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Sample records for alamos hiv sequence

  1. HIV Sequence Compendium 2015

    SciTech Connect

    Foley, Brian Thomas; Leitner, Thomas Kenneth; Apetrei, Cristian; Hahn, Beatrice; Mizrachi, Ilene; Mullins, James; Rambaut, Andrew; Wolinsky, Steven; Korber, Bette Tina Marie

    2015-10-05

    This compendium is an annual printed summary of the data contained in the HIV sequence database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2015. Hence, though it is published in 2015 and called the 2015 Compendium, its contents correspond to the 2014 curated alignments on our website. The number of sequences in the HIV database is still increasing. In total, at the end of 2014, there were 624,121 sequences in the HIV Sequence Database, an increase of 7% since the previous year. This is the first year that the number of new sequences added to the database has decreased compared to the previous year. The number of near complete genomes (>7000 nucleotides) increased to 5834 by end of 2014. However, as in previous years, the compendium alignments contain only a fraction of these. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/ content/sequence/NEWALIGN/align.html As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  2. HIV Sequence Compendium 2010

    SciTech Connect

    Kuiken, Carla; Foley, Brian; Leitner, Thomas; Apetrei, Christian; Hahn, Beatrice; Mizrachi, Ilene; Mullins, James; Rambaut, Andrew; Wolinsky, Steven; Korber, Bette

    2010-12-31

    This compendium is an annual printed summary of the data contained in the HIV sequence database. In these compendia we try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2010. Hence, though it is called the 2010 Compendium, its contents correspond to the 2009 curated alignments on our website. The number of sequences in the HIV database is still increasing exponentially. In total, at the time of printing, there were 339,306 sequences in the HIV Sequence Database, an increase of 45% since last year. The number of near complete genomes (>7000 nucleotides) increased to 2576 by end of 2009, reflecting a smaller increase than in previous years. However, as in previous years, the compendium alignments contain only a small fraction of these. Included in the alignments are a small number of sequences representing each of the subtypes and the more prevalent circulating recombinant forms (CRFs) such as 01 and 02, as well as a few outgroup sequences (group O and N and SIV-CPZ). Of the rarer CRFs we included one representative each. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html. Reprints are available from our website in the form of both HTML and PDF files. As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  3. HIV sequence compendium 2002

    SciTech Connect

    Kuiken, Carla; Foley, Brian; Freed, Eric; Hahn, Beatrice; Marx, Preston; McCutchan, Francine; Mellors, John; Wolinsky, Steven; Korber, Bette

    2002-12-31

    This compendium is an annual printed summary of the data contained in the HIV sequence database. In these compendia we try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Traditionally, we present the sequence data themselves in the form of alignments: Section II, an alignment of a selection of HIV-1/SIVcpz full-length genomes (a lot of LAI-like sequences, for example, have been omitted because they are so similar that they bias the alignment); Section III, a combined HIV-1/HIV-2/SIV whole genome alignment; Sections IV–VI, amino acid alignments for HIV-1/SIV-cpz, HIV-2/SIV, and SIVagm. The HIV-2/SIV and SIVagm amino acid alignments are separate because the genetic distances between these groups are so great that presenting them in one alignment would make it very elongated because of the large number of gaps that have to be inserted. As always, tables with extensive background information gathered from the literature accompany the whole genome alignments. The collection of whole-gene sequences in the database is now large enough that we have abundant representation of most subtypes. For many subtypes, and especially for subtype B, a large number of sequences that span entire genes were not included in the printed alignments to conserve space. A more complete version of all alignments is available on our website, http://hiv-web.lanl.gov/content/hiv-db/ALIGN_CURRENT/ALIGN-INDEX.html. Importantly, all these alignments have been edited to include only one sequence per person, based on phylogenetic trees that were created for all of them, as well as on the literature. Because of the number of sequences available, we have decided to use a different selection principle this year, based on the epidemiological importance of the subtypes. Subtypes A–D and CRFs 01 and 02 are by far the most widespread variants, and for these (when available) we have included 8–10 representatives in the alignments. The other

  4. Integrated sequence and immunology filovirus database at Los Alamos

    SciTech Connect

    Yusim, Karina; Yoon, Hyejin; Foley, Brian; Feng, Shihai; Macke, Jennifer; Dimitrijevic, Mira; Abfalterer, Werner; Szinger, James; Fischer, Will; Kuiken, Carla; Korber, Bette

    2016-01-01

    The Ebola outbreak of 2013–15 infected more than 28,000 people and claimed more lives than all previous filovirus outbreaks combined. Governmental agencies, clinical teams, and the world scientific community pulled together in a multifaceted response ranging from prevention and disease control, to evaluating vaccines and therapeutics in human trials. We report that as this epidemic is finally coming to a close, refocusing on long-term prevention strategies becomes paramount. Given the very real threat of future filovirus outbreaks, and the inherent uncertainty of the next outbreak virus and geographic location, it is prudent to consider the extent and implications of known natural diversity in advancing vaccines and therapeutic approaches. To facilitate such consideration, we have updated and enhanced the content of the filovirus portion of Los Alamos Hemorrhagic Fever Viruses Database. We have integrated and performed baseline analysis of all family Filoviridae sequences deposited into GenBank, with associated immune response data, and metadata, and we have added new computational tools with web-interfaces to assist users with analysis. Here, we (i) describe the main features of updated database, (ii) provide integrated views and some basic analyses summarizing evolutionary patterns as they relate to geo-temporal data captured in the database and (iii) highlight the most conserved regions in the proteome that may be useful for a T cell vaccine strategy.

  5. Integrated sequence and immunology filovirus database at Los Alamos

    DOE PAGESBeta

    Yusim, Karina; Yoon, Hyejin; Foley, Brian; Feng, Shihai; Macke, Jennifer; Dimitrijevic, Mira; Abfalterer, Werner; Szinger, James; Fischer, Will; Kuiken, Carla; et al

    2016-01-01

    The Ebola outbreak of 2013–15 infected more than 28,000 people and claimed more lives than all previous filovirus outbreaks combined. Governmental agencies, clinical teams, and the world scientific community pulled together in a multifaceted response ranging from prevention and disease control, to evaluating vaccines and therapeutics in human trials. We report that as this epidemic is finally coming to a close, refocusing on long-term prevention strategies becomes paramount. Given the very real threat of future filovirus outbreaks, and the inherent uncertainty of the next outbreak virus and geographic location, it is prudent to consider the extent and implications of knownmore » natural diversity in advancing vaccines and therapeutic approaches. To facilitate such consideration, we have updated and enhanced the content of the filovirus portion of Los Alamos Hemorrhagic Fever Viruses Database. We have integrated and performed baseline analysis of all family Filoviridae sequences deposited into GenBank, with associated immune response data, and metadata, and we have added new computational tools with web-interfaces to assist users with analysis. Here, we (i) describe the main features of updated database, (ii) provide integrated views and some basic analyses summarizing evolutionary patterns as they relate to geo-temporal data captured in the database and (iii) highlight the most conserved regions in the proteome that may be useful for a T cell vaccine strategy.« less

  6. Integrated sequence and immunology filovirus database at Los Alamos

    PubMed Central

    Yoon, Hyejin; Foley, Brian; Feng, Shihai; Macke, Jennifer; Dimitrijevic, Mira; Abfalterer, Werner; Szinger, James; Fischer, Will; Kuiken, Carla; Korber, Bette

    2016-01-01

    The Ebola outbreak of 2013–15 infected more than 28 000 people and claimed more lives than all previous filovirus outbreaks combined. Governmental agencies, clinical teams, and the world scientific community pulled together in a multifaceted response ranging from prevention and disease control, to evaluating vaccines and therapeutics in human trials. As this epidemic is finally coming to a close, refocusing on long-term prevention strategies becomes paramount. Given the very real threat of future filovirus outbreaks, and the inherent uncertainty of the next outbreak virus and geographic location, it is prudent to consider the extent and implications of known natural diversity in advancing vaccines and therapeutic approaches. To facilitate such consideration, we have updated and enhanced the content of the filovirus portion of Los Alamos Hemorrhagic Fever Viruses Database. We have integrated and performed baseline analysis of all family Filoviridae sequences deposited into GenBank, with associated immune response data, and metadata, and we have added new computational tools with web-interfaces to assist users with analysis. Here, we (i) describe the main features of updated database, (ii) provide integrated views and some basic analyses summarizing evolutionary patterns as they relate to geo-temporal data captured in the database and (iii) highlight the most conserved regions in the proteome that may be useful for a T cell vaccine strategy. Database URL: www.hfv.lanl.gov PMID:27103629

  7. Integrated sequence and immunology filovirus database at Los Alamos.

    PubMed

    Yusim, Karina; Yoon, Hyejin; Foley, Brian; Feng, Shihai; Macke, Jennifer; Dimitrijevic, Mira; Abfalterer, Werner; Szinger, James; Fischer, Will; Kuiken, Carla; Korber, Bette

    2016-01-01

    The Ebola outbreak of 2013-15 infected more than 28 000 people and claimed more lives than all previous filovirus outbreaks combined. Governmental agencies, clinical teams, and the world scientific community pulled together in a multifaceted response ranging from prevention and disease control, to evaluating vaccines and therapeutics in human trials. As this epidemic is finally coming to a close, refocusing on long-term prevention strategies becomes paramount. Given the very real threat of future filovirus outbreaks, and the inherent uncertainty of the next outbreak virus and geographic location, it is prudent to consider the extent and implications of known natural diversity in advancing vaccines and therapeutic approaches. To facilitate such consideration, we have updated and enhanced the content of the filovirus portion of Los Alamos Hemorrhagic Fever Viruses Database. We have integrated and performed baseline analysis of all family ITALIC! Filoviridaesequences deposited into GenBank, with associated immune response data, and metadata, and we have added new computational tools with web-interfaces to assist users with analysis. Here, we (i) describe the main features of updated database, (ii) provide integrated views and some basic analyses summarizing evolutionary patterns as they relate to geo-temporal data captured in the database and (iii) highlight the most conserved regions in the proteome that may be useful for a T cell vaccine strategy.Database URL:www.hfv.lanl.gov. PMID:27103629

  8. V3 sequences and paired HIV isolates from 52 non-subtype B HIV type 1-infected patients.

    PubMed

    Monno, Laura; Brindicci, Gaetano; Saracino, Annalisa; Punzi, Grazia; Cibelli, Donatella; Lagioia, Antonella; Angarano, Gioacchino

    2010-03-01

    Viral isolation and V3 sequencing were performed for 52 patients with non-subtype B viruses. The HIV-1 isolation rate was 93%, and 98% of isolates were characterized as NSI. V3 sequences corresponding to NSI isolates were compared to non-subtype B sequences with corresponding SI isolates from the Los Alamos database. The two sequence groups significantly differed in number of sequences with 35 amino acids, net charge, Brigg's coefficient, loss of NGS at positions 6-8, and 11/25 genotype (p < 0.0001). Substantial discrepancies in V3 variability were also observed. Basic amino acids at positions 8, 21, 23, and 24 were more frequent in SI sequences as were uncharged amino acids at positions 5, 6, 7, 8, 12, 13, 25, and 34. When characterizing paired viral isolates and V3 sequences from patients with non-subtype B HIV-1, current V3 sequence-based criteria from subtype B appeared to discriminate well between NSI and SI sequences from non-subtype B patients. PMID:20334572

  9. A Pan-HIV Strategy for Complete Genome Sequencing.

    PubMed

    Berg, Michael G; Yamaguchi, Julie; Alessandri-Gradt, Elodie; Tell, Robert W; Plantier, Jean-Christophe; Brennan, Catherine A

    2016-04-01

    Molecular surveillance is essential to monitor HIV diversity and track emerging strains. We have developed a universal library preparation method (HIV-SMART [i.e.,switchingmechanismat 5' end ofRNAtranscript]) for next-generation sequencing that harnesses the specificity of HIV-directed priming to enable full genome characterization of all HIV-1 groups (M, N, O, and P) and HIV-2. Broad application of the HIV-SMART approach was demonstrated using a panel of diverse cell-cultured virus isolates. HIV-1 non-subtype B-infected clinical specimens from Cameroon were then used to optimize the protocol to sequence directly from plasma. When multiplexing 8 or more libraries per MiSeq run, full genome coverage at a median ∼2,000× depth was routinely obtained for either sample type. The method reproducibly generated the same consensus sequence, consistently identified viral sequence heterogeneity present in specimens, and at viral loads of ≤4.5 log copies/ml yielded sufficient coverage to permit strain classification. HIV-SMART provides an unparalleled opportunity to identify diverse HIV strains in patient specimens and to determine phylogenetic classification based on the entire viral genome. Easily adapted to sequence any RNA virus, this technology illustrates the utility of next-generation sequencing (NGS) for viral characterization and surveillance. PMID:26699702

  10. Complete Genome Sequence of the WHO International Standard for HIV-2 RNA Determined by Deep Sequencing

    PubMed Central

    Ham, Claire; Morris, Clare

    2016-01-01

    The World Health Organization (WHO) International Standard for HIV-2 RNA nucleic acid assays was characterized by complete genome deep sequencing. The entire coding sequence and flanking long terminal repeats (LTRs), including minority species, were assigned subtype A. This information will aid design, development, and evaluation of HIV-2 RNA amplification assays. PMID:26847885

  11. Molecular Characterization of Mexican HIV-1 Vif Sequences.

    PubMed

    Guerra-Palomares, Sandra E; Hernandez-Sanchez, Pedro G; Esparza-Perez, Mario A; Arguello, J Rafael; Noyola, Daniel E; Garcia-Sepulveda, Christian A

    2016-03-01

    The viral infectivity factor (Vif) is an HIV accessory protein that counteracts host antiviral proteins of the APOBEC3 family. Accumulating evidence highlights the pivotal role that accessory HIV proteins have on disease pathogenesis, a fact that has made them targets of interest for novel therapeutic and preventive strategies. Little is known about Vif sequence diversity outside of African or white populations. Mexico is home to Americas' third largest HIV-affected population and Mexican Hispanics represent an ever-increasing U.S. minority. This study provides a detailed analysis of the diversity seen in 77 Mexican Vif protein sequences. Phylogenetic analysis shows that most sequences cluster with HIV-1 subtype B, while less than 10% exhibit greater similarity to subtype D and A subtypes. Although most functional motifs are conserved among the Mexican sequences, substantial diversity was seen in some APOBEC binding sites, the nuclear localization inhibitory signal, and the CBFβ interaction sites. PMID:26529466

  12. High-accuracy identification of incident HIV-1 infections using a sequence clustering based diversity measure.

    PubMed

    Xia, Xia-Yu; Ge, Meng; Hsi, Jenny H; He, Xiang; Ruan, Yu-Hua; Wang, Zhi-Xin; Shao, Yi-Ming; Pan, Xian-Ming

    2014-01-01

    Accurate estimates of HIV-1 incidence are essential for monitoring epidemic trends and evaluating intervention efforts. However, the long asymptomatic stage of HIV-1 infection makes it difficult to effectively distinguish incident infections from chronic ones. Current incidence assays based on serology or viral sequence diversity are both still lacking in accuracy. In the present work, a sequence clustering based diversity (SCBD) assay was devised by utilizing the fact that viral sequences derived from each transmitted/founder (T/F) strain tend to cluster together at early stage, and that only the intra-cluster diversity is correlated with the time since HIV-1 infection. The dot-matrix pairwise alignment was used to eliminate the disproportional impact of insertion/deletions (indels) and recombination events, and so was the proportion of clusterable sequences (Pc) as an index to identify late chronic infections with declined viral genetic diversity. Tested on a dataset containing 398 incident and 163 chronic infection cases collected from the Los Alamos HIV database (last modified 2/8/2012), our SCBD method achieved 99.5% sensitivity and 98.8% specificity, with an overall accuracy of 99.3%. Further analysis and evaluation also suggested its performance was not affected by host factors such as the viral subtypes and transmission routes. The SCBD method demonstrated the potential of sequencing based techniques to become useful for identifying incident infections. Its use may be most advantageous for settings with low to moderate incidence relative to available resources. The online service is available at http://www.bioinfo.tsinghua.edu.cn:8080/SCBD/index.jsp. PMID:24925130

  13. Deep sequencing of HIV: clinical and research applications.

    PubMed

    Chabria, Shiven B; Gupta, Shaili; Kozal, Michael J

    2014-01-01

    Human immunodeficiency virus (HIV) exhibits remarkable diversity in its genomic makeup and exists in any given individual as a complex distribution of closely related but nonidentical genomes called a viral quasispecies, which is subject to genetic variation, competition, and selection. This viral diversity clinically manifests as a selection of mutant variants based on viral fitness in treatment-naive individuals and based on drug-selective pressure in those on antiretroviral therapy (ART). The current standard-of-care ART consists of a combination of antiretroviral agents, which ensures maximal viral suppression while preventing the emergence of drug-resistant HIV variants. Unfortunately, transmission of drug-resistant HIV does occur, affecting 5% to >20% of newly infected individuals. To optimize therapy, clinicians rely on viral genotypic information obtained from conventional population sequencing-based assays, which cannot reliably detect viral variants that constitute <20% of the circulating viral quasispecies. These low-frequency variants can be detected by highly sensitive genotyping methods collectively grouped under the moniker of deep sequencing. Low-frequency variants have been correlated to treatment failures and HIV transmission, and detection of these variants is helping to inform strategies for vaccine development. Here, we discuss the molecular virology of HIV, viral heterogeneity, drug-resistance mutations, and the application of deep sequencing technologies in research and the clinical care of HIV-infected individuals. PMID:24821496

  14. Performance of genotypic tools for prediction of tropism in HIV-1 subtype C V3 loop sequences.

    PubMed

    Gupta, Soham; Neogi, Ujjwal; Srinivasa, Hiresave; Shet, Anita

    2015-01-01

    Currently, there is no consensus on the genotypic tools to be used for tropism analysis in HIV-1 subtype C strains. Thus, the aim of the study was to evaluate the performance of the different V3 loop-based genotypic algorithms available. We compiled a dataset of 645 HIV-1 subtype C V3 loop sequences of known coreceptor phenotypes (531 R5-tropic/non-syncytium-inducing and 114 X4-tropic/R5X4-tropic/syncytium-inducing sequences) from the Los Alamos database (http://www.hiv.lanl.gov/) and previously published literature. Coreceptor usage was predicted based on this dataset using different software-based machine-learning algorithms as well as simple classical rules. All the sophisticated machine-learning methods showed a good concordance of above 85%. Geno2Pheno (false-positive rate cutoff of 5-15%) and CoRSeqV3-C were found to have a high predicting capability in determining both HIV-1 subtype C X4-tropic and R5-tropic strains. The current sophisticated genotypic tropism tools based on V3 loop perform well for tropism prediction in HIV-1 subtype C strains and can be used in clinical settings. PMID:25573618

  15. Triple NF-kB binding sites and LTR sequence similarities in HIV-1C isolates irrespective of helminth co-infection

    PubMed Central

    2014-01-01

    Background Helminth infections as well as structural alternations in the long-terminal repeat (LTR) regions of HIV-1 are known to contribute to elevated HIV RNA level and enhance HIV-1 diseases progression. However, the impact of helminths infections on the occurrences of triple NF-κB and genetic variability in LTR region of HIV-1C isolates is not known. We aimed to examine the presence of genetic variability in the LTR region of HIV-1C isolates during chronic HIV-helminth co-infection. Methods HIV-1C infected Ethiopians with (n = 22) and without (n = 20) helminth infection were included. The LTR region of HIV was amplified and sequenced. Sequences were aligned with reference set from the Los Alamos HIV database. Phylogenetic analysis and frequency of polymorphic changes was performed by the neighbour-joining method using Geneious Basic software. Results All LTR sequences from patients with or without of helminth co-infection clustered with HIV-1 subtype C with two distinct subclusters (C and C’). The enhancer element was found to have three copies of 10-base pair binding sites for NF-κBs which is an evidence for predominance of triple NF-κB sites (94%) in HIV-1C isolates irrespective of helminths co-infection and subclusters. Moreover, irrespective of helminth co-infection and C/C’ subclusters high sequences similarity in LTR was observed. There was no significant difference in plasma HIV RNA level between HIV-1 C and C’ subclusters. Conclusions Despite the small sample size, the predominance of triple NF-κB binding sites and high sequence similarities in LTR region irrespective of helminths infection suggest the natural occurrence of the three NF-κB binding sites in HIV-1C isolates without the influence of secondary infection. Thus, the higher HIV-1C viraemia in helminth co-infected individuals is more likely a result of immune activation rather than LTR sequence variation. Moreover, the lack of significant difference in plasma HIV RNA level

  16. Dynamics of immunoglobulin sequence diversity in HIV-1 infected individuals.

    PubMed

    Hoehn, Kenneth B; Gall, Astrid; Bashford-Rogers, Rachael; Fidler, S J; Kaye, S; Weber, J N; McClure, M O; Kellam, Paul; Pybus, Oliver G

    2015-09-01

    Advances in immunoglobulin (Ig) sequencing technology are leading to new perspectives on immune system dynamics. Much research in this nascent field has focused on resolving immune responses to viral infection. However, the dynamics of B-cell diversity in early HIV infection, and in response to anti-retroviral therapy, are still poorly understood. Here, we investigate these dynamics through bulk Ig sequencing of samples collected over 2 years from a group of eight HIV-1 infected patients, five of whom received anti-retroviral therapy during the first half of the study period. We applied previously published methods for visualizing and quantifying B-cell sequence diversity, including the Gini index, and compared their efficacy to alternative measures. While we found significantly greater clonal structure in HIV-infected patients versus healthy controls, within HIV patients, we observed no significant relationships between statistics of B-cell clonal expansion and clinical variables such as viral load and CD4(+) count. Although there are many potential explanations for this, we suggest that important factors include poor sampling resolution and complex B-cell dynamics that are difficult to summarize using simple summary statistics. Importantly, we find a significant association between observed Gini indices and sequencing read depth, and we conclude that more robust analytical methods and a closer integration of experimental and theoretical work is needed to further our understanding of B-cell repertoire diversity during viral infection. PMID:26194755

  17. Dynamics of immunoglobulin sequence diversity in HIV-1 infected individuals

    PubMed Central

    Hoehn, Kenneth B.; Gall, Astrid; Bashford-Rogers, Rachael; Fidler, S. J.; Kaye, S.; Weber, J. N.; McClure, M. O.; Kellam, Paul; Pybus, Oliver G.

    2015-01-01

    Advances in immunoglobulin (Ig) sequencing technology are leading to new perspectives on immune system dynamics. Much research in this nascent field has focused on resolving immune responses to viral infection. However, the dynamics of B-cell diversity in early HIV infection, and in response to anti-retroviral therapy, are still poorly understood. Here, we investigate these dynamics through bulk Ig sequencing of samples collected over 2 years from a group of eight HIV-1 infected patients, five of whom received anti-retroviral therapy during the first half of the study period. We applied previously published methods for visualizing and quantifying B-cell sequence diversity, including the Gini index, and compared their efficacy to alternative measures. While we found significantly greater clonal structure in HIV-infected patients versus healthy controls, within HIV patients, we observed no significant relationships between statistics of B-cell clonal expansion and clinical variables such as viral load and CD4+ count. Although there are many potential explanations for this, we suggest that important factors include poor sampling resolution and complex B-cell dynamics that are difficult to summarize using simple summary statistics. Importantly, we find a significant association between observed Gini indices and sequencing read depth, and we conclude that more robust analytical methods and a closer integration of experimental and theoretical work is needed to further our understanding of B-cell repertoire diversity during viral infection. PMID:26194755

  18. Improved therapy-success prediction with GSS estimated from clinical HIV-1 sequences

    PubMed Central

    Pironti, Alejandro; Pfeifer, Nico; Kaiser, Rolf; Walter, Hauke; Lengauer, Thomas

    2014-01-01

    Introduction Rules-based HIV-1 drug-resistance interpretation (DRI) systems disregard many amino-acid positions of the drug's target protein. The aims of this study are (1) the development of a drug-resistance interpretation system that is based on HIV-1 sequences from clinical practice rather than hard-to-get phenotypes, and (2) the assessment of the benefit of taking all available amino-acid positions into account for DRI. Materials and Methods A dataset containing 34,934 therapy-naïve and 30,520 drug-exposed HIV-1 pol sequences with treatment history was extracted from the EuResist database and the Los Alamos National Laboratory database. 2,550 therapy-change-episode baseline sequences (TCEB) were assigned to test set A. Test set B contains 1,084 TCEB from the HIVdb TCE repository. Sequences from patients absent in the test sets were used to train three linear support vector machines to produce scores that predict drug exposure pertaining to each of 20 antiretrovirals: the first one uses the full amino-acid sequences (DEfull), the second one only considers IAS drug-resistance positions (DEonlyIAS), and the third one disregards IAS drug-resistance positions (DEnoIAS). For performance comparison, test sets A and B were evaluated with DEfull, DEnoIAS, DEonlyIAS, geno2pheno[resistance], HIVdb, ANRS, HIV-GRADE, and REGA. Clinically-validated cut-offs were used to convert the continuous output of the first four methods into susceptible-intermediate-resistant (SIR) predictions. With each method, a genetic susceptibility score (GSS) was calculated for each therapy episode in each test set by converting the SIR prediction for its compounds to integer: S=2, I=1, and R=0. The GSS were used to predict therapy success as defined by the EuResist standard datum definition. Statistical significance was assessed using a Wilcoxon signed-rank test. Results A comparison of the therapy-success prediction performances among the different interpretation systems for test set A can be

  19. HIV-1 Quasispecies Delineation by Tag Linkage Deep Sequencing

    PubMed Central

    Wu, Nicholas C.; De La Cruz, Justin; Al-Mawsawi, Laith Q.; Olson, C. Anders; Qi, Hangfei; Luan, Harding H.; Nguyen, Nguyen; Du, Yushen; Le, Shuai; Wu, Ting-Ting; Li, Xinmin; Lewis, Martha J.; Yang, Otto O.; Sun, Ren

    2014-01-01

    Trade-offs between throughput, read length, and error rates in high-throughput sequencing limit certain applications such as monitoring viral quasispecies. Here, we describe a molecular-based tag linkage method that allows assemblage of short sequence reads into long DNA fragments. It enables haplotype phasing with high accuracy and sensitivity to interrogate individual viral sequences in a quasispecies. This approach is demonstrated to deduce ∼2000 unique 1.3 kb viral sequences from HIV-1 quasispecies in vivo and after passaging ex vivo with a detection limit of ∼0.005% to ∼0.001%. Reproducibility of the method is validated quantitatively and qualitatively by a technical replicate. This approach can improve monitoring of the genetic architecture and evolution dynamics in any quasispecies population. PMID:24842159

  20. Deep Sequencing of the Vaginal Microbiota of Women with HIV

    PubMed Central

    Hummelen, Ruben; Fernandes, Andrew D.; Macklaim, Jean M.; Dickson, Russell J.; Changalucha, John

    2010-01-01

    Background Women living with HIV and co-infected with bacterial vaginosis (BV) are at higher risk for transmitting HIV to a partner or newborn. It is poorly understood which bacterial communities constitute BV or the normal vaginal microbiota among this population and how the microbiota associated with BV responds to antibiotic treatment. Methods and Findings The vaginal microbiota of 132 HIV positive Tanzanian women, including 39 who received metronidazole treatment for BV, were profiled using Illumina to sequence the V6 region of the 16S rRNA gene. Of note, Gardnerella vaginalis and Lactobacillus iners were detected in each sample constituting core members of the vaginal microbiota. Eight major clusters were detected with relatively uniform microbiota compositions. Two clusters dominated by L. iners or L. crispatus were strongly associated with a normal microbiota. The L. crispatus dominated microbiota were associated with low pH, but when L. crispatus was not present, a large fraction of L. iners was required to predict a low pH. Four clusters were strongly associated with BV, and were dominated by Prevotella bivia, Lachnospiraceae, or a mixture of different species. Metronidazole treatment reduced the microbial diversity and perturbed the BV-associated microbiota, but rarely resulted in the establishment of a lactobacilli-dominated microbiota. Conclusions Illumina based microbial profiling enabled high though-put analyses of microbial samples at a high phylogenetic resolution. The vaginal microbiota among women living with HIV in Sub-Saharan Africa constitutes several profiles associated with a normal microbiota or BV. Recurrence of BV frequently constitutes a different BV-associated profile than before antibiotic treatment. PMID:20711427

  1. Identification of HIV-1 Genitourinary Tract Compartmentalization by Analyzing the env Gene Sequences in Urine

    PubMed Central

    BLASI, Maria; CARPENTER, J. Harris; BALAKUMARAN, Bala; CARA, Andrea; GAO, Feng; KLOTMAN, Mary E.

