal from a Pb(NO3)2 aqueous solution, CMNP showed a recovery efficacy of 100%, which makes them attractive for using in heavy metals ion removal from waste water.

  11. One-step synthesis and microstructure of CuO-SDC composites

    Energy Technology Data Exchange (ETDEWEB)

    Firmino, H.C.T.; Araujo, A.J.M.; Dutra, R.P.S.; Macedo, D.A., E-mail: hellentorrano@hotmail.com, E-mail: allanjp1993@hotmail.com, E-mail: ricardopsd@gmail.com, E-mail: damaced@gmail.com [Universidade Federal da Paraiba (UFPB), Joao Pessoa, PB (Brazil); Nascimento, R.M., E-mail: rmaribondo@ufrnet.br [Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN (Brazil); Rajesh, S., E-mail: rajeshayr@gmail.com [University of Aveiro (Portugal)

    2017-01-15

    An in situ one step synthesis route based on the polymeric precursor method was used to produce dual phase CuO-samaria doped ceria (SDC) nanocomposite powders. This chemical route allowed to obtain composite powders with reduced particle size and uniform distribution of Cu, Ce and Sm elements. The particulate material was characterized by powder X-ray diffraction (XRD) combined with Rietveld refinement. CuO-SDC sintered in air between 950 to 1050 °C and subsequently reduced to Cu-SDC cermets were further characterized by XRD and scanning electron microscopy. The open porosity was measured using the Archimedes' principle. Suitable microstructures for both charge transfer and mass transport processes (30 to 45% porosity) were attained in Cu-SDC cermets previously fired at 1000 to 1050 °C. Overall results indicated that CuO-SDC composites and Cu-SDC cermets with potential application as anodes for solid oxide fuel cells (SOFCs) can be obtained by microstructural design. An anode supported half-cell was prepared by co-pressing and co-firing gadolinia doped ceria (CGO) and the herein synthesized CuO-SDC nanocomposite powder. (author)

  12. Fluorinated alkyne-derived monolayers on oxide-free silicon nanowires via one-step hydrosilylation

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen Minh, Quyen [Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen (Netherlands); Nanosens, IJsselkade 7, 7201 HB Zutphen (Netherlands); Pujari, Sidharam P. [Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen (Netherlands); Wang, Bin [The Department of Chemical Engineering and Russell Berrie Nanotechnology Institute, Technion – Israel Institute of Technology, Haifa 3200003 (Israel); Wang, Zhanhua [Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen (Netherlands); Haick, Hossam [The Department of Chemical Engineering and Russell Berrie Nanotechnology Institute, Technion – Israel Institute of Technology, Haifa 3200003 (Israel); Zuilhof, Han [Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen (Netherlands); Rijn, Cees J.M. van, E-mail: cees.vanrijn@wur.nl [Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen (Netherlands)

    2016-11-30

    Highlights: • Oxide-free H-terminated silicon nanowires undergo efficient surface modification by reaction with fluorinated 1-alkynes (HC≡C−(CH{sub 2}){sub 6}C{sub 8}H{sub 17−x}F{sub x}; x = 0–17). • These surface-modified Si NWs are chemically stable under range of conditions (including acid, base). • The surface coating yields efficient electrical passivation as demonstrated by a near-zero electrochemical activity of the surface. - Abstract: Passivation of oxide-free silicon nanowires (Si NWs) by the formation of high-quality fluorinated 1-hexadecyne-derived monolayers with varying fluorine content has been investigated. Alkyl chain monolayers (C{sub 16}H{sub 30−x}F{sub x}) with a varying number of fluorine substituents (x = 0, 1, 3, 9, 17) were attached onto hydrogen-terminated silicon (Si−H) surfaces with an effective one-step hydrosilylation. This surface chemistry gives well-defined monolayers on nanowires that have a cylindrical core–shell structure, as characterized by X-ray photoelectron spectroscopy (XPS), Fourier transform infrared spectroscopy (FT-IR) and static contact angle (SCA) analysis. The monolayers were stable under acidic and basic conditions, as well as under extreme conditions (such as UV exposure), and provide excellent surface passivation, which opens up applications in the fields of field effect transistors, optoelectronics and especially for disease diagnosis.

  13. InGaN directional coupler made with a one-step etching technique

    Science.gov (United States)

    Gao, Xumin; Yuan, Jialei; Yang, Yongchao; Zhang, Shuai; Shi, Zheng; Li, Xin; Wang, Yongjin

    2017-06-01

    We propose, fabricate and characterize an on-chip integration of light source, InGaN waveguide, directional coupler and photodiode, in which AlGaN layers are used as top and bottom optical claddings to form an InGaN waveguide for guiding the in-plane emitted light from the InGaN/GaN multiple-quantum-well light-emitting diode (MQW-LED). The difference in etch rate caused by different exposure windows leads to an etching depth discrepancy using the one-step etching technique, which forms the InGaN directional coupler with the overlapped underlying slab. Light propagation results directly confirm effective light coupling in the InGaN directional coupler, which is achieved through high-order guided modes. The InGaN waveguide couples the modulated light from the InGaN/GaN MQW-LED and transfers part of light to the coupled waveguide via the InGaN directional coupler. The in-plane InGaN/GaN MQW-photodiode absorbs the guided light by the coupled InGaN waveguide and induces the photocurrent. The on-chip InGaN photonic integration experimentally demonstrates an in-plane light communication with a data transmission of 50 Mbps.

  14. One-step synthesis and microstructure of CuO-SDC composites

    Directory of Open Access Journals (Sweden)

    H. C. T. Firmino

    Full Text Available Abstract An in situ one step synthesis route based on the polymeric precursor method was used to produce dual phase CuO-samaria doped ceria (SDC nanocomposite powders. This chemical route allowed to obtain composite powders with reduced particle size and uniform distribution of Cu, Ce and Sm elements. The particulate material was characterized by powder X-ray diffraction (XRD combined with Rietveld refinement. CuO-SDC sintered in air between 950 to 1050 °C and subsequently reduced to Cu-SDC cermets were further characterized by XRD and scanning electron microscopy. The open porosity was measured using the Archimedes’ principle. Suitable microstructures for both charge transfer and mass transport processes (30 to 45% porosity were attained in Cu-SDC cermets previously fired at 1000 to 1050 °C. Overall results indicated that CuO-SDC composites and Cu-SDC cermets with potential application as anodes for solid oxide fuel cells (SOFCs can be obtained by microstructural design. An anode supported half-cell was prepared by co-pressing and co-firing gadolinia doped ceria (CGO and the herein synthesized CuO-SDC nanocomposite powder.

  15. One-step electrochemical deposition of Schiff base cobalt complex as effective water oxidation catalyst

    Science.gov (United States)

    Huang, Binbin; Wang, Yan; Zhan, Shuzhong; Ye, Jianshan

    2017-02-01

    Schiff base metal complexes have been applied in many fields, especially, a potential homogeneous catalyst for water splitting. However, the high overpotential, time consumed synthesis process and complicated working condition largely limit their application. In the present work, a one-step approach to fabricate Schiff base cobalt complex modified electrode is developed. Microrod clusters (MRC) and rough spherical particles (RSP) can be obtained on the ITO electrode through different electrochemical deposition condition. Both of the MRC and RSP present favorable activity for oxygen evolution reaction (OER) compared to the commercial Co3O4, taking an overpotential of 650 mV and 450 mV to drive appreciable catalytic current respectively. The highly active and stable RSP shows a Tafel plot of 84 mV dec-1 and negligible decrease of the current density for 12 h bulk electrolysis. The synthesis strategy of effective and stable catalyst in this work provide a simple method to fabricate heterogeneous OER catalyst with Schiff base metal complex.

  16. ONE-STEP PROCESS TO MAKE ELECTRICALLY CONDUCTIVE THERMOPLASTIC VULCANIZATES FILLED WITH MWCNTs

    Institute of Scientific and Technical Information of China (English)

    Hao-sheng Wang; Xiao-hong Zhang; Yi-lei Zhu; Zhi-hai Song; Jin-liang Qiao

    2012-01-01

    Electrically conductive thermoplastic vulcanizates (TPVs) filled by multi-walled carbon nanotubes (MWCNTs)are prepared by a simple one-step melt mixing process,based on linear low density polyethylene (LLDPE) and ultrafine full-vulcanized rubber particles (UFRP).An ideal morphology with controlled localization of MWCNTs in continuous LLDPE matrix and appropriate size of finely-dispersed UFRP can be achieved at the same time.The controlled localization of MWCNTs in the continuous phase facilitates the formation of conductive pathway,and thus the volume resistivity of the as-prepared LLDPE/UFRP/MWCNTs thermoplastic vulcanizates is significantly decreased.The results show that both the blend ratio of LLDPE/UFRP and the loading of MWCNTs have remarkable effect on the volume resistivity.Significantly,the electrically conductive TPVs exhibit good mechanical properties duo to the fine dispersion of UFRP in LLDPE.The added MWCNTs are capable of imparting reinforcement effects to thermoplastic vulcanizates with just a slight loss of stretchability and elasticity.

  17. One step gold (bio)functionalisation based on CS{sub 2}-amine reaction

    Energy Technology Data Exchange (ETDEWEB)

    Almeida, Ines [Centro de Quimica e Bioquimica, Faculdade de Ciencias da Universidade de Lisboa, Ed. C8, Campo Grande, 1749-016 Lisboa (Portugal); Cascalheira, Antonio C. [Lumisense, Lda, Campus Faculdade de Ciencias da Universidade de Lisboa, Ed. ICAT, Campo Grande, 1749-016 Lisboa (Portugal); Viana, Ana S., E-mail: anaviana@fc.ul.p [Centro de Quimica e Bioquimica, Faculdade de Ciencias da Universidade de Lisboa, Ed. C8, Campo Grande, 1749-016 Lisboa (Portugal)

    2010-12-01

    Dithiocarbamates have been regarded as alternative anchor groups to thiols on gold surfaces, and claimed to be formed in situ through the reaction between secondary amines and carbon disulphide. In this paper, we further exploit this methodology for a convenient one step biomolecule immobilisation onto gold surfaces. First, the reactivity between CS{sub 2} and electroactive compounds containing amines, primary (dopamine), secondary (epinephrine), and an amino acid (tryptophan) has been investigated by electrochemical methods. Cyclic voltammetric characterisation of the modified electrodes confirmed the immobilisation of all the target compounds, allowing the estimation of their surface concentration. The best result was obtained with epinephrine, a secondary amine, for which a typical quasi-reversible behaviour of surface confined electroactive species could be clearly depicted. Electrochemical reductive desorption studies enabled to infer on the extent of the reaction and on the relative stability of the generated monolayers. Bio-functionalisation studies have been accomplished through the reaction of CS{sub 2} with glucose oxidase in aqueous medium, and the catalytic activity of the immobilised enzyme was evaluated towards glucose, by electrochemical methods in the presence of a redox mediator. Scanning tunnelling microscopy (STM) and Atomic force microscopy (AFM) were used respectively, to characterize the gold electrodes and Glucose Oxidase coverage and distribution on the modified surfaces.

  18. Enhancement of valve metal osteoconductivity by one-step hydrothermal treatment

    Energy Technology Data Exchange (ETDEWEB)

    Zuldesmi, Mansjur, E-mail: mzuldesmi@yahoo.com [Department of Materials Science and Engineering, Graduate School of Engineering, Nagoya University, Nagoya (Japan); Department of Mechanical Engineering, Manado State University (UNIMA) (Indonesia); Waki, Atsushi [Department of Materials Science and Engineering, Graduate School of Engineering, Nagoya University, Nagoya (Japan); Kuroda, Kensuke; Okido, Masazumi [EcoTopia Science Institute, Nagoya University, Nagoya (Japan)

    2014-09-01

    In this study, we produced super-hydrophilic surfaces of valve metals (Ti, Nb, Ta and Zr) by one-step hydrothermal treatment. Their surface characteristics and osteoconductivity using an in vivo test were then assessed. These data were compared with that of as-polished, as-anodized and both anodized + hydrothermally treated samples. Changes in surface chemistry, surface morphology and structure were investigated by X-ray photoelectron spectroscopy, scanning electron microscopy, and X-ray diffractometry. The results revealed that the water contact angles of valve metals were decreased by hydrothermal treatment and continued to reduce dramatically until lower than 10° after being immersed in phosphate buffered solution. By producing super-hydrophilic surfaces, the osteoconductivity of these hydrothermally treated valve metals was enhanced by up to 55%. - Highlights: • Hydrothermal treatment in distilled water was applied to valve metals. • Surface characteristics and osteoconductivity by in vivo test were evaluated. • Water contact angles of valve metals were decreased by hydrothermal treatment. • Osteoconductivity of valve metals improved notably by hydrothermal treatment.

  19. One-step preparation of hydrogenated ZrO2 microspheres by cathode plasma electrolysis

    Science.gov (United States)

    Liu, Chenxu; Xiang, Qingyun; Yang, Mu; Wang, Shengdian; Wang, Linxiu; Zhang, Jin; He, Yedong

    2017-07-01

    Hydrogenated ZrO2 microspheres were directly prepared by cathode plasma electrolysis (CPE) in an aqueous solution of Zr(NO3)4•5H2O. Owing to the energy of plasma and the cathodic hydrogen evolution reactions, the CPE method combined the preparation of ZrO2 ceramic and the hydrogen treatment into only one step. The results showed regular microspheres consisting of tetragonal-ZrO2 and monoclinic-ZrO2 with 1-10 µm in diameter were formed at relatively high concentration of Zr(NO3)3•5H2O. These ZrO2 microspheres contained about 52.54 µg g-1 hydrogen which caused a narrow band gap (3.10 eV). Thus, the microspheres showed good photocatalytic activity under simulated sunlight, and the degradation of RhB dye reached nearly 58% for 3 h of irradiation, much better than the ZrO2 microspheres after dehydrogenation treatment.

  20. One-step sol-gel imprint lithography for guided-mode resonance structures.

    Science.gov (United States)

    Huang, Yin; Liu, Longju; Johnson, Michael; C Hillier, Andrew; Lu, Meng

    2016-03-01

    Guided-mode resonance (GMR) structures consisting of sub-wavelength periodic gratings are capable of producing narrow-linewidth optical resonances. This paper describes a sol-gel-based imprint lithography method for the fabrication of submicron 1D and 2D GMR structures. This method utilizes a patterned polydimethylsiloxane (PDMS) mold to fabricate the grating coupler and waveguide for a GMR device using a sol-gel thin film in a single step. An organic-inorganic hybrid sol-gel film was selected as the imprint material because of its relatively high refractive index. The optical responses of several sol-gel GMR devices were characterized, and the experimental results were in good agreement with the results of electromagnetic simulations. The influence of processing parameters was investigated in order to determine how finely the spectral response and resonant wavelength of the GMR devices could be tuned. As an example potential application, refractometric sensing experiments were performed using a 1D sol-gel device. The results demonstrated a refractive index sensitivity of 50 nm/refractive index unit. This one-step fabrication process offers a simple, rapid, and low-cost means of fabricating GMR structures. We anticipate that this method can be valuable in the development of various GMR-based devices as it can readily enable the fabrication of complex shapes and allow the doping of optically active materials into sol-gel thin film.

