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Sample records for amplicon va derived

  1. Herpes simplex virus type 1-derived recombinant and amplicon vectors.

    PubMed

    Fraefel, Cornel; Marconi, Peggy; Epstein, Alberto L

    2011-01-01

    Herpes simplex virus type 1 (HSV-1) is a human pathogen whose lifestyle is based on a long-term dual interaction with the infected host, being able to establish both lytic and latent infections. The virus genome is a 153 kbp double-stranded DNA molecule encoding more than 80 genes. The interest of HSV-1 as gene transfer vector stems from its ability to infect many different cell types, both quiescent and proliferating cells, the very high packaging capacity of the virus capsid, the outstanding neurotropic adaptations that this virus has evolved, and the fact that it never integrates into the cellular chromosomes, thus avoiding the risk of insertional mutagenesis. Two types of vectors can be derived from HSV-1, recombinant vectors and amplicon vectors, and different methodologies have been developed to prepare large stocks of each type of vector. This chapter summarizes (1) the two approaches most commonly used to prepare recombinant vectors through homologous recombination, either in eukaryotic cells or in bacteria, and (2) the two methodologies currently used to generate helper-free amplicon vectors, either using a bacterial artificial chromosome (BAC)-based approach or a Cre/loxP site-specific recombination strategy.

  2. Functional Overexpression of Vomeronasal Receptors Using a Herpes Simplex Virus Type 1 (HSV-1)-Derived Amplicon

    PubMed Central

    Stein, Benjamin; Alonso, María Teresa; Zufall, Frank; Leinders-Zufall, Trese; Chamero, Pablo

    2016-01-01

    In mice, social behaviors such as mating and aggression are mediated by pheromones and related chemosignals. The vomeronasal organ (VNO) detects olfactory information from other individuals by sensory neurons tuned to respond to specific chemical cues. Receptors expressed by vomeronasal neurons are implicated in selective detection of these cues. Nearly 400 receptor genes have been identified in the mouse VNO, but the tuning properties of individual receptors remain poorly understood, in part due to the lack of a robust heterologous expression system. Here we develop a herpes virus-based amplicon delivery system to overexpress three types of vomeronasal receptor genes and to characterize cell responses to their proposed ligands. Through Ca2+ imaging in native VNO cells we show that virus-induced overexpression of V1rj2, V2r1b or Fpr3 caused a pronounced increase of responsivity to sulfated steroids, MHC-binding peptide or the synthetic hexapeptide W-peptide, respectively. Other related ligands were not recognized by infected individual neurons, indicating a high degree of selectivity by the overexpressed receptor. Removal of G-protein signaling eliminates Ca2+ responses, indicating that the endogenous second messenger system is essential for observing receptor activation. Our results provide a novel expression system for vomeronasal receptors that should be useful for understanding the molecular logic of VNO ligand detection. Functional expression of vomeronasal receptors and their deorphanization provides an essential requirement for deciphering the neural mechanisms controlling behavior. PMID:27195771

  3. Functional Overexpression of Vomeronasal Receptors Using a Herpes Simplex Virus Type 1 (HSV-1)-Derived Amplicon.

    PubMed

    Stein, Benjamin; Alonso, María Teresa; Zufall, Frank; Leinders-Zufall, Trese; Chamero, Pablo

    2016-01-01

    In mice, social behaviors such as mating and aggression are mediated by pheromones and related chemosignals. The vomeronasal organ (VNO) detects olfactory information from other individuals by sensory neurons tuned to respond to specific chemical cues. Receptors expressed by vomeronasal neurons are implicated in selective detection of these cues. Nearly 400 receptor genes have been identified in the mouse VNO, but the tuning properties of individual receptors remain poorly understood, in part due to the lack of a robust heterologous expression system. Here we develop a herpes virus-based amplicon delivery system to overexpress three types of vomeronasal receptor genes and to characterize cell responses to their proposed ligands. Through Ca2+ imaging in native VNO cells we show that virus-induced overexpression of V1rj2, V2r1b or Fpr3 caused a pronounced increase of responsivity to sulfated steroids, MHC-binding peptide or the synthetic hexapeptide W-peptide, respectively. Other related ligands were not recognized by infected individual neurons, indicating a high degree of selectivity by the overexpressed receptor. Removal of G-protein signaling eliminates Ca2+ responses, indicating that the endogenous second messenger system is essential for observing receptor activation. Our results provide a novel expression system for vomeronasal receptors that should be useful for understanding the molecular logic of VNO ligand detection. Functional expression of vomeronasal receptors and their deorphanization provides an essential requirement for deciphering the neural mechanisms controlling behavior. PMID:27195771

  4. A Novel Ligustrazine Derivative T-VA Prevents Neurotoxicity in Differentiated PC12 Cells and Protects the Brain against Ischemia Injury in MCAO Rats

    PubMed Central

    Li, Guoling; Tian, Yufei; Zhang, Yuzhong; Hong, Ying; Hao, Yingzhi; Chen, Chunxiao; Wang, Penglong; Lei, Haimin

    2015-01-01

    Broad-spectrum drugs appear to be more promising for the treatment of acute ischemic stroke. In our previous work, a new ligustrazine derivative (3,5,6-trimethylpyrazin-2-yl) methyl 3-methoxy-4-[(3,5,6-trimethylpyrazin-2-yl)methoxy]benzoate (T-VA) showed neuroprotective effect on injured PC12 cells (EC50 = 4.249 µM). In the current study, we show that this beneficial effect was due to the modulation of nuclear transcription factor-κB/p65 (NF-κB/p65) and cyclooxygenase-2 (COX-2) expressions. We also show that T-VA exhibited neuroprotective effect in a rat model of ischemic stroke with concomitant improvement of motor functions. We propose that the protective effect observed in vivo is owing to increased vascular endothelial growth factor (VEGF) expression, decreased oxidative stress, and up-regulation of Ca2+–Mg2+ ATP enzyme activity. Altogether, our results warrant further studies on the utility of T-VA for the potential treatment of ischemic brain injuries, such as stroke. PMID:26370988

  5. Amplicon –Based Metagenomic Analysis of Mixed Fungal Samples Using Proton Release Amplicon Sequencing

    PubMed Central

    Tonge, Daniel P.; Pashley, Catherine H.; Gant, Timothy W.

    2014-01-01

    Next generation sequencing technology has revolutionised microbiology by allowing concurrent analysis of whole microbial communities. Here we developed and verified similar methods for the analysis of fungal communities using a proton release sequencing platform with the ability to sequence reads of up to 400 bp in length at significant depth. This read length permits the sequencing of amplicons from commonly used fungal identification regions and thereby taxonomic classification. Using the 400 bp sequencing capability, we have sequenced amplicons from the ITS1, ITS2 and LSU fungal regions to a depth of approximately 700,000 raw reads per sample. Representative operational taxonomic units (OTUs) were chosen by the USEARCH algorithm, and identified taxonomically through nucleotide blast (BLASTn). Combination of this sequencing technology with the bioinformatics pipeline allowed species recognition in two controlled fungal spore populations containing members of known identity and concentration. Each species included within the two controlled populations was found to correspond to a representative OTU, and these OTUs were found to be highly accurate representations of true biological sequences. However, the absolute number of reads attributed to each OTU differed among species. The majority of species were represented by an OTU derived from all three genomic regions although in some cases, species were only represented in two of the regions due to the absence of conserved primer binding sites or due to sequence composition. It is apparent from our data that proton release sequencing technologies can deliver a qualitative assessment of the fungal members comprising a sample. The fact that some fungi cannot be amplified by specific “conserved” primer pairs confirms our recommendation that a multi-region approach be taken for other amplicon-based metagenomic studies. PMID:24728005

  6. Association of Myosin Va and Schwann cells-derived RNA in mammal myelinated axons, analyzed by immunocytochemistry and confocal FRET microscopy.

    PubMed

    Canclini, Lucía; Wallrabe, Horst; Di Paolo, Andrés; Kun, Alejandra; Calliari, Aldo; Sotelo-Silveira, José Roberto; Sotelo, José Roberto

    2014-03-15

    Evidence from multiple sources supports the hypothesis that Schwann cells in the peripheral nervous system transfer messenger RNA and ribosomes to the axons they ensheath. Several technical and methodological difficulties exist for investigators to unravel this process in myelinated axons - a complex two-cell unit. We present an experimental design to demonstrate that newly synthesized RNA is transferred from Schwann cells to axons in association with Myosin Va. The use of quantitative confocal FRET microscopy to track newly-synthesized RNA and determine the molecular association with Myosin Va, is described in detail.

  7. Cooperative epigenetic modulation by cancer amplicon genes.

    PubMed

    Rui, Lixin; Emre, N C Tolga; Kruhlak, Michael J; Chung, Hye-Jung; Steidl, Christian; Slack, Graham; Wright, George W; Lenz, Georg; Ngo, Vu N; Shaffer, Arthur L; Xu, Weihong; Zhao, Hong; Yang, Yandan; Lamy, Laurence; Davis, R Eric; Xiao, Wenming; Powell, John; Maloney, David; Thomas, Craig J; Möller, Peter; Rosenwald, Andreas; Ott, German; Muller-Hermelink, Hans Konrad; Savage, Kerry; Connors, Joseph M; Rimsza, Lisa M; Campo, Elias; Jaffe, Elaine S; Delabie, Jan; Smeland, Erlend B; Weisenburger, Dennis D; Chan, Wing C; Gascoyne, Randy D; Levens, David; Staudt, Louis M

    2010-12-14

    Chromosome band 9p24 is frequently amplified in primary mediastinal B cell lymphoma (PMBL) and Hodgkin lymphoma (HL). To identify oncogenes in this amplicon, we screened an RNA interference library targeting amplicon genes and thereby identified JAK2 and the histone demethylase JMJD2C as essential genes in these lymphomas. Inhibition of JAK2 and JMJD2C cooperated in killing these lymphomas by decreasing tyrosine 41 phosphorylation and increasing lysine 9 trimethylation of histone H3, promoting heterochromatin formation. MYC, a major target of JAK2-mediated histone phosphorylation, was silenced after JAK2 and JMJD2C inhibition, with a corresponding increase in repressive chromatin. Hence, JAK2 and JMJD2C cooperatively remodel the PMBL and HL epigenome, offering a mechanistic rationale for the development of JAK2 and JMJD2C inhibitors in these diseases. PMID:21156283

  8. Cooperative Epigenetic Modulation by Cancer Amplicon Genes

    PubMed Central

    Rui, Lixin; Tolga Emre, N. C.; Kruhlak, Michael J.; Chung, Hye-Jung; Steidl, Christian; Slack, Graham; Wright, George W.; Lenz, Georg; Ngo, Vu N.; Shaffer, Arthur L.; Xu, Weihong; Zhao, Hong; Yang, Yandan; Lamy, Laurence; Davis, R. Eric; Xiao, Wenming; Powell, John; Maloney, David; Thomas, Craig J.; Möller, Peter; Rosenwald, Andreas; Ott, German; Muller-Hermelink, Hans Konrad; Savage, Kerry; Connors, Joseph M.; Rimsza, Lisa M.; Campo, Elias; Jaffe, Elaine S.; Delabie, Jan; Smeland, Erlend B.; Weisenburger, Dennis D.; Chan, Wing C.; Gascoyne, Randy D.; Levens, David; Staudt, Louis M.

    2010-01-01

    Chromosome band 9p24 is frequently amplified in primary mediastinal B-cell lymphoma (PMBL) and Hodgkin lymphoma (HL). To identify oncogenes in this amplicon, we screened an RNA interference library targeting amplicon genes and thereby identified JAK2 and the histone demethylase JMJD2C as essential genes in these lymphomas. Inhibition of JAK2 and JMJD2C cooperated in killing these lymphomas by decreasing tyrosine 41 phosphorylation and increasing lysine 9 trimethylation of histone H3, promoting heterochromatin formation. MYC, a major target of JAK2-mediated histone phosphorylation, was silenced following JAK2 and JMJD2C inhibition, with a corresponding increase in repressive chromatin. Hence, JAK2 and JMJD2C cooperatively remodel the PMBL and HL epigenome, offering a mechanistic rationale for the development of JAK2 and JMJD2C inhibitors in these diseases. PMID:21156283

  9. Silencing Status Epilepticus-Induced BDNF Expression with Herpes Simplex Virus Type-1 Based Amplicon Vectors.

    PubMed

    Falcicchia, Chiara; Trempat, Pascal; Binaschi, Anna; Perrier-Biollay, Coline; Roncon, Paolo; Soukupova, Marie; Berthommé, Hervé; Simonato, Michele

    2016-01-01

    Brain-derived neurotrophic factor (BDNF) has been found to produce pro- but also anti-epileptic effects. Thus, its validity as a therapeutic target must be verified using advanced tools designed to block or to enhance its signal. The aim of this study was to develop tools to silence the BDNF signal. We generated Herpes simplex virus type 1 (HSV-1) derived amplicon vectors, i.e. viral particles containing a genome of 152 kb constituted of concatameric repetitions of an expression cassette, enabling the expression of the gene of interest in multiple copies. HSV-1 based amplicon vectors are non-pathogenic and have been successfully employed in the past for gene delivery into the brain of living animals. Therefore, amplicon vectors should represent a logical choice for expressing a silencing cassette, which, in multiple copies, is expected to lead to an efficient knock-down of the target gene expression. Here, we employed two amplicon-based BDNF silencing strategies. The first, antisense, has been chosen to target and degrade the cytoplasmic mRNA pool of BDNF, whereas the second, based on the convergent transcription technology, has been chosen to repress transcription at the BDNF gene. Both these amplicon vectors proved to be effective in down-regulating BDNF expression in vitro, in BDNF-expressing mesoangioblast cells. However, only the antisense strategy was effective in vivo, after inoculation in the hippocampus in a model of status epilepticus in which BDNF mRNA levels are strongly increased. Interestingly, the knocking down of BDNF levels induced with BDNF-antisense was sufficient to produce significant behavioral effects, in spite of the fact that it was produced only in a part of a single hippocampus. In conclusion, this study demonstrates a reliable effect of amplicon vectors in knocking down gene expression in vitro and in vivo. Therefore, this approach may find broad applications in neurobiological studies.

  10. Silencing Status Epilepticus-Induced BDNF Expression with Herpes Simplex Virus Type-1 Based Amplicon Vectors

    PubMed Central

    Falcicchia, Chiara; Trempat, Pascal; Binaschi, Anna; Perrier-Biollay, Coline; Roncon, Paolo; Soukupova, Marie; Berthommé, Hervé; Simonato, Michele

    2016-01-01

    Brain-derived neurotrophic factor (BDNF) has been found to produce pro- but also anti-epileptic effects. Thus, its validity as a therapeutic target must be verified using advanced tools designed to block or to enhance its signal. The aim of this study was to develop tools to silence the BDNF signal. We generated Herpes simplex virus type 1 (HSV-1) derived amplicon vectors, i.e. viral particles containing a genome of 152 kb constituted of concatameric repetitions of an expression cassette, enabling the expression of the gene of interest in multiple copies. HSV-1 based amplicon vectors are non-pathogenic and have been successfully employed in the past for gene delivery into the brain of living animals. Therefore, amplicon vectors should represent a logical choice for expressing a silencing cassette, which, in multiple copies, is expected to lead to an efficient knock-down of the target gene expression. Here, we employed two amplicon-based BDNF silencing strategies. The first, antisense, has been chosen to target and degrade the cytoplasmic mRNA pool of BDNF, whereas the second, based on the convergent transcription technology, has been chosen to repress transcription at the BDNF gene. Both these amplicon vectors proved to be effective in down-regulating BDNF expression in vitro, in BDNF-expressing mesoangioblast cells. However, only the antisense strategy was effective in vivo, after inoculation in the hippocampus in a model of status epilepticus in which BDNF mRNA levels are strongly increased. Interestingly, the knocking down of BDNF levels induced with BDNF-antisense was sufficient to produce significant behavioral effects, in spite of the fact that it was produced only in a part of a single hippocampus. In conclusion, this study demonstrates a reliable effect of amplicon vectors in knocking down gene expression in vitro and in vivo. Therefore, this approach may find broad applications in neurobiological studies. PMID:26954758

  11. Metabarcoding Marine Sediments: Preparation of Amplicon Libraries.

    PubMed

    Fonseca, Vera G; Lallias, Delphine

    2016-01-01

    The accurate assessment of community composition and ultimately species identification is of utmost importance in any ecological and evolutionary study. Advances in sequencing technologies have allowed the unraveling of levels of biodiversity never imagined before when applied to large-scale environmental DNA studies (also termed metabarcoding/metagenetics/metasystematics/environmental barcoding). Here, we describe a detailed protocol to assess eukaryotic biodiversity in marine sediments, identifying key steps that should not be neglected when preparing Next-Generation Sequencing (NGS) amplicon libraries: DNA extraction, multiple PCR amplification of DNA barcode markers with index/ tag-primers, and final Illumina MiSeq sequencing library preparation. PMID:27460378

  12. Determining VA physician requirements through empirically based models.

    PubMed Central

    Lipscomb, J; Kilpatrick, K E; Lee, K L; Pieper, K S

    1995-01-01

    OBJECTIVE: As part of a project to estimate physician requirements for the Department of Veterans Affairs, the Institute of Medicine (IOM) developed and tested empirically based models of physician staffing, by specialty, that could be applied to each VA facility. DATA SOURCE/STUDY SETTING. These analyses used selected data on all patient encounters and all facilities in VA's management information systems for FY 1989. STUDY DESIGN. Production functions (PFs), with patient workload dependent on physicians, other providers, and nonpersonnel factors, were estimated for each of 14 patient care areas in a VA medical center. Inverse production functions (IPFs), with physician staffing levels dependent on workload and other factors, were estimated for each of 11 specialty groupings. These models provide complementary approaches to deriving VA physician requirements for patient care and medical education. DATA COLLECTION/EXTRACTION METHODS. All data were assembled by VA and put in analyzable SAS data sets containing FY 1989 workload and staffing variables used in the PFs and IPFs. All statistical analyses reported here were conducted by the IOM. PRINCIPAL FINDINGS. Existing VA data can be used to develop statistically strong, clinically plausible, empirically based models for calculating physician requirements, by specialty. These models can (1) compare current physician staffing in a given setting with systemwide norms and (2) yield estimates of future staffing requirements conditional on future workload. CONCLUSIONS. Empirically based models can play an important role in determining VA physician staffing requirements. VA should test, evaluate, and revise these models on an ongoing basis. PMID:7860320

  13. PCR Amplicon Prediction from Multiplex Degenerate Primer and Probe Sets

    2013-08-08

    Assessing primer specificity and predicting both desired and off-target amplification products is an essential step for robust PCR assay design. Code is described to predict potential polymerase chain reaction (PCR) amplicons in a large sequence database such as NCBI nt from either singleplex or a large multiplexed set of primers, allowing degenerate primer and probe bases, with target mismatch annotates amplicons with gene information automatically downloaded from NCBI, and optionally it can predict whether theremore » are also TaqMan/Luminex probe matches within predicted amplicons.« less

  14. PCR Amplicon Prediction from Multiplex Degenerate Primer and Probe Sets

    SciTech Connect

    Gardner, S. N.

    2013-08-08

    Assessing primer specificity and predicting both desired and off-target amplification products is an essential step for robust PCR assay design. Code is described to predict potential polymerase chain reaction (PCR) amplicons in a large sequence database such as NCBI nt from either singleplex or a large multiplexed set of primers, allowing degenerate primer and probe bases, with target mismatch annotates amplicons with gene information automatically downloaded from NCBI, and optionally it can predict whether there are also TaqMan/Luminex probe matches within predicted amplicons.

  15. Optimal Activation of Isopsoralen To Prevent Amplicon Carryover

    PubMed Central

    Fahle, Gary A.; Gill, Vee J.; Fischer, Steven H.

    1999-01-01

    We compared the efficiencies of activation of the photochemical isopsoralen compound 10 and its resulting amplicon neutralizations under conditions with a UV transilluminator box at room temperature (RT) and a HRI-300 UV photothermal reaction chamber at RT and at 5°C. Our data suggest that use of the HRI-300 reaction chamber at 5°C results in a statistically significantly higher degree of amplicon neutralization. PMID:9854109

  16. Virion-associated cofactor high-mobility group DNA-binding protein-1 facilitates transposition from the herpes simplex virus/Sleeping Beauty amplicon vector platform.

    PubMed

    de Silva, Suresh; Lotta, Louis T; Burris, Clark A; Bowers, William J

    2010-11-01

    The development of the integration-competent, herpes simplex virus/Sleeping Beauty (HSV/SB) amplicon vector platform has created a means to efficiently and stably deliver therapeutic transcription units (termed "transgenons") to neurons within the mammalian brain. Furthermore, an investigation into the transposition capacity of the HSV/SB vector system revealed that the amplicon genome provides an optimal substrate for the transposition of transgenons at least 12 kb in length [de Silva, S., Mastrangelo, M.A., Lotta, L.T., Jr., Burris, C.A., Federoff, H.J., and Bowers, W.J. ( 2010 ). Gene Ther. 17, 424-431]. These results prompted an investigation into the factors that may contribute toward efficient transposition from the HSV/SB amplicon. One of the cellular cofactors known to play a key role during SB-mediated transposition is the high-mobility group DNA-binding protein-1 (HMGB1). Our present investigation into the role of HMGB1 during amplicon-based transposition revealed that transposition is not strictly dependent on the presence of cellular HMGB1, contrary to what had been previously demonstrated with plasmid-based SB transposition. We have shown for the first time that during amplicon preparation, biologically active HMGB1 derived from the packaging cell line is copackaged into amplicon vector particles. As a result, HSV/SB amplicon virions arrive prearmed with HMGB1 protein at levels sufficient for facilitating SB-mediated transposition in the transduced mammalian cell. PMID:20568967

  17. Induction of humoral responses to BHV-1 glycoprotein D expressed by HSV-1 amplicon vectors

    PubMed Central

    Blanc, Andrea Maria; Berois, Mabel Beatriz; Tomé, Lorena Magalí; Epstein, Alberto L.

    2012-01-01

    Herpes simplex virus type-1 (HSV-1) amplicon vectors are versatile and useful tools for transferring genes into cells that are capable of stimulating a specific immune response to their expressed antigens. In this work, two HSV-1-derived amplicon vectors were generated. One of these expressed the full-length glycoprotein D (gD) of bovine herpesvirus 1 while the second expressed the truncated form of gD (gDtr) which lacked the trans-membrane region. After evaluating gD expression in the infected cells, the ability of both vectors to induce a specific gD immune response was tested in BALB/c mice that were intramuscularly immunized. Specific serum antibody responses were detected in mice inoculated with both vectors, and the response against truncated gD was higher than the response against full-length gD. These results reinforce previous findings that HSV-1 amplicon vectors can potentially deliver antigens to animals and highlight the prospective use of these vectors for treating infectious bovine rhinotracheitis disease. PMID:22437537

  18. Fast, accurate and easy-to-pipeline methods for amplicon sequence processing

    NASA Astrophysics Data System (ADS)

    Antonielli, Livio; Sessitsch, Angela

    2016-04-01

    Next generation sequencing (NGS) technologies established since years as an essential resource in microbiology. While on the one hand metagenomic studies can benefit from the continuously increasing throughput of the Illumina (Solexa) technology, on the other hand the spreading of third generation sequencing technologies (PacBio, Oxford Nanopore) are getting whole genome sequencing beyond the assembly of fragmented draft genomes, making it now possible to finish bacterial genomes even without short read correction. Besides (meta)genomic analysis next-gen amplicon sequencing is still fundamental for microbial studies. Amplicon sequencing of the 16S rRNA gene and ITS (Internal Transcribed Spacer) remains a well-established widespread method for a multitude of different purposes concerning the identification and comparison of archaeal/bacterial (16S rRNA gene) and fungal (ITS) communities occurring in diverse environments. Numerous different pipelines have been developed in order to process NGS-derived amplicon sequences, among which Mothur, QIIME and USEARCH are the most well-known and cited ones. The entire process from initial raw sequence data through read error correction, paired-end read assembly, primer stripping, quality filtering, clustering, OTU taxonomic classification and BIOM table rarefaction as well as alternative "normalization" methods will be addressed. An effective and accurate strategy will be presented using the state-of-the-art bioinformatic tools and the example of a straightforward one-script pipeline for 16S rRNA gene or ITS MiSeq amplicon sequencing will be provided. Finally, instructions on how to automatically retrieve nucleotide sequences from NCBI and therefore apply the pipeline to targets other than 16S rRNA gene (Greengenes, SILVA) and ITS (UNITE) will be discussed.

  19. Reproducibility and quantitation of amplicon sequencing-based detection.

    PubMed

    Zhou, Jizhong; Wu, Liyou; Deng, Ye; Zhi, Xiaoyang; Jiang, Yi-Huei; Tu, Qichao; Xie, Jianping; Van Nostrand, Joy D; He, Zhili; Yang, Yunfeng

    2011-08-01

    To determine the reproducibility and quantitation of the amplicon sequencing-based detection approach for analyzing microbial community structure, a total of 24 microbial communities from a long-term global change experimental site were examined. Genomic DNA obtained from each community was used to amplify 16S rRNA genes with two or three barcode tags as technical replicates in the presence of a small quantity (0.1% wt/wt) of genomic DNA from Shewanella oneidensis MR-1 as the control. The technical reproducibility of the amplicon sequencing-based detection approach is quite low, with an average operational taxonomic unit (OTU) overlap of 17.2%±2.3% between two technical replicates, and 8.2%±2.3% among three technical replicates, which is most likely due to problems associated with random sampling processes. Such variations in technical replicates could have substantial effects on estimating β-diversity but less on α-diversity. A high variation was also observed in the control across different samples (for example, 66.7-fold for the forward primer), suggesting that the amplicon sequencing-based detection approach could not be quantitative. In addition, various strategies were examined to improve the comparability of amplicon sequencing data, such as increasing biological replicates, and removing singleton sequences and less-representative OTUs across biological replicates. Finally, as expected, various statistical analyses with preprocessed experimental data revealed clear differences in the composition and structure of microbial communities between warming and non-warming, or between clipping and non-clipping. Taken together, these results suggest that amplicon sequencing-based detection is useful in analyzing microbial community structure even though it is not reproducible and quantitative. However, great caution should be taken in experimental design and data interpretation when the amplicon sequencing-based detection approach is used for quantitative

  20. VA telemental health: suicide assessment.

    PubMed

    Godleski, Linda; Nieves, J Edwin; Darkins, Adam; Lehmann, Laurent

    2008-01-01

    The Department of Veterans Affairs (VA) encompasses one of the largest telemental health networks in the world, with over 45,000 videoconferencing and over 5,000 home telemental health encounters annually. Recently, the VA designated suicide prevention as a major priority, with telehealth modalities providing opportunities for remote interventions. Suicide risk assessments, using videoconferencing, are now documented in the literature, as are current studies that find telemental health to be equivalent to face-to-face treatment. Remote assessment of suicidality, however, involves complex legal issues: licensing requirements for remote delivery of care, legal procedures for involuntary detainment and commitment of potentially harmful patients, and liability questions related to the remote nature of the mental health service. VA best practices for remote suicide risk assessment include paradigms for establishing procedures in the context of legal challenges (licensing and involuntary detainment/commitment), for utilizing clinical assessment and triage decision protocols, and for contingency planning to optimize patient care and reduce liability.

  1. Barcoded primers used in multiplex amplicon pyrosequencing bias amplification.

    PubMed

    Berry, David; Ben Mahfoudh, Karim; Wagner, Michael; Loy, Alexander

    2011-11-01

    "Barcode-tagged" PCR primers used for multiplex amplicon sequencing generate a thus-far-overlooked amplification bias that produces variable terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing data from the same environmental DNA template. We propose a simple two-step PCR approach that increases reproducibility and consistently recovers higher genetic diversity in pyrosequencing libraries. PMID:21890669

  2. Herpes simplex virus type 1-based amplicon vectors for fundamental research in neurosciences and gene therapy of neurological diseases.

    PubMed

    Jerusalinsky, Diana; Baez, María Verónica; Epstein, Alberto Luis

    2012-01-01

    Somatic manipulation of the nervous system without the involvement of the germinal line appears as a powerful counterpart of the transgenic strategy. The use of viral vectors to produce specific, transient and localized knockout, knockdown, ectopic expression or overexpression of a gene, leads to the possibility of analyzing both in vitro and in vivo molecular basis of neural function. In this approach, viral particles engineered to carry transgenic sequences are delivered into discrete brain regions, to transduce cells that will express the transgenic products. Amplicons are replication-incompetent helper-dependent vectors derived from herpes simplex virus type 1 (HSV-1), with several advantages that potentiate their use in neurosciences: (1) minimal toxicity: amplicons do not encode any virus proteins, are neither toxic for the infected cells nor pathogenic for the inoculated animals and elicit low levels of adaptive immune responses; (2) extensive transgene capacity to carry up to 150-kb of foreign DNA; i.e., entire genes with regulatory sequences could be delivered; (3) widespread cellular tropism: amplicons can experimentally infect several cell types including glial cells, though naturally the virus infects mainly neurons and epithelial cells; (4) since the viral genome does not integrate into cellular chromosomes there is low probability to induce insertional mutagenesis. Recent investigations on gene transfer into the brain using these vectors, have focused on gene therapy of inherited genetic diseases affecting the nervous system, such as ataxias, or on neurodegenerative disorders using experimental models of Parkinson's or Alzheimer's disease. Another group of studies used amplicons to investigate complex neural functions such as neuroplasticity, anxiety, learning and memory. In this short review, we summarize recent data supporting the potential of HSV-1 based amplicon vector model for gene delivery and modulation of gene expression in primary cultures

  3. SNP discovery by amplicon sequencing and multiplex SNP genotyping in the allopolyploid species Brassica napus.

    PubMed

    Durstewitz, G; Polley, A; Plieske, J; Luerssen, H; Graner, E M; Wieseke, R; Ganal, M W

    2010-11-01

    Oilseed rape (Brassica napus) is an allotetraploid species consisting of two genomes, derived from B. rapa (A genome) and B. oleracea (C genome). The presence of these two genomes makes single nucleotide polymorphism (SNP) marker identification and SNP analysis more challenging than in diploid species, as for a given locus usually two versions of a DNA sequence (based on the two ancestral genomes) have to be analyzed simultaneously during SNP identification and analysis. One hundred amplicons derived from expressed sequence tag (ESTs) were analyzed to identify SNPs in a panel of oilseed rape varieties and within two sister species representing the ancestral genomes. A total of 604 SNPs were identified, averaging one SNP in every 42 bp. It was possible to clearly discriminate SNPs that are polymorphic between different plant varieties from SNPs differentiating the two ancestral genomes. To validate the identified SNPs for their use in genetic analysis, we have developed Illumina GoldenGate assays for some of the identified SNPs. Through the analysis of a number of oilseed rape varieties and mapping populations with GoldenGate assays, we were able to identify a number of different segregation patterns in allotetraploid oilseed rape. The majority of the identified SNP markers can be readily used for genetic mapping, showing that amplicon sequencing and Illumina GoldenGate assays can be used to reliably identify SNP markers in tetraploid oilseed rape and to convert them into successful SNP assays that can be used for genetic analysis.

  4. Grinder: a versatile amplicon and shotgun sequence simulator

    PubMed Central

    Angly, Florent E.; Willner, Dana; Rohwer, Forest; Hugenholtz, Philip; Tyson, Gene W.

    2012-01-01

    We introduce Grinder (http://sourceforge.net/projects/biogrinder/), an open-source bioinformatic tool to simulate amplicon and shotgun (genomic, metagenomic, transcriptomic and metatranscriptomic) datasets from reference sequences. This is the first tool to simulate amplicon datasets (e.g. 16S rRNA) widely used by microbial ecologists. Grinder can create sequence libraries with a specific community structure, α and β diversities and experimental biases (e.g. chimeras, gene copy number variation) for commonly used sequencing platforms. This versatility allows the creation of simple to complex read datasets necessary for hypothesis testing when developing bioinformatic software, benchmarking existing tools or designing sequence-based experiments. Grinder is particularly useful for simulating clinical or environmental microbial communities and complements the use of in vitro mock communities. PMID:22434876

  5. Systems consequences of amplicon formation in human breast cancer.

    PubMed

    Inaki, Koichiro; Menghi, Francesca; Woo, Xing Yi; Wagner, Joel P; Jacques, Pierre-Étienne; Lee, Yi Fang; Shreckengast, Phung Trang; Soon, Wendy WeiJia; Malhotra, Ankit; Teo, Audrey S M; Hillmer, Axel M; Khng, Alexis Jiaying; Ruan, Xiaoan; Ong, Swee Hoe; Bertrand, Denis; Nagarajan, Niranjan; Karuturi, R Krishna Murthy; Miranda, Alfredo Hidalgo; Liu, Edison T

    2014-10-01

    Chromosomal structural variations play an important role in determining the transcriptional landscape of human breast cancers. To assess the nature of these structural variations, we analyzed eight breast tumor samples with a focus on regions of gene amplification using mate-pair sequencing of long-insert genomic DNA with matched transcriptome profiling. We found that tandem duplications appear to be early events in tumor evolution, especially in the genesis of amplicons. In a detailed reconstruction of events on chromosome 17, we found large unpaired inversions and deletions connect a tandemly duplicated ERBB2 with neighboring 17q21.3 amplicons while simultaneously deleting the intervening BRCA1 tumor suppressor locus. This series of events appeared to be unusually common when examined in larger genomic data sets of breast cancers albeit using approaches with lesser resolution. Using siRNAs in breast cancer cell lines, we showed that the 17q21.3 amplicon harbored a significant number of weak oncogenes that appeared consistently coamplified in primary tumors. Down-regulation of BRCA1 expression augmented the cell proliferation in ERBB2-transfected human normal mammary epithelial cells. Coamplification of other functionally tested oncogenic elements in other breast tumors examined, such as RIPK2 and MYC on chromosome 8, also parallel these findings. Our analyses suggest that structural variations efficiently orchestrate the gain and loss of cancer gene cassettes that engage many oncogenic pathways simultaneously and that such oncogenic cassettes are favored during the evolution of a cancer. PMID:25186909

  6. AmpliconDuo: A Split-Sample Filtering Protocol for High-Throughput Amplicon Sequencing of Microbial Communities

    PubMed Central

    Lange, Anja; Jost, Steffen; Heider, Dominik; Bock, Christina; Budeus, Bettina; Schilling, Elmar; Strittmatter, Axel; Boenigk, Jens; Hoffmann, Daniel

    2015-01-01

    High throughput sequencing (HTSeq) of small ribosomal subunit amplicons has the potential for a comprehensive characterization of microbial community compositions, down to rare species. However, the error-prone nature of the multi-step experimental process requires that the resulting raw sequences are subjected to quality control procedures. These procedures often involve an abundance cutoff for rare sequences or clustering of sequences, both of which limit genetic resolution. Here we propose a simple experimental protocol that retains the high genetic resolution granted by HTSeq methods while effectively removing many low abundance sequences that are likely due to PCR and sequencing errors. According to this protocol, we split samples and submit both halves to independent PCR and sequencing runs. The resulting sequence data is graphically and quantitatively characterized by the discordance between the two experimental branches, allowing for a quick identification of problematic samples. Further, we discard sequences that are not found in both branches (“AmpliconDuo filter”). We show that the majority of sequences removed in this way, mostly low abundance but also some higher abundance sequences, show features expected from random modifications of true sequences as introduced by PCR and sequencing errors. On the other hand, the filter retains many low abundance sequences observed in both branches and thus provides a more reliable census of the rare biosphere. We find that the AmpliconDuo filter increases biological resolution as it increases apparent community similarity between biologically similar communities, while it does not affect apparent community similarities between biologically dissimilar communities. The filter does not distort overall apparent community compositions. Finally, we quantitatively explain the effect of the AmpliconDuo filter by a simple mathematical model. PMID:26523925

  7. Multiplex amplicon sequencing for microbe identification in community-based culture collections.

    PubMed

    Armanhi, Jaderson Silveira Leite; de Souza, Rafael Soares Correa; de Araújo, Laura Migliorini; Okura, Vagner Katsumi; Mieczkowski, Piotr; Imperial, Juan; Arruda, Paulo

    2016-01-01

    Microbiome analysis using metagenomic sequencing has revealed a vast microbial diversity associated with plants. Identifying the molecular functions associated with microbiome-plant interaction is a significant challenge concerning the development of microbiome-derived technologies applied to agriculture. An alternative to accelerate the discovery of the microbiome benefits to plants is to construct microbial culture collections concomitant with accessing microbial community structure and abundance. However, traditional methods of isolation, cultivation, and identification of microbes are time-consuming and expensive. Here we describe a method for identification of microbes in culture collections constructed by picking colonies from primary platings that may contain single or multiple microorganisms, which we named community-based culture collections (CBC). A multiplexing 16S rRNA gene amplicon sequencing based on two-step PCR amplifications with tagged primers for plates, rows, and columns allowed the identification of the microbial composition regardless if the well contains single or multiple microorganisms. The multiplexing system enables pooling amplicons into a single tube. The sequencing performed on the PacBio platform led to recovery near-full-length 16S rRNA gene sequences allowing accurate identification of microorganism composition in each plate well. Cross-referencing with plant microbiome structure and abundance allowed the estimation of diversity and abundance representation of microorganism in the CBC. PMID:27404280

  8. Multiplex amplicon sequencing for microbe identification in community-based culture collections.

    PubMed

    Armanhi, Jaderson Silveira Leite; de Souza, Rafael Soares Correa; de Araújo, Laura Migliorini; Okura, Vagner Katsumi; Mieczkowski, Piotr; Imperial, Juan; Arruda, Paulo

    2016-07-12

    Microbiome analysis using metagenomic sequencing has revealed a vast microbial diversity associated with plants. Identifying the molecular functions associated with microbiome-plant interaction is a significant challenge concerning the development of microbiome-derived technologies applied to agriculture. An alternative to accelerate the discovery of the microbiome benefits to plants is to construct microbial culture collections concomitant with accessing microbial community structure and abundance. However, traditional methods of isolation, cultivation, and identification of microbes are time-consuming and expensive. Here we describe a method for identification of microbes in culture collections constructed by picking colonies from primary platings that may contain single or multiple microorganisms, which we named community-based culture collections (CBC). A multiplexing 16S rRNA gene amplicon sequencing based on two-step PCR amplifications with tagged primers for plates, rows, and columns allowed the identification of the microbial composition regardless if the well contains single or multiple microorganisms. The multiplexing system enables pooling amplicons into a single tube. The sequencing performed on the PacBio platform led to recovery near-full-length 16S rRNA gene sequences allowing accurate identification of microorganism composition in each plate well. Cross-referencing with plant microbiome structure and abundance allowed the estimation of diversity and abundance representation of microorganism in the CBC.

  9. Multiplex amplicon sequencing for microbe identification in community-based culture collections

    PubMed Central

    Armanhi, Jaderson Silveira Leite; de Souza, Rafael Soares Correa; de Araújo, Laura Migliorini; Okura, Vagner Katsumi; Mieczkowski, Piotr; Imperial, Juan; Arruda, Paulo

    2016-01-01

    Microbiome analysis using metagenomic sequencing has revealed a vast microbial diversity associated with plants. Identifying the molecular functions associated with microbiome-plant interaction is a significant challenge concerning the development of microbiome-derived technologies applied to agriculture. An alternative to accelerate the discovery of the microbiome benefits to plants is to construct microbial culture collections concomitant with accessing microbial community structure and abundance. However, traditional methods of isolation, cultivation, and identification of microbes are time-consuming and expensive. Here we describe a method for identification of microbes in culture collections constructed by picking colonies from primary platings that may contain single or multiple microorganisms, which we named community-based culture collections (CBC). A multiplexing 16S rRNA gene amplicon sequencing based on two-step PCR amplifications with tagged primers for plates, rows, and columns allowed the identification of the microbial composition regardless if the well contains single or multiple microorganisms. The multiplexing system enables pooling amplicons into a single tube. The sequencing performed on the PacBio platform led to recovery near-full-length 16S rRNA gene sequences allowing accurate identification of microorganism composition in each plate well. Cross-referencing with plant microbiome structure and abundance allowed the estimation of diversity and abundance representation of microorganism in the CBC. PMID:27404280

  10. Mutascope: sensitive detection of somatic mutations from deep amplicon sequencing

    PubMed Central

    Yost, Shawn E.; Alakus, Hakan; Matsui, Hiroko; Schwab, Richard B.; Jepsen, Kristen; Frazer, Kelly A.; Harismendy, Olivier

    2013-01-01

    Summary: We present Mutascope, a sequencing analysis pipeline specifically developed for the identification of somatic variants present at low-allelic fraction from high-throughput sequencing of amplicons from matched tumor-normal specimen. Using datasets reproducing tumor genetic heterogeneity, we demonstrate that Mutascope has a higher sensitivity and generates fewer false-positive calls than tools designed for shotgun sequencing or diploid genomes. Availability: Freely available on the web at http://sourceforge.net/projects/mutascope/. Contact: oharismendy@ucsd.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23712659

  11. KaVA ESTEMA project

    NASA Astrophysics Data System (ADS)

    Oyadomari, Miyako; Imai, Hiroshi; Cho, Se-Hyung; Asaki, Yoshiharu; Choi, Yoon-Kyong; Kim, Jaeheon; Yun, Youngjoo; Matsumoto, Naoko; Min, Cheul-Hong; Oyama, Tomoaki; Yoon, Sung-Chul; Yoon, Dong-Hwan; Kim, Dong-Jin; Dodson, Richard; Rioja, Maria; Burns, Ross; Orosz, Gabor; Nakagawa, Akiharu; Chibueze O, James; Nakashima, Jun-ichi; Sobolev, Andrey

    2016-07-01

    The ESTEMA (Expanded Study on Stellar Masers) project is one of three Large Programs of the KaVA (the combined array of the Korean VLBI Network and Japanese VLBI Exploration of Radio Astrometry), and conducted in 2015-2016. It aims to publish a database of the largest sample of VLBI images of circumstellar water (H2O) and silicon-monoxide (SiO) maser sources towards circumstellar envelopes (CSEs) of 80 evolved stars in late AGB to early post-AGB phase. Here we present the specifications of the ESTEMA observations and the planned scientific goals in order to share the basic information of the ESTEMA with astronomical community and encourage future collaborations with the ESTEMA and future follow-up observations for the targeted stars.

  12. 77 FR 70967 - Authorization for Non-VA Medical Services

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-28

    ..., Alcoholism, Claims, Day care, Dental health, Drug abuse, Government contracts, Grant programs--health... its regulation governing payment by VA for non-VA outpatient care under VA's statutory authority to provide non-VA care. Under this authority, VA may contract for certain hospital care (inpatient care)...

  13. The VA-Medical School Partnership: The Medical School Perspective.

    ERIC Educational Resources Information Center

    Petersdorf, Robert G.

    1987-01-01

    Issues in the relationship between the Veterans' Administration (VA) and medical schools are discussed, including VA faculty recruitment and retention, ambulatory care in VA teaching hospitals, governance and growth of research within VA medical centers, and effects of cost containment and competition on teaching and training in VA hospitals. (MSE)

  14. 48 CFR 801.690 - VA's COCP.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 48 Federal Acquisition Regulations System 5 2014-10-01 2014-10-01 false VA's COCP. 801.690 Section 801.690 Federal Acquisition Regulations System DEPARTMENT OF VETERANS AFFAIRS GENERAL DEPARTMENT OF... Responsibilities 801.690 VA's COCP....

  15. Agreement Between HEDIS Performance Assessments in the VA and Medicare Advantage: Is Quality in the Eye of the Beholder?

    PubMed

    Trivedi, Amal N; Wilson, Ira B; Charlton, Mary E; Kizer, Kenneth W

    2016-01-01

    Medicare Advantage (MA) plans and the Veterans Affairs (VA) health care system assess quality of care using standardized Healthcare Effectiveness Data and Information Set (HEDIS) performance measures. Little is known, however, about the relative accuracy of quality indicators for persons receiving care in more than one health care system. Among Veterans dually enrolled in an MA plan, we examined the agreement between MA and VA HEDIS assessments. Our study tested the hypothesis that private health plans underreport quality of care relative to a fully integrated delivery system utilizing a comprehensive electronic health record. Despite assessing the same individuals using identical measure specifications, reported VA performance was significantly better than reported MA performance for all 12 HEDIS measures. The VA's performance advantage ranged from 9.8% (glycosylated hemoglobin [HbA1c] < 7.0% in diabetes) to 54.7% (blood pressure < 140/90 mm Hg in diabetes). The overall agreement between VA and MA HEDIS assessments ranged from 38.5% to 62.6%. Performance rates derived from VA and MA aggregate data were 1.6% to 14.3% higher than those reported by VA alone. This analysis suggests that neither MA plans nor the VA fully capture quality of care information for dually enrolled persons. However, the VA's system-wide electronic health record may allow for more complete capture of quality information across multiple providers and settings. PMID:27033565

  16. Agreement Between HEDIS Performance Assessments in the VA and Medicare Advantage: Is Quality in the Eye of the Beholder?

    PubMed

    Trivedi, Amal N; Wilson, Ira B; Charlton, Mary E; Kizer, Kenneth W

    2016-01-01

    Medicare Advantage (MA) plans and the Veterans Affairs (VA) health care system assess quality of care using standardized Healthcare Effectiveness Data and Information Set (HEDIS) performance measures. Little is known, however, about the relative accuracy of quality indicators for persons receiving care in more than one health care system. Among Veterans dually enrolled in an MA plan, we examined the agreement between MA and VA HEDIS assessments. Our study tested the hypothesis that private health plans underreport quality of care relative to a fully integrated delivery system utilizing a comprehensive electronic health record. Despite assessing the same individuals using identical measure specifications, reported VA performance was significantly better than reported MA performance for all 12 HEDIS measures. The VA's performance advantage ranged from 9.8% (glycosylated hemoglobin [HbA1c] < 7.0% in diabetes) to 54.7% (blood pressure < 140/90 mm Hg in diabetes). The overall agreement between VA and MA HEDIS assessments ranged from 38.5% to 62.6%. Performance rates derived from VA and MA aggregate data were 1.6% to 14.3% higher than those reported by VA alone. This analysis suggests that neither MA plans nor the VA fully capture quality of care information for dually enrolled persons. However, the VA's system-wide electronic health record may allow for more complete capture of quality information across multiple providers and settings.

  17. Inconsistent Denoising and Clustering Algorithms for Amplicon Sequence Data.

    PubMed

    Koskinen, Kaisa; Auvinen, Petri; Björkroth, K Johanna; Hultman, Jenni

    2015-08-01

    Natural microbial communities have been studied for decades using the 16S rRNA gene as a marker. In recent years, the application of second-generation sequencing technologies has revolutionized our understanding of the structure and function of microbial communities in complex environments. Using these highly parallel techniques, a detailed description of community characteristics are constructed, and even the rare biosphere can be detected. The new approaches carry numerous advantages and lack many features that skewed the results using traditional techniques, but we are still facing serious bias, and the lack of reliable comparability of produced results. Here, we contrasted publicly available amplicon sequence data analysis algorithms by using two different data sets, one with defined clone-based structure, and one with food spoilage community with well-studied communities. We aimed to assess which software and parameters produce results that resemble the benchmark community best, how large differences can be detected between methods, and whether these differences are statistically significant. The results suggest that commonly accepted denoising and clustering methods used in different combinations produce significantly different outcome: clustering method impacts greatly on the number of operational taxonomic units (OTUs) and denoising algorithm influences more on taxonomic affiliations. The magnitude of the OTU number difference was up to 40-fold and the disparity between results seemed highly dependent on the community structure and diversity. Statistically significant differences in taxonomies between methods were seen even at phylum level. However, the application of effective denoising method seemed to even out the differences produced by clustering. PMID:25525895

  18. Integrated Microfluidic Nucleic Acid Isolation, Isothermal Amplification, and Amplicon Quantification

    PubMed Central

    Mauk, Michael G.; Liu, Changchun; Song, Jinzhao; Bau, Haim H.

    2015-01-01

    Microfluidic components and systems for rapid (<60 min), low-cost, convenient, field-deployable sequence-specific nucleic acid-based amplification tests (NAATs) are described. A microfluidic point-of-care (POC) diagnostics test to quantify HIV viral load from blood samples serves as a representative and instructive example to discuss the technical issues and capabilities of “lab on a chip” NAAT devices. A portable, miniaturized POC NAAT with performance comparable to conventional PCR (polymerase-chain reaction)-based tests in clinical laboratories can be realized with a disposable, palm-sized, plastic microfluidic chip in which: (1) nucleic acids (NAs) are extracted from relatively large (~mL) volume sample lysates using an embedded porous silica glass fiber or cellulose binding phase (“membrane”) to capture sample NAs in a flow-through, filtration mode; (2) NAs captured on the membrane are isothermally (~65 °C) amplified; (3) amplicon production is monitored by real-time fluorescence detection, such as with a smartphone CCD camera serving as a low-cost detector; and (4) paraffin-encapsulated, lyophilized reagents for temperature-activated release are pre-stored in the chip. Limits of Detection (LOD) better than 103 virons/sample can be achieved. A modified chip with conduits hosting a diffusion-mode amplification process provides a simple visual indicator to readily quantify sample NA template. In addition, a companion microfluidic device for extracting plasma from whole blood without a centrifuge, generating cell-free plasma for chip-based molecular diagnostics, is described. Extensions to a myriad of related applications including, for example, food testing, cancer screening, and insect genotyping are briefly surveyed.

  19. Integrated Microfluidic Nucleic Acid Isolation, Isothermal Amplification, and Amplicon Quantification

    PubMed Central

    Mauk, Michael G.; Liu, Changchun; Song, Jinzhao; Bau, Haim H.

    2015-01-01

    Microfluidic components and systems for rapid (<60 min), low-cost, convenient, field-deployable sequence-specific nucleic acid-based amplification tests (NAATs) are described. A microfluidic point-of-care (POC) diagnostics test to quantify HIV viral load from blood samples serves as a representative and instructive example to discuss the technical issues and capabilities of “lab on a chip” NAAT devices. A portable, miniaturized POC NAAT with performance comparable to conventional PCR (polymerase-chain reaction)-based tests in clinical laboratories can be realized with a disposable, palm-sized, plastic microfluidic chip in which: (1) nucleic acids (NAs) are extracted from relatively large (~mL) volume sample lysates using an embedded porous silica glass fiber or cellulose binding phase (“membrane”) to capture sample NAs in a flow-through, filtration mode; (2) NAs captured on the membrane are isothermally (~65 °C) amplified; (3) amplicon production is monitored by real-time fluorescence detection, such as with a smartphone CCD camera serving as a low-cost detector; and (4) paraffin-encapsulated, lyophilized reagents for temperature-activated release are pre-stored in the chip. Limits of Detection (LOD) better than 103 virons/sample can be achieved. A modified chip with conduits hosting a diffusion-mode amplification process provides a simple visual indicator to readily quantify sample NA template. In addition, a companion microfluidic device for extracting plasma from whole blood without a centrifuge, generating cell-free plasma for chip-based molecular diagnostics, is described. Extensions to a myriad of related applications including, for example, food testing, cancer screening, and insect genotyping are briefly surveyed. PMID:27600235

  20. Do Older Rural and Urban Veterans Experience Different Rates of Unplanned Readmission to VA and Non-VA Hospitals?

    ERIC Educational Resources Information Center

    Weeks, William B.; Lee, Richard E.; Wallace, Amy E.; West, Alan N.; Bagian, James P.

    2009-01-01

    Context: Unplanned readmission within 30 days of discharge is an indicator of hospital quality. Purpose: We wanted to determine whether older rural veterans who were enrolled in the VA had different rates of unplanned readmission to VA or non-VA hospitals than their urban counterparts. Methods: We used the combined VA/Medicare dataset to examine…

  1. Taxonomic Assessment of Rumen Microbiota Using Total RNA and Targeted Amplicon Sequencing Approaches

    PubMed Central

    Li, Fuyong; Henderson, Gemma; Sun, Xu; Cox, Faith; Janssen, Peter H.; Guan, Le Luo

    2016-01-01

    Taxonomic characterization of active gastrointestinal microbiota is essential to detect shifts in microbial communities and functions under various conditions. This study aimed to identify and quantify potentially active rumen microbiota using total RNA sequencing and to compare the outcomes of this approach with the widely used targeted RNA/DNA amplicon sequencing technique. Total RNA isolated from rumen digesta samples from five beef steers was subjected to Illumina paired-end sequencing (RNA-seq), and bacterial and archaeal amplicons of partial 16S rRNA/rDNA were subjected to 454 pyrosequencing (RNA/DNA Amplicon-seq). Taxonomic assessments of the RNA-seq, RNA Amplicon-seq, and DNA Amplicon-seq datasets were performed using a pipeline developed in house. The detected major microbial phylotypes were common among the three datasets, with seven bacterial phyla, fifteen bacterial families, and five archaeal taxa commonly identified across all datasets. There were also unique microbial taxa detected in each dataset. Elusimicrobia and Verrucomicrobia phyla; Desulfovibrionaceae, Elusimicrobiaceae, and Sphaerochaetaceae families; and Methanobrevibacter woesei were only detected in the RNA-Seq and RNA Amplicon-seq datasets, whereas Streptococcaceae was only detected in the DNA Amplicon-seq dataset. In addition, the relative abundances of four bacterial phyla, eight bacterial families and one archaeal taxon were different among the three datasets. This is the first study to compare the outcomes of rumen microbiota profiling between RNA-seq and RNA/DNA Amplicon-seq datasets. Our results illustrate the differences between these methods in characterizing microbiota both qualitatively and quantitatively for the same sample, and so caution must be exercised when comparing data. PMID:27446027

  2. Taxonomic Assessment of Rumen Microbiota Using Total RNA and Targeted Amplicon Sequencing Approaches.

    PubMed

    Li, Fuyong; Henderson, Gemma; Sun, Xu; Cox, Faith; Janssen, Peter H; Guan, Le Luo

    2016-01-01

    Taxonomic characterization of active gastrointestinal microbiota is essential to detect shifts in microbial communities and functions under various conditions. This study aimed to identify and quantify potentially active rumen microbiota using total RNA sequencing and to compare the outcomes of this approach with the widely used targeted RNA/DNA amplicon sequencing technique. Total RNA isolated from rumen digesta samples from five beef steers was subjected to Illumina paired-end sequencing (RNA-seq), and bacterial and archaeal amplicons of partial 16S rRNA/rDNA were subjected to 454 pyrosequencing (RNA/DNA Amplicon-seq). Taxonomic assessments of the RNA-seq, RNA Amplicon-seq, and DNA Amplicon-seq datasets were performed using a pipeline developed in house. The detected major microbial phylotypes were common among the three datasets, with seven bacterial phyla, fifteen bacterial families, and five archaeal taxa commonly identified across all datasets. There were also unique microbial taxa detected in each dataset. Elusimicrobia and Verrucomicrobia phyla; Desulfovibrionaceae, Elusimicrobiaceae, and Sphaerochaetaceae families; and Methanobrevibacter woesei were only detected in the RNA-Seq and RNA Amplicon-seq datasets, whereas Streptococcaceae was only detected in the DNA Amplicon-seq dataset. In addition, the relative abundances of four bacterial phyla, eight bacterial families and one archaeal taxon were different among the three datasets. This is the first study to compare the outcomes of rumen microbiota profiling between RNA-seq and RNA/DNA Amplicon-seq datasets. Our results illustrate the differences between these methods in characterizing microbiota both qualitatively and quantitatively for the same sample, and so caution must be exercised when comparing data. PMID:27446027

  3. Implementing amplicon-based next generation sequencing in the diagnosis of small cell lung carcinoma metastases.

    PubMed

    Meder, Lydia; König, Katharina; Fassunke, Jana; Ozretić, Luka; Wolf, Jürgen; Merkelbach-Bruse, Sabine; Heukamp, Lukas C; Buettner, Reinhard

    2015-12-01

    Small cell lung carcinoma (SCLC) is the most aggressive entity of lung cancer. Rapid cancer progression and early formation of systemic metastases drive the deadly outcome of SCLC. Recent advances in identifying oncogenes by cancer whole genome sequencing improved the understanding of SCLC carcinogenesis. However, tumor material is often limited in the clinic. Thus, it is a compulsive issue to improve SCLC diagnostics by combining established immunohistochemistry and next generation sequencing. We implemented amplicon-based next generation deep sequencing in our routine diagnostics pipeline to analyze RB1, TP53, EP300 and CREBBP, frequently mutated in SCLC. Thereby, our pipeline combined routine SCLC histology and identification of somatic mutations. We comprehensively analyzed fifty randomly collected SCLC metastases isolated from trachea and lymph nodes in comparison to specimens derived from primary SCLC. SCLC lymph node metastases showed enhanced proliferation and frequently a collapsed keratin cytoskeleton compared to SCLC metastases isolated from trachea. We identified characteristic synchronous mutations in RB1 and TP53 and non-synchronous CREBBP and EP300 mutations. Our data showed the benefit of implementing deep sequencing into routine diagnostics. We here identify oncogenic drivers and simultaneously gain further insights into SCLC tumor biology.