    2015-01-01

    Objective HIV-1 persists indefinitely in memory CD4+ T cells and other long-lived cellular reservoirs despite antiretroviral therapy (ART). Our group had previously demonstrated that HIV-1 can establish a productive infection in renal epithelial cells and that the kidney represents a separate compartment for HIV-1 replication. Here, to better understand the viruses in this unique site, we genetically characterized and compared the viruses in blood and urine specimens from twenty-four HIV-1 infected subjects with detectable viremia. Design and Methods Blood and urine samples were obtained from 35 HIV-1 positive subjects. Single-genome amplification was performed on HIV-1 env RNA and DNA isolated from urine supernatants and urine derived cell pellets respectively, as well as from plasma and PBMC from the same individuals. Neighbor-joining trees were constructed under the Kimura 2-parameter mode. Results We amplified and sequenced the full-length HIV-1 envelope (env) gene from twelve of the twenty-four individuals, indicating that fifty percent (50%) of the viremic HIV-1 positive patients had viral RNA in their urine. Phylogenetic analysis of the env sequences from four subjects with more than fifteen urine-derived env sequences showed that the majority of the sequences from urine formed distinct cluster(s) independent of those PBMC and plasma-derived sequences, consistent with viral compartmentalization in the urine. Conclusions Our results suggest the presence of a distinct HIV compartment in the genitourinary tract. PMID:26372275

  2. Quantifying Next Generation Sequencing Sample Pre-Processing Bias in HIV-1 Complete Genome Sequencing.

    PubMed

    Vrancken, Bram; Trovão, Nídia Sequeira; Baele, Guy; van Wijngaerden, Eric; Vandamme, Anne-Mieke; van Laethem, Kristel; Lemey, Philippe

    2016-01-01

    Genetic analyses play a central role in infectious disease research. Massively parallelized "mechanical cloning" and sequencing technologies were quickly adopted by HIV researchers in order to broaden the understanding of the clinical importance of minor drug-resistant variants. These efforts have, however, remained largely limited to small genomic regions. The growing need to monitor multiple genome regions for drug resistance testing, as well as the obvious benefit for studying evolutionary and epidemic processes makes complete genome sequencing an important goal in viral research. In addition, a major drawback for NGS applications to RNA viruses is the need for large quantities of input DNA. Here, we use a generic overlapping amplicon-based near full-genome amplification protocol to compare low-input enzymatic fragmentation (Nextera™) with conventional mechanical shearing for Roche 454 sequencing. We find that the fragmentation method has only a modest impact on the characterization of the population composition and that for reliable results, the variation introduced at all steps of the procedure--from nucleic acid extraction to sequencing--should be taken into account, a finding that is also relevant for NGS technologies that are now more commonly used. Furthermore, by applying our protocol to deep sequence a number of pre-therapy plasma and PBMC samples, we illustrate the potential benefits of a near complete genome sequencing approach in routine genotyping. PMID:26751471

  3. Importance of Viral Sequence Length and Number of Variable and Informative Sites in Analysis of HIV Clustering

    PubMed Central

    Novitsky, Vlad; Moyo, Sikhulile; Lei, Quanhong; DeGruttola, Victor

    2015-01-01

    Abstract To improve the methodology of HIV cluster analysis, we addressed how analysis of HIV clustering is associated with parameters that can affect the outcome of viral clustering. The extent of HIV clustering and tree certainty was compared between 401 HIV-1C near full-length genome sequences and subgenomic regions retrieved from the LANL HIV Database. Sliding window analysis was based on 99 windows of 1,000 bp and 45 windows of 2,000 bp. Potential associations between the extent of HIV clustering and sequence length and the number of variable and informative sites were evaluated. The near full-length genome HIV sequences showed the highest extent of HIV clustering and the highest tree certainty. At the bootstrap threshold of 0.80 in maximum likelihood (ML) analysis, 58.9% of near full-length HIV-1C sequences but only 15.5% of partial pol sequences (ViroSeq) were found in clusters. Among HIV-1 structural genes, pol showed the highest extent of clustering (38.9% at a bootstrap threshold of 0.80), although it was significantly lower than in the near full-length genome sequences. The extent of HIV clustering was significantly higher for sliding windows of 2,000 bp than 1,000 bp. We found a strong association between the sequence length and proportion of HIV sequences in clusters, and a moderate association between the number of variable and informative sites and the proportion of HIV sequences in clusters. In HIV cluster analysis, the extent of detectable HIV clustering is directly associated with the length of viral sequences used, as well as the number of variable and informative sites. Near full-length genome sequences could provide the most informative HIV cluster analysis. Selected subgenomic regions with a high extent of HIV clustering and high tree certainty could also be considered as a second choice. PMID:25560745

  4. HIV gp120 sequence variability associated with HAND in Hispanic Women

    PubMed Central

    Colón, Krystal; Vázquez-Santiago, Fabián; Rivera-Amill, Vanessa; Delgado, Gisela; Massey, Steven E.; Wojna, Valerie; Noel, Richard J.; Meléndez, Loyda M.

    2016-01-01

    Objective HIV-1 variants with different tropisms are associated with various neuropathologies. This study intends to determine if this correlation is determined by unique viral env sequences. We hypothesize that HIV-1 envelope gene sequence changes are associated with cognition status Methods Viral RNA was extracted from peripheral blood mononuclear cells (PBMCs) co-cultures derived from HIV-1 infected Hispanic women that had been characterized for HIV associated neurocognitive disorders (HAND). Results Analyses of the C2V4 region of HIV gp120 demonstrated that increased sequence diversity correlates with cognition status as sequences derived from subjects with normal cognition exhibited less diversity than sequences derived from subjects with cognitive impairment. In addition, differences in V3 and V4 loop charges were also noted as well as differences in the N-glycosylation of the V4 region. Conclusions Our data suggest that the genetic signature within the C2V4 region may contribute to the pathogenesis of HAND. HIV env sequence characteristics for the isolates grouped in milder forms of HAND can provide insightful information of prognostic value to assess neurocognitive status in HIV+ subjects, particularly during the era of highly prevalent milder forms of HAND.

  5. Quantifying Next Generation Sequencing Sample Pre-Processing Bias in HIV-1 Complete Genome Sequencing

    PubMed Central

    Vrancken, Bram; Trovão, Nídia Sequeira; Baele, Guy; van Wijngaerden, Eric; Vandamme, Anne-Mieke; van Laethem, Kristel; Lemey, Philippe

    2016-01-01

    Genetic analyses play a central role in infectious disease research. Massively parallelized “mechanical cloning” and sequencing technologies were quickly adopted by HIV researchers in order to broaden the understanding of the clinical importance of minor drug-resistant variants. These efforts have, however, remained largely limited to small genomic regions. The growing need to monitor multiple genome regions for drug resistance testing, as well as the obvious benefit for studying evolutionary and epidemic processes makes complete genome sequencing an important goal in viral research. In addition, a major drawback for NGS applications to RNA viruses is the need for large quantities of input DNA. Here, we use a generic overlapping amplicon-based near full-genome amplification protocol to compare low-input enzymatic fragmentation (Nextera™) with conventional mechanical shearing for Roche 454 sequencing. We find that the fragmentation method has only a modest impact on the characterization of the population composition and that for reliable results, the variation introduced at all steps of the procedure—from nucleic acid extraction to sequencing—should be taken into account, a finding that is also relevant for NGS technologies that are now more commonly used. Furthermore, by applying our protocol to deep sequence a number of pre-therapy plasma and PBMC samples, we illustrate the potential benefits of a near complete genome sequencing approach in routine genotyping. PMID:26751471

  6. Newly Exerted T Cell Pressures on Mutated Epitopes following Transmission Help Maintain Consensus HIV-1 Sequences

    PubMed Central

    Eriksson, Emily M.; Liegler, Teri; Keh, Chris E.; Karlsson, Annika C.; Holditch, Sara J.; Pilcher, Christopher D.; Loeb, Lisa; Nixon, Douglas F.; Hecht, Frederick M.

    2015-01-01

    CD8+ T cells are important for HIV-1 virus control, but are also a major contributing factor that drives HIV-1 virus sequence evolution. Although HIV-1 cytotoxic T cell (CTL) escape mutations are a common aspect during HIV-1 infection, less is known about the importance of T cell pressure in reversing HIV-1 virus back to a consensus sequences. In this study we aimed to assess the frequency with which reversion of transmitted mutations in T cell epitopes were associated with T cell responses to the mutation. This study included 14 HIV-1 transmission pairs consisting of a ‘source’ (virus-donor) and a ‘recipient’ (newly infected individual). Non-consensus B sequence amino acids (mutations) in T cell epitopes in HIV-1 gag regions p17, p24, p2 and p7 were identified in each pair and transmission of mutations to the recipient was verified with population viral sequencing. Longitudinal analyses of the recipient’s viral sequence were used to identify whether reversion of mutations back to the consensus B sequence occurred. Autologous 12-mer peptides overlapping by 11 were synthesized, representing the sequence region surrounding each reversion and longitudinal analysis of T cell responses to source-derived mutated and reverted epitopes were assessed. We demonstrated that mutations in the source were frequently transmitted to the new host and on an average 17 percent of mutated epitopes reverted to consensus sequence in the recipient. T cell responses to these mutated epitopes were detected in 7 of the 14 recipients in whom reversion occurred. Overall, these findings indicate that transmitted non-consensus B epitopes are frequently immunogenic in HLA-mismatched recipients and new T cell pressures to T cell escape mutations following transmission play a significant role in maintaining consensus HIV-1 sequences. PMID:25919393

  7. Use of Four Next-Generation Sequencing Platforms to Determine HIV-1 Coreceptor Tropism

    PubMed Central

    Henry, Kenneth; Winner, Dane; Gibson, Richard; Lee, Lawrence; Paxinos, Ellen; Arts, Eric J.; Robertson, David L.; Mimms, Larry; Quiñones-Mateu, Miguel E.

    2012-01-01

    HIV-1 coreceptor tropism assays are required to rule out the presence of CXCR4-tropic (non-R5) viruses prior treatment with CCR5 antagonists. Phenotypic (e.g., Trofile™, Monogram Biosciences) and genotypic (e.g., population sequencing linked to bioinformatic algorithms) assays are the most widely used. Although several next-generation sequencing (NGS) platforms are available, to date all published deep sequencing HIV-1 tropism studies have used the 454™ Life Sciences/Roche platform. In this study, HIV-1 co-receptor usage was predicted for twelve patients scheduled to start a maraviroc-based antiretroviral regimen. The V3 region of the HIV-1 env gene was sequenced using four NGS platforms: 454™, PacBio® RS (Pacific Biosciences), Illumina®, and Ion Torrent™ (Life Technologies). Cross-platform variation was evaluated, including number of reads, read length and error rates. HIV-1 tropism was inferred using Geno2Pheno, Web PSSM, and the 11/24/25 rule and compared with Trofile™ and virologic response to antiretroviral therapy. Error rates related to insertions/deletions (indels) and nucleotide substitutions introduced by the four NGS platforms were low compared to the actual HIV-1 sequence variation. Each platform detected all major virus variants within the HIV-1 population with similar frequencies. Identification of non-R5 viruses was comparable among the four platforms, with minor differences attributable to the algorithms used to infer HIV-1 tropism. All NGS platforms showed similar concordance with virologic response to the maraviroc-based regimen (75% to 80% range depending on the algorithm used), compared to Trofile (80%) and population sequencing (70%). In conclusion, all four NGS platforms were able to detect minority non-R5 variants at comparable levels suggesting that any NGS-based method can be used to predict HIV-1 coreceptor usage. PMID:23166726

  8. HIV drug resistance testing by high-multiplex "wide" sequencing on the MiSeq instrument.

    PubMed

    Lapointe, H R; Dong, W; Lee, G Q; Bangsberg, D R; Martin, J N; Mocello, A R; Boum, Y; Karakas, A; Kirkby, D; Poon, A F Y; Harrigan, P R; Brumme, C J

    2015-11-01

    Limited access to HIV drug resistance testing in low- and middle-income countries impedes clinical decision-making at the individual patient level. An efficient protocol to address this issue must be established to minimize negative therapeutic outcomes for HIV-1-infected individuals in such settings. This is an observational study to ascertain the potential of newer genomic sequencing platforms, such as the Illumina MiSeq instrument, to provide accurate HIV drug resistance genotypes for hundreds of samples simultaneously. Plasma samples were collected from Canadian patients during routine drug resistance testing (n = 759) and from a Ugandan study cohort (n = 349). Amplicons spanning HIV reverse transcriptase codons 90 to 234 were sequenced with both MiSeq sequencing and conventional Sanger sequencing methods. Sequences were evaluated for nucleotide concordance between methods, using coverage and mixture parameters for quality control. Consensus sequences were also analyzed for disparities in the identification of drug resistance mutations. Sanger and MiSeq sequencing was successful for 881 samples (80%) and 892 samples (81%), respectively, with 832 samples having results from both methods. Most failures were for samples with viral loads of <3.0 log10 HIV RNA copies/ml. Overall, 99.3% nucleotide concordance between methods was observed. MiSeq sequencing achieved 97.4% sensitivity and 99.3% specificity in detecting resistance mutations identified by Sanger sequencing. Findings suggest that the Illumina MiSeq platform can yield high-quality data with a high-multiplex "wide" sequencing approach. This strategy can be used for multiple HIV subtypes, demonstrating the potential for widespread individual testing and annual population surveillance in resource-limited settings. PMID:26282425

  9. HIV Whole-Genome Sequencing Now: Answering Still-Open Questions.

    PubMed

    Metzner, Karin J

    2016-04-01

    Diversity, evolution, and epidemiology of HIV are directly relevant to HIV transmission and pathogenesis; hence, they play a key role in antiretroviral treatment and vaccine design. Global HIV whole-genome sequencing would provide a treasure chest of data to answer many questions still open in these fields. An article by Berg et al. in this issue of theJournal of Clinical Microbiologydescribes a universal strategy to amplify and sequence heterogeneous HIV whole genomes (M. G. Berg, J. Yamaguchi, E. Alessandri-Gradt, R. W. Tell, J.-C. Plantier, and C. A. Brennan, J Clin Microbiol 54:868-882, 2016,http://dx.doi.org/10.1128/JCM.02479-15). PMID:26791367

  10. Transcriptome Sequencing of Gene Expression in the Brain of the HIV-1 Transgenic Rat

    PubMed Central

    Li, Ming D.; Cao, Junran; Wang, Shaolin; Wang, Ju; Sarkar, Sraboni; Vigorito, Michael; Ma, Jennie Z.; Chang, Sulie L.

    2013-01-01

    The noninfectious HIV-1 transgenic (HIV-1Tg) rat was developed as a model of AIDs-related pathology and immune dysfunction by manipulation of a noninfectious HIV-1gag-pol virus with a deleted 3-kb SphI-MscI fragment containing the 3′ -region of gag and the 5′ region of pol into F344 rats. Our previous studies revealed significant behavioral differences between HIV-1Tg and F344 control rats in their performance in the Morris water maze and responses to psychostimulants. However, the molecular mechanisms underlying these behavioral differences remain largely unknown. The primary goal of this study was to identify differentially expressed genes and enriched pathways affected by the gag-pol-deleted HIV-1 genome. Using RNA deep sequencing, we sequenced RNA transcripts in the prefrontal cortex, hippocampus, and striatum of HIV-1Tg and F344 rats. A total of 72 RNA samples were analyzed (i.e., 12 animals per group × 2 strains × 3 brain regions). Following deep-sequencing analysis of 50-bp paired-end reads of RNA-Seq, we used Bowtie/Tophat/Cufflinks suites to align these reads into transcripts based on the Rn4 rat reference genome and to measure the relative abundance of each transcript. Statistical analyses on each brain region in the two strains revealed that immune response- and neurotransmission-related pathways were altered in the HIV-1Tg rats, with brain region differences. Other neuronal survival-related pathways, including those encoding myelin proteins, growth factors, and translation regulators, were altered in the HIV-1Tg rats in a brain region-dependent manner. This study is the first deep-sequencing analysis of RNA transcripts associated the HIV-1Tg rat. Considering the functions of the pathways and brain regions examined in this study, our findings of abnormal gene expression patterns in HIV-1Tg rats suggest mechanisms underlying the deficits in learning and memory and vulnerability to drug addiction and other psychiatric disorders observed in HIV

  11. Reconstructing the Dynamics of HIV Evolution within Hosts from Serial Deep Sequence Data

    PubMed Central

    Poon, Art F. Y.; Swenson, Luke C.; Bunnik, Evelien M.; Edo-Matas, Diana; Schuitemaker, Hanneke; van 't Wout, Angélique B.; Harrigan, P. Richard

    2012-01-01

    At the early stage of infection, human immunodeficiency virus (HIV)-1 predominantly uses the CCR5 coreceptor for host cell entry. The subsequent emergence of HIV variants that use the CXCR4 coreceptor in roughly half of all infections is associated with an accelerated decline of CD4+ T-cells and rate of progression to AIDS. The presence of a ‘fitness valley’ separating CCR5- and CXCR4-using genotypes is postulated to be a biological determinant of whether the HIV coreceptor switch occurs. Using phylogenetic methods to reconstruct the evolutionary dynamics of HIV within hosts enables us to discriminate between competing models of this process. We have developed a phylogenetic pipeline for the molecular clock analysis, ancestral reconstruction, and visualization of deep sequence data. These data were generated by next-generation sequencing of HIV RNA extracted from longitudinal serum samples (median 7 time points) from 8 untreated subjects with chronic HIV infections (Amsterdam Cohort Studies on HIV-1 infection and AIDS). We used the known dates of sampling to directly estimate rates of evolution and to map ancestral mutations to a reconstructed timeline in units of days. HIV coreceptor usage was predicted from reconstructed ancestral sequences using the geno2pheno algorithm. We determined that the first mutations contributing to CXCR4 use emerged about 16 (per subject range 4 to 30) months before the earliest predicted CXCR4-using ancestor, which preceded the first positive cell-based assay of CXCR4 usage by 10 (range 5 to 25) months. CXCR4 usage arose in multiple lineages within 5 of 8 subjects, and ancestral lineages following alternate mutational pathways before going extinct were common. We observed highly patient-specific distributions and time-scales of mutation accumulation, implying that the role of a fitness valley is contingent on the genotype of the transmitted variant. PMID:23133358

  12. Spin models inferred from patient-derived viral sequence data faithfully describe HIV fitness landscapes

    NASA Astrophysics Data System (ADS)

    Shekhar, Karthik; Ruberman, Claire F.; Ferguson, Andrew L.; Barton, John P.; Kardar, Mehran; Chakraborty, Arup K.

    2013-12-01

    Mutational escape from vaccine-induced immune responses has thwarted the development of a successful vaccine against AIDS, whose causative agent is HIV, a highly mutable virus. Knowing the virus' fitness as a function of its proteomic sequence can enable rational design of potent vaccines, as this information can focus vaccine-induced immune responses to target mutational vulnerabilities of the virus. Spin models have been proposed as a means to infer intrinsic fitness landscapes of HIV proteins from patient-derived viral protein sequences. These sequences are the product of nonequilibrium viral evolution driven by patient-specific immune responses and are subject to phylogenetic constraints. How can such sequence data allow inference of intrinsic fitness landscapes? We combined computer simulations and variational theory á la Feynman to show that, in most circumstances, spin models inferred from patient-derived viral sequences reflect the correct rank order of the fitness of mutant viral strains. Our findings are relevant for diverse viruses.

  13. Sources of variation in ancestral sequence reconstruction for HIV-1 envelope genes

    PubMed Central

    Ross, Howard A.; Nickle, David C.; Liu, Yi; Heath, Laura; Jensen, Mark A.; Rodrigo, Allen G.; Mullins, James I.

    2007-01-01

    We characterized the variation in the reconstructed ancestor of 118 HIV-1 envelope gene sequences arising from the methods used for (a) estimating and (b) rooting the phylogenetic tree, and (c) reconstructing the ancestor on that tree, from (d) the sequence format, and from (e) the number of input sequences. The method of rooting the tree was responsible for most of the sequence variation both among the reconstructed ancestral sequences and between the ancestral and observed sequences. Variation in predicted 3-D structural properties of the ancestors mirrored their sequence variation. The observed sequence consensus and ancestral sequences from center-rooted trees were most similar in all predicted attributes. Only for the predicted number of N-glycosylation sites was there a difference between MP and ML methods of reconstruction. Taxon sampling effects were observed only for outgroup-rooted trees, not center-rooted, reflecting the occurrence of several divergent basal sequences. Thus, for sequences exhibiting a radial phylogenetic tree, as does HIV-1, most of the variation in the estimated ancestor arises from the method of rooting the phylogenetic tree. Those investigating the ancestors of genes exhibiting such a radial tree should pay particular attention to alternate rooting methods in order to obtain a representative sample of ancestors. PMID:19455202

  14. Los Alamos National Laboratory Overview

    SciTech Connect

    Neu, Mary

    2010-06-02

    Mary Neu, Associate Director for Chemistry, Life and Earth Sciences at Los Alamos National Laboratory, delivers opening remarks at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  15. Coalescent Inference Using Serially Sampled, High-Throughput Sequencing Data from Intrahost HIV Infection.

    PubMed

    Dialdestoro, Kevin; Sibbesen, Jonas Andreas; Maretty, Lasse; Raghwani, Jayna; Gall, Astrid; Kellam, Paul; Pybus, Oliver G; Hein, Jotun; Jenkins, Paul A

    2016-04-01

    Human immunodeficiency virus (HIV) is a rapidly evolving pathogen that causes chronic infections, so genetic diversity within a single infection can be very high. High-throughput "deep" sequencing can now measure this diversity in unprecedented detail, particularly since it can be performed at different time points during an infection, and this offers a potentially powerful way to infer the evolutionary dynamics of the intrahost viral population. However, population genomic inference from HIV sequence data is challenging because of high rates of mutation and recombination, rapid demographic changes, and ongoing selective pressures. In this article we develop a new method for inference using HIV deep sequencing data, using an approach based on importance sampling of ancestral recombination graphs under a multilocus coalescent model. The approach further extends recent progress in the approximation of so-calledconditional sampling distributions, a quantity of key interest when approximating coalescent likelihoods. The chief novelties of our method are that it is able to infer rates of recombination and mutation, as well as the effective population size, while handling sampling over different time points and missing data without extra computational difficulty. We apply our method to a data set of HIV-1, in which several hundred sequences were obtained from an infected individual at seven time points over 2 years. We find mutation rate and effective population size estimates to be comparable to those produced by the software BEAST. Additionally, our method is able to produce local recombination rate estimates. The software underlying our method, Coalescenator, is freely available. PMID:26857628

  16. Sequence-specific alterations of epitope production by HIV Protease Inhibitors

    PubMed Central

    Kourjian, Georgio; Xu, Yang; Mondesire-Crump, Ijah; Shimada, Mariko; Gourdain, Pauline; Le Gall, Sylvie

    2014-01-01

    Antigen processing by intracellular proteases and peptidases and epitope presentation are critical for recognition of pathogen-infected cells by CD8+ T lymphocytes. First generation HIV protease inhibitors (PIs) alter proteasome activity, but the effect of first or second generation PIs on other cellular peptidases, the underlying mechanism and impact on antigen processing and epitope presentation to CTL are still unknown. Here we demonstrate that several HIV PIs altered not only proteasome but also aminopeptidase activities in PBMC. Using an in vitro degradation assay involving PBMC cytosolic extracts we showed that PIs altered the degradation patterns of oligopeptides and peptide production in a sequence-specific manner, enhancing the cleavage of certain residues and reducing others’. PIs affected the sensitivity of peptides to intracellular degradation, altered the kinetics and amount of HIV epitopes produced intracellularly. Accordingly the endogenous degradation of incoming virions in the presence of PIs led to variations in CTL-mediated killing of HIV-infected cells. By altering host protease activities and the degradation patterns of proteins in a sequence-specific manner, HIV PIs may diversify peptides available for MHC-I presentation to CTL, alter the patters of CTL responses, and may provide a complementary approach to current therapies for the CTL-mediated clearance of abnormal cells in infection, cancer or other immune disease. PMID:24616479

  17. In Silico Prediction of Mutant HIV-1 Proteases Cleaving a Target Sequence

    PubMed Central

    Jensen, Jan H.; Willemoës, Martin; Winther, Jakob R.; De Vico, Luca

    2014-01-01

    HIV-1 protease represents an appealing system for directed enzyme re-design, since it has various different endogenous targets, a relatively simple structure and it is well studied. Recently Chaudhury and Gray (Structure (2009) 17: 1636–1648) published a computational algorithm to discern the specificity determining residues of HIV-1 protease. In this paper we present two computational tools aimed at re-designing HIV-1 protease, derived from the algorithm of Chaudhuri and Gray. First, we present an energy-only based methodology to discriminate cleavable and non cleavable peptides for HIV-1 proteases, both wild type and mutant. Secondly, we show an algorithm we developed to predict mutant HIV-1 proteases capable of cleaving a new target substrate peptide, different from the natural targets of HIV-1 protease. The obtained in silico mutant enzymes were analyzed in terms of cleavability and specificity towards the target peptide using the energy-only methodology. We found two mutant proteases as best candidates for specificity and cleavability towards the target sequence. PMID:24796579

  18. HIV-1 sequence variation between isolates from mother-infant transmission pairs

    SciTech Connect

    Wike, C.M.; Daniels, M.R.; Furtado, M.; Wolinsky, M.; Korber, B.; Hutto, C.; Munoz, J.; Parks, W.; Saah, A.