  1. One-step electrolytic preparation of Si-Fe alloys as anodes for lithium ion batteries

    Science.gov (United States)

    Wang, Hailong; Sun, Diankun; Song, Qiqi; Xie, Wenqi; Jiang, Xu; Zhang, Bo

    2016-06-01

    One-step electrolytic formation of uniform crystalline Si-Fe alloy particles was successfully demonstrated in direct electro-reduction of solid mixed oxides of SiO2 and Fe2O3 in molten CaCl2 at 900∘C. Upon constant voltage electrolysis of solid mixed oxides at 2.8V between solid oxide cathode and graphite anode for 5h, electrolytic Si-Fe with the same Si/Fe stoichimetry of the precursory oxides was generated. The firstly generated Fe could function as depolarizers to enhance reduction rate of SiO2, resulting in the enhanced reduction kinetics to the electrolysis of individual SiO2. When evaluated as anode for lithium ion batteries, the prepared SiFe electrode showed a reversible lithium storage capacity as high as 470mAh g-1 after 100 cycles at 200mA g-1, promising application in high-performance lithium ion batteries.

  2. Biocompatible gold nanorods: one-step surface functionalization, highly colloidal stability, and low cytotoxicity.

    Science.gov (United States)

    Liu, Kang; Zheng, Yuanhui; Lu, Xun; Thai, Thibaut; Lee, Nanju Alice; Bach, Udo; Gooding, J Justin

    2015-05-05

    The conjugation of gold nanorods (AuNRs) with polyethylene glycol (PEG) is one of the most effective ways to reduce their cytotoxicity arising from the cetyltrimethylammonium bromide (CTAB) and silver ions used in their synthesis. However, typical PEGylation occurs only at the tips of the AuNRs, producing partially modified AuNRs. To address this issue, we have developed a novel, facile, one-step surface functionalization method that involves the use of Tween 20 to stabilize AuNRs, bis(p-sulfonatophenyl)phenylphosphine (BSPP) to activate the AuNR surface for the subsequent PEGylation, and NaCl to etch silver from the AuNRs. This method allows for the complete removal of the surface-bound CTAB and the most active surface silver from the AuNRs. The produced AuNRs showed far lower toxicity than other methods to PEGylate AuNRs, with no apparent toxicity when their concentration is lower than 5 μg/mL. Even at a high concentration of 80 μg/mL, their cell viability is still four times higher than that of the tip-modified AuNRs.

  3. Rapid synthesis of gold nanorods using a one-step photochemical strategy.

    Science.gov (United States)

    Ahmed, Marya; Narain, Ravin

    2010-12-07

    Rapid synthesis of gold nanorods of controlled dimensions is one of the desired aspects of nanotechnology as a result of the potential of these nanomaterials for biomedical applications. The synthesis of gold nanorods has been achieved using a photoinitiator as an instant source of ketyl radicals, which allows the synthesis of gold nanorods in minutes. This is the first report providing a one-step synthesis of nanorods of controlled dimensions in 20-30 min using photoinitiator I-2959 as a source of ketyl radicals. Furthermore, the role of UV intensity, the concentration of silver ions, and the presence of cosolvents and a cosurfactant have been studied in detail in an effort to produce nanorods with controlled dimensions in higher yields. The role of acetone in nanorod synthesis has been explored in detail, and it has been demonstrated that, for the photochemical synthesis of nanorods using a photoinitiator, acetone is not a critical component and can be replaced by other water-miscible solvents, thus the successful synthesis of nanorods in tetrahydrofuran (THF) has been demonstrated. It has also been found that a cosurfactant and an organic solvent are not required for the synthesis of nanorods; however, their presence is found to improve the monodispersity of nanorod samples, in addition to providing a higher yield.

  4. One-step Solution Processing of Ag, Au and Pd@MXene Hybrids for SERS

    Science.gov (United States)

    Satheeshkumar, Elumalai; Makaryan, Taron; Melikyan, Armen; Minassian, Hayk; Gogotsi, Yury; Yoshimura, Masahiro

    2016-08-01

    We report on one-step hybridization of silver, gold and palladium nanoparticles from solution onto exfoliated two-dimensional (2D) Ti3C2 titanium carbide (MXene) nanosheets. The produced hybrid materials can be used as substrates for surface-enhanced Raman spectroscopy (SERS). An approximate analytical approach is also developed for the calculation of the surface plasmon resonance (SPR) frequency of nanoparticles immersed in a medium, near the interface of two dielectric media with different dielectric constants. We obtained a good match with the experimental data for SPR wavelengths, 440 nm and 558 nm, respectively for silver and gold nanoparticles. In the case of palladium, our calculated SPR wavelength for the planar geometry was 160 nm, demonstrating that non-spherical palladium nanoparticles coupled with 2D MXene yield a broad, significanlty red-shifted SPR band with a peak at 230 nm. We propose a possible mechanism of the plasmonic hybridization of nanoparticles with MXene. The as-prepared noble metal nanoparticles on MXene show a highly sensitive SERS detection of methylene blue (MB) with calculated enhancement factors on the order of 105. These findings open a pathway for extending visible-range SERS applications of novel 2D hybrid materials in sensors, catalysis, and biomedical applications.

  5. Synthesis and Characteristics of Mesoporous Silica Aerogels with One-step Solvent Exchange/Surface Modification

    Institute of Scientific and Technical Information of China (English)

    WANG Lijiu; ZHAO Shanyu

    2009-01-01

    The synthesis procedures and physical properties of the ambient dried hydrophobic silica aerogels by using different contents of ethanol(EtOH)/trimethylchlorosilane(TMCS)/n-Hexane as surface modification agent were investigated.One-step solvent exchange and surface modification were simultaneously progressed by immersing silica hydrogels in EtOH/TMCS/n-Hexane solution.It is found that microstructures as well as properties of silica aerogels like porosity,specific density and specific surface area are affected by the contents of surface modification agent in the sol from the re-sults of SEM,TEM morphology,FT-IR chemical structure,BET surface area and BJH pore size analyses.The volume of TMCS is of 10%and 20%of hydrogels,and the final product is hydrophilic xerogels.When TMCS's percent(v/v)is elevated to 75%-100%,hydrophobic silica aerogels with good performance are synthesized,the porosities of aerogels are in the range of 93.5%-95.8%and the av-erage pore size diameter is less than 20 nm.

  6. Anisotropic wetting of copper alloys induced by one-step laser micro-patterning

    Energy Technology Data Exchange (ETDEWEB)

    Hans, M., E-mail: michael.hans@mx.uni-saarland.de [Chair of Functional Materials, Faculty of Natural Sciences and Technology, Saarland University, 66123 Saarbruecken (Germany); Mueller, F.; Grandthyll, S.; Huefner, S. [Experimental Physics, Faculty of Natural Sciences and Technology, Saarland University, 66123 Saarbruecken (Germany); Muecklich, F. [Chair of Functional Materials, Faculty of Natural Sciences and Technology, Saarland University, 66123 Saarbruecken (Germany)

    2012-12-15

    Highlights: Black-Right-Pointing-Pointer One-step, contactless micro-patterning of copper alloys has been achieved. Black-Right-Pointing-Pointer Anisotropic wetting properties are tailored by line-like structures. Black-Right-Pointing-Pointer Both topographical and chemical patterns contribute to the phenomenon. Black-Right-Pointing-Pointer The topographic shape and homogeneity are found to be governing factors. - Abstract: Copper alloys (CuSn8, CuZn23Al3Co) have been micro-patterned with line-like geometries by Laser Interference Surface Structuring (LISS). In the presented study two high power pulsed laser beams are recombined to create unique, line-like intensity distributions with a chosen, constant periodicity of 10 {mu}m at varying laser fluencies. Anisotropic wetting properties on these surfaces have been confirmed by drop shape analysis and static contact angle measurements, which were conducted parallel and perpendicular to the structures revealing up to 25% difference in contact angle. The topography and chemistry of the tailored line structures have been characterized and analyzed by white light interferometry, spatial frequency distribution, AFM and X-ray photoelectron spectroscopy. The topographic shape and homogeneity are considered as key parameters for anisotropic wetting design, although it is concluded that both, the geometry as well as the locally varying chemical composition of the surface structures contribute to the phenomenon. Parallel capillarity effects and perpendicular contact line pinning are found to be the governing mechanisms.

  7. Epoxy Resins Toughened with Surface Modified Epoxidized Natural Rubber Fibers by One-Step Electrospinning.

    Science.gov (United States)

    Kim, Joo Ran; Kim, Jung J

    2017-04-27

    Epoxidized natural rubber fibers (ERFs) are developed through one-step electrospinning and directly deposited into epoxy resins without collecting and distributing of fibers. The shape of ERFs shows rough surface due to different evaporation rate of solvent mixture consisting of chloroform and dichloromethane and the average diameter of ERFs is 6.2 µm. The increase of ERFs loading from 0 to 20 wt % into the epoxy resin increases the fracture strain significantly from 1.2% to 13% and toughness from 0.3 MPa to 1.9 MPa by a factor of 7. However, the tensile strength and Young's modulus decrease about 34% from 58 MPa to 34 MPa and from 1.4 GPa to 0.9 GPa, respectively. Due to the crosslinking reactions between oxirane groups of ERFs and amine groups in the resin, surface roughness and the high aspect ratio of ERFs, ERFs result in more effective toughening effect with the minimum loss of tensile properties in epoxy resins.

  8. Optimisation of one-step desolvation and scale-up of gelatine nanoparticle production.

    Science.gov (United States)

    Geh, Katharina J; Hubert, Madlen; Winter, Gerhard

    2016-11-01

    Gelatine nanoparticles (GNPs) are biodegradable and biocompatible drug delivery systems with excellent clinical performances. A two-step desolvation is commonly used for their preparation, although this methodology has several shortcomings: lack of reproducibility, small scales and low yields. A straightforward and more consistent GNP preparation approach is presented here focusing on the development of a one-step desolvation with the use of a commercially available gelatine type. Controlled stirring conditions and ultrafiltration are used to achieve large-scale production of nanoparticles of up to 2.6 g per batch. Particle size distributions are conserved and comparable to those determined for two-step desolvation on small scale. Additionally, a range of cross-linking agents is examined for their effectiveness in stabilising GNPs as an alternative to glutaraldehyde. Glyceraldehyde demonstrated outstanding properties, which led to high colloidal stability. This approach optimises the manufacturing process and the scale-up of the production capacity, providing a clear potential for future applications.

  9. Parallel multifunctionalization of nanoparticles: a one-step modular approach for in vivo imaging.

    Science.gov (United States)

    Groult, Hugo; Ruiz-Cabello, Jesús; Pellico, Juan; Lechuga-Vieco, Ana V; Bhavesh, Riju; Zamai, Moreno; Almarza, Elena; Martín-Padura, Inés; Cantelar, Eugenio; Martínez-Alcázar, María P; Herranz, Fernando

    2015-01-21

    Multifunctional nanoparticles are usually produced by sequential synthesis, with long multistep protocols. Our study reports a generic modular strategy for the parallel one-step multifunctionalization of different hydrophobic nanoparticles. The method was designed and developed by taking advantage of the natural noncovalent interactions between the fatty acid binding sites of the bovine serum albumin (BSA) and the aliphatic surfactants on different inorganic nanomaterials. As a general example of the approach, three different nanoparticles-iron oxide, upconverting nanophosphors, and gold nanospheres-were nanoemulsified in water with BSA. To support specific applications, multifunctional capability was incorporated with a variety of previously modified BSA modules. These modules include different conjugated groups, such as chelating agents for (68)Ga or (89)Zr and ligand molecules for enhanced in vivo targeting. A large library of 13 multimodal contrast agents was developed with this convergent strategy. This platform allows a highly versatile and easy tailoring option for efficient incorporation of functional groups. Finally, as demonstration of this versatility, a bimodal (PET/MRI) probe including a maleimide-conjugated BSA was selectively synthesized with an RGD peptide for in vivo imaging detection of tumor angiogenesis.

  10. Cryopreservation of Pistacia spp. seeds by dehydration and one-step freezing.

    Science.gov (United States)

    Ozden-Tokatli, Y; Ozudogru, E A; Gumusel, F; Lambardi, M

    2007-01-01

    Cryopreservation protocols by dehydration and one-step freezing were developed for seeds from three Pistacia species, i.e., P. vera, P. terebinthus and P. lentiscus, which were characterised by different initial germination percentages (100%, 17% and 81%, respectively). In P. vera, a maximum of 90% germination was obtained following 8 hours drying in silica gel (corresponding to 11.7% moisture content on a FW basis) and direct immersion in LN. In P. terebinthus and P. lentiscus, shorter periods of dehydration (1 hour and 15 min, respectively) were sufficient to reduce their moisture content to about 20%, which resulted in peak seed germination percentages from cryostorage of 16% and 47%, respectively. Following cryopreservation, the seeds germinated better on semi-solid MS medium, than on cotton wool wetted with dH(2)O or liquid MS medium. Finally, in P. vera and P. lentiscus, high and significant correlation coefficients were obtained between the TTC viability test and seed germinability after recovery from LN, provided that seeds which were considered positive in the test showed completely or partially red embryonic axes coupled to completely red cotyledons.

  11. Demosaicking by alternating projections: theory and fast one-step implementation.

    Science.gov (United States)

    Lu, Yue M; Karzand, Mina; Vetterli, Martin

    2010-08-01

    Color image demosaicking is a key process in the digital imaging pipeline. In this paper, we study a well-known and influential demosaicking algorithm based upon alternating projections (AP), proposed by Gunturk, Altunbasak and Mersereau in 2002. Since its publication, the AP algorithm has been widely cited and compared against in a series of more recent papers in the demosaicking literature. Despite good performances, a limitation of the AP algorithm is its high computational complexity. We provide three main contributions in this paper. First, we present a rigorous analysis of the convergence property of the AP demosaicking algorithm, showing that it is a contraction mapping, with a unique fixed point. Second, we show that this fixed point is in fact the solution to a constrained quadratic minimization problem, thus, establishing the optimality of the AP algorithm. Finally, using the tool of polyphase representation, we show how to obtain the results of the AP algorithm in a single step, implemented as linear filtering in the polyphase domain. Replacing the original iterative procedure by the proposed one-step solution leads to substantial computational savings, by about an order of magnitude in our experiments.