  4. JRC GMO-Amplicons: a collection of nucleic acid sequences related to genetically modified organisms.

    PubMed

    Petrillo, Mauro; Angers-Loustau, Alexandre; Henriksson, Peter; Bonfini, Laura; Patak, Alex; Kreysa, Joachim

    2015-01-01

    The DNA target sequence is the key element in designing detection methods for genetically modified organisms (GMOs). Unfortunately this information is frequently lacking, especially for unauthorized GMOs. In addition, patent sequences are generally poorly annotated, buried in complex and extensive documentation and hard to link to the corresponding GM event. Here, we present the JRC GMO-Amplicons, a database of amplicons collected by screening public nucleotide sequence databanks by in silico determination of PCR amplification with reference methods for GMO analysis. The European Union Reference Laboratory for Genetically Modified Food and Feed (EU-RL GMFF) provides these methods in the GMOMETHODS database to support enforcement of EU legislation and GM food/feed control. The JRC GMO-Amplicons database is composed of more than 240 000 amplicons, which can be easily accessed and screened through a web interface. To our knowledge, this is the first attempt at pooling and collecting publicly available sequences related to GMOs in food and feed. The JRC GMO-Amplicons supports control laboratories in the design and assessment of GMO methods, providing inter-alia in silico prediction of primers specificity and GM targets coverage. The new tool can assist the laboratories in the analysis of complex issues, such as the detection and identification of unauthorized GMOs. Notably, the JRC GMO-Amplicons database allows the retrieval and characterization of GMO-related sequences included in patents documentation. Finally, it can help annotating poorly described GM sequences and identifying new relevant GMO-related sequences in public databases. The JRC GMO-Amplicons is freely accessible through a web-based portal that is hosted on the EU-RL GMFF website. Database URL: http://gmo-crl.jrc.ec.europa.eu/jrcgmoamplicons/. PMID:26424080

  5. JRC GMO-Amplicons: a collection of nucleic acid sequences related to genetically modified organisms

    PubMed Central

    Petrillo, Mauro; Angers-Loustau, Alexandre; Henriksson, Peter; Bonfini, Laura; Patak, Alex; Kreysa, Joachim

    2015-01-01

    The DNA target sequence is the key element in designing detection methods for genetically modified organisms (GMOs). Unfortunately this information is frequently lacking, especially for unauthorized GMOs. In addition, patent sequences are generally poorly annotated, buried in complex and extensive documentation and hard to link to the corresponding GM event. Here, we present the JRC GMO-Amplicons, a database of amplicons collected by screening public nucleotide sequence databanks by in silico determination of PCR amplification with reference methods for GMO analysis. The European Union Reference Laboratory for Genetically Modified Food and Feed (EU-RL GMFF) provides these methods in the GMOMETHODS database to support enforcement of EU legislation and GM food/feed control. The JRC GMO-Amplicons database is composed of more than 240 000 amplicons, which can be easily accessed and screened through a web interface. To our knowledge, this is the first attempt at pooling and collecting publicly available sequences related to GMOs in food and feed. The JRC GMO-Amplicons supports control laboratories in the design and assessment of GMO methods, providing inter-alia in silico prediction of primers specificity and GM targets coverage. The new tool can assist the laboratories in the analysis of complex issues, such as the detection and identification of unauthorized GMOs. Notably, the JRC GMO-Amplicons database allows the retrieval and characterization of GMO-related sequences included in patents documentation. Finally, it can help annotating poorly described GM sequences and identifying new relevant GMO-related sequences in public databases. The JRC GMO-Amplicons is freely accessible through a web-based portal that is hosted on the EU-RL GMFF website. Database URL: http://gmo-crl.jrc.ec.europa.eu/jrcgmoamplicons/ PMID:26424080

  6. JRC GMO-Amplicons: a collection of nucleic acid sequences related to genetically modified organisms.

    PubMed

    Petrillo, Mauro; Angers-Loustau, Alexandre; Henriksson, Peter; Bonfini, Laura; Patak, Alex; Kreysa, Joachim

    2015-01-01

    The DNA target sequence is the key element in designing detection methods for genetically modified organisms (GMOs). Unfortunately this information is frequently lacking, especially for unauthorized GMOs. In addition, patent sequences are generally poorly annotated, buried in complex and extensive documentation and hard to link to the corresponding GM event. Here, we present the JRC GMO-Amplicons, a database of amplicons collected by screening public nucleotide sequence databanks by in silico determination of PCR amplification with reference methods for GMO analysis. The European Union Reference Laboratory for Genetically Modified Food and Feed (EU-RL GMFF) provides these methods in the GMOMETHODS database to support enforcement of EU legislation and GM food/feed control. The JRC GMO-Amplicons database is composed of more than 240 000 amplicons, which can be easily accessed and screened through a web interface. To our knowledge, this is the first attempt at pooling and collecting publicly available sequences related to GMOs in food and feed. The JRC GMO-Amplicons supports control laboratories in the design and assessment of GMO methods, providing inter-alia in silico prediction of primers specificity and GM targets coverage. The new tool can assist the laboratories in the analysis of complex issues, such as the detection and identification of unauthorized GMOs. Notably, the JRC GMO-Amplicons database allows the retrieval and characterization of GMO-related sequences included in patents documentation. Finally, it can help annotating poorly described GM sequences and identifying new relevant GMO-related sequences in public databases. The JRC GMO-Amplicons is freely accessible through a web-based portal that is hosted on the EU-RL GMFF website. Database URL: http://gmo-crl.jrc.ec.europa.eu/jrcgmoamplicons/.

  7. 76 FR 75509 - Autopsies at VA Expense

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-02

    ... that amendment, VA promulgated 38 CFR 17.38, on October 6, 1999, 64 FR 54212. Section 17.38, inter alia... spouse or, in a proper case, the next of kin, unless the patient or domiciled person was abandoned by the... next preceding his death, he or she shall be deemed to have been abandoned. (b) If there is no...

  8. 78 FR 32126 - VA Dental Insurance Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-29

    ...) Resin-based composite restorations. (iv) Endodontic services. (A) Pulp capping. (B) Pulpotomy and... in the Federal Register (77 FR 12517) a proposed rule to amend VA regulations to establish VADIP, a... coverage capabilities as determined during the Federal contracting process. See 77 FR 12518. Although...

  9. 48 CFR 801.690 - VA's COCP.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 48 Federal Acquisition Regulations System 5 2011-10-01 2011-10-01 false VA's COCP. 801.690 Section 801.690 Federal Acquisition Regulations System DEPARTMENT OF VETERANS AFFAIRS GENERAL DEPARTMENT OF VETERANS AFFAIRS ACQUISITION REGULATION SYSTEM Career Development, Contracting Authority,...

  10. 75 FR 24757 - Virginia Disaster #VA-00029

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-05

    ... ADMINISTRATION Virginia Disaster VA-00029 AGENCY: U.S. Small Business Administration. ACTION: Notice. SUMMARY: This is a Notice of the Presidential declaration of a major disaster for Public Assistance Only for the... of Disaster Assistance, U.S. Small Business Administration, 409 3rd Street, SW., Suite...

  11. 76 FR 70804 - Virginia Disaster #VA-00037

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-15

    ... ADMINISTRATION Virginia Disaster VA-00037 AGENCY: U.S. Small Business Administration. ACTION: Notice. SUMMARY: This is a Notice of the Presidential declaration of a major disaster for the Commonwealth of Virginia... INFORMATION CONTACT: A. Escobar, Office of Disaster Assistance, U.S. Small Business Administration, 409...

  12. 76 FR 72994 - Virginia Disaster #VA-00041

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-28

    ... ADMINISTRATION Virginia Disaster VA-00041 AGENCY: U.S. Small Business Administration. ACTION: Notice. SUMMARY: This is a Notice of the Presidential declaration of a major disaster for Public Assistance Only for the... Disaster Assistance, U.S. Small Business Administration, 409 3rd Street SW., Suite 6050, Washington,...

  13. 76 FR 56861 - Virginia Disaster #VA-00038

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-14

    ... ADMINISTRATION Virginia Disaster VA-00038 AGENCY: U.S. Small Business Administration. ACTION: Notice. SUMMARY... Commonwealth of Virginia (FEMA-4024-DR), dated 09/03/2011. Incident: Hurricane Irene. Incident Period: 08/26..., Southampton, Suffolk City, Sussex, Virginia Beach City, Westmoreland, Williamsburg City, York. The...

  14. 77 FR 73510 - Virginia Disaster #VA-00052

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-10

    ... From the Federal Register Online via the Government Publishing Office SMALL BUSINESS ADMINISTRATION Virginia Disaster VA-00052 AGENCY: U.S. Small Business Administration. ACTION: Notice. SUMMARY... State of Virginia (FEMA- 4092-DR), dated 11/26/2012. Incident: Hurricane Sandy Incident Period:...

  15. 75 FR 9006 - Virginia Disaster #VA-00028

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-26

    ... From the Federal Register Online via the Government Publishing Office SMALL BUSINESS ADMINISTRATION Virginia Disaster VA-00028 AGENCY: U.S. Small Business Administration. ACTION: Notice. SUMMARY... Commonwealth of Virginia (FEMA-1874-DR), dated 02/16/2010. Incident: Severe Winter Storm and...

  16. 76 FR 40766 - Virginia Disaster #VA-00032

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-07-11

    ... ADMINISTRATION Virginia Disaster VA-00032 AGENCY: U.S. Small Business Administration. ACTION: Notice. SUMMARY: This is a notice of an Administrative declaration of a disaster for the Commonwealth of Virginia dated... determined to be adversely affected by the disaster: Primary Counties: Pulaski. Contiguous Counties:...

  17. 76 FR 72020 - Virginia Disaster #VA-00039

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-21

    ... ADMINISTRATION Virginia Disaster VA-00039 AGENCY: U.S. Small Business Administration. ACTION: Notice. SUMMARY: This is a notice of an Administrative declaration of a disaster for the Commonwealth of Virginia dated... adversely affected by the disaster: Primary Counties: Fairfax, Prince William. Contiguous Counties:...

  18. 76 FR 59765 - Virginia Disaster # VA-00036

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-27

    ... ADMINISTRATION Virginia Disaster VA-00036 AGENCY: U.S. Small Business Administration. ACTION: Notice SUMMARY: This is a notice of an Administrative declaration of a disaster for the Commonwealth of Virginia dated...: Virginia: Charles City, Chesterfield, Colonial Heights City, Dinwiddie, Hanover, Henrico, James City,...

  19. 76 FR 72022 - Virginia Disaster #VA-00040

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-21

    ... From the Federal Register Online via the Government Publishing Office SMALL BUSINESS ADMINISTRATION Virginia Disaster VA-00040 AGENCY: U.S. Small Business Administration. ACTION: Notice. SUMMARY... State of Virginia (FEMA- 4042-DR), dated 11/10/2011. Incident: Earthquake. Incident Period:...

  20. 76 FR 40765 - Virginia Disaster #VA-00034

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-07-11

    ... ADMINISTRATION Virginia Disaster VA-00034 AGENCY: U.S. Small Business Administration. ACTION: Notice. SUMMARY: This is a notice of an Administrative declaration of a disaster for the Commonwealth of Virginia dated...: Virginia: Bristol City, Grayson, Russell, Scott, Smyth. Tennessee: Johnson, Sullivan. The Interest...

  1. 77 FR 74908 - Virginia Disaster #VA-00051

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-18

    ... ADMINISTRATION Virginia Disaster VA-00051 AGENCY: U.S. Small Business Administration. ACTION: Notice. SUMMARY: This is a notice of an Administrative declaration of a disaster for the Commonwealth of Virginia dated... adversely affected by the disaster: Primary Counties: Accomack. Contiguous Counties: Virginia:...

  2. Intrachromosomal homologous recombination between inverted amplicons on opposing Y-chromosome arms.

    PubMed

    Lange, Julian; Noordam, Michiel J; van Daalen, Saskia K M; Skaletsky, Helen; Clark, Brian A; Macville, Merryn V; Page, David C; Repping, Sjoerd

    2013-10-01

    Amplicons--large, nearly identical repeats in direct or inverted orientation--are abundant in the male-specific region of the human Y chromosome (MSY) and provide targets for intrachromosomal non-allelic homologous recombination (NAHR). Thus far, NAHR events resulting in deletions, duplications, inversions, or isodicentric chromosomes have been reported only for amplicon pairs located exclusively on the short arm (Yp) or the long arm (Yq). Here we report our finding of four men with Y chromosomes that evidently formed by intrachromosomal NAHR between inverted repeat pairs comprising one amplicon on Yp and one amplicon on Yq. In two men with spermatogenic failure, sister-chromatid crossing-over resulted in pseudoisoYp chromosome formation and loss of distal Yq. In two men with normal spermatogenesis, intrachromatid crossing-over generated pericentric inversions. These findings highlight the recombinogenic nature of the MSY, as intrachromosomal NAHR occurs for nearly all Y-chromosome amplicon pairs, even those located on opposing chromosome arms.

  3. Electroanalytical study of proflavine intercalation in 5-methyl or inosine-containing amplicons.

    PubMed

    Alexiadou, Despina K; Ioannou, Andrea K; Kouidou-Andreou, Sofia A; Voulgaropoulos, Anastasios N; Girousi, Stella Th

    2008-10-01

    Amplicons corresponding to the GC-rich p53 exon 5 and its analogues, synthesized by substituting 60% of cytosine by 5-methyl-cytosine, or 60% of guanosine by inosine and GC-poor p53 exon 6 were synthesized and investigated electrochemically, in the presence and absence of proflavine, by differential pulse voltammetry (DPV). Incorporation of base analogues and the thermal stability of the resulting amplicons were tested in the presence of a fluorescent probe (Sybr-Green). Peak current at 1.0 V was lower for methylated than for unmethylated PCR amplicons and was similarly affected by proflavine intercalation. In contrast, considerable peak current differences were observed in the presence of proflavine for unmodified exon 5 v.s. exon 6 or inosine-containing amplicons. Thermal analysis verified the expected shifts in melting temperature (T (m)) due to the base analogue incorporation and GC-content variations. In conclusion, methylated and unmethylated PCR amplicons could be distinguished in model DNA systems using differential pulse voltammetry (DPV) and use of proflavine could serve as an electrochemical probe for identifying different DNA conformations.

  4. A flexible and economical barcoding approach for highly multiplexed amplicon sequencing of diverse target genes.

    PubMed

    Herbold, Craig W; Pelikan, Claus; Kuzyk, Orest; Hausmann, Bela; Angel, Roey; Berry, David; Loy, Alexander

    2015-01-01

    High throughput sequencing of phylogenetic and functional gene amplicons provides tremendous insight into the structure and functional potential of complex microbial communities. Here, we introduce a highly adaptable and economical PCR approach to barcoding and pooling libraries of numerous target genes. In this approach, we replace gene- and sequencing platform-specific fusion primers with general, interchangeable barcoding primers, enabling nearly limitless customized barcode-primer combinations. Compared to barcoding with long fusion primers, our multiple-target gene approach is more economical because it overall requires lower number of primers and is based on short primers with generally lower synthesis and purification costs. To highlight our approach, we pooled over 900 different small-subunit rRNA and functional gene amplicon libraries obtained from various environmental or host-associated microbial community samples into a single, paired-end Illumina MiSeq run. Although the amplicon regions ranged in size from approximately 290 to 720 bp, we found no significant systematic sequencing bias related to amplicon length or gene target. Our results indicate that this flexible multiplexing approach produces large, diverse, and high quality sets of amplicon sequence data for modern studies in microbial ecology. PMID:26236305

  5. Integration of complete chloroplast genome sequences with small amplicon datasets improves phylogenetic resolution in Acacia.

    PubMed

    Williams, Anna V; Miller, Joseph T; Small, Ian; Nevill, Paul G; Boykin, Laura M

    2016-03-01

    Combining whole genome data with previously obtained amplicon sequences has the potential to increase the resolution of phylogenetic analyses, particularly at low taxonomic levels or where recent divergence, rapid speciation or slow genome evolution has resulted in limited sequence variation. However, the integration of these types of data for large scale phylogenetic studies has rarely been investigated. Here we conduct a phylogenetic analysis of the whole chloroplast genome and two nuclear ribosomal loci for 65 Acacia species from across the most recent Acacia phylogeny. We then combine this data with previously generated amplicon sequences (four chloroplast loci and two nuclear ribosomal loci) for 508 Acacia species. We use several phylogenetic methods, including maximum likelihood bootstrapping (with and without constraint) and ExaBayes, in order to determine the success of combining a dataset of 4000bp with one of 189,000bp. The results of our study indicate that the inclusion of whole genome data gave a far better resolved and well supported representation of the phylogenetic relationships within Acacia than using only amplicon sequences, with the greatest support observed when using a whole genome phylogeny as a constraint on the amplicon sequences. Our study therefore provides methods for optimal integration of genomic and amplicon sequences.

  6. Integration of complete chloroplast genome sequences with small amplicon datasets improves phylogenetic resolution in Acacia.

    PubMed

    Williams, Anna V; Miller, Joseph T; Small, Ian; Nevill, Paul G; Boykin, Laura M

    2016-03-01

    Combining whole genome data with previously obtained amplicon sequences has the potential to increase the resolution of phylogenetic analyses, particularly at low taxonomic levels or where recent divergence, rapid speciation or slow genome evolution has resulted in limited sequence variation. However, the integration of these types of data for large scale phylogenetic studies has rarely been investigated. Here we conduct a phylogenetic analysis of the whole chloroplast genome and two nuclear ribosomal loci for 65 Acacia species from across the most recent Acacia phylogeny. We then combine this data with previously generated amplicon sequences (four chloroplast loci and two nuclear ribosomal loci) for 508 Acacia species. We use several phylogenetic methods, including maximum likelihood bootstrapping (with and without constraint) and ExaBayes, in order to determine the success of combining a dataset of 4000bp with one of 189,000bp. The results of our study indicate that the inclusion of whole genome data gave a far better resolved and well supported representation of the phylogenetic relationships within Acacia than using only amplicon sequences, with the greatest support observed when using a whole genome phylogeny as a constraint on the amplicon sequences. Our study therefore provides methods for optimal integration of genomic and amplicon sequences. PMID:26702955

  7. Telephone Enrollment in the VA Healthcare System. Interim final rule.

    PubMed

    2016-03-16

    This rulemaking amends VA's medical regulations to allow veterans to complete applications for health care enrollment by telephone by providing application information to a VA employee, agreeing to VA's provisions regarding copayment liability and assignment of third-party insurance benefits, and attesting to the accuracy and authenticity of the information provided over the phone. This action will make it easier for veterans to apply to enroll and will speed VA processing of applications. PMID:26987128

  8. Payment for non-VA physician services associated with either outpatient or inpatient care provided at non-VA facilities--VA. Proposed rule.

    PubMed

    1997-07-22

    This document proposes to amend Department of Veterans Affairs (VA) medical regulations concerning payment for non-VA physician services that are associated with either outpatient or inpatient care provided to eligible VA beneficiaries at non-VA facilities. We propose that when a service specific reimbursement amount has been calculated under Medicare's Participating Physician Fee Schedule, VA would pay the lesser of the actual billed charge or the calculated amount. We also propose that when an amount has not been calculated, VA would pay the amount calculated under a 75th percentile formula or, in certain limited circumstances, VA would pay the usual and customary rate. In our view, adoption of this proposal would establish reimbursement consistency among federal health benefits programs, would ensure that amounts paid to physicians better represent the relative resource inputs used to furnish a service, and, would, as reflected by a recent VA Office of Inspector General (OIG) audit of the VA fee-basis program, achieve program cost reductions. Further, consistent with statutory requirements, the regulations would continue to specify that VA payment constitutes payment in full.

  9. 48 CFR 819.7109 - VA review of application.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false VA review of application... SOCIOECONOMIC PROGRAMS SMALL BUSINESS PROGRAMS VA Mentor-Protégé Program 819.7109 VA review of application. (a... that the information that is in VAAR 819.7108 is included. If the application relates to a...

  10. 78 FR 76061 - Authorization for Non-VA Medical Services

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-16

    ... Administrative practice and procedure, Alcohol abuse, Alcoholism, Claims, Day care, Dental health, Drug abuse...-VA medical care. In the Federal Register on November 28, 2012, VA proposed to remove an outdated regulatory limitation on veterans' eligibility to be referred for non- VA medical care. On the same date,...

  11. Assessing a new approach to verbal autopsy interpretation in a rural Ethiopian community: the InterVA model.

    PubMed Central

    Fantahun, Mesganaw; Fottrell, Edward; Berhane, Yemane; Wall, Stig; Högberg, Ulf; Byass, Peter

    2006-01-01

    OBJECTIVE: Verbal autopsy (VA) -- the interviewing of family members or caregivers about the circumstances of a death after the event -- is an established tool in areas where routine death registration is non-existent or inadequate. We assessed the performance of a probabilistic model (InterVA) for interpreting community-based VA interviews, in order to investigate patterns of cause-specific mortality in a rural Ethiopian community. We compared results with those obtained after review of the VA by local physicians, with a view to validating the model as a community-based tool. METHODS: Two-hundred and eighty-nine VA interviews were successfully completed; these included most deaths occurring in a defined community over a 1-year period. The VA interviews were interpreted by physicians and by the model, and cause-specific mortality fractions were derived for the whole community and for particular age groups using both approaches. FINDINGS: The results of the two approaches to interpretation correlated well in this example from Ethiopia. Four major cause groups accounted for over 60% of all mortality, and patterns within specific age groups were consistent with expectations for an underdeveloped high-mortality community in sub-Saharan Africa. CONCLUSION: Compared with interpretation by physicians, the InterVA model is much less labour intensive and offers 100% consistency. It is a valuable new tool for characterizing patterns of cause-specific mortality in communities without death registration and for comparing patterns of mortality in different populations. PMID:16583079

  12. Use of AmpliWax to optimize amplicon sterilization by isopsoralen.

    PubMed

    De la Viuda, M; Fille, M; Ruiz, J; Aslanzadeh, J

    1996-12-01

    The photochemical inactivation of amplicons by isopsoralen (IP-10) has been suggested as a possible means to prevent PCR carryover contamination. To evaluate the technique, serial dilutions of amplicons (10(11) to 10(3)) from the Borrelia burgdorferi OSP A gene were amplified in the presence of 0, 25, 50, and 100 micrograms of IP-10 per ml for 45 cycles. The PCR products were exposed to UV light for 15 min to activate IP-10 and sterilize the amplicons. One microliter of each sterilized sample was reamplified for an additional 45 cycles. The PCR products were then resolved in an agarose gel, blotted onto a nylon membrane, and probed with an alkaline phosphatase-conjugated chemiluminescent probe. Although IP-10 at concentrations of 50 and 100 micrograms/ml effectively sterilized up to 10(11) amplicons, the compound was inhibitory to PCR. IP-10 at a concentration of 25 micrograms/ml had slight inhibitory effect on PCR and did not completely sterilized all of the amplicons. Therefore, in subsequent experiments AmpliWax was substituted for mineral oil, and PCR was performed on 10(9) to 10(3) amplicons as described above. Following the amplification, the PCR tubes were cooled to solidify the AmpliWax and inoculated with various concentrations of IP-10. With this technique, PCR products produced from as many as 10(9) target amplicons were effectively sterilized with 200 micrograms of IP-10 per ml. Similarly, the addition of IP-10 (50 micrograms/ml) before and after PCR was evaluated for the detection of B. burgdorferi in 62 ticks from a region of Southern Connecticut where the organism is highly endemic. PCR performed in the presence of 50 micrograms of IP-10 per ml detected B. burgdorferi-specific DNA in 17 of 62 ticks (27%) following gel electrophoresis and in 34 of 62 ticks (55%) following Southern blot hybridization of the PCR products. In contrast, post-PCR addition of IP-10 detected borrelia-specific DNA in 31 of 62 ticks (50%) following gel electrophoresis and in

  13. Use of AmpliWax to optimize amplicon sterilization by isopsoralen.

    PubMed Central

    De la Viuda, M; Fille, M; Ruiz, J; Aslanzadeh, J

    1996-01-01

    The photochemical inactivation of amplicons by isopsoralen (IP-10) has been suggested as a possible means to prevent PCR carryover contamination. To evaluate the technique, serial dilutions of amplicons (10(11) to 10(3)) from the Borrelia burgdorferi OSP A gene were amplified in the presence of 0, 25, 50, and 100 micrograms of IP-10 per ml for 45 cycles. The PCR products were exposed to UV light for 15 min to activate IP-10 and sterilize the amplicons. One microliter of each sterilized sample was reamplified for an additional 45 cycles. The PCR products were then resolved in an agarose gel, blotted onto a nylon membrane, and probed with an alkaline phosphatase-conjugated chemiluminescent probe. Although IP-10 at concentrations of 50 and 100 micrograms/ml effectively sterilized up to 10(11) amplicons, the compound was inhibitory to PCR. IP-10 at a concentration of 25 micrograms/ml had slight inhibitory effect on PCR and did not completely sterilized all of the amplicons. Therefore, in subsequent experiments AmpliWax was substituted for mineral oil, and PCR was performed on 10(9) to 10(3) amplicons as described above. Following the amplification, the PCR tubes were cooled to solidify the AmpliWax and inoculated with various concentrations of IP-10. With this technique, PCR products produced from as many as 10(9) target amplicons were effectively sterilized with 200 micrograms of IP-10 per ml. Similarly, the addition of IP-10 (50 micrograms/ml) before and after PCR was evaluated for the detection of B. burgdorferi in 62 ticks from a region of Southern Connecticut where the organism is highly endemic. PCR performed in the presence of 50 micrograms of IP-10 per ml detected B. burgdorferi-specific DNA in 17 of 62 ticks (27%) following gel electrophoresis and in 34 of 62 ticks (55%) following Southern blot hybridization of the PCR products. In contrast, post-PCR addition of IP-10 detected borrelia-specific DNA in 31 of 62 ticks (50%) following gel electrophoresis and in

  14. 38 CFR 1.9 - Description, use, and display of VA seal and flag.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... stationery. (B) Official VA identification cards and security credentials. (C) Business cards for VA employees. (D) Official VA signs. (E) Official publications or graphics issued by and attributed to VA,...

  15. 38 CFR 1.9 - Description, use, and display of VA seal and flag.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... stationery. (B) Official VA identification cards and security credentials. (C) Business cards for VA employees. (D) Official VA signs. (E) Official publications or graphics issued by and attributed to VA,...

  16. 48 CFR 853.215-70 - VA Form 10-1170, Application for Furnishing Nursing Home Care to Beneficiaries of VA.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ..., Application for Furnishing Nursing Home Care to Beneficiaries of VA. 853.215-70 Section 853.215-70 Federal... 853.215-70 VA Form 10-1170, Application for Furnishing Nursing Home Care to Beneficiaries of VA. VA Form 10-1170, Application for Furnishing Nursing Home Care to Beneficiaries of VA, will be used...

  17. 48 CFR 853.215-70 - VA Form 10-1170, Application for Furnishing Nursing Home Care to Beneficiaries of VA.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ..., Application for Furnishing Nursing Home Care to Beneficiaries of VA. 853.215-70 Section 853.215-70 Federal... 853.215-70 VA Form 10-1170, Application for Furnishing Nursing Home Care to Beneficiaries of VA. VA Form 10-1170, Application for Furnishing Nursing Home Care to Beneficiaries of VA, will be used...

  18. 48 CFR 853.215-70 - VA Form 10-1170, Application for Furnishing Nursing Home Care to Beneficiaries of VA.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ..., Application for Furnishing Nursing Home Care to Beneficiaries of VA. 853.215-70 Section 853.215-70 Federal... 853.215-70 VA Form 10-1170, Application for Furnishing Nursing Home Care to Beneficiaries of VA. VA Form 10-1170, Application for Furnishing Nursing Home Care to Beneficiaries of VA, will be used...

  19. 48 CFR 853.215-70 - VA Form 10-1170, Application for Furnishing Nursing Home Care to Beneficiaries of VA.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ..., Application for Furnishing Nursing Home Care to Beneficiaries of VA. 853.215-70 Section 853.215-70 Federal... 853.215-70 VA Form 10-1170, Application for Furnishing Nursing Home Care to Beneficiaries of VA. VA Form 10-1170, Application for Furnishing Nursing Home Care to Beneficiaries of VA, will be used...

  20. 48 CFR 853.215-70 - VA Form 10-1170, Application for Furnishing Nursing Home Care to Beneficiaries of VA.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ..., Application for Furnishing Nursing Home Care to Beneficiaries of VA. 853.215-70 Section 853.215-70 Federal... 853.215-70 VA Form 10-1170, Application for Furnishing Nursing Home Care to Beneficiaries of VA. VA Form 10-1170, Application for Furnishing Nursing Home Care to Beneficiaries of VA, will be used...

  1. High-Throughput Amplicon Sequencing Reveals Distinct Communities within a Corroding Concrete Sewer System

    PubMed Central

    Dennis, Paul G.; Keller, Jurg; Tyson, Gene W.

    2012-01-01

    Microbially induced concrete corrosion (MICC) is an important problem in sewers. Here, small-subunit (SSU) rRNA gene amplicon pyrosequencing was used to characterize MICC communities. Microbial community composition differed between wall- and ceiling-associated MICC layers. Acidithiobacillus spp. were present at low abundances, and the communities were dominated by other sulfur-oxidizing-associated lineages. PMID:22843532

  2. High-throughput amplicon sequencing reveals distinct communities within a corroding concrete sewer system.

    PubMed

    Cayford, Barry I; Dennis, Paul G; Keller, Jurg; Tyson, Gene W; Bond, Philip L

    2012-10-01

    Microbially induced concrete corrosion (MICC) is an important problem in sewers. Here, small-subunit (SSU) rRNA gene amplicon pyrosequencing was used to characterize MICC communities. Microbial community composition differed between wall- and ceiling-associated MICC layers. Acidithiobacillus spp. were present at low abundances, and the communities were dominated by other sulfur-oxidizing-associated lineages. PMID:22843532

  3. Bacterial metabarcoding by 16S rRNA gene ion torrent amplicon sequencing.

    PubMed

    Fantini, Elio; Gianese, Giulio; Giuliano, Giovanni; Fiore, Alessia

    2015-01-01

    Ion Torrent is a next generation sequencing technology based on the detection of hydrogen ions produced during DNA chain elongation; this technology allows analyzing and characterizing genomes, genes, and species. Here, we describe an Ion Torrent procedure applied to the metagenomic analysis of 16S rRNA gene amplicons to study the bacterial diversity in food and environmental samples. PMID:25343859

  4. High-throughput amplicon sequencing reveals distinct communities within a corroding concrete sewer system.

    PubMed

    Cayford, Barry I; Dennis, Paul G; Keller, Jurg; Tyson, Gene W; Bond, Philip L

    2012-10-01

    Microbially induced concrete corrosion (MICC) is an important problem in sewers. Here, small-subunit (SSU) rRNA gene amplicon pyrosequencing was used to characterize MICC communities. Microbial community composition differed between wall- and ceiling-associated MICC layers. Acidithiobacillus spp. were present at low abundances, and the communities were dominated by other sulfur-oxidizing-associated lineages.

  5. Characterizing partial AZFc deletions of the Y chromosome with amplicon-specific sequence markers

    PubMed Central

    Navarro-Costa, Paulo; Pereira, Luísa; Alves, Cíntia; Gusmão, Leonor; Proença, Carmen; Marques-Vidal, Pedro; Rocha, Tiago; Correia, Sónia C; Jorge, Sónia; Neves, António; Soares, Ana P; Nunes, Joaquim; Calhaz-Jorge, Carlos; Amorim, António; Plancha, Carlos E; Gonçalves, João

    2007-01-01

    Background The AZFc region of the human Y chromosome is a highly recombinogenic locus containing multi-copy male fertility genes located in repeated DNA blocks (amplicons). These AZFc gene families exhibit slight sequence variations between copies which are considered to have functional relevance. Yet, partial AZFc deletions yield phenotypes ranging from normospermia to azoospermia, thwarting definite conclusions on their real impact on fertility. Results The amplicon content of partial AZFc deletion products was characterized with novel amplicon-specific sequence markers. Data indicate that partial AZFc deletions are a male infertility risk [odds ratio: 5.6 (95% CI: 1.6–30.1)] and although high diversity of partial deletion products and sequence conversion profiles were recorded, the AZFc marker profiles detected in fertile men were also observed in infertile men. Additionally, the assessment of rearrangement recurrence by Y-lineage analysis indicated that while partial AZFc deletions occurred in highly diverse samples, haplotype diversity was minimal in fertile men sharing identical marker profiles. Conclusion Although partial AZFc deletion products are highly heterogeneous in terms of amplicon content, this plasticity is not sufficient to account for the observed phenotypical variance. The lack of causative association between the deletion of specific gene copies and infertility suggests that AZFc gene content might be part of a multifactorial network, with Y-lineage evolution emerging as a possible phenotype modulator. PMID:17903263

  6. Bacterial metabarcoding by 16S rRNA gene ion torrent amplicon sequencing.

    PubMed

    Fantini, Elio; Gianese, Giulio; Giuliano, Giovanni; Fiore, Alessia

    2015-01-01

    Ion Torrent is a next generation sequencing technology based on the detection of hydrogen ions produced during DNA chain elongation; this technology allows analyzing and characterizing genomes, genes, and species. Here, we describe an Ion Torrent procedure applied to the metagenomic analysis of 16S rRNA gene amplicons to study the bacterial diversity in food and environmental samples.

  7. PANGEA: pipeline for analysis of next generation amplicons.

    PubMed

    Giongo, Adriana; Crabb, David B; Davis-Richardson, Austin G; Chauliac, Diane; Mobberley, Jennifer M; Gano, Kelsey A; Mukherjee, Nabanita; Casella, George; Roesch, Luiz F W; Walts, Brandon; Riva, Alberto; King, Gary; Triplett, Eric W

    2010-07-01

    High-throughput DNA sequencing can identify organisms and describe population structures in many environmental and clinical samples. Current technologies generate millions of reads in a single run, requiring extensive computational strategies to organize, analyze and interpret those sequences. A series of bioinformatics tools for high-throughput sequencing analysis, including pre-processing, clustering, database matching and classification, have been compiled into a pipeline called PANGEA. The PANGEA pipeline was written in Perl and can be run on Mac OSX, Windows or Linux. With PANGEA, sequences obtained directly from the sequencer can be processed quickly to provide the files needed for sequence identification by BLAST and for comparison of microbial communities. Two different sets of bacterial 16S rRNA sequences were used to show the efficiency of this workflow. The first set of 16S rRNA sequences is derived from various soils from Hawaii Volcanoes National Park. The second set is derived from stool samples collected from diabetes-resistant and diabetes-prone rats. The workflow described here allows the investigator to quickly assess libraries of sequences on personal computers with customized databases. PANGEA is provided for users as individual scripts for each step in the process or as a single script where all processes, except the chi(2) step, are joined into one program called the 'backbone'.

  8. Medical Student Psychiatry Examination Performance at VA and Non-VA Clerkship Sites

    ERIC Educational Resources Information Center

    Tucker, Phebe; von Schlageter, Margo Shultes; Park, EunMi; Rosenberg, Emily; Benjamin, Ashley B.; Nawar, Ola

    2009-01-01

    Objective: The authors examined the effects of medical student assignment to U.S. Department of Veterans Affairs (VA) Medical Center inpatient and outpatient psychiatry clerkship sites versus other university and community sites on the performance outcome measure of National Board of Medical Examiners (NBME) subject examination scores. Methods:…

  9. Improvements in VA health services for women veterans.

    PubMed

    Weiss, T W

    1995-01-01

    Since the early 1980s, health care for women veterans in the Department of Veterans Affairs (VA) has improved considerably, although problems still remain. The lack of privacy for women at many VA facilities and the provision of incomplete physical examinations for women continue to be problematic issues. A 1992 congressional appropriation of $7.5 million has substantially increased the awareness of women veterans health care in the VA. This appropriation, from Public Law 102-585, Veterans Health Care Act of 1992, Title I-Women Veterans Health Programs, has allowed VA to expand services for women veterans. Using these funds, VA has established eight comprehensive women veterans health centers, 23 full-time women veterans coordinators, and four regional stress disorder teams. This paper describes these and other important new initiatives and discusses how they will serve as the foundation on which VA expands care for women within the context of a changing health care system.

  10. Telephone Enrollment in the VA Healthcare System. Final rule.

    PubMed

    2016-09-12

    The Department of Veterans Affairs (VA) adopts as final, without change, an interim final rule amending its medical regulations. Specifically, this rule allows veterans to complete applications for health care enrollment by providing application information, agreeing to VA's provisions regarding copayment liability and assignment of third-party insurance benefits, and attesting to the accuracy and authenticity of the information provided to a VA employee over the phone. This action makes it easier for veterans to apply to enroll and speeds VA processing of applications. PMID:27632804

  11. Telephone Enrollment in the VA Healthcare System. Final rule.

    PubMed

    2016-09-12

    The Department of Veterans Affairs (VA) adopts as final, without change, an interim final rule amending its medical regulations. Specifically, this rule allows veterans to complete applications for health care enrollment by providing application information, agreeing to VA's provisions regarding copayment liability and assignment of third-party insurance benefits, and attesting to the accuracy and authenticity of the information provided to a VA employee over the phone. This action makes it easier for veterans to apply to enroll and speeds VA processing of applications.

  12. Simultaneous Amplicon Sequencing to Explore Co-Occurrence Patterns of Bacterial, Archaeal and Eukaryotic Microorganisms in Rumen Microbial Communities

    PubMed Central

    Kittelmann, Sandra; Seedorf, Henning; Walters, William A.; Clemente, Jose C.; Knight, Rob; Gordon, Jeffrey I.; Janssen, Peter H.

    2013-01-01

    Ruminants rely on a complex rumen microbial community to convert dietary plant material to energy-yielding products. Here we developed a method to simultaneously analyze the community's bacterial and archaeal 16S rRNA genes, ciliate 18S rRNA genes and anaerobic fungal internal transcribed spacer 1 genes using 12 DNA samples derived from 11 different rumen samples from three host species (Ovis aries, Bos taurus, Cervus elephas) and multiplex 454 Titanium pyrosequencing. We show that the mixing ratio of the group-specific DNA templates before emulsion PCR is crucial to compensate for differences in amplicon length. This method, in contrast to using a non-specific universal primer pair, avoids sequencing non-targeted DNA, such as plant- or endophyte-derived rRNA genes, and allows increased or decreased levels of community structure resolution for each microbial group as needed. Communities analyzed with different primers always grouped by sample origin rather than by the primers used. However, primer choice had a greater impact on apparent archaeal community structure than on bacterial community structure, and biases for certain methanogen groups were detected. Co-occurrence analysis of microbial taxa from all three domains of life suggested strong within- and between-domain correlations between different groups of microorganisms within the rumen. The approach used to simultaneously characterize bacterial, archaeal and eukaryotic components of a microbiota should be applicable to other communities occupying diverse habitats. PMID:23408926

  13. Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities.

    PubMed

    Kittelmann, Sandra; Seedorf, Henning; Walters, William A; Clemente, Jose C; Knight, Rob; Gordon, Jeffrey I; Janssen, Peter H

    2013-01-01

    Ruminants rely on a complex rumen microbial community to convert dietary plant material to energy-yielding products. Here we developed a method to simultaneously analyze the community's bacterial and archaeal 16S rRNA genes, ciliate 18S rRNA genes and anaerobic fungal internal transcribed spacer 1 genes using 12 DNA samples derived from 11 different rumen samples from three host species (Ovis aries, Bos taurus, Cervus elephas) and multiplex 454 Titanium pyrosequencing. We show that the mixing ratio of the group-specific DNA templates before emulsion PCR is crucial to compensate for differences in amplicon length. This method, in contrast to using a non-specific universal primer pair, avoids sequencing non-targeted DNA, such as plant- or endophyte-derived rRNA genes, and allows increased or decreased levels of community structure resolution for each microbial group as needed. Communities analyzed with different primers always grouped by sample origin rather than by the primers used. However, primer choice had a greater impact on apparent archaeal community structure than on bacterial community structure, and biases for certain methanogen groups were detected. Co-occurrence analysis of microbial taxa from all three domains of life suggested strong within- and between-domain correlations between different groups of microorganisms within the rumen. The approach used to simultaneously characterize bacterial, archaeal and eukaryotic components of a microbiota should be applicable to other communities occupying diverse habitats.

  14. Neuronal precursor-restricted transduction via in utero CNS gene delivery of a novel bipartite HSV amplicon/transposase hybrid vector.

    PubMed

    Bowers, William J; Mastrangelo, Michael A; Howard, Darlene F; Southerland, Hilary A; Maguire-Zeiss, Kathleen A; Federoff, Howard J

    2006-03-01

    The ability to modify genetically in utero the precursors of neuronal lineage contributing to multiple postmitotic cell types in the adult central nervous system would provide a means to evaluate strategies to ameliorate conditions affecting cellular patterning, metabolism, or survival. The herpes simplex virus (HSV)-derived amplicon, a vector devoid of viral genes and with the largest known payload capacity, normally exists episomally within nuclei of transduced cells, thus precluding conveyance during mitosis. Herein, we modify the Tc1-like Sleeping Beauty (SB) transposon system to create an integrating amplicon vector platform wherein provision of transposase in trans effectively catalyzes integration of a transgenomic segment. Cotransduction with a Rous sarcoma virus promoter-driven beta-galactosidase-neomycin (betageo) fusion flanked by SB terminal repeats (HSVT-betageo) and a second expressing the SB transposase gene under HSV immediate-early 4/5 gene promoter control (HSVsb) resulted in integration and extension of expression duration. Most notably, in utero intraventricular application led to extensive transgene expression within neuronal precursors and their derivatives without attendant adverse consequences, suggesting this new platform could be used to evaluate prenatally the function of gene products in neuronal lineages and evaluate therapeutic strategies for correction of genetic abnormalities affecting the developing CNS. PMID:16412694

  15. One-way sequencing of multiple amplicons from tandem repetitive mitochondrial DNA control region.

    PubMed

    Xu, Jiawu; Fonseca, Dina M

    2011-10-01

    Repetitive DNA sequences not only exist abundantly in eukaryotic nuclear genomes, but also occur as tandem repeats in many animal mitochondrial DNA (mtDNA) control regions. Due to concerted evolution, these repetitive sequences are highly similar or even identical within a genome. When long repetitive regions are the targets of amplification for the purpose of sequencing, multiple amplicons may result if one primer has to be located inside the repeats. Here, we show that, without separating these amplicons by gel purification or cloning, directly sequencing the mitochondrial repeats with the primer outside repetitive region is feasible and efficient. We exemplify it by sequencing the mtDNA control region of the mosquito Aedes albopictus, which harbors typical large tandem DNA repeats. This one-way sequencing strategy is optimal for population surveys.

  16. Comparison of normalization methods for construction of large, multiplex amplicon pools for next-generation sequencing.

    PubMed

    Harris, J Kirk; Sahl, Jason W; Castoe, Todd A; Wagner, Brandie D; Pollock, David D; Spear, John R

    2010-06-01

    Constructing mixtures of tagged or bar-coded DNAs for sequencing is an important requirement for the efficient use of next-generation sequencers in applications where limited sequence data are required per sample. There are many applications in which next-generation sequencing can be used effectively to sequence large mixed samples; an example is the characterization of microbial communities where amplicon are mixed. Here we compare three approaches (spectroscopy, size-restricted spectroscopy, and quantitative binding) for normalization of large, multiplex amplicon pools for performance and efficiency. We found that the quantitative binding approach was superior and represents an efficient scalable process for construction of very large, multiplex pools with hundreds and perhaps thousands of individual amplicons included. We demonstrate the increased sequence diversity identified with higher throughput. Massively parallel sequencing can dramatically accelerate microbial ecology studies by allowing appropriate replication of sequence acquisition to account for temporal and spatial variations. Further, population studies to examine genetic variation, which require even lower levels of sequencing, should be possible where thousands of individual bar-coded amplicons are examined in parallel. PMID:20418443

  17. Amplicon Sequencing of Colorectal Cancer: Variant Calling in Frozen and Formalin-Fixed Samples

    PubMed Central

    Betge, Johannes; Kerr, Grainne; Miersch, Thilo; Leible, Svenja; Erdmann, Gerrit; Galata, Christian L.; Zhan, Tianzuo; Gaiser, Timo; Post, Stefan; Ebert, Matthias P.; Horisberger, Karoline; Boutros, Michael

    2015-01-01

    Next generation sequencing (NGS) is an emerging technology becoming relevant for genotyping of clinical samples. Here, we assessed the stability of amplicon sequencing from formalin-fixed paraffin-embedded (FFPE) and paired frozen samples from colorectal cancer metastases with different analysis pipelines. 212 amplicon regions in 48 cancer related genes were sequenced with Illumina MiSeq using DNA isolated from resection specimens from 17 patients with colorectal cancer liver metastases. From ten of these patients, paired fresh frozen and routinely processed FFPE tissue was available for comparative study. Sample quality of FFPE tissues was determined by the amount of amplifiable DNA using qPCR, sequencing libraries were evaluated using Bioanalyzer. Three bioinformatic pipelines were compared for analysis of amplicon sequencing data. Selected hot spot mutations were reviewed using Sanger sequencing. In the sequenced samples from 16 patients, 29 non-synonymous coding mutations were identified in eleven genes. Most frequent were mutations in TP53 (10), APC (7), PIK3CA (3) and KRAS (2). A high concordance of FFPE and paired frozen tissue samples was observed in ten matched samples, revealing 21 identical mutation calls and only two mutations differing. Comparison of these results with two other commonly used variant calling tools, however, showed high discrepancies. Hence, amplicon sequencing can potentially be used to identify hot spot mutations in colorectal cancer metastases in frozen and FFPE tissue. However, remarkable differences exist among results of different variant calling tools, which are not only related to DNA sample quality. Our study highlights the need for standardization and benchmarking of variant calling pipelines, which will be required for translational and clinical applications. PMID:26010451

  18. Massively parallel sequencing of 17 commonly used forensic autosomal STRs and amelogenin with small amplicons.

    PubMed

    Kim, Eun Hye; Lee, Hwan Young; Yang, In Seok; Jung, Sang-Eun; Yang, Woo Ick; Shin, Kyoung-Jin

    2016-05-01

    The next-generation sequencing (NGS) method has been utilized to analyze short tandem repeat (STR) markers, which are routinely used for human identification purposes in the forensic field. Some researchers have demonstrated the successful application of the NGS system to STR typing, suggesting that NGS technology may be an alternative or additional method to overcome limitations of capillary electrophoresis (CE)-based STR profiling. However, there has been no available multiplex PCR system that is optimized for NGS analysis of forensic STR markers. Thus, we constructed a multiplex PCR system for the NGS analysis of 18 markers (13CODIS STRs, D2S1338, D19S433, Penta D, Penta E and amelogenin) by designing amplicons in the size range of 77-210 base pairs. Then, PCR products were generated from two single-sources, mixed samples and artificially degraded DNA samples using a multiplex PCR system, and were prepared for sequencing on the MiSeq system through construction of a subsequent barcoded library. By performing NGS and analyzing the data, we confirmed that the resultant STR genotypes were consistent with those of CE-based typing. Moreover, sequence variations were detected in targeted STR regions. Through the use of small-sized amplicons, the developed multiplex PCR system enables researchers to obtain successful STR profiles even from artificially degraded DNA as well as STR loci which are analyzed with large-sized amplicons in the CE-based commercial kits. In addition, successful profiles can be obtained from mixtures up to a 1:19 ratio. Consequently, the developed multiplex PCR system, which produces small size amplicons, can be successfully applied to STR NGS analysis of forensic casework samples such as mixtures and degraded DNA samples. PMID:26799314

  19. Ioncopy: a novel method for calling copy number alterations in amplicon sequencing data including significance assessment

    PubMed Central

    Budczies, Jan; Pfarr, Nicole; Stenzinger, Albrecht; Treue, Denise; Endris, Volker; Ismaeel, Fakher; Bangemann, Nikola; Blohmer, Jens-Uwe; Dietel, Manfred; Loibl, Sibylle; Klauschen, Frederick; Weichert, Wilko; Denkert, Carsten

    2016-01-01

    Recently, it has been demonstrated that calling of copy number alterations (CNAs) from amplicon sequencing (AS) data is feasible. Most approaches, however, require non-tumor (germline) DNA for data normalization. Here, we present the method Ioncopy for CNA detection which requires no normal controls and includes a significance assessment for each detected alteration. Ioncopy was evaluated in a cohort of 184 clinically annotated breast carcinomas. A total number of 252 amplifications were detected, of which 183 (72.6%) could be validated by a call of an additional amplicon interrogating the same gene. Moreover, a total number of 33 deletions were found, whereof 27 (81.8%) could be validated. Analyzing the 16 most frequently amplified genes, validation rates of over 89% could be achieved for 11 of these genes. 11 of the top 16 genes showed significant overexpression in the amplified tumors. 89.5% of the HER2-amplified tumors were GRB7 and STARD3 co-amplified, whereas 68.4% of the HER2-amplified tumors had additional MED1 amplifications. Correlations between CNAs measured by amplicons in HER2 exons 19, 20 and 21 were strong (all R > 0.93). AS based detection of HER2 amplifications had a sensitivity of 90.0% and a specificity of 98.8% compared to the gold standard of HER2 immunohistochemistry combined with in situ hybridization. In summary, we developed and validated a novel method for detection and significance assessment of CNAs in amplicon sequencing data. Using Ioncopy, AS offers a straightforward and efficient approach to simultaneously analyze gene amplifications and gene deletions together with simple somatic mutations in a single assay. PMID:26910888

  20. Characterization of FGFR1 Locus in sqNSCLC Reveals a Broad and Heterogeneous Amplicon

    PubMed Central

    Rooney, Claire; Geh, Catherine; Williams, Victoria; Heuckmann, Johannes M.; Menon, Roopika; Schneider, Petra; Al-Kadhimi, Katherine; Dymond, Michael; Smith, Neil R.; Baker, Dawn; French, Tim; Smith, Paul D.; Harrington, Elizabeth A.; Barrett, J. Carl; Kilgour, Elaine

    2016-01-01

    FGFR1 amplification occurs in ~20% of sqNSCLC and trials with FGFR inhibitors have selected FGFR1 amplified patients by FISH. Lung cancer cell lines were profiled for sensitivity to AZD4547, a potent, selective inhibitor of FGFRs 1–3. Sensitivity to FGFR inhibition was associated with but not wholly predicted by increased FGFR1 gene copy number. Additional biomarker assays evaluating expression of FGFRs and correlation between amplification and expression in clinical tissues are therefore warranted. We validated nanoString for mRNA expression analysis of 194 genes, including FGFRs, from clinical tumour tissue. In a panel of sqNSCLC tumours 14.4% (13/90) were FGFR1 amplified by FISH. Although mean FGFR1 expression was significantly higher in amplified samples, there was significant overlap in the range of expression levels between the amplified and non-amplified cohorts with several non-amplified samples expressing FGFR1 to levels equivalent to amplified samples. Statistical analysis revealed increased expression of FGFR1 neighboring genes on the 8p12 amplicon (BAG4, LSM1 and WHSC1L1) in FGFR1 amplified tumours, suggesting a broad rather than focal amplicon and raises the potential for codependencies. High resolution aCGH analysis of pre-clinical and clinical samples supported the presence of a broad and heterogeneous amplicon around the FGFR1 locus. In conclusion, the range of FGFR1 expression levels in both FGFR1 amplified and non-amplified NSCLC tissues, together with the breadth and intra-patient heterogeneity of the 8p amplicon highlights the need for gene expression analysis of clinical samples to inform the understanding of determinants of response to FGFR inhibitors. In this respect the nanoString platform provides an attractive option for RNA analysis of FFPE clinical samples. PMID:26905262

  1. Characterization of FGFR1 Locus in sqNSCLC Reveals a Broad and Heterogeneous Amplicon.

    PubMed

    Rooney, Claire; Geh, Catherine; Williams, Victoria; Heuckmann, Johannes M; Menon, Roopika; Schneider, Petra; Al-Kadhimi, Katherine; Dymond, Michael; Smith, Neil R; Baker, Dawn; French, Tim; Smith, Paul D; Harrington, Elizabeth A; Barrett, J Carl; Kilgour, Elaine

    2016-01-01

    FGFR1 amplification occurs in ~20% of sqNSCLC and trials with FGFR inhibitors have selected FGFR1 amplified patients by FISH. Lung cancer cell lines were profiled for sensitivity to AZD4547, a potent, selective inhibitor of FGFRs 1-3. Sensitivity to FGFR inhibition was associated with but not wholly predicted by increased FGFR1 gene copy number. Additional biomarker assays evaluating expression of FGFRs and correlation between amplification and expression in clinical tissues are therefore warranted. We validated nanoString for mRNA expression analysis of 194 genes, including FGFRs, from clinical tumour tissue. In a panel of sqNSCLC tumours 14.4% (13/90) were FGFR1 amplified by FISH. Although mean FGFR1 expression was significantly higher in amplified samples, there was significant overlap in the range of expression levels between the amplified and non-amplified cohorts with several non-amplified samples expressing FGFR1 to levels equivalent to amplified samples. Statistical analysis revealed increased expression of FGFR1 neighboring genes on the 8p12 amplicon (BAG4, LSM1 and WHSC1L1) in FGFR1 amplified tumours, suggesting a broad rather than focal amplicon and raises the potential for codependencies. High resolution aCGH analysis of pre-clinical and clinical samples supported the presence of a broad and heterogeneous amplicon around the FGFR1 locus. In conclusion, the range of FGFR1 expression levels in both FGFR1 amplified and non-amplified NSCLC tissues, together with the breadth and intra-patient heterogeneity of the 8p amplicon highlights the need for gene expression analysis of clinical samples to inform the understanding of determinants of response to FGFR inhibitors. In this respect the nanoString platform provides an attractive option for RNA analysis of FFPE clinical samples. PMID:26905262

  2. From Benchtop to Desktop: Important Considerations when Designing Amplicon Sequencing Workflows

    PubMed Central

    Murray, Dáithí C.; Coghlan, Megan L.; Bunce, Michael

    2015-01-01

    Amplicon sequencing has been the method of choice in many high-throughput DNA sequencing (HTS) applications. To date there has been a heavy focus on the means by which to analyse the burgeoning amount of data afforded by HTS. In contrast, there has been a distinct lack of attention paid to considerations surrounding the importance of sample preparation and the fidelity of library generation. No amount of high-end bioinformatics can compensate for poorly prepared samples and it is therefore imperative that careful attention is given to sample preparation and library generation within workflows, especially those involving multiple PCR steps. This paper redresses this imbalance by focusing on aspects pertaining to the benchtop within typical amplicon workflows: sample screening, the target region, and library generation. Empirical data is provided to illustrate the scope of the problem. Lastly, the impact of various data analysis parameters is also investigated in the context of how the data was initially generated. It is hoped this paper may serve to highlight the importance of pre-analysis workflows in achieving meaningful, future-proof data that can be analysed appropriately. As amplicon sequencing gains traction in a variety of diagnostic applications from forensics to environmental DNA (eDNA) it is paramount workflows and analytics are both fit for purpose. PMID:25902146

  3. From benchtop to desktop: important considerations when designing amplicon sequencing workflows.

    PubMed

    Murray, Dáithí C; Coghlan, Megan L; Bunce, Michael

    2015-01-01

    Amplicon sequencing has been the method of choice in many high-throughput DNA sequencing (HTS) applications. To date there has been a heavy focus on the means by which to analyse the burgeoning amount of data afforded by HTS. In contrast, there has been a distinct lack of attention paid to considerations surrounding the importance of sample preparation and the fidelity of library generation. No amount of high-end bioinformatics can compensate for poorly prepared samples and it is therefore imperative that careful attention is given to sample preparation and library generation within workflows, especially those involving multiple PCR steps. This paper redresses this imbalance by focusing on aspects pertaining to the benchtop within typical amplicon workflows: sample screening, the target region, and library generation. Empirical data is provided to illustrate the scope of the problem. Lastly, the impact of various data analysis parameters is also investigated in the context of how the data was initially generated. It is hoped this paper may serve to highlight the importance of pre-analysis workflows in achieving meaningful, future-proof data that can be analysed appropriately. As amplicon sequencing gains traction in a variety of diagnostic applications from forensics to environmental DNA (eDNA) it is paramount workflows and analytics are both fit for purpose.