    1991-12-31

    To examine the sequence diversity of human immunodeficiency virus type 1 (HIV-1) between known transmission sets, sequences from the V3 and V4-V5 region of the env gene from 4 mother-infant pairs were analyzed. The mean interpatient sequence variation between isolates from linked mother-infant pairs was comparable to the sequence diversity found between isolates from other close contacts. The mean intrapatient variation was significantly less in the infants` isolates then the isolates from both their mothers and other characterized intrapatient sequence sets. In addition, a distinct and characteristic difference in the glycosylation pattern preceding the V3 loop was found between each linked transmission pair. These findings indicate that selection of specific genotypic variants, which may play a role in some direct transmission sets, and the duration of infection are important factors in the degree of diversity seen between the sequence sets.

  19. HIV-1 sequence variation between isolates from mother-infant transmission pairs

    SciTech Connect

    Wike, C.M.; Daniels, M.R.; Furtado, M.; Wolinsky, M.; Korber, B.; Hutto, C.; Munoz, J.; Parks, W.; Saah, A.

    1991-01-01

    To examine the sequence diversity of human immunodeficiency virus type 1 (HIV-1) between known transmission sets, sequences from the V3 and V4-V5 region of the env gene from 4 mother-infant pairs were analyzed. The mean interpatient sequence variation between isolates from linked mother-infant pairs was comparable to the sequence diversity found between isolates from other close contacts. The mean intrapatient variation was significantly less in the infants' isolates then the isolates from both their mothers and other characterized intrapatient sequence sets. In addition, a distinct and characteristic difference in the glycosylation pattern preceding the V3 loop was found between each linked transmission pair. These findings indicate that selection of specific genotypic variants, which may play a role in some direct transmission sets, and the duration of infection are important factors in the degree of diversity seen between the sequence sets.

  20. Focused Evolution of HIV-1 Neutralizing Antibodies Revealed by Structures and Deep Sequencing

    SciTech Connect

    Wu, Xueling; Zhou, Tongqing; Zhu, Jiang; Zhang, Baoshan; Georgiev, Ivelin; Wang, Charlene; Chen, Xuejun; Longo, Nancy S.; Louder, Mark; McKee, Krisha; O’Dell, Sijy; Perfetto, Stephen; Schmidt, Stephen D.; Shi, Wei; Wu, Lan; Yang, Yongping; Yang, Zhi-Yong; Yang, Zhongjia; Zhang, Zhenhai; Bonsignori, Mattia; Crump, John A.; Kapiga, Saidi H.; Sam, Noel E.; Haynes, Barton F.; Simek, Melissa; Burton, Dennis R.; Koff, Wayne C.; Doria-Rose, Nicole A.; Connors, Mark; Mullikin, James C.; Nabel, Gary J.; Roederer, Mario; Shapiro, Lawrence; Kwong, Peter D.; Mascola, John R.

    2013-03-04

    Antibody VRC01 is a human immunoglobulin that neutralizes about 90% of HIV-1 isolates. To understand how such broadly neutralizing antibodies develop, we used x-ray crystallography and 454 pyrosequencing to characterize additional VRC01-like antibodies from HIV-1-infected individuals. Crystal structures revealed a convergent mode of binding for diverse antibodies to the same CD4-binding-site epitope. A functional genomics analysis of expressed heavy and light chains revealed common pathways of antibody-heavy chain maturation, confined to the IGHV1-2*02 lineage, involving dozens of somatic changes, and capable of pairing with different light chains. Broadly neutralizing HIV-1 immunity associated with VRC01-like antibodies thus involves the evolution of antibodies to a highly affinity-matured state required to recognize an invariant viral structure, with lineages defined from thousands of sequences providing a genetic roadmap of their development.

  1. HIV-1 intrapatient sequence diversity in the immunogenic V3 region

    SciTech Connect

    Korber, B.; Myers, G. ); Wolinsky, S.; Kunstman, K.; Levy, R.; Furtado, M.; Otto, P. . Medical School); Haynes, B. . Dept. of Medicine)

    1991-11-12

    The third hypervariable domain (V3) of the human immunodeficiency virus type-1 (HIV-1) envelope protein (env) can serve as an epitope for potent type-specific neutralizing antibodies (NAbs) -- thus short peptides predicted on the most commonly found variants of the antigenic tip of the V3 loop have been considered as potential candidates for an HIV peptide vaccine. To evaluate the extent of intrapatient variation in the immunogenic crest of the V3 loop, sequence sets were analyzed from individuals for whom multiple V3 sequences were available. Several strategies for selecting the best sets of hexapeptides to represent the variable tip of the V3 loop were considered and their effectiveness was evaluated by comparing them with the sequence sets from individuals. Most individuals carried at least one, and frequently many, variants that did not match any of the sequences from among the ten most common hexapeptides. Intrapatient viral sequence variation was increased by including sequences derived from brain biopsy specimens as well as from blood. Additionally, sequences obtained from brain specimens of different individuals had common elements which were not conserved in the corresponding blood samples, suggesting that certain amino acids in the V3 loop may be requisite for viral propagation in the CNS.

  2. Utility of Metagenomic Next-Generation Sequencing for Characterization of HIV and Human Pegivirus Diversity

    PubMed Central

    Naccache, Samia N.; Kabre, Beniwende; Federman, Scot; Mbanya, Dora; Kaptué, Lazare; Chiu, Charles Y.; Brennan, Catherine A.; Hackett, John

    2015-01-01

    Given the dynamic changes in HIV-1 complexity and diversity, next-generation sequencing (NGS) has the potential to revolutionize strategies for effective HIV global surveillance. In this study, we explore the utility of metagenomic NGS to characterize divergent strains of HIV-1 and to simultaneously screen for other co-infecting viruses. Thirty-five HIV-1-infected Cameroonian blood donor specimens with viral loads of >4.4 log10 copies/ml were selected to include a diverse representation of group M strains. Random-primed NGS libraries, prepared from plasma specimens, resulted in greater than 90% genome coverage for 88% of specimens. Correct subtype designations based on NGS were concordant with sub-region PCR data in 31 of 35 (89%) cases. Complete genomes were assembled for 25 strains, including circulating recombinant forms with relatively limited data available (7 CRF11_cpx, 2 CRF13_cpx, 1 CRF18_cpx, and 1 CRF37_cpx), as well as 9 unique recombinant forms. HPgV (formerly designated GBV-C) co-infection was detected in 9 of 35 (25%) specimens, of which eight specimens yielded complete genomes. The recovered HPgV genomes formed a diverse cluster with genotype 1 sequences previously reported from Ghana, Uganda, and Japan. The extensive genome coverage obtained by NGS improved accuracy and confidence in phylogenetic classification of the HIV-1 strains present in the study population relative to conventional sub-region PCR. In addition, these data demonstrate the potential for metagenomic analysis to be used for routine characterization of HIV-1 and identification of other viral co-infections. PMID:26599538

  3. Sequence-specific interaction between HIV-1 matrix protein and viral genomic RNA revealed by in vitro genetic selection.

    PubMed Central

    Purohit, P; Dupont, S; Stevenson, M; Green, M R

    2001-01-01

    The human immunodeficiency virus type-1 matrix protein (HIV-1 MA) is a multifunctional structural protein synthesized as part of the Pr55 gag polyprotein. We have used in vitro genetic selection to identify an RNA consensus sequence that specifically interacts with MA (Kd = 5 x 10(-7) M). This 13-nt MA binding consensus sequence bears a high degree of homology (77%) to a region (nt 1433-1446) within the POL open reading frame of the HIV-1 genome (consensus sequence from 38 HIV-1 strains). Chemical interference experiments identified the nucleotides within the MA binding consensus sequence involved in direct contact with MA. We further demonstrate that this RNA-protein interaction is mediated through a stretch of basic amino acids within MA. Mutations that disrupt the interaction between MA and its RNA binding site within the HIV-1 genome resulted in a measurable decrease in viral replication. PMID:11345436

  4. Quantification of the Epitope Diversity of HIV-1-Specific Binding Antibodies by Peptide Microarrays for Global HIV-1 Vaccine Development

    PubMed Central

    Stephenson, Kathryn E.; Neubauer, George H.; Reimer, Ulf; Pawlowski, Nikolaus; Knaute, Tobias; Zerweck, Johannes; Korber, Bette T.; Barouch, Dan H.

    2014-01-01

    An effective vaccine against human immunodeficiency virus type 1 (HIV-1) will have to provide protection against a vast array of different HIV-1 strains. Current methods to measure HIV-1-specific binding antibodies following immunization typically focus on determining the magnitude of antibody responses, but the epitope diversity of antibody responses has remained largely unexplored. Here we describe the development of a global HIV-1 peptide microarray that contains 6,564 peptides from across the HIV-1 proteome and covers the majority of HIV-1 sequences in the Los Alamos National Laboratory global HIV-1 sequence database. Using this microarray, we quantified the magnitude, breadth, and depth of IgG binding to linear HIV-1 sequences in HIV-1-infected humans and HIV-1-vaccinated humans, rhesus monkeys and guinea pigs. The microarray measured potentially important differences in antibody epitope diversity, particularly regarding the depth of epitope variants recognized at each binding site. Our data suggest that the global HIV-1 peptide microarray may be a useful tool for both preclinical and clinical HIV-1 research. PMID:25445329

  5. Quantification of the epitope diversity of HIV-1-specific binding antibodies by peptide microarrays for global HIV-1 vaccine development

    SciTech Connect

    Stephenson, Kathryn E.; Neubauer, George H.; Reimer, Ulf; Pawlowski, Nikolaus; Knaute, Tobias; Zerweck, Johannes; Korber, Bette T.; Barouch, Dan H.

    2014-11-14

    An effective vaccine against human immunodeficiency virus type 1 (HIV-1) will have to provide protection against a vast array of different HIV-1 strains. Current methods to measure HIV-1-specific binding antibodies following immunization typically focus on determining the magnitude of antibody responses, but the epitope diversity of antibody responses has remained largely unexplored. Here we describe the development of a global HIV-1 peptide microarray that contains 6564 peptides from across the HIV-1 proteome and covers the majority of HIV-1 sequences in the Los Alamos National Laboratory global HIV-1 sequence database. Using this microarray, we quantified the magnitude, breadth, and depth of IgG binding to linear HIV-1 sequences in HIV-1-infected humans and HIV-1-vaccinated humans, rhesus monkeys and guinea pigs. The microarray measured potentially important differences in antibody epitope diversity, particularly regarding the depth of epitope variants recognized at each binding site. Our data suggest that the global HIV-1 peptide microarray may be a useful tool for both preclinical and clinical HIV-1 research.

  6. Quantification of the epitope diversity of HIV-1-specific binding antibodies by peptide microarrays for global HIV-1 vaccine development

    DOE PAGESBeta

    Stephenson, Kathryn E.; Neubauer, George H.; Reimer, Ulf; Pawlowski, Nikolaus; Knaute, Tobias; Zerweck, Johannes; Korber, Bette T.; Barouch, Dan H.

    2014-11-14

    An effective vaccine against human immunodeficiency virus type 1 (HIV-1) will have to provide protection against a vast array of different HIV-1 strains. Current methods to measure HIV-1-specific binding antibodies following immunization typically focus on determining the magnitude of antibody responses, but the epitope diversity of antibody responses has remained largely unexplored. Here we describe the development of a global HIV-1 peptide microarray that contains 6564 peptides from across the HIV-1 proteome and covers the majority of HIV-1 sequences in the Los Alamos National Laboratory global HIV-1 sequence database. Using this microarray, we quantified the magnitude, breadth, and depth ofmore » IgG binding to linear HIV-1 sequences in HIV-1-infected humans and HIV-1-vaccinated humans, rhesus monkeys and guinea pigs. The microarray measured potentially important differences in antibody epitope diversity, particularly regarding the depth of epitope variants recognized at each binding site. Our data suggest that the global HIV-1 peptide microarray may be a useful tool for both preclinical and clinical HIV-1 research.« less

  7. Phylogenetic Analysis of Near Full-Length HIV Type 1 Genomic Sequences from 21 Korean Individuals

    PubMed Central

    Kim, Jung-Eun; Foley, Brian T.

    2013-01-01

    Abstract The Korean subclade of subtype B (KSB) is the most prevalent HIV-1 strain found in Korea. To date, only two near full-length HIV-1 sequences from Korean patients have been reported. Here, we analyzed a total of 24 near full-length genomes of HIV-1 strains that were isolated from 17 antiretroviral therapy (ART)-naive patients and four ART-exposed patients. Proviral DNA from peripheral blood mononuclear cells was PCR amplified and directly sequenced. Phylogenetic analyses were used to classify viruses from 19 patients as KSB, from one patient as subtype B, from one patient as subtype D, and three viruses from one patient as CRF02_AG. All KSB viruses demonstrated TAAAA instead of TATAA at the TATA box in the LTR. Of the 19 KSB patients, their sequence identities at the nucleotide level ranged from 89.8% to 97.1% from the lowest env gene to the highest pol gene. Other than the CRF02_AG viruses, no recombination events were noted in any of the 19 KSB patients, which is consistent with our previous studies on the pol, vif, and nef genes. Except for one strain, all of the strains were classified as non-syncytium-inducing strains. This is the first report to describe near full-length KSB. PMID:23199052

  8. Genotypic Resistance Tests Sequences Reveal the Role of Marginalized Populations in HIV-1 Transmission in Switzerland

    PubMed Central

    Shilaih, Mohaned; Marzel, Alex; Yang, Wan Lin; Scherrer, Alexandra U.; Schüpbach, Jörg; Böni, Jürg; Yerly, Sabine; Hirsch, Hans H.; Aubert, Vincent; Cavassini, Matthias; Klimkait, Thomas; Vernazza, Pietro L.; Bernasconi, Enos; Furrer, Hansjakob; Günthard, Huldrych F.; Kouyos, Roger; Battegay, Manuel; Braun, Dominique; Bucher, Heiner; Burton-Jeangros, Claudine; Calmy, Alexandra; Dollenmaier, Günter; Egger, Matthias; Elzi, Luigia; Fehr, Jan; Fellay, Jaque; Fux, Christoph; Gorgievski, Meri; Haerry, David; Hasse, Barbara; Hoffmann, Matthias; Hösli, Irene; Kahlert, Christian; Kaiser, Laurent; Keiser, Olivia; Kovari, Helen; Ledergerber, Bruno; Martinetti, Gladys; de Tejada, Begoña Martinez; Marzolini, Catia; Metzner, Karin; Müller, Nicolas; Nadal, David; Nicca, Dunja; Pantaleo, Giuseppe; Rauch, Andre; Regenass, Stephan; Rudin, Christoph; Schöni-Affolter, Franziska; Schmid, Patrick; Speck, Roberto; Stöckle, Marcel; Tarr, Philip; Trkola, Alexandra; Weber, Reiner

    2016-01-01

    Targeting hard-to-reach/marginalized populations is essential for preventing HIV-transmission. A unique opportunity to identify such populations in Switzerland is provided by a database of all genotypic-resistance-tests from Switzerland, including both sequences from the Swiss HIV Cohort Study (SHCS) and non-cohort sequences. A phylogenetic tree was built using 11,127 SHCS and 2,875 Swiss non-SHCS sequences. Demographics were imputed for non-SHCS patients using a phylogenetic proximity approach. Factors associated with non-cohort outbreaks were determined using logistic regression. Non-B subtype (univariable odds-ratio (OR): 1.9; 95% confidence interval (CI): 1.8–2.1), female gender (OR: 1.6; 95% CI: 1.4–1.7), black ethnicity (OR: 1.9; 95% CI: 1.7–2.1) and heterosexual transmission group (OR:1.8; 95% CI: 1.6–2.0), were all associated with underrepresentation in the SHCS. We found 344 purely non-SHCS transmission clusters, however, these outbreaks were small (median 2, maximum 7 patients) with a strong overlap with the SHCS’. 65% of non-SHCS sequences were part of clusters composed of >= 50% SHCS sequences. Our data suggests that marginalized-populations are underrepresented in the SHCS. However, the limited size of outbreaks among non-SHCS patients in-care implies that no major HIV outbreak in Switzerland was missed by the SHCS surveillance. This study demonstrates the potential of sequence data to assess and extend the scope of infectious-disease surveillance. PMID:27297284

  9. Genotypic Resistance Tests Sequences Reveal the Role of Marginalized Populations in HIV-1 Transmission in Switzerland.

    PubMed

    Shilaih, Mohaned; Marzel, Alex; Yang, Wan Lin; Scherrer, Alexandra U; Schüpbach, Jörg; Böni, Jürg; Yerly, Sabine; Hirsch, Hans H; Aubert, Vincent; Cavassini, Matthias; Klimkait, Thomas; Vernazza, Pietro L; Bernasconi, Enos; Furrer, Hansjakob; Günthard, Huldrych F; Kouyos, Roger

    2016-01-01

    Targeting hard-to-reach/marginalized populations is essential for preventing HIV-transmission. A unique opportunity to identify such populations in Switzerland is provided by a database of all genotypic-resistance-tests from Switzerland, including both sequences from the Swiss HIV Cohort Study (SHCS) and non-cohort sequences. A phylogenetic tree was built using 11,127 SHCS and 2,875 Swiss non-SHCS sequences. Demographics were imputed for non-SHCS patients using a phylogenetic proximity approach. Factors associated with non-cohort outbreaks were determined using logistic regression. Non-B subtype (univariable odds-ratio (OR): 1.9; 95% confidence interval (CI): 1.8-2.1), female gender (OR: 1.6; 95% CI: 1.4-1.7), black ethnicity (OR: 1.9; 95% CI: 1.7-2.1) and heterosexual transmission group (OR:1.8; 95% CI: 1.6-2.0), were all associated with underrepresentation in the SHCS. We found 344 purely non-SHCS transmission clusters, however, these outbreaks were small (median 2, maximum 7 patients) with a strong overlap with the SHCS'. 65% of non-SHCS sequences were part of clusters composed of >= 50% SHCS sequences. Our data suggests that marginalized-populations are underrepresented in the SHCS. However, the limited size of outbreaks among non-SHCS patients in-care implies that no major HIV outbreak in Switzerland was missed by the SHCS surveillance. This study demonstrates the potential of sequence data to assess and extend the scope of infectious-disease surveillance. PMID:27297284

  10. Identification of HIV Mutation as Diagnostic Biomarker through Next Generation Sequencing

    PubMed Central

    Shaw, Wen Hui; Lin, Qianqian; Muhammad, Zikry Zhiwei Bin Roslee; Lee, Jia Jun; Khong, Wei Xin; Ng, Oon Tek; Tan, Eng Lee

    2016-01-01

    Introduction Current clinical detection of Human immunodeficiency virus 1 (HIV-1) is used to target viral genes and proteins. However, the immunoassay, such as viral culture or Polymerase Chain Reaction (PCR), lacks accuracy in the diagnosis, as these conventional assays rely on the stable genome and HIV-1 is a highly-mutated virus. Next generation sequencing (NGS) promises to be transformative for the practice of infectious disease, and the rapidly reducing cost and processing time mean that this will become a feasible technology in diagnostic and research laboratories in the near future. The technology offers the superior sensitivity to detect the pathogenic viruses, including unknown and unexpected strains. Aim To leverage the NGS technology in order to improve current HIV-1 diagnosis and genotyping methods. Materials and Methods Ten blood samples were collected from HIV-1 infected patients which were diagnosed by RT PCR at Singapore Communicable Disease Centre, Tan Tock Seng Hospital from October 2014 to March 2015. Viral RNAs were extracted from blood plasma and reversed into cDNA. The HIV-1 cDNA samples were cleaned up using a PCR purification kit and the sequencing library was prepared and identified through MiSeq. Results Two common mutations were observed in all ten samples. The common mutations were identified at genome locations 1908 and 2104 as missense and silent mutations respectively, conferring S37N and S3S found on aspartic protease and reverse transcriptase subunits. Conclusion The common mutations identified in this study were not previously reported, therefore suggesting the potential for them to be used for identification of viral infection, disease transmission and drug resistance. This was especially the case for, missense mutation S37N which could cause an amino acid change in viral proteases thus reducing the binding affinity of some protease inhibitors. Thus, the unique common mutations identified in this study could be used as diagnostic

  11. HIV-1 in genital tract and plasma of women: Compartmentalization of viral sequences, coreceptor usage, and glycosylation

    PubMed Central

    Kemal, Kimdar Sherefa; Foley, Brian; Burger, Harold; Anastos, Kathryn; Minkoff, Howard; Kitchen, Christina; Philpott, Sean M.; Gao, Wei; Robison, Esther; Holman, Susan; Dehner, Carolyn; Beck, Suzanne; Meyer, William A.; Landay, Alan; Kovacs, Andrea; Bremer, James; Weiser, Barbara

    2003-01-01

    Worldwide, 90% of HIV-1 infections are transmitted heterosexually. Because the genital mucosa are the sites of initial contact with HIV-1 for most exposed individuals, study of the virus from the genital tract is critical for the development of vaccines and therapeutics. Previous analyses of HIV-1 in various tissues have documented compartmentalization of viral genomes. Whether compartmentalization was associated with viral phenotypic differences or immune status, however, was not well understood. We compared HIV-1 gp120 env sequences from the genital tract and plasma of 12 women. Eight women displayed compartmentalized HIV-1 RNA genomes, with viral sequences from each site that were clearly discrete, yet phylogenetically related. The remaining four exhibited env sequences that were intermingled between the two sites. Women with compartmentalized HIV-1 genomes had higher CD4+ cell counts than those displaying intermingled strains (P = 0.02). Intrapatient HIV-1 recombinants comprising sequences that were characteristic of both sites were identified. We next compared viral phenotypes in each compartment. HIV-1 coreceptor usage was often compartmentalized (P ≤ 0.01). The number of N-linked glycosylation sites, associated with neutralization resistance, also differed between compartments (P < 0.01). Furthermore, disparities between the density of gp120 glycosylations in each compartment correlated with higher CD4+ counts (P = 0.03). These data demonstrate that the genital tract and plasma can harbor populations of replicating HIV-1 with different phenotypes. The association of higher CD4+ cell counts with compartmentalization of viral genomes and density of gp120 glycosylations suggests that the immune response influences the development of viral genotypes in each compartment. These findings are relevant to the prevention and control of HIV-1 infection. PMID:14557540

  12. Improving HIV coreceptor usage prediction in the clinic using hints from next-generation sequencing data

    PubMed Central

    Pfeifer, Nico; Lengauer, Thomas

    2012-01-01

    Motivation: Due to the high mutation rate of human immunodeficiency virus (HIV), drug-resistant-variants emerge frequently. Therefore, researchers are constantly searching for new ways to attack the virus. One new class of anti-HIV drugs is the class of coreceptor antagonists that block cell entry by occupying a coreceptor on CD4 cells. This type of drug just has an effect on the subset of HIVs that use the inhibited coreceptor. A good prediction of whether the viral population inside a patient is susceptible to the treatment is hence very important for therapy decisions and pre-requisite to administering the respective drug. The first prediction models were based on data from Sanger sequencing of the V3 loop of HIV. Recently, a method based on next-generation sequencing (NGS) data was introduced that predicts labels for each read separately and decides on the patient label through a percentage threshold for the resistant viral minority. Results: We model the prediction problem on the patient level taking the information of all reads from NGS data jointly into account. This enables us to improve prediction performance for NGS data, but we can also use the trained model to improve predictions based on Sanger sequencing data. Therefore, also laboratories without NGS capabilities can benefit from the improvements. Furthermore, we show which amino acids at which position are important for prediction success, giving clues on how the interaction mechanism between the V3 loop and the particular coreceptors might be influenced. Availability: A webserver is available at http://coreceptor.bioinf.mpi-inf.mpg.de. Contact: nico.pfeifer@mpi-inf.mpg.de PMID:22962486

  13. Assessment of Ambiguous Base Calls in HIV-1 pol Population Sequences as a Biomarker for Identification of Recent Infections in HIV-1 Incidence Studies

    PubMed Central

    Hauser, Andrea; Jansen, Klaus; Yousef, Kaveh Pouran; Fiedler, Stefan; von Kleist, Max; Norley, Stephen; Somogyi, Sybille; Hamouda, Osamah; Bannert, Norbert; Bartmeyer, Barbara; Kücherer, Claudia

    2014-01-01

    An increase in the proportion of ambiguous base calls in HIV-1 pol population sequences during the course of infection has been demonstrated in different study populations, and sequence ambiguity thresholds to classify infections as recent or nonrecent have been suggested. The aim of our study was to evaluate sequence ambiguities as a candidate biomarker for use in an HIV-1 incidence assay using samples from antiretroviral treatment-naive seroconverters with known durations of infection (German HIV-1 Seroconverter Study). We used 2,203 HIV-1 pol population sequences derived from 1,334 seroconverters to assess the sequence ambiguity method (SAM). We then compared the serological incidence BED capture enzyme immunoassay (BED-CEIA) with the SAM for a subset of 723 samples from 495 seroconverters and evaluated a multianalyte algorithm that includes BED-CEIA results, SAM results, viral loads, and CD4 cell counts for 453 samples from 325 seroconverters. We observed a significant increase in the proportion of sequence ambiguities with the duration of infection. A sequence ambiguity threshold of 0.5% best identified recent infections with 76.7% accuracy. The mean duration of recency was determined to be 208 (95% confidence interval, 196 to 221) days. In the subset analysis, BED-CEIA achieved a significantly higher accuracy than the SAM (84.6 versus 75.5%, P < 0.001) and results were concordant for 64.2% (464/723) of the samples. Also, the multianalyte algorithm did not show better accuracy than the BED-CEIA (83.4 versus 84.3%, P = 0.786). In conclusion, the SAM and the multianalyte algorithm including SAM were inferior to the BED-CEIA, and the proportion of sequence ambiguities is therefore not a preferable biomarker for HIV-1 incidence testing. PMID:24920768

  14. HIV Drug Resistance Testing by High-Multiplex “Wide” Sequencing on the MiSeq Instrument

    PubMed Central

    Lapointe, H. R.; Dong, W.; Lee, G. Q.; Bangsberg, D. R.; Martin, J. N.; Mocello, A. R.; Boum, Y.; Karakas, A.; Kirkby, D.; Poon, A. F. Y.