  12. tCRISPRi: tunable and reversible, one-step control of gene expression

    Science.gov (United States)

    Li, Xin-Tian; Jun, Yonggun; Erickstad, Michael J.; Brown, Steven D.; Parks, Adam; Court, Donald L.; Jun, Suckjoon

    2016-12-01

    The ability to control the level of gene expression is a major quest in biology. A widely used approach employs deletion of a nonessential gene of interest (knockout), or multi-step recombineering to move a gene of interest under a repressible promoter (knockdown). However, these genetic methods are laborious, and limited for quantitative study. Here, we report a tunable CRISPR-cas system, “tCRISPRi”, for precise and continuous titration of gene expression by more than 30-fold. Our tCRISPRi system employs various previous advancements into a single strain: (1) We constructed a new strain containing a tunable arabinose operon promoter PBAD to quantitatively control the expression of CRISPR-(d)Cas protein over two orders of magnitude in a plasmid-free system. (2) tCRISPRi is reversible, and gene expression is repressed under knockdown conditions. (3) tCRISPRi shows significantly less than 10% leaky expression. (4) Most important from a practical perspective, construction of tCRISPRi to target a new gene requires only one-step of oligo recombineering. Our results show that tCRISPRi, in combination with recombineering, provides a simple and easy-to-implement tool for gene expression control, and is ideally suited for construction of both individual strains and high-throughput tunable knockdown libraries.

  13. One-step bone marrow-derived cell transplantation in talarosteochondral lesions: mid-term results.

    Science.gov (United States)

    Buda, Roberto; Vannini, Francesca; Cavallo, Marco; Baldassarri, Matteo; Natali, Simone; Castagnini, Francesco; Giannini, Sandro

    2013-01-01

    to verify the capability of scaffold-supported bone marrow-derived cells to be used in the repair of osteochondral lesions of the talus. using a device to concentrate bone marrow-derived cells, a scaffold (collagen powder or hyaluronic acid membrane) for cell support and platelet gel, a one-step arthroscopic technique was developed for cartilage repair. In a prospective clinical study, we investigated the ability of this technique to repair talar osteochondral lesions in 64 patients. The mean follow-up was 53 months. Clinical results were evaluated using the American Orthopaedic Foot and Ankle Society (AOFAS) scale score. We also considered the influence of scaffold type, lesion area, previous surgery, and lesion depth. the mean preoperative AOFAS scale score was 65.2 ± 13.9. The clinical results peaked at 24 months, before declining gradually to settle at a score of around 80 at the maximum follow-up of 72 months. the use of bone marrow-derived cells supported by scaffolds to repair osteochondral lesions of the talus resulted in significant clinical improvement, which was maintained over time. level IV, therapeutic case series.

  14. One-Step Preparation of Silver Hexagonal Microsheets as Electrically Conductive Adhesive Fillers for Printed Electronics.

    Science.gov (United States)

    Ren, Hu-Ming; Guo, Ying; Huang, Sheng-Yun; Zhang, Kai; Yuen, Matthew M F; Fu, Xian-Zhu; Yu, Shuhui; Sun, Rong; Wong, Ching-Ping

    2015-06-24

    A facile one-step solution-phase chemical reduction method has been developed to synthesize Ag microsheets at room temperature. The morphology of Ag sheets is a regular hexagon more than 1 μm in size and about 200 nm in thickness. The hexagonal Ag microsheets possess a smoother and straighter surface compared with that of the commercial Ag micrometer-sized flakes prepared by ball milling for electrically conductive adhesives (ECAs). The function of the reagents and the formation mechanism of Ag hexagonal microsheets are also investigated. For the polyvinylpyrrolidone (PVP) and citrate facet-selective capping, the Ag atoms freshly reduced by N2H4 would orientationally grow alone on the {111} facet of Ag seeds, with the synergistically selective etching of irregular and small Ag particles by H2O2, to form Ag hexagonal microsheets. The hexagonal Ag microsheet-filled epoxy adhesives, as electrically conductive materials, can be easily printed on various substrates such as polyethylene terephthalate (PET), epoxy, glass, and flexible papers. The hexagonal Ag microsheet filled ECAs demonstrate lower bulk resistivity (approximately 8 × 10(-5) Ω cm) than that of the traditional Ag micrometer-sized-flake-filled ECAs with the same Ag content of 80 wt % (approximately 1.2 × 10(-4) Ω cm).

  15. A Facile One Step Solution Route to Synthesize Cuprous Oxide Nanofluid

    Directory of Open Access Journals (Sweden)

    Shenoy U. Sandhya

    2013-05-01

    Full Text Available A cuprous oxide nanofluid stabilized by sodium lauryl sulfate, synthesized by using the one step method, has been reported. Nanofluids were synthesized by using a well‐ controlled surfactant‐assisted solution phase synthesis. The method involved reduction of copper acetate by glucose in a mixture of water and ethylene glycol serving as the base fluid. The synthesized fluid was characterized by X‐ray and electron diffraction techniques, in addition, transmission and field emission microscopic techniques and Fourier transform infra red spectroscopic analysis was undertaken. The rheological property, as well as the thermal conductivity of the fluid, were measured. The variation of reaction parameters considerably affected the size of the particles as well as the reaction rate. The uniform dispersion of the particles in the base fluid led to a stability period of three months under stationary state, augmenting the thermal conductivity of the nanofluid. The method is found to be simple, reliable and fast for the synthesis of Newtonian nanofluids containing cuprous oxide nanoparticles.

  16. IDENTIFICATION OF SEQUENCE SPECIFIC PCR PRIMERS FOR DETECTION OF THE TOXIGENIC FUNGAL SPECIES STACHYBOTRYS CHARTARUM

    Science.gov (United States)

    The nucleotide sequence of a 936 bp segment of the nuclear rRNA gene operon was determined for the toxigenic fungal species Stachybotrys chartarum and for other species of Stachybotrys and the related genus Memnoniella. This information was used to infer the phylogenitic relati...

  17. IDENTIFICATION OF PUTATIVE SEQUENCE SPECIFIC PCR PRIMERS FOR DETECTION OF THE TOXIGENIC FUNGAL SPECIES STACHYBOTRYS CHARTARUM

    Science.gov (United States)

    The nucleotide sequence of a c 936 bp segment of the nuclear rRNA gene operon was determined for the toxigenic fungal species Stachybotrys chartarum and for other species of Stachbotrys and the related genus Memnoniella. This information was used to infer the phylogenetic relatio...

  18. Homology-integrated CRISPR-Cas (HI-CRISPR) system for one-step multigene disruption in Saccharomyces cerevisiae.

    Science.gov (United States)

    Bao, Zehua; Xiao, Han; Liang, Jing; Zhang, Lu; Xiong, Xiong; Sun, Ning; Si, Tong; Zhao, Huimin

    2015-05-15

    One-step multiple gene disruption in the model organism Saccharomyces cerevisiae is a highly useful tool for both basic and applied research, but it remains a challenge. Here, we report a rapid, efficient, and potentially scalable strategy based on the type II Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR associated proteins (Cas) system to generate multiple gene disruptions simultaneously in S. cerevisiae. A 100 bp dsDNA mutagenizing homologous recombination donor is inserted between two direct repeats for each target gene in a CRISPR array consisting of multiple donor and guide sequence pairs. An ultrahigh copy number plasmid carrying iCas9, a variant of wild-type Cas9, trans-encoded RNA (tracrRNA), and a homology-integrated crRNA cassette is designed to greatly increase the gene disruption efficiency. As proof of concept, three genes, CAN1, ADE2, and LYP1, were simultaneously disrupted in 4 days with an efficiency ranging from 27 to 87%. Another three genes involved in an artificial hydrocortisone biosynthetic pathway, ATF2, GCY1, and YPR1, were simultaneously disrupted in 6 days with 100% efficiency. This homology-integrated CRISPR (HI-CRISPR) strategy represents a powerful tool for creating yeast strains with multiple gene knockouts.

  19. Combining real-time PCR and next-generation DNA sequencing to provide quantitative comparisons of fungal aerosol populations

    Science.gov (United States)

    Dannemiller, Karen C.; Lang-Yona, Naama; Yamamoto, Naomichi; Rudich, Yinon; Peccia, Jordan

    2014-02-01

    We examined fungal communities associated with the PM10 mass of Rehovot, Israel outdoor air samples collected in the spring and fall seasons. Fungal communities were described by 454 pyrosequencing of the internal transcribed spacer (ITS) region of the fungal ribosomal RNA encoding gene. To allow for a more quantitative comparison of fungal exposure in humans, the relative abundance values of specific taxa were transformed to absolute concentrations through multiplying these values by the sample's total fungal spore concentration (derived from universal fungal qPCR). Next, the sequencing-based absolute concentrations for Alternaria alternata, Cladosporium cladosporioides, Epicoccum nigrum, and Penicillium/Aspergillus spp. were compared to taxon-specific qPCR concentrations for A. alternata, C. cladosporioides, E. nigrum, and Penicillium/Aspergillus spp. derived from the same spring and fall aerosol samples. Results of these comparisons showed that the absolute concentration values generated from pyrosequencing were strongly associated with the concentration values derived from taxon-specific qPCR (for all four species, p 0.70). The correlation coefficients were greater for species present in higher concentrations. Our microbial aerosol population analyses demonstrated that fungal diversity (number of fungal operational taxonomic units) was higher in the spring compared to the fall (p = 0.02), and principal coordinate analysis showed distinct seasonal differences in taxa distribution (ANOSIM p = 0.004). Among genera containing allergenic and/or pathogenic species, the absolute concentrations of Alternaria, Aspergillus, Fusarium, and Cladosporium were greater in the fall, while Cryptococcus, Penicillium, and Ulocladium concentrations were greater in the spring. The transformation of pyrosequencing fungal population relative abundance data to absolute concentrations can improve next-generation DNA sequencing-based quantitative aerosol exposure assessment.

  20. RT-PCR and sequence analysis of the full-length fusion protein of Canine Distemper Virus from domestic dogs.

    Science.gov (United States)

    Romanutti, Carina; Gallo Calderón, Marina; Keller, Leticia; Mattion, Nora; La Torre, José

    2016-02-01

    During 2007-2014, 84 out of 236 (35.6%) samples from domestic dogs submitted to our laboratory for diagnostic purposes were positive for Canine Distemper Virus (CDV), as analyzed by RT-PCR amplification of a fragment of the nucleoprotein gene. Fifty-nine of them (70.2%) were from dogs that had been vaccinated against CDV. The full-length gene encoding the Fusion (F) protein of fifteen isolates was sequenced and compared with that of those of other CDVs, including wild-type and vaccine strains. Phylogenetic analysis using the F gene full-length sequences grouped all the Argentinean CDV strains in the SA2 clade. Sequence identity with the Onderstepoort vaccine strain was 89.0-90.6%, and the highest divergence was found in the 135 amino acids corresponding to the F protein signal-peptide, Fsp (64.4-66.7% identity). In contrast, this region was highly conserved among the local strains (94.1-100% identity). One extra putative N-glycosylation site was identified in the F gene of CDV Argentinean strains with respect to the vaccine strain. The present report is the first to analyze full-length F protein sequences of CDV strains circulating in Argentina, and contributes to the knowledge of molecular epidemiology of CDV, which may help in understanding future disease outbreaks.

  1. Citrus psorosis virus: nucleotide sequencing of the coat protein gene and detection by hybridization and RT-PCR.

    Science.gov (United States)

    Barthe, G A; Ceccardi, T L; Manjunath, K L; Derrick, K S

    1998-06-01

    Citrus psorosis virus (CPV) is a multicomponent ssRNA virus with a coat protein of approximately 48 kDa. The viral genome is encapsidated in short and long particles that are readily separated by sucrose density-gradient centrifugation. CPV particles are spiral filaments that are referred to as spiroviruses (SV). A cDNA library of purified short particles from isolate CPV-4 was prepared in a Lambda vector and screened for expression of the coat protein gene (CPG) with a monoclonal antibody to the coat protein. Sequencing of immunopositive clones indicated a single ORF encoding a 49 kDa protein. This ORF, when expressed in E. coli, gave a protein identical in size and immunoreactivity to the CPV coat protein. A full-length clone of the CPG was transcribed and used in Northern hybridization assays to establish that short particle RNA of CPV is negative sense and contains the CPG. Moreover, the CPG was not found on RNA extracted from long particles or on the sedimentable dsRNA from CPV infected tissue. RT-PCR assays were developed for the amplification of a 600 bp fragment of CPG and for the complete CPG (1317 bp). The 600 bp fragment from a biologically and serologically different isolate, CPV-6, was cloned, sequenced and found to share 86% (nucleotide) and 96% (amino acid) identity with CPV-4. BLAST analysis of sequences from CPV-4 and CPV-6 detected no significant nucleic acid or protein similarity with any known viral sequences.

  2. The functional potential of high Arctic permafrost revealed by metagenomic sequencing, qPCR and microarray analyses.

    Science.gov (United States)

    Yergeau, Etienne; Hogues, Hervé; Whyte, Lyle G; Greer, Charles W

    2010-09-01

    The fate of the carbon stocked in permafrost following global warming and permafrost thaw is of major concern in view of the potential for increased CH(4) and CO(2) emissions from these soils. Complex carbon compound degradation and greenhouse gas emissions are due to soil microbial communities, but no comprehensive study has yet addressed their composition and functional potential in permafrost. Here, a 2-m deep permafrost sample and its overlying active layer soil were subjected to metagenomic sequencing, quantitative PCR (qPCR) and microarray analyses. The active layer soil and the 2-m permafrost microbial community structures were very similar, with Actinobacteria being the dominant phylum. The two samples also possessed a highly similar spectrum of functional genes, especially when compared with other already published metagenomes. Key genes related to methane generation, methane oxidation and organic matter degradation were highly diverse for both samples in the metagenomic libraries and some (for example, pmoA) showed relatively high abundance in qPCR assays. Genes related to nitrogen fixation and ammonia oxidation, which could have important roles following climatic change in these nitrogen-limited environments, showed low diversity but high abundance. The 2-m permafrost showed lower abundance and diversity for all the assessed genes and taxa. Experimental biases were also evaluated using qPCR and showed that the whole-community genome amplification technique used caused representational biases in the metagenomic libraries by increasing the abundance of Bacteroidetes and decreasing the abundance of Actinobacteria. This study describes for the first time the detailed functional potential of permafrost-affected soils.