  4. Double minute chromosomes in glioblastoma multiforme are revealed by precise reconstruction of oncogenic amplicons

    PubMed Central

    Sanborn, J. Zachary; Salama, Sofie R.; Grifford, Mia; Brennan, Cameron W.; Mikkelsen, Tom; Jhanwar, Suresh; Katzman, Sol; Chin, Lynda; Haussler, David

    2013-01-01

    DNA sequencing offers a powerful tool in oncology based on the precise definition of structural rearrangements, copy number in tumor genomes. Here we describe the development of methods to compute copy number and detect structural variants with data synthesis to locally reconstruct highly rearranged regions of the tumor genome with high precision from standard short read, paired-end sequencing datasets. We find that circular assemblies are the most parsimonious explanation for a set of highly amplified tumor regions in a subset of glioblastoma multiforme (GBM) samples sequenced by The Cancer Genome Atlas (TCGA) consortium, revealing evidence for double minute chromosomes (DM) in these tumors. Further, we find that some samples harbor multiple circular amplicons and in some cases further rearrangements occurred after the initial amplicon-generating event. Fluorescence in situ hybridization (FISH) analysis offered an initial confirmation of the presence of DMs. Gene content in these assemblies helps identify likely driver oncogenes for these amplicons. RNA-seq data available for one DM offered additional support for our local tumor genome assemblies, identifying the birth of a novel exon made possible through rearranged sequences present in the DM. Consistent with previous estimates, our method was also useful for analysis of a larger set of GBM tumors for which exome sequencing data is available, finding evidence for oncogenic DMs in over 20% of clinical specimens examined. PMID:23940299

  5. 38 CFR 1.203 - Information to be reported to VA Police.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... reported to VA Police. 1.203 Section 1.203 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS... be reported to VA Police. Information about actual or possible violations of criminal laws related to... occurs on VA premises, will be reported by VA management officials to the VA police component...

  6. 38 CFR 1.203 - Information to be reported to VA Police.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... reported to VA Police. 1.203 Section 1.203 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS... be reported to VA Police. Information about actual or possible violations of criminal laws related to... occurs on VA premises, will be reported by VA management officials to the VA police component...

  7. 38 CFR 1.203 - Information to be reported to VA Police.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... reported to VA Police. 1.203 Section 1.203 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS... be reported to VA Police. Information about actual or possible violations of criminal laws related to... occurs on VA premises, will be reported by VA management officials to the VA police component...

  8. 38 CFR 1.203 - Information to be reported to VA Police.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... reported to VA Police. 1.203 Section 1.203 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS... be reported to VA Police. Information about actual or possible violations of criminal laws related to... occurs on VA premises, will be reported by VA management officials to the VA police component...

  9. 38 CFR 1.203 - Information to be reported to VA Police.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... reported to VA Police. 1.203 Section 1.203 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS... be reported to VA Police. Information about actual or possible violations of criminal laws related to... occurs on VA premises, will be reported by VA management officials to the VA police component...

  10. Home Health Care and Patterns of Subsequent VA and Medicare Health Care Utilization for Veterans

    ERIC Educational Resources Information Center

    Van Houtven, Courtney Harold; Jeffreys, Amy S.; Coffman, Cynthia J.

    2008-01-01

    Purpose: The Veterans Affairs or VA health care system is in the process of significantly expanding home health care (HOC) nationwide. We describe VA HHC use in 2003 for all VA HHC users from 2002; we examine whether VA utilization across a broad spectrum of services differed for a sample of VA HHC users and their propensity-score-matched…

  11. 77 FR 67063 - VA Directive 0005 on Scientific Integrity

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-08

    ... April 9, 2012 (77 FR 21158). FOR FURTHER INFORMATION CONTACT: Billy E. Jones, M.D., Senior Advisor to... http://www1.va.gov/vapubs/ . Directive 0005 establishes VA policies that: Foster a culture of... technological information from political or commercial influence; Prohibit suppression or alteration...

  12. FACILITIES FOR EDUCATION IN VA HOSPITALS. FINAL REPORT.

    ERIC Educational Resources Information Center

    GREEN, ALAN C.; AND OTHERS

    THIS STUDY WAS AUTHORIZED BY THE VA DEPARTMENT OF MEDICINE AND SURGERY FOR THE PURPOSE OF IDENTIFYING AND DETERMINING THE FACILITIES NEEDED TO PROPERLY HOUSE AND SUPPORT EDUCATION ACTIVITIES IN EXISTING AND FUTURE VA HOSPITALS AND TO PRODUCE ARCHITECTURAL GUIDANCE IN THE DESIGN OF THE FACILITIES. CURRENT PRACTICES AND SIGNIFICANT TRENDS IN MEDICAL…

  13. 38 CFR 74.27 - How will VA store information?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2010-07-01 2010-07-01 false How will VA store information? 74.27 Section 74.27 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) VETERANS SMALL BUSINESS REGULATIONS Records Management § 74.27 How will VA store information?...

  14. 78 FR 63143 - VA Dental Insurance Program-Federalism

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-23

    ... AFFAIRS 38 CFR Part 17 RIN 2900-AO86 VA Dental Insurance Program--Federalism AGENCY: Department of... its regulations related to the VA Dental Insurance Program (VADIP), a pilot program to offer premium-based dental insurance to enrolled veterans and certain survivors and dependents of...

  15. 78 FR 62441 - VA Dental Insurance Program-Federalism

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-22

    ... AFFAIRS 38 CFR Part 17 RIN 2900-AO85 VA Dental Insurance Program--Federalism AGENCY: Department of... direct final action to amend its regulations related to the VA Dental Insurance Program (VADIP), a pilot program to offer premium-based dental insurance to enrolled veterans and certain survivors and...

  16. 33 CFR 80.510 - Chesapeake Bay Entrance, VA.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Chesapeake Bay Entrance, VA. 80.510 Section 80.510 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Fifth District § 80.510 Chesapeake Bay Entrance, VA....

  17. 33 CFR 80.510 - Chesapeake Bay Entrance, VA.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Chesapeake Bay Entrance, VA. 80.510 Section 80.510 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Fifth District § 80.510 Chesapeake Bay Entrance, VA....

  18. 33 CFR 80.510 - Chesapeake Bay Entrance, VA.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Chesapeake Bay Entrance, VA. 80.510 Section 80.510 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Fifth District § 80.510 Chesapeake Bay Entrance, VA....

  19. 33 CFR 80.510 - Chesapeake Bay Entrance, VA.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Chesapeake Bay Entrance, VA. 80.510 Section 80.510 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Fifth District § 80.510 Chesapeake Bay Entrance, VA....

  20. 33 CFR 80.510 - Chesapeake Bay Entrance, VA.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Chesapeake Bay Entrance, VA. 80.510 Section 80.510 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Fifth District § 80.510 Chesapeake Bay Entrance, VA....

  1. DOE Spent Nuclear Fuel Information In Support of TSPA-VA

    SciTech Connect

    A. Brewer; D. Cresap; D. Fillmore; H. Loo; M. Ebner; R. McCormack

    1998-09-01

    RW has started the viability assessment (VA) effort to determine the feasibility of Yucca Mountain as the first geologic repository for spent nuclear fuel (SNF) and high-level waste. One component of the viability assessment will be a total system performance assessment (TSPA), based on the design concept and the scientific data and analysis available, describing the repository's probable behavior relative to the overall system performance standards. Thus, all the data collected from the Exploratory Studies Facility to-date have been incorporated into the latest TSPA model. In addition, the Repository Integration Program, an integrated probabilistic simulator, used in the TSPA has also been updated by Golder Associates Incorporated at December 1997. To ensure that the Department of Energy-owned (DOE-owned) SNF continues to be acceptable for disposal in the repository, it will be included in the TSPA-VA evaluation. A number of parameters are needed in the TSPA-VA models to predict the performance of the DOE-owned SNF materials placed into the potential repository. This report documents all of the basis and/or derivation for each of these parameters. A number of properties were not readily available at the time the TSPA-VA data was requested. Thus, expert judgement and opinion was utilized to determine a best property value. The performance of the DOE-owned SNF will be published as part of the TSPA-VA report. Each DOE site will be collecting better data as the DOE SNF program moves closer to repository license application. As required by the RW-0333P, the National Spent Nuclear Fuel Program will be assisting each site in qualifying the information used to support the performance assessment evaluations.

  2. 75 FR 78806 - Agency Information Collection (Create Payment Request for the VA Funding Fee Payment System (VA...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-16

    ... AFFAIRS Agency Information Collection (Create Payment Request for the VA Funding Fee Payment System (VA... Officer, OMB Human Resources and Housing Branch, New Executive Office Building, Room 10235, Washington, DC... Administration (VBA), Department of Veterans Affairs, will submit the collection of information abstracted...

  3. The depiction of Alboran Sea Gyre during Donde Va? using remote sensing and conventional data

    NASA Technical Reports Server (NTRS)

    Laviolette, P. E.

    1984-01-01

    Experienced oceanographic investigators have come to realize that remote sensing techniques are most successful when applied as part of programs of integrated measurements aimed at solving specific oceanographic problems. A good example of such integration occurred during the multi-platform international experiment, Donde Va? in the Alboran Sea during the period June through October, 1982. The objective of Donde Va? was to derive the interrelationship of the Atlantic waters entering the Mediterranean Sea and the Alboran Sea Gyre. The experimental plan conceived solely with this objective in mind consisted of a variety of remote sensing and conventional platforms: three ships, three aircraft, five current moorings, two satellites and a specialized beach radar (CODAR). Integrated analyses of these multiple-data sets are still being conducted. However, the initial results show detailed structure of the incoming Atlantic jet and Alboran Sea Gyre that would not have been possible by conventional means.

  4. Regional effects on chimera formation in 454 pyrosequenced amplicons from a mock community.

    PubMed

    Shin, Sunguk; Lee, Tae Kwon; Han, Jung Min; Park, Joonhong

    2014-07-01

    Chimeras are a frequent artifact in polymerase chain reaction and could be the underlying causes of erroneous taxonomic identifications, overestimated microbial diversity, and spurious sequences. However, little is known about the regional effects on chimera formation. Therefore, we investigated the chimera formation rates in different regions of phylogenetically important biomarker genes to test the regional effects on chimera formation. An empirical study of chimera formation rates was performed using the Roche GSFLX™ system with sequences of the V1/V2/V3 and V4/V5 regions of the 16S rRNA gene and sequences of the nifH gene from a mock microbial community. The chimera formation rates for the 16S V1/V2/V3 region, V4/V5 region, and nifH gene were 22.1-38.5%, 3.68-3.88%, and 0.31-0.98%, respectively. Some amplicons from the V1/V2/V3 regions were shorter than the typical length (∼7-31%), reflecting incomplete extension. In the V1/V2/V3 and V4/V5 regions, conserved and hypervariable regions were identified. Chimeric hot spots were located in parts of conserved regions near the ends of the amplicons. The 16S V1/V2/V3 region had the highest chimera formation rate, likely because of long template lengths and incomplete extension. The amplicons of the nifH gene had the lowest frequency of chimera formation most likely because of variations in their wobble positions in triplet codons. Our results suggest that the main reasons for chimera formation are sequence similarity and premature termination of DNA extension near primer regions. Other housekeeping genes can be a good substitute for 16S rRNA genes in molecular microbial studies to reduce the effects of chimera formation.

  5. Regional effects on chimera formation in 454 pyrosequenced amplicons from a mock community.

    PubMed

    Shin, Sunguk; Lee, Tae Kwon; Han, Jung Min; Park, Joonhong

    2014-07-01

    Chimeras are a frequent artifact in polymerase chain reaction and could be the underlying causes of erroneous taxonomic identifications, overestimated microbial diversity, and spurious sequences. However, little is known about the regional effects on chimera formation. Therefore, we investigated the chimera formation rates in different regions of phylogenetically important biomarker genes to test the regional effects on chimera formation. An empirical study of chimera formation rates was performed using the Roche GSFLX™ system with sequences of the V1/V2/V3 and V4/V5 regions of the 16S rRNA gene and sequences of the nifH gene from a mock microbial community. The chimera formation rates for the 16S V1/V2/V3 region, V4/V5 region, and nifH gene were 22.1-38.5%, 3.68-3.88%, and 0.31-0.98%, respectively. Some amplicons from the V1/V2/V3 regions were shorter than the typical length (∼7-31%), reflecting incomplete extension. In the V1/V2/V3 and V4/V5 regions, conserved and hypervariable regions were identified. Chimeric hot spots were located in parts of conserved regions near the ends of the amplicons. The 16S V1/V2/V3 region had the highest chimera formation rate, likely because of long template lengths and incomplete extension. The amplicons of the nifH gene had the lowest frequency of chimera formation most likely because of variations in their wobble positions in triplet codons. Our results suggest that the main reasons for chimera formation are sequence similarity and premature termination of DNA extension near primer regions. Other housekeeping genes can be a good substitute for 16S rRNA genes in molecular microbial studies to reduce the effects of chimera formation. PMID:24879347

  6. Using Amplicon Sequencing To Characterize and Monitor Bacterial Diversity in Drinking Water Distribution Systems

    PubMed Central

    Shaw, Jennifer L. A.; Weyrich, Laura S.; Sawade, Emma; Drikas, Mary; Cooper, Alan J.

    2015-01-01

    Drinking water assessments use a variety of microbial, physical, and chemical indicators to evaluate water treatment efficiency and product water quality. However, these indicators do not allow the complex biological communities, which can adversely impact the performance of drinking water distribution systems (DWDSs), to be characterized. Entire bacterial communities can be studied quickly and inexpensively using targeted metagenomic amplicon sequencing. Here, amplicon sequencing of the 16S rRNA gene region was performed alongside traditional water quality measures to assess the health, quality, and efficiency of two distinct, full-scale DWDSs: (i) a linear DWDS supplied with unfiltered water subjected to basic disinfection before distribution and (ii) a complex, branching DWDS treated by a four-stage water treatment plant (WTP) prior to disinfection and distribution. In both DWDSs bacterial communities differed significantly after disinfection, demonstrating the effectiveness of both treatment regimes. However, bacterial repopulation occurred further along in the DWDSs, and some end-user samples were more similar to the source water than to the postdisinfection water. Three sample locations appeared to be nitrified, displaying elevated nitrate levels and decreased ammonia levels, and nitrifying bacterial species, such as Nitrospira, were detected. Burkholderiales were abundant in samples containing large amounts of monochloramine, indicating resistance to disinfection. Genera known to contain pathogenic and fecal-associated species were also identified in several locations. From this study, we conclude that metagenomic amplicon sequencing is an informative method to support current compliance-based methods and can be used to reveal bacterial community interactions with the chemical and physical properties of DWDSs. PMID:26162884

  7. Using Amplicon Sequencing To Characterize and Monitor Bacterial Diversity in Drinking Water Distribution Systems.

    PubMed

    Shaw, Jennifer L A; Monis, Paul; Weyrich, Laura S; Sawade, Emma; Drikas, Mary; Cooper, Alan J

    2015-09-01

    Drinking water assessments use a variety of microbial, physical, and chemical indicators to evaluate water treatment efficiency and product water quality. However, these indicators do not allow the complex biological communities, which can adversely impact the performance of drinking water distribution systems (DWDSs), to be characterized. Entire bacterial communities can be studied quickly and inexpensively using targeted metagenomic amplicon sequencing. Here, amplicon sequencing of the 16S rRNA gene region was performed alongside traditional water quality measures to assess the health, quality, and efficiency of two distinct, full-scale DWDSs: (i) a linear DWDS supplied with unfiltered water subjected to basic disinfection before distribution and (ii) a complex, branching DWDS treated by a four-stage water treatment plant (WTP) prior to disinfection and distribution. In both DWDSs bacterial communities differed significantly after disinfection, demonstrating the effectiveness of both treatment regimes. However, bacterial repopulation occurred further along in the DWDSs, and some end-user samples were more similar to the source water than to the postdisinfection water. Three sample locations appeared to be nitrified, displaying elevated nitrate levels and decreased ammonia levels, and nitrifying bacterial species, such as Nitrospira, were detected. Burkholderiales were abundant in samples containing large amounts of monochloramine, indicating resistance to disinfection. Genera known to contain pathogenic and fecal-associated species were also identified in several locations. From this study, we conclude that metagenomic amplicon sequencing is an informative method to support current compliance-based methods and can be used to reveal bacterial community interactions with the chemical and physical properties of DWDSs.

  8. Viability-qPCR for detecting Legionella: Comparison of two assays based on different amplicon lengths.

    PubMed

    Ditommaso, Savina; Giacomuzzi, Monica; Ricciardi, Elisa; Zotti, Carla M

    2015-08-01

    Two different real-time quantitative PCR (PMA-qPCR) assays were applied for quantification of Legionella spp. by targeting a long amplicon (approx 400 bp) of 16S rRNA gene and a short amplicon (approx. 100 bp) of 5S rRNA gene. Purified DNA extracts from pure cultures of Legionella spp. and from environmental water samples were quantified. Application of the two assays to quantify Legionella in artificially contaminated water achieved that both assays were able to detect Legionella over a linear range of 10 to 10(5) cells ml(-1). A statistical analysis of the standard curves showed that both assays were linear with a good correlation coefficient (R(2) = 0.99) between the Ct and the copy number. Amplification with the reference assay was the most effective for detecting low copy numbers (1 bacterium per PCR mixture). Using selective quantification of viable Legionella by the PMA-qPCR method we obtained a greater inhibition of the amplification of the 400-bp 16S gene fragment (Δlog(10) = 3.74 ± 0.39 log(10) GU ml(-1)). A complete inhibition of the PCR signal was obtained when heat-killed cells in a concentration below 1 × 10(5) cells ml(-1) were pretreated with PMA. Analysing short amplicon sizes led to only 2.08 log reductions in the Legionella dead-cell signal. When we tested environmental water samples, the two qPCR assays were in good agreement according to the kappa index (0.741). Applying qPCR combined with PMA treatment, we also obtained a good agreement (kappa index 0.615). The comparison of quantitative results shows that both assays yielded the same quantification sensitivity (mean log = 4.59 vs mean log = 4.31).

  9. Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

    PubMed Central

    Sanschagrin, Sylvie; Yergeau, Etienne

    2014-01-01

    One of the major questions in microbial ecology is “who is there?” This question can be answered using various tools, but one of the long-lasting gold standards is to sequence 16S ribosomal RNA (rRNA) gene amplicons generated by domain-level PCR reactions amplifying from genomic DNA. Traditionally, this was performed by cloning and Sanger (capillary electrophoresis) sequencing of PCR amplicons. The advent of next-generation sequencing has tremendously simplified and increased the sequencing depth for 16S rRNA gene sequencing. The introduction of benchtop sequencers now allows small labs to perform their 16S rRNA sequencing in-house in a matter of days. Here, an approach for 16S rRNA gene amplicon sequencing using a benchtop next-generation sequencer is detailed. The environmental DNA is first amplified by PCR using primers that contain sequencing adapters and barcodes. They are then coupled to spherical particles via emulsion PCR. The particles are loaded on a disposable chip and the chip is inserted in the sequencing machine after which the sequencing is performed. The sequences are retrieved in fastq format, filtered and the barcodes are used to establish the sample membership of the reads. The filtered and binned reads are then further analyzed using publically available tools. An example analysis where the reads were classified with a taxonomy-finding algorithm within the software package Mothur is given. The method outlined here is simple, inexpensive and straightforward and should help smaller labs to take advantage from the ongoing genomic revolution. PMID:25226019

  10. Analysis and Visualization Tool for Targeted Amplicon Bisulfite Sequencing on Ion Torrent Sequencers.

    PubMed

    Pabinger, Stephan; Ernst, Karina; Pulverer, Walter; Kallmeyer, Rainer; Valdes, Ana M; Metrustry, Sarah; Katic, Denis; Nuzzo, Angelo; Kriegner, Albert; Vierlinger, Klemens; Weinhaeusel, Andreas

    2016-01-01

    Targeted sequencing of PCR amplicons generated from bisulfite deaminated DNA is a flexible, cost-effective way to study methylation of a sample at single CpG resolution and perform subsequent multi-target, multi-sample comparisons. Currently, no platform specific protocol, support, or analysis solution is provided to perform targeted bisulfite sequencing on a Personal Genome Machine (PGM). Here, we present a novel tool, called TABSAT, for analyzing targeted bisulfite sequencing data generated on Ion Torrent sequencers. The workflow starts with raw sequencing data, performs quality assessment, and uses a tailored version of Bismark to map the reads to a reference genome. The pipeline visualizes results as lollipop plots and is able to deduce specific methylation-patterns present in a sample. The obtained profiles are then summarized and compared between samples. In order to assess the performance of the targeted bisulfite sequencing workflow, 48 samples were used to generate 53 different Bisulfite-Sequencing PCR amplicons from each sample, resulting in 2,544 amplicon targets. We obtained a mean coverage of 282X using 1,196,822 aligned reads. Next, we compared the sequencing results of these targets to the methylation level of the corresponding sites on an Illumina 450k methylation chip. The calculated average Pearson correlation coefficient of 0.91 confirms the sequencing results with one of the industry-leading CpG methylation platforms and shows that targeted amplicon bisulfite sequencing provides an accurate and cost-efficient method for DNA methylation studies, e.g., to provide platform-independent confirmation of Illumina Infinium 450k methylation data. TABSAT offers a novel way to analyze data generated by Ion Torrent instruments and can also be used with data from the Illumina MiSeq platform. It can be easily accessed via the Platomics platform, which offers a web-based graphical user interface along with sample and parameter storage. TABSAT is freely

  11. Analysis and Visualization Tool for Targeted Amplicon Bisulfite Sequencing on Ion Torrent Sequencers

    PubMed Central

    Pabinger, Stephan; Ernst, Karina; Pulverer, Walter; Kallmeyer, Rainer; Valdes, Ana M.; Metrustry, Sarah; Katic, Denis; Nuzzo, Angelo; Kriegner, Albert; Vierlinger, Klemens; Weinhaeusel, Andreas

    2016-01-01

    Targeted sequencing of PCR amplicons generated from bisulfite deaminated DNA is a flexible, cost-effective way to study methylation of a sample at single CpG resolution and perform subsequent multi-target, multi-sample comparisons. Currently, no platform specific protocol, support, or analysis solution is provided to perform targeted bisulfite sequencing on a Personal Genome Machine (PGM). Here, we present a novel tool, called TABSAT, for analyzing targeted bisulfite sequencing data generated on Ion Torrent sequencers. The workflow starts with raw sequencing data, performs quality assessment, and uses a tailored version of Bismark to map the reads to a reference genome. The pipeline visualizes results as lollipop plots and is able to deduce specific methylation-patterns present in a sample. The obtained profiles are then summarized and compared between samples. In order to assess the performance of the targeted bisulfite sequencing workflow, 48 samples were used to generate 53 different Bisulfite-Sequencing PCR amplicons from each sample, resulting in 2,544 amplicon targets. We obtained a mean coverage of 282X using 1,196,822 aligned reads. Next, we compared the sequencing results of these targets to the methylation level of the corresponding sites on an Illumina 450k methylation chip. The calculated average Pearson correlation coefficient of 0.91 confirms the sequencing results with one of the industry-leading CpG methylation platforms and shows that targeted amplicon bisulfite sequencing provides an accurate and cost-efficient method for DNA methylation studies, e.g., to provide platform-independent confirmation of Illumina Infinium 450k methylation data. TABSAT offers a novel way to analyze data generated by Ion Torrent instruments and can also be used with data from the Illumina MiSeq platform. It can be easily accessed via the Platomics platform, which offers a web-based graphical user interface along with sample and parameter storage. TABSAT is freely

  12. Single-stranded positive-sense RNA viruses generated in days using infectious subgenomic amplicons.

    PubMed

    Aubry, Fabien; Nougairède, Antoine; de Fabritus, Lauriane; Querat, Gilles; Gould, Ernest A; de Lamballerie, Xavier

    2014-11-01

    Reverse genetics is a key methodology for producing genetically modified RNA viruses and deciphering cellular and viral biological properties, but methods based on the preparation of plasmid-based complete viral genomes are laborious and unpredictable. Here, both wild-type and genetically modified infectious RNA viruses were generated in days using the newly described ISA (infectious-subgenomic-amplicons) method. This new versatile and simple procedure may enhance our capacity to obtain infectious RNA viruses from PCR-amplified genetic material. PMID:25053561

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

    PubMed

    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 <700 bp). Here, we describe an approach to sequence pooled amplicons of any length using the Illumina platform. Using this method, amplicons are pooled at equal volume rather than at equal concentration, thus eliminating the laborious purification and quantification steps. We then shear the pooled amplicons, repair the ends, add sample identifying linkers and pool multiple samples prior to Illumina library preparation. Data are then assembled using the transcriptome assembly program trinity, which is optimized to deal with templates of highly varying quantities. We demonstrated the utility of our approach by recovering 93.5% of the target amplicons (size up to 1650 bp) in full length for a 16 taxa × 101 loci project, using ~2.0 GB of Illumina 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. PMID:25959587

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

    PubMed

    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 <700 bp). Here, we describe an approach to sequence pooled amplicons of any length using the Illumina platform. Using this method, amplicons are pooled at equal volume rather than at equal concentration, thus eliminating the laborious purification and quantification steps. We then shear the pooled amplicons, repair the ends, add sample identifying linkers and pool multiple samples prior to Illumina library preparation. Data are then assembled using the transcriptome assembly program trinity, which is optimized to deal with templates of highly varying quantities. We demonstrated the utility of our approach by recovering 93.5% of the target amplicons (size up to 1650 bp) in full length for a 16 taxa × 101 loci project, using ~2.0 GB of Illumina 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.

  15. Exploration Day at Busch Gardens, Williamsburg, Va. - Aug. 5, 2011

    NASA Video Gallery

    Friday, August 8, was NASA Days at Busch Gardens Williamsburg, Va. NASA exhibits and educational specialists worked to inspire young and old, and NASA astronaut Susan Kilrain -- a veteran of two Sp...

  16. 75 FR 35511 - Virginia Disaster Number VA-00028

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-22

    ... From the Federal Register Online via the Government Publishing Office SMALL BUSINESS ADMINISTRATION Virginia Disaster Number VA-00028 AGENCY: Small Business Administration. ACTION: Amendment 3... Federal Domestic Assistance Numbers 59002 and 59008) Roger B. Garland, Acting Associate Administrator...

  17. Amplicon-based metagenomics identified candidate organisms in soils that caused yield decline in strawberry

    PubMed Central

    Xu, Xiangming; Passey, Thomas; Wei, Feng; Saville, Robert; Harrison, Richard J.

    2015-01-01

    A phenomenon of yield decline due to weak plant growth in strawberry was recently observed in non-chemo-fumigated soils, which was not associated with the soil fungal pathogen Verticillium dahliae, the main target of fumigation. Amplicon-based metagenomics was used to profile soil microbiota in order to identify microbial organisms that may have caused the yield decline. A total of 36 soil samples were obtained in 2013 and 2014 from four sites for metagenomic studies; two of the four sites had a yield-decline problem, the other two did not. More than 2000 fungal or bacterial operational taxonomy units (OTUs) were found in these samples. Relative abundance of individual OTUs was statistically compared for differences between samples from sites with or without yield decline. A total of 721 individual comparisons were statistically significant – involving 366 unique bacterial and 44 unique fungal OTUs. Based on further selection criteria, we focused on 34 bacterial and 17 fungal OTUs and found that yield decline resulted probably from one or more of the following four factors: (1) low abundance of Bacillus and Pseudomonas populations, which are well known for their ability of supressing pathogen development and/or promoting plant growth; (2) lack of the nematophagous fungus (Paecilomyces species); (3) a high level of two non-specific fungal root rot pathogens; and (4) wet soil conditions. This study demonstrated the usefulness of an amplicon-based metagenomics approach to profile soil microbiota and to detect differential abundance in microbes. PMID:26504572

  18. CASPER: context-aware scheme for paired-end reads from high-throughput amplicon sequencing

    PubMed Central

    2014-01-01

    Merging the forward and reverse reads from paired-end sequencing is a critical task that can significantly improve the performance of downstream tasks, such as genome assembly and mapping, by providing them with virtually elongated reads. However, due to the inherent limitations of most paired-end sequencers, the chance of observing erroneous bases grows rapidly as the end of a read is approached, which becomes a critical hurdle for accurately merging paired-end reads. Although there exist several sophisticated approaches to this problem, their performance in terms of quality of merging often remains unsatisfactory. To address this issue, here we present a context-aware scheme for paired-end reads (CASPER): a computational method to rapidly and robustly merge overlapping paired-end reads. Being particularly well suited to amplicon sequencing applications, CASPER is thoroughly tested with both simulated and real high-throughput amplicon sequencing data. According to our experimental results, CASPER significantly outperforms existing state-of-the art paired-end merging tools in terms of accuracy and robustness. CASPER also exploits the parallelism in the task of paired-end merging and effectively speeds up by multithreading. CASPER is freely available for academic use at http://best.snu.ac.kr/casper. PMID:25252785

  19. Bioinformatic Amplicon Read Processing Strategies Strongly Affect Eukaryotic Diversity and the Taxonomic Composition of Communities.

    PubMed

    Majaneva, Markus; Hyytiäinen, Kirsi; Varvio, Sirkka Liisa; Nagai, Satoshi; Blomster, Jaanika

    2015-01-01

    Amplicon read sequencing has revolutionized the field of microbial diversity studies. The technique has been developed for bacterial assemblages and has undergone rigorous testing with mock communities. However, due to the great complexity of eukaryotes and the numbers of different rDNA copies, analyzing eukaryotic diversity is more demanding than analyzing bacterial or mock communities, so studies are needed that test the methods of analyses on taxonomically diverse natural communities. In this study, we used 20 samples collected from the Baltic Sea ice, slush and under-ice water to investigate three program packages (UPARSE, mothur and QIIME) and 18 different bioinformatic strategies implemented in them. Our aim was to assess the impact of the initial steps of bioinformatic strategies on the results when analyzing natural eukaryotic communities. We found significant differences among the strategies in resulting read length, number of OTUs and estimates of diversity as well as clear differences in the taxonomic composition of communities. The differences arose mainly because of the variable number of chimeric reads that passed the pre-processing steps. Singleton removal and denoising substantially lowered the number of errors. Our study showed that the initial steps of the bioinformatic amplicon read processing strategies require careful consideration before applying them to eukaryotic communities.

  20. AMPLISAS: a web server for multilocus genotyping using next-generation amplicon sequencing data.

    PubMed

    Sebastian, Alvaro; Herdegen, Magdalena; Migalska, Magdalena; Radwan, Jacek

    2016-03-01

    Next-generation sequencing (NGS) technologies are revolutionizing the fields of biology and medicine as powerful tools for amplicon sequencing (AS). Using combinations of primers and barcodes, it is possible to sequence targeted genomic regions with deep coverage for hundreds, even thousands, of individuals in a single experiment. This is extremely valuable for the genotyping of gene families in which locus-specific primers are often difficult to design, such as the major histocompatibility complex (MHC). The utility of AS is, however, limited by the high intrinsic sequencing error rates of NGS technologies and other sources of error such as polymerase amplification or chimera formation. Correcting these errors requires extensive bioinformatic post-processing of NGS data. Amplicon Sequence Assignment (AMPLISAS) is a tool that performs analysis of AS results in a simple and efficient way, while offering customization options for advanced users. AMPLISAS is designed as a three-step pipeline consisting of (i) read demultiplexing, (ii) unique sequence clustering and (iii) erroneous sequence filtering. Allele sequences and frequencies are retrieved in excel spreadsheet format, making them easy to interpret. AMPLISAS performance has been successfully benchmarked against previously published genotyped MHC data sets obtained with various NGS technologies.

  1. Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing.

    PubMed

    Ranjan, Ravi; Rani, Asha; Metwally, Ahmed; McGee, Halvor S; Perkins, David L

    2016-01-22

    The human microbiome has emerged as a major player in regulating human health and disease. Translational studies of the microbiome have the potential to indicate clinical applications such as fecal transplants and probiotics. However, one major issue is accurate identification of microbes constituting the microbiota. Studies of the microbiome have frequently utilized sequencing of the conserved 16S ribosomal RNA (rRNA) gene. We present a comparative study of an alternative approach using whole genome shotgun sequencing (WGS). In the present study, we analyzed the human fecal microbiome compiling a total of 194.1 × 10(6) reads from a single sample using multiple sequencing methods and platforms. Specifically, after establishing the reproducibility of our methods with extensive multiplexing, we compared: 1) The 16S rRNA amplicon versus the WGS method, 2) the Illumina HiSeq versus MiSeq platforms, 3) the analysis of reads versus de novo assembled contigs, and 4) the effect of shorter versus longer reads. Our study demonstrates that whole genome shotgun sequencing has multiple advantages compared with the 16S amplicon method including enhanced detection of bacterial species, increased detection of diversity and increased prediction of genes. In addition, increased length, either due to longer reads or the assembly of contigs, improved the accuracy of species detection.

  2. Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform

    PubMed Central

    Schirmer, Melanie; Ijaz, Umer Z.; D'Amore, Rosalinda; Hall, Neil; Sloan, William T.; Quince, Christopher

    2015-01-01

    With read lengths of currently up to 2 × 300 bp, high throughput and low sequencing costs Illumina's MiSeq is becoming one of the most utilized sequencing platforms worldwide. The platform is manageable and affordable even for smaller labs. This enables quick turnaround on a broad range of applications such as targeted gene sequencing, metagenomics, small genome sequencing and clinical molecular diagnostics. However, Illumina error profiles are still poorly understood and programs are therefore not designed for the idiosyncrasies of Illumina data. A better knowledge of the error patterns is essential for sequence analysis and vital if we are to draw valid conclusions. Studying true genetic variation in a population sample is fundamental for understanding diseases, evolution and origin. We conducted a large study on the error patterns for the MiSeq based on 16S rRNA amplicon sequencing data. We tested state-of-the-art library preparation methods for amplicon sequencing and showed that the library preparation method and the choice of primers are the most significant sources of bias and cause distinct error patterns. Furthermore we tested the efficiency of various error correction strategies and identified quality trimming (Sickle) combined with error correction (BayesHammer) followed by read overlapping (PANDAseq) as the most successful approach, reducing substitution error rates on average by 93%. PMID:25586220

  3. Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing.

    PubMed

    Ranjan, Ravi; Rani, Asha; Metwally, Ahmed; McGee, Halvor S; Perkins, David L

    2016-01-22

    The human microbiome has emerged as a major player in regulating human health and disease. Translational studies of the microbiome have the potential to indicate clinical applications such as fecal transplants and probiotics. However, one major issue is accurate identification of microbes constituting the microbiota. Studies of the microbiome have frequently utilized sequencing of the conserved 16S ribosomal RNA (rRNA) gene. We present a comparative study of an alternative approach using whole genome shotgun sequencing (WGS). In the present study, we analyzed the human fecal microbiome compiling a total of 194.1 × 10(6) reads from a single sample using multiple sequencing methods and platforms. Specifically, after establishing the reproducibility of our methods with extensive multiplexing, we compared: 1) The 16S rRNA amplicon versus the WGS method, 2) the Illumina HiSeq versus MiSeq platforms, 3) the analysis of reads versus de novo assembled contigs, and 4) the effect of shorter versus longer reads. Our study demonstrates that whole genome shotgun sequencing has multiple advantages compared with the 16S amplicon method including enhanced detection of bacterial species, increased detection of diversity and increased prediction of genes. In addition, increased length, either due to longer reads or the assembly of contigs, improved the accuracy of species detection. PMID:26718401

  4. ICO amplicon NGS data analysis: a Web tool for variant detection in common high-risk hereditary cancer genes analyzed by amplicon GS Junior next-generation sequencing.

    PubMed

    Lopez-Doriga, Adriana; Feliubadaló, Lídia; Menéndez, Mireia; Lopez-Doriga, Sergio; Morón-Duran, Francisco D; del Valle, Jesús; Tornero, Eva; Montes, Eva; Cuesta, Raquel; Campos, Olga; Gómez, Carolina; Pineda, Marta; González, Sara; Moreno, Victor; Capellá, Gabriel; Lázaro, Conxi

    2014-03-01

    Next-generation sequencing (NGS) has revolutionized genomic research and is set to have a major impact on genetic diagnostics thanks to the advent of benchtop sequencers and flexible kits for targeted libraries. Among the main hurdles in NGS are the difficulty of performing bioinformatic analysis of the huge volume of data generated and the high number of false positive calls that could be obtained, depending on the NGS technology and the analysis pipeline. Here, we present the development of a free and user-friendly Web data analysis tool that detects and filters sequence variants, provides coverage information, and allows the user to customize some basic parameters. The tool has been developed to provide accurate genetic analysis of targeted sequencing of common high-risk hereditary cancer genes using amplicon libraries run in a GS Junior System. The Web resource is linked to our own mutation database, to assist in the clinical classification of identified variants. We believe that this tool will greatly facilitate the use of the NGS approach in routine laboratories.

  5. Identification and Evaluation of Single-Nucleotide Polymorphisms in Allotetraploid Peanut (Arachis hypogaea L.) Based on Amplicon Sequencing Combined with High Resolution Melting (HRM) Analysis.

    PubMed

    Hong, Yanbin; Pandey, Manish K; Liu, Ying; Chen, Xiaoping; Liu, Hong; Varshney, Rajeev K; Liang, Xuanqiang; Huang, Shangzhi

    2015-01-01

    The cultivated peanut (Arachis hypogaea L.) is an allotetraploid (AABB) species derived from the A-genome (Arachis duranensis) and B-genome (Arachis ipaensis) progenitors. Presence of two versions of a DNA sequence based on the two progenitor genomes poses a serious technical and analytical problem during single nucleotide polymorphism (SNP) marker identification and analysis. In this context, we have analyzed 200 amplicons derived from expressed sequence tags (ESTs) and genome survey sequences (GSS) to identify SNPs in a panel of genotypes consisting of 12 cultivated peanut varieties and two diploid progenitors representing the ancestral genomes. A total of 18 EST-SNPs and 44 genomic-SNPs were identified in 12 peanut varieties by aligning the sequence of A. hypogaea with diploid progenitors. The average frequency of sequence polymorphism was higher for genomic-SNPs than the EST-SNPs with one genomic-SNP every 1011 bp as compared to one EST-SNP every 2557 bp. In order to estimate the potential and further applicability of these identified SNPs, 96 peanut varieties were genotyped using high resolution melting (HRM) method. Polymorphism information content (PIC) values for EST-SNPs ranged between 0.021 and 0.413 with a mean of 0.172 in the set of peanut varieties, while genomic-SNPs ranged between 0.080 and 0.478 with a mean of 0.249. Total 33 SNPs were used for polymorphism detection among the parents and 10 selected lines from mapping population Y13Zh (Zhenzhuhei × Yueyou13). Of the total 33 SNPs, nine SNPs showed polymorphism in the mapping population Y13Zh, and seven SNPs were successfully mapped into five linkage groups. Our results showed that SNPs can be identified in allotetraploid peanut with high accuracy through amplicon sequencing and HRM assay. The identified SNPs were very informative and can be used for different genetic and breeding applications in peanut.

  6. Identification and Evaluation of Single-Nucleotide Polymorphisms in Allotetraploid Peanut (Arachis hypogaea L.) Based on Amplicon Sequencing Combined with High Resolution Melting (HRM) Analysis

    PubMed Central

    Hong, Yanbin; Pandey, Manish K.; Liu, Ying; Chen, Xiaoping; Liu, Hong; Varshney, Rajeev K.; Liang, Xuanqiang; Huang, Shangzhi

    2015-01-01

    The cultivated peanut (Arachis hypogaea L.) is an allotetraploid (AABB) species derived from the A-genome (Arachis duranensis) and B-genome (Arachis ipaensis) progenitors. Presence of two versions of a DNA sequence based on the two progenitor genomes poses a serious technical and analytical problem during single nucleotide polymorphism (SNP) marker identification and analysis. In this context, we have analyzed 200 amplicons derived from expressed sequence tags (ESTs) and genome survey sequences (GSS) to identify SNPs in a panel of genotypes consisting of 12 cultivated peanut varieties and two diploid progenitors representing the ancestral genomes. A total of 18 EST-SNPs and 44 genomic-SNPs were identified in 12 peanut varieties by aligning the sequence of A. hypogaea with diploid progenitors. The average frequency of sequence polymorphism was higher for genomic-SNPs than the EST-SNPs with one genomic-SNP every 1011 bp as compared to one EST-SNP every 2557 bp. In order to estimate the potential and further applicability of these identified SNPs, 96 peanut varieties were genotyped using high resolution melting (HRM) method. Polymorphism information content (PIC) values for EST-SNPs ranged between 0.021 and 0.413 with a mean of 0.172 in the set of peanut varieties, while genomic-SNPs ranged between 0.080 and 0.478 with a mean of 0.249. Total 33 SNPs were used for polymorphism detection among the parents and 10 selected lines from mapping population Y13Zh (Zhenzhuhei × Yueyou13). Of the total 33 SNPs, nine SNPs showed polymorphism in the mapping population Y13Zh, and seven SNPs were successfully mapped into five linkage groups. Our results showed that SNPs can be identified in allotetraploid peanut with high accuracy through amplicon sequencing and HRM assay. The identified SNPs were very informative and can be used for different genetic and breeding applications in peanut. PMID:26697032

  7. 78 FR 18425 - Proposed Information Collection VA Police Officer Pre-Employment Screening Checklist); Comment...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-26

    ... AFFAIRS Proposed Information Collection VA Police Officer Pre-Employment Screening Checklist); Comment... applicant's qualification and suitability as a VA police officer. DATES: Written comments and... information technology. Title: VA Police Officer Pre-Employment Screening Checklist, VA Form 0120. OMB...

  8. 78 FR 38452 - Agency Information Collection (VA Police Officer Pre-Employment Screening Checklist) Activities...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-26

    ... AFFAIRS Agency Information Collection (VA Police Officer Pre-Employment Screening Checklist) Activities... ``OMB Control No. 2900-0524.'' SUPPLEMENTARY INFORMATION: Title: VA Police Officer Pre-Employment... checks on applicants seeking employment as VA police officers. VA will use the data collected...

  9. The Bias Associated with Amplicon Sequencing Does Not Affect the Quantitative Assessment of Bacterial Community Dynamics

    PubMed Central

    Figuerola, Eva L. M.; Erijman, Leonardo

    2014-01-01

    The performance of two sets of primers targeting variable regions of the 16S rRNA gene V1–V3 and V4 was compared in their ability to describe changes of bacterial diversity and temporal turnover in full-scale activated sludge. Duplicate sets of high-throughput amplicon sequencing data of the two 16S rRNA regions shared a collection of core taxa that were observed across a series of twelve monthly samples, although the relative abundance of each taxon was substantially different between regions. A case in point was the changes in the relative abundance of filamentous bacteria Thiothrix, which caused a large effect on diversity indices, but only in the V1–V3 data set. Yet the relative abundance of Thiothrix in the amplicon sequencing data from both regions correlated with the estimation of its abundance determined using fluorescence in situ hybridization. In nonmetric multidimensional analysis samples were distributed along the first ordination axis according to the sequenced region rather than according to sample identities. The dynamics of microbial communities indicated that V1–V3 and the V4 regions of the 16S rRNA gene yielded comparable patterns of: 1) the changes occurring within the communities along fixed time intervals, 2) the slow turnover of activated sludge communities and 3) the rate of species replacement calculated from the taxa–time relationships. The temperature was the only operational variable that showed significant correlation with the composition of bacterial communities over time for the sets of data obtained with both pairs of primers. In conclusion, we show that despite the bias introduced by amplicon sequencing, the variable regions V1–V3 and V4 can be confidently used for the quantitative assessment of bacterial community dynamics, and provide a proper qualitative account of general taxa in the community, especially when the data are obtained over a convenient time window rather than at a single time point. PMID:24923665

  10. Preparation of Amplicon Libraries for Metabarcoding of Marine Eukaryotes Using Illumina MiSeq: The Adapter Ligation Method.

    PubMed

    Leray, Matthieu; Haenel, Quiterie; Bourlat, Sarah J

    2016-01-01

    Amplicon-based studies of marine microscopic eukaryotes, also referred to as metabarcoding studies, can be performed to analyze patterns of biodiversity or predator-prey interactions targeting the mitochondrial cytochrome oxidase 1 (CO1) or the small ribosomal subunit (SSU) markers. Because high-throughput sequencing (HTS) Illumina platforms provide millions of reads per run, hundreds of samples may be sequenced simultaneously. This protocol details the preparation of multiplexed amplicon libraries for Illumina MiSeq sequencing. We describe a strategy for sample multiplexing using a combination of tailed PCR primers and ligation of indexed adapters. PMID:27460380

  11. Pitfalls of haplotype phasing from amplicon-based long-read sequencing

    PubMed Central

    Laver, Thomas W.; Caswell, Richard C.; Moore, Karen A.; Poschmann, Jeremie; Johnson, Matthew B.; Owens, Martina M.; Ellard, Sian; Paszkiewicz, Konrad H.; Weedon, Michael N.

    2016-01-01

    The long-read sequencers from Pacific Bioscience (PacBio) and Oxford Nanopore Technologies (ONT) offer the opportunity to phase mutations multiple kilobases apart directly from sequencing reads. In this study, we used long-range PCR with ONT and PacBio sequencing to phase two variants 9 kb apart in the RET gene. We also re-analysed data from a recent paper which had apparently successfully used ONT to phase clinically important haplotypes at the CYP2D6 and HLA loci. From these analyses, we demonstrate PCR-chimera formation during PCR amplification and reference alignment bias are pitfalls that need to be considered when attempting to phase variants using amplicon-based long-read sequencing technologies. These methodological pitfalls need to be avoided if the opportunities provided by long-read sequencers are to be fully exploited. PMID:26883533

  12. 16S rRNA amplicon sequencing dataset for conventionalized and conventionally raised zebrafish larvae.

    PubMed

    Davis, Daniel J; Bryda, Elizabeth C; Gillespie, Catherine H; Ericsson, Aaron C

    2016-09-01

    Data presented here contains metagenomic analysis regarding the sequential conventionalization of germ-free zebrafish embryos. Zebrafish embryos that underwent a germ-free sterilization process immediately after fertilization were promptly exposed to and raised to larval stage in conventional fish water. At 6 days postfertilization (dpf), these "conventionalized" larvae were compared to zebrafish larvae that were raised in conventional fish water never undergoing the initial sterilization process. Bacterial 16S rRNA amplicon sequencing was performed on DNA isolated from homogenates of the larvae revealing distinct microbiota variations between the two groups. The dataset described here is also related to the research article entitled "Microbial modulation of behavior and stress responses in zebrafish larvae" (Davis et al., 2016) [1]. PMID:27508247

  13. Amplicon restriction patterns associated with nitrogenase activity of root nodules for selection of superior Myrica seedlings.

    PubMed

    Yanthan, Mhathung; Misra, Arvind K

    2013-11-01

    Trees of Myrica sp. grow abundantly in the forests of Meghalaya, India. These trees are actinorhizal and harbour nitrogen-fixing Frankia in their root nodules and contribute positively towards the enhancement of nitrogen status of forest areas. They can be used in rejuvenation of mine spoils and nitrogen-depleted fallow lands generated due to slash and burn agriculture practiced in the area. We have studied the association of amplicon restriction patterns (ARPs) of Myrica ribosomal RNA gene and internal transcribed spacer (ITS) region and nitrogenase activity of its root nodules. We found that ARPs thus obtained could be used as markers for early screening of seedlings that could support strains of Frankia that fix atmospheric nitrogen more efficiently. PMID:24287658

  14. Using Amplicon Deep Sequencing to Detect Genetic Signatures of Plasmodium vivax Relapse

    PubMed Central

    Lin, Jessica T.; Hathaway, Nicholas J.; Saunders, David L.; Lon, Chanthap; Balasubramanian, Sujata; Kharabora, Oksana; Gosi, Panita; Sriwichai, Sabaithip; Kartchner, Laurel; Chuor, Char Meng; Satharath, Prom; Lanteri, Charlotte; Bailey, Jeffrey A.; Juliano, Jonathan J.

    2015-01-01

    Plasmodium vivax infections often recur due to relapse of hypnozoites from the liver. In malaria-endemic areas, tools to distinguish relapse from reinfection are needed. We applied amplicon deep sequencing to P. vivax isolates from 78 Cambodian volunteers, nearly one-third of whom suffered recurrence at a median of 68 days. Deep sequencing at a highly variable region of the P. vivax merozoite surface protein 1 gene revealed impressive diversity—generating 67 unique haplotypes and detecting on average 3.6 cocirculating parasite clones within individuals, compared to 2.1 clones detected by a combination of 3 microsatellite markers. This diversity enabled a scheme to classify over half of recurrences as probable relapses based on the low probability of reinfection by multiple recurring variants. In areas of high P. vivax diversity, targeted deep sequencing can help detect genetic signatures of relapse, key to evaluating antivivax interventions and achieving a better understanding of relapse-reinfection epidemiology. PMID:25748326

  15. Using Amplicon Deep Sequencing to Detect Genetic Signatures of Plasmodium vivax Relapse.

    PubMed

    Lin, Jessica T; Hathaway, Nicholas J; Saunders, David L; Lon, Chanthap; Balasubramanian, Sujata; Kharabora, Oksana; Gosi, Panita; Sriwichai, Sabaithip; Kartchner, Laurel; Chuor, Char Meng; Satharath, Prom; Lanteri, Charlotte; Bailey, Jeffrey A; Juliano, Jonathan J

    2015-09-15

    Plasmodium vivax infections often recur due to relapse of hypnozoites from the liver. In malaria-endemic areas, tools to distinguish relapse from reinfection are needed. We applied amplicon deep sequencing to P. vivax isolates from 78 Cambodian volunteers, nearly one-third of whom suffered recurrence at a median of 68 days. Deep sequencing at a highly variable region of the P. vivax merozoite surface protein 1 gene revealed impressive diversity-generating 67 unique haplotypes and detecting on average 3.6 cocirculating parasite clones within individuals, compared to 2.1 clones detected by a combination of 3 microsatellite markers. This diversity enabled a scheme to classify over half of recurrences as probable relapses based on the low probability of reinfection by multiple recurring variants. In areas of high P. vivax diversity, targeted deep sequencing can help detect genetic signatures of relapse, key to evaluating antivivax interventions and achieving a better understanding of relapse-reinfection epidemiology.

  16. Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae.

    PubMed

    Lagkouvardos, Ilias; Weinmaier, Thomas; Lauro, Federico M; Cavicchioli, Ricardo; Rattei, Thomas; Horn, Matthias

    2014-01-01

    In the era of metagenomics and amplicon sequencing, comprehensive analyses of available sequence data remain a challenge. Here we describe an approach exploiting metagenomic and amplicon data sets from public databases to elucidate phylogenetic diversity of defined microbial taxa. We investigated the phylum Chlamydiae whose known members are obligate intracellular bacteria that represent important pathogens of humans and animals, as well as symbionts of protists. Despite their medical relevance, our knowledge about chlamydial diversity is still scarce. Most of the nine known families are represented by only a few isolates, while previous clone library-based surveys suggested the existence of yet uncharacterized members of this phylum. Here we identified more than 22,000 high quality, non-redundant chlamydial 16S rRNA gene sequences in diverse databases, as well as 1900 putative chlamydial protein-encoding genes. Even when applying the most conservative approach, clustering of chlamydial 16S rRNA gene sequences into operational taxonomic units revealed an unexpectedly high species, genus and family-level diversity within the Chlamydiae, including 181 putative families. These in silico findings were verified experimentally in one Antarctic sample, which contained a high diversity of novel Chlamydiae. In our analysis, the Rhabdochlamydiaceae, whose known members infect arthropods, represents the most diverse and species-rich chlamydial family, followed by the protist-associated Parachlamydiaceae, and a putative new family (PCF8) with unknown host specificity. Available information on the origin of metagenomic samples indicated that marine environments contain the majority of the newly discovered chlamydial lineages, highlighting this environment as an important chlamydial reservoir. PMID:23949660

  17. Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae

    PubMed Central

    Lagkouvardos, Ilias; Weinmaier, Thomas; Lauro, Federico M; Cavicchioli, Ricardo; Rattei, Thomas; Horn, Matthias

    2014-01-01

    In the era of metagenomics and amplicon sequencing, comprehensive analyses of available sequence data remain a challenge. Here we describe an approach exploiting metagenomic and amplicon data sets from public databases to elucidate phylogenetic diversity of defined microbial taxa. We investigated the phylum Chlamydiae whose known members are obligate intracellular bacteria that represent important pathogens of humans and animals, as well as symbionts of protists. Despite their medical relevance, our knowledge about chlamydial diversity is still scarce. Most of the nine known families are represented by only a few isolates, while previous clone library-based surveys suggested the existence of yet uncharacterized members of this phylum. Here we identified more than 22 000 high quality, non-redundant chlamydial 16S rRNA gene sequences in diverse databases, as well as 1900 putative chlamydial protein-encoding genes. Even when applying the most conservative approach, clustering of chlamydial 16S rRNA gene sequences into operational taxonomic units revealed an unexpectedly high species, genus and family-level diversity within the Chlamydiae, including 181 putative families. These in silico findings were verified experimentally in one Antarctic sample, which contained a high diversity of novel Chlamydiae. In our analysis, the Rhabdochlamydiaceae, whose known members infect arthropods, represents the most diverse and species-rich chlamydial family, followed by the protist-associated Parachlamydiaceae, and a putative new family (PCF8) with unknown host specificity. Available information on the origin of metagenomic samples indicated that marine environments contain the majority of the newly discovered chlamydial lineages, highlighting this environment as an important chlamydial reservoir. PMID:23949660

  18. Complementary Amplicon-Based Genomic Approaches for the Study of Fungal Communities in Humans

    PubMed Central

    Heisel, Timothy; Podgorski, Heather; Staley, Christopher M.; Knights, Dan; Sadowsky, Michael J.; Gale, Cheryl A.