    2015-01-01

    Limited access to HIV drug resistance testing in low- and middle-income countries impedes clinical decision-making at the individual patient level. An efficient protocol to address this issue must be established to minimize negative therapeutic outcomes for HIV-1-infected individuals in such settings. This is an observational study to ascertain the potential of newer genomic sequencing platforms, such as the Illumina MiSeq instrument, to provide accurate HIV drug resistance genotypes for hundreds of samples simultaneously. Plasma samples were collected from Canadian patients during routine drug resistance testing (n = 759) and from a Ugandan study cohort (n = 349). Amplicons spanning HIV reverse transcriptase codons 90 to 234 were sequenced with both MiSeq sequencing and conventional Sanger sequencing methods. Sequences were evaluated for nucleotide concordance between methods, using coverage and mixture parameters for quality control. Consensus sequences were also analyzed for disparities in the identification of drug resistance mutations. Sanger and MiSeq sequencing was successful for 881 samples (80%) and 892 samples (81%), respectively, with 832 samples having results from both methods. Most failures were for samples with viral loads of <3.0 log10 HIV RNA copies/ml. Overall, 99.3% nucleotide concordance between methods was observed. MiSeq sequencing achieved 97.4% sensitivity and 99.3% specificity in detecting resistance mutations identified by Sanger sequencing. Findings suggest that the Illumina MiSeq platform can yield high-quality data with a high-multiplex “wide” sequencing approach. This strategy can be used for multiple HIV subtypes, demonstrating the potential for widespread individual testing and annual population surveillance in resource-limited settings. PMID:26282425

  15. Nautilus: a bioinformatics package for the analysis of HIV type 1 targeted deep sequencing data.

    PubMed

    Kijak, Gustavo H; Pham, Phuc; Sanders-Buell, Eric; Harbolick, Elizabeth A; Eller, Leigh Anne; Robb, Merlin L; Michael, Nelson L; Kim, Jerome H; Tovanabutra, Sodsai

    2013-10-01

    The advent of next generation sequencing technologies is providing new insight into HIV-1 diversity and evolution, which has created the need for bioinformatics tools that could be applied to the characterization of viral quasispecies. Here we present Nautilus, a bioinformatics package for the analysis of HIV-1 targeted deep sequencing data. The DeepHaplo module determines the nucleotide base frequency and read depth at each position and computes the haplotype frequencies based on the linkage among polymorphisms in the same next generation sequence read. The Motifs module computes the frequency of the variants in the setting of their sequence context and mapping orientation, which allows for the validation of polymorphisms and haplotypes when strand bias is suspected. Both modules are accessed through a user-friendly GUI, which runs on Mac OS X (version 10.7.4 or later), and are based on Python, JAVA, and R scripts. Nautilus is available from www.hivresearch.org/research.php?ServiceID=5&SubServiceID=6 . PMID:23809062

  16. STD/HIV prevention in Turkey: planning a sequence of interventions.

    PubMed

    Aral, S O; Fransen, L

    1995-12-01

    This study was initiated to assess which mix of early STD/HIV prevention interventions would potentially be effective, cost-effective and sustainable in Turkey; and to program an intervention sequence to maximize synergy among the interventions. During rapid assessment we: 1) reviewed past issues of 3 leading newspapers; 2) collected information on TV coverage; 3) interviewed key informants including taxicab drivers, hotel employees, grocery store owners, academicians in public health and law, investigators of STD/HIV and reproductive tract infections, and officials in the ministry of health; 4) reviewed available evidence on STD/HIV morbidity, sexual behavior patterns, migration patterns and same/opposite gender sex trade. We found: 1) discrepancies between decision makers' perceptions and social realities with respect to the epidemiology of sexual behavior and STDs, and the state of public health programs; 2) discrepancies between sexual practices and public expression regarding sexual practices; 3) economic, demographic, and political pressures in Turkey and in surrounding countries for the expansion of prostitution; 4) a sexual double standard and gender specific migration patterns which sustain a high demand for commercial sex; 5) patterns of health care seeking behaviors and provision of STD clinical services which indicate other STDs may play a very important role in spread of HIV infection; 6) an important mass media role in opinion formation; 7) consensual denial of risk for the majority based on beliefs embedded in machismo, nationalism and religion, and a resulting marginalization and externalization of STD/HIV risk; 8) high prevalence of syphilis among both Turkish and immigrant female prostitutes in Istanbul (early latent 8 and 13%; late latent 0 and 4%; previous history 9 and 22%) 9) and high rates of syphilis among male prostitutes (early latent 11%, late latent 21% and previous history 58%). We concluded that interventions should initially include

  17. Short Communication Phylogenetic Characterization of HIV Type 1 CRF01_AE V3 Envelope Sequences in Pregnant Women in Northern Vietnam

    PubMed Central

    Caridha, Rozina; Ha, Tran Thi Thanh; Gaseitsiwe, Simani; Hung, Pham Viet; Anh, Nguyen Mai; Bao, Nguyen Huy; Khang, Dinh Duy; Hien, Nguyen Tran; Cam, Phung Dac; Chiodi, Francesca

    2012-01-01

    Abstract Characterization of HIV-1 strains is important for surveillance of the HIV-1 epidemic. In Vietnam HIV-1-infected pregnant women often fail to receive the care they are entitled to. Here, we analyzed phylogenetically HIV-1 env sequences from 37 HIV-1-infected pregnant women from Ha Noi (n=22) and Hai Phong (n=15), where they delivered in 2005–2007. All carried CRF01_AE in the gp120 V3 region. In 21 women CRF01_AE was also found in the reverse transcriptase gene. We compared their env gp120 V3 sequences phylogenetically in a maximum likelihood tree to those of 198 other CRF01_AE sequences in Vietnam and 229 from neighboring countries, predominantly Thailand, from the HIV-1 database. Altogether 464 sequences were analyzed. All but one of the maternal sequences colocalized with sequences from northern Vietnam. The maternal sequences had evolved the least when compared to sequences collected in Ha Noi in 2002, as shown by analysis of synonymous and nonsynonymous changes, than to other Vietnamese sequences collected earlier and/or elsewhere. Since the HIV-1 epidemic in women in Vietnam may still be underestimated, characterization of HIV-1 in pregnant women is important to observe how HIV-1 has evolved and follow its molecular epidemiology. PMID:21936713

  18. HIV-1 gp140 epitope recognition is influenced by immunoglobulin DH gene segment sequence.

    PubMed

    Wang, Yuge; Kapoor, Pratibha; Parks, Robert; Silva-Sanchez, Aaron; Alam, S Munir; Verkoczy, Laurent; Liao, Hua-Xin; Zhuang, Yingxin; Burrows, Peter; Levinson, Michael; Elgavish, Ada; Cui, Xiangqin; Haynes, Barton F; Schroeder, Harry

    2016-02-01

    Complementarity Determining Region 3 of the immunoglobulin (Ig) H chain (CDR-H3) lies at the center of the antigen-binding site where it often plays a decisive role in antigen recognition and binding. Amino acids encoded by the diversity (DH) gene segment are the main component of CDR-H3. Each DH has the potential to rearrange into one of six DH reading frames (RFs), each of which exhibits a characteristic amino acid hydrophobicity signature that has been conserved among jawed vertebrates by natural selection. A preference for use of RF1 promotes the incorporation of tyrosine into CDR-H3 while suppressing the inclusion of hydrophobic or charged amino acids. To test the hypothesis that these evolutionary constraints on DH sequence influence epitope recognition, we used mice with a single DH that has been altered to preferentially use RF2 or inverted RF1. B cells in these mice produce a CDR-H3 repertoire that is enriched for valine or arginine in place of tyrosine. We serially immunized this panel of mice with gp140 from HIV-1 JR-FL isolate and then used enzyme-linked immunosorbent assay (ELISA) or peptide microarray to assess antibody binding to key or overlapping HIV-1 envelope epitopes. By ELISA, serum reactivity to key epitopes varied by DH sequence. By microarray, sera with Ig CDR-H3s enriched for arginine bound to linear peptides with a greater range of hydrophobicity but had a lower intensity of binding than sera containing Ig CDR-H3s enriched for tyrosine or valine. We conclude that patterns of epitope recognition and binding can be heavily influenced by DH germ line sequence. This may help explain why antibodies in HIV-infected patients must undergo extensive somatic mutation in order to bind to specific viral epitopes and achieve neutralization. PMID:26687685

  19. HIV type 1 genetic diversity in Moyale, Mandera, and Turkana based on env-C2-V3 sequences.

    PubMed

    Khamadi, Samoel A; Lihana, Raphael W; Mwaniki, D L; Kinyua, Joyceline; Lagat, Nancy; Carter, Jane Y; Ichimura, Hiroshi; Oishi, Isao; Okoth, Fredrick A; Ochieng, Washington

    2008-12-01

    The genetic diversity of HIV-1 subtypes circulating in three districts of northern Kenya, i.e., Turkana, Mandera, and Moyale, was studied. DNA sequences encoding a portion of the env-C2-V3 region of the virus were amplified by PCR and sequenced directly. One hundred and fifty-nine samples were successfully sequenced in the env-C2-V3 region and analyzed. From the analysis, 57% were subtype A1, 27% were subtype C, 9% were subtype D, and the remaining 7% were unclassified. This study showed that HIV-1 subtype A1 was the dominant subtype in circulation in this region, though there was a significant percentage of HIV-1 subtype C in circulation there. PMID:19102688

  20. Lymphotropic herpes virus (EBV, HHV-6, HHV-8) DNA sequences in HIV negative Castleman's disease

    PubMed Central

    Barozzi, P; Luppi, M; Masini, L; Marasca, R; Savarino, M; Morselli, M; Ferrari, M G; Bevini, M; Bonacorsi, G; Torelli, G

    1996-01-01

    Aim—To evaluate the possible involvement of lymphotropic herpes viruses in Castleman's disease. Methods—Archival formalin fixed, paraffin wax embedded biopsy specimens from 16 HIV negative patients (11 with localised and five of multicentric disease) were studied. Epstein-Barr virus (EBV), human herpes virus-6 (HHV-6) and human herpes virus-8 (HHV-8) DNA was detected using PCR. PCR was also used to characterise the EBV genomes and the clonal status of the lesions. Results—EBV sequences were identified in nine (56%) cases. The main EBV genotype detected was type 1. Two (12%) cases were positive for both HHV-6 and EBV sequences. HHV-8 sequences were detected in one case of localised Castleman's disease, the sequence of which differed from that of the HHV-8 prototype. No clonal immunoglobulin gene rearrangements were found. Conclusions—EBV DNA was detected in a substantial proportion of cases, suggesting that it may have a role in the pathogenesis of Castleman's disease, unlike HHV-6 which was detected rarely. This is the first report of HHV-8 specific sequences in the localised from of the disease. Images PMID:16696081

  1. Comparison of Major and Minor Viral SNPs Identified through Single Template Sequencing and Pyrosequencing in Acute HIV-1 Infection

    PubMed Central

    Bouzek, Heather; Kim, Moon; Deng, Wenjie; Larsen, Brendan B.; Zhao, Hong; Bumgarner, Roger E.; Rolland, Morgane; Mullins, James I.

    2015-01-01

    Massively parallel sequencing (MPS) technologies, such as 454-pyrosequencing, allow for the identification of variants in sequence populations at lower levels than consensus sequencing and most single-template Sanger sequencing experiments. We sought to determine if the greater depth of population sampling attainable using MPS technology would allow detection of minor variants in HIV founder virus populations very early in infection in instances where Sanger sequencing detects only a single variant. We compared single nucleotide polymorphisms (SNPs) during acute HIV-1 infection from 32 subjects using both single template Sanger and 454-pyrosequencing. Pyrosequences from a median of 2400 viral templates per subject and encompassing 40% of the HIV-1 genome, were compared to a median of five individually amplified near full-length viral genomes sequenced using Sanger technology. There was no difference in the consensus nucleotide sequences over the 3.6kb compared in 84% of the subjects infected with single founders and 33% of subjects infected with multiple founder variants: among the subjects with disagreements, mismatches were found in less than 1% of the sites evaluated (of a total of nearly 117,000 sites across all subjects). The majority of the SNPs observed only in pyrosequences were present at less than 2% of the subject’s viral sequence population. These results demonstrate the utility of the Sanger approach for study of early HIV infection and provide guidance regarding the design, utility and limitations of population sequencing from variable template sources, and emphasize parameters for improving the interpretation of massively parallel sequencing data to address important questions regarding target sequence evolution. PMID:26317928

  2. Evaluation of the automatic editing tool RECall for HIV-1 pol and V3 loop sequences.

    PubMed

    Vinken, Lore; Megens, Sarah; Schrooten, Yoeri; Vandamme, Anne-Mieke; Van Laethem, Kristel

    2013-10-01

    Genotypic drug resistance testing is routine practice in HIV-1 clinical care. The visual interpretation of sequencing electropherograms is labour-intensive and subject to intra- and inter-assay variability because decisions are based on operators' judgments. In this study the performance of the automatic editing tool RECall was compared to the current standard of editing manually and editing using the tool ViroSeq. Using RECall a consensus sequence could be generated for 97% of the V3 loop and for 79% of the pol experiments. By comparison, using manual editing a consensus sequence could be reached for 87% of the V3 and 87% of the pol experiments. Using ViroSeq, a consensus sequence was generated for 68% of the pol experiments. On a predefined dataset, manual editing displayed the highest probability to accurately assign mixtures (0.91 vs. 0.88 by ViroSeq vs. 0.76 by RECall) and the lowest probability to inaccurately assign a mixture to a pure base call (0.002 vs. 0.019 by ViroSeq vs. 0.002 by RECall). As differences in base calling have little impact on drug resistance interpretation and hands-on-time could be substantially reduced, RECall could be a valuable tool for the standardization and acceleration of the editing process. PMID:23748120

  3. Sequence analysis of the dimerization initiation site of concordant and discordant viral variants superinfecting HIV type 1 patients.

    PubMed

    Mayr, Luzia; Powell, Rebecca; Kinge, Thompson; Nyambi, Phillipe N

    2011-11-01

    For HIV recombination to occur, the RNAs from two infecting strains within a cell must dimerize at the dimerization initiation site (DIS). We examined the sequence identity at the DIS (697-731 bp, Hxb2 numbering engine) in patients superinfected with concordant HIV-1 strains and compared them to those with discordant strains. Viral RNA in sequential plasma from four subjects superinfected with subtype-discordant and two subjects superinfected with subtype-concordant HIV-1 strains was extracted, amplified (5' LTR-early gag: 526-1200 bp, Hxb2 numbering engine), sequenced, and analyzed to determine their compatibility for dimerization in vivo. The concordant viruses infecting the two subjects exhibited identical sequences in the 35-bp-long DIS region while sequences from the discordant viruses revealed single nucleotide changes that were located in the DIS loop (715 bp), its flanking nucleotides (710 bp and 717 bp), and the DIS stem (719 bp). Evidence from in vitro experiments demonstrates that these in vivo changes identified can abolish dimerization and reduce recombination frequency. Therefore, these results revealing differences in the DIS of discordant strains versus the similarity noted for the concordant strains may contribute to the differences in the frequency of recombination in patients superinfected with such HIV-1 variants. PMID:21453132

  4. Structural and Functional Roles of HIV-1 gp41 Pretransmembrane Sequence Segmentation

    PubMed Central

    Sáez-Cirión, Asier; Arrondo, José L. R.; Gómara, María J.; Lorizate, Maier; Iloro, Ibón; Melikyan, Grigory; Nieva, José L.

    2003-01-01

    The membrane-proximal segment connecting the helical core with the transmembrane anchor of human immunodeficiency virus type 1 gp41 is accessible to broadly neutralizing antibodies and plays a crucial role in fusion activity. New predictive approaches including computation of interfacial affinity and the corresponding hydrophobic moments suggest that this region is functionally segmented into two consecutive subdomains: one amphipathic at the N-terminal side and one fully interfacial at the C-terminus. The N-terminal subdomain would extend α-helices from the preceding carboxy-terminal heptad repeat and provide, at the same time, a hydrophobic-at-interface surface. Experiments were performed to compare a wild-type representing pretransmembrane peptide with a nonamphipathic defective sequence, which otherwise conserved interfacial hydrophobicity at the carboxy-subdomain. Results confirmed that both penetrated equally well into lipid monolayers and both were able to partition into membrane interfaces. However only the functional sequence: 1), adopted helical structures in solution and in membranes; 2), formed homo-oligomers in solution and membranes; and 3), inhibited gp41-induced cell-cell fusion. These data support two roles for gp41 aromatic-rich pretransmembrane sequence: 1), oligomerization of gp41; and 2), immersion into the viral membrane interface. Accessibility to membrane interfaces and subsequent adoption of the low-energy structure may augment helical bundle formation and perhaps be related to a concomitant loss of immunoreactivity. These results may have implications in the development of HIV-1 fusion inhibitors and vaccines. PMID:14645067

  5. Multilocus sequence typing of Cryptococcus neoformans in non-HIV associated cryptococcosis in Nagasaki, Japan.

    PubMed

    Mihara, Tomo; Izumikawa, Koichi; Kakeya, Hiroshi; Ngamskulrungroj, Popchai; Umeyama, Takashi; Takazono, Takahiro; Tashiro, Masato; Nakamura, Shigeki; Imamura, Yoshifumi; Miyazaki, Taiga; Ohno, Hideaki; Yamamoto, Yoshihiro; Yanagihara, Katsunori; Miyzaki, Yoshitsugu; Kohno, Shigeru

    2013-04-01

    Cryptococcosis is primarily caused by two Cryptococcus species, i.e., Cryptococcus neoformans and C. gattii. Both include several genetically diverse subgroups that can be differentiated using various molecular strain typing methods. Since little is known about the molecular epidemiology of the C. neoformans/C. gattii species complex in Japan, we conducted a molecular epidemiological analysis of 35 C. neoformans isolates from non-HIV patients in Nagasaki, Japan and 10 environmental isolates from Thailand. All were analyzed using URA5-restriction fragment length polymorphism (RFLP) and multilocus sequence typing (MLST). Combined sequence data for all isolates were evaluated with the neighbor-joining method. All were found to be serotype A and mating type MATα. Thirty-two of the 35 clinical isolates molecular type VNI, while the three remaining isolates were VNII as determined through the URA5-RFLP method. Thirty-one of the VNI isolates were identified as MLST sequence type (ST) 5, the remaining one was ST 32 and the three VNII isolates were found to be ST 43. All the environmental isolates were identified as molecular type VNI (four MLST ST 5 and six ST 4). Our study shows that C. neoformans isolates in Nagasaki are genetically homogeneous, with most of the isolates being ST 5. PMID:22901045

  6. Production of Mucosally Transmissible SHIV Challenge Stocks from HIV-1 Circulating Recombinant Form 01_AE env Sequences

    PubMed Central

    Tartaglia, Lawrence J.; Chang, Hui-Wen; Lee, Benjamin C.; Abbink, Peter; Ng’ang’a, David; Boyd, Michael; Lavine, Christy L.; Lim, So-Yon; Sanisetty, Srisowmya; Whitney, James B.; Seaman, Michael S.; Rolland, Morgane; Tovanabutra, Sodsai; Ananworanich, Jintanat; Robb, Merlin L.; Kim, Jerome H.; Michael, Nelson L.; Barouch, Dan H.

    2016-01-01

    Simian-human immunodeficiency virus (SHIV) challenge stocks are critical for preclinical testing of vaccines, antibodies, and other interventions aimed to prevent HIV-1. A major unmet need for the field has been the lack of a SHIV challenge stock expressing circulating recombinant form 01_AE (CRF01_AE) env sequences. We therefore sought to develop mucosally transmissible SHIV challenge stocks containing HIV-1 CRF01_AE env derived from acutely HIV-1 infected individuals from Thailand. SHIV-AE6, SHIV-AE6RM, and SHIV-AE16 contained env sequences that were >99% identical to the original HIV-1 isolate and did not require in vivo passaging. These viruses exhibited CCR5 tropism and displayed a tier 2 neutralization phenotype. These challenge stocks efficiently infected rhesus monkeys by the intrarectal route, replicated to high levels during acute infection, and established chronic viremia in a subset of animals. SHIV-AE16 was titrated for use in single, high dose as well as repetitive, low dose intrarectal challenge studies. These SHIV challenge stocks should facilitate the preclinical evaluation of vaccines, monoclonal antibodies, and other interventions targeted at preventing HIV-1 CRF01_AE infection. PMID:26849216

  7. Quantitative Deep Sequencing Reveals Dynamic HIV-1 Escape and Large Population Shifts during CCR5 Antagonist Therapy In Vivo

    PubMed Central

    Tsibris, Athe M. N.; Russ, Carsten; Lo, Chien-Chi; Leitner, Thomas; Gaschen, Brian; Theiler, James; Paredes, Roger; Su, Zhaohui; Hughes, Michael D.; Gulick, Roy M.; Greaves, Wayne; Coakley, Eoin; Flexner, Charles; Nusbaum, Chad; Kuritzkes, Daniel R.

    2009-01-01

    High-throughput sequencing platforms provide an approach for detecting rare HIV-1 variants and documenting more fully quasispecies diversity. We applied this technology to the V3 loop-coding region of env in samples collected from 4 chronically HIV-infected subjects in whom CCR5 antagonist (vicriviroc [VVC]) therapy failed. Between 25,000–140,000 amplified sequences were obtained per sample. Profound baseline V3 loop sequence heterogeneity existed; predicted CXCR4-using populations were identified in a largely CCR5-using population. The V3 loop forms associated with subsequent virologic failure, either through CXCR4 use or the emergence of high-level VVC resistance, were present as minor variants at 0.8–2.8% of baseline samples. Extreme, rapid shifts in population frequencies toward these forms occurred, and deep sequencing provided a detailed view of the rapid evolutionary impact of VVC selection. Greater V3 diversity was observed post-selection. This previously unreported degree of V3 loop sequence diversity has implications for viral pathogenesis, vaccine design, and the optimal use of HIV-1 CCR5 antagonists. PMID:19479085

  8. HIV

    PubMed Central

    Chawla, Sumit; Sahoo, Soumya Swaroop; Jain, Rambilas; Khanna, Pardeep; Mehta, Bharti; Singh, Inderjeet

    2014-01-01

    Getting to zero: zero new HIV infections, zero deaths from AIDS-related illness, zero discrimination is the theme of World AIDS Day 2012. Given the spread of the epidemic today, getting to zero may sound difficult, but significant progress is underway. The total annual loss for the entire country due to HIV is 7% of GDP, which exceeds India’s annual health expenditure in 2004. The additional loss due to loss of labor income and increased medical expenditure as measured by the external transfers, account for 5% of the country’s health expenditure and 0.23% of GDP. Given that the HIV incidence rate is only 0.27% in India, these losses are quite staggering. Despite the remarkable achievements in development of anti-retroviral therapies against HIV and the recent advances in new prevention technologies, the rate of new HIV infections continue to outpace efforts on HIV prevention and control. Thus, the development of a safe and effective vaccine for prevention and control of AIDS remains a global public health priority and the greatest opportunity to eventually end the AIDS pandemic. PMID:24056755

  9. Structure-function studies of HIV-1: influence of long terminal repeat U3 region sequences on virus production.

    PubMed

    Velpandi, A; Nagashunmugam, T; Otsuka, T; Cartas, M; Srinivasan, A

    1992-06-01

    DNA sequence analyses of several human immunodeficiency virus (HIV) isolates revealed extensive genetic diversity in the env gene and, to a lesser extent, in other regions of the viral genome, including the long terminal repeat (LTR) sequences. Since the LTRs contain elements responsible for the control of transcription, the difference in the LTR region may play a crucial role in the overall replication rate of HIV. To evaluate the role of the LTR, we have constructed a number of infectious hybrid HIV molecular clones containing LTRs from different proviral DNAs linked to the body of the viral genome, and analyzed them in a transient expression system. Both parental and hybrid proviral DNAs were transfected into human rhabdomyosarcoma cells for monitoring virus production. Proviral DNA designate pZ6 (HIVZr6) showed a high level of virus in the medium of the transfected culture in comparison to the pHXB2 (HIVHTLV-III) and pARV (HIVSF-2) DNAs. Hybrid proviral DNAs containing viral genes from pZ6, linked to LTR U3 sequences of pHXB2 and pARV at the 5' end, showed virus production similar to the levels observed with pZ6. These results indicate that the extent of virus production does not correlate with the LTR U3 sequences, and may involve other regions of the viral genome. PMID:1351391

  10. The highly conserved codon following the slippery sequence supports -1 frameshift efficiency at the HIV-1 frameshift site.

    PubMed

    Mathew, Suneeth F; Crowe-McAuliffe, Caillan; Graves, Ryan; Cardno, Tony S; McKinney, Cushla; Poole, Elizabeth S; Tate, Warren P

    2015-01-01

    HIV-1 utilises -1 programmed ribosomal frameshifting to translate structural and enzymatic domains in a defined proportion required for replication. A slippery sequence, U UUU UUA, and a stem-loop are well-defined RNA features modulating -1 frameshifting in HIV-1. The GGG glycine codon immediately following the slippery sequence (the 'intercodon') contributes structurally to the start of the stem-loop but has no defined role in current models of the frameshift mechanism, as slippage is inferred to occur before the intercodon has reached the ribosomal decoding site. This GGG codon is highly conserved in natural isolates of HIV. When the natural intercodon was replaced with a stop codon two different decoding molecules-eRF1 protein or a cognate suppressor tRNA-were able to access and decode the intercodon prior to -1 frameshifting. This implies significant slippage occurs when the intercodon is in the (perhaps distorted) ribosomal A site. We accommodate the influence of the intercodon in a model of frame maintenance versus frameshifting in HIV-1. PMID:25807539

  11. Comparison of a High-Resolution Melting Assay to Next-Generation Sequencing for Analysis of HIV Diversity

    PubMed Central

    Cousins, Matthew M.; Ou, San-San; Wawer, Maria J.; Munshaw, Supriya; Swan, David; Magaret, Craig A.; Mullis, Caroline E.; Serwadda, David; Porcella, Stephen F.; Gray, Ronald H.; Quinn, Thomas C.; Donnell, Deborah; Eshleman, Susan H.