  3. An efficient one-step site-directed deletion, insertion, single and multiple-site plasmid mutagenesis protocol

    Directory of Open Access Journals (Sweden)

    Naismith James H

    2008-12-01

    Full Text Available Abstract Background Mutagenesis plays an essential role in molecular biology and biochemistry. It has also been used in enzymology and protein science to generate proteins which are more tractable for biophysical techniques. The ability to quickly and specifically mutate a residue(s in protein is important for mechanistic and functional studies. Although many site-directed mutagenesis methods have been developed, a simple, quick and multi-applicable method is still desirable. Results We have developed a site-directed plasmid mutagenesis protocol that preserved the simple one step procedure of the QuikChange™ site-directed mutagenesis but enhanced its efficiency and extended its capability for multi-site mutagenesis. This modified protocol used a new primer design that promoted primer-template annealing by eliminating primer dimerization and also permitted the newly synthesized DNA to be used as the template in subsequent amplification cycles. These two factors we believe are the main reasons for the enhanced amplification efficiency and for its applications in multi-site mutagenesis. Conclusion Our modified protocol significantly increased the efficiency of single mutation and also allowed facile large single insertions, deletions/truncations and multiple mutations in a single experiment, an option incompatible with the standard QuikChange™. Furthermore the new protocol required significantly less parental DNA which facilitated the DpnI digestion after the PCR amplification and enhanced the overall efficiency and reliability. Using our protocol, we generated single site, multiple single-site mutations and a combined insertion/deletion mutations. The results demonstrated that this new protocol imposed no additional reagent costs (beyond basic QuikChange™ but increased the overall success rates.

  4. PCR-RFLP Provides Discrimination for Total flaA Sequence Analysis in Clinical Campylobacter jejuni Isolates.

    Science.gov (United States)

    Ghorbanalizadgan, Mahdi; Bakhshi, Bita; Najar-Peerayeh, Shahin

    2016-09-21

    The aims of this study were to determine the genetic relatedness among 20 clinical Campylobacter jejuni samples isolated from children with diarrhea in Iran and to introduce the best method of discrimination based on flagellin gene (flaA) sequence divergence. A total of 400 stool specimens were obtained from children under 5 years of age from July 2012 to June 2013. Primers were designed based on conserved sequences flanking the flaA gene that encompassed and amplified the entire flaA gene and followed by sequencing and data analysis with MEGA version 6.0.6 software. Ninety amino acids and 560 nucleotide polymorphic sequences were detected within 1,681 bp of the flaA sequence of which 43 (2.5%) and 12 (0.7%) were singletons, respectively. New repeat boxes within the flaA sequences were found in this study. Unweighted Pair Group Method with Arithmetic Mean dendrogram based on nucleotides of the full length flaA gene, the flaA short variable region gene and the in silico flaA phylogenic tree of DdeI restriction fragment length polymorphism (RFLP) profiles produced very similar clustering with a diversity index of 0.86 for each of the 3 methods. We conclude that flaA typing based on DdeI RFLP of the PCR products is a cheap, rapid, and reliable method for the epidemiological study of C. jejuni isolates of clinical origin in resource-limited regions or in large-scale population surveillance.

  5. Analysis of 525 samples to determine the usefulness of PCR amplification and sequencing of the 16S rRNA gene for diagnosis of bone and joint infections.

    Science.gov (United States)

    Fenollar, Florence; Roux, Véronique; Stein, Andréas; Drancourt, Michel; Raoult, Didier

    2006-03-01

    The 16S rRNA gene PCR in the diagnosis of bone and joint infections has not been systematically tested. Five hundred twenty-five bone and joint samples collected from 525 patients were cultured and submitted to 16S rRNA gene PCR detection of bacteria in parallel. The amplicons with mixed sequences were also cloned. When discordant results were observed, culture and PCR were performed once again. Bacteria were detected in 139 of 525 samples. Culture and 16S rRNA gene PCR yielded identical documentation in 475 samples. Discrepancies were linked to 13 false-positive culture results, 5 false-positive PCR results, 9 false-negative PCR results, 16 false-negative culture results, and 7 mixed infections. Cloning and sequencing of 16S rRNA gene amplicons in 6 of 8 patients with mixed infections identified 2 to 8 bacteria per sample. Rarely described human pathogens such as Alcaligenes faecalis, Comamonas terrigena, and 21 anaerobes were characterized. We also detected, by 16S rRNA gene PCR, four previously identified bacteria never reported in human infection, Alkanindiges illinoisensis, dehydroabietic acid-degrading bacterium DhA-73, unidentified Hailaer soda lake bacterium, and uncultured bacterium clone HuCa4. Seven organisms representing new potential species were also detected. PCR followed by cloning and sequencing may help to identify new pathogens involved in mixed bone infection.

  6. Magnetic studies of mesoporous nanostructured iron oxide materials synthesized by one-step soft-templating.

    Science.gov (United States)

    Jin, Jing; Hines, William A; Kuo, Chung-Hao; Perry, David M; Poyraz, Altug S; Xia, Yan; Zaidi, Taha; Nieh, Mu-Ping; Suib, Steven L

    2015-07-14

    A combined magnetization and (57)Fe spin-echo nuclear magnetic resonance (NMR) study has been carried out on mesoporous nanostructured materials consisting of the magnetite (Fe3O4) and maghemite (γ-Fe2O3) phases. Two series of samples were synthesized using a recently developed one-step soft-templating approach with systematic variations in calcination temperature and reaction atmosphere. Nuclear magnetic resonance has been shown to be a valuable tool for distinguishing between the two magnetic iron oxide spinel phases, Fe3O4 and γ-Fe2O3, on the nanoscale as well as monitoring phase transformation resulting from oxidation. For the Fe3O4 and γ-Fe2O3 phases, peaks in the NMR spectra are attributed to Fe in the tetrahedral (A) sites and octahedral (B) sites. The magnetic field dependence of the peaks was observed and confirmed the site assignments. Fe3O4 on a nanoscale readily oxidizes to form γ-Fe2O3 and this was clearly evident in the NMR spectra. As evidenced by transmission electron microscope (TEM) images, the porous mesostructure for the iron oxide materials is formed by a random close-packed aggregation of nanoparticles; correspondingly, superparamagnetic behavior was observed in the magnetic measurements. Although X-ray diffraction (XRD) shows the spinel structure for the Fe3O4 and γ-Fe2O3 phases, unlike NMR, it is difficult to distinguish between the two phases with XRD. Nitrogen sorption isotherms characterize the mesoporous structures of the materials, and yield BET surface area values and limited BJH pore size distribution curves.

  7. Nanomembrane Canister Architectures for the Visualization and Filtration of Oxyanion Toxins with One-Step Processing.

    Science.gov (United States)

    Aboelmagd, Ahmed; El-Safty, Sherif A; Shenashen, Mohamed A; Elshehy, Emad A; Khairy, Mohamed; Sakaic, Masaru; Yamaguchi, Hitoshi

    2015-11-01

    Nanomembrane canister-like architectures were fabricated by using hexagonal mesocylinder-shaped aluminosilica nanotubes (MNTs)-porous anodic alumina (PAA) hybrid nanochannels. The engineering pattern of the MNTs inside a 60 μm-long membrane channel enabled the creation of unique canister-like channel necks and cavities. The open-tubular canister architecture design provides controllable, reproducible, and one-step processing patterns of visual detection and rejection/permeation of oxyanion toxins such as selenite (SeO3(2-)) in aquatic environments (i.e., in ground and river water sources) in the Ibaraki Prefecture of Japan. The decoration of organic ligand moieties such as omega chrome black blue (OCG) into inorganic Al2O3@tubular SiO2/Al2O3 canister membrane channel cavities led to the fabrication of an optical nanomembrane sensor (ONS). The OCG ligand was not leached from the canister as observed in washing, sensing, and recovery assays of selenite anions in solution, which enabled its multiple reuse. The ONS makes a variety of alternate processing analyses of selective quantification, visual detection, rejection/permeation, and recovery of toxic selenite quick and simple without using complex instrumentation. Under optimal conditions, the ONS canister exhibited a high selectivity toward selenite anions relative to other ions and a low-level detection limit of 0.0093 μM. Real analytical data showed that approximately 96% of SeO3(2-) anions can be recovered from aquatic and wastewater samples. The ONS canister holds potential for field recovery applications of toxic selenite anions from water. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. One-step electrodeposition process of CuInSe2: Deposition time effect

    Indian Academy of Sciences (India)

    O Meglali; N Attaf; A Bouraiou; M S Aida; S Lakehal

    2014-10-01

    CuInSe2 thin films were prepared by one-step electrodeposition process using a simplified twoelectrodes system. The films were deposited, during 5, 10, 15 and 20 min, from the deionized water solution consisting of CuCl2, InCl3 and SeO2 onto ITO-coated glass substrates. As-deposited films have been annealed under vacuum at 300 °C during 30 min. The structural, optical band gap and electrical resistivity of elaborated films were studied, respectively, using X-ray diffraction (XRD), Raman spectroscopy, UV spectrophotometer and four-point probe method. The micro structural parameters like lattice constants, crystallite size, dislocation density and strain have been evaluated. The XRD investigation proved that the film deposited at 20 min present CuInSe2 single phase in its chalcopyrite structure and with preferred orientation along (1 1 2) direction, whereas the films deposited at 5, 10 and 15 min show the CuInSe2 chalcopyrite structure with the In2Se3 as secondary phase. We have found that the formation mechanism of CuInSe2 depends on the In2Se3 phase. The optical band gap of the films is found to decrease from 1.17 to 1.04 eV with increase in deposition time. All films show Raman spectra with a dominant A1 mode at 174 cm-1, confirming the chalcopyrite crystalline quality of these films. The films exhibited a range of resistivity varying from 2.3 × 10-3 to 4.4 × 10-1 cm.

  9. Dramatic improvement in dissolution rate of albendazole by a simple, one-step, industrially scalable technique

    Directory of Open Access Journals (Sweden)

    Saeed Ghanbarzadeh

    2016-01-01

    Full Text Available Low solubility and dissolution rate are the primary challenges in the drug development which substantially impact the oral absorption and bioavailability of drugs. Due to the poor water solubility, Albendazole (ABZ is poorly absorbed from the gastrointestinal tract and shows low oral bioavailability (5% which is a major disadvantage for the systemic use of ABZ. To improve the solubility and dissolution rate of ABZ, different classes of hydrophilic excipients such as sugars (lactose, sucrose, and glucose, polyols (mannitol and sorbitol, ionic surfactant (sodium lauryl sulfate and non-ionic surfactant (Cremophor A25 were co-spray dried with ABZ. The crystallinity changes in the processed drug were characterized by differential scanning calorimetry and X-Ray diffraction methods were used to interpret the enhanced solubility and dissolution rate of the drug. Results showed that the solubility and dissolution rate of ABZ were increased 1.8-2.6 folds and 3-25 folds, respectively. Unexpectedly, SLS decreased the solubility index of drug powder even lower than the unprocessed drug which was attributed to drug-SLS ionic interaction as depicted from Fourier transform infrared spectroscopy. It was concluded that by applying the facile, one-step, industrially scalable technique and the use of small amounts of excipient (only 4% of the formulation, a great improvement (21 folds in dissolution rate of ABZ was achieved. This finding may be used in the pharmaceutical industries for the formulation of therapeutically efficient dosage forms of class II and IV drugs classified in biopharmaceutical classification system.

  10. One step synthesis of polyacrylamide functionalized graphene and its application in Pb(II) removal

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Zhiwei; Zhang, Yaoyao; Qian, Xiaoming; Shi, Jie; Chen, Lei; Li, Baodong; Niu, Jiarong; Liu, Liangsen, E-mail: 83019163@163.com

    2014-10-15

    Highlights: • PAM-g-graphene is synthesized by the co-irradiation between GO and AM monomers. • PAM graft on GO has led to the exfoliation of GO into individual sheets. • The γ-ray induced reduction of GO. • PAM-g-graphene exhibits high adsorption capacities toward Pb(II) ions. • PAM-g-graphene provides a new idea for heavy metal pollutants’ removal in water. - Abstract: Polyacrylamide grafted graphene (PAM-g-graphene) from graphite oxide (GO) was successfully prepared by γ-ray irradiation with acrylamide monomers in aqueous at room temperature in this paper. Our strategy involves the PAM chains graft on the surface and between the layers of GO by in situ radical polymerization which led to the exfoliation of GO into individual sheets. Results show that the degree of grafting of PAM-g-graphene samples is 24.2%, and the thickness is measured to be 2.59 nm. Moreover, the as-prepared PAM-g-graphene with some amino from PAM and little oxygen functional groups exhibit superior adsorption of Pb(II) ions. The adsorption processes reach equilibrium in just 30 min and the adsorption isotherms are described well by Langmuir and Freundlich classical isotherms models. The determined adsorption capacity of PAM-g-graphene is 819.67 mg g{sup −1} (pH 6) for Pb(II), which is 20 times and 8 times capacities of that for graphene nanosheets and carbon nanotubes according to reports, respectively. This chemically modified graphene synthesized by this fast one-step approach, featuring a good versatility and adaptability, excellent adsorption capacity and rapid extraction, may provide a new idea for the global problem of heavy metal pollutants’ removal in water.

  11. Synthesis of carbon nanoparticles using one step green approach and their application as mercuric ion sensor

    Energy Technology Data Exchange (ETDEWEB)

    Roshni, V.; Ottoor, Divya, E-mail: divya@chem.unipune.ac.in

    2015-05-15

    Carbon nanoparticles (CNPs) have been evolved as a promising candidate for the metal sensing applications due to their synthesis from naturally occurring and easily available non-toxic molecular precursors by green chemistry. A simple and one step procedure is reported here for the synthesis of CNPs from coconut milk by thermal pyrolysis at a temperature of 120–150 °C for 2–5 min without using any carbonizing or passivating agent. On pyrolysis the coconut oil is separated from the carbon rich residue and the residue when dissolved in water showed blue fluorescence under UV light. The CNPs produced are found to show an emission maximum at 440 nm when excited at 360 nm. Synthesis by green approach makes CNPs a promising substitute for the metal sensing applications. Series of metal ions which have a hazardous impact on the ecological system have been taken for the analysis and it is observed that the fluorescence of CNPs gets remarkably quenched by mercuric ions. Fluorescence quenching was studied using standard Stern–Volmer quenching model. Limit of detection was found to be 16.5 nM Hg{sup 2+} concentration. - Highlights: • Green and economical synthesis of carbon nanoparticles (CNPs) from naturally abundant material. • Coconut milk is used as molecular precursor, which on thermal pyrolysis at 120 °C yielded CNPs. • Highly fluorescent CNPs show an emission maxima of 440 nm when excited at 360 nm. • Application of CNPs for metal ion sensing using fluorescence quenching phenomena. • Hg{sup 2+} is most effectively sensed with a detection limit of 16.5 nM.