    2015-01-01

    Recent studies highlight the importance of intestinal fungal microbiota in the development of human disease. Infants, in particular, are an important population in which to study intestinal microbiomes because microbial community structure and dynamics during this formative window of life have the potential to influence host immunity and metabolism. When compared to bacteria, much less is known about the early development of human fungal communities, owing partly to their lower abundance and the relative lack of established molecular and taxonomic tools for their study. Herein, we describe the development, validation, and use of complementary amplicon-based genomic strategies to characterize infant fungal communities and provide quantitative information about Candida, an important fungal genus with respect to intestinal colonization and human disease. Fungal communities were characterized from 11 infant fecal samples using primers that target the internal transcribed spacer (ITS) 2 locus, a region that provides taxonomic discrimination of medically relevant fungi. Each sample yielded an average of 27,553 fungal sequences and Candida albicans was the most abundant species identified by sequencing and quantitative PCR (qPCR). Low numbers of Candida krusei and Candida parapsilosis sequences were observed in several samples, but their presence was detected by species-specific qPCR in only one sample, highlighting a challenge inherent in the study of low-abundance organisms. Overall, the sequencing results revealed that infant fecal samples had fungal diversity comparable to that of bacterial communities in similar-aged infants, which correlated with the relative abundance of C. albicans. We conclude that targeted sequencing of fungal ITS2 amplicons in conjunction with qPCR analyses of specific fungi provides an informative picture of fungal community structure in the human intestinal tract. Our data suggests that the infant intestine harbors diverse fungal species and

  19. Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae.

    PubMed

    Lagkouvardos, Ilias; Weinmaier, Thomas; Lauro, Federico M; Cavicchioli, Ricardo; Rattei, Thomas; Horn, Matthias

    2014-01-01

    In the era of metagenomics and amplicon sequencing, comprehensive analyses of available sequence data remain a challenge. Here we describe an approach exploiting metagenomic and amplicon data sets from public databases to elucidate phylogenetic diversity of defined microbial taxa. We investigated the phylum Chlamydiae whose known members are obligate intracellular bacteria that represent important pathogens of humans and animals, as well as symbionts of protists. Despite their medical relevance, our knowledge about chlamydial diversity is still scarce. Most of the nine known families are represented by only a few isolates, while previous clone library-based surveys suggested the existence of yet uncharacterized members of this phylum. Here we identified more than 22,000 high quality, non-redundant chlamydial 16S rRNA gene sequences in diverse databases, as well as 1900 putative chlamydial protein-encoding genes. Even when applying the most conservative approach, clustering of chlamydial 16S rRNA gene sequences into operational taxonomic units revealed an unexpectedly high species, genus and family-level diversity within the Chlamydiae, including 181 putative families. These in silico findings were verified experimentally in one Antarctic sample, which contained a high diversity of novel Chlamydiae. In our analysis, the Rhabdochlamydiaceae, whose known members infect arthropods, represents the most diverse and species-rich chlamydial family, followed by the protist-associated Parachlamydiaceae, and a putative new family (PCF8) with unknown host specificity. Available information on the origin of metagenomic samples indicated that marine environments contain the majority of the newly discovered chlamydial lineages, highlighting this environment as an important chlamydial reservoir.

  20. Women in addictions treatment: comparing VA and community samples.

    PubMed

    Davis, Tania M; Carpenter, Kelly M; Malte, Carol A; Carney, Molly; Chambers, Sharon; Saxon, Andrew J

    2002-07-01

    Despite increasing awareness of gender issues in substance use treatment, women with substance use disorders (SUD) and gender-specific treatment remain understudied. This study examines differences, including identification of comorbid issues and patients' perceived treatment needs, between women in different SUD treatment settings: an intensive VA outpatient program (VA; N = 76) and a private residential/outpatient program (Residence XII; N = 308). In both settings the Addiction Severity Index (ASI) was administered at intake; ASI data were collected from retrospective chart review. Results support previous findings that women entering SUD treatment endorse high rates of psychiatric and medical comorbidity, and past abuse. Women in VA SUD treatment experienced more impairment on indices of medical, psychiatric, and employment issues whereas the private agency sample had higher alcohol and family/social composite scores. The differences between and similarities among the two treatment groups have implications for design of women-specific SUD treatment programs.

  1. Long amplicon (LA)-qPCR for the discrimination of infectious and noninfectious phix174 bacteriophages after UV inactivation.

    PubMed

    Ho, Johannes; Seidel, Michael; Niessner, Reinhard; Eggers, Jutta; Tiehm, Andreas

    2016-10-15

    Waterborne viruses are increasingly being considered in risk assessment schemes. In general, virus detection by culture methods is time consuming. In contrast, detection by quantitative polymerase chain reaction (qPCR) is more rapid and therefore, more suitable for monitoring. At present, qPCR lacks the essential ability for discriminating between infectious and non-infectious viruses, thus limiting its applicability for monitoring disinfection processes. In this study, a method was developed to quantify UV inactivation by long amplicon (LA)-qPCR. Bacteriophage phiX174 was used as a surrogate for human pathogenic viruses. A qPCR protocol was developed with new sets of primers, resulting in amplicon lengths of 108, 250, 456, 568, 955, 1063, 1544, and 1764 nucleotides. The log reduction of gene copies increased with increasing amplicon length. Additional treatment with the intercalating dye, PMA, had no effect, indicating that the bacteriophage capsids were not damaged by low pressure UV irradiation. A qPCR of nearly the complete genome (approx. 5000 nucleotides) showed similar results to the plaque assay. The log reduction in qPCR correlates with [specific amplicon length x UV dose]. The normalized DNA effect constant can be applied to calculate phiX174 inactivation based on qPCR detection. PMID:27450352

  2. Long amplicon (LA)-qPCR for the discrimination of infectious and noninfectious phix174 bacteriophages after UV inactivation.

    PubMed

    Ho, Johannes; Seidel, Michael; Niessner, Reinhard; Eggers, Jutta; Tiehm, Andreas

    2016-10-15

    Waterborne viruses are increasingly being considered in risk assessment schemes. In general, virus detection by culture methods is time consuming. In contrast, detection by quantitative polymerase chain reaction (qPCR) is more rapid and therefore, more suitable for monitoring. At present, qPCR lacks the essential ability for discriminating between infectious and non-infectious viruses, thus limiting its applicability for monitoring disinfection processes. In this study, a method was developed to quantify UV inactivation by long amplicon (LA)-qPCR. Bacteriophage phiX174 was used as a surrogate for human pathogenic viruses. A qPCR protocol was developed with new sets of primers, resulting in amplicon lengths of 108, 250, 456, 568, 955, 1063, 1544, and 1764 nucleotides. The log reduction of gene copies increased with increasing amplicon length. Additional treatment with the intercalating dye, PMA, had no effect, indicating that the bacteriophage capsids were not damaged by low pressure UV irradiation. A qPCR of nearly the complete genome (approx. 5000 nucleotides) showed similar results to the plaque assay. The log reduction in qPCR correlates with [specific amplicon length x UV dose]. The normalized DNA effect constant can be applied to calculate phiX174 inactivation based on qPCR detection.

  3. 78 FR 2708 - Virginia Disaster Number VA-00052

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-14

    ... From the Federal Register Online via the Government Publishing Office SMALL BUSINESS ADMINISTRATION Virginia Disaster Number VA-00052 AGENCY: U.S. Small Business Administration. ACTION: Amendment 1... completed loan applications to: U.S. Small Business Administration, Processing and Disbursement...

  4. 77 FR 25591 - Drawbridge Operation Regulation; Intracoastal Waterway, Chesapeake, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-01

    ...The Commander Fifth Coast Guard District has issued a temporary deviation from the regulations governing the operation of the Norfolk Southern 7 Railroad Bridge, across the Intracoastal Waterway, mile 5.8, in Chesapeake, VA. The deviation is necessary to facilitate replacing the lift joints of the drawbridge. This deviation restricts operation of the draw span, allowing it to remain......

  5. 78 FR 72002 - Amendment of Class E Airspace; Danville, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-02

    ... Class E surface area airspace at Danville Regional Airport, Danville, VA. (78 FR, 48079). Interested... rule'' under DOT Regulatory Policies and Procedures (44 FR 11034; February 26, 1979); and (3) does not..., 40113, 40120; E.O. 10854, 24 FR 9565, 3 CFR, 1959-1963 Comp., p. 389. Sec. 71.1 0 2. The...

  6. 77 FR 51100 - Virginia Disaster No. VA-00048

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-23

    ... ADMINISTRATION Virginia Disaster No. VA-00048 AGENCY: U.S. Small Business Administration. ACTION: Amendment 1.... ADDRESSES: Submit completed loan applications to: U.S. Small Business Administration, Processing and..., Office of Disaster Assistance, U.S. Small Business Administration, 409 3rd Street, SW., Suite...

  7. 76 FR 77270 - Board Meeting; January 9, 2012, Arlington, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-12

    ... From the Federal Register Online via the Government Publishing Office NUCLEAR WASTE TECHNICAL REVIEW BOARD Board Meeting; January 9, 2012, Arlington, VA The U.S. Nuclear Waste Technical Review Board... under section 5051 of Public Law 100-203, Nuclear Waste Policy Amendments Act of 1987, the U.S....

  8. 76 FR 34576 - Amendment of Class E Airspace; Waynesboro, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-14

    ...) to amend Class E airspace at Eagle's Nest Airport, Waynesboro, VA (75 FR 14820) Docket No. FAA-2010..., 40113, 40120; E.O. 10854, 24 FR 9565, 3 CFR, 1959-1963 Comp., p. 389. Sec. 71.1 0 2. The incorporation... Executive Order 12866; (2) is not a ``significant rule'' under DOT Regulatory Policies and Procedures (44...

  9. 48 CFR 801.695 - VA's Appointment of HCAs Program.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 48 Federal Acquisition Regulations System 5 2011-10-01 2011-10-01 false VA's Appointment of HCAs Program. 801.695 Section 801.695 Federal Acquisition Regulations System DEPARTMENT OF VETERANS AFFAIRS GENERAL DEPARTMENT OF VETERANS AFFAIRS ACQUISITION REGULATION SYSTEM Career Development,...

  10. Military and VA General Dentistry Training: A National Resource.

    ERIC Educational Resources Information Center

    Atchison, Kathryn A.; Bachand, William; Buchanan, C. Richard; Lefever, Karen H.; Lin, Sylvia; Engelhardt, Rita

    2002-01-01

    Compared the program characteristics of the postgraduate general dentistry (PGD) training programs sponsored by the military and the Veterans Health Administration (VA). Gathered information on program infrastructure and emphasis, resident preparation prior to entering the program, and patients served and types of services provided. Programs…

  11. Medical care collection or recovery--VA. Notice.

    PubMed

    1998-10-13

    In a companion document published in the "Proposed Rules" section of this issue of the Federal Register, we proposed to amend VA's medical regulations concerning collection or recovery by VA for medical care or services provided or furnished to a veteran: (i) For a non-service connected disability for which the veteran is entitled to care (or the payment of expenses of care) under a health-plan contract; (ii) For a non-service connected disability incurred incident to the veteran's employment and covered under a worker's compensation law or plan that provides reimbursement or indemnification for such care and services; or (iii) For a non-service connected disability incurred as a result of a motor vehicle accident in a State that requires automobile accident reparations insurance. The proposed rule includes methodology for establishing charges for VA medical care or services. Using this methodology, information for calculating proposed charge amounts at individual VA facilities for inpatient facility charges, skilled nursing facility/sub-acute inpatient facility charges, outpatient facility charges, and physician charges is set forth below. If this methodology were adopted subsequently as a final rule, the applicable data in this document, designed for the period August 1998 through September 1999, would be used for the period from the effective date of the final rule through September 1999. Accordingly, interested parties may wish to retain this document for future reference.

  12. 76 FR 43575 - Amendment of Class E Airspace; Staunton, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-07-21

    ... Valley Regional Airport, Staunton, VA (76 FR 14822) Docket No. FAA- 2010-1285. Interested parties were... Executive Order 12866; (2) is not a ``significant rule'' under DOT Regulatory Policies and Procedures (44 FR... FR 9565, 3 CFR, 1959-1963 Comp., p. 389. Sec. 71.1 0 2. The incorporation by reference in 14 CFR...

  13. 75 FR 41247 - Virginia Disaster Number VA-00028

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-15

    ... ADMINISTRATION Virginia Disaster Number VA-00028 AGENCY: U.S. Small Business Administration. ACTION: Amendment 4... Only for the Commonwealth of Virginia (FEMA-1874-DR), dated 02/16/2010. Incident: Severe Winter Storm... disaster declaration for Private Non-Profit organizations in the Commonwealth of Virginia, dated...

  14. 77 FR 530 - Virginia Disaster Number VA-00037

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-05

    ... ADMINISTRATION Virginia Disaster Number VA-00037 AGENCY: U.S. Small Business Administration. ACTION: Amendment 1... Virginia (FEMA-4042-DR), dated 11/04/2011. Incident: Earthquake. Incident Period: 08/23/2011 through 10/25... major disaster declaration for the Commonwealth of Virginia, dated 11/04/2011 is hereby amended...

  15. 76 FR 62132 - Virginia Disaster Number VA-00038

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-06

    ... ADMINISTRATION Virginia Disaster Number VA-00038 AGENCY: U.S. Small Business Administration. ACTION: Amendment 2... only for the State of Virginia (FEMA-4024-DR), dated 09/03/2011. Incident: Hurricane Irene. Incident... Non-Profit organizations in the State of Virginia, dated 09/03/2011, is hereby amended to include...

  16. 75 FR 26813 - VIRGINIA Disaster Number VA-00028

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-12

    ... ADMINISTRATION VIRGINIA Disaster Number VA-00028 AGENCY: U.S. Small Business Administration. ACTION: Amendment 2... Only for the Commonwealth of VIRGINIA (FEMA-1874-DR), dated 02/16/2010. Incident: Severe Winter Storm... disaster declaration for Private Non-Profit organizations in the Commonwealth of VIRGINIA, dated...

  17. 76 FR 74837 - Virginia Disaster Number VA-00040

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-01

    ... ADMINISTRATION Virginia Disaster Number VA-00040 AGENCY: U.S. Small Business Administration. ACTION: Amendment 1... Only for the State of Virginia (FEMA-4042-DR), dated 11/10/2011. Incident: Earthquake. Incident Period... non-profit organizations in the State of Virginia, dated 11/10/2011, is hereby amended to include...

  18. 77 FR 1547 - Virginia Disaster Number VA-00040

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-10

    ... ADMINISTRATION Virginia Disaster Number VA-00040 AGENCY: U.S. Small Business Administration. ACTION: Amendment 3... Only for the Commonwealth of Virginia (FEMA--4042-DR), dated 11/10/2011. Incident: Earthquake. Incident... Non-Profit organizations in the Commonwealth of Virginia, dated 11/10/2011, is hereby amended...

  19. 77 FR 1547 - Virginia Disaster Number VA-00037

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-10

    ... ADMINISTRATION Virginia Disaster Number VA-00037 AGENCY: U.S. Small Business Administration. ACTION: Amendment 2... Virginia (FEMA-4042-DR), dated 11/04/ 2011. Incident: Earthquake. Incident Period: 08/23/2011 Through 10/25... disaster declaration for the State of Virginia, dated 11/04/2011 is hereby amended to include the...

  20. 75 FR 21370 - Virginia Disaster Number VA-00028

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-23

    ... ADMINISTRATION Virginia Disaster Number VA-00028 AGENCY: U.S. Small Business Administration. ACTION: Amendment 1... Only for the Commonwealth of Virginia (FEMA-1874-DR), dated 02/16/2010. Incident: Severe Winter Storm... disaster declaration for Private Non-Profit organizations in the Commonwealth of Virginia, dated...

  1. 76 FR 78957 - Virginia Disaster Number VA-00040

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-20

    ... ADMINISTRATION Virginia Disaster Number VA-00040 AGENCY: U.S. Small Business Administration. ACTION: Amendment 2... Only for the Commonwealth of Virginia (FEMA--4042--DR), dated 11/10/2011. Incident: Earthquake... Private Non-Profit organizations in the Commonwealth of Virginia, dated 11/10/2011, is hereby amended...

  2. 76 FR 52230 - Establishment of Class E Airspace; Forest, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-22

    ..., VA (76 FR 34196) Docket No. FAA-2011-0378. Interested parties were invited to participate in this... Procedures (44 FR 11034; February 26, 1979); and (3) does not warrant preparation of a Regulatory Evaluation.... 106(g); 40103, 40113, 40120; E.O. 10854, 24 FR 9565, 3 CFR, 1959-1963 Comp., p. 389. Sec. 71.1 0...

  3. 76 FR 72838 - Amendment of Class E Airspace; Luray, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-28

    ... Luray, VA, to accommodate the new Area Navigation (RNAV) Global Positioning System (GPS) Standard... Support Group, Eastern Service Center, Federal Aviation Administration, P.O. Box 20636, Atlanta, Georgia... FR 52292). Interested parties were invited to participate in this rulemaking effort by...

  4. 38 CFR 1.920 - Referral of VA debts.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... purpose of salary offset shall be done in accordance with 38 CFR 1.980 through 1.995 and regulations prescribed by the Director of the Office of Personnel Management (OPM) in 5 CFR part 550, subpart K... 38 Pensions, Bonuses, and Veterans' Relief 1 2011-07-01 2011-07-01 false Referral of VA debts....

  5. 38 CFR 1.920 - Referral of VA debts.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... purpose of salary offset shall be done in accordance with 38 CFR 1.980 through 1.995 and regulations prescribed by the Director of the Office of Personnel Management (OPM) in 5 CFR part 550, subpart K... 38 Pensions, Bonuses, and Veterans' Relief 1 2010-07-01 2010-07-01 false Referral of VA debts....

  6. VA Library Service--Today's look at Tomorrow's Library.

    ERIC Educational Resources Information Center

    Veterans Administration, Washington, DC.

    The Conference Poceedings are divided into three broad topics: systems planning, audiovisuals in biomedical communication, and automation and networking. Speakers from within the Veterans Administration (VA), from the National Medical Audiovisual Center, and the Lister Hill National Center for Biomedical Communications, National Library of…

  7. 76 FR 60713 - Establishment of Class E Airspace; Bumpass, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-30

    ... establish Class E airspace at Bumpass, VA (76 FR 45479) Docket No. FAA-2011-0377. Interested parties were...: Authority: 49 U.S.C. 106(g); 40103, 40113, 40120; E.O. 10854, 24 FR 9565, 3 CFR, 1959-1963 Comp., p. 389... Policies and Procedures (44 FR 11034; February 26, 1979); and (3) does not warrant preparation of...

  8. 32 CFR 105.10 - SARC and SAPR VA procedures.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... to accept reports of sexual assault along with the SAPR VA and healthcare personnel. (6) Report directly to the installation commander in accordance with 32 CFR part 103, to include providing regular... criminal investigative personnel on the SAPR policy and program and the roles and responsibilities of...

  9. 12 CFR 324.205 - VaR-based measure.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... risk-based capital requirements. The FDIC-supervised institution must update data sets at least monthly... observation period of at least one year. Data used to determine the VaR-based measure must be relevant to the... portfolio over a full business cycle. An FDIC-supervised institution using this option must update its...

  10. 12 CFR 3.205 - VaR-based measure.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... bank or Federal savings association must update data sets at least monthly or more frequently as... be based on a historical observation period of at least one year. Data used to determine the VaR... using this option must update its data more frequently than monthly and in a manner appropriate for...

  11. 12 CFR 217.205 - VaR-based measure.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... requirements. The Board-regulated institution must update data sets at least monthly or more frequently as... year. Data used to determine the VaR-based measure must be relevant to the Board-regulated institution.... A Board-regulated institution using this option must update its data more frequently than...

  12. 78 FR 71041 - VA Compensation and Pension Regulation Rewrite Project

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-27

    ... effect of the proposed revisions is to assist claimants, beneficiaries, veterans' representatives, and VA... quoted at length from NPRM AM 01, 72 FR 28770, May 22, 2007, to rebut the Secretary's assertion that his... noted that the NPRM stated that it explained any substantive changes between part 3 and part 5, 72...

  13. Geropsychology Training in a VA Nursing Home Setting

    ERIC Educational Resources Information Center

    Karel, Michele J.; Moye, Jennifer

    2005-01-01

    There is a growing need for professional psychology training in nursing home settings, and nursing homes provide a rich environment for teaching geropsychology competencies. We describe the nursing home training component of our Department of Veterans Affairs (VA) Predoctoral Internship and Geropsychology Postdoctoral Fellowship programs. Our…

  14. 75 FR 79295 - Establishment of Class E Airspace; Crewe, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-20

    ... Federal Register a notice of proposed rulemaking to establish Class E airspace at Crewe, VA (75 FR 57215...: Authority: 49 U.S.C. 106(g); 40103, 40113, 40120; E.O. 10854, 24 FR 9565, 3 CFR, 1959-1963 Comp., p. 389... ``significant rule'' under DOT Regulatory Policies and Procedures (44 FR 11034; February 26, 1979); and (3)...

  15. Polymicrobial Nature of Chronic Diabetic Foot Ulcer Biofilm Infections Determined Using Bacterial Tag Encoded FLX Amplicon Pyrosequencing (bTEFAP)

    PubMed Central

    Dowd, Scot E.; Wolcott, Randall D.; Sun, Yan; McKeehan, Trevor; Smith, Ethan; Rhoads, Daniel

    2008-01-01

    Background Diabetic extremity ulcers are associated with chronic infections. Such ulcer infections are too often followed by amputation because there is little or no understanding of the ecology of such infections or how to control or eliminate this type of chronic infection. A primary impediment to the healing of chronic wounds is biofilm phenotype infections. Diabetic foot ulcers are the most common, disabling, and costly complications of diabetes. Here we seek to derive a better understanding of the polymicrobial nature of chronic diabetic extremity ulcer infections. Methods and Findings Using a new bacterial tag encoded FLX amplicon pyrosequencing (bTEFAP) approach we have evaluated the bacterial diversity of 40 chronic diabetic foot ulcers from different patients. The most prevalent bacterial genus associated with diabetic chronic wounds was Corynebacterium spp. Findings also show that obligate anaerobes including Bacteroides, Peptoniphilus, Fingoldia, Anaerococcus, and Peptostreptococcus spp. are ubiquitous in diabetic ulcers, comprising a significant portion of the wound biofilm communities. Other major components of the bacterial communities included commonly cultured genera such as Streptococcus, Serratia, Staphylococcus and Enterococcus spp. Conclusions In this article, we highlight the patterns of population diversity observed in the samples and introduce preliminary evidence to support the concept of functional equivalent pathogroups (FEP). Here we introduce FEP as consortia of genotypically distinct bacteria that symbiotically produce a pathogenic community. According to this hypothesis, individual members of these communities when they occur alone may not cause disease but when they coaggregate or consort together into a FEP the synergistic effect provides the functional equivalence of well-known pathogens, such as Staphylococcus aureus, giving the biofilm community the factors necessary to maintain chronic biofilm infections. Further work is

  16. 75 FR 41577 - VBA/VHA Musculoskeletal Forum: Improving VA's Disability Evaluation Criteria

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-16

    ... presentations made by subject matter experts. VA plans to use this information to update the sections of VA's... system. See 38 CFR 4.40-4.73. Specifically, diagnostic code descriptors and evaluation criteria will...

  17. 77 FR 24268 - Agency Information Collection (Dependents' Application for VA Educational Benefits) Activity...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-23

    ... AFFAIRS Agency Information Collection (Dependents' Application for VA Educational Benefits) Activity Under... INFORMATION: Title: Dependents' Application for VA Educational Benefits (Under Provisions of Chapters 33 and... spouses and children of veterans or servicemembers to apply for Survivors' and Dependents'...

  18. 31. FELGATES CREEK BRIDGE (HAER No. VA48I), VIEW FROM WEST ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    31. FELGATES CREEK BRIDGE (HAER No. VA-48-I), VIEW FROM WEST END. NOTE ALUMINUM RAILING ON EAST SIDE FOR CANTILEVERED BIKE PATH. - Colonial Parkway, Yorktown to Jamestown Island, Yorktown, York County, VA

  19. Shedding light on the microbial community of the macropod foregut using 454-amplicon pyrosequencing.

    PubMed

    Gulino, Lisa-Maree; Ouwerkerk, Diane; Kang, Alicia Y H; Maguire, Anita J; Kienzle, Marco; Klieve, Athol V

    2013-01-01

    Twenty macropods from five locations in Queensland, Australia, grazing on a variety of native pastures were surveyed and the bacterial community of the foregut was examined using 454-amplicon pyrosequencing. Specifically, the V3/V4 region of 16S rRNA gene was examined. A total of 5040 OTUs were identified in the data set (post filtering). Thirty-two OTUs were identified as 'shared' OTUS (i.e. present in all samples) belonging to either Firmicutes or Bacteroidetes (Clostridiales/Bacteroidales). These phyla predominated the general microbial community in all macropods. Genera represented within the shared OTUs included: unclassified Ruminococcaceae, unclassified Lachnospiraceae, unclassified Clostridiales, Peptococcus sp. Coprococcus spp., Streptococcus spp., Blautia sp., Ruminoccocus sp., Eubacterium sp., Dorea sp., Oscillospira sp. and Butyrivibrio sp. The composition of the bacterial community of the foregut samples of each the host species (Macropus rufus, Macropus giganteus and Macropus robustus) was significantly different allowing differentiation between the host species based on alpha and beta diversity measures. Specifically, eleven dominant OTUs that separated the three host species were identified and classified as: unclassified Ruminococcaceae, unclassified Bacteroidales, Prevotella spp. and a Syntrophococcus sucromutans. Putative reductive acetogens and fibrolytic bacteria were also identified in samples. Future work will investigate the presence and role of fibrolytics and acetogens in these ecosystems. Ideally, the isolation and characterization of these organisms will be used for enhanced feed efficiency in cattle, methane mitigation and potentially for other industries such as the biofuel industry.

  20. Rare amplicons implicate frequent deregulation of cell fate specification pathways in oral squamous cell carcinoma.

    PubMed

    Snijders, Antoine M; Schmidt, Brian L; Fridlyand, Jane; Dekker, Nusi; Pinkel, Daniel; Jordan, Richard C K; Albertson, Donna G

    2005-06-16

    Genomes of solid tumors are characterized by gains and losses of regions, which may contribute to tumorigenesis by altering gene expression. Often the aberrations are extensive, encompassing whole chromosome arms, which makes identification of candidate genes in these regions difficult. Here, we focused on narrow regions of gene amplification to facilitate identification of genetic pathways important in oral squamous cell carcinoma (SCC) development. We used array comparative genomic hybridization (array CGH) to define minimum common amplified regions and then used expression analysis to identify candidate driver genes in amplicons that spanned <3 Mb. We found genes involved in integrin signaling (TLN1), survival (YAP1, BIRC2), and adhesion and migration (TLN1, LAMA3, MMP7), as well as members of the hedgehog (GLI2) and notch (JAG1, RBPSUH, FJX1) pathways to be amplified and overexpressed. Deregulation of these and other members of the hedgehog and notch pathways (HHIP, SMO, DLL1, NOTCH4) implicates deregulation of developmental and differentiation pathways, cell fate misspecification, in oral SCC development. PMID:15824737

  1. Flow cytometry community fingerprinting and amplicon sequencing for the assessment of landfill leachate cellulolytic bioaugmentation.

    PubMed

    Kinet, R; Dzaomuho, P; Baert, J; Taminiau, B; Daube, G; Nezer, C; Brostaux, Y; Nguyen, F; Dumont, G; Thonart, P; Delvigne, F

    2016-08-01

    Flow cytometry (FCM) is a high throughput single cell technology that is actually becoming widely used for studying phenotypic and genotypic diversity among microbial communities. This technology is considered in this work for the assessment of a bioaugmentation treatment in order to enhance cellulolytic potential of landfill leachate. The experimental results reveal the relevant increase of leachate cellulolytic potential due to bioaugmentation. Cytometric monitoring of microbial dynamics along these assays is then realized. The flow FP package is used to establish microbial samples fingerprint from initial 2D cytometry histograms. This procedure allows highlighting microbial communities' variation along the assays. Cytometric and 16S rRNA gene sequencing fingerprinting methods are then compared. The two approaches give same evidence about microbial dynamics throughout digestion assay. There are however a lack of significant correlation between cytometric and amplicon sequencing fingerprint at genus or species level. Same phenotypical profiles of microbiota during assays matched to several 16S rRNA gene sequencing ones. Flow cytometry fingerprinting can thus be considered as a promising routine on-site method suitable for the detection of stability/variation/disturbance of complex microbial communities involved in bioprocesses. PMID:27160955

  2. Swarm v2: highly-scalable and high-resolution amplicon clustering

    PubMed Central

    Quince, Christopher; de Vargas, Colomban; Dunthorn, Micah

    2015-01-01

    Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global clustering thresholds and input-order dependency. Swarm v1 worked with an initial phase that used iterative single-linkage with a local clustering threshold (d), followed by a phase that used the internal abundance structures of clusters to break chained OTUs. Here we present Swarm v2, which has two important novel features: (1) a new algorithm for d = 1 that allows the computation time of the program to scale linearly with increasing amounts of data; and (2) the new fastidious option that reduces under-grouping by grafting low abundant OTUs (e.g., singletons and doubletons) onto larger ones. Swarm v2 also directly integrates the clustering and breaking phases, dereplicates sequencing reads with d = 0, outputs OTU representatives in fasta format, and plots individual OTUs as two-dimensional networks. PMID:26713226

  3. The development of reduced size STR amplicons as tools for analysis of degraded DNA.

    PubMed

    Butler, John M; Shen, Yin; McCord, Bruce R

    2003-09-01

    New multiplex PCR sets of commonly used short tandem repeat (STR) markers have been developed to produce PCR products that are reduced in size when compared to standard commercial STR kits. The reduction in size of these amplicons can facilitate the examination and analysis of degraded DNA evidence by improving amplification efficiency. This "miniSTR" approach will permit current forensic practitioners to use STR markers and instrumentation already present in their laboratories and to generate genotyping data that is directly comparable to reference samples and searchable through the FBI's Combined DNA Index System (CODIS) databases. This paper discusses the development of these new primer sets and presents some initial results in the analysis of degraded and aged DNA samples. A method for removal of problematic fluorescent dye artifacts is also described. Comparison studies in over 100 samples have verified that these miniSTR primers can provide fully concordant results to commercial STR kits and can provide improved signal from degraded DNA specimens. These miniplex sets should prove valuable in the analysis of samples where allele dropout and reduced sensitivity of larger STR alleles occurs.

  4. Extracellular DNA amplicon sequencing reveals high levels of benthic eukaryotic diversity in the central Red Sea.

    PubMed

    Pearman, John K; Irigoien, Xabier; Carvalho, Susana

    2016-04-01

    The present study aims to characterize the benthic eukaryotic biodiversity patterns at a coarse taxonomic level in three areas of the central Red Sea (a lagoon, an offshore area in Thuwal and a shallow coastal area near Jeddah) based on extracellular DNA. High-throughput amplicon sequencing targeting the V9 region of the 18S rRNA gene was undertaken for 32 sediment samples. High levels of alpha-diversity were detected with 16,089 operational taxonomic units (OTUs) being identified. The majority of the OTUs were assigned to Metazoa (29.2%), Alveolata (22.4%) and Stramenopiles (17.8%). Stramenopiles (Diatomea) and Alveolata (Ciliophora) were frequent in a lagoon and in shallower coastal stations, whereas metazoans (Arthropoda: Maxillopoda) were dominant in deeper offshore stations. Only 24.6% of total OTUs were shared among all areas. Beta-diversity was generally lower between the lagoon and Jeddah (nearshore) than between either of those and the offshore area, suggesting a nearshore-offshore biodiversity gradient. The current approach allowed for a broad-range of benthic eukaryotic biodiversity to be analysed with significantly less labour than would be required by other traditional taxonomic approaches. Our findings suggest that next generation sequencing techniques have the potential to provide a fast and standardised screening of benthic biodiversity at large spatial and temporal scales.

  5. Shedding Light on the Microbial Community of the Macropod Foregut Using 454-Amplicon Pyrosequencing

    PubMed Central

    Gulino, Lisa-Maree; Ouwerkerk, Diane; Kang, Alicia Y. H.; Maguire, Anita J.; Kienzle, Marco; Klieve, Athol V.

    2013-01-01

    Twenty macropods from five locations in Queensland, Australia, grazing on a variety of native pastures were surveyed and the bacterial community of the foregut was examined using 454-amplicon pyrosequencing. Specifically, the V3/V4 region of 16S rRNA gene was examined. A total of 5040 OTUs were identified in the data set (post filtering). Thirty-two OTUs were identified as ‘shared’ OTUS (i.e. present in all samples) belonging to either Firmicutes or Bacteroidetes (Clostridiales/Bacteroidales). These phyla predominated the general microbial community in all macropods. Genera represented within the shared OTUs included: unclassified Ruminococcaceae, unclassified Lachnospiraceae, unclassified Clostridiales, Peptococcus sp. Coprococcus spp., Streptococcus spp., Blautia sp., Ruminoccocus sp., Eubacterium sp., Dorea sp., Oscillospira sp. and Butyrivibrio sp. The composition of the bacterial community of the foregut samples of each the host species (Macropus rufus, Macropus giganteus and Macropus robustus) was significantly different allowing differentiation between the host species based on alpha and beta diversity measures. Specifically, eleven dominant OTUs that separated the three host species were identified and classified as: unclassified Ruminococcaceae, unclassified Bacteroidales, Prevotella spp. and a Syntrophococcus sucromutans. Putative reductive acetogens and fibrolytic bacteria were also identified in samples. Future work will investigate the presence and role of fibrolytics and acetogens in these ecosystems. Ideally, the isolation and characterization of these organisms will be used for enhanced feed efficiency in cattle, methane mitigation and potentially for other industries such as the biofuel industry. PMID:23626688

  6. Allelic Selection of Amplicons in Glioblastoma Revealed by Combining Somatic and Germline Analysis

    PubMed Central

    Wilkins, Katherine; Pe'er, Itsik; Freedman, Matthew L.

    2010-01-01

    Cancer is a disease driven by a combination of inherited risk alleles coupled with the acquisition of somatic mutations, including amplification and deletion of genomic DNA. Potential relationships between the inherited and somatic aspects of the disease have only rarely been examined on a genome-wide level. Applying a novel integrative analysis of SNP and copy number measurements, we queried the tumor and normal-tissue genomes of 178 glioblastoma patients from the Cancer Genome Atlas project for preferentially amplified alleles, under the hypothesis that oncogenic germline variants will be selectively amplified in the tumor environment. Selected alleles are revealed by allelic imbalance in amplification across samples. This general approach is based on genetic principles and provides a method for identifying important tumor-related alleles. We find that SNP alleles that are most significantly overrepresented in amplicons tend to occur in genes involved with regulation of kinase and transferase activity, and many of these genes are known contributors to gliomagenesis. The analysis also implicates variants in synapse genes. By incorporating gene expression data, we demonstrate synergy between preferential allelic amplification and expression in DOCK4 and EGFR. Our results support the notion that combining germline and tumor genetic data can identify regions relevant to cancer biology. PMID:20824129

  7. Digital fragment analysis of short tandem repeats by high-throughput amplicon sequencing.

    PubMed

    Darby, Brian J; Erickson, Shay F; Hervey, Samuel D; Ellis-Felege, Susan N

    2016-07-01

    High-throughput sequencing has been proposed as a method to genotype microsatellites and overcome the four main technical drawbacks of capillary electrophoresis: amplification artifacts, imprecise sizing, length homoplasy, and limited multiplex capability. The objective of this project was to test a high-throughput amplicon sequencing approach to fragment analysis of short tandem repeats and characterize its advantages and disadvantages against traditional capillary electrophoresis. We amplified and sequenced 12 muskrat microsatellite loci from 180 muskrat specimens and analyzed the sequencing data for precision of allele calling, propensity for amplification or sequencing artifacts, and for evidence of length homoplasy. Of the 294 total alleles, we detected by sequencing, only 164 alleles would have been detected by capillary electrophoresis as the remaining 130 alleles (44%) would have been hidden by length homoplasy. The ability to detect a greater number of unique alleles resulted in the ability to resolve greater population genetic structure. The primary advantages of fragment analysis by sequencing are the ability to precisely size fragments, resolve length homoplasy, multiplex many individuals and many loci into a single high-throughput run, and compare data across projects and across laboratories (present and future) with minimal technical calibration. A significant disadvantage of fragment analysis by sequencing is that the method is only practical and cost-effective when performed on batches of several hundred samples with multiple loci. Future work is needed to optimize throughput while minimizing costs and to update existing microsatellite allele calling and analysis programs to accommodate sequence-aware microsatellite data. PMID:27386092

  8. Detection of human tumor cells by amplicon fusion site polymerase chain reaction (AFS-PCR)

    PubMed Central

    Weber, Axel; Taube, Sylvia; Starke, Sven; Bergmann, Eckhard; Christiansen, Nina Merete; Christiansen, Holger

    2011-01-01

    Reliable diagnostic strategies for individuals with cancer demand practical methods for highly sensitive and specific detection of tumor cells. Amplification of genomic regions that include putative oncogenes is common in tumor cells of various types. Genomic array platforms offer the opportunity to identify and precisely map amplified genomic regions (ampGRs). The stable existence of these tumor cell–specific genomic aberrations during and after therapy, in theory, make ampGRs optimal targets for cancer diagnostics. In this study, we mapped ampGRs around the proto-oncogene MYCN of human neuroblastomas using a high-resolution tiling array (HR-TA). Based on the HR-TA data, we were able to precisely describe the telomeric and centromeric borders of the ampGRs and deduce virtual fusion sites of the joined ampGRs (amplicon fusion sites [AFSs]). These AFSs served as blueprints for the subsequent design of AFS bridging PCR assays (AFS-PCRs). Strikingly, these assays were absolutely tumor cell specific and capable of detecting 1 tumor cell in 1 × 106 to 8 × 106 control cells. We successfully proved the in vivo practicability of AFS-PCR by detecting and quantifying the specific AFS DNA of human MYCN-amplified neuroblastomas in the patients’ corresponding peripheral blood and bone marrow samples. Thus, we believe AFS-PCR could become a powerful and nevertheless feasible personalized diagnostic tool applicable to a large number of cancer patients, including children with MYCN-amplified neuroblastomas. PMID:21293059

  9. Detection of human tumor cells by amplicon fusion site polymerase chain reaction (AFS-PCR).

    PubMed

    Weber, Axel; Taube, Sylvia; Starke, Sven; Bergmann, Eckhard; Christiansen, Nina Merete; Christiansen, Holger

    2011-02-01

    Reliable diagnostic strategies for individuals with cancer demand practical methods for highly sensitive and specific detection of tumor cells. Amplification of genomic regions that include putative oncogenes is common in tumor cells of various types. Genomic array platforms offer the opportunity to identify and precisely map amplified genomic regions (ampGRs). The stable existence of these tumor cell–specific genomic aberrations during and after therapy, in theory, make ampGRs optimal targets for cancer diagnostics. In this study, we mapped ampGRs around the proto-oncogene MYCN of human neuroblastomas using a high-resolution tiling array (HR-TA). Based on the HR-TA data, we were able to precisely describe the telomeric and centromeric borders of the ampGRs and deduce virtual fusion sites of the joined ampGRs (amplicon fusion sites [AFSs]). These AFSs served as blueprints for the subsequent design of AFS bridging PCR assays (AFS-PCRs). Strikingly, these assays were absolutely tumor cell specific and capable of detecting 1 tumor cell in 1 × 10(6) to 8 × 10(6) control cells. We successfully proved the in vivo practicability of AFS-PCR by detecting and quantifying the specific AFS DNA of human MYCN-amplified neuroblastomas in the patients’ corresponding peripheral blood and bone marrow samples. Thus, we believe AFS-PCR could become a powerful and nevertheless feasible personalized diagnostic tool applicable to a large number of cancer patients, including children with MYCN-amplified neuroblastomas.

  10. Electroanalytical study of SYBR Green I and ethidium bromide intercalation in methylated and unmethylated amplicons.

    PubMed

    Ioannou, Andrea K; Alexiadou, Despina K; Kouidou, Sofia A; Voulgaropoulos, Anastasios N; Girousi, Stella Th

    2010-01-11

    This work involves the electrochemical study of the interaction of SYBR Green I (SG) with native DNA using differential pulse voltammetry at a carbon paste electrode (CPE) and alternating current voltammetry at a hanging mercury drop electrode (HMDE). At the CPE the peak current intensity at 1.0 V decreased by increasing the concentration of SG. At the HMDE, a decrease in the current intensity of the DNA peak at -1.2 V was also observed by increasing the concentration of SG. These results electrochemically confirmed that SG intercalates within the DNA double helix and changes its conformation. Through the present work the differentiation of differently methylated analytes was achieved by application of alternative current and differential pulse voltammetric techniques. Amplicons (PCR products) corresponding to the GC-rich p53 exon 5 containing cytosine and its methylated analogue, synthesized by substituting 60% of cytosine by 5-methyl-cytosine, were amplified and investigated electrochemically in the presence of SG and ethidium bromide (EtBr) by differential pulse voltammetry. Considerable peak current differences were observed in the presence of SG and EtBr for unmethylated exon 5 vs. methylated. Therefore, both SG and EtBr could serve as electrochemical probes for identifying different DNA conformations.

  11. Amplicon pyrosequencing reveals the soil microbial diversity associated with invasive Japanese barberry (Berberis thunbergii DC.).

    PubMed

    Coats, V C; Pelletreau, K N; Rumpho, M E

    2014-03-01

    The soil microbial community acts as a reservoir of microbes that directly influences the structure and composition of the aboveground plant community, promotes plant growth, increases stress tolerance and mediates local patterns of nutrient cycling. Direct interactions between plants and rhizosphere-dwelling microorganisms occur at, or near, the surface of the root. Upon introduction and establishment, invasive plants modify the soil microbial communities and soil biochemistry affecting bioremediation efforts and future plant communities. Here, we used tag-encoded FLX amplicon 454 pyrosequencing (TEFAP) to characterize the bacterial and fungal community diversity in the rhizosphere of Berberis thunbergii DC. (Japanese barberry) from invasive stands in coastal Maine to investigate effects of soil type, soil chemistry and surrounding plant cover on the soil microbial community structure. Acidobacteria, Actinobacteria, Proteobacteria and Verrucomicrobia were the dominant bacterial phyla, whereas fungal communities were comprised mostly of Ascomycota and Basidiomycota phyla members, including Agaricomycetes and Sordariomycetes. Bulk soil chemistry had more effect on the bacterial community structure than the fungal community. An effect of geographic location was apparent in the rhizosphere microbial communities, yet it was less significant than the effect of surrounding plant cover. These data demonstrate a high degree of spatial variation in the rhizosphere microbial communities of Japanese barberry with apparent effects of soil chemistry, location and canopy cover on the microbial community structure.

  12. Flow cytometry community fingerprinting and amplicon sequencing for the assessment of landfill leachate cellulolytic bioaugmentation.

    PubMed

    Kinet, R; Dzaomuho, P; Baert, J; Taminiau, B; Daube, G; Nezer, C; Brostaux, Y; Nguyen, F; Dumont, G; Thonart, P; Delvigne, F

    2016-08-01

    Flow cytometry (FCM) is a high throughput single cell technology that is actually becoming widely used for studying phenotypic and genotypic diversity among microbial communities. This technology is considered in this work for the assessment of a bioaugmentation treatment in order to enhance cellulolytic potential of landfill leachate. The experimental results reveal the relevant increase of leachate cellulolytic potential due to bioaugmentation. Cytometric monitoring of microbial dynamics along these assays is then realized. The flow FP package is used to establish microbial samples fingerprint from initial 2D cytometry histograms. This procedure allows highlighting microbial communities' variation along the assays. Cytometric and 16S rRNA gene sequencing fingerprinting methods are then compared. The two approaches give same evidence about microbial dynamics throughout digestion assay. There are however a lack of significant correlation between cytometric and amplicon sequencing fingerprint at genus or species level. Same phenotypical profiles of microbiota during assays matched to several 16S rRNA gene sequencing ones. Flow cytometry fingerprinting can thus be considered as a promising routine on-site method suitable for the detection of stability/variation/disturbance of complex microbial communities involved in bioprocesses.

  13. Accuracy of the high-throughput amplicon sequencing to identify species within the genus Aspergillus.

    PubMed

    Lee, Seungeun; Yamamoto, Naomichi

    2015-12-01

    This study characterized the accuracy of high-throughput amplicon sequencing to identify species within the genus Aspergillus. To this end, we sequenced the internal transcribed spacer 1 (ITS1), β-tubulin (BenA), and calmodulin (CaM) gene encoding sequences as DNA markers from eight reference Aspergillus strains with known identities using 300-bp sequencing on the Illumina MiSeq platform, and compared them with the BLASTn outputs. The identifications with the sequences longer than 250 bp were accurate at the section rank, with some ambiguities observed at the species rank due to mostly cross detection of sibling species. Additionally, in silico analysis was performed to predict the identification accuracy for all species in the genus Aspergillus, where 107, 210, and 187 species were predicted to be identifiable down to the species rank based on ITS1, BenA, and CaM, respectively. Finally, air filter samples were analysed to quantify the relative abundances of Aspergillus species in outdoor air. The results were reproducible across biological duplicates both at the species and section ranks, but not strongly correlated between ITS1 and BenA, suggesting the Aspergillus detection can be taxonomically biased depending on the selection of the DNA markers and/or primers.

  14. The Impact of VA's Geriatric Research, Education and Clinical Centers on Academic Affiliates

    ERIC Educational Resources Information Center

    Bragg, Elizabeth J.; Meganathan, Karthikeyan; Shay, Kenneth; Gilman, Stuart C.; Zeiss, Robert A.; Hettler, Debbie L.

    2011-01-01

    The education mission of the Department of Veterans Affairs (VA) is to train health professionals to benefit VA and the United States. One approach for achieving that mission, along with VA's research and clinical missions, was the establishment of Geriatric Research, Education and Clinical Centers (GRECCs) in 1975. These were developed at VA…

  15. 78 FR 76412 - Agency Information Collection (VA National Rehabilitation Special Events, Event Registration...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-17

    ...-0759''. SUPPLEMENTARY INFORMATION: Titles: a. National Disabled Veterans Winter Sports Clinic... sports Clinic Event Application, VA Form 0928a, c. l. Volunteer Application, VA Form 0928h. m. Surfing... already approved collection. Abstract: Veterans who are enrolled for VA health care may apply...

  16. 78 FR 26250 - Payment for Home Health Services and Hospice Care to Non-VA Providers

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-06

    ... November 21, 2011 (76 FR 71920), VA proposed to amend its regulations concerning the billing methodology... AFFAIRS 38 CFR Part 17 RIN 2900-AN98 Payment for Home Health Services and Hospice Care to Non-VA Providers... services and hospice care. Because the newly applicable methodology cannot supersede rates for which VA...

  17. 78 FR 11094 - Drawbridge Operation Regulation; James River, Between Isle of Wight and Newport News, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-15

    ... and Newport News, VA AGENCY: Coast Guard, DHS. ACTION: Notice of deviation from drawbridge regulation... News, VA. This deviation is necessary to facilitate generator replacement on the James River Draw... operating schedule, the James River Bridge, mile 5.0, between Isle of Isle and Newport News, VA opens...

  18. 48 CFR 853.236-70 - VA Form 10-6298, Architect-Engineer Fee Proposal.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 48 Federal Acquisition Regulations System 5 2011-10-01 2011-10-01 false VA Form 10-6298, Architect... VETERANS AFFAIRS CLAUSES AND FORMS FORMS Prescription of Forms 853.236-70 VA Form 10-6298, Architect-Engineer Fee Proposal. VA Form 10-6298, Architect-Engineer Fee Proposal, shall be used as prescribed in...

  19. 75 FR 78808 - Agency Information Collection (VA Request for Determination of Reasonable Value) Activity Under...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-16

    ... AFFAIRS Agency Information Collection (VA Request for Determination of Reasonable Value) Activity Under... comment. The PRA submission describes the nature of the information collection and its expected cost and... INFORMATION: Title: VA Request for Determination of Reasonable Value VA Form 26- 1805 and 26-1805-1....

  20. 78 FR 59773 - Proposed Information Collection (VA Request for Determination of Reasonable Value) Activity...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-27

    ... AFFAIRS Proposed Information Collection (VA Request for Determination of Reasonable Value) Activity... solicits comments for information needed to determine the reasonable value of properties for guaranteed or... information technology. Title: VA Request for Determination of Reasonable Value, VA Form 26-1805 and...

  1. 38 CFR 26.9 - Information on and public participation in VA environmental process.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... participation in VA environmental process. 26.9 Section 26.9 Pensions, Bonuses, and Veterans' Relief DEPARTMENT...) ACTIONS § 26.9 Information on and public participation in VA environmental process. (a) During the..., the Office of Environmental Affairs, or a VA element, information is available by writing to...

  2. 76 FR 63357 - VA National Academic Affiliations Council; Notice of Establishment

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-12

    ... AFFAIRS VA National Academic Affiliations Council; Notice of Establishment As required by Section 9(a)(2... establishment of the Department of Veterans Affairs (VA) National Academic Affiliations Council. The Secretary... partnerships between VA and its academic affiliates. The Council will provide a forum for discussion and...

  3. VA-086 methacrylate gelatine photopolymerizable hydrogels: A parametric study for highly biocompatible 3D cell embedding.

    PubMed

    Occhetta, Paola; Visone, Roberta; Russo, Laura; Cipolla, Laura; Moretti, Matteo; Rasponi, Marco

    2015-06-01

    The ability to replicate in vitro the native extracellular matrix (ECM) features and to control the three-dimensional (3D) cell organization plays a fundamental role in obtaining functional engineered bioconstructs. In tissue engineering (TE) applications, hydrogels have been successfully implied as biomatrices for 3D cell embedding, exhibiting high similarities to the natural ECM and holding easily tunable mechanical properties. In the present study, we characterized a promising photocrosslinking process to generate cell-laden methacrylate gelatin (GelMA) hydrogels in the presence of VA-086 photoinitiator using a ultraviolet LED source. We investigated the influence of prepolymer concentration and light irradiance on mechanical and biomimetic properties of resulting hydrogels. In details, the increasing of gelatin concentration resulted in enhanced rheological properties and shorter polymerization time. We then defined and validated a reliable photopolymerization protocol for cell embedding (1.5% VA-086, LED 2 mW/cm2) within GelMA hydrogels, which demonstrated to support bone marrow stromal cells viability when cultured up to 7 days. Moreover, we showed how different mechanical properties, derived from different crosslinking parameters, strongly influence cell behavior. In conclusion, this protocol can be considered a versatile tool to obtain biocompatible cell-laden hydrogels with properties easily adaptable for different TE applications.

  4. Analysis of β-Subunit-dependent GABAA Receptor Modulation and Behavioral Effects of Valerenic Acid Derivatives

    PubMed Central

    Hintersteiner, J.; Luger, D.; Haider, M.; Pototschnig, G.; Mihovilovic, M. D.; Schwarzer, C.; Hering, S.

    2016-01-01

    Valerenic acid (VA)—a β2/3-selective GABA type A (GABAA) receptor modulator—displays anxiolytic and anticonvulsive effects in mice devoid of sedation, making VA an interesting drug candidate. Here we analyzed β-subunit-dependent enhancement of GABA-induced chloride currents (IGABA) by a library of VA derivatives and studied their effects on pentylenetetrazole (PTZ)-induced seizure threshold and locomotion. Compound-induced IGABA enhancement was determined in oocytes expressing α1β1γ2S, α1β2γ2S, or α1β3γ2S receptors. Effects on seizure threshold and locomotion were studied using C57BL/6N mice and compared with saline-treated controls. β2/3-selective VA derivatives such as VA-amide (VA-A) modulating α1β3γ2S (VA-A: Emax = 972 ± 69%, n = 6, P < 0.05) and α1β2γ2S receptors (Emax = 1119 ± 72%, n = 6, P < 0.05) more efficaciously than VA (α1β3γ2S: VA: Emax = 632 ± 88%, n = 9 versus α1β2γ2S: VA: Emax = 721 ± 68%, n = 6) displayed significantly more pronounced seizure threshold elevation than VA (saline control: 40.4 ± 1.4 mg/kg PTZ versus VA 10 mg/kg: 49.0 ± 1.8 mg/kg PTZ versus VA-A 3 mg/kg: 57.9 ± 1.9 mg/kg PTZ, P < 0.05). Similarly, VA’s methylamide (VA-MA) enhancing IGABA through β3-containing receptors more efficaciously than VA (Emax = 1043 ± 57%, P < 0.01, n = 6) displayed stronger anticonvulsive effects. Increased potency of IGABA enhancement and anticonvulsive effects at lower doses compared with VA were observed for VA-tetrazole (α1β3γ2S: VA-TET: EC50 = 6.0 ± 1.0 μM, P < 0.05; VA-TET: 0.3 mg/kg: 47.3 ± 0.5 mg/kg PTZ versus VA: 10 mg/kg: 49.0 ± 1.8 mg/kg PTZ, P < 0.05). At higher doses (≥10 mg/kg), VA-A, VA-MA, and VA-TET reduced locomotion. In contrast, unselective VA derivatives induced anticonvulsive effects only at high doses (30 mg/kg) or did not display any behavioral effects. Our data indicate that the β2/3-selective compounds VA-A, VA-MA, and VA-TET induce anticonvulsive effects at low doses (≤10 mg

  5. Groundtruthing Next-Gen Sequencing for Microbial Ecology–Biases and Errors in Community Structure Estimates from PCR Amplicon Pyrosequencing

    PubMed Central

    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. PMID:22970184

  6. Comparison of Normalization Methods for Construction of Large, Multiplex Amplicon Pools for Next-Generation Sequencing▿ †

    PubMed Central

    Harris, J. Kirk; Sahl, Jason W.; Castoe, Todd A.; Wagner, Brandie D.; Pollock, David D.; Spear, John R.

    2010-01-01

    Constructing mixtures of tagged or bar-coded DNAs for sequencing is an important requirement for the efficient use of next-generation sequencers in applications where limited sequence data are required per sample. There are many applications in which next-generation sequencing can be used effectively to sequence large mixed samples; an example is the characterization of microbial communities where ≤1,000 sequences per samples are adequate to address research questions. Thus, it is possible to examine hundreds to thousands of samples per run on massively parallel next-generation sequencers. However, the cost savings for efficient utilization of sequence capacity is realized only if the production and management costs associated with construction of multiplex pools are also scalable. One critical step in multiplex pool construction is the normalization process, whereby equimolar amounts of each amplicon are mixed. Here we compare three approaches (spectroscopy, size-restricted spectroscopy, and quantitative binding) for normalization of large, multiplex amplicon pools for performance and efficiency. We found that the quantitative binding approach was superior and represents an efficient scalable process for construction of very large, multiplex pools with hundreds and perhaps thousands of individual amplicons included. We demonstrate the increased sequence diversity identified with higher throughput. Massively parallel sequencing can dramatically accelerate microbial ecology studies by allowing appropriate replication of sequence acquisition to account for temporal and spatial variations. Further, population studies to examine genetic variation, which require even lower levels of sequencing, should be possible where thousands of individual bar-coded amplicons are examined in parallel. PMID:20418443

  7. Electrochemical detection of PCR amplicons of Escherichia coli genome based on DNA nanostructural probes and polyHRP enzyme.