    2012-01-01

    Next-generation sequencing (NGS) has recently been used for analysis of HIV diversity, but this method is labor-intensive, costly, and requires complex protocols for data analysis. We compared diversity measures obtained using NGS data to those obtained using a diversity assay based on high-resolution melting (HRM) of DNA duplexes. The HRM diversity assay provides a single numeric score that reflects the level of diversity in the region analyzed. HIV gag and env from individuals in Rakai, Uganda, were analyzed in a previous study using NGS (n = 220 samples from 110 individuals). Three sequence-based diversity measures were calculated from the NGS sequence data (percent diversity, percent complexity, and Shannon entropy). The amplicon pools used for NGS were analyzed with the HRM diversity assay. HRM scores were significantly associated with sequence-based measures of HIV diversity for both gag and env (P < 0.001 for all measures). The level of diversity measured by the HRM diversity assay and NGS increased over time in both regions analyzed (P < 0.001 for all measures except for percent complexity in gag), and similar amounts of diversification were observed with both methods (P < 0.001 for all measures except for percent complexity in gag). Diversity measures obtained using the HRM diversity assay were significantly associated with those from NGS, and similar increases in diversity over time were detected by both methods. The HRM diversity assay is faster and less expensive than NGS, facilitating rapid analysis of large studies of HIV diversity and evolution. PMID:22785188

  12. Characterization of HIV Transmission in South-East Austria

    PubMed Central

    Kessler, Harald H.; Haas, Bernhard; Stelzl, Evelyn; Weninger, Karin; Little, Susan J.; Mehta, Sanjay R.

    2016-01-01

    To gain deeper insight into the epidemiology of HIV-1 transmission in South-East Austria we performed a retrospective analysis of 259 HIV-1 partial pol sequences obtained from unique individuals newly diagnosed with HIV infection in South-East Austria from 2008 through 2014. After quality filtering, putative transmission linkages were inferred when two sequences were ≤1.5% genetically different. Multiple linkages were resolved into putative transmission clusters. Further phylogenetic analyses were performed using BEAST v1.8.1. Finally, we investigated putative links between the 259 sequences from South-East Austria and all publicly available HIV polymerase sequences in the Los Alamos National Laboratory HIV sequence database. We found that 45.6% (118/259) of the sampled sequences were genetically linked with at least one other sequence from South-East Austria forming putative transmission clusters. Clustering individuals were more likely to be men who have sex with men (MSM; p<0.001), infected with subtype B (p<0.001) or subtype F (p = 0.02). Among clustered males who reported only heterosexual (HSX) sex as an HIV risk, 47% clustered closely with MSM (either as pairs or within larger MSM clusters). One hundred and seven of the 259 sequences (41.3%) from South-East Austria had at least one putative inferred linkage with sequences from a total of 69 other countries. In conclusion, analysis of HIV-1 sequences from newly diagnosed individuals residing in South-East Austria revealed a high degree of national and international clustering mainly within MSM. Interestingly, we found that a high number of heterosexual males clustered within MSM networks, suggesting either linkage between risk groups or misrepresentation of sexual risk behaviors by subjects. PMID:26967154

  13. Requirement for HIV-1 TAR sequences for Tat activation in rodent cells.

    PubMed

    Sutton, J A; Braddock, M; Kingsman, A J; Kingsman, S M

    1995-01-10

    HIV-1 gene expression is activated via an interaction between the virally encoded Tat protein and a target RNA, TAR. TAR is located at the immediate 5' end of all viral mRNAs and comprises a partially base-paired stem with a tripyrimidine bulge in the upper stem and a hexanucleotide loop. In vitro, Tat binds specifically to the bulge and upper stem region with no requirement for the loop. In contrast, when Tat activation is analyzed in primate cells, mutations in the loop abolish activation, suggesting a critical role for loop binding cellular factors. However, in rodent cells the reverse is true. Messages with a mutation in the TAR loop are activated whereas messages harboring a wild-type TAR sequence are not activated. By testing the effect of mutations in the bulge and stem in the context of mutation in the loop we now show that this loop-independent activation by Tat in rodent cells requires the critical bulge-stem sequences needed for Tat binding in vitro. These data suggest that in rodent cells, as in vitro, Tat does not require a loop binding cofactor. In rodent cells containing human chromosome 12 (CHO12), however, Tat activation is both bulge and loop dependent. It appears that rodent cells, but not CHO12 cells, are refractory to the normal Tat/TAR activation pathway not by virtue of lacking a loop binding cofactor, but rather by the presence of a loop binding inhibitor of either Tat binding or the activation process. PMID:7530399

  14. HIV-1 Nef sequence and functional compartmentalization in the gut is not due to differential cytotoxic T lymphocyte selective pressure.

    PubMed

    Lewis, Martha J; Frohnen, Patricia; Ibarrondo, F Javier; Reed, Diane; Iyer, Varun; Ng, Hwee L; Elliott, Julie; Yang, Otto O; Anton, Peter

    2013-01-01

    The gut is the largest lymphoid organ in the body and a site of active HIV-1 replication and immune surveillance. The gut is a reservoir of persistent infection in some individuals with fully suppressed plasma viremia on combination antiretroviral therapy (cART) although the cause of this persistence is unknown. The HIV-1 accessory protein Nef contributes to persistence through multiple functions including immune evasion and increasing infectivity. Previous studies showed that Nef's function is shaped by cytotoxic T lymphocyte (CTL) responses and that there are distinct populations of Nef within tissue compartments. We asked whether Nef's sequence and/or function are compartmentalized in the gut and how compartmentalization relates to local CTL immune responses. Primary nef quasispecies from paired plasma and sigmoid colon biopsies from chronically infected subjects not on therapy were sequenced and cloned into Env(-) Vpu(-) pseudotyped reporter viruses. CTL responses were mapped by IFN-γ ELISpot using expanded CD8+ cells from blood and gut with pools of overlapping peptides covering the entire HIV proteome. CD4 and MHC Class I Nef-mediated downregulation was measured by flow cytometry. Multiple tests indicated compartmentalization of nef sequences in 5 of 8 subjects. There was also compartmentalization of function with MHC Class I downregulation relatively well preserved, but significant loss of CD4 downregulation specifically by gut quasispecies in 5 of 7 subjects. There was no compartmentalization of CTL responses in 6 of 8 subjects, and the selective pressure on quasispecies correlated with the magnitude CTL response regardless of location. These results demonstrate that Nef adapts via diverse pathways to local selective pressures within gut mucosa, which may be predominated by factors other than CTL responses such as target cell availability. The finding of a functionally distinct population within gut mucosa offers some insight into how HIV-1 may persist in

  15. Genetic Characteristics, Coreceptor Usage Potential and Evolution of Nigerian HIV-1 Subtype G and CRF02_AG Isolates

    PubMed Central

    Ajoge, Hannah O.; Gordon, Michelle L.; de Oliveira, Tulio; Green, Taryn N.; Ibrahim, Sani; Shittu, Oladapo S.; Olonitola, Stephen O.; Ahmad, Aliyu A.; Ndung'u, Thumbi

    2011-01-01

    HIV-1 CRF02_AG and subtype G (HIV-1G) account for most HIV infections in Nigeria, but their evolutionary trends have not been well documented. To better elucidate the dynamics of the epidemic in Nigeria we characterised the gag and env genes of North-Central Nigerian HIV-1 isolates from pregnant women. Of 28 samples sequenced in both genes, the predominant clades were CRF02_AG (39%) and HIV-1G (32%). Higher predicted proportion of CXCR4-tropic (X4) HIV-1G isolates was noted compared to CRF02_AG (p = 0.007, Fisher's exact test). Phylogenetic and Bayesian analysis conducted on our sequences and all the dated available Nigerian sequences on the Los Alamos data base showed that CRF02_AG and HIV-1G entered into Nigeria through multiple entries, with presence of HIV-1G dating back to early 1980s. This study underlines the genetic complexity of the HIV-1 epidemic in Nigeria, possible subtype-specific differences in co-receptor usage, and the evolutionary trends of the predominant HIV-1 strains in Nigeria, which may have implications for the design of biomedical interventions and better understanding of the epidemic. PMID:21423811

  16. The C-Terminal Sequence of IFITM1 Regulates Its Anti-HIV-1 Activity

    PubMed Central

    Pan, Qinghua; Liu, Shan-Lu; Qiao, Wentao; Liang, Chen

    2015-01-01

    The interferon-inducible transmembrane (IFITM) proteins inhibit a wide range of viruses. We previously reported the inhibition of human immunodeficiency virus type 1 (HIV-1) strain BH10 by human IFITM1, 2 and 3. It is unknown whether other HIV-1 strains are similarly inhibited by IFITMs and whether there exists viral countermeasure to overcome IFITM inhibition. We report here that the HIV-1 NL4-3 strain (HIV-1NL4-3) is not restricted by IFITM1 and its viral envelope glycoprotein is partly responsible for this insensitivity. However, HIV-1NL4-3 is profoundly inhibited by an IFITM1 mutant, known as Δ(117–125), which is deleted of 9 amino acids at the C-terminus. In contrast to the wild type IFITM1, which does not affect HIV-1 entry, the Δ(117–125) mutant diminishes HIV-1NL4-3 entry by 3-fold. This inhibition correlates with the predominant localization of Δ(117–125) to the plasma membrane where HIV-1 entry occurs. In spite of strong conservation of IFITM1 among most species, mouse IFITM1 is 19 amino acids shorter at its C-terminus as compared to human IFITM1 and, like the human IFITM1 mutant Δ(117–125), mouse IFITM1 also inhibits HIV-1 entry. This is the first report illustrating the role of viral envelope protein in overcoming IFITM1 restriction. The results also demonstrate the importance of the C-terminal region of IFITM1 in modulating the antiviral function through controlling protein subcellular localization. PMID:25738301

  17. Phenotypic assays and sequencing are less sensitive than point mutation assays for detection of resistance in mixed HIV-1 genotypic populations.

    PubMed

    Van Laethem, K; Van Vaerenbergh, K; Schmit, J C; Sprecher, S; Hermans, P; De Vroey, V; Schuurman, R; Harrer, T; Witvrouw, M; Van Wijngaerden, E; Stuyver, L; Van Ranst, M; Desmyter, J; De Clercq, E; Vandamme, A M

    1999-10-01

    The sensitivity and discriminatory power of the 151 and 215 amplification refractory mutation system (ARMS) were evaluated, and their performance for the detection of drug resistance in mixed genotypic populations of the reverse transcription (RT) gene of HIV-1 were compared with T7 sequencing, cycle sequencing, the line probe assay (LiPA) HIV-1 RT test, and the recombinant virus assay (RVA). ARMS and the LiPA HIV-1 RT test were shown to be able to detect minor variants that in particular cases comprised only 1%. T7 sequencing on an ALF semiautomated sequencer could correctly score mixtures only when variants were present at 50%. Cycle sequencing on an ABI PRISM 310 improved the sensitivity for mixtures to about 25%. Using RVA, it was shown that at least 50% of the virus population needed to carry the resistance mutation at codon 184 to afford phenotypic resistance against lamivudine. The two point mutation assays therefore proved to be more sensitive methods than sequencing and RVA to reliably determine a gradual shift in HIV-1 drug resistance mutations in follow-up of patients infected with HIV-1. In 4 of 5 treated patients who were followed by ARMS, a gradual shift in resistant genotypic populations was observed during a period of 6 to 19 months. For 1 patient, a shift from wild to mutant type at position 151 occurred within 2 months, without mixed genotypic intermediate type's being detected. PMID:10843523

  18. Antigen Load and Viral Sequence Diversification Determine the Functional Profile of HIV-1–Specific CD8+ T Cells

    PubMed Central

    Streeck, Hendrik; Brumme, Zabrina L; Anastario, Michael; Cohen, Kristin W; Jolin, Jonathan S; Meier, Angela; Brumme, Chanson J; Rosenberg, Eric S; Alter, Galit; Allen, Todd M; Walker, Bruce D; Altfeld, Marcus

    2008-01-01

    Background Virus-specific CD8+ T lymphocytes play a key role in the initial reduction of peak viremia during acute viral infections, but display signs of increasing dysfunction and exhaustion under conditions of chronic antigen persistence. It has been suggested that virus-specific CD8+ T cells with a “polyfunctional” profile, defined by the capacity to secrete multiple cytokines or chemokines, are most competent in controlling viral replication in chronic HIV-1 infection. We used HIV-1 infection as a model of chronic persistent viral infection to investigate the process of exhaustion and dysfunction of virus-specific CD8+ T cell responses on the single-epitope level over time, starting in primary HIV-1 infection. Methods and Findings We longitudinally analyzed the polyfunctional epitope-specific CD8+ T cell responses of 18 patients during primary HIV-1 infection before and after therapy initiation or sequence variation in the targeted epitope. Epitope-specific CD8+ T cells responded with multiple effector functions to antigenic stimulation during primary HIV-1 infection, but lost their polyfunctional capacity in response to antigen and up-regulated programmed death 1 (PD-1) expression with persistent viremic infection. This exhausted phenotype significantly decreased upon removal of stimulation by antigen, either in response to antiretroviral therapy or by reduction of epitope-specific antigen load in the presence of ongoing viral replication, as a consequence of in vivo selection of cytotoxic T lymphocyte escape mutations in the respective epitopes. Monofunctionality increased in CD8+ T cell responses directed against conserved epitopes from 49% (95% confidence interval 27%–72%) to 76% (56%–95%) (standard deviation [SD] of the effect size 0.71), while monofunctionality remained stable or slightly decreased for responses directed against escaped epitopes from 61% (47%–75%) to 56% (42%–70%) (SD of the effect size 0.18) (p < 0.05). Conclusion These data

  19. Los Alamos National Laboratory.

    ERIC Educational Resources Information Center

    Hammel, Edward F., Jr.

    1982-01-01

    Current and post World War II scientific research at the Los Alamos National Laboratory (New Mexico) is discussed. The operation of the laboratory, the Los Alamos consultant program, and continuation education, and continuing education activities at the laboratory are also discussed. (JN)

  20. Certification assays for HIV-1-based vectors: frequent passage of gag sequences without evidence of replication-competent viruses.

    PubMed

    Sastry, Lakshmi; Xu, Yi; Johnson, Terry; Desai, Kunal; Rissing, David; Marsh, Jonathan; Cornetta, Kenneth

    2003-11-01

    A principal concern regarding the safety of HIV-1-based vectors is replication-competent lentivirus (RCL). We have developed two PCR assays for detecting RCL; the first detects recombination between gag regions in the transfer vector and the packaging construct (sensitivity of detection approximately 10-100 copies of target sequence). The second assay uses real-time PCR to detect vesicular stomatitis virus glycoprotein (VSVG) envelope DNA (sensitivity approximately 5-50 VSVG sequences). In an attempt to amplify any RCL, test vectors were used to transduce C8166 and 293 cells, which were then screened weekly for 3 weeks. Psi-gag recombinants were routinely detected (20 of 21 analyses) in four transductions using the RRL-CMV-GFP vector. In contrast, VSVG sequences were detected only once in 21 analyses. Interestingly, p24 levels (as measured by ELISA) were occasionally detectable after 3 weeks of culture. To determine if a true RCL was present, 21-day cell-free medium was used to transduce naïve cells. No evidence of psi-gag or VSVG transfer was detected, indicating that the recombination events were insufficient to reconstitute a true RCL. These findings have important implications for the design and safety of HIV-1-based vectors intended for clinical applications. PMID:14599817

  1. Subtype-independent near full-length HIV-1 genome sequencing and assembly to be used in large molecular epidemiological studies and clinical management

    PubMed Central

    Grossmann, Sebastian; Nowak, Piotr; Neogi, Ujjwal

    2015-01-01

    Introduction HIV-1 near full-length genome (HIV-NFLG) sequencing from plasma is an attractive multidimensional tool to apply in large-scale population-based molecular epidemiological studies. It also enables genotypic resistance testing (GRT) for all drug target sites allowing effective intervention strategies for control and prevention in high-risk population groups. Thus, the main objective of this study was to develop a simplified subtype-independent, cost- and labour-efficient HIV-NFLG protocol that can be used in clinical management as well as in molecular epidemiological studies. Methods Plasma samples (n=30) were obtained from HIV-1B (n=10), HIV-1C (n=10), CRF01_AE (n=5) and CRF01_AG (n=5) infected individuals with minimum viral load >1120 copies/ml. The amplification was performed with two large amplicons of 5.5 kb and 3.7 kb, sequenced with 17 primers to obtain HIV-NFLG. GRT was validated against ViroSeq™ HIV-1 Genotyping System. Results After excluding four plasma samples with low-quality RNA, a total of 26 samples were attempted. Among them, NFLG was obtained from 24 (92%) samples with the lowest viral load being 3000 copies/ml. High (>99%) concordance was observed between HIV-NFLG and ViroSeq™ when determining the drug resistance mutations (DRMs). The N384I connection mutation was additionally detected by NFLG in two samples. Conclusions Our high efficiency subtype-independent HIV-NFLG is a simple and promising approach to be used in large-scale molecular epidemiological studies. It will facilitate the understanding of the HIV-1 pandemic population dynamics and outline effective intervention strategies. Furthermore, it can potentially be applicable in clinical management of drug resistance by evaluating DRMs against all available antiretrovirals in a single assay. PMID:26115688

  2. Replication fitness of multiple nonnucleoside reverse transcriptase-resistant HIV-1 variants in the presence of etravirine measured by 454 deep sequencing.

    PubMed

    Brumme, Chanson J; Huber, Kelly D; Dong, Winnie; Poon, Art F Y; Harrigan, P Richard; Sluis-Cremer, Nicolas

    2013-08-01

    We applied an efficient method to characterize the relative fitness levels of multiple nonnucleoside reverse transcriptase (NNRTI)-resistant HIV-1 variants by simultaneous competitive culture and 454 deep sequencing. Using this method, we show that the Y181V mutation in the HIV-1 reverse transcriptase in particular confers a clear selective advantage to the virus over 14 other NNRTI resistance mutations in the presence of etravirine in vitro. PMID:23720723

  3. Conserved sequences in the current strains of HIV-1 subtype A in Russia are effectively targeted by artificial RNAi in vitro.

    PubMed

    Tchurikov, Nickolai A; Fedoseeva, Daria M; Gashnikova, Natalya M; Sosin, Dmitri V; Gorbacheva, Maria A; Alembekov, Ildar R; Chechetkin, Vladimir R; Kravatsky, Yuri V; Kretova, Olga V

    2016-05-25

    Highly active antiretroviral therapy has greatly reduced the morbidity and mortality of AIDS. However, many of the antiretroviral drugs are toxic with long-term use, and all currently used anti-HIV agents generate drug-resistant mutants. Therefore, there is a great need for new approaches to AIDS therapy. RNAi is a powerful means of inhibiting HIV-1 production in human cells. We propose to use RNAi for gene therapy of HIV/AIDS. Previously we identified a number of new biologically active siRNAs targeting several moderately conserved regions in HIV-1 transcripts. Here we analyze the heterogeneity of nucleotide sequences in three RNAi targets in sequences encoding the reverse transcriptase and integrase domains of current isolates of HIV-1 subtype A in Russia. These data were used to generate genetic constructs expressing short hairpin RNAs 28-30-bp in length that could be processed in cells into siRNAs. After transfection of the constructs we observed siRNAs that efficiently attacked the selected targets. We expect that targeting several viral genes important for HIV-1 reproduction will help overcome the problem of viral adaptation and will prevent the appearance of RNAi escape mutants in current virus strains, an important feature of gene therapy of HIV/AIDS. PMID:26947394

  4. Recombination of HIV type 1C (C'/C") in Ethiopia: possible link of EthHIV-1C' to subtype C sequences from the high-prevalence epidemics in India and Southern Africa.

    PubMed

    Pollakis, Georgios; Abebe, Almaz; Kliphuis, Aletta; De Wit, Tobias F Rinke; Fisseha, Bitew; Tegbaru, Belete; Tesfaye, Girma; Negassa, Hailu; Mengistu, Yohannes; Fontanet, Arnaud L; Cornelissen, Marion; Goudsmit, Jaap

    2003-11-01

    The magnitude and complexity of the HIV-1 genetic diversity are major challenges for vaccine development. Investigation of the genotypes circulating in areas of high incidence, as well as their interactions, will be a milestone in the development of an efficacious vaccine. Because HIV-1 subtype C (HIV-1C) is responsible for most of the 36 million infections worldwide we investigated the HIV-1C strains circulating in Ethiopia in a retrospective, cross-sectional study. Serum samples from HIV-1-positive individuals were collected in seven Ethiopian cities and towns. Nucleotide sequences of the gag, pol, and env genes were analyzed. We performed phylogenetic analysis by the neighbor-joining and maximum-likelihood methods with sequences from 30 isolates, and we determined recombination by the bootscanning method as implemented in the SIMPLOT program. Sequence analyses of a 2600-nucleotide fragment (including the gag gene, the protease, and the 5' half of reverse transcriptase of the pol gene) and the corresponding V1V2/C2V3 envelope regions confirmed that two distinct HIV-1C genotypes (C' and C") are cocirculating in Ethiopia, as shown previously by the analysis of the C2V3 envelope region. We have identified intrasubtype recombination between the two HIV-1C genotypes, C' and C", with 6 of the 30 (20%) analyzed viruses being recombinants. The C' sequences were phylogenetically linked to the fast spreading viruses in India and southern Africa. Furthermore, all the recombinant viruses shared the C' V1V3 region of the envelope, suggesting that the prevalence of viruses with the C' envelope is increasing compared to the C" envelope. The possibility that viruses with a C' envelope have a biological advantage over the viruses with a C" envelope should be further investigated in biological and epidemiological studies. PMID:14678607

  5. Order of Orifices: Sequence of Condom Use and Ejaculation by Orifice during Anal Intercourse among Women, Implications for HIV Transmission

    PubMed Central

    Gorbach, Pamina M.; Pines, Heather; Javanbakht, Marjan; Weiss, Robert E.; Jeffries, Robin; Cranston, Ross D.; Fuchs, Edward J; Hezerah, Marjan; Brown, Stephen; Voskanian, Alen; Anton, Peter

    2014-01-01

    Background For women the order of penile insertion, condom use, and ejaculation by orifice during sexual events affects the probability of HIV transmission and design of HIV prevention methods. Methods From October 2006-June 2009, 431 women in Los Angeles and Baltimore in a rectal health study reported the sequence of penile insertion, condom use, and ejaculation by orifice location by computer assisted self-interview. Multinomial logistic regression identified predictors of condom use by orifice among women who reported vaginal intercourse (VI) during their last anal intercourse (AI) event. Results Of the 192 reporting on a last AI event, 96.3% (180/187) reported VI. Of these, 83.1% had VI before AI; 66.1% reported ejaculation during VI and 45.2% during AI. Only one third used a condom for both VI and AI, less than 10% for VI only or AI only; and half used no condoms. After adjusting for race, partner type, and substance use, compared to women who used condoms for both VI and AI at last AI, being older (units=5 years) (adjusted odds ratio [AOR]=0.76, 95% confidence interval [CI]: 0.60, 0.96), with serodiscordant partners (AOR=0.22, 95% CI: 0.08, 0.61) and HIV-positive with seroconcordant partners (AOR = 0.15; 95% CI: 0.04, 0.54) were inversely associated with non-condom use. Conclusions For most of the women in our study VI accompanied AI, with AI usually occurring after VI. This evidence for use of multiple orifices during the same sexual encounter and low use of condoms across orifices supports the need for a multi-compartment HIV prevention strategy. PMID:25356778

  6. Stockpile Stewardship: Los Alamos

    SciTech Connect

    McMillan, Charlie; Morgan, Nathanial; Goorley, Tom; Merrill, Frank; Funk, Dave; Korzekwa, Deniece; Laintz, Ken

    2012-01-26

    "Heritage of Science" is a short video that highlights the Stockpile Stewardship program at Los Alamos National Laboratory. Stockpile Stewardship was conceived in the early 1990s as a national science-based program that could assure the safety, security, and effectiveness of the U.S. nuclear deterrent without the need for full-scale underground nuclear testing. This video was produced by Los Alamos National Laboratory for screening at the Lab's Bradbury Science Museum in Los Alamos, NM and is narrated by science correspondent Miles O'Brien.

  7. Stockpile Stewardship: Los Alamos

    ScienceCinema

    McMillan, Charlie; Morgan, Nathanial; Goorley, Tom; Merrill, Frank; Funk, Dave; Korzekwa, Deniece; Laintz, Ken

    2014-08-12

    "Heritage of Science" is a short video that highlights the Stockpile Stewardship program at Los Alamos National Laboratory. Stockpile Stewardship was conceived in the early 1990s as a national science-based program that could assure the safety, security, and effectiveness of the U.S. nuclear deterrent without the need for full-scale underground nuclear testing. This video was produced by Los Alamos National Laboratory for screening at the Lab's Bradbury Science Museum in Los Alamos, NM and is narrated by science correspondent Miles O'Brien.

  8. Primer ID Informs Next-Generation Sequencing Platforms and Reveals Preexisting Drug Resistance Mutations in the HIV-1 Reverse Transcriptase Coding Domain

    PubMed Central

    Keys, Jessica R.; Zhou, Shuntai; Anderson, Jeffrey A.; Eron, Joseph J.; Rackoff, Lauren A.; Jabara, Cassandra

    2015-01-01

    Abstract Sequencing of a bulk polymerase chain reaction (PCR) product to identify drug resistance mutations informs antiretroviral therapy selection but has limited sensitivity for minority variants. Alternatively, deep sequencing is capable of detecting minority variants but is subject to sequencing errors and PCR resampling due to low input templates. We screened for resistance mutations among 184 HIV-1-infected, therapy-naive subjects using the 454 sequencing platform to sequence two amplicons spanning HIV-1 reverse transcriptase codons 34–245. Samples from 19 subjects were also analyzed using the MiSeq sequencing platform for comparison. Errors and PCR resampling were addressed by tagging each HIV-1 RNA template copy (i.e., cDNA) with a unique sequence tag (Primer ID), allowing a consensus sequence to be constructed for each original template from resampled sequences. In control reactions, Primer ID reduced 454 and MiSeq errors from 71 to 2.6 and from 24 to 1.2 errors/10,000 nucleotides, respectively. MiSeq also allowed accurate sequencing of codon 65, an important drug resistance position embedded in a homopolymeric run that is poorly resolved by the 454 platform. Excluding homopolymeric positions, 14% of subjects had evidence of ≥1 resistance mutation among Primer ID consensus sequences, compared to 2.7% by bulk population sequencing. When calls were restricted to mutations that appeared twice among consensus sequence populations, 6% of subjects had detectable resistance mutations. The use of Primer ID revealed 5–15% template utilization on average, limiting the depth of deep sequencing sampling and revealing sampling variation due to low template utilization. Primer ID addresses important limitations of deep sequencing and produces less biased estimates of low-level resistance mutations in the viral population. PMID:25748056

  9. Primer ID Informs Next-Generation Sequencing Platforms and Reveals Preexisting Drug Resistance Mutations in the HIV-1 Reverse Transcriptase Coding Domain.