  12. One-step extraction of polar drugs from plasma by parallel artificial liquid membrane extraction.

    Science.gov (United States)

    Pilařová, Veronika; Sultani, Mumtaz; Ask, Kristine Skoglund; Nováková, Lucie; Pedersen-Bjergaard, Stig; Gjelstad, Astrid

    2017-02-01

    The new microextraction technique named parallel artificial liquid membrane extraction (PALME) was introduced as an alternative approach to liquid-liquid extraction of charged analytes from aqueous samples. The concept is based on extraction of analytes across a supported liquid membrane sustained in the pores of a thin polymeric membrane, a well-known extraction principle also used in hollow fiber liquid-phase microextraction (HF-LPME). However, the new PALME technique offers a more user-friendly setup in which the supported liquid membrane is incorporated in a 96 well plate system. Thus, high-throughput is achievable, in addition to the green chemistry offered by using PALME. The consumption of organic solvent is minimized to 3-5μL per sample. With a sample volume of 250μL and acceptor solution volume of 50μL, a maximal enrichment factor of five is achievable. Based on these parameters, a new method for extraction of polar basic drugs was developed in the present work. The basic drugs hydralazine, ephedrine, metaraminol, salbutamol, and cimetidine were used as model analytes, and were extracted from alkalized human plasma into an aqueous solution via the supported liquid membrane. The extraction was promoted by a carrier dissolved in the membrane, creating a temporary ion-pair complex between the hydrophilic drug and the carrier. As the model analytes were extracted directly into an aqueous solution, there was no need for evaporation of the extract before injection into LC-MS. Hence, the sample preparation is performed in one step. With optimized conditions, the extraction recoveries were in the range 50-89% from human plasma after 45min extraction. The data from the method evaluation were satisfactory and in line with current guidelines, and revealed an extraction method with substantial potential for high throughput bioanalysis of polar basic drugs.

  13. One-step high-efficiency CRISPR/Cas9-mediated genome editing in Streptomyces.

    Science.gov (United States)

    Huang, He; Zheng, Guosong; Jiang, Weihong; Hu, Haifeng; Lu, Yinhua

    2015-04-01

    The RNA-guided DNA editing technology CRISPRs (clustered regularly interspaced short palindromic repeats)/Cas9 had been used to introduce double-stranded breaks into genomes and to direct subsequent site-specific insertions/deletions or the replacement of genetic material in bacteria, such as Escherichia coli, Streptococcus pneumonia, and Lactobacillus reuteri. In this study, we established a high-efficiency CRISPR/Cas9 genome editing plasmid pKCcas9dO for use in Streptomyces genetic manipulation, which comprises a target-specific guide RNA, a codon-optimized cas9, and two homology-directed repair templates. By delivering pKCcas9dO series editing plasmids into the model strain Streptomyces coelicolor M145, through one-step intergeneric transfer, we achieved the genome editing at different levels with high efficiencies of 60%-100%, including single gene deletion, such as actII-orf4, redD, and glnR, and single large-size gene cluster deletion, such as the antibiotic biosynthetic clusters of actinorhodin (ACT) (21.3 kb), undecylprodigiosin (RED) (31.6 kb), and Ca(2+)-dependent antibiotic (82.8 kb). Furthermore, we also realized simultaneous deletions of actII-orf4 and redD, and of the ACT and RED biosynthetic gene clusters with high efficiencies of 54% and 45%, respectively. Finally, we applied this system to introduce nucleotide point mutations into the rpsL gene, which conferred the mutants with resistance to streptomycin. Notably, using this system, the time required for one round of genome modification is reduced by one-third or one-half of those for conventional methods. These results clearly indicate that the established CRISPR/Cas9 genome editing system substantially improves the genome editing efficiency compared with the currently existing methods in Streptomyces, and it has promise for application to genome modification in other Actinomyces species.

  14. One-Step Synthesis of Zeolite Membranes Containing Catalytic Metal Nanoclusters.

    Science.gov (United States)

    Kim, Seok-Jhin; Tan, Shuai; Taborga Claure, Micaela; Briones Gil, Laura; More, Karren L; Liu, Yujun; Moore, Jason S; Dixit, Ravindra S; Pendergast, John G; Sholl, David S; Jones, Christopher W; Nair, Sankar

    2016-09-21

    Metal-loaded zeolitic membranes are promising candidates as catalytic membrane reactors. We report a one-step synthesis method to synthesize zeolite membranes containing metal nanoclusters, that has advantages in comparison to multistep methods such as impregnation and ion exchange. Pure-silica MFI zeolite-Pt hybrid membranes were prepared by hydrothermal synthesis with addition of 3-mercaptopropyl-trimethoxysilane (MPS) and a platinum precursor. Composition analysis and mapping by energy-dispersive X-ray spectroscopy (EDX) reveal that Pt ions/clusters are uniformly distributed along the membrane cross-section. High-magnification scanning transmission electron microscopy (STEM) analysis shows that Pt metal clusters in the hybrid zeolite membrane have a diameter distribution in the range of 0.5-2.0 nm. In contrast, a pure-silica MFI membrane synthesized from an MPS-free solution shows negligible incorporation of Pt metal clusters. To characterize the properties of the hybrid (zeolite/metal) membrane, it was used as a catalytic membrane reactor (CMR) for high-temperature propane dehydrogenation (PDH) at 600 °C and 1 atm. The results indicate that Pt metal clusters formed within the MFI zeolite membrane can serve as effective catalysts for high-temperature PDH reaction along with H2 removal via membrane permeation, thereby increasing both conversion and selectivity in relation to a conventional membrane reactor containing an equivalent amount of packed Pt catalyst in contact with an MFI membrane. The hybrid zeolite-Pt CMR also showed stable conversion and selectivity upon extended high-temperature operation (12 h), indicating that encapsulation in the zeolite allowed thermal stabilization of the Pt nanoclusters and reduced catalyst deactivation.

  15. Vygotsky's Principle "One Step in Learning - One Hundred Steps In Development": From Idea To Practice

    Directory of Open Access Journals (Sweden)

    Zaretsky V.K.,

    2016-12-01

    Full Text Available The article reviews Lev Vygotsky’s published works to trace the evolution of his understanding of child development. The authors believe that his assumption that one step in learning may mean one hundred steps in development, is as important as the two other key postulates of the cultural-historical theory: the principle that learning precedes development and the concept of zone of proximal development. The authors provide a rationale for utilization of these assumptions in the practice of development-facilitating psychological and educational assistance. A mechanism of this learning-development relationship is hypothesized. The article outlines a multidimensional model of the zone of proximal development illustrating the above mechanism. This model is one of the conceptual tools of the Reflection and Activity Approach helping children overcome learning difficulties and promoting their development. Having given the account of how they proceeded “from the idea to the problem” and “from the idea to the mechanism”, the authors provide case studies showing how this mechanism allows working with learning difficulties to trigger simultaneous improvement in multiple developmental dimensions. The article reports on the experience of running special Summer Schools for children with learning difficulties, implementing the “Chess for General Development” Project, and assisting orphaned children with severe somatic conditions. A case study of a female college student displaying signs of the learned helplessness syndrome is presented. The authors infer that Vygotsky’s idea of a specific relationship between learning and development may be of fundamental theoretical and practical value, especially for working with children with special needs.

  16. Identification of Mycobacterium ulcerans in the environment from regions in Southeast Australia in which it is endemic with sequence capture-PCR.

    Science.gov (United States)

    Stinear, T; Davies, J K; Jenkin, G A; Hayman, J A; Oppedisano, F; Johnson, P D

    2000-08-01

    We recently described the use of PCR to identify the environmental source of Mycobacterium ulcerans during an outbreak of ulcerative disease that occurred in a localized region of southeast Australia. The PCR used was based on amplification of the M. ulcerans-specific insertion sequence, IS2404. In this study we developed a new test that is a substantial improvement over the original PCR method in terms of sensitivity, reliability, and ease of use. In the new method magnetic bead sequence capture-PCR is used to detect two M. ulcerans sequences (IS2404 and IS2606) and total mycobacterial 16S ribosomal DNA. We used sequence capture-PCR to test water and plant material collected over a 12-month period during 1998 and 1999 from sites near the centers of two distinct foci of M. ulcerans infections. A golf course irrigation system in one area and a small shallow lake in another area repeatedly were PCR positive for M. ulcerans. Nearby sites and sites unrelated to the endemic areas were negative. Based on the PCR data, a most-probable-number method was used to estimate the concentration of M. ulcerans cells in positive samples from both regions. This procedure resulted in average concentrations of 0.5 cell per 100 ml of water and 40 cells per 100 g of detritus. Loss of the PCR signal coincided with a decrease in ulcerative disease in each area. These results provide further evidence that M. ulcerans may be transmitted from a point environmental source and demonstrate the utility of magnetic bead sequence capture-PCR for identification of nonculturable microbial pathogens in the environment.

  17. Somatic Mutation Screening Using Archival Formalin-Fixed, Paraffin-Embedded Tissues by Fluidigm Multiplex PCR and Illumina Sequencing.

    Science.gov (United States)

    Wang, Ming; Escudero-Ibarz, Leire; Moody, Sarah; Zeng, Naiyan; Clipson, Alexandra; Huang, Yuanxue; Xue, Xuemin; Grigoropoulos, Nicholas F; Barrans, Sharon; Worrillow, Lisa; Forshew, Tim; Su, Jing; Firth, Andrew; Martin, Howard; Jack, Andrew; Brugger, Kim; Du, Ming-Qing

    2015-09-01

    High-throughput somatic mutation screening using FFPE tissues is a major challenge because of a lack of established methods and validated variant calling algorithms. We aimed to develop a targeted sequencing protocol by Fluidigm multiplex PCR and Illumina sequencing and to establish a companion variant calling algorithm. The experimental protocol and variant calling algorithm were first developed and optimized against a series of somatic mutations (147 substitutions, 12 indels ranging from 1 to 33 bp) in seven genes, previously detected by Sanger sequencing of DNA from 163 FFPE lymphoma biopsy specimens. The optimized experimental protocol and variant calling algorithm were further ascertained in two separate experiments by including the seven genes as a part of larger gene panels (22 or 13 genes) using FFPE and high-molecular-weight lymphoma DNAs, respectively. We found that most false-positive variants were due to DNA degradation, deamination, and Taq polymerase errors, but they were nonreproducible and could be efficiently eliminated by duplicate experiments. A small fraction of false-positive variants appeared in duplicate, but they were at low alternative allele frequencies and could be separated from mutations when appropriate threshold value was used. In conclusion, we established a robust practical approach for high-throughput mutation screening using archival FFPE tissues.

  18. Capillary-driven multiparametric microfluidic chips for one-step immunoassays.

    Science.gov (United States)

    Gervais, Luc; Hitzbleck, Martina; Delamarche, Emmanuel

    2011-09-15

    Here we present a capillary-driven microfluidic chip for "one-step" immunoassays. The chip allows for easy modification of several assay parameters such as the flow rates of sample, the volumes of samples for tests, and the type of reagents and receptors for detecting analytes. We therefore term such a chip a multiparametric chip and illustrate this concept with the integration and release of anti-C-reactive protein (CRP) detection antibodies (dAbs) together with splitting flow of samples containing CRP across lines of anti-CRP capture antibodies (cAbs). The microfluidic chip is fabricated in Si and is sealed with polydimethylsiloxane (PDMS) patterned with cAbs. The microfluidic chip is ∼1.7×3.4 cm(2) and is capable of analyzing 20 μL of human serum in 6 parallel flow paths with a range of flow rates from 3.3 nL s(-1) to 0.46 nL s(-1). An inkjet spotter was used to deposit 10.6 nL of dAb solution in a structure vicinal to the main flow path of the chip. The consequent asymmetric release of dAbs in a stream of human serum is compensated by a Dean flow mixer having 9 mixing loops and a footprint of 2.8 mm × 0.78 mm. The quantity of dAb present in the half of the flow path close to the spotting region decreases from 83% at the entrance of the mixer to 52% in the region after the mixer. The sample is then equally split into 6 reaction chambers and proceeds via connecting channels to 2 μL capillary pumps. The hydraulic resistance of the connecting channels is designed to vary flow rates, and therefore the kinetics of capture of CRP-dAb complexes, from 10 min to 72 min. The increased incubation time leads to a fourfold increase in detection signal in the reaction chamber with the longer incubation time. The concept presented here is flexible and suited for implementing various surface fluorescence immunoassays on a capillary-driven microfluidic chip.