    PubMed

    Wen, Yanli; Wang, LeLe; Xu, Li; Li, Lanying; Ren, Suzhen; Cao, Chengming; Jia, Nengqin; Aldalbahi, Ali; Song, Shiping; Shi, Jiye; Xia, Jiaoyun; Liu, Gang; Zuo, Xiaolei

    2016-09-21

    Fast, portable and sensitive analysis of E. coli is becoming an important challenge in many critical fields (e.g., food safety, environmental monitoring and clinical diagnosis). Thus, electrochemical biosensing of PCR amplicons from the bacterial genome has attracted reasonable research attention. In this work, we utilized a 3D DNA tetrahedral probe to establish a "sandwich-type" electrochemical DNA biosensor for sensitive and specific analysis of a 250 bp unpurified PCR amplicon from the uidA gene of the E. coli genome. Asymmetric PCR was used to produce single-stranded PCR products. Streptavidin-polyHRP80 was employed to improve the signal gain during electrochemical detection. We optimized important experimental conditions for DNA sensing, including the streptavidin-polyHRP, the signal probe and the ion strength. Finally, we achieved a remarkable sensitivity of 10 fM synthetic DNA target, and successfully performed the analysis of PCR amplicons from as low as 0.2 pg μL(-1) of E. coli genome. Compared with traditional single stranded DNA (ssDNA) probe based detection, our present work demonstrated 3 orders of magnitude improvement in sensitivity. In addition, our electrochemical DNA biosensor was 4 orders of magnitude more sensitive than normal electrophoretic analysis of PCR products. Our work made important progress in DNA nanostructured probe-based biosensors toward application in real applications. PMID:27460969

  8. Analysis of the mouse gut microbiome using full-length 16S rRNA amplicon sequencing.

    PubMed

    Shin, Jongoh; Lee, Sooin; Go, Min-Jeong; Lee, Sang Yup; Kim, Sun Chang; Lee, Chul-Ho; Cho, Byung-Kwan

    2016-01-01

    Demands for faster and more accurate methods to analyze microbial communities from natural and clinical samples have been increasing in the medical and healthcare industry. Recent advances in next-generation sequencing technologies have facilitated the elucidation of the microbial community composition with higher accuracy and greater throughput than was previously achievable; however, the short sequencing reads often limit the microbial composition analysis at the species level due to the high similarity of 16S rRNA amplicon sequences. To overcome this limitation, we used the nanopore sequencing platform to sequence full-length 16S rRNA amplicon libraries prepared from the mouse gut microbiota. A comparison of the nanopore and short-read sequencing data showed that there were no significant differences in major taxonomic units (89%) except one phylotype and three taxonomic units. Moreover, both sequencing data were highly similar at all taxonomic resolutions except the species level. At the species level, nanopore sequencing allowed identification of more species than short-read sequencing, facilitating the accurate classification of the bacterial community composition. Therefore, this method of full-length 16S rRNA amplicon sequencing will be useful for rapid, accurate and efficient detection of microbial diversity in various biological and clinical samples. PMID:27411898

  9. Analysis of the mouse gut microbiome using full-length 16S rRNA amplicon sequencing

    PubMed Central

    Shin, Jongoh; Lee, Sooin; Go, Min-Jeong; Lee, Sang Yup; Kim, Sun Chang; Lee, Chul-Ho; Cho, Byung-Kwan

    2016-01-01

    Demands for faster and more accurate methods to analyze microbial communities from natural and clinical samples have been increasing in the medical and healthcare industry. Recent advances in next-generation sequencing technologies have facilitated the elucidation of the microbial community composition with higher accuracy and greater throughput than was previously achievable; however, the short sequencing reads often limit the microbial composition analysis at the species level due to the high similarity of 16S rRNA amplicon sequences. To overcome this limitation, we used the nanopore sequencing platform to sequence full-length 16S rRNA amplicon libraries prepared from the mouse gut microbiota. A comparison of the nanopore and short-read sequencing data showed that there were no significant differences in major taxonomic units (89%) except one phylotype and three taxonomic units. Moreover, both sequencing data were highly similar at all taxonomic resolutions except the species level. At the species level, nanopore sequencing allowed identification of more species than short-read sequencing, facilitating the accurate classification of the bacterial community composition. Therefore, this method of full-length 16S rRNA amplicon sequencing will be useful for rapid, accurate and efficient detection of microbial diversity in various biological and clinical samples. PMID:27411898

  10. Water Surface Turbulance and Internal Waves, Norfolk, VA, USA

    NASA Technical Reports Server (NTRS)

    1991-01-01

    Norfolk and the mouth of the Chesapeake Bay, VA, (37.5N, 75.5W) was exposed in sunglint conditions to emphasizes water surface patterns. Outgoing tides from the bay generate considerable turbulence as they encounter coastal ocean currents and can be observed as differences in the reflective properties of the water surface. Smooth flowing water has high reflectivity. Turbulent water has a rough surface and low reflectance. Ship wakes can also be seen.

  11. 'Baby talk' attracts neighbors to new Manassas, Va., birthing center.

    PubMed

    Botvin, Judith D

    2005-01-01

    An dollar 80 million expansion plan recently was launched by Prince William Hospital, Manassas, Va. The cornerstone of the plan is the new Hylton Family Birthing Center. The hospital employed a full range of tactics to promote the opening of the birthing center. These ranged from quarterly newsletters to billboards; from tours and radio spots to a newly revised web site. The campaign is characterized by infant testimonials, gentle humor and bright colors. PMID:15971721

  12. Prerequisites for amplicon pyrosequencing of microbial methanol utilizers in the environment

    PubMed Central

    Kolb, Steffen; Stacheter, Astrid

    2013-01-01

    The commercial availability of next generation sequencing (NGS) technologies facilitated the assessment of functional groups of microorganisms in the environment with high coverage, resolution, and reproducibility. Soil methylotrophs were among the first microorganisms in the environment that were assessed with molecular tools, and nowadays, as well with NGS technologies. Studies in the past years re-attracted notice to the pivotal role of methylotrophs in global conversions of methanol, which mainly originates from plants, and is involved in oxidative reactions and ozone formation in the atmosphere. Aerobic methanol utilizers belong to Bacteria, yeasts, Ascomycota, and molds. Numerous bacterial methylotrophs are facultatively aerobic, and also contribute to anaerobic methanol oxidation in the environment, whereas strict anaerobic methanol utilizers belong to methanogens and acetogens. The diversity of enzymes catalyzing the initial oxidation of methanol is considerable, and comprises at least five different enzyme types in aerobes, and one in strict anaerobes. Only the gene of the large subunit of pyrroloquinoline quinone (PQQ)-dependent methanol dehydrogenase (MDH; mxaF) has been analyzed by environmental pyrosequencing. To enable a comprehensive assessment of methanol utilizers in the environment, new primers targeting genes of the PQQ MDH in Methylibium (mdh2), of the nicotinamide adenine dinucleotide-dependent MDH (mdh), of the methanol oxidoreductase of Actinobacteria (mdo), of the fungal flavin adenine nucleotide-dependent alcohol oxidase (mod1, mod2, and homologs), and of the gene of the large subunit of the methanol:corrinoid methyltransferases (mtaC) in methanogens and acetogens need to be developed. Combined stable isotope probing of nucleic acids or proteins with amplicon-based NGS are straightforward approaches to reveal insights into functions of certain methylotrophic taxa in the global methanol cycle. PMID:24046766

  13. Amplicon-based semiconductor sequencing of human exomes: performance evaluation and optimization strategies.

    PubMed

    Damiati, E; Borsani, G; Giacopuzzi, Edoardo

    2016-05-01

    The Ion Proton platform allows to perform whole exome sequencing (WES) at low cost, providing rapid turnaround time and great flexibility. Products for WES on Ion Proton system include the AmpliSeq Exome kit and the recently introduced HiQ sequencing chemistry. Here, we used gold standard variants from GIAB consortium to assess the performances in variants identification, characterize the erroneous calls and develop a filtering strategy to reduce false positives. The AmpliSeq Exome kit captures a large fraction of bases (>94 %) in human CDS, ClinVar genes and ACMG genes, but with 2,041 (7 %), 449 (13 %) and 11 (19 %) genes not fully represented, respectively. Overall, 515 protein coding genes contain hard-to-sequence regions, including 90 genes from ClinVar. Performance in variants detection was maximum at mean coverage >120×, while at 90× and 70× we measured a loss of variants of 3.2 and 4.5 %, respectively. WES using HiQ chemistry showed ~71/97.5 % sensitivity, ~37/2 % FDR and ~0.66/0.98 F1 score for indels and SNPs, respectively. The proposed low, medium or high-stringency filters reduced the amount of false positives by 10.2, 21.2 and 40.4 % for indels and 21.2, 41.9 and 68.2 % for SNP, respectively. Amplicon-based WES on Ion Proton platform using HiQ chemistry emerged as a competitive approach, with improved accuracy in variants identification. False-positive variants remain an issue for the Ion Torrent technology, but our filtering strategy can be applied to reduce erroneous variants.

  14. Validation of KENO V.a Comparison with Critical Experiments

    SciTech Connect

    Jordan, W.C.

    1999-01-01

    Section 1 of this report documents the validation of KENO V.a against 258 critical experiments. Experiments considered were primarily high or low enriched uranium systems. The results indicate that the KENO V.a Monte Carlo Criticality Program accurately calculates a broad range of critical experiments. A substantial number of the calculations showed a positive or negative bias in excess of 1 1/2% in k-effective (k{sub eff}). Classes of criticals which show a bias include 3% enriched green blocks, highly enriched uranyl fluoride slab arrays, and highly enriched uranyl nitrate arrays. If these biases are properly taken into account, the KENO V.a code can be used with confidence for the design and criticality safety analysis of uranium-containing systems. Section 2 of this report documents the results of investigation into the cause of the bias observed in Sect. 1. The results of this study indicate that the bias seen in Sect. 1 is caused by code bias, cross-section bias, reporting bias, and modeling bias. There is evidence that many of the experiments used in this validation and in previous validations are not adequately documented. The uncertainty in the experimental parameters overshadows bias caused by the code and cross sections and prohibits code validation to better than about 1% in k{sub eff}.

  15. Gene-specific amplicons from metagenomes as an alternative to directed evolution for enzyme screening: a case study using phenylacetaldehyde reductases.

    PubMed

    Itoh, Nobuya; Kazama, Miki; Takeuchi, Nami; Isotani, Kentaro; Kurokawa, Junji

    2016-06-01

    Screening gene-specific amplicons from metagenomes (S-GAM) is a highly promising technique for the isolation of genes encoding enzymes for biochemical and industrial applications. From metagenomes, we isolated phenylacetaldehyde reductase (par) genes, which code for an enzyme that catalyzes the production of various Prelog's chiral alcohols. Nearly full-length par genes were amplified by PCR from metagenomic DNA, the products of which were fused with engineered par sequences at both terminal regions of the expression vector to ensure proper expression and then used to construct Escherichia coli plasmid libraries. Sequence- and activity-based screening of these libraries identified different homologous par genes, Hpar-001 to -036, which shared more than 97% amino acid sequence identity with PAR. Comparative characterization of these active homologs revealed a wide variety of enzymatic properties including activity, substrate specificity, and thermal stability. Moreover, amino acid substitutions in these genes coincided with those of Sar268 and Har1 genes, which were independently engineered by error-prone PCR to exhibit increased activity in the presence of concentrated 2-propanol. The comparative data from both approaches suggest that sequence information from homologs isolated from metagenomes is quite useful for enzyme engineering. Furthermore, by examining the GAM-based sequence dataset derived from soil metagenomes, we easily found amino acid substitutions that increase the thermal stability of PAR/PAR homologs. Thus, GAM-based approaches can provide not only useful homologous enzymes but also an alternative to directed evolution methodologies. PMID:27419059

  16. The VA Maryland Health Care System's telemental health program.

    PubMed

    Koch, Edward F

    2012-05-01

    The VA Maryland Health Care System introduced videoconferencing technology to provide psychiatry, evidenced-based psychotherapy, case management, and patient education at rural clinics where it was difficult to recruit providers. Telemental health services enable rural clinics to offer additional services, such as case management and patient education. Services have been expanded to urban outpatient clinics where a limited number of mental health clinic hours are available. This technology expands the availability of mental health providers and services, allowing patients to receive services from providers located at distant medical centers.

  17. Genotyping-in-Thousands by sequencing (GT-seq): A cost effective SNP genotyping method based on custom amplicon sequencing.

    PubMed

    Campbell, Nathan R; Harmon, Stephanie A; Narum, Shawn R

    2015-07-01

    Genotyping-in-Thousands by sequencing (GT-seq) is a method that uses next-generation sequencing of multiplexed PCR products to generate genotypes from relatively small panels (50-500) of targeted single-nucleotide polymorphisms (SNPs) for thousands of individuals in a single Illumina HiSeq lane. This method uses only unlabelled oligos and PCR master mix in two thermal cycling steps for amplification of targeted SNP loci. During this process, sequencing adapters and dual barcode sequence tags are incorporated into the amplicons enabling thousands of individuals to be pooled into a single sequencing library. Post sequencing, reads from individual samples are split into individual files using their unique combination of barcode sequences. Genotyping is performed with a simple perl script which counts amplicon-specific sequences for each allele, and allele ratios are used to determine the genotypes. We demonstrate this technique by genotyping 2068 individual steelhead trout (Oncorhynchus mykiss) samples with a set of 192 SNP markers in a single library sequenced in a single Illumina HiSeq lane. Genotype data were 99.9% concordant to previously collected TaqMan(™) genotypes at the same 192 loci, but call rates were slightly lower with GT-seq (96.4%) relative to Taqman (99.0%). Of the 192 SNPs, 187 were genotyped in ≥90% of the individual samples and only 3 SNPs were genotyped in <70% of samples. This study demonstrates amplicon sequencing with GT-seq greatly reduces the cost of genotyping hundreds of targeted SNPs relative to existing methods by utilizing a simple library preparation method and massive efficiency of scale.

  18. CloVR-ITS: Automated internal transcribed spacer amplicon sequence analysis pipeline for the characterization of fungal microbiota

    PubMed Central

    2013-01-01

    Background Besides the development of comprehensive tools for high-throughput 16S ribosomal RNA amplicon sequence analysis, there exists a growing need for protocols emphasizing alternative phylogenetic markers such as those representing eukaryotic organisms. Results Here we introduce CloVR-ITS, an automated pipeline for comparative analysis of internal transcribed spacer (ITS) pyrosequences amplified from metagenomic DNA isolates and representing fungal species. This pipeline performs a variety of steps similar to those commonly used for 16S rRNA amplicon sequence analysis, including preprocessing for quality, chimera detection, clustering of sequences into operational taxonomic units (OTUs), taxonomic assignment (at class, order, family, genus, and species levels) and statistical analysis of sample groups of interest based on user-provided information. Using ITS amplicon pyrosequencing data from a previous human gastric fluid study, we demonstrate the utility of CloVR-ITS for fungal microbiota analysis and provide runtime and cost examples, including analysis of extremely large datasets on the cloud. We show that the largest fractions of reads from the stomach fluid samples were assigned to Dothideomycetes, Saccharomycetes, Agaricomycetes and Sordariomycetes but that all samples were dominated by sequences that could not be taxonomically classified. Representatives of the Candida genus were identified in all samples, most notably C. quercitrusa, while sequence reads assigned to the Aspergillus genus were only identified in a subset of samples. CloVR-ITS is made available as a pre-installed, automated, and portable software pipeline for cloud-friendly execution as part of the CloVR virtual machine package (http://clovr.org). Conclusion The CloVR-ITS pipeline provides fungal microbiota analysis that can be complementary to bacterial 16S rRNA and total metagenome sequence analysis allowing for more comprehensive studies of environmental and host-associated microbial

  19. The VA advantage: the gold standard in clinical informatics.

    PubMed

    Morgan, Matthew W

    2005-01-01

    How does a healthcare organization undergo such transformation as described in the lead paper in eight short years? Just imagine being part of an organization that achieved the following transformations: (1) reduction in hospital and long-term-care beds from 92,000 to 53,000 and an increase in outpatient clinics from 200 to 850 (2) a 75% increase in the number of patients treated on an annual basis (from 2.8 million to 4.9 million) with only a 32% cumulative increase in budget (from $19 billion to $25 billion) (3) clinicians who have access to complete medical records for almost all patient visits and all care settings (4) clinicians who willingly enter medication orders 94% of the time (5) patients who are increasingly satisfied with their care, ranking the service consistently higher than the competition (6) improved patient outcomes, achieved at costs 25% less than the competition. Such transformation is impossible to achieve without vision, leadership, talent, teamwork and tools. I will restrict my comments to a discussion of the tools, specifically the VA's clinical information system (VistA, HealtheVet, My HealtheVet. However, it is important to note that the results described in this paper would not be possible without the VA's transformational leadership and dedicated teams of professionals capable of executing the vision.

  20. Use of VA and Medicare Services By Dually Eligible Veterans with Psychiatric Problems

    PubMed Central

    Carey, Kathleen; Montez-Rath, Maria E; Rosen, Amy K; Christiansen, Cindy L; Loveland, Susan; Ettner, Susan L

    2008-01-01

    Objective To examine how service accessibility measured by geographic distance affects service sector choices for veterans who are dually eligible for veterans affairs (VA) and Medicare services and who are diagnosed with mental health and/or substance abuse (MH/SA) disorders. Data Sources Primary VA data sources were the Patient Treatment (acute care), Extended Care (long-term care), and Outpatient Clinic files. VA cost data were obtained from (1) inpatient and outpatient cost files developed by the VA Health Economics and Resource Center and (2) outpatient VA Decision Support System files. Medicare data sources were the denominator, Medicare Provider Analysis Review (MEDPAR), Provider-of-Service, Outpatient Standard Analytic and Physician/Supplier Standard Analytic files. Additional sources included the Area Resource File and Census Bureau data. Study Design We identified dually eligible veterans who had either an inpatient or outpatient MH/SA diagnosis in the VA system during fiscal year (FY)'99. We then estimated one- and two-part regression models to explain the effects of geographic distance on both VA and Medicare total and MH/SA costs. Principal Findings Results provide evidence for substitution between the VA and Medicare, demonstrating that poorer geographic access to VA inpatient and outpatient clinics decreased VA expenditures but increased Medicare expenditures, while poorer access to Medicare-certified general and psychiatric hospitals decreased Medicare expenditures but increased VA expenditures. Conclusions As geographic distance to VA medical facility increases, Medicare plays an increasingly important role in providing mental health services to veterans. PMID:18355256

  1. KENO V.a Primer: A Primer for Criticality Calculations with SCALE/KENO V.a Using CSPAN for Input

    SciTech Connect

    Busch, R.D.

    2003-01-17

    The SCALE (Standardized Computer Analyses for Licensing Evaluation) computer software system developed at Oak Ridge National Laboratory (ORNL) is widely used and accepted around the world for criticality safety analyses. The well-known KENO V.a three-dimensional Monte Carlo criticality computer code is the primary criticality safety analysis tool in SCALE. The KENO V.a primer is designed to help a new user understand and use the SCALE/KENO V.a Monte Carlo code for nuclear criticality safety analyses. It assumes that the user has a college education in a technical field. There is no assumption of familiarity with Monte Carlo codes in general or with SCALE/KENO V.a in particular. The primer is designed to teach by example, with each example illustrating two or three features of SCALE/KENO V.a that are useful in criticality analyses. The primer is based on SCALE 4.4a, which includes the Criticality Safety Processor for Analysis (CSPAN) input processor for Windows personal computers (PCs). A second edition of the primer, which uses the new KENO Visual Editor, is currently under development at ORNL and is planned for publication in late 2003. Each example in this first edition of the primer uses CSPAN to provide the framework for data input. Starting with a Quickstart section, the primer gives an overview of the basic requirements for SCALE/KENO V.a input and allows the user to quickly run a simple criticality problem with SCALE/KENO V.a. The sections that follow Quickstart include a list of basic objectives at the beginning that identifies the goal of the section and the individual SCALE/KENO V.a features which are covered in detail in the example problems in that section. Upon completion of the primer, a new user should be comfortable using CSPAN to set up criticality problems in SCALE/KENO V.a.

  2. Improved Efficiency and Reliability of NGS Amplicon Sequencing Data Analysis for Genetic Diagnostic Procedures Using AGSA Software

    PubMed Central

    Poulet, Axel; Privat, Maud; Viala, Sandrine; Decousus, Stephanie; Perin, Axel; Lafarge, Laurence; Ollier, Marie; El Saghir, Nagi S.

    2016-01-01

    Screening for BRCA mutations in women with familial risk of breast or ovarian cancer is an ideal situation for high-throughput sequencing, providing large amounts of low cost data. However, 454, Roche, and Ion Torrent, Thermo Fisher, technologies produce homopolymer-associated indel errors, complicating their use in routine diagnostics. We developed software, named AGSA, which helps to detect false positive mutations in homopolymeric sequences. Seventy-two familial breast cancer cases were analysed in parallel by amplicon 454 pyrosequencing and Sanger dideoxy sequencing for genetic variations of the BRCA genes. All 565 variants detected by dideoxy sequencing were also detected by pyrosequencing. Furthermore, pyrosequencing detected 42 variants that were missed with Sanger technique. Six amplicons contained homopolymer tracts in the coding sequence that were systematically misread by the software supplied by Roche. Read data plotted as histograms by AGSA software aided the analysis considerably and allowed validation of the majority of homopolymers. As an optimisation, additional 250 patients were analysed using microfluidic amplification of regions of interest (Access Array Fluidigm) of the BRCA genes, followed by 454 sequencing and AGSA analysis. AGSA complements a complete line of high-throughput diagnostic sequence analysis, reducing time and costs while increasing reliability, notably for homopolymer tracts. PMID:27656653

  3. Quantitation of parvovirus B19 DNA sequences by competitive PCR: differential hybridization of the amplicons and immunoenzymatic detection on microplate.

    PubMed

    Gallinella, G; Zerbini, M; Musiani, M; Venturoli, S; Gentilomi, G; Manaresi, E

    1997-04-01

    A competitive PCR assay was developed to quantify B19 DNA sequences. Target and internal standard sequences were co-amplified by the same set of primers. The internal standard competitor was constructed by recombinant PCR and differed from the original genome sequence in a 21-bp mutagenized fragment, internal to the region amplified by the same set of primers. The internal standard competitor was cloned in a plasmid vector and the cloned fragment used in all the experiments. Target and internal standard sequences were labelled with digoxigenin during the co-amplification reaction and the different amplicons were detected in two separate hybridization reactions by biotinylated probes specific for the original 21-bp sequence or the mutagenized one. Hybridized amplicons were captured onto streptavidin-oated microtitre wells and detected by anti-digoxigenin antibodies conjugated to peroxidase. The chromogenic reaction for peroxidase was quantitatively evaluated by optical density determination. The titration curve subsequently developed showed a linear relationship over the range 10(2) to 10(5) genome copies, thus obtaining an exact quantitative evaluation over a wide range together with good sensitivity. Nine reference serum samples positive for B19 DNA and eight negative serum samples were tested by the competitive PCR assay for the quantitation of B19 DNA sequences.

  4. Improved Efficiency and Reliability of NGS Amplicon Sequencing Data Analysis for Genetic Diagnostic Procedures Using AGSA Software

    PubMed Central

    Poulet, Axel; Privat, Maud; Viala, Sandrine; Decousus, Stephanie; Perin, Axel; Lafarge, Laurence; Ollier, Marie; El Saghir, Nagi S.

    2016-01-01

    Screening for BRCA mutations in women with familial risk of breast or ovarian cancer is an ideal situation for high-throughput sequencing, providing large amounts of low cost data. However, 454, Roche, and Ion Torrent, Thermo Fisher, technologies produce homopolymer-associated indel errors, complicating their use in routine diagnostics. We developed software, named AGSA, which helps to detect false positive mutations in homopolymeric sequences. Seventy-two familial breast cancer cases were analysed in parallel by amplicon 454 pyrosequencing and Sanger dideoxy sequencing for genetic variations of the BRCA genes. All 565 variants detected by dideoxy sequencing were also detected by pyrosequencing. Furthermore, pyrosequencing detected 42 variants that were missed with Sanger technique. Six amplicons contained homopolymer tracts in the coding sequence that were systematically misread by the software supplied by Roche. Read data plotted as histograms by AGSA software aided the analysis considerably and allowed validation of the majority of homopolymers. As an optimisation, additional 250 patients were analysed using microfluidic amplification of regions of interest (Access Array Fluidigm) of the BRCA genes, followed by 454 sequencing and AGSA analysis. AGSA complements a complete line of high-throughput diagnostic sequence analysis, reducing time and costs while increasing reliability, notably for homopolymer tracts.

  5. |SE|S|AM|E| Barcode: NGS-oriented software for amplicon characterization--application to species and environmental barcoding.

    PubMed

    Piry, S; Guivier, E; Realini, A; Martin, J-F

    2012-11-01

    Progress in NGS technologies has opened up new opportunities for characterizing biodiversity, both for individual specimen identification and for environmental barcoding. Although the amount of data available to biologist is increasing, user-friendly tools to facilitate data analysis have yet to be developed. Our aim, with |SE|S|AM|E| Barcode, is to provide such support through a unified platform. The sequences are analysed through a pipeline that (i) processes NGS amplicon runs, filtering markers and samples, (ii) builds reference libraries and finally (iii) identifies (barcodes) the sequences in each amplicon from the reference library. We use a simulated data set for specimen identification and a recently published data set for environmental barcoding to validate the method. The results obtained are consistent with the expected characterizations (in silico and previously published, respectively). |SE|S|AM|E| Barcode and its documentation are freely available under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported Licence for Windows and Linux from http://www1.montpellier.inra.fr/CBGP/NGS/.

  6. RiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to metagenomes

    PubMed Central

    Zhang, Yanming; Ji, Peifeng; Wang, Jinfeng; Zhao, Fangqing

    2016-01-01

    16S rRNA amplicon analysis and shotgun metagenome sequencing are two main culture-independent strategies to explore the genetic landscape of various microbial communities. Recently, numerous studies have employed these two approaches together, but downstream data analyses were performed separately, which always generated incongruent or conflict signals on both taxonomic and functional classifications. Here we propose a novel approach, RiboFR-Seq (Ribosomal RNA gene flanking region sequencing), for capturing both ribosomal RNA variable regions and their flanking protein-coding genes simultaneously. Through extensive testing on clonal bacterial strain, salivary microbiome and bacterial epibionts of marine kelp, we demonstrated that RiboFR-Seq could detect the vast majority of bacteria not only in well-studied microbiomes but also in novel communities with limited reference genomes. Combined with classical amplicon sequencing and shotgun metagenome sequencing, RiboFR-Seq can link the annotations of 16S rRNA and metagenomic contigs to make a consensus classification. By recognizing almost all 16S rRNA copies, the RiboFR-seq approach can effectively reduce the taxonomic abundance bias resulted from 16S rRNA copy number variation. We believe that RiboFR-Seq, which provides an integrated view of 16S rRNA profiles and metagenomes, will help us better understand diverse microbial communities. PMID:26984526

  7. A Method for Amplicon Deep Sequencing of Drug Resistance Genes in Plasmodium falciparum Clinical Isolates from India.

    PubMed

    Rao, Pavitra N; Uplekar, Swapna; Kayal, Sriti; Mallick, Prashant K; Bandyopadhyay, Nabamita; Kale, Sonal; Singh, Om P; Mohanty, Akshaya; Mohanty, Sanjib; Wassmer, Samuel C; Carlton, Jane M

    2016-06-01

    A major challenge to global malaria control and elimination is early detection and containment of emerging drug resistance. Next-generation sequencing (NGS) methods provide the resolution, scalability, and sensitivity required for high-throughput surveillance of molecular markers of drug resistance. We have developed an amplicon sequencing method on the Ion Torrent PGM platform for targeted resequencing of a panel of six Plasmodium falciparum genes implicated in resistance to first-line antimalarial therapy, including artemisinin combination therapy, chloroquine, and sulfadoxine-pyrimethamine. The protocol was optimized using 12 geographically diverse P. falciparum reference strains and successfully applied to multiplexed sequencing of 16 clinical isolates from India. The sequencing results from the reference strains showed 100% concordance with previously reported drug resistance-associated mutations. Single-nucleotide polymorphisms (SNPs) in clinical isolates revealed a number of known resistance-associated mutations and other nonsynonymous mutations that have not been implicated in drug resistance. SNP positions containing multiple allelic variants were used to identify three clinical samples containing mixed genotypes indicative of multiclonal infections. The amplicon sequencing protocol has been designed for the benchtop Ion Torrent PGM platform and can be operated with minimal bioinformatics infrastructure, making it ideal for use in countries that are endemic for the disease to facilitate routine large-scale surveillance of the emergence of drug resistance and to ensure continued success of the malaria treatment policy.

  8. A portable automatic endpoint detection system for amplicons of loop mediated isothermal amplification on microfluidic compact disk platform.

    PubMed

    Uddin, Shah Mukim; Ibrahim, Fatimah; Sayad, Abkar Ahmed; Thiha, Aung; Pei, Koh Xiu; Mohktar, Mas S; Hashim, Uda; Cho, Jongman; Thong, Kwai Lin

    2015-01-01

    In recent years, many improvements have been made in foodborne pathogen detection methods to reduce the impact of food contamination. Several rapid methods have been developed with biosensor devices to improve the way of performing pathogen detection. This paper presents an automated endpoint detection system for amplicons generated by loop mediated isothermal amplification (LAMP) on a microfluidic compact disk platform. The developed detection system utilizes a monochromatic ultraviolet (UV) emitter for excitation of fluorescent labeled LAMP amplicons and a color sensor to detect the emitted florescence from target. Then it processes the sensor output and displays the detection results on liquid crystal display (LCD). The sensitivity test has been performed with detection limit up to 2.5 × 10(-3) ng/µL with different DNA concentrations of Salmonella bacteria. This system allows a rapid and automatic endpoint detection which could lead to the development of a point-of-care diagnosis device for foodborne pathogens detection in a resource-limited environment. PMID:25751077

  9. A Method for Amplicon Deep Sequencing of Drug Resistance Genes in Plasmodium falciparum Clinical Isolates from India

    PubMed Central

    Rao, Pavitra N.; Uplekar, Swapna; Kayal, Sriti; Mallick, Prashant K.; Bandyopadhyay, Nabamita; Kale, Sonal; Singh, Om P.; Mohanty, Akshaya; Mohanty, Sanjib; Wassmer, Samuel C.

    2016-01-01

    A major challenge to global malaria control and elimination is early detection and containment of emerging drug resistance. Next-generation sequencing (NGS) methods provide the resolution, scalability, and sensitivity required for high-throughput surveillance of molecular markers of drug resistance. We have developed an amplicon sequencing method on the Ion Torrent PGM platform for targeted resequencing of a panel of six Plasmodium falciparum genes implicated in resistance to first-line antimalarial therapy, including artemisinin combination therapy, chloroquine, and sulfadoxine-pyrimethamine. The protocol was optimized using 12 geographically diverse P. falciparum reference strains and successfully applied to multiplexed sequencing of 16 clinical isolates from India. The sequencing results from the reference strains showed 100% concordance with previously reported drug resistance-associated mutations. Single-nucleotide polymorphisms (SNPs) in clinical isolates revealed a number of known resistance-associated mutations and other nonsynonymous mutations that have not been implicated in drug resistance. SNP positions containing multiple allelic variants were used to identify three clinical samples containing mixed genotypes indicative of multiclonal infections. The amplicon sequencing protocol has been designed for the benchtop Ion Torrent PGM platform and can be operated with minimal bioinformatics infrastructure, making it ideal for use in countries that are endemic for the disease to facilitate routine large-scale surveillance of the emergence of drug resistance and to ensure continued success of the malaria treatment policy. PMID:27008882

  10. A Portable Automatic Endpoint Detection System for Amplicons of Loop Mediated Isothermal Amplification on Microfluidic Compact Disk Platform

    PubMed Central

    Uddin, Shah Mukim; Ibrahim, Fatimah; Sayad, Abkar Ahmed; Thiha, Aung; Pei, Koh Xiu; Mohktar, Mas S.; Hashim, Uda; Cho, Jongman; Thong, Kwai Lin

    2015-01-01

    In recent years, many improvements have been made in foodborne pathogen detection methods to reduce the impact of food contamination. Several rapid methods have been developed with biosensor devices to improve the way of performing pathogen detection. This paper presents an automated endpoint detection system for amplicons generated by loop mediated isothermal amplification (LAMP) on a microfluidic compact disk platform. The developed detection system utilizes a monochromatic ultraviolet (UV) emitter for excitation of fluorescent labeled LAMP amplicons and a color sensor to detect the emitted florescence from target. Then it processes the sensor output and displays the detection results on liquid crystal display (LCD). The sensitivity test has been performed with detection limit up to 2.5 × 10−3 ng/µL with different DNA concentrations of Salmonella bacteria. This system allows a rapid and automatic endpoint detection which could lead to the development of a point-of-care diagnosis device for foodborne pathogens detection in a resource-limited environment. PMID:25751077

  11. Employing 454 amplicon pyrosequencing to reveal intragenomic divergence in the internal transcribed spacer rDNA region in fungi

    PubMed Central

    Lindner, Daniel L; Carlsen, Tor; Henrik Nilsson, R; Davey, Marie; Schumacher, Trond; Kauserud, Håvard

    2013-01-01

    The rDNA internal transcribed spacer (ITS) region has been accepted as a DNA barcoding marker for fungi and is widely used in phylogenetic studies; however, intragenomic ITS variability has been observed in a broad range of taxa, including prokaryotes, plants, animals, and fungi, and this variability has the potential to inflate species richness estimates in molecular investigations of environmental samples. In this study 454 amplicon pyrosequencing of the ITS1 region was applied to 99 phylogenetically diverse axenic single-spore cultures of fungi (Dikarya: Ascomycota and Basidiomycota) to investigate levels of intragenomic variation. Three species (one Basidiomycota and two Ascomycota), in addition to a positive control species known to contain ITS paralogs, displayed levels of molecular variation indicative of intragenomic variation; taxon inflation due to presumed intragenomic variation was ≈9%. Intragenomic variability in the ITS region appears to be widespread but relatively rare in fungi (≈3–5% of species investigated in this study), suggesting this problem may have minor impacts on species richness estimates relative to PCR and/or pyrosequencing errors. Our results indicate that 454 amplicon pyrosequencing represents a powerful tool for investigating levels of ITS intragenomic variability across taxa, which may be valuable for better understanding the fundamental mechanisms underlying concerted evolution of repetitive DNA regions. PMID:23789083

  12. HSV-1 amplicon vectors that direct the in situ production of foot-and-mouth disease virus antigens in mammalian cells can be used for genetic immunization.

    PubMed

    D'Antuono, Alejandra; Laimbacher, Andrea S; La Torre, Jose; Tribulatti, Virginia; Romanutti, Carina; Zamorano, Patricia; Quattrocchi, Valeria; Schraner, Elisabeth M; Ackermann, Mathias; Fraefel, Cornel; Mattion, Nora

    2010-10-28

    HSV-1 amplicon vectors encoding heterologous antigens were capable to mediate in situ generation of protein synthesis and to generate a specific immune response to the corresponding antigens. In this study, foot-and-mouth disease (FMD) virus antigens were used to generate a genetic vaccine prototype. The amplicons were designed to provide a high safety profile as they do not express any HSV-1 genes when packaged using a helper virus-free system, and they are able to encapsidate several copies of the transgene or allow the simultaneous expression of different genes. Virus-like particles were produced after cell processing of the delivered DNA. Inoculation of mice with 5 × 10(5) transducing units of amplicon vectors resulted in FMDV-specific humoral responses in the absence of adjuvants, which were dependent on the in situ de novo production of the vector-encoded antigens. Challenge of mice vaccinated with these amplicons with a high dose of live virus, resulted in partial protection, with a significant reduction of viremia. This work highlights the potential use of a HSV-1 amplicon vector platform for generation of safe genetic vaccines. PMID:20851082

  13. Upregulated, 7q21-22 amplicon candidate gene SHFM1 confers oncogenic advantage by suppressing p53 function in gastric cancer.

    PubMed

    Tamilzhalagan, Sembulingam; Muthuswami, Muthulakshmi; Periasamy, Jayaprakash; Lee, Ming Hui; Rha, Sun Young; Tan, Patrick; Ganesan, Kumaresan

    2015-06-01

    Chromosomal aberrations are hallmarks of cancers and the locus of frequent genomic amplifications often harbors key cancer driver genes. Many genomic amplicons remain larger with hundreds of genes and the key drivers remain to be identified by an amplification-wide systematic analysis. The 7q21.12-q22.3 genomic amplification is frequent in gastric cancers which occur in ~10% of the patients and multiple cell lines. This 7q21.12-q22.3 amplicon has not yet been completely analyzed towards identifying the driver genes and their functional contribution in oncogenesis. The amplitude and prevalence indicate the important role conferred by this amplicon in gastric cancers. Among the 159 genes of this amplicon, 12 genes are found over-expressed in primary gastric tumors and cell lines. Many of the over-expressed genes show negative association with p53 transcriptional activity. RNAi based functional screening of the genes reveal, SHFM1 as key gastric cancer driver gene. SHFM1 confers cell cycle progression and resistance to p53 stabilizing drugs in gastric cancer cells. SHFM1 also activates Src, MAPK/ERK and PI3K/Akt signaling pathways. This is the first integrative genomic investigation of 7q21.12-q22.3 amplicon revealing the potential oncogenic candidacy of 12 genes. The oncogenic contribution of SHFM1, mediated by the p53 suppressive feature has been demonstrated in gastric cancer cells.

  14. HSV-1 amplicon vectors that direct the in situ production of foot-and-mouth disease virus antigens in mammalian cells can be used for genetic immunization.

    PubMed

    D'Antuono, Alejandra; Laimbacher, Andrea S; La Torre, Jose; Tribulatti, Virginia; Romanutti, Carina; Zamorano, Patricia; Quattrocchi, Valeria; Schraner, Elisabeth M; Ackermann, Mathias; Fraefel, Cornel; Mattion, Nora

    2010-10-28

    HSV-1 amplicon vectors encoding heterologous antigens were capable to mediate in situ generation of protein synthesis and to generate a specific immune response to the corresponding antigens. In this study, foot-and-mouth disease (FMD) virus antigens were used to generate a genetic vaccine prototype. The amplicons were designed to provide a high safety profile as they do not express any HSV-1 genes when packaged using a helper virus-free system, and they are able to encapsidate several copies of the transgene or allow the simultaneous expression of different genes. Virus-like particles were produced after cell processing of the delivered DNA. Inoculation of mice with 5 × 10(5) transducing units of amplicon vectors resulted in FMDV-specific humoral responses in the absence of adjuvants, which were dependent on the in situ de novo production of the vector-encoded antigens. Challenge of mice vaccinated with these amplicons with a high dose of live virus, resulted in partial protection, with a significant reduction of viremia. This work highlights the potential use of a HSV-1 amplicon vector platform for generation of safe genetic vaccines.

  15. Calculations on various total cross-sections of electron impact on group VA - atoms-threshold to 2000 eV

    NASA Astrophysics Data System (ADS)

    Joshipura, K. N.; Gangopadhyay, Sumona; Kothari, Harshit N.; Shelat, Foram A.

    2009-11-01

    In this paper we have calculated various total cross-sections of Nitrogen, Phosphorus, Arsenic, Antimony and Bismuth (Group VA-atoms) in the energy range of 15 to 2000 eV. Spherical Complex potential formalism is used to derive total as well as inelastic cross-sections. We have developed CSP-ic method by which we can extract ionization cress-section from the inelastic cross-section. Our results are compared with available theoretical and experimental data.

  16. Parallelization of KENO-Va Monte Carlo code

    NASA Astrophysics Data System (ADS)

    Ramón, Javier; Peña, Jorge

    1995-07-01

    KENO-Va is a code integrated within the SCALE system developed by Oak Ridge that solves the transport equation through the Monte Carlo Method. It is being used at the Consejo de Seguridad Nuclear (CSN) to perform criticality calculations for fuel storage pools and shipping casks. Two parallel versions of the code: one for shared memory machines and other for distributed memory systems using the message-passing interface PVM have been generated. In both versions the neutrons of each generation are tracked in parallel. In order to preserve the reproducibility of the results in both versions, advanced seeds for random numbers were used. The CONVEX C3440 with four processors and shared memory at CSN was used to implement the shared memory version. A FDDI network of 6 HP9000/735 was employed to implement the message-passing version using proprietary PVM. The speedup obtained was 3.6 in both cases.

  17. Development of 30 kVA class fully superconducting generator

    SciTech Connect

    Tsukamoto, O.; Amemiya, N.; Takao, T. . Faculty of Engineering); Akita, S. ); Ohishi, K.; Shimuzu, H.; Tanaka, Y. ); Uchikawa, Y. )

    1992-01-01

    This paper reports that the authors are developing a 4 poles 30 kVA class fully superconducting generator to investigate the characteristics of superconducting armature winding subject to the rotating magnetic field produced by the superconducting rotor and behavior of a superconducting generator connected to an electric power utility grid. A static test of the armature winding have been performed by applying 50 Hz AC current. AC quench currents of the armature windings have reached to 200 Arms after several quenches which was well over the rated current. A static test of the field windings have been also performed to verify its rated performance. In the paper, detailed configurations and electrical test results of the generator are shown.

  18. The Impact of VA and Navy Hospital Collaboration on Medical School Education

    ERIC Educational Resources Information Center

    Atre-Vaidya, Nutan; Ross, Arthur, III; Sandu, Ioana C.; Hassan, Tariq

    2009-01-01

    Objective: The U.S. Department of Veterans Affairs (VA) is the largest single provider of medical education in the United States and is often the preferred training site for medical students and residents. However, changing priorities of patients and the marketplace are forcing medical schools and the VA to consider new ways of practicing medicine…

  19. 30 CFR 57.22229 - Weekly testing (I-A, III, and V-A mines).

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Weekly testing (I-A, III, and V-A mines). 57.22229 Section 57.22229 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR...-A, III, and V-A mines). (a) The mine atmosphere shall be tested for methane and carbon monoxide...

  20. 30 CFR 57.22229 - Weekly testing (I-A, III, and V-A mines).

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 30 Mineral Resources 1 2014-07-01 2014-07-01 false Weekly testing (I-A, III, and V-A mines). 57.22229 Section 57.22229 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR...-A, III, and V-A mines). (a) The mine atmosphere shall be tested for methane and carbon monoxide...

  1. 30 CFR 57.22229 - Weekly testing (I-A, III, and V-A mines).

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Weekly testing (I-A, III, and V-A mines). 57.22229 Section 57.22229 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR...-A, III, and V-A mines). (a) The mine atmosphere shall be tested for methane and carbon monoxide...

  2. Making Bullying Prevention a Priority in Finnish Schools: The KiVa Antibullying Program

    ERIC Educational Resources Information Center

    Salmivalli, Christina; Poskiparta, Elisa

    2012-01-01

    The KiVa antibullying program has been widely implemented in Finnish comprehensive schools since 2009. The program is predicated on the idea that a positive change in the behaviors of classmates can reduce the rewards gained by the perpetrators of bullying and consequently their motivation to bully in the first place. KiVa involves both universal…

  3. 48 CFR 852.219-9 - VA Small business subcontracting plan minimum requirements.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... review of personnel in the Office of Small and Disadvantaged Business Utilization. (e) The contractor may... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false VA Small business... Provisions and Clauses 852.219-9 VA Small business subcontracting plan minimum requirements. As prescribed...

  4. 77 FR 21158 - VA Directive 0005 on Scientific Integrity: Availability for Review and Comment

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-09

    ... AFFAIRS VA Directive 0005 on Scientific Integrity: Availability for Review and Comment AGENCY: Office of... (VA) Directive 0005 on Scientific Integrity. The Draft Directive incorporates the principles of scientific integrity contained in the Presidential Memorandum of March 9, 2009, and the Director, Office...

  5. 33 CFR 334.350 - Chesapeake Bay off Fort Monroe, Va.; firing range danger zone.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ..., Va.; firing range danger zone. 334.350 Section 334.350 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE DANGER ZONE AND RESTRICTED AREA REGULATIONS § 334.350 Chesapeake Bay off Fort Monroe, Va.; firing range danger zone. (a) The danger zone. All of...

  6. 33 CFR 80.515 - Cape Henry, VA to Cape Hatteras, NC.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Cape Henry, VA to Cape Hatteras, NC. 80.515 Section 80.515 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Fifth District § 80.515 Cape Henry, VA...

  7. 33 CFR 80.515 - Cape Henry, VA to Cape Hatteras, NC.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Cape Henry, VA to Cape Hatteras, NC. 80.515 Section 80.515 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Fifth District § 80.515 Cape Henry, VA...

  8. 33 CFR 80.515 - Cape Henry, VA to Cape Hatteras, NC.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Cape Henry, VA to Cape Hatteras, NC. 80.515 Section 80.515 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Fifth District § 80.515 Cape Henry, VA...

  9. 33 CFR 80.515 - Cape Henry, VA to Cape Hatteras, NC.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Cape Henry, VA to Cape Hatteras, NC. 80.515 Section 80.515 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Fifth District § 80.515 Cape Henry, VA...

  10. 33 CFR 80.515 - Cape Henry, VA to Cape Hatteras, NC.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Cape Henry, VA to Cape Hatteras, NC. 80.515 Section 80.515 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Fifth District § 80.515 Cape Henry, VA...

  11. 78 FR 28949 - Fund Availability Under VA's Homeless Providers Grant and Per Diem Program (Rehabilitation)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-16

    ... AFFAIRS Fund Availability Under VA's Homeless Providers Grant and Per Diem Program (Rehabilitation) AGENCY... announces the availability of rehabilitation funds under VA's Homeless Providers Grant and Per Diem Program... local or state codes. Each rehabilitation funded program will submit quarterly reports to the Grant...

  12. Myosin Va Transports Dense Core Secretory Vesicles in Pancreatic MIN6 β-CellsV⃞

    PubMed Central

    Varadi, Aniko; Tsuboi, Takashi; Rutter, Guy A.

    2005-01-01

    The role of unconventional myosins in neuroendocrine cells is not fully understood, with involvement suggested in the movement of both secretory vesicles and mitochondria. Here, we demonstrate colocalization of myosin Va (MyoVa) with insulin in pancreatic β-cells and show that MyoVa copurifies with insulin in density gradients and with the vesicle marker phogrin-enhanced green fluorescent protein upon fluorescence-activated sorting of vesicles. By contrast, MyoVa immunoreactivity was poorly colocalized with mitochondrial or other markers. Demonstrating an important role for MyoVa in the recruitment of secretory vesicles to the cell surface, a reduction of MyoVa protein levels achieved by RNA interference caused a significant decrease in glucose- or depolarization-stimulated insulin secretion. Similarly, expression of the dominant-negative–acting globular tail domain of MyoVa decreased by ∼50% the number of vesicles docked at the plasma membrane and by 87% the number of depolarization-stimulated exocytotic events detected by total internal reflection fluorescence microscopy. We conclude that MyoVa-driven movements of vesicles along the cortical actin network are essential for the terminal stages of regulated exocytosis in β-cells. PMID:15788565

  13. 77 FR 23204 - VA Acquisition Regulation: Electronic Submission of Payment Requests

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-18

    ... waste in other agency programs and operations. Executive Order 13520 of November 20, 2009 (``Reducing... Electronic Invoicing Could Further Reduce Late Payments'' (GAO-06-358). The report confirmed the... using under VA's current interim electronic invoicing clause. See 74 FR 32223. VA's Electronic...

  14. 77 FR 3841 - Proposed Information Collection (Survey of Veteran Enrollees (Quality and Efficiency of VA Health...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-25

    ... Care)) Activities Under OMB Review AGENCY: Veterans Health Administration, Department of Veterans... VA Health Care), VA Form 10-21088. OMB Control Number: 2900-0725. Type of Review: Extension of a... promote quality and efficient delivery of health care through the use of health information...

  15. 76 FR 70831 - Proposed Information Collection (Survey of Veteran Enrollees (Quality and Efficiency of VA Health...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-15

    ... Care)) Activity; Comment Request AGENCY: Veterans Health Administration, Department of Veterans Affairs... Efficiency of VA Health Care), VA Form 10-21088. OMB Control Number: 2900-0725. Type of Review: Extension of... necessary to promote quality and efficient delivery of health care through the use of health...

  16. 33 CFR 334.130 - Atlantic Ocean off Wallops Island and Chincoteague Inlet, Va.; danger zone.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 3 2014-07-01 2014-07-01 false Atlantic Ocean off Wallops Island and Chincoteague Inlet, Va.; danger zone. 334.130 Section 334.130 Navigation and Navigable Waters... REGULATIONS § 334.130 Atlantic Ocean off Wallops Island and Chincoteague Inlet, Va.; danger zone. (a) The...

  17. 78 FR 56151 - Safety Zone, North Atlantic Ocean; Virginia Beach, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-12

    ... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone, North Atlantic Ocean; Virginia Beach, VA... zone on the navigable waters of the North Atlantic Ocean in Virginia Beach, VA to support the Virginia... over the navigable waters of the Atlantic Ocean. Due to the need to protect mariners and...

  18. 48 CFR 853.236-70 - VA Form 10-6298, Architect-Engineer Fee Proposal.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false VA Form 10-6298, Architect-Engineer Fee Proposal. 853.236-70 Section 853.236-70 Federal Acquisition Regulations System DEPARTMENT OF...-Engineer Fee Proposal. VA Form 10-6298, Architect-Engineer Fee Proposal, shall be used as prescribed in...

  19. 48 CFR 853.236-70 - VA Form 10-6298, Architect-Engineer Fee Proposal.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 48 Federal Acquisition Regulations System 5 2014-10-01 2014-10-01 false VA Form 10-6298, Architect-Engineer Fee Proposal. 853.236-70 Section 853.236-70 Federal Acquisition Regulations System DEPARTMENT OF...-Engineer Fee Proposal. VA Form 10-6298, Architect-Engineer Fee Proposal, shall be used as prescribed in...

  20. 48 CFR 853.236-70 - VA Form 10-6298, Architect-Engineer Fee Proposal.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 48 Federal Acquisition Regulations System 5 2012-10-01 2012-10-01 false VA Form 10-6298, Architect-Engineer Fee Proposal. 853.236-70 Section 853.236-70 Federal Acquisition Regulations System DEPARTMENT OF...-Engineer Fee Proposal. VA Form 10-6298, Architect-Engineer Fee Proposal, shall be used as prescribed in...

  1. 75 FR 54771 - Safety Zone; Thunder on the Bay, Chesapeake Bay, Buckroe Beach Park, Hampton, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-09

    ... Beach Park, Hampton, VA AGENCY: Coast Guard, DHS. ACTION: Temporary final rule. SUMMARY: The Coast Guard... a fireworks display on the Buckroe Beach Park Fishing Pier over the navigable waters of the...). This safety zone will be established in the vicinity of Buckroe Beach Park in Hampton, VA from 9:15...

  2. 77 FR 12697 - VA Homeless Providers Grant and Per Diem Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-01

    ...We propose to revise and reorganize regulations which contain the Department of Veterans Affairs' (VA) Homeless Providers Grant and Per Diem Program. This rulemaking would update our current regulations, implement and authorize new VA policies, and generally improve the clarity of part...

  3. 77 FR 39404 - Safety Zone; Wicomico Community Fireworks Rain Date, Great Wicomico River, Mila, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-03

    ... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; Wicomico Community Fireworks Rain Date..., VA in support of the Wicomico Community Rain Date Fireworks event. This action is necessary to.... 165.T05-0425 Safety Zone; Wicomico Community Fireworks Rain Date, Great Wicomico River, Mila, VA....

  4. Expanded Access to Non-VA Care Through the Veterans Choice Program. Interim final rule.

    PubMed

    2015-12-01

    The Department of Veterans Affairs (VA) revises its medical regulations that implement section 101 of the Veterans Access, Choice, and Accountability Act of 2014 (hereafter referred to as "the Choice Act"), which requires VA to establish a program to furnish hospital care and medical services through eligible non-VA health care providers to eligible veterans who either cannot be seen within the wait-time goals of the Veterans Health Administration (VHA) or who qualify based on their place of residence (hereafter referred to as the "Veterans Choice Program" or the "Program"). These regulatory revisions are required by the most recent amendments to the Choice Act made by the Construction Authorization and Choice Improvement Act of 2014, and by the Surface Transportation and Veterans Health Care Choice Improvement Act of 2015. The Construction Authorization and Choice Improvement Act of 2014 amended the Choice Act to define additional criteria that VA may use to determine that a veteran's travel to a VA medical facility is an "unusual or excessive burden," and the Surface Transportation and Veterans Health Care Choice Improvement Act of 2015 amended the Choice Act to cover all veterans enrolled in the VA health care system, remove the 60-day limit on an episode of care, modify the wait-time and 40-mile distance eligibility criteria, and expand provider eligibility based on criteria as determined by VA. This interim final rule revises VA regulations consistent with the changes made to the Choice Act as described above.

  5. 33 CFR 334.290 - Elizabeth River, Southern Branch, Va., naval restricted areas.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ..., Va., naval restricted areas. 334.290 Section 334.290 Navigation and Navigable Waters CORPS OF....290 Elizabeth River, Southern Branch, Va., naval restricted areas. (a) The areas—(1) St. Helena Annex Area. Beginning at a point at St. Helena Annex of the Norfolk Naval Shipyard, on the eastern shore...

  6. 75 FR 20774 - Establishment of Class E Airspace; Fort A.P. Hill, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-21

    ... final rule with a request for comments in the Federal Register on December 7, 2009 (74 FR 63974), Docket... Federal Aviation Administration 14 CFR Part 71 Establishment of Class E Airspace; Fort A.P. Hill, VA... Register December 7, 2009 that establishes Class E airspace at Fort A.P. Hill, VA. DATES: Effective...

  7. 78 FR 77204 - Proposed Information Collection (VA National Veterans Sports Programs and Special Event Surveys...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-20

    ... AFFAIRS Proposed Information Collection (VA National Veterans Sports Programs and Special Event Surveys... solicits comments on the information needed to evaluate the National Veterans Sports Programs and Special... ``OMB Control No. 2900-NEW (VA National Veterans Sports Programs and Special Event Surveys)'' in...

  8. 77 FR 48127 - Foreign-Trade Zone 20-Suffolk, VA; Notification of Proposed Production Activity, Usui...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-13

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF COMMERCE Foreign-Trade Zones Board Foreign-Trade Zone 20--Suffolk, VA; Notification of Proposed Production Activity, Usui International Corporation, (Diesel Engine Fuel Lines), Chesapeake, VA The Virginia Port Authority, grantee of FTZ 20, submitted a...

  9. 30 CFR 57.22309 - Methane monitors (V-A mines).

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 30 CFR part 18, and prevent starting of such equipment when methane levels reach 1.5 percent; and (3... 30 Mineral Resources 1 2014-07-01 2014-07-01 false Methane monitors (V-A mines). 57.22309 Section... Standards for Methane in Metal and Nonmetal Mines Equipment § 57.22309 Methane monitors (V-A mines)....

  10. 30 CFR 57.22309 - Methane monitors (V-A mines).

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 30 CFR part 18, and prevent starting of such equipment when methane levels reach 1.5 percent; and (3... 30 Mineral Resources 1 2013-07-01 2013-07-01 false Methane monitors (V-A mines). 57.22309 Section... Standards for Methane in Metal and Nonmetal Mines Equipment § 57.22309 Methane monitors (V-A mines)....