    PubMed

    Keys, Jessica R; Zhou, Shuntai; Anderson, Jeffrey A; Eron, Joseph J; Rackoff, Lauren A; Jabara, Cassandra; Swanstrom, Ronald

    2015-06-01

    Sequencing of a bulk polymerase chain reaction (PCR) product to identify drug resistance mutations informs antiretroviral therapy selection but has limited sensitivity for minority variants. Alternatively, deep sequencing is capable of detecting minority variants but is subject to sequencing errors and PCR resampling due to low input templates. We screened for resistance mutations among 184 HIV-1-infected, therapy-naive subjects using the 454 sequencing platform to sequence two amplicons spanning HIV-1 reverse transcriptase codons 34-245. Samples from 19 subjects were also analyzed using the MiSeq sequencing platform for comparison. Errors and PCR resampling were addressed by tagging each HIV-1 RNA template copy (i.e., cDNA) with a unique sequence tag (Primer ID), allowing a consensus sequence to be constructed for each original template from resampled sequences. In control reactions, Primer ID reduced 454 and MiSeq errors from 71 to 2.6 and from 24 to 1.2 errors/10,000 nucleotides, respectively. MiSeq also allowed accurate sequencing of codon 65, an important drug resistance position embedded in a homopolymeric run that is poorly resolved by the 454 platform. Excluding homopolymeric positions, 14% of subjects had evidence of ≥1 resistance mutation among Primer ID consensus sequences, compared to 2.7% by bulk population sequencing. When calls were restricted to mutations that appeared twice among consensus sequence populations, 6% of subjects had detectable resistance mutations. The use of Primer ID revealed 5-15% template utilization on average, limiting the depth of deep sequencing sampling and revealing sampling variation due to low template utilization. Primer ID addresses important limitations of deep sequencing and produces less biased estimates of low-level resistance mutations in the viral population. PMID:25748056

  10. Genome sequence of a novel HIV-1 circulating recombinant form 54_01B from Malaysia.

    PubMed

    Ng, Kim Tien; Ong, Lai Yee; Takebe, Yutaka; Kamarulzaman, Adeeba; Tee, Kok Keng

    2012-10-01

    We report here the first novel HIV-1 circulating recombinant form (CRF) 54_01B (CRF54_01B) isolated from three epidemiologically unlinked subjects of different risk groups in Malaysia. These recently sampled recombinants showed a complex genome organization composed of parental subtype B' and CRF01_AE, with identical recombination breakpoints observed in the gag, pol, and vif genes. Such a discovery highlights the ongoing active generation and spread of intersubtype recombinants involving the subtype B' and CRF01_AE lineages and indicates the potential of the new CRF in bridging HIV-1 transmission among different risk groups in Southeast Asia. PMID:22997423

  11. Identification of novel human papillomavirus lineages and sublineages in HIV/HPV-coinfected pregnant women by next-generation sequencing.

    PubMed

    Siqueira, Juliana D; Alves, Brunna M; Prellwitz, Isabel M; Furtado, Carolina; Meyrelles, Ângela R; Machado, Elizabeth S; Seuánez, Héctor N; Soares, Marcelo A; Soares, Esmeralda A

    2016-06-01

    Infection by human papillomavirus (HPV) is a necessary condition for development of cervical cancer, and has also been associated with malignancies of other body anatomical sites. Specific HPV types have been associated with premalignant lesions and invasive carcinoma, but mounting evidence suggests that within-type lineages and sublineages also display distinct biological characteristics associated with persistent infections and evolution to cervical cancer. In the present study, we have assessed HPV multiple infection and variation from a cohort of highly susceptible, HIV(+) pregnant women using next-generation sequencing and an in-house pipeline for HPV full-length genome assembly. Seventy-two consensus sequences representing complete or near-complete (>97%) HPV genomes were assembled, spanning 28 different types. Genetic distance and phylogenetic analyses allowed us to propose the classification of novel HPV lineages and sublineages across nine HPV types, including two high-risk types. HPV diversity may be a hallmark of immunosuppressed patients upon HIV infection and AIDS progression. PMID:27060563

  12. U3 Region in the HIV-1 Genome Adopts a G-Quadruplex Structure in Its RNA and DNA Sequence

    PubMed Central

    2015-01-01

    Genomic regions rich in G residues are prone to adopt G-quadruplex structure. Multiple Sp1-binding motifs arranged in tandem have been suggested to form this structure in promoters of cancer-related genes. Here, we demonstrate that the G-rich proviral DNA sequence of the HIV-1 U3 region, which serves as a promoter of viral transcription, adopts a G-quadruplex structure. The sequence contains three binding elements for transcription factor Sp1, which is involved in the regulation of HIV-1 latency, reactivation, and high-level virus expression. We show that the three Sp1 binding motifs can adopt different forms of G-quadruplex structure and that the Sp1 protein can recognize and bind to its site folded into a G-quadruplex. In addition, a c-kit2 specific antibody, designated hf2, binds to two different G-quadruplexes formed in Sp1 sites. Since U3 is encoded at both viral genomic ends, the G-rich sequence is also present in the RNA genome. We demonstrate that the RNA sequence of U3 forms dimers with characteristics known for intermolecular G-quadruplexes. Together with previous reports showing G-quadruplex dimers in the gag and cPPT regions, these results suggest that integrity of the two viral genomes is maintained through numerous intermolecular G-quadruplexes formed in different RNA genome locations. Reconstituted reverse transcription shows that the potassium-dependent structure formed in U3 RNA facilitates RT template switching, suggesting that the G-quadruplex contributes to recombination in U3. PMID:24735378

  13. Acquisition of HIV by African-Born Residents of Victoria, Australia: Insights from Molecular Epidemiology

    PubMed Central

    Lemoh, Chris; Ryan, Claire E.; Sekawi, Zamberi; Hearps, Anna C.; Aleksic, Eman; Chibo, Doris; Grierson, Jeffrey; Baho, Samia; Street, Alan; Hellard, Margaret; Biggs, Beverley-Ann; Crowe, Suzanne M.

    2013-01-01

    African-born Australians are a recognised “priority population” in Australia's Sixth National HIV/AIDS Strategy. We compared exposure location and route for African-born people living with HIV (PLHIV) in Victoria, Australia, with HIV-1 pol subtype from drug resistance assays and geographical origin suggested by phylogenetic analysis of env gene. Twenty adult HIV positive African-born Victorian residents were recruited via treating doctors. HIV exposure details were obtained from interviews and case notes. Viral RNA was extracted from participant stored plasma or whole blood. The env V3 region was sequenced and compared to globally representative reference HIV-1 sequences in the Los Alamos National Library HIV Database. Twelve participants reported exposure via heterosexual sex and two via iatrogenic blood exposures; four were men having sex with men (MSM); two were exposed via unknown routes. Eight participants reported exposure in their countries of birth, seven in Australia, three in other countries and two in unknown locations. Genotype results (pol) were available for ten participants. HIV env amplification was successful in eighteen cases. HIV-1 subtype was identified in all participants: eight both pol and env; ten env alone and two pol alone. Twelve were subtype C, four subtype B, three subtype A and one subtype CRF02_AG. Reported exposure location was consistent with the phylogenetic clustering of env sequences. African Australians are members of multiple transnational social and sexual networks influencing their exposure to HIV. Phylogenetic analysis may complement traditional surveillance to discern patterns of HIV exposure, providing focus for HIV prevention programs in mobile populations. PMID:24391866

  14. Acquisition of HIV by African-born residents of Victoria, Australia: insights from molecular epidemiology.

    PubMed

    Lemoh, Chris; Ryan, Claire E; Sekawi, Zamberi; Hearps, Anna C; Aleksic, Eman; Chibo, Doris; Grierson, Jeffrey; Baho, Samia; Street, Alan; Hellard, Margaret; Biggs, Beverley-Ann; Crowe, Suzanne M

    2013-01-01

    African-born Australians are a recognised "priority population" in Australia's Sixth National HIV/AIDS Strategy. We compared exposure location and route for African-born people living with HIV (PLHIV) in Victoria, Australia, with HIV-1 pol subtype from drug resistance assays and geographical origin suggested by phylogenetic analysis of env gene. Twenty adult HIV positive African-born Victorian residents were recruited via treating doctors. HIV exposure details were obtained from interviews and case notes. Viral RNA was extracted from participant stored plasma or whole blood. The env V3 region was sequenced and compared to globally representative reference HIV-1 sequences in the Los Alamos National Library HIV Database. Twelve participants reported exposure via heterosexual sex and two via iatrogenic blood exposures; four were men having sex with men (MSM); two were exposed via unknown routes. Eight participants reported exposure in their countries of birth, seven in Australia, three in other countries and two in unknown locations. Genotype results (pol) were available for ten participants. HIV env amplification was successful in eighteen cases. HIV-1 subtype was identified in all participants: eight both pol and env; ten env alone and two pol alone. Twelve were subtype C, four subtype B, three subtype A and one subtype CRF02_AG. Reported exposure location was consistent with the phylogenetic clustering of env sequences. African Australians are members of multiple transnational social and sexual networks influencing their exposure to HIV. Phylogenetic analysis may complement traditional surveillance to discern patterns of HIV exposure, providing focus for HIV prevention programs in mobile populations. PMID:24391866

  15. Relative Resistance of HLA-B to Downregulation by Naturally Occurring HIV-1 Nef Sequences

    PubMed Central

    Mahiti, Macdonald; Toyoda, Mako; Jia, Xiaofei; Kuang, Xiaomei T.; Mwimanzi, Francis; Mwimanzi, Philip; Walker, Bruce D.; Xiong, Yong; Brumme, Zabrina L.; Brockman, Mark A.

    2016-01-01

    ABSTRACT HIV-1 Nef binds to the cytoplasmic region of HLA-A and HLA-B and downregulates these molecules from the surface of virus-infected cells, thus evading immune detection by CD8+ T cells. Polymorphic residues within the HLA cytoplasmic region may affect Nef’s downregulation activity. However, the effects of HLA polymorphisms on recognition by primary Nef isolates remain elusive, as do the specific Nef regions responsible for downregulation of HLA-A versus HLA-B. Here, we examined 46 Nef clones isolated from chronically HIV-1 subtype B-infected subjects for their ability to downregulate various HLA-A, HLA-B, and HLA-C molecules on the surface of virus-infected cells. Overall, HLA-B exhibited greater resistance to Nef-mediated downregulation than HLA-A, regardless of the cell type examined. As expected, no Nef clone downregulated HLA-C. Importantly, the differential abilities of patient-derived Nef clones to downregulate HLA-A and HLA-B correlated inversely with the sensitivities of HIV-infected target cells to recognition by effector cells expressing an HIV-1 Gag-specific T cell receptor. Nef codon function analysis implicated amino acid variation at position 202 (Nef-202) in differentially affecting the ability to downregulate HLA-A and HLA-B, an observation that was subsequently confirmed by experiments using Nef mutants constructed by site-directed mutagenesis. The in silico and mutagenesis analyses further suggested that Nef-202 may interact with the C-terminal Cys-Lys-Val residues of HLA-A, which are absent in HLA-B. Taken together, the results show that natural polymorphisms within Nef modulate its interaction with natural polymorphisms in the HLA cytoplasmic tails, thereby affecting the efficiency of HLA downregulation and consequent recognition by HIV-specific T cells. These results thus extend our understanding of this complex pathway of retroviral immune evasion. PMID:26787826

  16. Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of Low-frequency drug resistance mutations in HIV-1 DNA

    PubMed Central

    2013-01-01

    Background 454 sequencing technology is a promising approach for characterizing HIV-1 populations and for identifying low frequency mutations. The utility of 454 technology for determining allele frequencies and linkage associations in HIV infected individuals has not been extensively investigated. We evaluated the performance of 454 sequencing for characterizing HIV populations with defined allele frequencies. Results We constructed two HIV-1 RT clones. Clone A was a wild type sequence. Clone B was identical to clone A except it contained 13 introduced drug resistant mutations. The clones were mixed at ratios ranging from 1% to 50% and were amplified by standard PCR conditions and by PCR conditions aimed at reducing PCR-based recombination. The products were sequenced using 454 pyrosequencing. Sequence analysis from standard PCR amplification revealed that 14% of all sequencing reads from a sample with a 50:50 mixture of wild type and mutant DNA were recombinants. The majority of the recombinants were the result of a single crossover event which can happen during PCR when the DNA polymerase terminates synthesis prematurely. The incompletely extended template then competes for primer sites in subsequent rounds of PCR. Although less often, a spectrum of other distinct crossover patterns was also detected. In addition, we observed point mutation errors ranging from 0.01% to 1.0% per base as well as indel (insertion and deletion) errors ranging from 0.02% to nearly 50%. The point errors (single nucleotide substitution errors) were mainly introduced during PCR while indels were the result of pyrosequencing. We then used new PCR conditions designed to reduce PCR-based recombination. Using these new conditions, the frequency of recombination was reduced 27-fold. The new conditions had no effect on point mutation errors. We found that 454 pyrosequencing was capable of identifying minority HIV-1 mutations at frequencies down to 0.1% at some nucleotide positions. Conclusion

  17. Short Communication: Investigating a Chain of HIV Transmission Events Due to Homosexual Exposure and Blood Transfusion Based on a Next Generation Sequencing Method.

    PubMed

    Zhao, Qi; Zhang, Chen; Jiang, Yan; Wen, Yujie; Pan, Pinliang; Li, Yang; Zhang, Guiyun; Zhang, Lei; Qiu, Maofeng

    2015-12-01

    This study investigates a chain of HIV transmission events due to homosexual exposure and blood transfusion in China. The MiSeq platform, a next generation sequencing (NGS) system, was used to obtain genetic details of the HIV-1 env region (336 base pairs). Evolutionary analysis combined with epidemiologic evidence suggests a transmission chain from patient T3 to T2 through homosexual exposure and subsequently to T1 through blood transfusion. More importantly, a phylogenetic study suggested a likely genetic bottleneck for HIV in homosexual transmission from T3 to T2, while T1 inherited the majority of variants from T2. The result from the MiSeq platform is consistent with findings from the epidemiologic survey. The MiSeq platform is a powerful tool for tracing HIV transmissions and intrapersonal evolution. PMID:26355677

  18. Deep Sequencing and Circos Analyses of Antibody Libraries Reveal Antigen-driven Selection of Ig VH Genes during HIV-1 Infection

    PubMed Central

    Xiao, Madelyne; Ponraj, Prabakaran; Chen, Weizao; Kessing, Bailey; Dimitrov, Dimiter S.

    2013-01-01

    The vast diversity of antibody repertoires is largely attributed to heavy chain (VH) recombination of variable (V), diversity (D) and joining (J) gene segments. We used 454 sequencing information of the variable domains of the antibody heavy chain repertoires from neonates, normal adults and an HIV-1-infected individual, to analyze, with Circos software, the VDJ pairing patterns at birth, adulthood and a time-dependent response to HIV-1 infection. Our comparative analyses of the Ig VDJ repertoires from these libraries indicated that, from birth to adulthood, VDJ recombination patterns remain the same with some slight changes, whereas some VH families are selected and preferentially expressed after long-term infection with HIV-1. We also demonstrated that the immune system responds to HIV-1 chronic infection by selectively expanding certain HV families in an attempt to combat infection. Our findings may have implications for understanding immune responses in pathology as well as for development of new therapeutics and vaccines. PMID:24158018

  19. Sequences in Gibbon Ape Leukemia Virus Envelope That Confer Sensitivity to HIV-1 Accessory Protein Vpu▿†

    PubMed Central

    Janaka, Sanath Kumar; Lucas, Tiffany M.; Johnson, Marc C.

    2011-01-01

    HIV-1 efficiently forms pseudotyped particles with many gammaretrovirus glycoproteins, such as Friend murine leukemia virus (F-MLV) Env, but not with the related gibbon ape leukemia virus (GaLV) Env or with a chimeric F-MLV Env with a GaLV cytoplasmic tail domain (CTD). This incompatibility is modulated by the HIV-1 accessory protein Vpu. Because the GaLV Env CTD does not resemble tetherin or CD4, the well-studied targets of Vpu, we sought to characterize the modular sequence in the GaLV Env CTD required for this restriction in the presence of Vpu. Using a systematic mutagenesis scan, we determined that the motif that makes GaLV Env sensitive to Vpu is INxxIxxVKxxVxRxK. This region in the CTD of GaLV Env is predicted to form a helix. Mutations in the CTD that would break this helix abolish sensitivity to Vpu. Although many of these positions can be replaced with amino acids with similar biophysical properties without disrupting the Vpu sensitivity, the final lysine residue is required. This Vpu sensitivity sequence appears to be modular, as the unrelated Rous sarcoma virus (RSV) Env can be made Vpu sensitive by replacing its CTD with the GaLV Env CTD. In addition, F-MLV Env can be made Vpu sensitive by mutating two amino acids in its cytoplasmic tail to make it resemble more closely the Vpu sensitivity motif. Surprisingly, the core components of this Vpu sensitivity sequence are also present in the host surface protein CD4, which is also targeted by Vpu through its CTD. PMID:21917962

  20. The Effect of Clade-Specific Sequence Polymorphisms on HIV-1 Protease Activity and Inhibitor Resistance Pathways

    SciTech Connect

    Bandaranayake, Rajintha M.; Kolli, Madhavi; King, Nancy M.; Nalivaika, Ellen A.; Heroux, Annie; Kakizawa, Junko; Sugiura, Wataru; Schiffer, Celia A.

    2010-09-08

    The majority of HIV-1 infections around the world result from non-B clade HIV-1 strains. The CRF01{_}AE (AE) strain is seen principally in Southeast Asia. AE protease differs by {approx}10% in amino acid sequence from clade B protease and carries several naturally occurring polymorphisms that are associated with drug resistance in clade B. AE protease has been observed to develop resistance through a nonactive-site N88S mutation in response to nelfinavir (NFV) therapy, whereas clade B protease develops both the active-site mutation D30N and the nonactive-site mutation N88D. Structural and biochemical studies were carried out with wild-type and NFV-resistant clade B and AE protease variants. The relationship between clade-specific sequence variations and pathways to inhibitor resistance was also assessed. AE protease has a lower catalytic turnover rate than clade B protease, and it also has weaker affinity for both NFV and darunavir (DRV). This weaker affinity may lead to the nonactive-site N88S variant in AE, which exhibits significantly decreased affinity for both NFV and DRV. The D30N/N88D mutations in clade B resulted in a significant loss of affinity for NFV and, to a lesser extent, for DRV. A comparison of crystal structures of AE protease shows significant structural rearrangement in the flap hinge region compared with those of clade B protease and suggests insights into the alternative pathways to NFV resistance. In combination, our studies show that sequence polymorphisms within clades can alter protease activity and inhibitor binding and are capable of altering the pathway to inhibitor resistance.

  1. Detection of GB virus C genomic sequence in the cerebrospinal fluid of a HIV-infected patient in China: a case report and literature review.

    PubMed

    Liu, Z; Zhang, Y; Wei, F; Xu, M; Mou, D; Zhang, T; Li, W; Chen, D; Wu, H

    2016-01-01

    Hepatitis G virus or GB virus C (GBV-C) is a human virus of the Flaviviridae family that is structurally and epidemiologically closest to hepatitis C virus, but replicates primarily in lymphocytes. Co-infection with GBV-C has been reported to confer beneficial outcomes in some HIV-positive patients. Up to now, however, studies on GBV-C infection in the central nervous system (CNS) of HIV-infected patient have rarely been reported. Herein, we report on a 32-year-old HIV-1-infected patient with cerebral toxoplasmosis and fungal encephalitis. GBV-C viral loads were detected in CSF by quantitative real-time reverse transcription polymerase chain reaction (RT-PCR), and the results showed that GBV-C viral load was 6·5 log copies/ml. We amplified and sequenced the E2 and 5'-untranslated regions from the purified viral RNA from CSF by RT-PCR. Both sequences belong to genotype 3 and there were some minor nucleotide divergence among the E2 sequences from the CSF of the patient. These data suggest that GBV-C may be able to penetrate the blood-brain barrier and colonize the CNS of HIV-infected patients. However, the exact mechanisms and potential effect of the infected GBV-C in CNS on HIV-associated neuropathy needs to be further explored. PMID:26081197

  2. HIV-1 Tropism Dynamics and Phylogenetic Analysis from Longitudinal Ultra-Deep Sequencing Data of CCR5- and CXCR4-Using Variants

    PubMed Central

    Sede, Mariano M.; Moretti, Franco A.; Laufer, Natalia L.

    2014-01-01

    Objective Coreceptor switch from CCR5 to CXCR4 is associated with HIV disease progression. The molecular and evolutionary mechanisms underlying the CCR5 to CXCR4 switch are the focus of intense recent research. We studied the HIV-1 tropism dynamics in relation to coreceptor usage, the nature of quasispecies from ultra deep sequencing (UDPS) data and their phylogenetic relationships. Methods Here, we characterized C2-V3-C3 sequences of HIV obtained from 19 patients followed up for 54 to 114 months using UDPS, with further genotyping and phylogenetic analysis for coreceptor usage. HIV quasispecies diversity and variability as well as HIV plasma viral load were measured longitudinally and their relationship with the HIV coreceptor usage was analyzed. The longitudinal UDPS data were submitted to phylogenetic analysis and sampling times and coreceptor usage were mapped onto the trees obtained. Results Although a temporal viral genetic structuring was evident, the persistence of several viral lineages evolving independently along the infection was statistically supported, indicating a complex scenario for the evolution of viral quasispecies. HIV X4-using variants were present in most of our patients, exhibiting a dissimilar inter- and intra-patient predominance as the component of quasispecies even on antiretroviral therapy. The viral populations from some of the patients studied displayed evidences of the evolution of X4 variants through fitness valleys, whereas for other patients the data favored a gradual mode of emergence. Conclusions CXCR4 usage can emerge independently, in multiple lineages, along the course of HIV infection. The mode of emergence, i.e. gradual or through fitness valleys seems to depend on both virus and patient factors. Furthermore, our analyses suggest that, besides becoming dominant after population-level switches, minor proportions of X4 viruses might exist along the infection, perhaps even at early stages of it. The fate of these minor

  3. Bioinformatic analysis of neurotropic HIV envelope sequences identifies polymorphisms in the gp120 bridging sheet that increase macrophage-tropism through enhanced interactions with CCR5

    SciTech Connect

    Mefford, Megan E.; Kunstman, Kevin; Wolinsky, Steven M.; Gabuzda, Dana

    2015-07-15

    Macrophages express low levels of the CD4 receptor compared to T-cells. Macrophage-tropic HIV strains replicating in brain of untreated patients with HIV-associated dementia (HAD) express Envs that are adapted to overcome this restriction through mechanisms that are poorly understood. Here, bioinformatic analysis of env sequence datasets together with functional studies identified polymorphisms in the β3 strand of the HIV gp120 bridging sheet that increase M-tropism. D197, which results in loss of an N-glycan located near the HIV Env trimer apex, was detected in brain in some HAD patients, while position 200 was estimated to be under positive selection. D197 and T/V200 increased fusion and infection of cells expressing low CD4 by enhancing gp120 binding to CCR5. These results identify polymorphisms in the HIV gp120 bridging sheet that overcome the restriction to macrophage infection imposed by low CD4 through enhanced gp120–CCR5 interactions, thereby promoting infection of brain and other macrophage-rich tissues. - Highlights: • We analyze HIV Env sequences and identify amino acids in beta 3 of the gp120 bridging sheet that enhance macrophage tropism. • These amino acids at positions 197 and 200 are present in brain of some patients with HIV-associated dementia. • D197 results in loss of a glycan near the HIV Env trimer apex, which may increase exposure of V3. • These variants may promote infection of macrophages in the brain by enhancing gp120–CCR5 interactions.

  4. In Vitro HIV-1 LTR Integration into T-Cell Activation Gene CD27 Segment and the Decoy Effect of Modified-Sequence DNA

    PubMed Central

    Ohmori, Rei; Tsuruyama, Tatsuaki

    2012-01-01

    Integration into the host genome is an essential step in the HIV-1 life cycle. However, the host genome sequence that is favored by HIV-1 during integration has never been documented. Here, we report that CD27, a T cell activation gene, includes a sequence that is a target for in vitro HIV-1 cDNA integration. This sequence has a high affinity for integrase, and the target nucleotides responsible for this higher affinity were identified using a crystal microbalance assay. In experiments involving a segment of the CD27 gene, integration converged in the target nucleotides and flanking sequence DNA, indicating that integration is probably dependent upon the secondary structure of the substrate DNA. Notably, decoy modified CD27 sequence DNAs in which the target nucleotides were replaced suppressed integration when accompanying the original CD27 sequence DNA. Our identified CD27 sequence DNA is useful for investigating the biochemistry of integrase and for in vitro assessment of integrase-binding inhibitors. PMID:23209625

  5. Source identification in two criminal cases using phylogenetic analysis of HIV-1 DNA sequences.

    PubMed

    Scaduto, Diane I; Brown, Jeremy M; Haaland, Wade C; Zwickl, Derrick J; Hillis, David M; Metzker, Michael L

    2010-12-14

    Phylogenetic analysis has been widely used to test the a priori hypothesis of epidemiological clustering in suspected transmission chains of HIV-1. Among studies showing strong support for relatedness between HIV samples obtained from infected individuals, evidence for the direction of transmission between epidemiologically related pairs has been lacking. During transmission of HIV, a genetic bottleneck occurs, resulting in the paraphyly of source viruses with respect to those of the recipient. This paraphyly establishes the direction of transmission, from which the source can then be inferred. Here, we present methods and results from two criminal cases, State of Washington v Anthony Eugene Whitfield, case number 04-1-0617-5 (Superior Court of the State of Washington, Thurston County, 2004) and State of Texas v Philippe Padieu, case numbers 219-82276-07, 219-82277-07, 219-82278-07, 219-82279-07, 219-82280-07, and 219-82705-07 (219th Judicial District Court, Collin County, TX, 2009), which provided evidence that direction can be established from blinded case samples. The observed paraphyly from each case study led to the identification of an inferred source (i.e., index case), whose identity was revealed at trial to be that of the defendant. PMID:21078965

  6. HIV-1 Transmission Patterns in Antiretroviral Therapy-Naïve, HIV-Infected North Americans Based on Phylogenetic Analysis by Population Level and Ultra-Deep DNA Sequencing

    PubMed Central

    Ross, Lisa L.; Horton, Joseph; Hasan, Samiul; Brown, James R.; Murphy, Daniel; DeJesus, Edwin; Potter, Martin; LaMarca, Anthony; Melendez-Rivera, Ivan; Ward, Douglas; Uy, Jonathon; Shaefer, Mark S.