  19. A new deterministic Ensemble Kalman Filter with one-step-ahead smoothing for storm surge forecasting

    KAUST Repository

    Raboudi, Naila

    2016-11-01

    The Ensemble Kalman Filter (EnKF) is a popular data assimilation method for state-parameter estimation. Following a sequential assimilation strategy, it breaks the problem into alternating cycles of forecast and analysis steps. In the forecast step, the dynamical model is used to integrate a stochastic sample approximating the state analysis distribution (called analysis ensemble) to obtain a forecast ensemble. In the analysis step, the forecast ensemble is updated with the incoming observation using a Kalman-like correction, which is then used for the next forecast step. In realistic large-scale applications, EnKFs are implemented with limited ensembles, and often poorly known model errors statistics, leading to a crude approximation of the forecast covariance. This strongly limits the filter performance. Recently, a new EnKF was proposed in [1] following a one-step-ahead smoothing strategy (EnKF-OSA), which involves an OSA smoothing of the state between two successive analysis. At each time step, EnKF-OSA exploits the observation twice. The incoming observation is first used to smooth the ensemble at the previous time step. The resulting smoothed ensemble is then integrated forward to compute a "pseudo forecast" ensemble, which is again updated with the same observation. The idea of constraining the state with future observations is to add more information in the estimation process in order to mitigate for the sub-optimal character of EnKF-like methods. The second EnKF-OSA "forecast" is computed from the smoothed ensemble and should therefore provide an improved background. In this work, we propose a deterministic variant of the EnKF-OSA, based on the Singular Evolutive Interpolated Ensemble Kalman (SEIK) filter. The motivation behind this is to avoid the observations perturbations of the EnKF in order to improve the scheme\\'s behavior when assimilating big data sets with small ensembles. The new SEIK-OSA scheme is implemented and its efficiency is demonstrated

  20. Patient satisfaction with a novel one-step hydrogen peroxide solution

    Directory of Open Access Journals (Sweden)

    Schafer J

    2014-10-01

    Full Text Available Jeffery Schafer, Robert Steffen, Marjorie J Rah Bausch & Lomb Incorporated, Rochester, NY, USA Purpose: We aimed to evaluate the product performance of a novel one-step hydrogen ­peroxide cleaning and disinfecting solution, PeroxiClear (“Test” solution, when used by habitual Clear Care users to bilaterally clean and disinfect their soft contact lenses, for approximately 2 weeks.Methods: This was a 2-week, open-label, bilateral eye study designed to include subjects ­ranging in age from 18 to 55 years, inclusive. All subjects were habitual users of the Clear Care peroxide regimen for cleaning, disinfecting, and storage of their soft contact lenses, for at least 6 months prior to enrolling in the study. Subjects were examined at two study visits: a screening/­dispensing visit and a 2-week follow-up visit. The primary end point, patient preference for the Test solution, was evaluated with an online survey administered after 7 days of using the Test cleaning and disinfecting solution. Respondents could answer questions with neutral or nonneutral responses (better or worse. Statistical analyses were conducted to compare differences for nonneutral responses.Results: Of the 299 eligible subjects enrolled, 297 completed the study, conducted at 21 sites by 21 investigators in the United States. A significantly higher proportion of nonneutral respondents reported the Test solution was better overall (85.9% than their habitual contact lens solution (14.1% (P<0.001. The proportion of subjects who preferred the Test solution over their habitual solution was significantly higher for each of the preference questions regarding comfort (85.4% vs 14.6%, moistness (90.0% vs 10.0%, cleanness (91.6% vs 8.4%, and clarity of vision (85.8% vs 14.2%.Conclusion: After 7 days of using the Test cleaning and disinfecting solution, survey results indicated high levels of patient satisfaction and preference over the habitual solution, particularly in the areas of

  1. A versatile one-step CRISPR-Cas9 based approach to plasmid-curing

    DEFF Research Database (Denmark)

    Lauritsen, Ida; Porse, Andreas; Sommer, Morten Otto Alexander

    2017-01-01

    tool enabling rapid removal of plasmids from bacterial cells is lacking. Results Based on replicon abundance and sequence conservation analysis, we show that the vast majority of bacterial cloning and expression vectors share sequence similarities that allow for broad CRISPR-Cas9 targeting. We have...... widely used for expression and engineering purposes. By virtue of the CRISPR-Cas9 targeting, our platform is highly expandable and can be applied in a broad host context. We exemplify the wide applicability of our system in Gram-negative bacteria by demonstrating the successful application in both...

  2. The potential role of incorporating real-time PCR and DNA sequencing for amplification and detection of 16S rRNA gene signatures in neonatal sepsis.

    Science.gov (United States)

    Midan, Dina A; Abo El Fotoh, Wafaa Moustafa M; El Shalakany, Abeer H

    2017-06-01

    This study aimed to explore whether 16S rRNA gene amplification by real time PCR and sequencing could serve as genetic-based methods in rapid and accurate diagnosis of neonatal sepsis. This case control study was conducted on 40 neonates suffering from sepsis like manifestations recruited from the neonatal intensive care unit of Menoufia university hospital over a period of 6 months. Their blood samples were used for paired analysis of bacterial growth using BACTEC 9050 instrument and real time PCR assay with subsequent DNA sequencing for bacterial species identification. The detection rate of culture proven sepsis was 70%. By using real time 16S r RNA PCR amplification method, the detection of bacteria was improved to 80%. Real time PCR revealed sensitivity, specificity, positive predictive value and negative predictive value of [100%, 66.7%, 87.5% and 100%] respectively. Compared to culture, the 16S rRNA real time PCR demonstrated a high negative value for ruling out neonatal sepsis. There was significant statistical difference between the PCR positive and negative cases as regards the hematological sepsis score. The results demonstrated the ability of DNA sequencing to recognize 4 pathogens which were negative by blood culture. The time consumed to detect sepsis using blood culture was up to 5 days while it took up to 16 h only by PCR and sequencing methods. 16S rRNA gene amplification by real time PCR and sequence analysis could be served as ideal and reliable genetic-based methods to diagnose and rule out sepsis with provision of additional data that cannot be obtained by routine laboratory tests with a shorter turnaround time than those with culture-based protocols.

  3. In silico and in vitro evaluation of PCR-based assays for the detection of Bacillus anthracis chromosomal signature sequences.

    Science.gov (United States)

    Ågren, Joakim; Hamidjaja, Raditijo A; Hansen, Trine; Ruuls, Robin; Thierry, Simon; Vigre, Håkan; Janse, Ingmar; Sundström, Anders; Segerman, Bo; Koene, Miriam; Löfström, Charlotta; Van Rotterdam, Bart; Derzelle, Sylviane

    2013-11-15

    Bacillus anthracis, the causative agent of anthrax, is a zoonotic pathogen that is relatively common throughout the world and may cause life threatening diseases in animals and humans. There are many PCR-based assays in use for the detection of B. anthracis. While most of the developed assays rely on unique markers present on virulence plasmids pXO1 and pXO2, relatively few assays incorporate chromosomal DNA markers due to the close relatedness of B. anthracis to the B. cereus group strains. For the detection of chromosomal DNA, different genes have been used, such as BA813, rpoB, gyrA, plcR, S-layer, and prophage-lambda. Following a review of the literature, an in silico analysis of all signature sequences reported for identification of B. anthracis was conducted. Published primer and probe sequences were compared for specificity against 134 available Bacillus spp. genomes. Although many of the chromosomal targets evaluated are claimed to be specific to B. anthracis, cross-reactions with closely related B. cereus and B. thuringiensis strains were often observed. Of the 35 investigated PCR assays, only 4 were 100% specific for the B. anthracis chromosome. An interlaboratory ring trial among five European laboratories was then performed to evaluate six assays, including the WHO recommended procedures, using a collection of 90 Bacillus strains. Three assays performed adequately, yielding no false positive or negative results. All three assays target chromosomal markers located within the lambdaBa03 prophage region (PL3, BA5345, and BA5357). Detection limit was further assessed for one of these highly specific assays.

  4. PCR-SSCP-DNA sequencing method in detecting PTEN gene mutation and its significance in human gastric cancer

    Institute of Scientific and Technical Information of China (English)

    Chuan-Yong Guo; Xuan-Fu Xu; Jian-Ye Wu; Shu-Fang Liu

    2008-01-01

    AIM: To discuss the possible effect of PTEN gene mutations on occurrence and development of gastric cancer.METHODS: Fifty-three gastric cancer specimens were selected to probe PTEN gene mutations in genome of gastric cancer and paracancerous tissues using PCR-SSCP-DNA sequencing method based on microdissection and to observe the protein expression by immunohistochemistry technique.RESULTS: PCR-SSCP-DNA sequencing indicated that 4 kinds of mutation sites were found in 5 of 53 gastric cancer specimens.One kind of mutation was found in exons.AA-TCC mutation was located at 40bp upstream of 3' lateral exert 7 (115946 AA-TCC).Such mutations led to terminator formation in the 297th codon of the PTEN gene.The other 3 kinds of mutation were found in introns,including a G-C point mutation at 91 bp upstream of 5' lateral exon 5(90896 G-C),a T-G point mutation at 24 bp upstream of 5' lateral exon 5 (90963 T-G),and a single base A mutation at 7 bp upstream of 5' lateral exon 5 (90980 A del).The PTEN protein expression in gastric cancer and paracancerous tissues detected using immunohistochemistry technique indicated that the total positive rate of PTEN protein expression was 66% in gastric cancer tissue,which was significantly lower than that (100%) in paracancerous tissues (P<0.005).CONCLUSION: PTEN gene mutation and expression may play an important role in the occurrence and development of gastric cancer.(C)2008 The WJG Press.All rights reserved.

  5. THE IMPROVEMENT OF RT-PCR TECHNIQUE ON DETECTING ROTAVIRUS

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Objective To establish a speed and effective method to detect rotavirus. Methods Using ELISA and one step RT-PCR to detect 196 clinic samples from Xi'an area. Results Compared with ELISA method, one step RT PCR was more sensitive and specific (P <0.05). Conclusion One step RT-PCR is a simple, speed, sensitive and spe cific method for clinic and epidemic studies of rotavirus.

  6. Preparing a re-sequencing DNA library of 2 cancer candidate genes using the ligation-by-amplification protocol by two PCR reactions

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    To meet the needs of large-scale genomic/genetic studies, the next-generation massively parallelized sequencing technologies provide high throughput, low cost and low labor-intensive sequencing service, with subsequent bioinformatic software and laboratory methods developed to expand their applications in various types of research. PCR-based genomic/genetic studies, which have significant usage in association studies like cancer research, haven’t benefited much from those next-generation sequencing technologies, because the shortgun re-sequencing strategy used by such sequencing machines as the Illumina/Solexa Genome Analyzer may not be applied to direct re-sequencing of short-length target regions like those in PCR-based genomic/genetic studies. Although several methods have been proposed to solve this problem, including microarray-based genomic selections and selector-based technologies, they require advanced equipment and procedures which limit their applications in many laboratories. By contrast, we overcame such potential drawbacks by utilizing a ligation by amplification (LBA) protocol, a method using a pair of Universal Adapters to randomly ligate target regions in a two-step-PCR procedure, whose Long LBA products were easily fragmented and sequenced on the next-generation sequencing machine. In this concept-proven study, we chose the consensus coding sequences of two human cancer genes: BRCA1 and BRCA2 as target regions, specifically designed LBA primer pairs to amplify and randomly ligate them. 70 target sequences were successfully amplified and ligated into Long LBA products, which were then fragmented to construct DNA libraries for sequencing on both a conventional Sanger sequencer ABI 3730xl DNA Analyzer and the next-generation ’synthesis by sequencing technology’ Illumina/Solexa Genome Analyzer. Bioinformatic analysis demonstrated the utility and efficiency (including the coverage and depth of each target sequence and the SNPs detection

  7. Preparing a re-sequencing DNA library of 2 cancer candidate genes using the ligation-by-amplification protocol by two PCR reactions

    Institute of Scientific and Technical Information of China (English)

    SU YeYang; LIN Lin; TIAN Geng; CHEN Chen; LIU Tao; XU Xingya; QI XinPeng; ZHANG XiuQing; YANG HuanMing

    2009-01-01

    To meet the needs of large-scale genomic/genetic studies, the next-generation massively parallelized sequencing technologies provide high throughput, low cost and low labor-intensive sequencing ser-vice, with subsequent bioinformatic software and laboratory methods developed to expand their ap-plications in various types of research. PCR-based genomic/genetic studies, which have significant usage in association studies like cancer research, haven't benefited much from those next-generation sequencing technologies, because the shortgun re-sequencing strategy used by such sequencing machines as the Illumina/Solexa Genome Analyzer may not be applied to direct re-sequencing of short-length target regions like those in PCR-based genomic/genetic studies. Although several meth-ods have been proposed to solve this problem, including microarray-based genomic selections and selector-based technologies, they require advanced equipment and procedures which limit their ap-plications in many laboratories. By contrast, we overcame such potential drawbacks by utilizing a liga-tion by amplification (LBA) protocol, a method using a pair of Universal Adapters to randomly ligate target regions in a two-step-PCR procedure, whose Long LBA products were easily fragmented and sequenced on the next-generation sequencing machine. In this concept-proven study, we chose the consensus coding sequences of two human cancer genes: BRCA1 and BRCA2 as target regions, spe-cifically designed LBA primer pairs to amplify and randomly ligate them. 70 target sequences were successfully amplified and ligated into Long LBA products, which were then fragmented to construct DNA libraries for sequencing on both a conventional Sanger sequencer ABI 3730xl DNA Analyzer and the next-generation 'synthesis by sequencing technology' IlluminalSolexa Genome Analyzer. Bioin-formatic analysis demonstrated the utility and efficiency (including the coverage and depth of each target sequence and the SNPs detection

  8. Identification of new flagellin-encoding fliC genes in Escherichia coli isolated from domestic animals using RFLP-PCR and sequencing methods

    Directory of Open Access Journals (Sweden)

    Cláudia de Moura

    2013-04-01

    Full Text Available Identification of Escherichia coli requires knowledge regarding the prevalent serotypes and virulence factors profiles allows the classification in pathogenic/non-pathogenic. However, some of these bacteria do not express flagellar antigen invitro. In this case the PCR-restriction fragment length polymorphism (RFLP-PCR and sequencing of the fliC may be suitable for the identification of antigens by replacing the traditional serology. We studied 17 samples of E. coli isolated from animals and presenting antigen H nontypeable (HNT. The H antigens were characterized by PCR-RFLP and sequencing of fliC gene. Three new flagellin genes were identified, for which specific antisera were obtained. The PCR-RFLP was shown to be faster than the serotyping H antigen in E. coli, provided information on some characteristics of these antigens and indicated the presence of new genes fliC.

  9. A Rapid and Sensitive PCR Strategy Employed for Amplification and Sequencing of por A from a Single Colony-Forming Unit of Neisseria meningitidis

    Science.gov (United States)

    1993-01-01

    of 103-105 per sample (Mullis and Faloona, 1987; lished porA sequences (Barlow et al., 1989; Maiden et al., Arnheim and Erlich, 1992). When the copy...by the culture and Gram- stain techniques, and also by standard PCR protocols ( Arnheim and Erlich, 1992). These samples contained either no...iii) denaturation of DNA at 94 C to the 3-end of the primer by the highly active DNA pol)- initiate the first PCR cycle ( Arnheim and Erlich, 1992

  10. Cloning of ribosomal ITS PCR products creates frequent, non-random chimeric sequences – a test involving heterozygotes between Gymnopus dichrous taxa I and II

    Directory of Open Access Journals (Sweden)

    Karen W. Hughes

    2015-06-01

    Full Text Available Gymnopus dichrous exists in the southern Appalachians (USA as two distinct entities with essentially identical nuclear ribosomal ITS1 sequences but differing ITS2 and LSU sequences (for convenience, called G. dichrous I and II. F1 ITS heterozygotes between the two are routinely collected from nature. Cloning of ITS PCR products from F1 heterozygotes produced sequences of both parental haplotypes but also numerous chimeric sequences (21.9%. The location of template switching was non-random leading to recovery of the same chimera several times and the chimeric region varied from 45bp to 300bp. By comparison, single-basidiospore isolates from heterozygote F1 fruitbodies showed no recombinant haplotypes within the ITS + LSU span and clones derived from P1 homozygotes were identical to the P1 parent. Thus, chimeric sequences are likely an artifact of the PCR-cloning process and not a consequence of natural recombination events found in nature, nor are they due to hidden existing variation within the ribosomal repeat. Chimeras and PCR-induced mutations are common in cloned PCR products and may result in incorrect sequence information in public databases.