  11. 30 CFR 57.22309 - Methane monitors (V-A mines).

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 30 CFR part 18, and prevent starting of such equipment when methane levels reach 1.5 percent; and (3... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Methane monitors (V-A mines). 57.22309 Section... Standards for Methane in Metal and Nonmetal Mines Equipment § 57.22309 Methane monitors (V-A mines)....

  12. 38 CFR 74.26 - What types of business information will VA collect?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... VETERANS AFFAIRS (CONTINUED) VETERANS SMALL BUSINESS REGULATIONS Records Management § 74.26 What types of business information will VA collect? VA will examine a variety of business records. See § 74.12, “What is... 38 Pensions, Bonuses, and Veterans' Relief 2 2010-07-01 2010-07-01 false What types of...

  13. 78 FR 55777 - Proposed Information Collection (VA, National Veterans Sports Programs and Special Events, Event...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-11

    ... AFFAIRS Proposed Information Collection (VA, National Veterans Sports Programs and Special Events, Event... Events, Department of Veterans Affairs. ACTION: Notice. SUMMARY: The Office of National Veterans Sports Programs and Special Events (NVSP), Department of Veterans Affairs (VA), is announcing an opportunity...

  14. 38 CFR 17.96 - Medication prescribed by non-VA physicians.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2010-07-01 2010-07-01 false Medication prescribed by non-VA physicians. 17.96 Section 17.96 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS MEDICAL Outpatient Treatment § 17.96 Medication prescribed by non-VA physicians. Any prescription, which is not part of...

  15. 78 FR 56271 - FY 2014-2020 Draft VA Strategic Plan

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-12

    ... AFFAIRS FY 2014-2020 Draft VA Strategic Plan AGENCY: Department of Veterans Affairs. ACTION: Notice of... availability of the FY 2014-2020 Draft VA Strategic Plan (Strategic Plan) for public review and comment, as...). The Strategic Plan provides the Department's long-term direction and places a stronger emphasis...

  16. 75 FR 61858 - Proposed Information Collection (VA Request for Determination of Reasonable Value) Activity...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-06

    ... AFFAIRS Proposed Information Collection (VA Request for Determination of Reasonable Value) Activity... solicits comments for information needed to determine the reasonable value of properties for guaranteed or... Request for Determination of Reasonable Value, VA Form 26-1805 and 26-1805-1. OMB Control Number:...

  17. VA and HRS Local Coordination of Florida's Home-Based Services to the Elderly.

    ERIC Educational Resources Information Center

    Bradham, Douglas D.; Chico, Innette Mary

    Florida's District 12 Veterans Administration (VA) wanted to deliver medical case-management services to veterans not receiving home-based services due to the geographic restrictions of the VA's Hospital-Based Home Care Program. The Florida Department of Health and Rehabilitative Services (HRS) desired to demonstrate the effectiveness of nurse…

  18. 33 CFR 334.350 - Chesapeake Bay off Fort Monroe, Va.; firing range danger zone.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 3 2011-07-01 2011-07-01 false Chesapeake Bay off Fort Monroe, Va.; firing range danger zone. 334.350 Section 334.350 Navigation and Navigable Waters CORPS OF....350 Chesapeake Bay off Fort Monroe, Va.; firing range danger zone. (a) The danger zone. All of...

  19. 33 CFR 334.220 - Chesapeake Bay, south of Tangier Island, Va.; naval firing range.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 3 2011-07-01 2011-07-01 false Chesapeake Bay, south of Tangier Island, Va.; naval firing range. 334.220 Section 334.220 Navigation and Navigable Waters CORPS OF....220 Chesapeake Bay, south of Tangier Island, Va.; naval firing range. (a) The danger zone....

  20. 33 CFR 334.350 - Chesapeake Bay off Fort Monroe, Va.; firing range danger zone.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 3 2013-07-01 2013-07-01 false Chesapeake Bay off Fort Monroe, Va.; firing range danger zone. 334.350 Section 334.350 Navigation and Navigable Waters CORPS OF....350 Chesapeake Bay off Fort Monroe, Va.; firing range danger zone. (a) The danger zone. All of...

  1. 33 CFR 334.350 - Chesapeake Bay off Fort Monroe, Va.; firing range danger zone.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 3 2012-07-01 2012-07-01 false Chesapeake Bay off Fort Monroe, Va.; firing range danger zone. 334.350 Section 334.350 Navigation and Navigable Waters CORPS OF....350 Chesapeake Bay off Fort Monroe, Va.; firing range danger zone. (a) The danger zone. All of...

  2. 33 CFR 334.220 - Chesapeake Bay, south of Tangier Island, Va.; naval firing range.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 3 2014-07-01 2014-07-01 false Chesapeake Bay, south of Tangier Island, Va.; naval firing range. 334.220 Section 334.220 Navigation and Navigable Waters CORPS OF....220 Chesapeake Bay, south of Tangier Island, Va.; naval firing range. (a) The danger zone....

  3. 33 CFR 334.350 - Chesapeake Bay off Fort Monroe, Va.; firing range danger zone.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 3 2014-07-01 2014-07-01 false Chesapeake Bay off Fort Monroe, Va.; firing range danger zone. 334.350 Section 334.350 Navigation and Navigable Waters CORPS OF....350 Chesapeake Bay off Fort Monroe, Va.; firing range danger zone. (a) The danger zone. All of...

  4. 33 CFR 334.220 - Chesapeake Bay, south of Tangier Island, Va.; naval firing range.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 3 2012-07-01 2012-07-01 false Chesapeake Bay, south of Tangier Island, Va.; naval firing range. 334.220 Section 334.220 Navigation and Navigable Waters CORPS OF....220 Chesapeake Bay, south of Tangier Island, Va.; naval firing range. (a) The danger zone....

  5. 76 FR 67561 - Proposed Information Collection (VA Enrollment Certification) Activity: Comment Request

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-01

    ... information needed to determine the amount of educational benefits payable to claimants pursuing approved... use of other forms of information technology. Title: VA Enrollment Certification, VA Form 22-1999. OMB... educational program. The data is used to determine the amount of benefits payable and whether the...

  6. 77 FR 27118 - Safety Zone; Rocketts Red Glare Fireworks, Ancarrows Landing Park, James River, Richmond, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-09

    ..., VA in the Federal Register (76 FR 13525). We ] received no comments on the proposed rule. No public... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; Rocketts Red Glare Fireworks, Ancarrows... in Richmond, VA in support of the Rocketts Red Glare Fireworks event. This action is necessary...

  7. 78 FR 27882 - VA Veteran-Owned Small Business (VOSB) Verification Guidelines

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-13

    ... AFFAIRS 38 CFR Part 74 RIN 2900-AO63 VA Veteran-Owned Small Business (VOSB) Verification Guidelines AGENCY... and Disadvantaged Business Utilization (OSDBU) is currently reviewing its regulations governing the Department of Veterans Affairs (VA) Veteran-Owned Small Business (VOSB) Verification Program. OSDBU...

  8. 30 CFR 57.22309 - Methane monitors (V-A mines).

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 CFR part 18, and prevent starting of such equipment when methane levels reach 1.5 percent; and (3... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Methane monitors (V-A mines). 57.22309 Section... Standards for Methane in Metal and Nonmetal Mines Equipment § 57.22309 Methane monitors (V-A mines)....

  9. VA Health Professional Scholarship and Visual Impairment and Orientation and Mobility Professional Scholarship Programs. Final rule.

    PubMed

    2013-08-20

    The Department of Veterans Affairs (VA) is amending its VA Health Professional Scholarship Program (HPSP) regulations. VA is also establishing regulations for a new program, the Visual Impairment and Orientation and Mobility Professional Scholarship Program (VIOMPSP). These regulations comply with and implement sections 302 and 603 of the Caregivers and Veterans Omnibus Health Services Act of 2010 (the 2010 Act). Section 302 of the 2010 Act established the VIOMPSP, which authorizes VA to provide financial assistance to certain students seeking a degree in visual impairment or orientation or mobility, in order to increase the supply of qualified blind rehabilitation specialists for VA and the United States. Section 603 of the 2010 Act reauthorized and modified HPSP, a program that provides scholarships for education or training in certain health care occupations.

  10. Empirical analysis on future-cash arbitrage risk with portfolio VaR

    NASA Astrophysics Data System (ADS)

    Chen, Rongda; Li, Cong; Wang, Weijin; Wang, Ze

    2014-03-01

    This paper constructs the positive arbitrage position by alternating the spot index with Chinese Exchange Traded Fund (ETF) portfolio and estimating the arbitrage-free interval of futures with the latest trade data. Then, an improved Delta-normal method was used, which replaces the simple linear correlation coefficient with tail dependence correlation coefficient, to measure VaR (Value-at-risk) of the arbitrage position. Analysis of VaR implies that the risk of future-cash arbitrage is less than that of investing completely in either futures or spot market. Then according to the compositional VaR and the marginal VaR, we should increase the futures position and decrease the spot position appropriately to minimize the VaR, which can minimize risk subject to certain revenues.

  11. VA Health Professional Scholarship and Visual Impairment and Orientation and Mobility Professional Scholarship Programs. Final rule.

    PubMed

    2013-08-20

    The Department of Veterans Affairs (VA) is amending its VA Health Professional Scholarship Program (HPSP) regulations. VA is also establishing regulations for a new program, the Visual Impairment and Orientation and Mobility Professional Scholarship Program (VIOMPSP). These regulations comply with and implement sections 302 and 603 of the Caregivers and Veterans Omnibus Health Services Act of 2010 (the 2010 Act). Section 302 of the 2010 Act established the VIOMPSP, which authorizes VA to provide financial assistance to certain students seeking a degree in visual impairment or orientation or mobility, in order to increase the supply of qualified blind rehabilitation specialists for VA and the United States. Section 603 of the 2010 Act reauthorized and modified HPSP, a program that provides scholarships for education or training in certain health care occupations. PMID:23977714

  12. Identifying Homelessness among Veterans Using VA Administrative Data: Opportunities to Expand Detection Criteria.

    PubMed

    Peterson, Rachel; Gundlapalli, Adi V; Metraux, Stephen; Carter, Marjorie E; Palmer, Miland; Redd, Andrew; Samore, Matthew H; Fargo, Jamison D

    2015-01-01

    Researchers at the U.S. Department of Veterans Affairs (VA) have used administrative criteria to identify homelessness among U.S. Veterans. Our objective was to explore the use of these codes in VA health care facilities. We examined VA health records (2002-2012) of Veterans recently separated from the military and identified as homeless using VA conventional identification criteria (ICD-9-CM code V60.0, VA specific codes for homeless services), plus closely allied V60 codes indicating housing instability. Logistic regression analyses examined differences between Veterans who received these codes. Health care services and co-morbidities were analyzed in the 90 days post-identification of homelessness. VA conventional criteria identified 21,021 homeless Veterans from Operations Enduring Freedom, Iraqi Freedom, and New Dawn (rate 2.5%). Adding allied V60 codes increased that to 31,260 (rate 3.3%). While certain demographic differences were noted, Veterans identified as homeless using conventional or allied codes were similar with regards to utilization of homeless, mental health, and substance abuse services, as well as co-morbidities. Differences were noted in the pattern of usage of homelessness-related diagnostic codes in VA facilities nation-wide. Creating an official VA case definition for homelessness, which would include additional ICD-9-CM and other administrative codes for VA homeless services, would likely allow improved identification of homeless and at-risk Veterans. This also presents an opportunity for encouraging uniformity in applying these codes in VA facilities nationwide as well as in other large health care organizations.

  13. Amplicon-plus targeting technology (APTT) for rapid production of a highly unstable vaccine protein in tobacco plants.

    PubMed

    Azhakanandam, Kasi; Weissinger, Sandra M; Nicholson, Jennifer S; Qu, Rongda; Weissinger, Arthur K

    2007-02-01

    High-level expression of transgenes is essential for cost-effective production of valuable pharmaceutical proteins in plants. However, transgenic proteins often accumulate in plants at low levels. Low levels of protein accumulation can be caused by many factors including post-transcriptional gene silencing (PTGS) and/or rapid turnover of the transgenic proteins. We have developed an Amplicon-plus Targeting Technology (APTT), by using novel combination of known techniques that appears to overcome both of these factors. By using this technology, we have successfully expressed the highly-labile L1 protein of canine oral papillomavirus (COPV L1) by infecting transgenic tobacco plants expressing a suppressor of post-transcriptional gene silencing (PTGS) with a PVX amplicon carrying a gene encoding L1, and targeting the vaccine protein into the chloroplasts. Further, a scalable "wound-and-agrospray" inoculation method has been developed that will permit high-throughput Agrobacterium inoculation of Nicotiana tabacum, and a spray-only method (named "agrospray") for use with N. benthamiana to allow large-scale application of this technology. The good yield and short interval from inoculation to harvest characteristic of APTT, combined with the potential for high-throughput achieved by use of the agrospray inoculation protocol, make this system a very promising technology for producing high value recombinant proteins, especially those known to be highly labile, in plants for a wide range of applications including producing vaccines against rapidly evolving pathogens and for the rapid response needed to meet bio-defense emergencies. PMID:17221361

  14. Quantification of minimal residual disease (MRD) in acute lymphoblastic leukemia (ALL) using amplicon-fusion-site polymerase chain reaction (AFS-PCR)

    PubMed Central

    2012-01-01

    The amplification of putative oncogenes is a common finding within the genome of various cancer types. Identification and further targeting of specific junction sites within the sequence of genomic amplicons (amplicon fusion sites, AFS) by PCR (AFS-PCR) is suitable for quantification of minimal residual disease (MRD). This approach has recently been developed and described for MYCN amplified neuroblastomas. To compare AFS-PCR directly to routinely used MRD diagnostic strategies, we mapped the amplified genomic regions (ampGR) of an iAMP21-amplicon in high resolution of a patient with acute lymphoblastic leukemia (ALL). Successfully, we established AFS-PCR covering junction sites between ampGR within the iAMP21-amplicon. Quantification of MRD by AFS-PCR was directly comparable to IgH/TCR based real time quantitative PCR and fluorescence activated cell sorting (FACS) analysis in consecutive bone marrow (BM) specimens. Our data give an additional proof of concept of AFS-PCR for quantification of MRD. The method could be taken into account for ALL patients with genomic amplifications as alternative MRD diagnostic, if no or qualitatively poor Ig/TCR-PCRs are available. PMID:23210797

  15. Investigation of Microbial Diversity in Geothermal Hot Springs in Unkeshwar, India, Based on 16S rRNA Amplicon Metagenome Sequencing.

    PubMed

    Mehetre, Gajanan T; Paranjpe, Aditi; Dastager, Syed G; Dharne, Mahesh S

    2016-02-25

    Microbial diversity in geothermal waters of the Unkeshwar hot springs in Maharashtra, India, was studied using 16S rRNA amplicon metagenomic sequencing. Taxonomic analysis revealed the presence of Bacteroidetes, Proteobacteria, Cyanobacteria, Actinobacteria, Archeae, and OD1 phyla. Metabolic function prediction analysis indicated a battery of biological information systems indicating rich and novel microbial diversity, with potential biotechnological applications in this niche.

  16. Characteristics and VA Health Care Utilization of U.S. Veterans Who Completed Suicide in Oregon between 2000 and 2005

    ERIC Educational Resources Information Center

    Basham, Chandra; Denneson, Lauren M.; Millet, Lisa; Shen, Xun; Duckart, Jonathan; Dobscha, Steven K.

    2011-01-01

    Oregon Violent Death Reporting System data were linked with Veterans Affairs (VA) administrative data to identify and describe veterans who completed suicide in Oregon from 2000 to 2005 (n = 968), and to describe their VA health care utilization in the year prior to death. Twenty-two percent had received health care in the VA system. Of these, 57%…

  17. 76 FR 67257 - Computer Matching Program Between the Department of Veterans Affairs (VA) and the Department of...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-31

    ... education benefit payments under the Post-9/11 GI Bill. These benefit records are contained in a VA system of records identified as 58VA21/ 22/28 entitled: Compensation, Pension, Education and Vocational Rehabilitation and Employment Records--VA, first published in the Federal Register at 74 FR 9294 (March 3,...

  18. Prevalence and costs of chronic conditions in the VA health care system.

    PubMed

    Yu, Wei; Ravelo, Arliene; Wagner, Todd H; Phibbs, Ciaran S; Bhandari, Aman; Chen, Shuo; Barnett, Paul G

    2003-09-01

    Chronic conditions are among the most common causes of death and disability in the United States. Patients with such conditions receive disproportionate amounts of health care services and therefore cost more per capita than the average patient. This study assesses the prevalence among the Department of Veterans Affairs (VA) health care users and VA expenditures (costs) of 29 common chronic conditions. The authors used regression to identify the marginal impact of these conditions on total, inpatient, outpatient, and pharmacy costs. Excluding costs of contracted medical services at non-VA facilities, total VA health care expenditures in fiscal year 1999 (FY1999) were $14.3 billion. Among the 3.4 million VA patients in FY1999, 72 percent had 1 or more of the 29 chronic conditions, and these patients accounted for 96 percent of the total costs ($13.7 billion). In addition, 35 percent (1.2 million) of VA health care users had 3 or more of the 29 chronic conditions. These individuals accounted for 73 percent of the total cost. Overall, VA health care users have more chronic diseases than the general population. PMID:15095551

  19. Homeless and nonhomeless VA service users likely eligible for Medicaid expansion.

    PubMed

    Tsai, Jack; Rosenheck, Robert A

    2014-01-01

    Administrative data on the population of Department of Veterans Affairs (VA) service users in 2010 under the age of 65 (n = 3,841,225) were analyzed to identify the number and characteristics of homeless and nonhomeless VA service users who are likely to be eligible for the Medicaid expansion (LEME) option under the Affordable Care Act. Results showed that, estimating conservatively, about 1.2 million (21%) current VA users are LEME if all states implement the expansion. Homeless service users were twice as likely to be eligible than nonhomeless users (64% vs 30%). VA service users who are LEME, regardless of housing status, were physically healthier than those not LEME but were more likely to have substance use disorders and posttraumatic stress disorder. These findings suggest that many VA service users are LEME, particularly those who are homeless and/or have mental health needs. Cross-system use of VA and Medicaid-funded services may be advantageous for veterans with extensive medical and psychiatric needs but also risks fragmented care. Information and education for VA clinicians and their patients about possible implications of the Affordable Care Act may be important. PMID:25358031

  20. Electrical Resistivity Study of a Pleistocene Riverbed in Saltville, VA

    NASA Astrophysics Data System (ADS)

    Herman, R. B.; Whisonant, R. C.

    2008-05-01

    A shallow capacitively coupled resistivity survey was performed in Saltville, VA, in an area of suspected buried Pleistocene river deposits. Previous excavations in the sediments beneath the Saltville valley floor had been performed to recover late Pleistocene megafaunal remains and possible Clovis-age human artifacts. These digs encountered a zone, one to two meters deep, of gravel-sized rock fragments, including some boulders up to 75 cm. in diameter. These large clasts are rounded, show some imbrication (shingle-like overlapping indicative of current flow), and have been interpreted as river channel deposits. Carbon 14 dates from the megafaunal bones within and just above the gravel bed yielded dates of 14,500 years BP. Resistivity signals in a number of locations were consistent with cobbles and boulders deposited in a river channel. These signals are generally bowl- shaped areas with large circular (2-d scans) anomalies near the center, and smaller circular anomalies tapering out towards both sides. The bowl-shaped anomalies are within 3 meters of the surface. With several lines imaged in this survey a rough path of the riverbed, along with a number of branchings is traceable in the survey area. An exploratory hole confirmed the presence of a layer of rounded cobbles and boulders 1.3 meters deep beneath one of the survey lines.

  1. Distinct and opposing roles for Rab27a/Mlph/MyoVa and Rab27b/Munc13-4 in mast cell secretion.

    PubMed

    Singh, Rajesh K; Mizuno, Koichi; Wasmeier, Christina; Wavre-Shapton, Silene T; Recchi, Chiara; Catz, Sergio D; Futter, Clare; Tolmachova, Tanya; Hume, Alistair N; Seabra, Miguel C

    2013-02-01

    Mediator release from mast cells is a critical step in allergic and inflammatory disease. However, the processes regulating the latter stages of granule release are yet to be fully understood. Rab27 small GTPases regulate release of secretory lysosomes in a variety of cells, including mast cell granules. In the present study, using murine bone marrow-derived mast cells (BMMC) from Rab27-deficient mutant mice, we found that, in contrast to Rab27b, Rab27a primarily plays an inhibitory role in regulating degranulation. Immunofluorescence analysis revealed that resting Rab27a-deficient (ashen) BMMCs display abnormal cortical F-actin distribution. Actin disassembly prior to IgE cross-linking increased wild-type BMMC secretion to ashen levels, suggesting that changes in the integrity of cortical F-actin underlie the ashen phenotype. Comparison of the secretory impairment of Rab27b knockout and Rab27a/b double knockout BMMCs highlighted a secondary positive role for Rab27a in enhancing degranulation. Rab27 is known to interact with actin via its effectors melanophilin (Mlph) and myosin Va (MyoVa) in other cell types. To better understand the differing roles of Rab27 proteins, we analysed the secretory phenotype of BMMCs derived from mice lacking Rab27 effector proteins. These experiments revealed that the phenotype of BMMCs deficient in Mlph (leaden) and BMMCs deficient in MyoVa (dilute) resembles the hyper-secretion of ashen BMMCs, while Munc13-4-deficient (jinx) BMMCs phenocopy the Rab27b knockout and double Rab27a/b knockout secretory impairment. We conclude that Rab27a and Rab27b regulate distinct steps in the BMMC degranulation pathway, with Rab27a/Mlph/MyoVa regulating cortical actin stability upstream of Rab27a/b/Munc13-4-dependent granule exocytosis.

  2. Effects of inspired CO2, hyperventilation, and time on VA/Q inequality in the dog

    NASA Technical Reports Server (NTRS)

    Tsukimoto, K.; Arcos, J. P.; Schaffartzik, W.; Wagner, P. D.; West, J. B.

    1992-01-01

    In a recent study by Tsukimoto et al. (J. Appl. Physiol. 68: 2488-2493, 1990), CO2 inhalation appeared to reduce the size of the high ventilation-perfusion ratio (VA/Q) mode commonly observed in anesthetized mechanically air-ventilated dogs. In that study, large tidal volumes (VT) were used during CO2 inhalation to preserve normocapnia. To separate the influences of CO2 and high VT on the VA/Q distribution in the present study, we examined the effect of inspired CO2 on the high VA/Q mode using eight mechanically ventilated dogs (4 given CO2, 4 controls). The VA/Q distribution was measured first with normal VT and then with increased VT. In the CO2 group at high VT, data were collected before, during, and after CO2 inhalation. With normal VT, there was no difference in the size of the high VA/Q mode between groups [10.5 +/- 3.5% (SE) of ventilation in the CO2 group, 11.8 +/- 5.2% in the control group]. Unexpectedly, the size of the high VA/Q mode decreased similarly in both groups over time, independently of the inspired PCO2, at a rate similar to the fall in cardiac output over time. The reduction in the high VA/Q mode together with a simultaneous increase in alveolar dead space (estimated by the difference between inert gas dead space and Fowler dead space) suggests that poorly perfused high VA/Q areas became unperfused over time. A possible mechanism is that elevated alveolar pressure and decreased cardiac output eliminate blood flow from corner vessels in nondependent high VA/Q regions.

  3. KAT6A, a chromatin modifier from the 8p11-p12 amplicon is a candidate oncogene in luminal breast cancer.

    PubMed

    Turner-Ivey, Brittany; Guest, Stephen T; Irish, Jonathan C; Kappler, Christiana S; Garrett-Mayer, Elizabeth; Wilson, Robert C; Ethier, Stephen P

    2014-08-01

    The chromosome 8p11-p12 amplicon is present in 12% to 15% of breast cancers, resulting in an increase in copy number and expression of several chromatin modifiers in these tumors, including KAT6A. Previous analyses in SUM-52 breast cancer cells showed amplification and overexpression of KAT6A, and subsequent RNAi screening identified KAT6A as a potential driving oncogene. KAT6A is a histone acetyltransferase previously identified as a fusion partner with CREB binding protein in acute myeloid leukemia. Knockdown of KAT6A in SUM-52 cells, a luminal breast cancer cell line harboring the amplicon, resulted in reduced growth rate compared to non-silencing controls and profound loss of clonogenic capacity both in mono-layer and in soft agar. The normal cell line MCF10A, however, did not exhibit slower growth with knockdown of KAT6A. SUM-52 cells with KAT6A knockdown formed fewer mammospheres in culture compared to controls, suggesting a possible role for KAT6A in self-renewal. Previous data from our laboratory identified FGFR2 as a driving oncogene in SUM-52 cells. The colony forming efficiency of SUM-52 KAT6A knockdown cells in the presence of FGFR inhibition was significantly reduced compared to cells with KAT6A knockdown only. These data suggest that KAT6A may be a novel oncogene in breast cancers bearing the 8p11-p12 amplicon. While there are other putative oncogenes in the amplicon, the identification of KAT6A as a driving oncogene suggests that chromatin-modifying enzymes are a key class of oncogenes in these cancers, and play an important role in the selection of this amplicon in luminal B breast cancers. PMID:25220592

  4. KAT6A, a Chromatin Modifier from the 8p11-p12 Amplicon is a Candidate Oncogene in Luminal Breast Cancer

    PubMed Central

    Turner-Ivey, Brittany; Guest, Stephen T.; Irish, Jonathan C.; Kappler, Christiana S.; Garrett-Mayer, Elizabeth; Wilson, Robert C.; Ethier, Stephen P.

    2014-01-01

    The chromosome 8p11-p12 amplicon is present in 12% to 15% of breast cancers, resulting in an increase in copy number and expression of several chromatin modifiers in these tumors, including KAT6A. Previous analyses in SUM-52 breast cancer cells showed amplification and overexpression of KAT6A, and subsequent RNAi screening identified KAT6A as a potential driving oncogene. KAT6A is a histone acetyltransferase previously identified as a fusion partner with CREB binding protein in acute myeloid leukemia. Knockdown of KAT6A in SUM-52 cells, a luminal breast cancer cell line harboring the amplicon, resulted in reduced growth rate compared to non-silencing controls and profound loss of clonogenic capacity both in mono-layer and in soft agar. The normal cell line MCF10A, however, did not exhibit slower growth with knockdown of KAT6A. SUM-52 cells with KAT6A knockdown formed fewer mammospheres in culture compared to controls, suggesting a possible role for KAT6A in self-renewal. Previous data from our laboratory identified FGFR2 as a driving oncogene in SUM-52 cells. The colony forming efficiency of SUM-52 KAT6A knockdown cells in the presence of FGFR inhibition was significantly reduced compared to cells with KAT6A knockdown only. These data suggest that KAT6A may be a novel oncogene in breast cancers bearing the 8p11-p12 amplicon. While there are other putative oncogenes in the amplicon, the identification of KAT6A as a driving oncogene suggests that chromatin-modifying enzymes are a key class of oncogenes in these cancers, and play an important role in the selection of this amplicon in luminal B breast cancers. PMID:25220592

  5. Targeting the central nervous system with herpes simplex virus / Sleeping Beauty hybrid amplicon vectors.

    PubMed

    de Silva, Suresh; Bowers, William J

    2011-10-01

    The pursuits of sustainable treatments for diseases and disorders that afflict the central nervous system (CNS) have proven challenging for the field of viral vector-based gene therapy. However, recent advances in viral vector technology coupled with efficient delivery methods have opened up new avenues that show promise at the preclinical testing stage. The development of the Herpes Simplex Virus/Sleeping Beauty (HSV/SB) hybrid vector represents such an advance for devising treatments targeting the CNS with its potential for stably integrating large transgenomic segments of DNA within the genomes of transduced cells. In utero administration of this hybrid vector into the embryonic mouse brain has revealed the capacity for widespread transgene dissemination due to the targeting of a neuronal precursor cell population. This unique feature has provided the means to stably express a transgene throughout the brain for prolonged periods, which is a prerequisite for the treatment of progressive CNS disorders. In this review we provide a comprehensive breakdown of the characteristics of the HSV/SB vector system and how it can be efficiently employed in the derivation of CNS-targeted gene therapeutic strategies.

  6. Molecular characterization of a novel amplicon at 1q21-q22 frequently observed in human sarcomas.

    PubMed Central

    Forus, A.; Berner, J. M.; Meza-Zepeda, L. A.; Saeter, G.; Mischke, D.; Fodstad, O.; Myklebost, O.

    1998-01-01

    In a recent comparative genomic hybridization (CGH) study of a panel of sarcomas, we detected recurrent amplification of 1q21-q22 in soft tissue and bone tumours. Amplification of this region had not previously been associated with sarcoma development, but occasional amplification of CACY/S100A6 and MUC1 in 1q21 had been reported for melanoma and breast carcinoma respectively. Initial screening by Southern blot analysis showed amplification of S100A6, FLG and SPRR3 in several sarcomas and, in a first attempt to characterize the 1q21-q22 amplicon in more detail, we have now investigated the amplification status of these and 11 other markers in the region in 35 sarcoma samples. FLG was the most frequently amplified gene, and the markers located in the same 4.5-Mb region as FLG showed a higher incidence of amplification than the more distal ones. However, for most of the 14 markers, amplification levels were low, and only APOA2 and the anonymous marker D1S3620 showed high-level amplifications (> tenfold increases) in one sample each. We used fluorescence in situ hybridization (FISH) to determine the amplification patterns of two overlapping yeast artificial chromosomes (YACs) covering the region between D1S3620 and FLG (789f2 and 764a1), as well as two more distally located YACs in nine selected samples. Six samples had amplification of the YAC containing D1S3620 and, in three, 764a1 was also included. Five of these tumours showed normal copies of the more distal YACs; thus, it seems likely that an important gene may be located within 789f2, or very close. Two samples had high copy numbers of the most distal YACs. Taken together, FISH and molecular analyses indicate complex amplification patterns in 1q21-q22 with at least two amplicons: one located near D1S3620/789f2 and one more distal. Images Figure 1 Figure 2 Figure 3 PMID:9716033

  7. 77 FR 70212 - Agency Information Collection Activities Under OMB Review: VA MATIC Enrollment/Change

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-23

    ... MATIC or change their financial institution from which VA currently deducts his/her Government Life Insurance premium. An agency may not conduct or sponsor, and a person is not required to respond to...

  8. 78 FR 36642 - Proposed Information Collection (VA Loan Electronic Reporting Interface (VALERI) System) Activity...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-18

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF VETERANS...: Comment Request AGENCY: Veterans Benefits Administration, Department of Veterans Affairs. ACTION: Notice. SUMMARY: The Veterans Benefits Administration (VBA), Department of Veterans Affairs (VA), is announcing...

  9. 78 FR 60379 - Proposed Information Collection (Credit Underwriting Standards and Procedures for Processing VA...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-01

    ... Guaranteed Loans) Activity: Comment Request AGENCY: Veterans Benefits Administration, Department of Veterans Affairs. ACTION: Notice. SUMMARY: The Veterans Benefits Administration (VBA), Department of Veterans... the notice. This notice solicits comments on information needed to underwrite VA-guaranteed...

  10. 38 CFR 74.29 - When will VA dispose of records?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... (CONTINUED) VETERANS SMALL BUSINESS REGULATIONS Records Management § 74.29 When will VA dispose of records? The records, including those pertaining to businesses not determined to be eligible for the...

  11. 78 FR 66266 - Drawbridge Operation Regulation; Atlantic Intracoastal Waterway (AIWW), Chesapeake, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-05

    ... Chesapeake, VA. This deviation is necessary to facilitate maintenance work on the rotary span limit switches... 33 CFR 117.997(e), to facilitate maintenance of the moveable spans on the structure. The...

  12. 75 FR 9277 - Proposed Information Collection (VA National Rehabilitation Special Events, Event Registration...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-01

    ... AFFAIRS Proposed Information Collection (VA National Rehabilitation Special Events, Event Registration Applications); Comment Request AGENCY: Office of National Programs and Special Events, Department of Veterans Affairs. ACTION: Notice. SUMMARY: The Office of National Programs and Special Events (NPSE), Department...

  13. 77 FR 60746 - Proposed Information Collection (VA/DOD Joint Disability Evaluation Board Claim) Activity...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-04

    ... Interagency Task Force on Returning Global War on Terror Heroes, VA and the Department of Defense (DOD) have agreed to develop a joint process in which Global War on Terror (GWOT) service members are evaluated...

  14. 77 FR 74279 - Agency Information Collection (VA/DOD Joint Disability Evaluation Board Claim): Activity under...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-13

    ... President Bush's Interagency Task Force on Returning Global War on Terror Heroes, VA and the Department of Defense (DOD) have agreed to develop a joint process in which Global War on Terror (GWOT) service...

  15. 38 CFR 74.25 - What types of personally identifiable information will VA collect?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) VETERANS SMALL BUSINESS REGULATIONS Records Management § 74.25 What types of personally identifiable information will VA collect? In order to establish owner... in a specific business seeking to obtain verified status....

  16. 76 FR 40453 - Agency Information Collection (Application for VA Education Benefits) Activity Under OMB Review

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-07-08

    .... The PRA submission describes the nature of the information collection and its expected cost and burden....Regulations.gov or to VA's OMB Desk Officer, OMB Human Resources and Housing Branch, New Executive...

  17. 38 CFR 3.1706 - Burial allowance for a veteran who died while hospitalized by VA.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... within a State, or to the border limits of the United States. (2) VA may pay the plot or interment allowance for burial in a veterans cemetery under § 3.1707, Plot or interment allowance. (Authority: 38...

  18. 75 FR 54003 - Imperial Savings and Loan Association, Martinsville, VA; Notice of Appointment of Receiver

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-02

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF THE TREASURY Office of Thrift Supervision Imperial Savings and Loan Association, Martinsville, VA; Notice of... Insurance Corporation as sole Receiver for Imperial Savings and Loan Association, Martinsville,...

  19. 78 FR 34892 - Drawbridge Operation Regulation; Elizabeth River, Eastern Branch, Norfolk, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-11

    ..., VA. This deviation is necessary to facilitate thermite welding on rail joints on the Norfolk Southern... 33 CFR 117.5 to facilitate thermite welding on the rails. Under the regular operating schedule,...

  20. 79. Credit JTL. Detail of 2000 kVA generator (unit 2) ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    79. Credit JTL. Detail of 2000 kVA generator (unit 2) looking southwest. Note the elevated neutral on upper part of generator (added later). - Battle Creek Hydroelectric System, Battle Creek & Tributaries, Red Bluff, Tehama County, CA

  1. 12 CFR 3.206 - Stressed VaR-based measure.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 12 Banks and Banking 1 2014-01-01 2014-01-01 false Stressed VaR-based measure. 3.206 Section 3.206 Banks and Banking COMPTROLLER OF THE CURRENCY, DEPARTMENT OF THE TREASURY CAPITAL ADEQUACY STANDARDS Risk-Weighted Assets-Market Risk § 3.206 Stressed VaR-based measure. (a) General requirement. At least weekly, a national bank or Federal...

  2. 12 CFR 324.206 - Stressed VaR-based measure.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 12 Banks and Banking 5 2014-01-01 2014-01-01 false Stressed VaR-based measure. 324.206 Section 324.206 Banks and Banking FEDERAL DEPOSIT INSURANCE CORPORATION REGULATIONS AND STATEMENTS OF GENERAL POLICY CAPITAL ADEQUACY OF FDIC-SUPERVISED INSTITUTIONS Risk-Weighted Assets-Market Risk § 324.206 Stressed VaR-based measure. (a) General...

  3. 12 CFR 217.206 - Stressed VaR-based measure.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 12 Banks and Banking 2 2014-01-01 2014-01-01 false Stressed VaR-based measure. 217.206 Section 217.206 Banks and Banking FEDERAL RESERVE SYSTEM BOARD OF GOVERNORS OF THE FEDERAL RESERVE SYSTEM CAPITAL ADEQUACY OF BOARD-REGULATED INSTITUTIONS Risk-Weighted Assets-Market Risk § 217.206 Stressed VaR-based measure. (a) General requirement. At...

  4. 30 CFR 57.22240 - Actions at 2.0 percent methane (V-A mines).

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 30 Mineral Resources 1 2013-07-01 2013-07-01 false Actions at 2.0 percent methane (V-A mines). 57... MINES Safety Standards for Methane in Metal and Nonmetal Mines Ventilation § 57.22240 Actions at 2.0 percent methane (V-A mines). If methane reaches 2.0 percent in the mine atmosphere, all persons other...

  5. 30 CFR 57.22240 - Actions at 2.0 percent methane (V-A mines).

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Actions at 2.0 percent methane (V-A mines). 57... MINES Safety Standards for Methane in Metal and Nonmetal Mines Ventilation § 57.22240 Actions at 2.0 percent methane (V-A mines). If methane reaches 2.0 percent in the mine atmosphere, all persons other...

  6. 30 CFR 57.22240 - Actions at 2.0 percent methane (V-A mines).

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 30 Mineral Resources 1 2014-07-01 2014-07-01 false Actions at 2.0 percent methane (V-A mines). 57... MINES Safety Standards for Methane in Metal and Nonmetal Mines Ventilation § 57.22240 Actions at 2.0 percent methane (V-A mines). If methane reaches 2.0 percent in the mine atmosphere, all persons other...

  7. 46 CFR 7.55 - Cape Henry, VA to Cape Fear, NC.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 1 2013-10-01 2013-10-01 false Cape Henry, VA to Cape Fear, NC. 7.55 Section 7.55 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY PROCEDURES APPLICABLE TO THE PUBLIC BOUNDARY LINES Atlantic Coast § 7.55 Cape Henry, VA to Cape Fear, NC. (a) A line drawn from Rudee Inlet Jetty Light “2”...

  8. 46 CFR 7.55 - Cape Henry, VA to Cape Fear, NC.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 1 2014-10-01 2014-10-01 false Cape Henry, VA to Cape Fear, NC. 7.55 Section 7.55 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY PROCEDURES APPLICABLE TO THE PUBLIC BOUNDARY LINES Atlantic Coast § 7.55 Cape Henry, VA to Cape Fear, NC. (a) A line drawn from Rudee Inlet Jetty Light “2”...

  9. 46 CFR 7.55 - Cape Henry, VA to Cape Fear, NC.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 1 2011-10-01 2011-10-01 false Cape Henry, VA to Cape Fear, NC. 7.55 Section 7.55 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY PROCEDURES APPLICABLE TO THE PUBLIC BOUNDARY LINES Atlantic Coast § 7.55 Cape Henry, VA to Cape Fear, NC. (a) A line drawn from Rudee Inlet Jetty Light “2”...

  10. 46 CFR 7.55 - Cape Henry, VA to Cape Fear, NC.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 1 2010-10-01 2010-10-01 false Cape Henry, VA to Cape Fear, NC. 7.55 Section 7.55 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY PROCEDURES APPLICABLE TO THE PUBLIC BOUNDARY LINES Atlantic Coast § 7.55 Cape Henry, VA to Cape Fear, NC. (a) A line drawn from Rudee Inlet Jetty Light “2”...

  11. 46 CFR 7.55 - Cape Henry, VA to Cape Fear, NC.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 46 Shipping 1 2012-10-01 2012-10-01 false Cape Henry, VA to Cape Fear, NC. 7.55 Section 7.55 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY PROCEDURES APPLICABLE TO THE PUBLIC BOUNDARY LINES Atlantic Coast § 7.55 Cape Henry, VA to Cape Fear, NC. (a) A line drawn from Rudee Inlet Jetty Light “2”...

  12. Report on the evaluation of the VA/Seattle below-knee prosthesis.

    PubMed

    Ellepola, W; Sheredos, S J

    1993-01-01

    The Department of Veterans Affairs (VA), Rehabilitation Research and Development (Rehab R&D) Service, Technology Transfer Section (TTS) with collaboration from the Prosthetic and Sensory Aids Service (PSAS) managed clinical trials to evaluate the VA/Seattle Below-Knee (BK) Prosthetic System. The clinical trials were held at the Prosthetic Treatment Center (PTC), VA Medical Center, Hines, Illinois. Five other VA medical centers participated in the outreach program of the trials as satellite stations, with PTC Hines as the central fabrication facility. The VA/Seattle BK system is the first complete prosthetic system designed and developed by the Department of Veterans Affairs. It consists of a socket designed and fabricated using computer-aided, automated technology, and off-the-shelf modular components: a lightweight pylon and an ankle unit, and a lightweight, energy-storing foot. The computer-based socket design software, the modular components, and the prosthetic foot were developed with funds from the VA Rehab R&D Service. The evaluation trials were conducted to determine the efficacy of the VA/Seattle prosthesis, its reliability, and acceptance by veterans. The clinical trials began in April 1991 and were completed in August 1992. Forty-six BK amputee veterans were fitted with the VA/Seattle prosthesis. Their progress with the prosthesis was followed for a period of 6 months and data were gathered at intervals of 2 weeks, 3 months, and 6 months. Forty sets of subject data instruments were collected. In order to maintain the accuracy of the results, TTS used the 22 sets that were complete for data analysis.(ABSTRACT TRUNCATED AT 250 WORDS)

  13. VaRank: a simple and powerful tool for ranking genetic variants.

    PubMed

    Geoffroy, Véronique; Pizot, Cécile; Redin, Claire; Piton, Amélie; Vasli, Nasim; Stoetzel, Corinne; Blavier, André; Laporte, Jocelyn; Muller, Jean

    2015-01-01

    Background. Most genetic disorders are caused by single nucleotide variations (SNVs) or small insertion/deletions (indels). High throughput sequencing has broadened the catalogue of human variation, including common polymorphisms, rare variations or disease causing mutations. However, identifying one variation among hundreds or thousands of others is still a complex task for biologists, geneticists and clinicians. Results. We have developed VaRank, a command-line tool for the ranking of genetic variants detected by high-throughput sequencing. VaRank scores and prioritizes variants annotated either by Alamut Batch or SnpEff. A barcode allows users to quickly view the presence/absence of variants (with homozygote/heterozygote status) in analyzed samples. VaRank supports the commonly used VCF input format for variants analysis thus allowing it to be easily integrated into NGS bioinformatics analysis pipelines. VaRank has been successfully applied to disease-gene identification as well as to molecular diagnostics setup for several hundred patients. Conclusions. VaRank is implemented in Tcl/Tk, a scripting language which is platform-independent but has been tested only on Unix environment. The source code is available under the GNU GPL, and together with sample data and detailed documentation can be downloaded from http://www.lbgi.fr/VaRank/.

  14. VaRank: a simple and powerful tool for ranking genetic variants

    PubMed Central

    Geoffroy, Véronique; Pizot, Cécile; Redin, Claire; Piton, Amélie; Vasli, Nasim; Stoetzel, Corinne; Blavier, André; Laporte, Jocelyn

    2015-01-01

    Background. Most genetic disorders are caused by single nucleotide variations (SNVs) or small insertion/deletions (indels). High throughput sequencing has broadened the catalogue of human variation, including common polymorphisms, rare variations or disease causing mutations. However, identifying one variation among hundreds or thousands of others is still a complex task for biologists, geneticists and clinicians. Results. We have developed VaRank, a command-line tool for the ranking of genetic variants detected by high-throughput sequencing. VaRank scores and prioritizes variants annotated either by Alamut Batch or SnpEff. A barcode allows users to quickly view the presence/absence of variants (with homozygote/heterozygote status) in analyzed samples. VaRank supports the commonly used VCF input format for variants analysis thus allowing it to be easily integrated into NGS bioinformatics analysis pipelines. VaRank has been successfully applied to disease-gene identification as well as to molecular diagnostics setup for several hundred patients. Conclusions. VaRank is implemented in Tcl/Tk, a scripting language which is platform-independent but has been tested only on Unix environment. The source code is available under the GNU GPL, and together with sample data and detailed documentation can be downloaded from http://www.lbgi.fr/VaRank/. PMID:25780760

  15. Myosin Va bound to phagosomes binds to F-actin and delays microtubule-dependent motility.

    PubMed

    Al-Haddad, A; Shonn, M A; Redlich, B; Blocker, A; Burkhardt, J K; Yu, H; Hammer, J A; Weiss, D G; Steffen, W; Griffiths, G; Kuznetsov, S A

    2001-09-01

    We established a light microscopy-based assay that reconstitutes the binding of phagosomes purified from mouse macrophages to preassembled F-actin in vitro. Both endogenous myosin Va from mouse macrophages and exogenous myosin Va from chicken brain stimulated the phagosome-F-actin interaction. Myosin Va association with phagosomes correlated with their ability to bind F-actin in an ATP-regulated manner and antibodies to myosin Va specifically blocked the ATP-sensitive phagosome binding to F-actin. The uptake and retrograde transport of phagosomes from the periphery to the center of cells in bone marrow macrophages was observed in both normal mice and mice homozygous for the dilute-lethal spontaneous mutation (myosin Va null). However, in dilute-lethal macrophages the accumulation of phagosomes in the perinuclear region occurred twofold faster than in normal macrophages. Motion analysis revealed saltatory phagosome movement with temporarily reversed direction in normal macrophages, whereas almost no reversals in direction were observed in dilute-lethal macrophages. These observations demonstrate that myosin Va mediates phagosome binding to F-actin, resulting in a delay in microtubule-dependent retrograde phagosome movement toward the cell center. We propose an "antagonistic/cooperative mechanism" to explain the saltatory phagosome movement toward the cell center in normal macrophages. PMID:11553713

  16. Semi-nonparametric VaR forecasts for hedge funds during the recent crisis

    NASA Astrophysics Data System (ADS)

    Del Brio, Esther B.; Mora-Valencia, Andrés; Perote, Javier

    2014-05-01

    The need to provide accurate value-at-risk (VaR) forecasting measures has triggered an important literature in econophysics. Although these accurate VaR models and methodologies are particularly demanded for hedge fund managers, there exist few articles specifically devoted to implement new techniques in hedge fund returns VaR forecasting. This article advances in these issues by comparing the performance of risk measures based on parametric distributions (the normal, Student’s t and skewed-t), semi-nonparametric (SNP) methodologies based on Gram-Charlier (GC) series and the extreme value theory (EVT) approach. Our results show that normal-, Student’s t- and Skewed t- based methodologies fail to forecast hedge fund VaR, whilst SNP and EVT approaches accurately success on it. We extend these results to the multivariate framework by providing an explicit formula for the GC copula and its density that encompasses the Gaussian copula and accounts for non-linear dependences. We show that the VaR obtained by the meta GC accurately captures portfolio risk and outperforms regulatory VaR estimates obtained through the meta Gaussian and Student’s t distributions.

  17. Myosin-Va Mediates RNA Distribution in Primary Fibroblasts From Multiple Organs

    PubMed Central

    Salerno, Verônica P.; Calliari, Aldo; William Provance, D.; Sotelo-Silveira, José R.; Sotelo, José R.; Mercer, John A.

    2008-01-01

    Myosin-Va has been shown to have multiple functions in a variety of cell types, including a role in RNA transport in neurons. Using primary cultures of cells from organs of young dilute-lethal (Myo5ad-l/Myo5ad-l) null mutant mice and wild-type controls, we show that in some, but not all, tissues, RNA distribution is dramatically different in the homozygous null mutant cells. The dependence of RNA localization on myosin-Va correlates with the relative abundance of the brain-specific splicing pattern of the myosin-Va tail. We also show that myosin-Va is involved in RNA localization soon after synthesis, because the effects of its absence are diminished for RNAs that are more than 30 min old. Finally, we show that localization of β-actin mRNA is significantly changed by the absence of myosin-Va. These results suggest that myosin-Va is involved in a transient transport or tethering function in the perinuclear region. Cell Motil. PMID:18357619

  18. VaRank: a simple and powerful tool for ranking genetic variants.

    PubMed

    Geoffroy, Véronique; Pizot, Cécile; Redin, Claire; Piton, Amélie; Vasli, Nasim; Stoetzel, Corinne; Blavier, André; Laporte, Jocelyn; Muller, Jean

    2015-01-01

    Background. Most genetic disorders are caused by single nucleotide variations (SNVs) or small insertion/deletions (indels). High throughput sequencing has broadened the catalogue of human variation, including common polymorphisms, rare variations or disease causing mutations. However, identifying one variation among hundreds or thousands of others is still a complex task for biologists, geneticists and clinicians. Results. We have developed VaRank, a command-line tool for the ranking of genetic variants detected by high-throughput sequencing. VaRank scores and prioritizes variants annotated either by Alamut Batch or SnpEff. A barcode allows users to quickly view the presence/absence of variants (with homozygote/heterozygote status) in analyzed samples. VaRank supports the commonly used VCF input format for variants analysis thus allowing it to be easily integrated into NGS bioinformatics analysis pipelines. VaRank has been successfully applied to disease-gene identification as well as to molecular diagnostics setup for several hundred patients. Conclusions. VaRank is implemented in Tcl/Tk, a scripting language which is platform-independent but has been tested only on Unix environment. The source code is available under the GNU GPL, and together with sample data and detailed documentation can be downloaded from http://www.lbgi.fr/VaRank/. PMID:25780760

  19. US Veterans' Use Of VA Mental Health Services And Disability Compensation Increased From 2001 To 2010.

    PubMed

    Tsai, Jack; Rosenheck, Robert A

    2016-06-01

    There has been concern about the capacity of the Department of Veterans Affairs (VA) health care system to provide care for veterans returning from war zones in the Middle East and Afghanistan. We used two nationally representative surveys of US veterans in 2001 and 2010 to examine changes in the veteran population and veterans' use of health care services after a decade of war. The population was older and more diverse in 2010 than in 2001. In both years, veterans who served in the World War II era or earlier were more likely to have been exposed to combat-related trauma than veterans of more recent service eras. In 2010 veterans who served in the Persian Gulf War era (1990 through the wars in Iraq and Afghanistan) were more likely to have used VA mental health services and to have received VA disability compensation than veterans of previous service eras. Compared to veterans in 2001, those in 2010 were two times more likely to have used any VA health services and were more likely to have received VA disability compensation. These findings highlight changes in the veteran population over time that are important to consider in planning for future VA services. PMID:27269011

  20. A molecular-beacon-based asymmetric PCR assay for easy visualization of amplicons in the diagnosis of trichomoniasis.

    PubMed

    Sonkar, Subash C; Sachdev, Divya; Mishra, Prashant K; Kumar, Anita; Mittal, Pratima; Saluja, Daman

    2016-12-15

    The currently available nucleic acid amplification tests (NAATs) for trichomoniasis are accurate, quick and confirmative with superior sensitivity than traditional culture-based microbiology assays. However, these assays are associated with problems of carry over contamination, false positive results, requirement of technical expertise for performance and detection of end product. Hence, a diagnostic assay with easy visualization of the amplified product will be profitable. An in-house, rapid, sensitive, specific molecular-beacon-based PCR assay, using primers against pfoB gene of Trichomonas vaginalis, was developed and evaluated using dry ectocervical swabs (n=392) from symptomatic females with vaginal discharge. Total DNA was isolated and used as template for the PCR assays. The performance and reproducibility of PCR assay was evaluated by composite reference standard (CRS). For easy visualization of the amplified product, molecular-beacon was designed and amplicons were visualized directly using fluorescent handheld dark reader or by Micro-Plate Reader. Molecular-beacons are single-stranded hairpin shaped nucleic acid probes composed of a stem, with fluorophore/quencher pair and a loop region complementary to the desired DNA. The beacon-based PCR assay designed in the present study is highly specific as confirmed by competition experiments and extremely sensitive with detection limit of 20fg of genomic DNA (3-4 pathogens). The minimum infrastructure requirement and ease to perform the assay makes this method highly useful for resource poor countries for better disease management. PMID:27318568

  1. Amplicon-pyrosequencing-based detection of compositional shifts in bryophyte-associated fungal communities along an elevation gradient.

    PubMed

    Davey, Marie L; Heegaard, Einar; Halvorsen, Rune; Kauserud, Håvard; Ohlson, Mikael

    2013-01-01

    Although bryophytes are a dominant vegetation component of boreal and alpine ecosystems, little is known about their associated fungal communities. HPLC assays of ergosterol (fungal biomass) and amplicon pyrosequencing of the ITS2 region of rDNA were used to investigate how the fungal communities associated with four bryophyte species changed across an elevational gradient transitioning from conifer forest to the low-alpine. Fungal biomass and OTU richness associated with the four moss hosts did not vary significantly across the gradient (P > 0.05), and both were more strongly affected by host and tissue type. Despite largely constant levels of fungal biomass, distinct shifts in community composition of fungi associated with Hylocomium, Pleurozium and Polytrichum occurred between the elevation zones of the gradient. This likely is a result of influence on fungal communities by major environmental factors such as temperature, directly or indirectly mediated by, or interacting with, the response of other components of the vegetation (i.e. the dominant trees). Fungal communities associated with Dicranum were an exception, exhibiting spatial autocorrelation between plots, and no significant structuring by elevation. Nevertheless, the detection of distinct fungal assemblages associated with a single host growing in different elevation zones along an elevational gradient is of particular relevance in the light of the ongoing changes in vegetation patterns in boreal and alpine systems due to global climate warming.

  2. Simultaneous Whole Mitochondrial Genome Sequencing with Short Overlapping Amplicons Suitable for Degraded DNA Using the Ion Torrent Personal Genome Machine

    PubMed Central

    Chaitanya, Lakshmi; Ralf, Arwin; van Oven, Mannis; Kupiec, Tomasz; Chang, Joseph; Lagacé, Robert

    2015-01-01

    ABSTRACT Whole mitochondrial (mt) genome analysis enables a considerable increase in analysis throughput, and improves the discriminatory power to the maximum possible phylogenetic resolution. Most established protocols on the different massively parallel sequencing (MPS) platforms, however, invariably involve the PCR amplification of large fragments, typically several kilobases in size, which may fail due to mtDNA fragmentation in the available degraded materials. We introduce a MPS tiling approach for simultaneous whole human mt genome sequencing using 161 short overlapping amplicons (average 200 bp) with the Ion Torrent Personal Genome Machine. We illustrate the performance of this new method by sequencing 20 DNA samples belonging to different worldwide mtDNA haplogroups. Additional quality control, particularly regarding the potential detection of nuclear insertions of mtDNA (NUMTs), was performed by comparative MPS analysis using the conventional long‐range amplification method. Preliminary sensitivity testing revealed that detailed haplogroup inference was feasible with 100 pg genomic input DNA. Complete mt genome coverage was achieved from DNA samples experimentally degraded down to genomic fragment sizes of about 220 bp, and up to 90% coverage from naturally degraded samples. Overall, we introduce a new approach for whole mt genome MPS analysis from degraded and nondegraded materials relevant to resolve and infer maternal genetic ancestry at complete resolution in anthropological, evolutionary, medical, and forensic applications. PMID:26387877

  3. Simultaneous Whole Mitochondrial Genome Sequencing with Short Overlapping Amplicons Suitable for Degraded DNA Using the Ion Torrent Personal Genome Machine.