    2014-01-01

    Factors that contribute to the transmission of human immunodeficiency virus type 1 (HIV-1), especially drug-resistant HIV-1 variants remain a significant public health concern. In-depth phylogenetic analyses of viral sequences obtained in the screening phase from antiretroviral-naïve HIV-infected patients seeking enrollment in EPZ108859, a large open-label study in the USA, Canada and Puerto Rico (ClinicalTrials.gov NCT00440947) were examined for insights into the roles of drug resistance and epidemiological factors that could impact disease dissemination. Viral transmission clusters (VTCs) were initially predicted from a phylogenetic analysis of population level HIV-1 pol sequences obtained from 690 antiretroviral-naïve subjects in 2007. Subsequently, the predicted VTCs were tested for robustness by ultra deep sequencing (UDS) using pyrosequencing technology and further phylogenetic analyses. The demographic characteristics of clustered and non-clustered subjects were then compared. From 690 subjects, 69 were assigned to 1 of 30 VTCs, each containing 2 to 5 subjects. Race composition of VTCs were significantly more likely to be white (72% vs. 60%; p = 0.04). VTCs had fewer reverse transcriptase and major PI resistance mutations (9% vs. 24%; p = 0.002) than non-clustered sequences. Both men-who-have-sex-with-men (MSM) (68% vs. 48%; p = 0.001) and Canadians (29% vs. 14%; p = 0.03) were significantly more frequent in VTCs than non-clustered sequences. Of the 515 subjects who initiated antiretroviral therapy, 33 experienced confirmed virologic failure through 144 weeks while only 3/33 were from VTCs. Fewer VTCs subjects (as compared to those with non-clustering virus) had HIV-1 with resistance-associated mutations or experienced virologic failure during the course of the study. Our analysis shows specific geographical and drug resistance trends that correlate well with transmission clusters defined by HIV sequences of similarity. Furthermore, our

  7. Los Alamos offers Fellowships

    NASA Astrophysics Data System (ADS)

    Los Alamos National Laboratory in New Mexico is calling for applications for postdoctoral appointments and research fellowships. The positions are available in geoscience as well as other scientific disciplines.The laboratory, which is operated by the University of California for the Department of Energy, awards J. Robert Oppenheimer Research Fellowships to scientists that either have or will soon complete doctoral degrees. The appointments are for two years, are renewable for a third year, and carry a stipend of $51,865 per year. Potential applicants should send a resume or employment application and a statement of research goals to Carol M. Rich, Div. 89, Human Resources Development Division, MS P290, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 by mid-November.

  8. Comprehensive Sieve Analysis of Breakthrough HIV-1 Sequences in the RV144 Vaccine Efficacy Trial

    PubMed Central

    Edlefsen, Paul T.; Rolland, Morgane; Hertz, Tomer; Tovanabutra, Sodsai; Gartland, Andrew J.; deCamp, Allan C.; Magaret, Craig A.; Ahmed, Hasan; Gottardo, Raphael; Juraska, Michal; McCoy, Connor; Larsen, Brendan B.; Sanders-Buell, Eric; Carrico, Chris; Menis, Sergey; Bose, Meera; Arroyo, Miguel A.; O’Connell, Robert J.; Nitayaphan, Sorachai; Pitisuttithum, Punnee; Kaewkungwal, Jaranit; Rerks-Ngarm, Supachai; Robb, Merlin L.; Kirys, Tatsiana; Georgiev, Ivelin S.; Kwong, Peter D.; Scheffler, Konrad; Pond, Sergei L. Kosakovsky; Carlson, Jonathan M.; Michael, Nelson L.; Schief, William R.; Mullins, James I.; Kim, Jerome H.; Gilbert, Peter B.

    2015-01-01

    The RV144 clinical trial showed the partial efficacy of a vaccine regimen with an estimated vaccine efficacy (VE) of 31% for protecting low-risk Thai volunteers against acquisition of HIV-1. The impact of vaccine-induced immune responses can be investigated through sieve analysis of HIV-1 breakthrough infections (infected vaccine and placebo recipients). A V1/V2-targeted comparison of the genomes of HIV-1 breakthrough viruses identified two V2 amino acid sites that differed between the vaccine and placebo groups. Here we extended the V1/V2 analysis to the entire HIV-1 genome using an array of methods based on individual sites, k-mers and genes/proteins. We identified 56 amino acid sites or “signatures” and 119 k-mers that differed between the vaccine and placebo groups. Of those, 19 sites and 38 k-mers were located in the regions comprising the RV144 vaccine (Env-gp120, Gag, and Pro). The nine signature sites in Env-gp120 were significantly enriched for known antibody-associated sites (p = 0.0021). In particular, site 317 in the third variable loop (V3) overlapped with a hotspot of antibody recognition, and sites 369 and 424 were linked to CD4 binding site neutralization. The identified signature sites significantly covaried with other sites across the genome (mean = 32.1) more than did non-signature sites (mean = 0.9) (p < 0.0001), suggesting functional and/or structural relevance of the signature sites. Since signature sites were not preferentially restricted to the vaccine immunogens and because most of the associations were insignificant following correction for multiple testing, we predict that few of the genetic differences are strongly linked to the RV144 vaccine-induced immune pressure. In addition to presenting results of the first complete-genome analysis of the breakthrough infections in the RV144 trial, this work describes a set of statistical methods and tools applicable to analysis of breakthrough infection genomes in general vaccine efficacy

  9. Intercontinental Dispersal of HIV-1 Subtype B Associated with Transmission among Men Who Have Sex with Men in Japan

    PubMed Central

    Naito, Yuki; Raghwani, Jayna; Fearnhill, Esther; Sano, Takako; Kusagawa, Shigeru; Mbisa, Jean L.; Zhang, Hongyi; Matano, Tetsuro; Leigh Brown, Andrew J.; Pybus, Oliver G.; Dunn, David; Kondo, Makiko

    2014-01-01

    ABSTRACT Transmission clusters of HIV-1 subtype B uniquely associated with the epidemic among men who have sex with men (MSM) in East Asia have recently been identified. Using the Los Alamos HIV sequence database and the UK HIV drug resistance database, we explored possible links between HIV MSM epidemics in East Asia and the rest of the world by using phylogenetic and molecular clock analyses. We found that JP.MSM.B-1, a subtype B MSM variant that accounts for approximately one-third of the infections among Japanese MSM, was detected worldwide, in the United Kingdom (n = 13), mainland China (n = 3), the United States, Germany, Canada, and Taiwan (n = 1 each). Interestingly, 10 United Kingdom samples plus two from Germany and the United States formed a distinct monophyletic subgroup within JP.MSM.B-1. The estimated divergence times of JP.MSM.B-1 and the latter subgroup were ∼1989 and ∼1999, respectively. These dates suggest that JP.MSM.B-1 was circulating for many years in Japan among MSM before disseminating to other countries, most likely through global MSM networks. A significant number of other Asian MSM HIV lineages were also detected in the UK HIV drug resistance database. Our study provides insight into the regional and global dispersal of Asian MSM HIV lineages. Further study of these strains is warranted to elucidate viral migration and the interrelationship of HIV epidemics on a global scale. IMPORTANCE We previously identified several transmission clusters of HIV-1 subtype B uniquely associated with the epidemic among men who have sex with men (MSM) in East Asia. Using the Los Alamos HIV sequence database and the UK HIV drug resistance database, we explored the possible interplay of HIV MSM epidemics in the different geographic regions and found previously unrecognized interrelationships among the HIV-1 epidemics in East Asia, the United Kingdom, and the rest of the world. Our study provides insight into the regional and global dispersal of Asian MSM

  10. The Los Alamos primer

    SciTech Connect

    Serber, R.

    1992-01-01

    This book contains the 1943 lecture notes of Robert Serber. Serber was a protege of J. Robert Oppenheimer and member of the team that built the first atomic bomb - reveal what the Los Alamos scientists knew, and did not know, about the terrifying weapon they were building.

  11. Recoding method that removes inhibitory sequences and improves HIV gene expression

    DOEpatents

    Rabadan, Raul; Krasnitz, Michael; Robins, Harlan; Witten, Daniela; Levine, Arnold

    2016-08-23

    The invention relates to inhibitory nucleotide signal sequences or "INS" sequences in the genomes of lentiviruses. In particular the invention relates to the AGG motif present in all viral genomes. The AGG motif may have an inhibitory effect on a virus, for example by reducing the levels of, or maintaining low steady-state levels of, viral RNAs in host cells, and inducing and/or maintaining in viral latency. In one aspect, the invention provides vaccines that contain, or are produced from, viral nucleic acids in which the AGG sequences have been mutated. In another aspect, the invention provides methods and compositions for affecting the function of the AGG motif, and methods for identifying other INS sequences in viral genomes.

  12. Permeabilization and fusion of uncharged lipid vesicles induced by the HIV-1 fusion peptide adopting an extended conformation: dose and sequence effects.

    PubMed Central

    Pereira, F B; Goñi, F M; Muga, A; Nieva, J L

    1997-01-01

    The peptide HIV(arg), corresponding to a sequence of 23 amino acid residues at the N-terminus of HIV-1 gp41 (LAV1a strain), has the capacity to destabilize negatively charged large unilamellar vesicles. As revealed by infrared spectroscopy, the peptide associated with those vesicles showed conformational polymorphism: in the absence of cations the main structure was a pore-forming alpha-helix, whereas in the presence of Ca2+ the conformation switched to a fusogenic, predominantly extended beta-type structure. Here we show that an extended structure can also be involved in electrically neutral vesicle destabilization induced by the HIV-1 fusion peptide when it binds the vesicle from the aqueous phase. In the absence of cations, neutral liposomes composed of phosphatidylcholine, phosphatidylethanolamine, and cholesterol (molar ratio 1:1:1) selected for an extended structure that became fusogenic in a dose-dependent fashion. At subfusogenic doses this structure caused the release of trapped 8-aminonaphtalene-1,3,6-trisulfonic acid sodium salt/p-xylenebis(pyridinium)bromide from liposomes, indicating the existence of a peptide-mediated membrane destabilizing process before and independent of the development of fusion. When compared to HIV(arg), the fusion activity of HIV(ala) (bearing the R22 --> A substitution) was reduced by 70%. Fusogenicity was completely abolished when a second substitution (V2 --> E) was included to generate HIV(ala-E2), a sequence representing the N-terminus of an inactive gp41. However, the three sequences associated with vesicles to the same extent, and the three adopted a similar extended structure in the membrane. Whereas 1-(4-trimethylaminophenyl)-6-phenyl-1,3,5-hexatriene emission anisotropy was unaffected by the three peptides, DPH emission anisotropy in membranes was increased only by the fusogenic sequences. Taken together, our observations strongly argue that it is not an alpha-helical but an extended structure adopted by the HIV-1

  13. Hydrogen Exchange Mass Spectrometry of Related Proteins with Divergent Sequences: A Comparative Study of HIV-1 Nef Allelic Variants

    NASA Astrophysics Data System (ADS)

    Wales, Thomas E.; Poe, Jerrod A.; Emert-Sedlak, Lori; Morgan, Christopher R.; Smithgall, Thomas E.; Engen, John R.

    2016-03-01

    Hydrogen exchange mass spectrometry can be used to compare the conformation and dynamics of proteins that are similar in tertiary structure. If relative deuterium levels are measured, differences in sequence, deuterium forward- and back-exchange, peptide retention time, and protease digestion patterns all complicate the data analysis. We illustrate what can be learned from such data sets by analyzing five variants (Consensus G2E, SF2, NL4-3, ELI, and LTNP4) of the HIV-1 Nef protein, both alone and when bound to the human Hck SH3 domain. Regions with similar sequence could be compared between variants. Although much of the hydrogen exchange features were preserved across the five proteins, the kinetics of Nef binding to Hck SH3 were not the same. These observations may be related to biological function, particularly for ELI Nef where we also observed an impaired ability to downregulate CD4 surface presentation. The data illustrate some of the caveats that must be considered for comparison experiments and provide a framework for investigations of other protein relatives, families, and superfamilies with HX MS.

  14. Hydrogen Exchange Mass Spectrometry of Related Proteins with Divergent Sequences: A Comparative Study of HIV-1 Nef Allelic Variants.

    PubMed

    Wales, Thomas E; Poe, Jerrod A; Emert-Sedlak, Lori; Morgan, Christopher R; Smithgall, Thomas E; Engen, John R

    2016-06-01

    Hydrogen exchange mass spectrometry can be used to compare the conformation and dynamics of proteins that are similar in tertiary structure. If relative deuterium levels are measured, differences in sequence, deuterium forward- and back-exchange, peptide retention time, and protease digestion patterns all complicate the data analysis. We illustrate what can be learned from such data sets by analyzing five variants (Consensus G2E, SF2, NL4-3, ELI, and LTNP4) of the HIV-1 Nef protein, both alone and when bound to the human Hck SH3 domain. Regions with similar sequence could be compared between variants. Although much of the hydrogen exchange features were preserved across the five proteins, the kinetics of Nef binding to Hck SH3 were not the same. These observations may be related to biological function, particularly for ELI Nef where we also observed an impaired ability to downregulate CD4 surface presentation. The data illustrate some of the caveats that must be considered for comparison experiments and provide a framework for investigations of other protein relatives, families, and superfamilies with HX MS. Graphical Abstract ᅟ. PMID:27032648

  15. Hydrogen Exchange Mass Spectrometry of Related Proteins with Divergent Sequences: A Comparative Study of HIV-1 Nef Allelic Variants

    NASA Astrophysics Data System (ADS)

    Wales, Thomas E.; Poe, Jerrod A.; Emert-Sedlak, Lori; Morgan, Christopher R.; Smithgall, Thomas E.; Engen, John R.

    2016-06-01

    Hydrogen exchange mass spectrometry can be used to compare the conformation and dynamics of proteins that are similar in tertiary structure. If relative deuterium levels are measured, differences in sequence, deuterium forward- and back-exchange, peptide retention time, and protease digestion patterns all complicate the data analysis. We illustrate what can be learned from such data sets by analyzing five variants (Consensus G2E, SF2, NL4-3, ELI, and LTNP4) of the HIV-1 Nef protein, both alone and when bound to the human Hck SH3 domain. Regions with similar sequence could be compared between variants. Although much of the hydrogen exchange features were preserved across the five proteins, the kinetics of Nef binding to Hck SH3 were not the same. These observations may be related to biological function, particularly for ELI Nef where we also observed an impaired ability to downregulate CD4 surface presentation. The data illustrate some of the caveats that must be considered for comparison experiments and provide a framework for investigations of other protein relatives, families, and superfamilies with HX MS.

  16. Sequence Analysis of In Vivo-Expressed HIV-1 Spliced RNAs Reveals the Usage of New and Unusual Splice Sites by Viruses of Different Subtypes

    PubMed Central

    Vega, Yolanda; Delgado, Elena; de la Barrera, Jorge; Carrera, Cristina; Zaballos, Ángel; Cuesta, Isabel; Mariño, Ana; Ocampo, Antonio; Miralles, Celia; Pérez-Castro, Sonia; Álvarez, Hortensia; López-Miragaya, Isabel; García-Bodas, Elena; Díez-Fuertes, Francisco; Thomson, Michael M.

    2016-01-01

    HIV-1 RNAs are generated through a complex splicing mechanism, resulting in a great diversity of transcripts, which are classified in three major categories: unspliced, singly spliced (SS), and doubly spliced (DS). Knowledge on HIV-1 RNA splicing in vivo and by non-subtype B viruses is scarce. Here we analyze HIV-1 RNA splice site usage in CD4+CD25+ lymphocytes from HIV-1-infected individuals through pyrosequencing. HIV-1 DS and SS RNAs were amplified by RT-PCR in 19 and 12 samples, respectively. 13,108 sequences from HIV-1 spliced RNAs, derived from viruses of five subtypes (A, B, C, F, G), were identified. In four samples, three of non-B subtypes, five 3’ splice sites (3’ss) mapping to unreported positions in the HIV-1 genome were identified. Two, designated A4i and A4j, were used in 22% and 25% of rev RNAs in two viruses of subtypes B and A, respectively. Given their close proximity (one or two nucleotides) to A4c and A4d, respectively, they could be viewed as variants of these sites. Three 3’ss, designated A7g, A7h, and A7i, located 20, 32, and 18 nucleotides downstream of A7, respectively, were identified in a subtype C (A7g, A7h) and a subtype G (A7i) viruses, each in around 2% of nef RNAs. The new splice sites or variants of splice sites were associated with the usual sequence features of 3’ss. Usage of unusual 3’ss A4d, A4e, A5a, A7a, and A7b was also detected. A4f, previously identified in two subtype C viruses, was preferentially used by rev RNAs of a subtype C virus. These results highlight the great diversity of in vivo splice site usage by HIV-1 RNAs. The fact that four of five newly identified splice sites or variants of splice sites were detected in non-subtype B viruses allows anticipating an even greater diversity of HIV-1 splice site usage than currently known. PMID:27355361

  17. A Short Sequence Motif in the 5′ Leader of the HIV-1 Genome Modulates Extended RNA Dimer Formation and Virus Replication*

    PubMed Central

    van Bel, Nikki; Das, Atze T.; Cornelissen, Marion; Abbink, Truus E. M.; Berkhout, Ben

    2014-01-01

    The 5′ leader of the HIV-1 RNA genome encodes signals that control various steps in the replication cycle, including the dimerization initiation signal (DIS) that triggers RNA dimerization. The DIS folds a hairpin structure with a palindromic sequence in the loop that allows RNA dimerization via intermolecular kissing loop (KL) base pairing. The KL dimer can be stabilized by including the DIS stem nucleotides in the intermolecular base pairing, forming an extended dimer (ED). The role of the ED RNA dimer in HIV-1 replication has hardly been addressed because of technical challenges. We analyzed a set of leader mutants with a stabilized DIS hairpin for in vitro RNA dimerization and virus replication in T cells. In agreement with previous observations, DIS hairpin stability modulated KL and ED dimerization. An unexpected previous finding was that mutation of three nucleotides immediately upstream of the DIS hairpin significantly reduced in vitro ED formation. In this study, we tested such mutants in vivo for the importance of the ED in HIV-1 biology. Mutants with a stabilized DIS hairpin replicated less efficiently than WT HIV-1. This defect was most severe when the upstream sequence motif was altered. Virus evolution experiments with the defective mutants yielded fast replicating HIV-1 variants with second site mutations that (partially) restored the WT hairpin stability. Characterization of the mutant and revertant RNA molecules and the corresponding viruses confirmed the correlation between in vitro ED RNA dimer formation and efficient virus replication, thus indicating that the ED structure is important for HIV-1 replication. PMID:25368321

  18. Deep Sequencing of Protease Inhibitor Resistant HIV Patient Isolates Reveals Patterns of Correlated Mutations in Gag and Protease

    PubMed Central

    Tan, Zhiqiang; Oliveira, Glenn; Yuan, Jinyun; Okulicz, Jason F.; Torbett, Bruce E.; Levy, Ronald M.

    2015-01-01

    While the role of drug resistance mutations in HIV protease has been studied comprehensively, mutations in its substrate, Gag, have not been extensively cataloged. Using deep sequencing, we analyzed a unique collection of longitudinal viral samples from 93 patients who have been treated with therapies containing protease inhibitors (PIs). Due to the high sequence coverage within each sample, the frequencies of mutations at individual positions were calculated with high precision. We used this information to characterize the variability in the Gag polyprotein and its effects on PI-therapy outcomes. To examine covariation of mutations between two different sites using deep sequencing data, we developed an approach to estimate the tight bounds on the two-site bivariate probabilities in each viral sample, and the mutual information between pairs of positions based on all the bounds. Utilizing the new methodology we found that mutations in the matrix and p6 proteins contribute to continued therapy failure and have a major role in the network of strongly correlated mutations in the Gag polyprotein, as well as between Gag and protease. Although covariation is not direct evidence of structural propensities, we found the strongest correlations between residues on capsid and matrix of the same Gag protein were often due to structural proximity. This suggests that some of the strongest inter-protein Gag correlations are the result of structural proximity. Moreover, the strong covariation between residues in matrix and capsid at the N-terminus with p1 and p6 at the C-terminus is consistent with residue-residue contacts between these proteins at some point in the viral life cycle. PMID:25894830

  19. Comparison of HIV type 1 sequences from plasma, cell-free breast milk, and cell-associated breast milk viral populations in treated and untreated women in Mozambique.

    PubMed

    Andreotti, Mauro; Galluzzo, Clementina M; Guidotti, Giovanni; Germano, Paola; Altan, Annamaria Doro; Pirillo, Maria Franca; Marazzi, Maria Cristina; Vella, Stefano; Palombi, Leonardo; Giuliano, Marina

    2009-07-01

    We analyzed the sequences of the HIV viral populations obtained from plasma, cell-free breast milk, and breast milk cells of HAART-treated (23) and untreated (30) HIV-infected women to obtain information about the origin of the breast milk virus. Sequence analyses of viruses were performed using the TruGene HIV-1 assay. Direct sequences of the reverse transcriptase (RT) and protease (PR) genes were analyzed using the Phylip 3.68 suite of sequence analysis program and pairwise evolutionary distances were calculated with the Kimura two parameter model for estimation of distances. We found that the genetic distances between the plasma and the cell-free breast milk viruses and between the cell-free and cell-associated breast milk viruses for RT were higher in HAART-receiving women than in untreated women, suggesting viral evolution under selective drug pressure in breast milk. Our data support the hypothesis of the presence of an actively replicating viral population in the breast milk compartment, distinct from that present in plasma. PMID:19552594

  20. Comparison of SIV and HIV-1 genomic RNA structures reveals impact of sequence evolution on conserved and non-conserved structural motifs.

    PubMed

    Pollom, Elizabeth; Dang, Kristen K; Potter, E Lake; Gorelick, Robert J; Burch, Christina L; Weeks, Kevin M; Swanstrom, Ronald

    2013-01-01

    RNA secondary structure plays a central role in the replication and metabolism of all RNA viruses, including retroviruses like HIV-1. However, structures with known function represent only a fraction of the secondary structure reported for HIV-1(NL4-3). One tool to assess the importance of RNA structures is to examine their conservation over evolutionary time. To this end, we used SHAPE to model the secondary structure of a second primate lentiviral genome, SIVmac239, which shares only 50% sequence identity at the nucleotide level with HIV-1NL4-3. Only about half of the paired nucleotides are paired in both genomic RNAs and, across the genome, just 71 base pairs form with the same pairing partner in both genomes. On average the RNA secondary structure is thus evolving at a much faster rate than the sequence. Structure at the Gag-Pro-Pol frameshift site is maintained but in a significantly altered form, while the impact of selection for maintaining a protein binding interaction can be seen in the conservation of pairing partners in the small RRE stems where Rev binds. Structures that are conserved between SIVmac239 and HIV-1(NL4-3) also occur at the 5' polyadenylation sequence, in the plus strand primer sites, PPT and cPPT, and in the stem-loop structure that includes the first splice acceptor site. The two genomes are adenosine-rich and cytidine-poor. The structured regions are enriched in guanosines, while unpaired regions are enriched in adenosines, and functionaly important structures have stronger base pairing than nonconserved structures. We conclude that much of the secondary structure is the result of fortuitous pairing in a metastable state that reforms during sequence evolution. However, secondary structure elements with important function are stabilized by higher guanosine content that allows regions of structure to persist as sequence evolution proceeds, and, within the confines of selective pressure, allows structures to evolve. PMID:23593004

  1. Sequencing and Phylogenetic Analysis of Near Full-Length HIV-1 Subtypes A, B, G and Unique Recombinant AC and AD Viral Strains Identified in South Africa

    PubMed Central

    Wilkinson, Eduan; Holzmayer, Vera; Jacobs, Graeme B.; de Oliveira, Tulio; Brennan, Catherine A.; Hackett, John; van Rensburg, Estrelita Janse

    2015-01-01

    Abstract By the end of 2012, more than 6.1 million people were infected with HIV-1 in South Africa. Subtype C was responsible for the majority of these infections and more than 300 near full-length genomes (NFLGs) have been published. Currently very few non-subtype C isolates have been identified and characterized within the country, particularly full genome non-C isolates. Seven patients from the Tygerberg Virology (TV) cohort were previously identified as possible non-C subtypes and were selected for further analyses. RNA was isolated from five individuals (TV047, TV096, TV101, TV218, and TV546) and DNA from TV016 and TV1057. The NFLGs of these samples were amplified in overlapping fragments and sequenced. Online subtyping tools REGA version 3 and jpHMM were used to screen for subtypes and recombinants. Maximum likelihood (ML) phylogenetic analysis (phyML) was used to infer subtypes and SimPlot was used to confirm possible intersubtype recombinants. We identified three subtype B (TV016, TV047, and TV1057) isolates, one subtype A1 (TV096), one subtype G (TV546), one unique AD (TV101), and one unique AC (TV218) recombinant form. This is the first NFLG of subtype G that has been described in South Africa. The subtype B sequences described also increased the NFLG subtype B sequences in Africa from three to six. There is a need for more NFLG sequences, as partial HIV-1 sequences may underrepresent viral recombinant forms. It is also necessary to continue monitoring the evolution and spread of HIV-1 in South Africa, because understanding viral diversity may play an important role in HIV-1 prevention strategies. PMID:25492033

  2. Evaluation of internal transcribed spacer region of ribosomal DNA sequence analysis for molecular characterization of Candida albicans and Candida dubliniensis isolates from HIV-infected patients.

    PubMed

    Millon, L; Piarroux, R; Drobacheff, C; Monod, M; Grenouillet, F; Bulle, B; Bole, J; Blancard, A; Meillet, D

    2002-12-01

    Molecular typing systems have been needed to study Candida colonization in HIV-infected patients, particularly for investigating virulence and fluconazole resistance. Three methods--electrophoretic karyotyping (EK), detection of restriction fragment length polymorphisms (RFLP) and randomly amplified polymorphic DNA analysis (RAPD)--have been most frequently used. In this study, comparative sequence analysis of the internal transcribed spacer (ITS) region of rDNA was evaluated for delineation of Candida isolates from 14 HIV-infected patients. EK, ITS sequence analysis, RFLP and RAPD resulted in 11, 10, 9 and 8 DNA genotypes, respectively, from 39 Candida albicans isolates. The 10 genotypes observed using ITS sequence analysis were defined by six variation sites in the sequence. Molecular typing of sequential oral isolates showed the persistence of the same genotype of C. albicans in nine patients, and genotype variation in one patient. EK and RAPD showed that another patient was co-infected by two distinct genotypes and ITS analysis identified one of the two genotypes as Candida dubliniensis. Comparative ITS sequence analysis is a quick and reproducible method that provides clear and objective results, and it also identifies C. dubliniensis. The discriminatory power of this new typing approach could be improved by concomitant analysis of other DNA polymorphic sequences. PMID:12521117

  3. Sequence and peptide-binding motif for a variant of HLA-A*0214 (A*02142) in an HIV-1-resistant individual from the Nairobi Sex Worker cohort.