  11. Cloning and sequence of a processed p53 pseudogene from rat: a potential source of false 'mutations' in PCR fragments of tumor DNA.

    Science.gov (United States)

    Weghorst, C M; Buzard, G S; Calvert, R J; Hulla, J E; Rice, J M

    1995-12-12

    We describe here the nucleotide (nt) sequence of a p53 processed pseudogene (psi-gene) from the normal F344 rat genome. Exon-derived primers were utilized to amplify and clone a 1447-bp polymerase chain reaction (PCR) product corresponding to the coding regions of exons 2-11 of the functional gene. This psi-gene is a cDNA-like sequence possessing 87% homology with the functional rat p53. We have also partially characterized two additional and distinctly different putative rat p53 psi-genes, focussing on the sequences surrounding the reported rat p53 mutational hot spots of codons 202R and 211R within exon 6/7. Each of these three psi-gene sequences contained various single- and/or double-nt substitutions, small deletions and insertions that distinguish them from p53. One substitution, 211R CGG-->CAG, found both in the cloned psi-gene and in one of the partially characterized, putative psi-genes, corresponded precisely with the sequence that has been reported as a mutation at one of the hot spots. Co-amplification of one or more of the p53 psi-genes with portions of the functional p53 is likely, if exon-based primers are utilized for PCR amplification of rat p53. Consequently, psi-gene sequences are potential sources of sequence variations that can be misidentified as somatic cell mutations by direct sequencing of inappropriately generated PCR products.

  12. Direct Chromatin PCR (DC-PCR): Hypotonic Conditions Allow Differentiation of Chromatin States during Thermal Cycling

    Science.gov (United States)

    Vatolin, Sergei; Khan, Shahper N.; Reu, Frederic J.

    2012-01-01

    Current methods to study chromatin configuration are not well suited for high throughput drug screening since they require large cell numbers and multiple experimental steps that include centrifugation for isolation of nuclei or DNA. Here we show that site specific chromatin analysis can be achieved in one step by simply performing direct chromatin PCR (DC-PCR) on cells. The basic underlying observation was that standard hypotonic PCR buffers prevent global cellular chromatin solubilization during thermal cycling while more loosely organized chromatin can be amplified. Despite repeated heating to >90°C, 41 of 61 tested 5′ sequences of silenced genes (CDKN2A, PU.1, IRF4, FOSB, CD34) were not amplifiable while 47 could be amplified from expressing cells. Two gene regions (IRF4, FOSB) even required pre-heating of cells in isotonic media to allow this differentiation; otherwise none of 19 assayed sequences yielded PCR products. Cells with baseline expression or epigenetic reactivation gave similar DC-PCR results. Silencing during differentiation of CD34 positive cord blood cells closed respective chromatin while treatment of myeloma cells with an IRF4 transcriptional inhibitor opened a site to DC-PCR that was occupied by RNA polymerase II and NFκB as determined by ChIP. Translation into real-time PCR can not be achieved with commercial real-time PCR buffers which potently open chromatin, but even with simple ethidium bromide addition to standard PCR mastermix we were able to identify hits in small molecules screens that suppressed IRF4 expression or reactivated CDKN2A in myeloma cells using densitometry or visual inspection of PCR plates under UV light. While need in drug development inspired this work, application to genome-wide analysis appears feasible using phi29 for selective amplification of open cellular chromatin followed by library construction from supernatants since such supernatants yielded similar results as gene specific DC-PCR. PMID:22984542

  13. Direct chromatin PCR (DC-PCR: hypotonic conditions allow differentiation of chromatin states during thermal cycling.

    Directory of Open Access Journals (Sweden)

    Sergei Vatolin

    Full Text Available Current methods to study chromatin configuration are not well suited for high throughput drug screening since they require large cell numbers and multiple experimental steps that include centrifugation for isolation of nuclei or DNA. Here we show that site specific chromatin analysis can be achieved in one step by simply performing direct chromatin PCR (DC-PCR on cells. The basic underlying observation was that standard hypotonic PCR buffers prevent global cellular chromatin solubilization during thermal cycling while more loosely organized chromatin can be amplified. Despite repeated heating to >90 °C, 41 of 61 tested 5' sequences of silenced genes (CDKN2A, PU.1, IRF4, FOSB, CD34 were not amplifiable while 47 could be amplified from expressing cells. Two gene regions (IRF4, FOSB even required pre-heating of cells in isotonic media to allow this differentiation; otherwise none of 19 assayed sequences yielded PCR products. Cells with baseline expression or epigenetic reactivation gave similar DC-PCR results. Silencing during differentiation of CD34 positive cord blood cells closed respective chromatin while treatment of myeloma cells with an IRF4 transcriptional inhibitor opened a site to DC-PCR that was occupied by RNA polymerase II and NFκB as determined by ChIP. Translation into real-time PCR can not be achieved with commercial real-time PCR buffers which potently open chromatin, but even with simple ethidium bromide addition to standard PCR mastermix we were able to identify hits in small molecules screens that suppressed IRF4 expression or reactivated CDKN2A in myeloma cells using densitometry or visual inspection of PCR plates under UV light. While need in drug development inspired this work, application to genome-wide analysis appears feasible using phi29 for selective amplification of open cellular chromatin followed by library construction from supernatants since such supernatants yielded similar results as gene specific DC-PCR.

  14. Comparison of pulsed-field gel electrophoresis & repetitive sequence-based PCR methods for molecular epidemiological studies of Escherichia coli clinical isolates

    Directory of Open Access Journals (Sweden)

    Il Kwon Bae

    2014-01-01

    Full Text Available Background & objectives: PFGE, rep-PCR, and MLST are widely used to identify related bacterial isolates and determine epidemiologic associations during outbreaks. This study was performed to compare the ability of repetitive sequence-based PCR (rep-PCR and pulsed-field gel electrophoresis (PFGE to determine the genetic relationships among Escherichia coli isolates assigned to various sequence types (STs by two multilocus sequence typing (MLST schemes. Methods: A total of 41 extended-spectrum β-lactamase- (ESBL- and/or AmpC β-lactamase-producing E. coli clinical isolates were included in this study. MLST experiments were performed following the Achtman′s MLST scheme and the Whittam′s MLST scheme, respectively. Rep-PCR experiments were performed using the DiversiLab system. PFGE experiments were also performed. Results: A comparison of the two MLST methods demonstrated that these two schemes yielded compatible results. PFGE correctly segregated E. coli isolates belonging to different STs as different types, but did not group E. coli isolates belonging to the same ST in the same group. Rep-PCR accurately grouped E. coli isolates belonging to the same ST together, but this method demonstrated limited ability to discriminate between E. coli isolates belonging to different STs. Interpretation & conclusions: These results suggest that PFGE would be more effective when investigating outbreaks in a limited space, such as a specialty hospital or an intensive care unit, whereas rep-PCR should be used for nationwide or worldwide epidemiology studies.

  15. Phytoceramide in vertebrate tissues: one step chromatography separation for molecular characterization of ceramide species.

    Directory of Open Access Journals (Sweden)

    Somsankar Dasgupta

    Full Text Available Ceramide is a precursor for complex sphingolipids in vertebrates, while plants contain phytoceramide. By using a novel chromatography purification method we show that phytoceramide comprises a significant proportion of animal sphingolipids. Total ceramide including phytoceramide from mouse tissue (brain, heart, liver lipid extracts and cell culture (mouse primary astrocytes, human oligodendroglioma cells was eluted as a single homogenous fraction, and then analyzed by thin layer chromatography, and further characterized by gas chromatography-mass spectrometry (GC-MS. We detected a unique band that migrated between non-hydroxy fatty acyl ceramide and hydroxy fatty acyl ceramide, and identified it as phytoceramide. Using RT-PCR, we confirmed that mouse tissues expressed desaturase 2, an enzyme that has been reported to generate phytoceramide from dihydroceramide. Previously, only trace amounts of phytoceramide were reported in vertebrate intestine, kidney, and skin. While its function is still elusive, this is the first report of phytoceramide characterization in glial cells and vertebrate brain, heart, and liver.

  16. Comparison of IMRT planning with two-step and one-step optimization: a strategy for improving therapeutic gain and reducing the integral dose

    Science.gov (United States)

    Abate, A.; Pressello, M. C.; Benassi, M.; Strigari, L.

    2009-12-01

    The aim of this study was to evaluate the effectiveness and efficiency in inverse IMRT planning of one-step optimization with the step-and-shoot (SS) technique as compared to traditional two-step optimization using the sliding windows (SW) technique. The Pinnacle IMRT TPS allows both one-step and two-step approaches. The same beam setup for five head-and-neck tumor patients and dose-volume constraints were applied for all optimization methods. Two-step plans were produced converting the ideal fluence with or without a smoothing filter into the SW sequence. One-step plans, based on direct machine parameter optimization (DMPO), had the maximum number of segments per beam set at 8, 10, 12, producing a directly deliverable sequence. Moreover, the plans were generated whether a split-beam was used or not. Total monitor units (MUs), overall treatment time, cost function and dose-volume histograms (DVHs) were estimated for each plan. PTV conformality and homogeneity indexes and normal tissue complication probability (NTCP) that are the basis for improving therapeutic gain, as well as non-tumor integral dose (NTID), were evaluated. A two-sided t-test was used to compare quantitative variables. All plans showed similar target coverage. Compared to two-step SW optimization, the DMPO-SS plans resulted in lower MUs (20%), NTID (4%) as well as NTCP values. Differences of about 15-20% in the treatment delivery time were registered. DMPO generates less complex plans with identical PTV coverage, providing lower NTCP and NTID, which is expected to reduce the risk of secondary cancer. It is an effective and efficient method and, if available, it should be favored over the two-step IMRT planning.

  17. One-Step Generation of Scalable Multiparticle Entanglement for Hot Ions Driven by a Standing-Wave Laser

    Institute of Scientific and Technical Information of China (English)

    杨文星; 陈爱喜

    2011-01-01

    An alternative scheme is proposed for one-step generation of multiparticle cluster state with trapped ions in thermal motion. In this scheme, the ions are simultaneously illuminated by a standing-wave laser tuned to the carrier. During the operations, the vibrational mode is virtually excited, thus the quantum operations are insensitive to the heating. It is shown that the high fidelity multiparticle entanglement could be generated in just one step even including the small fluctuations of parameters. In addition, the ion does not need to be exactly positioned at the node of the standing wave, which is also important from the viewpoint of experiment.

  18. Synthesis of Carbon Nanotube/Graphene Composites by One-Step Chemical Vapor Deposition for Electrodes of Electrochemical Capacitors

    Directory of Open Access Journals (Sweden)

    Chuen-Chang Lin

    2015-01-01

    Full Text Available To control the packing density of carbon nanotubes (CNTs and the number of graphene layers, carbon nanotube/graphene composites are directly grown on cobalt (Co catalysts-coated nickel foam by one-step ambient pressure chemical vapor deposition (CVD at different temperatures and times. The carbon nanotube/graphene composites grown by one-step CVD at 850°C for 10 min possess the highest specific capacitance. Furthermore, a lower growing temperature leads to a higher packing density of CNTs and a smaller number of layers of graphene. A shorter growing time also leads to a smaller number of layers of graphene.

  19. COLD-PCR amplification of bisulfite-converted DNA allows the enrichment and sequencing of rare un-methylated genomic regions.

    Science.gov (United States)

    Castellanos-Rizaldos, Elena; Milbury, Coren A; Karatza, Elli; Chen, Clark C; Makrigiorgos, G Mike; Merewood, Anne

    2014-01-01

    Aberrant hypo-methylation of DNA is evident in a range of human diseases including cancer and diabetes. Development of sensitive assays capable of detecting traces of un-methylated DNA within methylated samples can be useful in several situations. Here we describe a new approach, fast-COLD-MS-PCR, which amplifies preferentially un-methylated DNA sequences. By employing an appropriate denaturation temperature during PCR of bi-sulfite converted DNA, fast-COLD-MS-PCR enriches un-methylated DNA and enables differential melting analysis or bisulfite sequencing. Using methylation on the MGMT gene promoter as a model, it is shown that serial dilutions of controlled methylation samples lead to the reliable sequencing of un-methylated sequences down to 0.05% un-methylated-to-methylated DNA. Screening of clinical glioma tumor and infant blood samples demonstrated that the degree of enrichment of un-methylated over methylated DNA can be modulated by the choice of denaturation temperature, providing a convenient method for analysis of partially methylated DNA or for revealing and sequencing traces of un-methylated DNA. Fast-COLD-MS-PCR can be useful for the detection of loss of methylation/imprinting in cancer, diabetes or diet-related methylation changes.

  20. Identification and molecular epidemiology of dermatophyte isolates by repetitive-sequence-PCR-based DNA fingerprinting using the DiversiLab system in Turkey.

    Science.gov (United States)

    Koc, A Nedret; Atalay, Mustafa A; Inci, Melek; Sariguzel, Fatma M; Sav, Hafize

    2017-05-01

    Dermatophyte species, isolation and identification in clinical samples are still difficult and take a long time. The identification and molecular epidemiology of dermatophytes commonly isolated in a clinical laboratory in Turkey by repetitive sequence-based PCR (rep-PCR) were assessed by comparing the results with those of reference identification. A total of 44 dermatophytes isolated from various clinical specimens of 20 patients with superficial mycoses in Kayseri and 24 patients in Hatay were studied. The identification of dermatophyte isolates was based on the reference identification and rep-PCR using the DiversiLab System (BioMerieux). The genotyping of dermatophyte isolates from different patients was determined by rep-PCR. In the identification of dermatophyte isolates, agreement between rep-PCR and conventional methods was 87.8 % ( 36 of 41). The dermatophyte strains belonged to four clones (A -D) which were determined by the use of rep-PCR. The dermatophyte strains in Clone B, D showed identical patterns with respect to the region. In conclusion, rep-PCR appears to be useful for evaluation of the identification and clonal relationships between Trichophyton rubrum species complex and Trichophyton mentagrophytes species complex isolates. The similarity and diversity of these isolates may be assessed according to different regions by rep-PCR. © 2017 Blackwell Verlag GmbH.

  1. Efficient multiplex simple sequence repeat genotyping of the oomycete plant pathogen Phytophthora infestans

    NARCIS (Netherlands)

    Li, Y.; Cooke, D.E.L.; Jacobsen, E.; Lee, van der T.A.J.