    PubMed

    Chaitanya, Lakshmi; Ralf, Arwin; van Oven, Mannis; Kupiec, Tomasz; Chang, Joseph; Lagacé, Robert; Kayser, Manfred

    2015-12-01

    Whole mitochondrial (mt) genome analysis enables a considerable increase in analysis throughput, and improves the discriminatory power to the maximum possible phylogenetic resolution. Most established protocols on the different massively parallel sequencing (MPS) platforms, however, invariably involve the PCR amplification of large fragments, typically several kilobases in size, which may fail due to mtDNA fragmentation in the available degraded materials. We introduce a MPS tiling approach for simultaneous whole human mt genome sequencing using 161 short overlapping amplicons (average 200 bp) with the Ion Torrent Personal Genome Machine. We illustrate the performance of this new method by sequencing 20 DNA samples belonging to different worldwide mtDNA haplogroups. Additional quality control, particularly regarding the potential detection of nuclear insertions of mtDNA (NUMTs), was performed by comparative MPS analysis using the conventional long-range amplification method. Preliminary sensitivity testing revealed that detailed haplogroup inference was feasible with 100 pg genomic input DNA. Complete mt genome coverage was achieved from DNA samples experimentally degraded down to genomic fragment sizes of about 220 bp, and up to 90% coverage from naturally degraded samples. Overall, we introduce a new approach for whole mt genome MPS analysis from degraded and nondegraded materials relevant to resolve and infer maternal genetic ancestry at complete resolution in anthropological, evolutionary, medical, and forensic applications.

  4. Potential applications of next generation DNA sequencing of 16S rRNA gene amplicons in microbial water quality monitoring.

    PubMed

    Vierheilig, J; Savio, D; Ley, R E; Mach, R L; Farnleitner, A H; Reischer, G H

    2015-01-01

    The applicability of next generation DNA sequencing (NGS) methods for water quality assessment has so far not been broadly investigated. This study set out to evaluate the potential of an NGS-based approach in a complex catchment with importance for drinking water abstraction. In this multi-compartment investigation, total bacterial communities in water, faeces, soil, and sediment samples were investigated by 454 pyrosequencing of bacterial 16S rRNA gene amplicons to assess the capabilities of this NGS method for (i) the development and evaluation of environmental molecular diagnostics, (ii) direct screening of the bulk bacterial communities, and (iii) the detection of faecal pollution in water. Results indicate that NGS methods can highlight potential target populations for diagnostics and will prove useful for the evaluation of existing and the development of novel DNA-based detection methods in the field of water microbiology. The used approach allowed unveiling of dominant bacterial populations but failed to detect populations with low abundances such as faecal indicators in surface waters. In combination with metadata, NGS data will also allow the identification of drivers of bacterial community composition during water treatment and distribution, highlighting the power of this approach for monitoring of bacterial regrowth and contamination in technical systems. PMID:26606090

  5. Fungi Sailing the Arctic Ocean: Speciose Communities in North Atlantic Driftwood as Revealed by High-Throughput Amplicon Sequencing.

    PubMed

    Rämä, Teppo; Davey, Marie L; Nordén, Jenni; Halvorsen, Rune; Blaalid, Rakel; Mathiassen, Geir H; Alsos, Inger G; Kauserud, Håvard

    2016-08-01

    High amounts of driftwood sail across the oceans and provide habitat for organisms tolerating the rough and saline environment. Fungi have adapted to the extremely cold and saline conditions which driftwood faces in the high north. For the first time, we applied high-throughput sequencing to fungi residing in driftwood to reveal their taxonomic richness, community composition, and ecology in the North Atlantic. Using pyrosequencing of ITS2 amplicons obtained from 49 marine logs, we found 807 fungal operational taxonomic units (OTUs) based on clustering at 97 % sequence similarity cut-off level. The phylum Ascomycota comprised 74 % of the OTUs and 20 % belonged to Basidiomycota. The richness of basidiomycetes decreased with prolonged submersion in the sea, supporting the general view of ascomycetes being more extremotolerant. However, more than one fourth of the fungal OTUs remained unassigned to any fungal class, emphasising the need for better DNA reference data from the marine habitat. Different fungal communities were detected in coniferous and deciduous logs. Our results highlight that driftwood hosts a considerably higher fungal diversity than currently known. The driftwood fungal community is not a terrestrial relic but a speciose assemblage of fungi adapted to the stressful marine environment and different kinds of wooden substrates found in it.

  6. High-resolution melting analysis using unlabeled probe and amplicon scanning simultaneously detects several lactase persistence variants.

    PubMed

    Janukonyté, Jurgita; Vestergaard, Else M; Ladefoged, Søren A; Nissen, Peter H

    2010-12-01

    Lactase persistence and thereby tolerance to lactose is a common trait in people of Northern European descent. It is linked to the LCT -13910C>T variant located in intron 13 of the MCM6 gene 13.9 kb upstream of the lactase (LCT) gene. In people of African and Middle Eastern descent, lactase persistence can be associated with other variants nearby the -13910C>T variant, limiting the use of the -13910C>T-based SNP analysis, e.g. TaqMan assays for the diagnosis of lactose intolerance. Using high-resolution melting analysis, we identified five samples that were heterozygous for the -13915T>G variant among 78 patients genotyped as -13910C/C by a TaqMan assay. All samples originated from patients of probable Middle Eastern descent. In order to detect the -13910 and -13915 variants simultaneously, we developed a new high-resolution melting (HRM) analysis assay based on unlabeled probe genotyping and simultaneous amplicon scanning analysis. By using this assay we were able to distinguish the -13910 and -13915 genotypes clearly. Furthermore, we identified two rare variants, the -13907C>G and -13913T>C. With this method, based on an inexpensive unlabeled probe, it is possible to simultaneously detect the -13910C>T and -13915T>G variants in addition to rarer variants surrounding the -13910 site. This new method may contribute to improve the diagnostic performance of the genetic analysis for lactose intolerance.

  7. A molecular-beacon-based asymmetric PCR assay for easy visualization of amplicons in the diagnosis of trichomoniasis.

    PubMed

    Sonkar, Subash C; Sachdev, Divya; Mishra, Prashant K; Kumar, Anita; Mittal, Pratima; Saluja, Daman

    2016-12-15

    The currently available nucleic acid amplification tests (NAATs) for trichomoniasis are accurate, quick and confirmative with superior sensitivity than traditional culture-based microbiology assays. However, these assays are associated with problems of carry over contamination, false positive results, requirement of technical expertise for performance and detection of end product. Hence, a diagnostic assay with easy visualization of the amplified product will be profitable. An in-house, rapid, sensitive, specific molecular-beacon-based PCR assay, using primers against pfoB gene of Trichomonas vaginalis, was developed and evaluated using dry ectocervical swabs (n=392) from symptomatic females with vaginal discharge. Total DNA was isolated and used as template for the PCR assays. The performance and reproducibility of PCR assay was evaluated by composite reference standard (CRS). For easy visualization of the amplified product, molecular-beacon was designed and amplicons were visualized directly using fluorescent handheld dark reader or by Micro-Plate Reader. Molecular-beacons are single-stranded hairpin shaped nucleic acid probes composed of a stem, with fluorophore/quencher pair and a loop region complementary to the desired DNA. The beacon-based PCR assay designed in the present study is highly specific as confirmed by competition experiments and extremely sensitive with detection limit of 20fg of genomic DNA (3-4 pathogens). The minimum infrastructure requirement and ease to perform the assay makes this method highly useful for resource poor countries for better disease management.

  8. Fungi Sailing the Arctic Ocean: Speciose Communities in North Atlantic Driftwood as Revealed by High-Throughput Amplicon Sequencing.

    PubMed

    Rämä, Teppo; Davey, Marie L; Nordén, Jenni; Halvorsen, Rune; Blaalid, Rakel; Mathiassen, Geir H; Alsos, Inger G; Kauserud, Håvard

    2016-08-01

    High amounts of driftwood sail across the oceans and provide habitat for organisms tolerating the rough and saline environment. Fungi have adapted to the extremely cold and saline conditions which driftwood faces in the high north. For the first time, we applied high-throughput sequencing to fungi residing in driftwood to reveal their taxonomic richness, community composition, and ecology in the North Atlantic. Using pyrosequencing of ITS2 amplicons obtained from 49 marine logs, we found 807 fungal operational taxonomic units (OTUs) based on clustering at 97 % sequence similarity cut-off level. The phylum Ascomycota comprised 74 % of the OTUs and 20 % belonged to Basidiomycota. The richness of basidiomycetes decreased with prolonged submersion in the sea, supporting the general view of ascomycetes being more extremotolerant. However, more than one fourth of the fungal OTUs remained unassigned to any fungal class, emphasising the need for better DNA reference data from the marine habitat. Different fungal communities were detected in coniferous and deciduous logs. Our results highlight that driftwood hosts a considerably higher fungal diversity than currently known. The driftwood fungal community is not a terrestrial relic but a speciose assemblage of fungi adapted to the stressful marine environment and different kinds of wooden substrates found in it. PMID:27147245

  9. Amplicon-Based Pyrosequencing Reveals High Diversity of Protistan Parasites in Ships' Ballast Water: Implications for Biogeography and Infectious Diseases.

    PubMed

    Pagenkopp Lohan, K M; Fleischer, R C; Carney, K J; Holzer, K K; Ruiz, G M

    2016-04-01

    Ships' ballast water (BW) commonly moves macroorganisms and microorganisms across the world's oceans and along coasts; however, the majority of these microbial transfers have gone undetected. We applied high-throughput sequencing methods to identify microbial eukaryotes, specifically emphasizing the protistan parasites, in ships' BW collected from vessels calling to the Chesapeake Bay (Virginia and Maryland, USA) from European and Eastern Canadian ports. We utilized tagged-amplicon 454 pyrosequencing with two general primer sets, amplifying either the V4 or V9 domain of the small subunit (SSU) of the ribosomal RNA (rRNA) gene complex, from total DNA extracted from water samples collected from the ballast tanks of bulk cargo vessels. We detected a diverse group of protistan taxa, with some known to contain important parasites in marine systems, including Apicomplexa (unidentified apicomplexans, unidentified gregarines, Cryptosporidium spp.), Dinophyta (Blastodinium spp., Euduboscquella sp., unidentified syndinids, Karlodinium spp., Syndinium spp.), Perkinsea (Parvilucifera sp.), Opisthokonta (Ichthyosporea sp., Pseudoperkinsidae, unidentified ichthyosporeans), and Stramenopiles (Labyrinthulomycetes). Further characterization of groups with parasitic taxa, consisting of phylogenetic analyses for four taxa (Cryptosporidium spp., Parvilucifera spp., Labyrinthulomycetes, and Ichthyosporea), revealed that sequences were obtained from both known and novel lineages. This study demonstrates that high-throughput sequencing is a viable and sensitive method for detecting parasitic protists when present and transported in the ballast water of ships. These data also underscore the potential importance of human-aided dispersal in the biogeography of these microbes and emerging diseases in the world's oceans. PMID:26476551

  10. Amplicon-Based Pyrosequencing Reveals High Diversity of Protistan Parasites in Ships' Ballast Water: Implications for Biogeography and Infectious Diseases.

    PubMed

    Pagenkopp Lohan, K M; Fleischer, R C; Carney, K J; Holzer, K K; Ruiz, G M

    2016-04-01

    Ships' ballast water (BW) commonly moves macroorganisms and microorganisms across the world's oceans and along coasts; however, the majority of these microbial transfers have gone undetected. We applied high-throughput sequencing methods to identify microbial eukaryotes, specifically emphasizing the protistan parasites, in ships' BW collected from vessels calling to the Chesapeake Bay (Virginia and Maryland, USA) from European and Eastern Canadian ports. We utilized tagged-amplicon 454 pyrosequencing with two general primer sets, amplifying either the V4 or V9 domain of the small subunit (SSU) of the ribosomal RNA (rRNA) gene complex, from total DNA extracted from water samples collected from the ballast tanks of bulk cargo vessels. We detected a diverse group of protistan taxa, with some known to contain important parasites in marine systems, including Apicomplexa (unidentified apicomplexans, unidentified gregarines, Cryptosporidium spp.), Dinophyta (Blastodinium spp., Euduboscquella sp., unidentified syndinids, Karlodinium spp., Syndinium spp.), Perkinsea (Parvilucifera sp.), Opisthokonta (Ichthyosporea sp., Pseudoperkinsidae, unidentified ichthyosporeans), and Stramenopiles (Labyrinthulomycetes). Further characterization of groups with parasitic taxa, consisting of phylogenetic analyses for four taxa (Cryptosporidium spp., Parvilucifera spp., Labyrinthulomycetes, and Ichthyosporea), revealed that sequences were obtained from both known and novel lineages. This study demonstrates that high-throughput sequencing is a viable and sensitive method for detecting parasitic protists when present and transported in the ballast water of ships. These data also underscore the potential importance of human-aided dispersal in the biogeography of these microbes and emerging diseases in the world's oceans.

  11. Potential applications of next generation DNA sequencing of 16S rRNA gene amplicons in microbial water quality monitoring.

    PubMed

    Vierheilig, J; Savio, D; Ley, R E; Mach, R L; Farnleitner, A H; Reischer, G H

    2015-01-01

    The applicability of next generation DNA sequencing (NGS) methods for water quality assessment has so far not been broadly investigated. This study set out to evaluate the potential of an NGS-based approach in a complex catchment with importance for drinking water abstraction. In this multi-compartment investigation, total bacterial communities in water, faeces, soil, and sediment samples were investigated by 454 pyrosequencing of bacterial 16S rRNA gene amplicons to assess the capabilities of this NGS method for (i) the development and evaluation of environmental molecular diagnostics, (ii) direct screening of the bulk bacterial communities, and (iii) the detection of faecal pollution in water. Results indicate that NGS methods can highlight potential target populations for diagnostics and will prove useful for the evaluation of existing and the development of novel DNA-based detection methods in the field of water microbiology. The used approach allowed unveiling of dominant bacterial populations but failed to detect populations with low abundances such as faecal indicators in surface waters. In combination with metadata, NGS data will also allow the identification of drivers of bacterial community composition during water treatment and distribution, highlighting the power of this approach for monitoring of bacterial regrowth and contamination in technical systems.

  12. Robust strand exchange reactions for the sequence-specific, real-time detection of nucleic acid amplicons.

    PubMed

    Jiang, Yu Sherry; Bhadra, Sanchita; Li, Bingling; Wu, Yuefeng Rose; Milligan, John N; Ellington, Andrew D

    2015-03-17

    Loop-mediated isothermal amplification (LAMP) of DNA is a powerful isothermal nucleic acid amplification method that can generate upward of 10(9) copies from less than 100 copies of template DNA within an hour. Unfortunately, although the amplification reactions are extremely powerful, real-time and specific detection of LAMP products remains analytically challenging. In order to both improve the specificity of LAMP detection and to make readout simpler and more reliable, we have replaced the intercalating dye typically used for monitoring in real-time fluorescence with a toehold-mediated strand exchange reaction termed one-step strand displacement (OSD). Due to the inherent sequence specificity of toehold-mediated strand exchange, the OSD reporter could successfully distinguish side products from true amplicons arising from templates corresponding to the biomedically relevant M. tuberculosis RNA polymerase (rpoB) and the melanoma-related biomarker BRAF. OSD allowed the Yes/No detection of rpoB in a complex mixture such as synthetic sputum and also demonstrated single nucleotide specificity in Yes/No detection of a mutant BRAF allele (V600E) in the presence of 20-fold more of the wild-type gene. Real-time detection of different genes in multiplex LAMP reactions also proved possible. The development of simple, readily designed, modular equivalents of TaqMan probes for isothermal amplification reactions should generally improve the applicability of these reactions and may eventually assist with the development of point-of-care tests.

  13. VA Education Benefits: VA Should Strengthen Its Efforts to Help Veterans Make Informed Education Choices. Report to Congressional Requesters. GAO-14-324

    ERIC Educational Resources Information Center

    Emrey-Arras, Melissa

    2014-01-01

    In fiscal year 2013, VA provided over $12 billion in benefits for veterans' postsecondary education; however, questions have been raised as to whether some schools are receiving these funds as a result of inappropriate recruiting practices. GAO was asked to examine issues related to schools' recruitment of veterans. This report examines (1) how…

  14. VA/Q distribution during heavy exercise and recovery in humans: implications for pulmonary edema

    NASA Technical Reports Server (NTRS)

    Schaffartzik, W.; Poole, D. C.; Derion, T.; Tsukimoto, K.; Hogan, M. C.; Arcos, J. P.; Bebout, D. E.; Wagner, P. D.

    1992-01-01

    Ventilation-perfusion (VA/Q) inequality has been shown to increase with exercise. Potential mechanisms for this increase include nonuniform pulmonary vasoconstriction, ventilatory time constant inequality, reduced large airway gas mixing, and development of interstitial pulmonary edema. We hypothesized that persistence of VA/Q mismatch after ventilation and cardiac output subside during recovery would be consistent with edema; however, rapid resolution would suggest mechanisms related to changes in ventilation and blood flow per se. Thirteen healthy males performed near-maximal cycle ergometry at an inspiratory PO2 of 91 Torr (because hypoxia accentuates VA/Q mismatch on exercise). Cardiorespiratory variables and inert gas elimination patterns were measured at rest, during exercise, and between 2 and 30 min of recovery. Two profiles of VA/Q distribution behavior emerged during heavy exercise: in group 1 an increase in VA/Q mismatch (log SDQ of 0.35 +/- 0.02 at rest and 0.44 +/- 0.02 at exercise; P less than 0.05, n = 7) and in group 2 no change in VA/Q mismatch (n = 6). There were no differences in anthropometric data, work rate, O2 uptake, or ventilation during heavy exercise between groups. Group 1 demonstrated significantly greater VA/Q inequality, lower vital capacity, and higher forced expiratory flow at 25-75% of forced vital capacity for the first 20 min during recovery than group 2. Cardiac index was higher in group 1 both during heavy exercise and 4 and 6 min postexercise. However, both ventilation and cardiac output returned toward baseline values more rapidly than did VA/Q relationships. Arterial pH was lower in group 1 during exercise and recovery. We conclude that greater VA/Q inequality in group 1 and its persistence during recovery are consistent with the hypothesis that edema occurs and contributes to the increase in VA/Q inequality during exercise. This is supported by observation of greater blood flows and acidosis and, presumably therefore

  15. 76 FR 27379 - Proposed Information Collection (Supplement to VA Forms 21-526, 21-534, and 21-535 (For...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-11

    ... AFFAIRS Proposed Information Collection (Supplement to VA Forms 21-526, 21-534, and 21-535 (For Philippine...: Supplement to VA Forms 21-526, 21-534, and 21-535 (For Philippine Claims), VA Form 21-4169. OMB Control Number: 2900-0094. Type of Review: Extension of a currently approved collection. Abstract: VA Form...

  16. Delivery of gender-sensitive comprehensive primary care to women veterans: implications for VA Patient Aligned Care Teams.

    PubMed

    Yano, Elizabeth M; Haskell, Sally; Hayes, Patricia

    2014-07-01

    The Veterans Health Administration (VA) has undertaken a major initiative to transform primary care delivery through implementation of Patient Aligned Care Teams (PACTs). Based on the patient-centered medical home concept, PACTs aim to improve access, continuity, coordination, and comprehensiveness using team-based care that is patient driven and patient centered. However, how PACT principles should be applied to meet the needs of special populations, including women veterans, is not entirely clear. While historical differences in military participation meant women veterans were rarely seen in VA healthcare settings, they now represent the fastest growing segment of new VA users. They also have complex healthcare needs, adding gender-specific services and other needs to the spectrum of services that the VA must deliver. These trends are changing the VA landscape, introducing challenges to how VA care is organized, how VA providers need to be trained, and how VA considers implementation of new initiatives, such as PACT. We briefly describe the evolution of VA primary care delivery for women veterans, review VA policy for delivering gender-sensitive comprehensive primary care for women, and discuss the challenges that women veterans' needs pose in the context of PACT implementation. We conclude with recommendations for addressing some of these challenges moving forward.

  17. Development of a control region-based mtDNA SNaPshot™ selection tool, integrated into a mini amplicon sequencing method.

    PubMed

    Weiler, Natalie E C; de Vries, Gerda; Sijen, Titia

    2016-03-01

    Mitochondrial DNA (mtDNA) analysis is regularly applied to forensic DNA samples with limited amounts of nuclear DNA (nDNA), such as hair shafts and bones. Generally, this mtDNA analysis involves examination of the hypervariable control region by Sanger sequencing of amplified products. When samples are severely degraded, small-sized amplicons can be applied and an earlier described mini-mtDNA method by Eichmann et al. [1] that accommodates ten mini amplicons in two multiplexes is found to be a very robust approach. However, in cases with large numbers of samples, like when searching for hairs with an mtDNA profile deviant from that of the victim, the method is time (and cost) consuming. Previously, Chemale et al. [2] described a SNaPshot™-based screening tool for a Brazilian population that uses standard-size amplicons for HVS-I and HVS-II. Here, we describe a similar tool adapted to the full control region and compatible with mini-mtDNA amplicons. Eighteen single nucleotide polymorphisms (SNPs) were selected based on their relative frequencies in a European population. They showed a high discriminatory power in a Dutch population (97.2%). The 18 SNPs are assessed in two SNaPshot™ multiplexes that pair to the two mini-mtDNA amplification multiplexes. Degenerate bases are included to limit allele dropout due to SNPs at primer binding site positions. Three SNPs provide haplogroup information. Reliability testing showed no differences with Sanger sequencing results. Since mini-mtSNaPshot screening uses only a small portion of the same PCR products used for Sanger sequencing, no additional DNA extract is consumed, which is forensically advantageous.

  18. Investigation of Microbial Diversity in Geothermal Hot Springs in Unkeshwar, India, Based on 16S rRNA Amplicon Metagenome Sequencing

    PubMed Central

    Mehetre, Gajanan T.; Paranjpe, Aditi; Dastager, Syed G.

    2016-01-01

    Microbial diversity in geothermal waters of the Unkeshwar hot springs in Maharashtra, India, was studied using 16S rRNA amplicon metagenomic sequencing. Taxonomic analysis revealed the presence of Bacteroidetes, Proteobacteria, Cyanobacteria, Actinobacteria, Archeae, and OD1 phyla. Metabolic function prediction analysis indicated a battery of biological information systems indicating rich and novel microbial diversity, with potential biotechnological applications in this niche. PMID:26950332

  19. Combined Amplicon Pyrosequencing Assays Reveal Presence of the Apicomplexan “type-N” (cf. Gemmocystis cylindrus) and Chromera velia on the Great Barrier Reef, Australia

    PubMed Central

    Šlapeta, Jan; Linares, Marjorie C.

    2013-01-01

    Background The coral is predominantly composed of the metabolically dependent coral host and the photosynthetic dinoflagellate Symbiodinium sp. The system as a whole interacts with symbiotic eukaryotes, bacteria and viruses. Gemmocystiscylindrus (cf. “type-N” symbiont) belonging to the obligatory parasitic phylum Apicomplexa (Alveolata) is ubiquitous in the Caribbean coral, but its presence in the Great Barrier Reef coral has yet to be documented. Approaches allowing identification of the healthy community from the pathogenic or saprobic organisms are needed for sustainable coral reef monitoring. Methods & Principal Findings We investigated the diversity of eukaryotes associated with a common reef-building corals from the southern Great Barrier Reef. We used three tag encoded 454 amplicon pyrosequencing assays targeting eukaryote small-subunit rRNA gene to demonstrate the presence of the apicomplexan type-N and a photosynthetic sister species to Apicomplexa - Chromeravelia. Amplicon pyrosequencing revealed presence of the small-subunit rRNA genes of known eukaryotic pathogens (Cryptosporidium and Cryptococcus). We therefore conducted bacterial tag encoded amplicon pyrosequencing assay for small-subunit rRNA gene to support effluent exposure of the coral. Bacteria of faecal origin (Enterobacteriales) formed 41% of total sequences in contrast to 0-2% of the coral-associated bacterial communities with and without C. velia, respectively. Significance This is the first time apicomplexan type-N has been detected in the Great Barrier Reef. Eukaryote tag encoded amplicon pyrosequencing assays demonstrate presence of apicomplexan type-N and C. Velia in total coral DNA. The data highlight the need for combined approaches for eukaryotic diversity studies coupled with bacterial community assessment to achieve a more realistic goals of defining the holobiont community and assessing coral disease. With increasing evidence of Apicomplexa in coral reef environments, it is

  20. Development of a control region-based mtDNA SNaPshot™ selection tool, integrated into a mini amplicon sequencing method.

    PubMed

    Weiler, Natalie E C; de Vries, Gerda; Sijen, Titia

    2016-03-01

    Mitochondrial DNA (mtDNA) analysis is regularly applied to forensic DNA samples with limited amounts of nuclear DNA (nDNA), such as hair shafts and bones. Generally, this mtDNA analysis involves examination of the hypervariable control region by Sanger sequencing of amplified products. When samples are severely degraded, small-sized amplicons can be applied and an earlier described mini-mtDNA method by Eichmann et al. [1] that accommodates ten mini amplicons in two multiplexes is found to be a very robust approach. However, in cases with large numbers of samples, like when searching for hairs with an mtDNA profile deviant from that of the victim, the method is time (and cost) consuming. Previously, Chemale et al. [2] described a SNaPshot™-based screening tool for a Brazilian population that uses standard-size amplicons for HVS-I and HVS-II. Here, we describe a similar tool adapted to the full control region and compatible with mini-mtDNA amplicons. Eighteen single nucleotide polymorphisms (SNPs) were selected based on their relative frequencies in a European population. They showed a high discriminatory power in a Dutch population (97.2%). The 18 SNPs are assessed in two SNaPshot™ multiplexes that pair to the two mini-mtDNA amplification multiplexes. Degenerate bases are included to limit allele dropout due to SNPs at primer binding site positions. Three SNPs provide haplogroup information. Reliability testing showed no differences with Sanger sequencing results. Since mini-mtSNaPshot screening uses only a small portion of the same PCR products used for Sanger sequencing, no additional DNA extract is consumed, which is forensically advantageous. PMID:26976467

  1. Topiramate Protects Pericytes from Glucotoxicity: Role for Mitochondrial CA VA in Cerebromicrovascular Disease in Diabetes

    PubMed Central

    Patrick, Ping; Price, Tulin O.; Diogo, Ana L.; Sheibani, Nader; Banks, William A.; Shah, Gul N.

    2015-01-01

    Hyperglycemia in diabetes mellitus causes oxidative stress and pericyte depletion from the microvasculature of the brain thus leading to the Blood-Brain Barrier (BBB) disruption. The compromised BBB exposes the brain to circulating substances, resulting in neurotoxicity and neuronal cell death. The decline in pericyte numbers in diabetic mouse brain and pericyte apoptosis in high glucose cultures are caused by excess superoxide produced during enhanced respiration (mitochondrial oxidative metabolism of glucose). Superoxide is precursor to all Reactive Oxygen Species (ROS) which, in turn, cause oxidative stress. The rate of respiration and thus the ROS production is regulated by mitochondrial carbonic anhydrases (mCA) VA and VB, the two isoforms expressed in the mitochondria. Inhibition of both mCA: decreases the oxidative stress and restores the pericyte numbers in diabetic brain; and reduces high glucose-induced respiration, ROS, oxidative stress, and apoptosis in cultured brain pericytes. However, the individual role of the two isoforms has not been established. To investigate the contribution of mCA VA in ROS production and apoptosis, a mCA VA overexpressing brain pericyte cell line was engineered. These cells were exposed to high glucose and analyzed for the changes in ROS and apoptosis. Overexpression of mCA VA significantly increased pericyte ROS and apoptosis. Inhibition of mCA VA with topiramate prevented increases both in glucose-induced ROS and pericyte death. These results demonstrate, for the first time, that mCA VA regulates the rate of pericyte respiration. These findings identify mCA VA as a novel and specific therapeutic target to protect the cerebromicrovascular bed in diabetes. PMID:26167540

  2. High-throughput amplicon sequencing of rRNA genes requires a copy number correction to accurately reflect the effects of management practices on soil nematode community structure.

    PubMed

    Darby, B J; Todd, T C; Herman, M A

    2013-11-01

    Nematodes are abundant consumers in grassland soils, but more sensitive and specific methods of enumeration are needed to improve our understanding of how different nematode species affect, and are affected by, ecosystem processes. High-throughput amplicon sequencing is used to enumerate microbial and invertebrate communities at a high level of taxonomic resolution, but the method requires validation against traditional specimen-based morphological identifications. To investigate the consistency between these approaches, we enumerated nematodes from a 25-year field experiment using both morphological and molecular identification techniques in order to determine the long-term effects of annual burning and nitrogen enrichment on soil nematode communities. Family-level frequencies based on amplicon sequencing were not initially consistent with specimen-based counts, but correction for differences in rRNA gene copy number using a genetic algorithm improved quantitative accuracy. Multivariate analysis of corrected sequence-based abundances of nematode families was consistent with, but not identical to, analysis of specimen-based counts. In both cases, herbivores, fungivores and predator/omnivores generally were more abundant in burned than nonburned plots, while bacterivores generally were more abundant in nonburned or nitrogen-enriched plots. Discriminate analysis of sequence-based abundances identified putative indicator species representing each trophic group. We conclude that high-throughput amplicon sequencing can be a valuable method for characterizing nematode communities at high taxonomic resolution as long as rRNA gene copy number variation is accounted for and accurate sequence databases are available. PMID:24103081

  3. The efficacy of uracil DNA glycosylase pretreatment in amplicon-based massively parallel sequencing with DNA extracted from archived formalin-fixed paraffin-embedded esophageal cancer tissues.

    PubMed

    Serizawa, Masakuni; Yokota, Tomoya; Hosokawa, Ayumu; Kusafuka, Kimihide; Sugiyama, Toshiro; Tsubosa, Yasuhiro; Yasui, Hirofumi; Nakajima, Takashi; Koh, Yasuhiro

    2015-09-01

    Advances in mutation testing for molecular-targeted cancer therapies have led to the increased use of archived formalin-fixed paraffin-embedded (FFPE) tumors. However, DNA extracted from FFPE tumors (FFPE DNA) is problematic for mutation testing, especially for amplicon-based massively parallel sequencing (MPS), owing to DNA fragmentation and artificial C:G > T:A single nucleotide variants (SNVs) caused by deamination of cytosine to uracil. Therefore, to reduce artificial C:G > T:A SNVs in amplicon-based MPS using FFPE DNA, we evaluated the efficacy of uracil DNA glycosylase (UDG) pretreatment, which can eliminate uracil-containing DNA molecules, with 126 archived FFPE esophageal cancer specimens. We also examined the association between the frequency of C:G > T:A SNVs and DNA quality, as assessed by a quantitative PCR (qPCR)-based assay. UDG pretreatment significantly lowered the frequency of C:G > T:A SNVs in highly fragmented DNA (by approximately 60%). This effect was not observed for good- to moderate-quality DNA, suggesting that a predictive assay (i.e., DNA quality assessment) needs to be performed prior to UDG pretreatment. These results suggest that UDG pretreatment is efficacious for mutation testing by amplicon-based MPS with fragmented DNA from FFPE samples.

  4. HSV-1 Amplicon Vectors Launch the Production of Heterologous Rotavirus-like Particles and Induce Rotavirus-specific Immune Responses in Mice

    PubMed Central

    Laimbacher, Andrea S; Esteban, Laura E; Castello, Alejandro A; Abdusetir Cerfoglio, Juan C; Argüelles, Marcelo H; Glikmann, Graciela; D'Antuono, Alejandra; Mattion, Nora; Berois, Mabel; Arbiza, Juan; Hilbe, Monika; Schraner, Elisabeth M; Seyffert, Michael; Dresch, Christiane; Epstein, Alberto L; Ackermann, Mathias; Fraefel, Cornel

    2012-01-01

    Virus-like particles (VLPs) are promising vaccine candidates because they represent viral antigens in the authentic conformation of the virion and are therefore readily recognized by the immune system. As VLPs do not contain genetic material they are safer than attenuated virus vaccines. In this study, herpes simplex virus type 1 (HSV-1) amplicon vectors were constructed to coexpress the rotavirus (RV) structural genes VP2, VP6, and VP7 and were used as platforms to launch the production of RV-like particles (RVLPs) in vector-infected mammalian cells. Despite the observed splicing of VP6 RNA, full-length VP6 protein and RVLPs were efficiently produced. Intramuscular injection of mice with the amplicon vectors as a two-dose regimen without adjuvants resulted in RV-specific humoral immune responses and, most importantly, immunized mice were partially protected at the mucosal level from challenge with live wild-type (wt) RV. This work provides proof of principle for the application of HSV-1 amplicon vectors that mediate the efficient production of heterologous VLPs as genetic vaccines. PMID:22713696

  5. High-throughput amplicon sequencing of rRNA genes requires a copy number correction to accurately reflect the effects of management practices on soil nematode community structure.

    PubMed

    Darby, B J; Todd, T C; Herman, M A

    2013-11-01

    Nematodes are abundant consumers in grassland soils, but more sensitive and specific methods of enumeration are needed to improve our understanding of how different nematode species affect, and are affected by, ecosystem processes. High-throughput amplicon sequencing is used to enumerate microbial and invertebrate communities at a high level of taxonomic resolution, but the method requires validation against traditional specimen-based morphological identifications. To investigate the consistency between these approaches, we enumerated nematodes from a 25-year field experiment using both morphological and molecular identification techniques in order to determine the long-term effects of annual burning and nitrogen enrichment on soil nematode communities. Family-level frequencies based on amplicon sequencing were not initially consistent with specimen-based counts, but correction for differences in rRNA gene copy number using a genetic algorithm improved quantitative accuracy. Multivariate analysis of corrected sequence-based abundances of nematode families was consistent with, but not identical to, analysis of specimen-based counts. In both cases, herbivores, fungivores and predator/omnivores generally were more abundant in burned than nonburned plots, while bacterivores generally were more abundant in nonburned or nitrogen-enriched plots. Discriminate analysis of sequence-based abundances identified putative indicator species representing each trophic group. We conclude that high-throughput amplicon sequencing can be a valuable method for characterizing nematode communities at high taxonomic resolution as long as rRNA gene copy number variation is accounted for and accurate sequence databases are available.

  6. Nuclear species-diagnostic SNP markers mined from 454 amplicon sequencing reveal admixture genomic structure of modern citrus varieties.

    PubMed

    Curk, Franck; Ancillo, Gema; Ollitrault, Frédérique; Perrier, Xavier; Jacquemoud-Collet, Jean-Pierre; Garcia-Lor, Andres; Navarro, Luis; Ollitrault, Patrick

    2015-01-01

    Most cultivated Citrus species originated from interspecific hybridisation between four ancestral taxa (C. reticulata, C. maxima, C. medica, and C. micrantha) with limited further interspecific recombination due to vegetative propagation. This evolution resulted in admixture genomes with frequent interspecific heterozygosity. Moreover, a major part of the phenotypic diversity of edible citrus results from the initial differentiation between these taxa. Deciphering the phylogenomic structure of citrus germplasm is therefore essential for an efficient utilization of citrus biodiversity in breeding schemes. The objective of this work was to develop a set of species-diagnostic single nucleotide polymorphism (SNP) markers for the four Citrus ancestral taxa covering the nine chromosomes, and to use these markers to infer the phylogenomic structure of secondary species and modern cultivars. Species-diagnostic SNPs were mined from 454 amplicon sequencing of 57 gene fragments from 26 genotypes of the four basic taxa. Of the 1,053 SNPs mined from 28,507 kb sequence, 273 were found to be highly diagnostic for a single basic taxon. Species-diagnostic SNP markers (105) were used to analyse the admixture structure of varieties and rootstocks. This revealed C. maxima introgressions in most of the old and in all recent selections of mandarins, and suggested that C. reticulata × C. maxima reticulation and introgression processes were important in edible mandarin domestication. The large range of phylogenomic constitutions between C. reticulata and C. maxima revealed in mandarins, tangelos, tangors, sweet oranges, sour oranges, grapefruits, and orangelos is favourable for genetic association studies based on phylogenomic structures of the germplasm. Inferred admixture structures were in agreement with previous hypotheses regarding the origin of several secondary species and also revealed the probable origin of several acid citrus varieties. The developed species-diagnostic SNP

  7. Uncultured bacterial diversity in a seawater recirculating aquaculture system revealed by 16S rRNA gene amplicon sequencing.

    PubMed

    Lee, Da-Eun; Lee, Jinhwan; Kim, Young-Mog; Myeong, Jeong-In; Kim, Kyoung-Ho

    2016-04-01

    Bacterial diversity in a seawater recirculating aquaculture system (RAS) was investigated using 16S rRNA amplicon sequencing to understand the roles of bacterial communities in the system. The RAS was operated at nine different combinations of temperature (15°C, 20°C, and 25°C) and salinity (20‰, 25‰, and 32.5‰). Samples were collected from five or six RAS tanks (biofilters) for each condition. Fifty samples were analyzed. Proteobacteria and Bacteroidetes were most common (sum of both phyla: 67.2% to 99.4%) and were inversely proportional to each other. Bacteria that were present at an average of ≥ 1% included Actinobacteria (2.9%) Planctomycetes (2.0%), Nitrospirae (1.5%), and Acidobacteria (1.0%); they were preferentially present in packed bed biofilters, mesh biofilters, and maturation biofilters. The three biofilters showed higher diversity than other RAS tanks (aerated biofilters, floating bed biofilters, and fish tanks) from phylum to operational taxonomic unit (OTU) level. Samples were clustered into several groups based on the bacterial communities. Major taxonomic groups related to family Rhodobacteraceae and Flavobacteriaceae were distributed widely in the samples. Several taxonomic groups like [Saprospiraceae], Cytophagaceae, Octadecabacter, and Marivita showed a cluster-oriented distribution. Phaeobacter and Sediminicola-related reads were detected frequently and abundantly at low temperature. Nitrifying bacteria were detected frequently and abundantly in the three biofilters. Phylogenetic analysis of the nitrifying bacteria showed several similar OTUs were observed widely through the biofilters. The diverse bacterial communities and the minor taxonomic groups, except for Proteobacteria and Bacteroidetes, seemed to play important roles and seemed necessary for nitrifying activity in the RAS, especially in packed bed biofilters, mesh biofilters, and maturation biofilters. PMID:27033205

  8. The Histone Variant H3.3 Is Enriched at Drosophila Amplicon Origins but Does Not Mark Them for Activation

    PubMed Central

    Paranjape, Neha P.; Calvi, Brian R.

    2016-01-01

    Eukaryotic DNA replication begins from multiple origins. The origin recognition complex (ORC) binds origin DNA and scaffolds assembly of a prereplicative complex (pre-RC), which is subsequently activated to initiate DNA replication. In multicellular eukaryotes, origins do not share a strict DNA consensus sequence, and their activity changes in concert with chromatin status during development, but mechanisms are ill-defined. Previous genome-wide analyses in Drosophila and other organisms have revealed a correlation between ORC binding sites and the histone variant H3.3. This correlation suggests that H3.3 may designate origin sites, but this idea has remained untested. To address this question, we examined the enrichment and function of H3.3 at the origins responsible for developmental gene amplification in the somatic follicle cells of the Drosophila ovary. We found that H3.3 is abundant at these amplicon origins. H3.3 levels remained high when replication initiation was blocked, indicating that H3.3 is abundant at the origins before activation of the pre-RC. H3.3 was also enriched at the origins during early oogenesis, raising the possibility that H3.3 bookmarks sites for later amplification. However, flies null mutant for both of the H3.3 genes in Drosophila did not have overt defects in developmental gene amplification or genomic replication, suggesting that H3.3 is not essential for the assembly or activation of the pre-RC at origins. Instead, our results imply that the correlation between H3.3 and ORC sites reflects other chromatin attributes that are important for origin function. PMID:27172191

  9. Screening of male breast cancer and of breast-ovarian cancer families for BRCA2 mutations using large bifluorescent amplicons

    PubMed Central

    Pages, S; Caux, V; Stoppa-Lyonnet, D; Tosi, M

    2001-01-01

    41 breast cancer or breast-ovarian cancer families, including 12 families with at least one affected first-degree male relative, were screened for mutations in the BRCA2 gene. Mutations had not been found in the BRCA1 gene of these families. Chemical cleavage of Mismatch was used to identify nucleotide changes within large PCR products (average size 1.2 kb) that carried strand-specific fluorescent end-labels. 15 amplicons were sufficient to scan 18 exons, including the large exon 11. The remaining 9 small exons were examined by Denaturing Gradient Gel Electrophoresis. The high sensitivity of this approach was documented by the detection, in these 41 patients, of all 9 exonic single nucleotide polymorphisms reported with heterozygosity >0.1. Truncating BRCA2 mutations were found in 7 of the 41 families. 3 of them were in the group of 12 families comprising cases of male breast cancer. Since the methods used here have no bias for particular types of mutations, these data confirm the high proportion of frameshifts among mutations in BRCA2. However, relevant single nucleotide substitutions were also found: one resulting in a stop codon and another one, present in a male patient, was the previously reported change Asp2723His, that affects a highly conserved region of the BRCA2 protein. This study indicates a BRCA2 contribution of 10% (95% CI 2.5–17.5) to our original cohort of 59 breast-ovarian cancer families, whereas the contribution of BRCA1 had been estimated at 46% (95% CI 33–59). © 2001 Cancer Research Campaign http://www.bjcancer.com PMID:11207042

  10. Redefining the Human Oral Mycobiome with Improved Practices in Amplicon-based Taxonomy: Discovery of Malassezia as a Prominent Commensal

    PubMed Central

    Dupuy, Amanda K.; David, Marika S.; Li, Lu; Heider, Thomas N.; Peterson, Jason D.; Montano, Elizabeth A.; Dongari-Bagtzoglou, Anna; Diaz, Patricia I.; Strausbaugh, Linda D.

    2014-01-01

    Fungi are a large, complex group, increasingly recognized as emerging threats. Their roles as modifiers of health mandate accurate portrayals of fungal communities in humans. As an entry point into the airways and gastrointestinal tract, fungi in the mouth are relevant to several biocompartments. We have revised current practices in sequence-based taxonomy assignments and employed the improvements to address the question of the fungal genera present in the healthy human mouth. The human oral mycobiome was surveyed using massively parallel, high throughput sequencing of internal transcribed spacer 1 (ITS1) amplicons from saliva following robust extraction methods. Taxonomy was assigned by comparison to a curated reference dataset, followed by filtering with an empirically determined BLAST E-value match statistic (10−42). Nomenclature corrections further refined results by conjoining redundant names for a single fungal genus. Following these curation steps, about two-thirds of the initially identified genera were eliminated. In comparison with the one similar metagenomic study and several earlier culture-based ones, our findings change the current conception of the oral mycobiome, especially with the discovery of the high prevalence and abundance of the genus Malassezia. Previously identified as an important pathogen of the skin, and recently reported as the predominant fungal genus at the nostril and backs of the head and ear, this is the first account of Malassezia in the human mouth. Findings from this study were in good agreement with others on the existence of many consensus members of the core mycobiome, and on unique patterns for individual subjects. This research offered a cautionary note about unconditional acceptance of lengthy lists of community members produced by automated assignments, provided a roadmap for enhancing the likely biological relevance of sequence-based fungal surveys, and built the foundation for understanding the role of fungi in health

  11. Nuclear Species-Diagnostic SNP Markers Mined from 454 Amplicon Sequencing Reveal Admixture Genomic Structure of Modern Citrus Varieties

    PubMed Central

    Curk, Franck; Ancillo, Gema; Ollitrault, Frédérique; Perrier, Xavier; Jacquemoud-Collet, Jean-Pierre; Garcia-Lor, Andres; Navarro, Luis; Ollitrault, Patrick

    2015-01-01

    Most cultivated Citrus species originated from interspecific hybridisation between four ancestral taxa (C. reticulata, C. maxima, C. medica, and C. micrantha) with limited further interspecific recombination due to vegetative propagation. This evolution resulted in admixture genomes with frequent interspecific heterozygosity. Moreover, a major part of the phenotypic diversity of edible citrus results from the initial differentiation between these taxa. Deciphering the phylogenomic structure of citrus germplasm is therefore essential for an efficient utilization of citrus biodiversity in breeding schemes. The objective of this work was to develop a set of species-diagnostic single nucleotide polymorphism (SNP) markers for the four Citrus ancestral taxa covering the nine chromosomes, and to use these markers to infer the phylogenomic structure of secondary species and modern cultivars. Species-diagnostic SNPs were mined from 454 amplicon sequencing of 57 gene fragments from 26 genotypes of the four basic taxa. Of the 1,053 SNPs mined from 28,507 kb sequence, 273 were found to be highly diagnostic for a single basic taxon. Species-diagnostic SNP markers (105) were used to analyse the admixture structure of varieties and rootstocks. This revealed C. maxima introgressions in most of the old and in all recent selections of mandarins, and suggested that C. reticulata × C. maxima reticulation and introgression processes were important in edible mandarin domestication. The large range of phylogenomic constitutions between C. reticulata and C. maxima revealed in mandarins, tangelos, tangors, sweet oranges, sour oranges, grapefruits, and orangelos is favourable for genetic association studies based on phylogenomic structures of the germplasm. Inferred admixture structures were in agreement with previous hypotheses regarding the origin of several secondary species and also revealed the probable origin of several acid citrus varieties. The developed species-diagnostic SNP

  12. Responses of soil microeukaryotic communities to short-term fumigation-incubation revealed by MiSeq amplicon sequencing

    PubMed Central

    Chen, Lin; Xu, Jianming; Feng, Youzhi; Wang, Juntao; Yu, Yongjie; Brookes, Philip C.

    2015-01-01

    In soil microbiology, there is a “paradox” of soil organic carbon (SOC) mineralization, which is that even though chloroform fumigation destroys majority of the soil microbial biomass, SOC mineralization continues at the same rate as in the non-fumigated soil during the incubation period. Soil microeukaryotes as important SOC decomposers, however, their community-level responses to chloroform fumigation are not well understood. Using the 18S rRNA gene amplicon sequencing, we analyzed the composition, diversity, and C-metabolic functions of a grassland soil and an arable soil microeukaryotic community in response to fumigation followed by a 30-day incubation. The grassland and arable soil microeukaryotic communities were dominated by the fungal Ascomycota (80.5–93.1% of the fungal sequences), followed by the protistan Cercozoa and Apicomplexa. In the arable soil fungal community, the predominance of the class Sordariomycetes was replaced by the class Eurotiomycetes after fumigation at days 7 and 30 of the incubation. Fumigation changed the microeukaryotic α-diversity in the grassland soil at days 0 and 7, and β-diversity in the arable soil at days 7 and 30. Network analysis indicated that after fumigation fungi were important groups closely related to other taxa. Most phylotypes (especially Sordariomycetes, Dothideomycetes, Coccidia, and uncultured Chytridiomycota) were inhibited, and only a few were positively stimulated by fumigation. Despite the inhibited Sordariomycetes, the fumigated communities mainly consisted of Eurotiomycetes and Sordariomycetes (21.9 and 36.5% relative frequency, respectively), which are able to produce hydrolytic enzymes associated with SOC mineralization. Our study suggests that fumigation not only decreases biomass size, but modulates the composition and diversity of the soil microeukaryotic communities, which are capable of driving SOC mineralization by release of hydrolytic enzymes during short-term fumigation-incubation. PMID

  13. Nuclear species-diagnostic SNP markers mined from 454 amplicon sequencing reveal admixture genomic structure of modern citrus varieties.

    PubMed

    Curk, Franck; Ancillo, Gema; Ollitrault, Frédérique; Perrier, Xavier; Jacquemoud-Collet, Jean-Pierre; Garcia-Lor, Andres; Navarro, Luis; Ollitrault, Patrick

    2015-01-01

    Most cultivated Citrus species originated from interspecific hybridisation between four ancestral taxa (C. reticulata, C. maxima, C. medica, and C. micrantha) with limited further interspecific recombination due to vegetative propagation. This evolution resulted in admixture genomes with frequent interspecific heterozygosity. Moreover, a major part of the phenotypic diversity of edible citrus results from the initial differentiation between these taxa. Deciphering the phylogenomic structure of citrus germplasm is therefore essential for an efficient utilization of citrus biodiversity in breeding schemes. The objective of this work was to develop a set of species-diagnostic single nucleotide polymorphism (SNP) markers for the four Citrus ancestral taxa covering the nine chromosomes, and to use these markers to infer the phylogenomic structure of secondary species and modern cultivars. Species-diagnostic SNPs were mined from 454 amplicon sequencing of 57 gene fragments from 26 genotypes of the four basic taxa. Of the 1,053 SNPs mined from 28,507 kb sequence, 273 were found to be highly diagnostic for a single basic taxon. Species-diagnostic SNP markers (105) were used to analyse the admixture structure of varieties and rootstocks. This revealed C. maxima introgressions in most of the old and in all recent selections of mandarins, and suggested that C. reticulata × C. maxima reticulation and introgression processes were important in edible mandarin domestication. The large range of phylogenomic constitutions between C. reticulata and C. maxima revealed in mandarins, tangelos, tangors, sweet oranges, sour oranges, grapefruits, and orangelos is favourable for genetic association studies based on phylogenomic structures of the germplasm. Inferred admixture structures were in agreement with previous hypotheses regarding the origin of several secondary species and also revealed the probable origin of several acid citrus varieties. The developed species-diagnostic SNP

  14. Uncultured bacterial diversity in a seawater recirculating aquaculture system revealed by 16S rRNA gene amplicon sequencing.

    PubMed

    Lee, Da-Eun; Lee, Jinhwan; Kim, Young-Mog; Myeong, Jeong-In; Kim, Kyoung-Ho

    2016-04-01

    Bacterial diversity in a seawater recirculating aquaculture system (RAS) was investigated using 16S rRNA amplicon sequencing to understand the roles of bacterial communities in the system. The RAS was operated at nine different combinations of temperature (15°C, 20°C, and 25°C) and salinity (20‰, 25‰, and 32.5‰). Samples were collected from five or six RAS tanks (biofilters) for each condition. Fifty samples were analyzed. Proteobacteria and Bacteroidetes were most common (sum of both phyla: 67.2% to 99.4%) and were inversely proportional to each other. Bacteria that were present at an average of ≥ 1% included Actinobacteria (2.9%) Planctomycetes (2.0%), Nitrospirae (1.5%), and Acidobacteria (1.0%); they were preferentially present in packed bed biofilters, mesh biofilters, and maturation biofilters. The three biofilters showed higher diversity than other RAS tanks (aerated biofilters, floating bed biofilters, and fish tanks) from phylum to operational taxonomic unit (OTU) level. Samples were clustered into several groups based on the bacterial communities. Major taxonomic groups related to family Rhodobacteraceae and Flavobacteriaceae were distributed widely in the samples. Several taxonomic groups like [Saprospiraceae], Cytophagaceae, Octadecabacter, and Marivita showed a cluster-oriented distribution. Phaeobacter and Sediminicola-related reads were detected frequently and abundantly at low temperature. Nitrifying bacteria were detected frequently and abundantly in the three biofilters. Phylogenetic analysis of the nitrifying bacteria showed several similar OTUs were observed widely through the biofilters. The diverse bacterial communities and the minor taxonomic groups, except for Proteobacteria and Bacteroidetes, seemed to play important roles and seemed necessary for nitrifying activity in the RAS, especially in packed bed biofilters, mesh biofilters, and maturation biofilters.

  15. Selective inhibition of the prothrombinase complex: factor Va alters macromolecular recognition of a tick anticoagulant peptide mutant by factor Xa.

    PubMed

    Betz, A; Vlasuk, G P; Bergum, P W; Krishnaswamy, S

    1997-01-01

    The prothrombinase complex assembles through reversible interactions between the protease, factor Xa, the cofactor, factor Va, and acidic phospholipid membranes in the presence of calcium ions. Changes in macromolecular recognition by factor Xa which may result from its interaction with factor Va in the prothrombinase complex have been probed using a recombinant derivative of tick anticoagulant peptide where Arg3 has been replaced with Ala (R3A-TAP). In contrast to the wild type inhibitor, R3A-TAP was a weak competitive inhibitor of factor Xa (Ki = 794 nM). The inhibition of the prothrombinase complex by R3A-TAP was characterized by slow, tight-binding kinetics with an increased affinity of approximately 4000-fold (Ki* = 0.195 nM) relative to that of solution-phase factor Xa. Stopped-flow measurements using p-aminobenzamidine (PAB) demonstrated that the reaction between solution-phase factor Xa and R3A-TAP could be adequately described by a single reversible step with rate constants that were consistent with equilibrium binding measurements. The rate-limiting bimolecular combination of R3A-TAP and factor Xa was competitive with PAB binding of the protease. In contrast, the reaction of R3A-TAP with prothrombinase measured using PAB yielded biphasic stopped-flow traces, indicating a multistep pathway for the reaction of the inhibitor with the enzyme complex. The kinetic measurements were consistent with the initial formation of a ternary complex between R3A-TAP, prothrombinase, and PAB followed by two unimolecular steps which lead to PAB dissociation from the enzyme. In this case, prior occupation of the active site by PAB had no effect on the bimolecular reaction between R3A-TAP and prothrombinase. Thus, the interaction of factor Xa with factor Va on the membrane surface alters recognition of R3A-TAP by the protease, leading to changes in the thermodynamics as well as in the observed kinetic mechanism for the reaction. Therefore, a single amino acid substitution in

  16. Haplotyping and copy number estimation of the highly polymorphic human beta-defensin locus on 8p23 by 454 amplicon sequencing

    PubMed Central

    2010-01-01

    Background The beta-defensin gene cluster (DEFB) at chromosome 8p23.1 is one of the most copy number (CN) variable regions of the human genome. Whereas individual DEFB CNs have been suggested as independent genetic risk factors for several diseases (e.g. psoriasis and Crohn's disease), the role of multisite sequence variations (MSV) is less well understood and to date has only been reported for prostate cancer. Simultaneous assessment of MSVs and CNs can be achieved by PCR, cloning and Sanger sequencing, however, these methods are labour and cost intensive as well as prone to methodological bias introduced by bacterial cloning. Here, we demonstrate that amplicon sequencing of pooled individual PCR products by the 454 technology allows in-depth determination of MSV haplotypes and estimation of DEFB CNs in parallel. Results Six PCR products spread over ~87 kb of DEFB and harbouring 24 known MSVs were amplified from 11 DNA samples, pooled and sequenced on a Roche 454 GS FLX sequencer. From ~142,000 reads, ~120,000 haplotype calls (HC) were inferred that identified 22 haplotypes ranging from 2 to 7 per amplicon. In addition to the 24 known MSVs, two additional sequence variations were detected. Minimal CNs were estimated from the ratio of HCs and compared to absolute CNs determined by alternative methods. Concordance in CNs was found for 7 samples, the CNs differed by one in 2 samples and the estimated minimal CN was half of the absolute in one sample. For 7 samples and 2 amplicons, the 454 haplotyping results were compared to those by cloning/Sanger sequencing. Intrinsic problems related to chimera formation during PCR and differences between haplotyping by 454 and cloning/Sanger sequencing are discussed. Conclusion Deep amplicon sequencing using the 454 technology yield thousands of HCs per amplicon for an affordable price and may represent an effective method for parallel haplotyping and CN estimation in small to medium-sized cohorts. The obtained haplotypes

  17. Recombinant adeno-associated virus type 2 replication and packaging is entirely supported by a herpes simplex virus type 1 amplicon expressing Rep and Cap.