    2013-01-01

    Genotyping is fundamental to population analysis. To accommodate fast, accurate and cost-effective genotyping, a one-step multiplex PCR method employing twelve simple sequence repeat (SSR) markers was developed for high-throughput screening of Phytophthora infestans populations worldwide. The SSR

  2. Sequence-specific "gene signatures" can be obtained by PCR with single specific primers at low stringency.

    OpenAIRE

    Pena, S D; Barreto, G.; Vago, A. R.; De Marco, L; Reinach,F. C.; Dias Neto, E; Simpson, A J

    1994-01-01

    Low-stringency single specific primer PCR (LSSP-PCR) is an extremely simple PCR-based technique that detects single or multiple mutations in gene-sized DNA fragments. A purified DNA fragment is subjected to PCR using high concentrations of a single specific oligonucleotide primer, large amounts of Taq polymerase, and a very low annealing temperature. Under these conditions the primer hybridizes specifically to its complementary region and nonspecifically to multiple sites wi...

  3. On the origins and genetic diversity of South American chickens: one step closer.

    Science.gov (United States)

    Luzuriaga-Neira, A; Villacís-Rivas, G; Cueva-Castillo, F; Escudero-Sánchez, G; Ulloa-Nuñez, A; Rubilar-Quezada, M; Monteiro, R; Miller, M R; Beja-Pereira, A

    2017-06-01

    Local chicken populations are a major source of food in the rural areas of South America. However, very little is known about their genetic composition and diversity. Here, we analyzed five populations from South America to investigate their maternal genetic origin and diversity, hoping to mitigate the lack of information on local chicken populations from this region. We also included three populations of chicken from the Iberian Peninsula and one from Easter Island, which are potential sources of the first chickens introduced in South America. The obtained sequencing data from South American chickens indicate the presence of four haplogroups (A, B, E and D) that can be further subdivided into nine sub-haplogroups. Of these, four (B1, D1a, E1a(b), E1b) were absent from local Iberian Peninsula chickens and one (D1a) was present only on Easter Island. The presence of the sub-haplogroups A1a(b) and E1a(b) in South America, previously only observed in Eastern Asia, and the significant population differentiation between Iberian Peninsula and South American populations, suggest a second maternal source of the extant genetic pool in South American chickens. © 2017 Stichting International Foundation for Animal Genetics.

  4. Use of the PCR and fluorescent probes to recover SSU rRNA gene sequences from single cells of the ciliate protozoon Spathidium.

    Science.gov (United States)

    Dyal, P L; Hope, S; Roberts, D M; Embley, T M

    1995-08-01

    A two-stage heminested PCR approach was developed to amplify small subunit (SSU) rDNA sequences, via two overlapping fragments, from single cells of microbial eucaryotes. The method was evaluated using the ciliate protozoon Spathidium when PCR products were obtained from nine of 10 cells tested. Southern blotting demonstrated that all fragments contained the same sequence in a region of SSU rDNA which is normally highly variable between species. A fluorescent oligonucleotide probe was used to demonstrate that this sequence also occurred in fixed cells of Spathidium. Fixatives containing mercuric salts preserved cell shape and allowed probe binding with little background autofluorescence. The Spathidium sequence is closely related to that from the haptorid Homalozoon vermiculare.

  5. Solving the maxwell equations by the Chebyshev method : A one-step finite-difference time-domain algorithm

    NARCIS (Netherlands)

    De Raedt, H; Michielsen, K; Kole, JS; Figge, MT

    2003-01-01

    We present a one-step algorithm that solves the Maxwell equations for systems with spatially varying permittivity and permeability by the Chebyshev method. We demonstrate that this algorithm may be orders of magnitude more efficient than current finite-difference time-domain (FDTD) algorithms.

  6. Direct construction of predictive models for describing growth Salmonella enteritidis in liquid eggs – a one-step approach

    Science.gov (United States)

    The objective of this study was to develop a new approach using a one-step approach to directly construct predictive models for describing the growth of Salmonella Enteritidis (SE) in liquid egg white (LEW) and egg yolk (LEY). A five-strain cocktail of SE, induced to resist rifampicin at 100 mg/L, ...

  7. One-step Synthesis of n-Butanol from Ethanol Condensation over Alumina-supported Metal Catalysts

    Institute of Scientific and Technical Information of China (English)

    Ke Wu YANG; Xuan Zhen JIANG; Wei Chao ZHANG

    2004-01-01

    One-step synthesis of n-butanol from bimolecular condensation of ethanol was firstly achieved over nickel supported gamma alumina catalyst. A mechanism of dehydration path for the growth of carbon chain by eliminating a hydroxy group from one ethanol molecule with a α-H of other ethanol molecule rather than aldol condensation was verified.

  8. A novel approach for one-step forming ε-caprolactam from cyclohexane nitrozation catalyzed by transition metal salt

    Institute of Scientific and Technical Information of China (English)

    Li Qiu Mao; BO Hua Wu; Du Lin Yin; Kui Yi You; Ping Le Liu; He An Luo

    2007-01-01

    The nitrozation reaction of cyclohexane in one-step reaction to form ε-caprolactam has been studied using transition metal salt as catalysts in this work. The results indicated that the catalysts play an especially important role. This method is expected to be a novel way to synthesize other lactam by similar reaction. The possible mechanism was suggested.

  9. Versatile, Fast, and Easy One-Step Method for the Synthesis of Hydrophilic Lanthanide-Doped Nanoparticles

    NARCIS (Netherlands)

    Grana Suarez, Laura; Verboom, Willem; Sarkar, Shyam; Mahalingam, V.; Huskens, Jurriaan

    2016-01-01

    The preparation of hydrophilic lanthanide-doped nanoparticles (NPs) following a versatile one-step colloidal method at low temperature and short reaction time with different doped lanthanides, capping ligands, and fluoride sources is presented. The photoluminescence of the particles, via both

  10. Treatment of fish processing wastewater in a one-step or two-step upflow anaerobic sludge blanket (UASB) reactor

    NARCIS (Netherlands)

    Paluenzuela-Rollon, A.; Zeeman, G.; Lubberding, H.J.; Lettinga, G.; Alaerts, G.J.

    2002-01-01

    The performance of one-step UASB reactors treating fish processing wastewater of different lipid levels was determined using artificially generated influent simulating that of the canning of sardines and tuna. The organic loading rates (OLR) and the hydraulic retention times (HRT) were 5-8 g COD.l(-

  11. One-Step Generation of Cluster States Assisted by a Strong Driving Classical Field in Cavity Quantum Electrodynamics

    Institute of Scientific and Technical Information of China (English)

    SHAO Xiao-Qiang; ZHANG Shou

    2008-01-01

    We propose a scheme for one-step generation of cluster states with atoms sent through a thermal cavity with strong classical driving field, based on the resonant atom-cavity interaction so that the operating time is sharply short, which is important in the view of decoherence.

  12. Fabrication of an all-polymer electrochemical sensor by using a one-step hot embossing procedure

    DEFF Research Database (Denmark)

    Kafka, Jan Robert; Larsen, Niels Bent; Skaarup, Steen

    2010-01-01

    We present a fast one-step hot embossing procedure for fabricating an all-polymer electrochemical sen¬sor based on a thin, conductive film of poly(3,4-ethylenedioxythiophene) (PEDOT), a few 100s of nano¬meters in thickness, polymerised on top of a non-conductive TOPAS® (Cyclic Olefin Copolymer...

  13. One-step implementation of maximally entangled states of many three-level atoms in microwave cavity QED

    Science.gov (United States)

    Zou, Xubo; Mathis, W.

    2004-09-01

    We propose an experimental scheme for one-step implementation of maximally entangled states of many three-level atoms in microwave cavity QED. In the scheme, many three-level atoms initially prepared in the same superposition states are simultaneously sent through one superconducting cavity, and maximally entangled states can be generated without requiring the measurement and individual addressing of the atoms.

  14. Treatment of fish processing wastewater in a one-step or two-step upflow anaerobic sludge blanket (UASB) reactor

    NARCIS (Netherlands)

    Paluenzuela-Rollon, A.; Zeeman, G.; Lubberding, H.J.; Lettinga, G.; Alaerts, G.J.

    2002-01-01

    The performance of one-step UASB reactors treating fish processing wastewater of different lipid levels was determined using artificially generated influent simulating that of the canning of sardines and tuna. The organic loading rates (OLR) and the hydraulic retention times (HRT) were 5-8 g

  15. Synthesis of Copper Oxalate Nanorods by a Simple One-step Solid-state Chemical Reaction Method

    Institute of Scientific and Technical Information of China (English)

    CAO Ya-li; JIA Dian-zeng; LIU Lang; XIAO Ding-quan; XIN Xin-quan

    2005-01-01

    Copper oxalate nanorods were successfully prepared by means of a simple one-step solid-state reaction method with the assistance of a suitable surfactant, polyethylene glycol 400. The product with uniform rodlike morphology was characterized by XRD, TEM and SEM. The formational mechanism of the rod-like structure was also preliminary discussed.

  16. Detection of genomic variations in BRCA1 and BRCA2 genes by long-range PCR and next-generation sequencing.

    Science.gov (United States)

    Hernan, Imma; Borràs, Emma; de Sousa Dias, Miguel; Gamundi, María José; Mañé, Begoña; Llort, Gemma; Agúndez, José A G; Blanca, Miguel; Carballo, Miguel

    2012-01-01

    Advances in sequencing technologies, such as next-generation sequencing (NGS), represent an opportunity to perform genetic testing in a clinical scenario. In this study, we developed and tested a method for the detection of mutations in the large BRCA1 and BRCA2 tumor suppressor genes, using long-range PCR (LR-PCR) and NGS, in samples from individuals with a personal and/or family history of breast and/or ovarian cancer. Eleven LR-PCR fragments, between 3000 and 15,300 bp, containing all coding exons and flanking splice junctions of BRCA1 and BRCA2, were obtained from DNA samples of five individuals carrying mutations in either BRCA1 or BRCA2. Libraries for NGS were prepared using an enzymatic (Nextera technology) method. We analyzed five individual samples in parallel by NGS and obtained complete coverage of all LR-PCR fragments, with an average coding sequence depth for each nucleotide of >30 reads, running from ×7 (in exon 22 of BRCA1) to >×150. We detected and confirmed 100% of the mutations that predispose to the risk of cancer, together with other genomic variations in BRCA1 and BRCA2. Our approach demonstrates that genomic LR-PCR, together with NGS, using the GS Junior 454 System platform, is an effective method for patient sample analysis of BRCA1 and BRCA2 genes. In addition, this method could be performed in regular molecular genetics laboratories.

  17. Comparison of rpoB gene sequencing, 16S rRNA gene sequencing, gyrB multiplex PCR, and the VITEK2 system for identification of Acinetobacter clinical isolates.

    Science.gov (United States)

    Lee, Min Jung; Jang, Sook Jin; Li, Xue Min; Park, Geon; Kook, Joong-Ki; Kim, Min Jung; Chang, Young-Hyo; Shin, Jong Hee; Kim, Soo Hyun; Kim, Dong-Min; Kang, Seong-Ho; Moon, Dae-Soo

    2014-01-01

    Since accurate identification of species is necessary for proper treatment of Acinetobacter infections, we compared the performances of 4 bacterial identification methods using 167 Acinetobacter clinical isolates to identify the best identification method. To secure more non-baumannii Acinetobacter (NBA) strains as target strains, we first identified Acinetobacter baumannii in a total of 495 Acinetobacter clinical isolates identified using the VITEK 2 system. Because 371 of 495 strains were identified as A. baumannii using gyrB multiplex 1 PCR and blaOXA51-like PCR, we performed rpoB gene sequencing and 16S rRNA gene sequencing on remaining 124 strains belonging to NBA and 52 strains of A. baumannii. For identification of Acinetobacter at the species level, the accuracy rates of rpoB gene sequencing, 16S rRNA gene sequencing, gyrB multiplex PCR, and the VITEK 2 were 98.2%, 93.4%, 77.2%, and 35.9%, respectively. The gyrB multiplex PCR seems to be very useful for the detection of ACB complex because its concordance rates to the final identification of strains of ACB complex were 100%. Both the rpoB gene sequencing and the 16S rRNA gene sequencing may be useful in identifying Acinetobacter.

  18. Quantitative analysis of herpes virus sequences from normal tissue and fibropapillomas of marine turtles with real-time PCR

    Science.gov (United States)

    Quackenbush, S.L.; Casey, R.N.; Murcek, R.J.; Paul, T.A.; Work, T.M.; Limpus, C.J.; Chaves, A.; duToit, L.; Perez, J.V.; Aguirre, A.A.; Spraker, T.R.; Horrocks, J.A.; Vermeer, L.A.; Balazs, G.S.; Casey, J.W.

    2001-01-01

    Quantitative real-time PCR has been used to measure fibropapilloma-associated turtle herpesvirus (FPTHV) pol DNA loads in fibropapillomas, fibromas, and uninvolved tissues of green, loggerhead, and olive ridley turtles from Hawaii, Florida, Costa Rica, Australia, Mexico, and the West Indies. The viral DNA loads from tumors obtained from terminal animals were relatively homogenous (range 2a??20 copies/cell), whereas DNA copy numbers from biopsied tumors and skin of otherwise healthy turtles displayed a wide variation (range 0.001a??170 copies/cell) and may reflect the stage of tumor development. FPTHV DNA loads in tumors were 2.5a??4.5 logs higher than in uninvolved skin from the same animal regardless of geographic location, further implying a role for FPTHV in the etiology of fibropapillomatosis. Although FPTHV pol sequences amplified from tumors are highly related to each other, single signature amino acid substitutions distinguish the Australia/Hawaii, Mexico/Costa Rica, and Florida/Caribbean groups.

  19. [Homologous Analysis Using Repetitive-sequence-based PCR Typing of Exfoliative Toxin-producing Staphylococcus aureus Isolated from Our Hospital].

    Science.gov (United States)

    Miyamoto, Hitoshi; Murakami, Shinobu; Nishimiya, Tatsuya; Suemori, Koichiro; Tauchi, Hisamichi

    2015-05-01

    We examined staphylococcal coagulase types and homologous analysis using the DiversiLab repetitive-sequence-based PCR system in exfoliative toxin (ET)-producing Staphylococcus aureus. Twenty-two isolates (17 methicillin-sensitive Staphylococcus aureus (MSSA) and 5 methicillin-resistant Staphylococcus aureus (MRSA) isolates) obtained in our hospital from January 2012 and December 2013 were used. Three groups were classified according to the coagulase types and serotypes of ET. The first group (4 MSSA) showed coagulase type I and ET-A, and the second group (3 MSSA and 2 MRSA) showed coagulase type I and ET-B. The third group (10 MSSA and 3 MRSA) showed coagulase type V and ET-B. An analysis by DiversiLab demonstrated that homology was high in both the first and second groups. The homogenousness was high among the third group isolates except for the ocular isolates. In our hospital, three important groups were present according to a coagulase type and an ET type, and the homology of ocular isolates could be different