    PubMed Central

    Conway, J E; Zolotukhin, S; Muzyczka, N; Hayward, G S; Byrne, B J

    1997-01-01

    Recombinant adeno-associated virus (AAV) type 2 (rAAV) vectors have recently been shown to have great utility as gene transfer agents both in vitro and in vivo. One of the problems associated with the use of rAAV vectors has been the difficulty of large-scale vector production. Low-efficiency plasmid transfection of the rAAV vector and complementing AAV type 2 (AAV-2) functions (rep and cap) followed by superinfection with adenovirus has been the standard approach to rAAV production. The objectives of this study were to demonstrate the ability of a recombinant herpes simplex virus type 1 (HSV-1) amplicon expressing AAV-2 Rep and Cap to support replication and packaging of rAAV vectors. HSV-1 amplicon vectors were constructed which contain the AAV-2 rep and cap genes under control of their native promoters (p5, p19, and p40). An HSV-1 amplicon vector, HSV-RC/KOS or HSV-RC/d27, was generated by supplying helper functions with either wild-type HSV-1 (KOS strain) or the ICP27-deleted mutant of HSV-1, d27-1, respectively. Replication of the amplicon stocks is not inhibited by the presence of AAV-2 Rep proteins, which highlights important differences between HSV-1 and adenovirus replication and the mechanism of providing helper function for productive AAV infection. Coinfection of rAAV and HSV-RC/KOS resulted in the replication and amplification of rAAV genomes. Similarly, rescue and replication of rAAV genomes occurred when rAAV vector plasmids were transfected into cells followed by HSV-RC/KOS infection and when two rAAV proviral cell lines were infected with HSV-RC/KOS or HSV-RC/d27. Production of infectious rAAV by rescue from two rAAV proviral cell lines has also been achieved with HSV-RC/KOS and HSV-RC/d27. The particle titer of rAAV produced with HSV-RC/d27 is equal to that achieved by supplying rep and cap by transfection followed by adenovirus superinfection. Importantly, no detectable wild-type AAV-2 is generated with this approach. These results demonstrate

  18. User and clinician perspectives on DEKA arm: results of VA study to optimize DEKA arm.

    PubMed

    Resnik, Linda; Klinger, Shana Lieberman; Etter, Katherine

    2014-01-01

    This article summarizes feedback from Department of Veterans Affairs (VA) subjects and clinicians gathered during the VA optimization study of the DEKA Arm. VA subjects and clinicians tested two DEKA Arm prototypes (second-generation [gen 2] and third-generation [gen 3]). Features of the prototypes in three configurations are described. DEKA used feedback from the VA optimization study and from their own subjects to refine the gen 2 prototype. Thirty-three unique subjects participated in the VA evaluation; 26 participated in the gen 2 evaluation (1 subject participated twice), 13 participated in the gen 3 evaluation, and 5 participated in both gen 2 and gen 3 evaluations. Subject data were gathered through structured and open-ended surveys, interviews, and audio- and videotaped sessions. Study prosthetists and therapists provided ongoing feedback and completed surveys at the end of each subject's protocol. Eleven categories of feedback were identified: weight, cosmesis, hand grips, wrist design, elbow design, end-point control, foot controls, batteries and chargers, visual notifications, tactor, and socket features. Final feedback on the gen 3 was generally positive, particularly regarding improvements in wrist design, visual notifications, foot controls, end-point control, and cosmesis. Additional refinements to make the device lighter in weight, eliminate external wires and cables, and eliminate the external battery may further enhance its perceived usability and acceptability.

  19. Improving Memory Subsystem Performance Using ViVA: Virtual Vector Architecture

    SciTech Connect

    Gebis, Joseph; Oliker, Leonid; Shalf, John; Williams, Samuel; Yelick, Katherine

    2009-01-12

    The disparity between microprocessor clock frequencies and memory latency is a primary reason why many demanding applications run well below peak achievable performance. Software controlled scratchpad memories, such as the Cell local store, attempt to ameliorate this discrepancy by enabling precise control over memory movement; however, scratchpad technology confronts the programmer and compiler with an unfamiliar and difficult programming model. In this work, we present the Virtual Vector Architecture (ViVA), which combines the memory semantics of vector computers with a software-controlled scratchpad memory in order to provide a more effective and practical approach to latency hiding. ViVA requires minimal changes to the core design and could thus be easily integrated with conventional processor cores. To validate our approach, we implemented ViVA on the Mambo cycle-accurate full system simulator, which was carefully calibrated to match the performance on our underlying PowerPC Apple G5 architecture. Results show that ViVA is able to deliver significant performance benefits over scalar techniques for a variety of memory access patterns as well as two important memory-bound compact kernels, corner turn and sparse matrix-vector multiplication -- achieving 2x-13x improvement compared the scalar version. Overall, our preliminary ViVA exploration points to a promising approach for improving application performance on leading microprocessors with minimal design and complexity costs, in a power efficient manner.

  20. 76 FR 71439 - Amendment to an Enhanced-Use Lease (EUL) of Department of Veterans Affairs (VA) Real Property for...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-17

    ... the Development of Permanent Housing in Battle Creek, MI AGENCY: Department of Veterans Affairs... Battle Creek VA Medical Center in Michigan. The existing lessee will finance, design, develop,...

  1. Conversion of Input Data between KENO V.a and MCNP File Formats, Version 5L.

    2007-10-31

    Version 00 The KENO2MCNP program was written to convert KENO V.a input files to MCNP Format. This program currently only works with KENO Va geometries and will not work with geometries that contain more than a single array. A C++ graphical user interface was created that was linked to Fortran routines from KENO V.a that read the material library and Fortran routines from the MCNP Visual Editor that generate the MCNP input file. Either SCALEmore » 5.0 or SCALE 5.1 cross section files will work with this release. This version of KENO2MCNP was tested with CCC-730/MCNP5 1.40 and with CCC-725/SCALE5.0 and CCC-732/SCALE 5.1. Note that this distribution does not include either MCNP or SCALE, which are available separately through either RSICC or the NEA Data Bank.« less

  2. Evidence for a novel mechanism for gene amplification in multiple myeloma: 1q12 pericentromeric heterochromatin mediates breakage-fusion-bridge cycles of a 1q12 approximately 23 amplicon.

    PubMed

    Sawyer, Jeffrey R; Tian, Erming; Thomas, Edward; Koller, Mark; Stangeby, Colin; Sammartino, Gael; Goosen, Linda; Swanson, Charles; Binz, Regina L; Barlogie, Bart; Shaughnessy, John

    2009-11-01

    Gene amplification is defined as a copy number (CN) increase in a restricted region of a chromosome arm, and is a mechanism for acquired drug resistance and oncogene activation. In multiple myeloma (MM), high CNs of genes in a 1q12 approximately 23 amplicon have been associated with disease progression and poor prognosis. To investigate the mechanisms for gene amplification in this region in MM, we performed a comprehensive metaphase analysis combining G-banding, fluorescence in situ hybridization, and spectral karyotyping in 67 patients with gain of 1q. In six patients (9%), evidence for at least one breakage-fusion-bridge (BFB) cycle was found. In three patients (4%), extended ladders of 1q12 approximately 23 amplicons were identified. Several key structures that are predicted intermediates in BFB cycles were observed, including: equal-spaced organization of amplicons, inverted repeat organization of amplicons along the same chromosome arm, and deletion of sequences distal to the amplified region. The 1q12 pericentromeric heterochromatin region served as both a recurrent breakpoint as well as a fusion point for sister chromatids, and ultimately bracketed both the proximal and distal boundaries of the amplicon. Our findings provide evidence for a novel BFB mechanism involving 1q12 pericentromeric breakage in the amplification of a large number of genes within a 1q12 approximately 23 amplicon.

  3. Effects of the KiVa antibullying program on cyberbullying and cybervictimization frequency among Finnish youth.

    PubMed

    Williford, Anne; Elledge, L Christian; Boulton, Aaron J; DePaolis, Kathryn J; Little, Todd D; Salmivalli, Christina

    2013-01-01

    Cyberbullying among school-aged children has received increased attention in recent literature. However, no empirical evidence currently exists on whether existing school-based antibullying programs are effective in targeting the unique aspects of cyberbullying. To address this important gap, the present study investigates the unique effects of the KiVa Antibullying Program on the frequency of cyberbullying and cybervictimization among elementary and middle school youth. Using data from a group randomized controlled trial, multilevel ordinal regression analyses were used to examine differences in the frequencies of cyberbullying and cybervictimization between intervention (N = 9,914) and control students (N = 8,498). The effects of age and gender on frequencies of cyber behaviors were also assessed across conditions. Results revealed a significant intervention effect on the frequency of cybervictimization; KiVa students reported lower frequencies of cybervictimization at posttest than students in a control condition. The effect of condition on the perpetration of cyberbullying was moderated by age. When student age was below the sample mean, KiVa students reported lower frequencies of cyberbullying than students in the control condition. We also found evidence of classroom level variation in cyberbullying and cybervictimization, suggesting cyberbullying is in part a classroom-level phenomenon. KiVa appears to be an efficacious program to address cyber forms of bullying and victimization. We discuss several unique aspects of KiVa that may account for the significant intervention effects. Results suggest that KiVa is an intervention option for schools concerned with reducing cyberbullying behavior and its deleterious effects on children's adjustment.

  4. Physical stability of solid dispersions with respect to thermodynamic solubility of tadalafil in PVP-VA.

    PubMed

    Wlodarski, K; Sawicki, W; Kozyra, A; Tajber, L

    2015-10-01

    The aim of this paper was to evaluate physical stability of solid dispersions in respect to the drug, tadalafil (Td), in vinylpyrrolidone and vinyl acetate block copolymer (PVP-VA). Nine solid dispersions of Td in PVP-VA (Td/PVP-VA) varied in terms of quantitative composition (1:9-9:1, w/w) were successfully produced by spray-drying. Their amorphous nature, supersaturated character and molecular level of mixing (a solid solution structure) were subsequently confirmed using DSC, PXRD, SEM and calculation of Hansen total solubility parameters. Due to thermal degradation of both components before the melting point of Td (302.3°C), an approach based on the drug crystallization from the supersaturated solid dispersion was selected to calculate the solubility of Td in the polymer. Annealing of the Td/PVP-VA solid dispersion (1:1, w/w) at selected temperatures above its Tg resulted in different stable solid dispersions. According to the Gordon-Taylor equation their new Tgs gave the information about the quantitative composition which corresponded to the thermodynamic solubility of Td in PVP-VA at given temperatures of annealing. The obtained relationship was fitted to the exponential function, with the calculated solubility of Td of 20.5% at 25°C. This value was in accordance with the results of hot stage polarizing light microscopy as well as stability tests carried out at 80°C and 0% RH, in which Td solid dispersions containing 10-20% of the drug were the only systems that did not crystallize within two months. A thermal analysis protocol utilizing a fast heating rate was shown to generate Td solubility data complementing the solid dispersion method. The Flory-Huggins model applied for the Td/PVP-VA system yielded the solubility value of 0.1% at 25°C, showing the lack of applicability in this case.

  5. Motor coupling through lipid membranes enhances transport velocities for ensembles of myosin Va

    PubMed Central

    Nelson, Shane R.; Trybus, Kathleen M.; Warshaw, David M.

    2014-01-01

    Myosin Va is an actin-based molecular motor responsible for transport and positioning of a wide array of intracellular cargoes. Although myosin Va motors have been well characterized at the single-molecule level, physiological transport is carried out by ensembles of motors. Studies that explore the behavior of ensembles of molecular motors have used nonphysiological cargoes such as DNA linkers or glass beads, which do not reproduce one key aspect of vesicular systems—the fluid intermotor coupling of biological lipid membranes. Using a system of defined synthetic lipid vesicles (100- to 650-nm diameter) composed of either 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) (fluid at room temperature) or 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) (gel at room temperature) with a range of surface densities of myosin Va motors (32–125 motors per μm2), we demonstrate that the velocity of vesicle transport by ensembles of myosin Va is sensitive to properties of the cargo. Gel-state DPPC vesicles bound with multiple motors travel at velocities equal to or less than vesicles with a single myosin Va (∼450 nm/s), whereas surprisingly, ensembles of myosin Va are able to transport fluid-state DOPC vesicles at velocities significantly faster (>700 nm/s) than a single motor. To explain these data, we developed a Monte Carlo simulation that suggests that these reductions in velocity can be attributed to two distinct mechanisms of intermotor interference (i.e., load-dependent modulation of stepping kinetics and binding-site exclusion), whereas faster transport velocities are consistent with a model wherein the normal stepping behavior of the myosin is supplemented by the preferential detachment of the trailing motor from the actin track. PMID:25201964

  6. Novel hydrogel obtained by chitosan and dextrin-VA co-polymerization.

    PubMed

    Ramos, Reinaldo; Carvalho, Vera; Gama, Miguel

    2006-08-01

    A novel hydrogel was obtained by reticulation of chitosan with dextrin enzymatically linked to vinyl acrylate (dextrin-VA), without cross-linking agents. The hydrogel had a solid-like behaviour with G' (storage modulus) > G'' (loss modulus). Glucose diffusion coefficients of 3.9 x 10(-6) +/- 1.3 x 10(-6) cm(2)/s and 2.9 x 10(-6) +/- 0.5 x 10(-6) cm(2)/s were obtained for different substitution degrees of the dextrin-VA (20% and 70% respectively). SEM observation revealed a porous structure, with pores ranging from 50 microm to 150 microm. PMID:16802098

  7. Influence of PVP/VA copolymer composition on drug-polymer solubility.

    PubMed

    Rask, Malte Bille; Knopp, Matthias Manne; Olesen, Niels Erik; Holm, René; Rades, Thomas

    2016-03-31

    In this study, the influence of copolymer composition on drug-polymer solubility was investigated. The solubility of the model drug celecoxib (CCX) in various polyvinylpyrrolidone/vinyl acetate (PVP/VA) copolymer compositions (70/30, 60/40, 50/50 and 30/70 w/w) and the pure homopolymers polyvinylpyrrolidone (PVP) and polyvinyl acetate (PVA) was predicted at 25 °C using a thermal analysis method based on the recrystallization of a supersaturated amorphous dispersion (recrystallization method). These solubilities were compared with a prediction based on the solubility of CCX in the liquid monomeric precursors of PVP/VA, N-vinylpyrrolidone (NVP) and vinyl acetate (VA), using the Flory-Huggins lattice theory (liquid monomer solubility approach). The solubilities predicted from the liquid monomer solubility approach increased linearly with increasing VP/VA ratio from 0.03-0.60 w/w. Even though the solubilities predicted from the recrystallization method also increased with increasing VP/VA ratio from 0.02-0.40 w/w, the predicted solubility seemed to approach a plateau at high VP/VA ratios. Increasing positive deviations from the Gordon-Taylor equation with increasing VP/VA ratio indicated strong interactions between CCX and the VP repeat unit, which was in accordance with the relatively high solubilities predicted using both methods. As the solubility plateau may be a consequence of steric hindrance caused by the size differences between CCX and the VP repeat units, it is likely that a CCX molecule interacting with a VP repeat unit hinders another CCX molecule from binding to the neighboring repeat units in the polymer chain. Therefore, it is possible that replacing these neighboring hygroscopic VP repeat units with hydrophobic VA repeat units, could increase the physical stability of an amorphous solid dispersion without compromising the drug-polymer solubility. This knowledge could be used advantageously in future development of amorphous drug delivery systems as

  8. Exploring the Gastrointestinal “Nemabiome”: Deep Amplicon Sequencing to Quantify the Species Composition of Parasitic Nematode Communities

    PubMed Central

    Avramenko, Russell W.; Redman, Elizabeth M.; Lewis, Roy; Yazwinski, Thomas A.; Wasmuth, James D.; Gilleard, John S.

    2015-01-01

    Parasitic helminth infections have a considerable impact on global human health as well as animal welfare and production. Although co-infection with multiple parasite species within a host is common, there is a dearth of tools with which to study the composition of these complex parasite communities. Helminth species vary in their pathogenicity, epidemiology and drug sensitivity and the interactions that occur between co-infecting species and their hosts are poorly understood. We describe the first application of deep amplicon sequencing to study parasitic nematode communities as well as introduce the concept of the gastro-intestinal “nemabiome”. The approach is analogous to 16S rDNA deep sequencing used to explore microbial communities, but utilizes the nematode ITS-2 rDNA locus instead. Gastro-intestinal parasites of cattle were used to develop the concept, as this host has many well-defined gastro-intestinal nematode species that commonly occur as complex co-infections. Further, the availability of pure mono-parasite populations from experimentally infected cattle allowed us to prepare mock parasite communities to determine, and correct for, species representation biases in the sequence data. We demonstrate that, once these biases have been corrected, accurate relative quantitation of gastro-intestinal parasitic nematode communities in cattle fecal samples can be achieved. We have validated the accuracy of the method applied to field-samples by comparing the results of detailed morphological examination of L3 larvae populations with those of the sequencing assay. The results illustrate the insights that can be gained into the species composition of parasite communities, using grazing cattle in the mid-west USA as an example. However, both the technical approach and the concept of the ‘nemabiome’ have a wide range of potential applications in human and veterinary medicine. These include investigations of host-parasite and parasite-parasite interactions

  9. Identification of amplified and highly expressed genes in amplicons of the T-cell line huT78 detected by cDNA microarray CGH

    PubMed Central

    Meléndez, Bárbara; Martínez-Delgado, Beatriz; Cuadros, Marta; Fernández, Victoria; Díaz-Uriarte, Ramón; Benítez, Javier

    2005-01-01

    Background Conventional Comparative Genomic Hybridization (CGH) has been widely used for detecting copy number alterations in cancer and for identifying regions containing candidate tumor responsible genes. Recently, several studies have shown the utility of cDNA microarray CGH for studing gene copy changes in various types of tumors. However, no such studies on T-cell lymphomas have been performed. To date T-cell lymphomas analyzed by the use of chromosome CGH have revealed only slight copy number alterations and not gene amplifications. Results In the present study, we describe the characterization of three amplicons of the T-cell line huT78 located at 2q34-q37, 8q23-q24 and 20p, where new amplified and overexpressed genes are found. The use of a cDNA microarray containing 7.657 transcripts allowed the identification of certain genes, such as BCLX, PCNA, FKBP1A, IGFBP2 and cMYC, that are amplified, highly expressed, and also contained in the amplicons on 20p and 2q. The expresion of these genes was analyzed in 39 T-cell lymphomas and 3 other T-cell lines. Conclusion By the use of conventional CGH and CGH and expression cDNA microarrays we defined three amplicons in the T-cell line huT78 and identified several novel gene amplifications (BCLX, PCNA, FKBP1A, IGFBP2 and cMYC). We showed that overexpression of the amplified genes could be attributable to gene dosage. We speculate that deregulation of those genes could be important in the development of T-cell lymphomas and/or in the maintenance of T-cell lines. PMID:15656903

  10. Combination vascular delivery of herpes simplex oncolytic viruses and amplicon mediated cytokine gene transfer is effective therapy for experimental liver cancer.

    PubMed Central

    Zager, J. S.; Delman, K. A.; Malhotra, S.; Ebright, M. I.; Bennett, J. J.; Kates, T.; Halterman, M.; Federoff, H.; Fong, Y.

    2001-01-01

    BACKGROUND: Herpes simplex type I (HSV)-based vectors have been used experimentally for suicide gene therapy, immunomodulatory gene delivery, and direct oncolytic therapy. The current study utilizes the novel concept of regional delivery of an oncolytic virus in combination with or serving as the helper virus for packaging herpes-based amplicon vectors carrying a cytokine transgene, with the goal of identifying if this combination is more efficacious than either modality alone. MATERIALS AND METHODS: A replication competent oncolytic HSV (G207) and a replication incompetent HSV amplicon carrying the gene for the immunomodulatory cytokine IL-2 (HSV-IL2) were tested in murine syngeneic colorectal carcinoma and in rat hepatocellular carcinoma models. Liver tumors were treated with vascular delivery of (1) phosphate-buffered saline (PBS), (2) G207, (3) HSV-IL2, (4) G207 and HSV-IL2 mixed in combination (mG207/HSV- IL2), and (5) G207 as the helper virus for packaging the construct HSV-IL2 (pG207/HSV-IL2). RESULTS: Tumor burden was significantly reduced in all treatment groups in both rats and mice treated with high-dose G207, HSV-IL2, or both (p < 0.02). When a low dose of virus was used in mice, anti-tumor efficacy was improved by use of G207 and HSV-IL2 in combination or with HSV-IL2 packaged by G207 (p < 0.001). This improvement was abolished when CD4(+) and CD8(+) lymphocytes were depleted, implying that the enhanced anti-tumor response to low-dose combined therapy is immune mediated. CONCLUSIONS: Vascular regional delivery of oncolytic and amplicon HSV vectors can be used to induce improved anti-tumor efficacy by combining oncolytic and immunostimulatory strategies. PMID:11591892

  11. 75 FR 24510 - Drug and Drug-Related Supply Promotion by Pharmaceutical Company Sales Representatives at VA...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-05

    ... limited to hospitals, CBOCs, nursing homes, and domiciliaries. We would define ``VA National Formulary... Veterans Nursing Home Care and 64.011 Veterans Dental Care. List of Subjects in 38 CFR Part 1... standard of permissible business practice at VA facilities. It would also facilitate mutually...

  12. 75 FR 51331 - Draft Tier II Environmental Impact Statement: Southeast High Speed Rail Corridor-Richmond, VA...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-19

    ... Federal Railroad Administration Draft Tier II Environmental Impact Statement: Southeast High Speed Rail... the Tier II Draft Environmental Impact Statement for the Southeast High Speed Rail, Richmond, VA to... the Draft Tier II Environmental Impact Statement for the Southeast High Speed Rail, Richmond, VA...

  13. 33 CFR 334.330 - Atlantic Ocean and connecting waters in vicinity of Myrtle Island, Va.; Air Force practice...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false Atlantic Ocean and connecting waters in vicinity of Myrtle Island, Va.; Air Force practice bombing, rocket firing, and gunnery range... waters in vicinity of Myrtle Island, Va.; Air Force practice bombing, rocket firing, and gunnery...

  14. 33 CFR 334.330 - Atlantic Ocean and connecting waters in vicinity of Myrtle Island, Va.; Air Force practice...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 3 2014-07-01 2014-07-01 false Atlantic Ocean and connecting waters in vicinity of Myrtle Island, Va.; Air Force practice bombing, rocket firing, and gunnery range... waters in vicinity of Myrtle Island, Va.; Air Force practice bombing, rocket firing, and gunnery...

  15. 33 CFR 334.330 - Atlantic Ocean and connecting waters in vicinity of Myrtle Island, Va.; Air Force practice...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 3 2011-07-01 2011-07-01 false Atlantic Ocean and connecting waters in vicinity of Myrtle Island, Va.; Air Force practice bombing, rocket firing, and gunnery range... waters in vicinity of Myrtle Island, Va.; Air Force practice bombing, rocket firing, and gunnery...

  16. 33 CFR 334.330 - Atlantic Ocean and connecting waters in vicinity of Myrtle Island, Va.; Air Force practice...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 3 2012-07-01 2012-07-01 false Atlantic Ocean and connecting waters in vicinity of Myrtle Island, Va.; Air Force practice bombing, rocket firing, and gunnery range... waters in vicinity of Myrtle Island, Va.; Air Force practice bombing, rocket firing, and gunnery...

  17. 33 CFR 334.330 - Atlantic Ocean and connecting waters in vicinity of Myrtle Island, Va.; Air Force practice...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 3 2013-07-01 2013-07-01 false Atlantic Ocean and connecting waters in vicinity of Myrtle Island, Va.; Air Force practice bombing, rocket firing, and gunnery range... waters in vicinity of Myrtle Island, Va.; Air Force practice bombing, rocket firing, and gunnery...

  18. 77 FR 23615 - Payment or Reimbursement for Emergency Services for Nonservice-Connected Conditions in Non-VA...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-20

    ... Sec. 17.1004(f). In a document published in the Federal Register on May 26, 2011 (76 FR 30598), VA... FR 79071), VA published an entirely separate final rule that added new paragraphs (c) and (d) to Sec... support of this rulemaking. Another commenter identified perceived inconsistencies between 38 U.S.C....

  19. 33 CFR 334.280 - James River between the entrance to Skiffes Creek and Mulberry Point, Va.; army training and...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 3 2013-07-01 2013-07-01 false James River between the entrance to Skiffes Creek and Mulberry Point, Va.; army training and small craft testing area. 334.280 Section... Creek and Mulberry Point, Va.; army training and small craft testing area. (a) The restricted...

  20. 33 CFR 334.280 - James River between the entrance to Skiffes Creek and Mulberry Point, Va.; army training and...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 3 2012-07-01 2012-07-01 false James River between the entrance to Skiffes Creek and Mulberry Point, Va.; army training and small craft testing area. 334.280 Section... Creek and Mulberry Point, Va.; army training and small craft testing area. (a) The restricted...

  1. 33 CFR 334.280 - James River between the entrance to Skiffes Creek and Mulberry Point, Va.; army training and...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 3 2014-07-01 2014-07-01 false James River between the entrance to Skiffes Creek and Mulberry Point, Va.; army training and small craft testing area. 334.280 Section... Creek and Mulberry Point, Va.; army training and small craft testing area. (a) The restricted...

  2. 38 CFR 17.56 - Payment for non-VA physician and other health care professional services.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...' (CMS) participating physician fee schedule for the period in which the service is provided (see 42 CFR...-VA physician and other health care professional services. (a) Except for anesthesia services, and... schedule or if the services constitute anesthesia services, payment for such non-VA health...

  3. Statistical Match of the VA 1979-1980 Recipient File against the 1979-1980 Basic Grant Recipient File. Revised.

    ERIC Educational Resources Information Center

    Applied Management Sciences, Inc., Silver Spring, MD.

    The amount of misreporting of Veterans Administration (VA) benefits was assessed, along with the impact of misreporting on the Basic Educational Opportunity Grant (BEOG) program. Accurate financial information is need to determine appropriate awards. The analysis revealed: over 97% of VA beneficiaries misreported benefits; the total net loss to…

  4. 33 CFR 334.280 - James River between the entrance to Skiffes Creek and Mulberry Point, Va.; army training and...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... to Skiffes Creek and Mulberry Point, Va.; army training and small craft testing area. 334.280 Section 334.280 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF... Creek and Mulberry Point, Va.; army training and small craft testing area. (a) The restricted...

  5. 33 CFR 334.250 - Gunston Cove, at Whitestone Point, Va.; U.S. Army restricted area.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ..., Va.; U.S. Army restricted area. 334.250 Section 334.250 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE DANGER ZONE AND RESTRICTED AREA REGULATIONS § 334.250 Gunston Cove, at Whitestone Point, Va.; U.S. Army restricted area. (a) The area. The waters...

  6. 33 CFR 334.280 - James River between the entrance to Skiffes Creek and Mulberry Point, Va.; army training and...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... to Skiffes Creek and Mulberry Point, Va.; army training and small craft testing area. 334.280 Section 334.280 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF... Creek and Mulberry Point, Va.; army training and small craft testing area. (a) The restricted...

  7. 33 CFR 334.250 - Gunston Cove, at Whitestone Point, Va.; U.S. Army restricted area.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ..., Va.; U.S. Army restricted area. 334.250 Section 334.250 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE DANGER ZONE AND RESTRICTED AREA REGULATIONS § 334.250 Gunston Cove, at Whitestone Point, Va.; U.S. Army restricted area. (a) The area. The waters...

  8. 77 FR 64388 - Agency Information Collection (Former POW Medical History), VA Form 10-0048 Activities Under OMB...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-19

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF VETERANS AFFAIRS Agency Information Collection (Former POW Medical History), VA Form 10-0048 Activities Under OMB....'' SUPPLEMENTARY INFORMATION: Title: Former POW Medical History, VA Form 10-0048. OMB Control Number:...

  9. Identification and mapping of adult plant stripe rust resistance in soft red winter wheat VA00W-38

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Virginia Tech experimental wheat (Triticum aestivum L.) line VA00W-38 has adult plant resistance to race PST-100, which was the predominant race of stripe rust (Puccinia striiformis f. sp. tritici) in the United States from 2003 to 2006. Resistance was characterized in a cross between VA00W-38 a...

  10. 38 CFR 58.15 - VA Form 10-0143-Department of Veterans Affairs Certification Regarding Drug-Free Workplace...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2010-07-01 2010-07-01 false VA Form 10-0143-Department of Veterans Affairs Certification Regarding Drug-Free Workplace Requirements for Grantees Other Than Individuals. 58.15 Section 58.15 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) FORMS § 58.15 VA Form...

  11. 75 FR 26160 - Drug and Drug-Related Supply Promotion by Pharmaceutical Company Sales Representatives at VA...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-11

    ... VA medical facilities, including but not limited to hospitals, CBOCs, nursing homes, and... Veterans Nursing Home Care and 64.011 Veterans Dental Care. Signing Authority The Secretary of Veterans... VA facilities, and provide sales representatives with a consistent standard of permissible...

  12. 48 CFR 852.219-72 - Evaluation factor for participation in the VA mentor-protégé program.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... program. As prescribed in 819.7115(b), insert the following clause: Evaluation Factor for Participation in the VA Mentor-Protégé Program (DEC2009) This solicitation contains an evaluation factor or sub-factor regarding participation in the VA Mentor-Protégé Program. In order to receive credit under the...

  13. 48 CFR 852.219-72 - Evaluation factor for participation in the VA mentor-protégé program.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... program. As prescribed in 819.7115(b), insert the following clause: Evaluation Factor for Participation in the VA Mentor-Protégé Program (DEC2009) This solicitation contains an evaluation factor or sub-factor regarding participation in the VA Mentor-Protégé Program. In order to receive credit under the...

  14. 48 CFR 852.219-72 - Evaluation factor for participation in the VA mentor-protégé program.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... program. As prescribed in 819.7115(b), insert the following clause: Evaluation Factor for Participation in the VA Mentor-Protégé Program (DEC2009) This solicitation contains an evaluation factor or sub-factor regarding participation in the VA Mentor-Protégé Program. In order to receive credit under the...

  15. 48 CFR 852.219-72 - Evaluation factor for participation in the VA mentor-protégé program.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... program. As prescribed in 819.7115(b), insert the following clause: Evaluation Factor for Participation in the VA Mentor-Protégé Program (DEC2009) This solicitation contains an evaluation factor or sub-factor regarding participation in the VA Mentor-Protégé Program. In order to receive credit under the...

  16. 48 CFR 852.219-72 - Evaluation factor for participation in the VA mentor-protégé program.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... program. As prescribed in 819.7115(b), insert the following clause: Evaluation Factor for Participation in the VA Mentor-Protégé Program (DEC2009) This solicitation contains an evaluation factor or sub-factor regarding participation in the VA Mentor-Protégé Program. In order to receive credit under the...

  17. 33 CFR 334.250 - Gunston Cove, at Whitestone Point, Va.; U.S. Army restricted area.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ..., Va.; U.S. Army restricted area. 334.250 Section 334.250 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE DANGER ZONE AND RESTRICTED AREA REGULATIONS § 334.250 Gunston Cove, at Whitestone Point, Va.; U.S. Army restricted area. (a) The area. The waters...

  18. 33 CFR 334.250 - Gunston Cove, at Whitestone Point, Va.; U.S. Army restricted area.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ..., Va.; U.S. Army restricted area. 334.250 Section 334.250 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE DANGER ZONE AND RESTRICTED AREA REGULATIONS § 334.250 Gunston Cove, at Whitestone Point, Va.; U.S. Army restricted area. (a) The area. The waters...

  19. 76 FR 70345 - Drawbridge Operation Regulations; Elizabeth River, Eastern Branch, Norfolk, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-14

    ...The Commander, Fifth Coast Guard District, has issued a temporary deviation from the regulations governing the operation of the Norfolk Southern 5 Railroad Bridge, mile 1.1, Norfolk, VA. Under this temporary deviation, the drawbridge may remain in the closed position on specific dates and times to facilitate laying new...

  20. 78 FR 49920 - Drawbridge Operation Regulation; Elizabeth River, Eastern Branch, Norfolk, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-16

    ...The Coast Guard has issued a temporary deviation from the operating schedule that governs the draw of the Norfolk Southern 5 Railroad Bridge, across the Elizabeth River Eastern Branch, mile 1.1, at Norfolk, VA. This deviation is necessary to facilitate replacing the broken tread plates and shimming the remaining tread plates to the proper elevation on the Norfolk Southern 5......

  1. 77 FR 74586 - Drawbridge Operation Regulation; Elizabeth River, Eastern Branch, Norfolk, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-17

    ...The Coast Guard has issued a temporary deviation from the operating schedule that governs the operation of the Norfolk Southern V2.8 Railroad Bridge across the Elizabeth River (Eastern Branch), mile 2.7, at Norfolk, VA. This deviation is necessary to facilitate replacing bearings on the Norfolk Southern V2.8 Railroad Bridge. This temporary deviation will allow the drawbridge......

  2. 48 CFR 852.219-71 - VA mentor-protégé program.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... Electronic Subcontracting Reporting System (eSRS). (e) Contractors interested in participating in the program... AFFAIRS CLAUSES AND FORMS SOLICITATION PROVISIONS AND CONTRACT CLAUSES Texts of Provisions and Clauses 852... contracts and subcontracts. (d) Large business prime contractors serving as mentors in the VA...

  3. 76 FR 44288 - Establishment of Class E Airspace; New Market, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-07-25

    ...; (2) is not a ``significant rule'' under DOT Regulatory Policies and Procedures (44 FR 11034; February...: Authority: 49 U.S.C. 106(g); 40103, 40113, 40120; E.O. 10854, 24 FR 9565, 3 CFR, 1959-1963 Comp., p. 389... Federal Aviation Administration 14 CFR Part 71 Establishment of Class E Airspace; New Market, VA...

  4. 76 FR 64236 - Establishment of Class E Airspace; New Market, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-18

    ... establish Class E airspace at New Market, VA (76 FR 44288). Interested parties were invited to participate... ``significant rule'' under DOT Regulatory Policies and Procedures (44 FR 11034; February 26, 1979); and (3) does... continues to read as follows: Authority: 49 U.S.C. 106(g); 40103, 40113, 40120; E.O. 10854, 24 FR 9565,...

  5. 77 FR 3844 - Proposed Information Collection (Dependents' Application for VA Educational Benefits) Activity...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-25

    ... Survivors' and Dependents' Educational Assistance and Fry Scholarship benefits. DATES: Written comments and... Sergeant John David Fry Scholarship (Fry Scholarship) benefits. VA will use the information collected to determine whether a claimant qualifies for DEA or Fry Scholarship benefits and if the program of...

  6. 77 FR 30050 - VA National Academic Affiliations Council, Notice of meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-21

    ... AFFAIRS VA National Academic Affiliations Council, Notice of meeting The Department of Veterans Affairs... the National Academic Affiliations Council will be held on June 5-6, 2012, in Suite 878 at 1800 G.... on June 5 and at 1 p.m. on June 6. The purpose of the Council is to advise the Secretary on...

  7. 30 CFR 57.22312 - Distribution boxes (II-A and V-A mines).

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... approved equipment shall be approved by MSHA under 30 CFR part 18. ... 30 Mineral Resources 1 2014-07-01 2014-07-01 false Distribution boxes (II-A and V-A mines). 57... MINES Safety Standards for Methane in Metal and Nonmetal Mines Equipment § 57.22312 Distribution...

  8. 30 CFR 57.22312 - Distribution boxes (II-A and V-A mines).

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... approved equipment shall be approved by MSHA under 30 CFR part 18. ... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Distribution boxes (II-A and V-A mines). 57... MINES Safety Standards for Methane in Metal and Nonmetal Mines Equipment § 57.22312 Distribution...

  9. 30 CFR 57.22312 - Distribution boxes (II-A and V-A mines).

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... approved equipment shall be approved by MSHA under 30 CFR part 18. ... 30 Mineral Resources 1 2012-07-01 2012-07-01 false Distribution boxes (II-A and V-A mines). 57... MINES Safety Standards for Methane in Metal and Nonmetal Mines Equipment § 57.22312 Distribution...

  10. 30 CFR 57.22312 - Distribution boxes (II-A and V-A mines).

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... approved equipment shall be approved by MSHA under 30 CFR part 18. ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Distribution boxes (II-A and V-A mines). 57... MINES Safety Standards for Methane in Metal and Nonmetal Mines Equipment § 57.22312 Distribution...

  11. 30 CFR 57.22312 - Distribution boxes (II-A and V-A mines).

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... approved equipment shall be approved by MSHA under 30 CFR part 18. ... 30 Mineral Resources 1 2013-07-01 2013-07-01 false Distribution boxes (II-A and V-A mines). 57... MINES Safety Standards for Methane in Metal and Nonmetal Mines Equipment § 57.22312 Distribution...

  12. 76 FR 34248 - Equestrian Stables at Meadowood Special Recreation Management Area, VA; Information Sharing Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-13

    ... Management Eastern States has scheduled a public meeting to share information about the condition of the... Equestrian Stables at Meadowood Special Recreation Management Area, VA; Information Sharing Meeting AGENCY... FURTHER INFORMATION CONTACT: E. Lynn Burkett, BLM-ES Lower Potomac Field Station Manager; phone:...

  13. 30 CFR 57.22229 - Weekly testing (I-A, III, and V-A mines).

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 30 Mineral Resources 1 2012-07-01 2012-07-01 false Weekly testing (I-A, III, and V-A mines). 57.22229 Section 57.22229 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR METAL AND NONMETAL MINE SAFETY AND HEALTH SAFETY AND HEALTH STANDARDS-UNDERGROUND METAL AND NONMETAL MINES Safety Standards for Methane in Metal...

  14. 30 CFR 57.22229 - Weekly testing (I-A, III, and V-A mines).

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 30 Mineral Resources 1 2013-07-01 2013-07-01 false Weekly testing (I-A, III, and V-A mines). 57.22229 Section 57.22229 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR METAL AND NONMETAL MINE SAFETY AND HEALTH SAFETY AND HEALTH STANDARDS-UNDERGROUND METAL AND NONMETAL MINES Safety Standards for Methane in Metal...

  15. 77 FR 33089 - OPSAIL 2012 Virginia, Port of Hampton Roads, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-06-05

    ... Acronyms DHS Department of Homeland Security FR Federal Register NPRM Notice of Proposed Rulemaking A...) entitled ``OPSAIL 2012 Virginia, Port of Hampton Roads, VA'' in the Federal Register (77 FR 19957). We... on the human environment. This rule involves implementation of regulations at 33 CFR part 100...

  16. 75 FR 34639 - Safety Zone; Reedville July 4th Celebration, Cockrell's Creek, Reedville, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-18

    ... the Reedville July 4th Celebration event. This action is intended to restrict vessel traffic movement... Celebration, Cockrell's Creek, Reedville, VA in the Federal Register (75 FR 26157). We received no comments on... standards bodies. This rule does not use technical standards. Therefore, we did not consider the use...

  17. 78 FR 52085 - VA Veteran-Owned Small Business Verification Guidelines

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-22

    ... requires the Department of Veterans Affairs (VA) to verify ownership and control of veteran- ] owned small... (77 FR 38181) an interim final rule that revised the requirement for re-verification of SDVOSB/VOSB... examination, the regulatory requirement of participants to report changes to ownership and control...

  18. 75 FR 22545 - Safety Zone; Private Fireworks, Wilson Creek, Gloucester, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-29

    ... Mandates Reform Act of 1995 (2 U.S.C. 1531-1538) requires Federal agencies to assess the effects of their... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; Private Fireworks, Wilson Creek, Gloucester... establishing a safety zone on Wilson Creek in the vicinity of Gloucester, VA in support of a private...

  19. 77 FR 70210 - Agency Information Collection (VA Subcontracting Report for Service Disabled Veteran-owned Small...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-23

    .... 2900-0741'' in any correspondence. FOR FURTHER INFORMATION CONTACT: Crystal Rennie, Enterprise Records...-7492, fax (202) 632-7583 or email crystal.rennie@va.gov . Please refer to ``OMB Control No. 2900-0741... Average Burden per Respondent: 2 Hours. Frequency of Response: One time. Estimated Number of...

  20. 48 CFR 852.219-71 - VA mentor-protégé program.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 48 Federal Acquisition Regulations System 5 2014-10-01 2014-10-01 false VA mentor-protégé program. 852.219-71 Section 852.219-71 Federal Acquisition Regulations System DEPARTMENT OF VETERANS AFFAIRS CLAUSES AND FORMS SOLICITATION PROVISIONS AND CONTRACT CLAUSES Texts of Provisions and Clauses...

  1. 48 CFR 852.219-9 - VA Small business subcontracting plan minimum requirements.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 48 Federal Acquisition Regulations System 5 2014-10-01 2014-10-01 false VA Small business subcontracting plan minimum requirements. 852.219-9 Section 852.219-9 Federal Acquisition Regulations System DEPARTMENT OF VETERANS AFFAIRS CLAUSES AND FORMS SOLICITATION PROVISIONS AND CONTRACT CLAUSES Texts...

  2. 75 FR 55615 - Hanesbrands, Inc., Galax, VA; Notice of Negative Determination on Reconsideration

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-13

    ... Employment and Training Administration Hanesbrands, Inc., Galax, VA; Notice of Negative Determination on.... The Department's Notice was published in the Federal Register on May 20, 2010 (75 FR 28295). The initial investigation resulted in a negative determination based on the finding that Parkdale...

  3. Belowground-system development of VA mycorrhiza in a restored tallgrass prairie community

    SciTech Connect

    Cook, B.D.; Jastrow, J.D.; Miller, R.M.; McGraw, A.C.

    1987-01-01

    This study was conducted to determine the relationship between root and VA mycorrhizal fungus development in a tallgrass prairie restoration chronosequence. Emphasis is placed on characterizing the relationship of root length, colonized root length, and percentage of root length occupied by the mycorrhizal fungus by differing root size classes. Mycorrhizal fungus composition and populations along the restoration chronosequence was determined. 3 refs., 1 fig.

  4. 38 CFR 21.9510 - Claims, VA's duty to assist, and time limits.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2014-07-01 2014-07-01 false Claims, VA's duty to assist, and time limits. 21.9510 Section 21.9510 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) VOCATIONAL REHABILITATION AND EDUCATION Post-9/11 GI Bill Claims...

  5. 38 CFR 21.9510 - Claims, VA's duty to assist, and time limits.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2010-07-01 2010-07-01 false Claims, VA's duty to assist, and time limits. 21.9510 Section 21.9510 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) VOCATIONAL REHABILITATION AND EDUCATION Post-9/11 GI Bill Claims...

  6. 38 CFR 21.9510 - Claims, VA's duty to assist, and time limits.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2012-07-01 2012-07-01 false Claims, VA's duty to assist, and time limits. 21.9510 Section 21.9510 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) VOCATIONAL REHABILITATION AND EDUCATION Post-9/11 GI Bill Claims...

  7. 38 CFR 21.9510 - Claims, VA's duty to assist, and time limits.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2011-07-01 2011-07-01 false Claims, VA's duty to assist, and time limits. 21.9510 Section 21.9510 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) VOCATIONAL REHABILITATION AND EDUCATION Post-9/11 GI Bill Claims...

  8. 38 CFR 21.9510 - Claims, VA's duty to assist, and time limits.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2013-07-01 2013-07-01 false Claims, VA's duty to assist, and time limits. 21.9510 Section 21.9510 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) VOCATIONAL REHABILITATION AND EDUCATION Post-9/11 GI Bill Claims...

  9. 33 CFR 334.220 - Chesapeake Bay, south of Tangier Island, Va.; naval firing range.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE DANGER ZONE AND RESTRICTED AREA REGULATIONS § 334.220 Chesapeake Bay, south of Tangier Island, Va.; naval firing range. (a) The danger zone. Beginning... by mechanical means or by sail at a speed greater than five knots may proceed through the danger...

  10. 33 CFR 334.260 - York River, Va.; naval restricted areas.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false York River, Va.; naval restricted areas. 334.260 Section 334.260 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE DANGER ZONE AND RESTRICTED AREA REGULATIONS § 334.260 York River,...

  11. 33 CFR 334.290 - Elizabeth River, Southern Branch, Va., naval restricted areas.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false Elizabeth River, Southern Branch, Va., naval restricted areas. 334.290 Section 334.290 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE DANGER ZONE AND RESTRICTED AREA REGULATIONS §...

  12. 30 CFR 57.22315 - Self-contained breathing apparatus (V-A mines).

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... throughout the mine. Such apparatus shall be approved by MSHA and NIOSH under 42 CFR part 84 and shall be... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Self-contained breathing apparatus (V-A mines... NONMETAL MINES Safety Standards for Methane in Metal and Nonmetal Mines Equipment § 57.22315...

  13. 30 CFR 57.22315 - Self-contained breathing apparatus (V-A mines).

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... throughout the mine. Such apparatus shall be approved by MSHA and NIOSH under 42 CFR part 84 and shall be... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Self-contained breathing apparatus (V-A mines... NONMETAL MINES Safety Standards for Methane in Metal and Nonmetal Mines Equipment § 57.22315...

  14. 75 FR 30782 - Reorganization/Expansion of Foreign-Trade Zone 20; Hampton Roads, VA, Area

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-02

    ... inviting public comment was given in the Federal Register (74 FR 20927, 5/6/09) and the application has... Foreign-Trade Zones Board Reorganization/Expansion of Foreign-Trade Zone 20; Hampton Roads, VA, Area..., and to add six new sites (proposed Sites 19- 24) in the Hampton Roads, Virginia, area within...

  15. 75 FR 76953 - Foreign-Trade Zone 238-Dublin, VA Site Renumbering Notice

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-10

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF COMMERCE Foreign-Trade Zones Board Foreign-Trade Zone 238--Dublin, VA Site Renumbering Notice Foreign-Trade Zone 238 was approved by the Foreign-Trade Zones Board on August 5, 1999 (Board Order 1047). FTZ...

  16. 75 FR 61417 - South River Watershed Dam No. 10A, Augusta County, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-05

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF AGRICULTURE Natural Resources Conservation Service South River Watershed Dam No. 10A, Augusta County, VA AGENCY... not being prepared for the rehabilitation of South River Watershed Dam No. 10A, Augusta...

  17. 75 FR 26157 - Safety Zone; Reedville July 4th Celebration, Cockrell's Creek, Reedville, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-11

    ... Federal Register (73 FR 3316). Public Meeting We do not now plan to hold a public meeting. But you may... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; Reedville July 4th Celebration, Cockrell's..., VA in support of the Reedville July 4th Celebration event. This action is intended to restrict...

  18. 38 CFR 26.7 - VA environmental decision making and documents.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... observing the provisions of these regulations, VA must act in accordance with CEQ Regulations, 40 CFR 1506... making and documents. 26.7 Section 26.7 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS... environmental decision making and documents. (a) Relevant environmental documents shall accompany other...

  19. 38 CFR 26.7 - VA environmental decision making and documents.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... observing the provisions of these regulations, VA must act in accordance with CEQ Regulations, 40 CFR 1506... making and documents. 26.7 Section 26.7 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS... environmental decision making and documents. (a) Relevant environmental documents shall accompany other...

  20. 38 CFR 26.7 - VA environmental decision making and documents.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... observing the provisions of these regulations, VA must act in accordance with CEQ Regulations, 40 CFR 1506... making and documents. 26.7 Section 26.7 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS... environmental decision making and documents. (a) Relevant environmental documents shall accompany other...

  1. 38 CFR 26.7 - VA environmental decision making and documents.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... observing the provisions of these regulations, VA must act in accordance with CEQ Regulations, 40 CFR 1506... making and documents. 26.7 Section 26.7 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS... environmental decision making and documents. (a) Relevant environmental documents shall accompany other...

  2. Veterans, children first. Consolidation of federal healthcare services leads some VA clinics to expand patient mix.

    PubMed

    Gardner, J

    1998-06-01

    Facing flat federal appropriations, the Department of Veterans Affairs is fattening its budget through service contracts with other agencies. That's meant young children and World War II veterans mix in some of its clinics. Although conceding that new funds are needed, veterans groups fear the VA's traditional customers will be shortchanged in the transition. PMID:10180477

  3. Forecasting VaR and ES of stock index portfolio: A Vine copula method

    NASA Astrophysics Data System (ADS)

    Zhang, Bangzheng; Wei, Yu; Yu, Jiang; Lai, Xiaodong; Peng, Zhenfeng

    2014-12-01

    Risk measurement has both theoretical and practical significance in risk management. Using daily sample of 10 international stock indices, firstly this paper models the internal structures among different stock markets with C-Vine, D-Vine and R-Vine copula models. Secondly, the Value-at-Risk (VaR) and Expected Shortfall (ES) of the international stock markets portfolio are forecasted using Monte Carlo method based on the estimated dependence of different Vine copulas. Finally, the accuracy of VaR and ES measurements obtained from different statistical models are evaluated by UC, IND, CC and Posterior analysis. The empirical results show that the VaR forecasts at the quantile levels of 0.9, 0.95, 0.975 and 0.99 with three kinds of Vine copula models are sufficiently accurate. Several traditional methods, such as historical simulation, mean-variance and DCC-GARCH models, fail to pass the CC backtesting. The Vine copula methods can accurately forecast the ES of the portfolio on the base of VaR measurement, and D-Vine copula model is superior to other Vine copulas.

  4. 76 FR 71920 - Payment for Home Health Services and Hospice Care by Non-VA Providers

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-21

    ... medical charges associated with non-VA outpatient care, provided under 38 CFR 17.52 or 17.120. 75 FR 78901.... See 75 FR 78901. We explained: Home Health Care and Hospice Care he pricing methodology adopted by...-day period was $2,537.40 in FY 2010. The average Medicare reimbursement level for skilled home...

  5. 77 FR 13519 - Safety Zone; Virginia Beach Oceanfront Air Show, Atlantic Ocean, Virginia Beach, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-07

    ..., Atlantic Ocean, Virginia Beach, VA AGENCY: Coast Guard, DHS. ACTION: Notice of proposed rulemaking. SUMMARY: The Coast Guard proposes establishing a safety zone on the navigable waters of the Atlantic Ocean in..., 2012 through June 3, 2012, the United States Navy will host an air show event over the Atlantic...

  6. 78 FR 31840 - Safety Zone; USO Patriotic Festival Air Show, Atlantic Ocean; Virginia Beach, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-28

    ... Guard is establishing a temporary safety zone on the navigable waters of the Atlantic Ocean in Virginia... Concerts Entertainment, Inc. will host an air show event over the Atlantic Ocean in Virginia Beach, VA. In... mariners and the public transiting the Atlantic Ocean immediately below the air show from...

  7. 77 FR 27120 - Safety Zone; Virginia Beach Oceanfront Air Show, Atlantic Ocean, Virginia Beach, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-09

    ..., Atlantic Ocean, Virginia Beach, VA AGENCY: Coast Guard, DHS. ACTION: Temporary final rule. SUMMARY: The Coast Guard will establish a temporary safety zone on the Atlantic Ocean in the vicinity of Virginia... restrict vessel traffic movement on the Atlantic Ocean to protect mariners from the hazards associated...

  8. VA Puget Sound Telemental Health Service to rural veterans: a growing program.

    PubMed

    Barnwell, Sara V Smucker; Juretic, Meghan A; Hoerster, Katherine D; Van de Plasch, Richard; Felker, Bradford L

    2012-05-01

    The VA Puget Sound Health Care System Telemental Health program connects veterans with psychologists, psychiatrists, and social workers via live clinical video teleconferencing. Providers deliver care to veterans in rural Veteran Affairs medical centers, community-based outpatient clinics and residences, and thus, increase access to specialty mental health care for rural and medically underserved veteran communities.

  9. 75 FR 70351 - Termination of Environmental Review Process Cities of Chesapeake and Virginia Beach, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-17

    ... of intent was published in the Federal Register on Wednesday December 24, 2003, at 68 FR 74698. A... was published in the Federal Register on June 10, 2005, at 70 FR 33901. The identified preferred... Virginia Beach, VA AGENCY: Federal Highway Administration (FHWA), DOT. ACTION: Termination of...

  10. 78 FR 76064 - Authorization for Non-VA Medical Services; Withdrawal

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-16

    .... DATES: The direct final rule published on November 28, 2013 (77 FR 70893), is withdrawn as of December... a direct final rule published in the Federal Register on November 28, 2012, 77 FR 70893, VA would... companion proposed rule on the same date, at 77 FR 70967, proposing the same amendments as the direct...

  11. 76 FR 38570 - Safety Zone; Fourth of July Fireworks Event, Pagan River, Smithfield, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-07-01

    ... establishing a 420-foot radius safety zone on the navigable waters of the Pagan River in Smithfield, VA in... other debris, vessel traffic will be temporarily restricted within 420 feet of the fireworks launch site... within the area bounded by a 420-foot radius circle centered on position 36 59'18'' N/076 37'45'' W...

  12. 75 FR 34372 - Safety Zone; Fourth of July Fireworks Event, Pagan River, Smithfield, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-17

    ... establishing a 420-foot radius safety zone on the navigable waters of the Pagan River in Smithfield, VA in..., and falling hot embers or other debris, vessel traffic will be temporarily restricted within 420 feet... navigable waters of the Pagan River within the area bounded by a 420-foot radius circle centered on...

  13. 77 FR 35848 - Safety Zone, Fourth of July Fireworks Event, Pagan River, Smithfield, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-06-15

    ... establishing a 420-foot radius safety zone on the navigable waters of the Pagan River in Smithfield, VA in... feet of the fireworks launch site. Discussion of Rule The Coast Guard is establishing a safety zone on the navigable waters of the Pagan River within the area bounded by a 420-foot radius circle...

  14. 77 FR 39346 - Proposed Information Collection (Statement of Accredited Representative in Appealed Case, VA Form...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-02

    ... AFFAIRS Proposed Information Collection (Statement of Accredited Representative in Appealed Case, VA Form 646) Activity: Comment Request AGENCY: The Board of Veterans' Appeals (BVA), Department of Veterans Affairs. ACTION: Notice. SUMMARY: The Board of Veterans' Appeals (BVA), Department of Veterans Affairs...

  15. 75 FR 48413 - Agency Information Collection (HUD/VA Addendum to Uniform Residential Loan Application) Activity...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-10

    ... Housing and Urban Development (HUD). Lenders and veterans use the form to apply for home loans. An agency... information through www.Regulations.gov ; or to VA's OMB Desk Officer, OMB Human Resources and Housing Branch... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF...

  16. 78 FR 53506 - Agency Information Collection (HUD/VA Addendum to Uniform Residential Loan Application) Activity...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-29

    ... application for both VA and the Department of Housing and Urban Development (HUD). Lenders and Veterans use... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF VETERANS... Under OMB Review AGENCY: Veterans Benefits Administration, Department of Veterans Affairs....

  17. The Effect of Increased Travel Reimbursement Rates on Health Care Utilization in the VA

    ERIC Educational Resources Information Center

    Nelson, Richard E.; Hicken, Bret; West, Alan; Rupper, Randall

    2012-01-01

    Purpose: The reimbursement rate that eligible veterans receive for travel to Department of Veterans Affairs (VA) facilities increased from 11 to 28.5 cents per mile on February 1, 2008. We examined the effect of this policy change on utilization of outpatient, inpatient, and pharmacy services, stratifying veterans based on distance from a VA…

  18. 76 FR 24567 - Proposed Information Collection (VA MATIC Authorization); Comment Request

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-02

    ... needed to deduct insurance premiums from policyholder's bank account. DATES: Written comments and.... Abstract: Veteran policyholders complete VA Form 29-0532-1 to authorize deduction of Government Life Insurance premiums from their bank account. Affected Public: Individuals or households. Estimated...

  19. 78 FR 79563 - Proposed Information Collection (VA MATIC Authorization); Comment Request

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-30

    ... needed to deduct insurance premiums from policyholder's bank account. DATES: Written comments and.... Abstract: Veteran policyholders complete VA Form 29-0532-1 to authorize deduction of Government Life Insurance premiums from their bank account. Affected Public: Individuals or households. Estimated...

  20. 78 FR 37710 - Safety Zone; Wicomico Community Fireworks Rain Date, Great Wicomico River, Heathsville, VA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-24

    ... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; Wicomico Community Fireworks Rain Date... Mila, VA for the Wicomico Community Fireworks event Rain Date. This action is necessary to provide for... not learn of the need for a rain date until insufficient time remained before the fireworks...