    PubMed

    Luscher, M A; MacDonald, K S; Bwayo, J J; Plummer, F A; Barber, B H

    2001-02-01

    As part of the ongoing study of natural HIV-1 resistance in the women of the Nairobi Sex Workers' study, we have examined a resistance-associated HLA class I allele at the molecular level. Typing by polymerase chain reaction using sequence-specific primers determined that this molecule is closely related to HLA-A*0214, one of a family of HLA-A2 supertype alleles which correlate with HIV-1 resistance in this population. Direct nucleotide sequencing shows that this molecule differs from A*0214, having a silent nucleotide substitution. We therefore propose to designate it HLA-A*02142. We have determined the peptide-binding motif of HLA-A*0214/02142 by peptide elution and bulk Edman degradative sequencing. The resulting motif, X-[Q,V]-X-X-X-K-X-X-[V,L], includes lysine as an anchor at position 6. The data complement available information on the peptide-binding characteristics of this molecule, and will be of use in identifying antigenic peptides from HIV-1 and other pathogens. PMID:11261925

  4. HIV Drug Resistance Mutations (DRMs) Detected by Deep Sequencing in Virologic Failure Subjects on Therapy from Hunan Province, China

    PubMed Central

    He, Jianmei; Zheng, Jun; Chiarella, Jennifer; Kozal, Michael J.

    2016-01-01

    Objective Determine HIV drug resistance mutations (DRMs) prevalence at low and high levels in ART-experienced patients experiencing virologic failure (VF). Methods 29 subjects from 18 counties in Hunan Province that experienced VF were evaluated for the prevalence of DRMs (Stanford DRMs with an algorithm value ≥15, include low-, intermediate and high-level resistance) by both Sanger sequencing (SS) and deep sequencing (DS) to 1% frequency levels. Results DS was performed on samples from 29 ART-experienced subjects; the median viral load 4.95×104 c/ml; 82.76% subtype CRF01_AE. 58 DRMs were detected by DS. 18 DRMs were detected by SS. Of the 58 mutations detected by DS, 40 were at levels <20% frequency (26 NNRTI, 12 NRTI and 2 PI) and the majority of these 95.00% (38/40) were not detected by standard genotyping. Of these 40 low-level DRMs, 16 (40%) were detected at frequency levels of 1–4% and 24 (60%) at levels of 5–19%. SS detected 15 of 17 (88.24%) DRMs at levels ≥ 20% that were detected by DS. The only variable associated with the detection of DRMs by DS was ART adherence (missed doses in the prior 7 days); all patients that reported missing a dose in the last 7 days had DRMs detected by DS. Conclusions DS of VF samples from treatment experienced subjects infected with primarily AE subtype frequently identified Stanford HIVdb NRTI and NNRTI resistance mutations with an algorithm value 15. Low frequency level resistant variants detected by DS were frequently missed by standard genotyping in VF specimens from antiretroviral-experienced subjects. PMID:26895182

  5. Primer ID Validates Template Sampling Depth and Greatly Reduces the Error Rate of Next-Generation Sequencing of HIV-1 Genomic RNA Populations

    PubMed Central

    Zhou, Shuntai; Jones, Corbin; Mieczkowski, Piotr

    2015-01-01

    ABSTRACT Validating the sampling depth and reducing sequencing errors are critical for studies of viral populations using next-generation sequencing (NGS). We previously described the use of Primer ID to tag each viral RNA template with a block of degenerate nucleotides in the cDNA primer. We now show that low-abundance Primer IDs (offspring Primer IDs) are generated due to PCR/sequencing errors. These artifactual Primer IDs can be removed using a cutoff model for the number of reads required to make a template consensus sequence. We have modeled the fraction of sequences lost due to Primer ID resampling. For a typical sequencing run, less than 10% of the raw reads are lost to offspring Primer ID filtering and resampling. The remaining raw reads are used to correct for PCR resampling and sequencing errors. We also demonstrate that Primer ID reveals bias intrinsic to PCR, especially at low template input or utilization. cDNA synthesis and PCR convert ca. 20% of RNA templates into recoverable sequences, and 30-fold sequence coverage recovers most of these template sequences. We have directly measured the residual error rate to be around 1 in 10,000 nucleotides. We use this error rate and the Poisson distribution to define the cutoff to identify preexisting drug resistance mutations at low abundance in an HIV-infected subject. Collectively, these studies show that >90% of the raw sequence reads can be used to validate template sampling depth and to dramatically reduce the error rate in assessing a genetically diverse viral population using NGS. IMPORTANCE Although next-generation sequencing (NGS) has revolutionized sequencing strategies, it suffers from serious limitations in defining sequence heterogeneity in a genetically diverse population, such as HIV-1 due to PCR resampling and PCR/sequencing errors. The Primer ID approach reveals the true sampling depth and greatly reduces errors. Knowing the sampling depth allows the construction of a model of how to maximize

  6. Deep sequencing and Circos analyses of antibody libraries reveal antigen-driven selection of Ig VH genes during HIV-1 infection.

    PubMed

    Xiao, Madelyne; Prabakaran, Ponraj; Chen, Weizao; Kessing, Bailey; Dimitrov, Dimiter S

    2013-12-01

    The vast diversity of antibody repertoires is largely attributed to heavy chain (V(H)) recombination of variable (V), diversity (D) and joining (J) gene segments. We used 454 sequencing information of the variable domains of the antibody heavy chain repertoires from neonates, normal adults and an HIV-1-infected individual, to analyze, with Circos software, the VDJ pairing patterns at birth, adulthood and a time-dependent response to HIV-1 infection. Our comparative analyses of the Ig VDJ repertoires from these libraries indicated that, from birth to adulthood, VDJ recombination patterns remain the same with some slight changes, whereas some V(H) families are selected and preferentially expressed after long-term infection with HIV-1. We also demonstrated that the immune system responds to HIV-1 chronic infection by selectively expanding certain HV families in an attempt to combat infection. Our findings may have implications for understanding immune responses in pathology as well as for development of new therapeutics and vaccines. PMID:24158018

  7. Preservation of Tetherin and CD4 Counter-Activities in Circulating Vpu Alleles despite Extensive Sequence Variation within HIV-1 Infected Individuals

    PubMed Central

    Pickering, Suzanne; Hué, Stephane; Kim, Eun-Young; Reddy, Susheel; Wolinsky, Steven M.; Neil, Stuart J. D.

    2014-01-01

    The HIV-1 Vpu protein is expressed from a bi-cistronic message late in the viral life cycle. It functions during viral assembly to maximise infectious virus release by targeting CD4 for proteosomal degradation and counteracting the antiviral protein tetherin (BST2/CD317). Single genome analysis of vpu repertoires throughout infection in 14 individuals infected with HIV-1 clade B revealed extensive amino acid diversity of the Vpu protein. For the most part, this variation in Vpu increases over the course of infection and is associated with predicted epitopes of the individual's MHC class I haplotype, suggesting CD8+ T cell pressure is the major driver of Vpu sequence diversity within the host. Despite this variability, the Vpu functions of targeting CD4 and counteracting both physical virus restriction and NF-κB activation by tetherin are rigorously maintained throughout HIV-1 infection. Only a minority of circulating alleles bear lesions in either of these activities at any given time, suggesting functional Vpu mutants are heavily selected against even at later stages of infection. Comparison of Vpu proteins defective for one or several functions reveals novel determinants of CD4 downregulation, counteraction of tetherin restriction, and inhibition of NF-κB signalling. These data affirm the importance of Vpu functions for in vivo persistence of HIV-1 within infected individuals, not simply for transmission, and highlight its potential as a target for antiviral therapy. PMID:24465210

  8. [Production and evaluation of immunologic characteristics of mzNLA-3, a non-infectious HIV-1 clone with a large deletion in the pol sequence].

    PubMed

    Aghasadeghi, M R; Zabihollahi, R; Sadat, S M; Salehi, M; Ashtiani, S H; Namazi, R; Kashanizadeh, N; Azadmanesh, K

    2013-01-01

    Inactivation ofintegrase and reverse transcriptase can revoke the replication of HIV virions, and non-infectious HIV particles are desirable virus-like particle (VLP) vaccine candidates. Here, we produced inactive in replication HIV-1 particles fit for vaccine and virological purposes by introducing a mutation into the pol sequence. Proviral DNA (pNLA-3) was cut at two points in the pol region using the Bal I restriction enzyme and then religated. HEK 293T cells were transfected with the resultant plasmid (pmzNL4-3) to produce mutated virions. To confirm a production of VLPs and evaluate their biological activity the p24 load and syncytium formation (MT2 cells) were analyzed. The assay indicated that mzNL4-3 virions were assembled and contained functional envelope glycoproteins (ENV). In addition, mzNL4-3 virions were not able to infect MT2 and HEK 293T cells. Furthermore, the immunogenicity of VLPs was investigated in a mouse model. According to the data on vaccinated mice, the titer of ENV-specific antibodies rose rapidly after a boosting injection. Moreover, lymphoid cells extracted from these mice proliferated after exposure to the antigen. The mzNL4-3 virus particles possessed immunogenic antigens of HIV and can effectively trigger humoral and CD4 immune responses. Non-infectious mzNL4-3 virions may also be used in biomedical experiments to improve the biological safety conditions. Moreover, the mzNL4-3 seems to be a promising candidate for further HIV-1 vaccine investigations. PMID:23808159

  9. Los Alamos National Laboratory

    SciTech Connect

    Dogliani, Harold O

    2011-01-19

    The purpose of the briefing is to describe general laboratory technical capabilities to be used for various groups such as military cadets or university faculty/students and post docs to recruit into a variety of Los Alamos programs. Discussed are: (1) development and application of high leverage science to enable effeictive, predictable and reliability outcomes; (2) deter, detect, characterize, reverse and prevent the proliferation of weapons of mass destruction and their use by adversaries and terrorists; (3) modeling and simulation to define complex processes, predict outcomes, and develop effective prevention, response, and remediation strategies; (4) energetic materials and hydrodynamic testing to develop materials for precise delivery of focused energy; (5) materials cience focused on fundamental understanding of materials behaviors, their quantum-molecular properties, and their dynamic responses, and (6) bio-science to rapidly detect and characterize pathogens, to develop vaccines and prophylactic remedies, and to develop attribution forensics.

  10. Ultra-Deep Sequencing of HIV-1 near Full-Length and Partial Proviral Genomes Reveals High Genetic Diversity among Brazilian Blood Donors

    PubMed Central

    Pessôa, Rodrigo; Loureiro, Paula; Esther Lopes, Maria; Carneiro-Proietti, Anna B. F.; Sabino, Ester C; Busch, Michael P.; Sanabani, Sabri S

    2016-01-01

    Background Here, we aimed to gain a comprehensive picture of the HIV-1 diversity in the northeast and southeast part of Brazil. To this end, a high-throughput sequencing-by-synthesis protocol and instrument were used to characterize the near full length (NFLG) and partial HIV-1 proviral genome in 259 HIV-1 infected blood donors at four major blood centers in Brazil: Pro-Sangue foundation (São Paulo state (SP), n 51), Hemominas foundation (Minas Gerais state (MG), n 41), Hemope foundation (Recife state (PE), n 96) and Hemorio blood bank (Rio de Janeiro (RJ), n 70). Materials and Methods A total of 259 blood samples were obtained from 195 donors with long-standing infections and 64 donors with a lack of stage information. DNA was extracted from the peripheral blood mononuclear cells (PBMCs) to amplify the HIV-1 NFLGs from five overlapping fragments. The amplicons were molecularly bar-coded, pooled, and sequenced by Illumina paired-end protocol. Results Of the 259 samples studied, 208 (80%) NFLGs and 49 (18.8%) partial fragments were de novo assembled into contiguous sequences and successfully subtyped. Of these 257 samples, 183 (71.2%) were pure subtypes consisting of clade B (n = 167, 65%), C (n = 10, 3.9%), F1 (n = 4, 1.5%), and D (n = 2, 0.7%). Recombinant viruses were detected in 74 (28.8%) samples and consist of unique BF1 (n = 41, 15.9%), BC (n = 7, 2.7%), BCF1 (n = 4, 1.5%), CF1 and CDK (n = 1, 0.4%, each), CRF70_BF1 (n = 4, 1.5%), CRF71_BF1 (n = 12, 4.7%), and CRF72_BF1 (n = 4, 1.5%). Evidence of dual infection was detected in four patients coinfected with the same subtype (n = 3) and distinct subtype (n = 1). Conclusion Based on this work, subtype B appears to be the prevalent subtype followed by a high proportion of intersubtype recombinants that appeared to be arising continually in this country. Our study represents the largest analysis of the viral NFLG ever undertaken worldwide and provides insights into the understanding the genesis of the HIV-1

  11. On the Physicochemical and Structural Modifications Associated with HIV-1 Subtype B Tropism Transition.

    PubMed

    Lamers, Susanna L; Fogel, Gary B; Liu, Enoch S; Salemi, Marco; McGrath, Michael S

    2016-08-01

    HIV-1 enters immune cells via binding the viral envelope to a host cell CD4 receptor, and then a secondary co-receptor, usually CCR5 (R5) or CXCR4 (X4), and some HIV can utilize both co-receptors (R5X4). Although a small set of amino-acid properties such as charge and sequence length applied to HIV-1 envelope V3 loop sequence data can be used to predict co-receptor usage, we sought to expand the fundamental understanding of the physiochemical basis of tropism by analyzing many, perhaps less obvious, amino-acid properties over a diverse array of HIV sequences. We examined 74 amino-acid physicochemical scales over 1,559 V3 loop sequences with biologically tested tropisms downloaded from the Los Alamos HIV sequence database. Linear regressions were then calculated for each feature relative to three tropism transitions (R5→X4; R5→R5X4; R5X4→X4). Independent correlations were rank ordered to determine informative features. A structural analysis of the V3 loop was performed to better interpret these findings relative to HIV tropism states. Similar structural changes are required for R5 and R5X4 to transition to X4, thus suggesting that R5 and R5X4 types are more similar than either phenotype is to X4. Overall, the analysis suggests a continuum of viral tropism that is only partially related to charge; in fact, the analysis suggests that charge modification may be primarily attributed to decreased R5 usage, and further structural changes, particularly those associated with β-sheet structure, are likely required for full X4 usage. PMID:27071630

  12. A zwitterionic 1D/2D polymer co-crystal and its polymorphic sub-components: a highly selective sensing platform for HIV ds-DNA sequences.

    PubMed

    Zhao, Hai-Qing; Yang, Shui-Ping; Ding, Ni-Ni; Qin, Liang; Qiu, Gui-Hua; Chen, Jin-Xiang; Zhang, Wen-Hua; Chen, Wen-Hua; Hor, T S Andy

    2016-03-15

    Polymorphic compounds {[Cu(dcbb)2(H2O)2]·10H2O}n (, 1D chain), [Cu(dcbb)2]n (, 2D layer) and their co-crystal {[Cu(dcbb)2(H2O)][Cu(dcbb)2]2}n () have been prepared from the coordination reaction of a 2D polymer [Na(dcbb)(H2O)]n (, H2dcbbBr = 1-(3,5-dicarboxybenzyl)-4,4'-bipyridinium bromide) with Cu(NO3)2·3H2O at different temperatures in water. Compounds have an identical metal-to-ligand stoichiometric ratio of 1 : 2, but absolutely differ in structure. Compound features a 2D layer structure with aromatic rings, positively charged pyridinium and free carboxylates on its surface, promoting electrostatic, π-stacking and/or hydrogen-bonding interactions with the carboxyfluorescein (FAM) labeled probe single-stranded DNA (probe ss-DNA, delineates as P-DNA). The resultant P-DNA@ system facilitated fluorescence quenching of FAM via a photoinduced electron transfer process. The P-DNA@ system functions as an efficient fluorescent sensor selective for HIV double-stranded DNA (HIV ds-DNA) due to the formation of a rigid triplex structure with the recovery of FAM fluorescence. The system reported herein also distinguishes complementary HIV ds-DNA from mismatched target DNA sequences with the detection limit of 1.42 nM. PMID:26883749

  13. Near-Full-Length Genome Sequences of a Novel HIV-1 Circulating Recombinant Form, CRF01_AE/B'/C (CRF78_cpx), in Yunnan, China.

    PubMed

    Song, Yindi; Feng, Yue; Miao, Zhijiang; Wang, Binghui; Yang, Ming; Zhang, A-Mei; Liu, Li; Xia, Xueshan

    2016-06-01

    We report a novel HIV circulating recombinant form (CRF78_cpx) composed mainly of CRF01_AE with inserts from subtypes B and C identified from three epidemiologically unlinked individuals in Yunnan province, China. Two of the subjects are heterosexual men and one is a male intravenous drug user. Sequencing and analyzing the near-full-length genome of these three isolates (YNTC88, YNTC19, and YNTC35) revealed identical recombination breakpoints in all three viruses, but considerable genetic diversity between them, across the genomes, indicating that this is not a newly created CRF, only newly detected. CRF78_cpx differs from previously documented CRF01-AE/B'/C forms in its distinct backbone, inserted fragment size, and breakpoints, and is not related to other described recombinants in the region such as CRF07_BC or CRF65_cpx (also composed of CRF01_AE, B', and C). Our present findings further enrich the diversity of the prevalent HIV-1 CRFs in Yunnan, which is considered as an epicenter of HIV-1 infections in China. PMID:26885715

  14. Microbiome in HIV infection

    PubMed Central

    Salas, January T.; Chang, Theresa L.

    2014-01-01

    HIV primary infection occurs at mucosa tissues, suggesting an intricate interplay between microbiome and HIV infection. Recent advanced technologies of high-throughput sequencing and bioinformatics allow researchers to explore nonculturable microbes including bacteria, virus and fungi and their association with diseases. HIV/SIV infection is associated with microbiome shifts and immune activation that may affect the outcome of disease progression. Similarly, altered microbiome and inflammation are associated with increased risks of HIV acquisition, suggesting the role of microbiome in HIV transmission. In this review, we will focus on microbiome in HIV infection at various mucosal compartments. Understanding the relationship between microbiome and HIV may offer insights into development of better strategies for HIV prevention and treatment. PMID:25439273

  15. Concordance of HIV Type 1 Tropism Phenotype to Predictions Using Web-Based Analysis of V3 Sequences: Composite Algorithms May Be Needed to Properly Assess Viral Tropism

    PubMed Central

    Cabral, Gabriela Bastos; Ferreira, João Leandro de Paula; Coelho, Luana Portes Osório; Fonsi, Mylva; Estevam, Denise Lotufo; Cavalcanti, Jaqueline Souza

    2012-01-01

    Abstract Genotypic prediction of HIV-1 tropism has been considered a practical surrogate for phenotypic tests and recently an European Consensus has set up recommendations for its use in clinical practice. Twenty-five antiretroviral-experienced patients, all heavily treated cases with a median of 16 years of antiretroviral therapy, had viral tropism determined by the Trofile assay and predicted by HIV-1 sequencing of partial env, followed by interpretation using web-based tools. Trofile determined 17/24 (71%) as X4 tropic or dual/mixed viruses, with one nonreportable result. The use of European consensus recommendations for single sequences (geno2pheno false-positive rates 20% cutoff) would lead to 4/24 (16.7%) misclassifications, whereas a composite algorithm misclassified 1/24 (4%). The use of the geno2pheno clinical option using CD4 T cell counts at collection was useful in resolving some discrepancies. Applying the European recommendations followed by additional web-based tools for cases around the recommended cutoff would resolve most misclassifications. PMID:21919801

  16. Concordance of HIV type 1 tropism phenotype to predictions using web-based analysis of V3 sequences: composite algorithms may be needed to properly assess viral tropism.

    PubMed

    Cabral, Gabriela Bastos; Ferreira, João Leandro de Paula; Coelho, Luana Portes Osório; Fonsi, Mylva; Estevam, Denise Lotufo; Cavalcanti, Jaqueline Souza; Brígido, Luis Fernando de Macedo

    2012-07-01

    Genotypic prediction of HIV-1 tropism has been considered a practical surrogate for phenotypic tests and recently an European Consensus has set up recommendations for its use in clinical practice. Twenty-five antiretroviral-experienced patients, all heavily treated cases with a median of 16 years of antiretroviral therapy, had viral tropism determined by the Trofile assay and predicted by HIV-1 sequencing of partial env, followed by interpretation using web-based tools. Trofile determined 17/24 (71%) as X4 tropic or dual/mixed viruses, with one nonreportable result. The use of European consensus recommendations for single sequences (geno2pheno false-positive rates 20% cutoff) would lead to 4/24 (16.7%) misclassifications, whereas a composite algorithm misclassified 1/24 (4%). The use of the geno2pheno clinical option using CD4 T cell counts at collection was useful in resolving some discrepancies. Applying the European recommendations followed by additional web-based tools for cases around the recommended cutoff would resolve most misclassifications. PMID:21919801

  17. Genome Sequence of Complex HIV-1 Unique Recombinant Forms Sharing a Common Recombination Breakpoint Identified in Malaysia

    PubMed Central

    Cheong, Hui Ting; Ng, Kim Tien; Ong, Lai Yee; Takebe, Yutaka; Chan, Kok Gan; Koh, Clayton; Al-Darraji, Haider Abdulrazzaq Abed; Kamarulzaman, Adeeba

    2015-01-01

    Three strains of HIV-1 unique recombinant forms (URFs) descended from subtypes B, B′, and CRF01_AE were identified among people who inject drugs in Kuala Lumpur, Malaysia. These three URFs shared a common recombination breakpoint in the reverse transcriptase region, indicating frequent linkage within the drug-injecting networks in Malaysia. PMID:26543107

  18. Deep Sequencing of HIV-1 RNA and DNA in Newly Diagnosed Patients with Baseline Drug Resistance Showed No Indications for Hidden Resistance and Is Biased by Strong Interference of Hypermutation.

    PubMed

    Dauwe, Kenny; Staelens, Delfien; Vancoillie, Leen; Mortier, Virginie; Verhofstede, Chris

    2016-06-01

    Deep sequencing of plasma RNA or proviral DNA may be an interesting alternative to population sequencing for the detection of baseline transmitted HIV-1 drug resistance. Using a Roche 454 GS Junior HIV-1 prototype kit, we performed deep sequencing of the HIV-1 protease and reverse transcriptase genes on paired plasma and buffy coat samples from newly diagnosed HIV-1-positive individuals. Selection was based on the outcome of population sequencing and included 12 patients with either a revertant amino acid at codon 215 of the reverse transcriptase or a singleton resistance mutation, 4 patients with multiple resistance mutations, and 4 patients with wild-type virus. Deep sequencing of RNA and DNA detected 6 and 43 mutations, respectively, that were not identified by population sequencing. A subsequently performed hypermutation analysis, however, revealed hypermutation in 61.19% of 3,188 DNA reads with a resistance mutation. The removal of hypermutated reads dropped the number of additional mutations in DNA from 43 to 17. No hypermutation evidence was found in the RNA reads. Five of the 6 additional RNA mutations and all additional DNA mutations, after full exclusion of hypermutation bias, were observed in the 3 individuals with multiple resistance mutations detected by population sequencing. Despite focused selection of patients with T215 revertants or singleton mutations, deep sequencing failed to identify the resistant T215Y/F or M184V or any other resistance mutation, indicating that in most of these cases there is no hidden resistance and that the virus detected at diagnosis by population sequencing is the original infecting variant. PMID:27076656

  19. Membrane-Active Sequences within gp41 Membrane Proximal External Region (MPER) Modulate MPER-Containing Peptidyl Fusion Inhibitor Activity and the Biosynthesis of HIV-1 Structural Proteins

    PubMed Central

    Zhang, Si Min; Jejcic, Alenka; Tam, James P.; Vahlne, Anders

    2015-01-01

    The membrane proximal external region (MPER) is a highly conserved membrane-active region located at the juxtamembrane positions within class I viral fusion glycoproteins and essential for membrane fusion events during viral entry. The MPER in the human immunodeficiency virus type I (HIV-1) envelope protein (Env) interacts with the lipid bilayers through a cluster of tryptophan (Trp) residues and a C-terminal cholesterol-interacting motif. The inclusion of the MPER N-terminal sequence contributes to the membrane reactivity and anti-viral efficacy of the first two anti-HIV peptidyl fusion inhibitors T20 and T1249. As a type I transmembrane protein, Env also interacts with the cellular membranes during its biosynthesis and trafficking. Here we investigated the roles of MPER membrane-active sequences during both viral entry and assembly, specifically, their roles in the design of peptidyl fusion inhibitors and the biosynthesis of viral structural proteins. We found that elimination of the membrane-active elements in MPER peptides, namely, penta Trp→alanine (Ala) substitutions and the disruption of the C-terminal cholesterol-interacting motif through deletion inhibited the anti-viral effect against the pseudotyped HIV-1. Furthermore, as compared to C-terminal dimerization, N-terminal dimerization of MPER peptides and N-terminal extension with five helix-forming residues enhanced their anti-viral efficacy substantially. The secondary structure study revealed that the penta-Trp→Ala substitutions also increased the helical content in the MPER sequence, which prompted us to study the biological relevance of such mutations in pre-fusion Env. We observed that Ala mutations of Trp664, Trp668 and Trp670 in MPER moderately lowered the intracellular and intraviral contents of Env while significantly elevating the content of another viral structural protein, p55/Gag and its derivative p24/capsid. The data suggest a role of the gp41 MPER in the membrane-reactive events during

  20. DNA-stabilized silver nanoclusters and carbon nanoparticles oxide: A sensitive platform for label-free fluorescence turn-on detection of HIV-DNA sequences.

    PubMed

    Ye, Yu-Dan; Xia, Li; Xu, Dang-Dang; Xing, Xiao-Jing; Pang, Dai-Wen; Tang, Hong-Wu

    2016-11-15

    Based on the remarkable difference between the interactions of carbon nanoparticles (CNPs) oxide with single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA), and the fact that fluorescence of DNA-stabilized silver nanoclusters (AgNCs) can be quenched by CNPs oxide, DNA-functionalized AgNCs were applied as label-free fluorescence probes and a novel fluorescence resonance energy transfer (FRET) sensor was successfully constructed for the detection of human immunodeficiency virus (HIV) DNA sequences. CNPs oxide were prepared with the oxidation of candle soot, hence it is simple, time-saving and low-cost. The strategy of dual AgNCs probes was applied to improve the detection sensitivity by using dual- probe capturing the same target DNA in a sandwich mode and as the fluorescence donor, and using CNPs oxide as the acceptor. In the presence of target DNA, a dsDNA hybrid forms, leading to the desorption of the ssDNA-AgNCs probes from CNPs oxide, and the recovering of fluorescence of the AgNCs in a HIV-DNA concentration-dependent manner. The results show that HIV-DNA can be detected in the range of 1-50nM with a detection limit of 0.40nM in aqueous buffer. The method is simple, rapid and sensitive with no need of labeled fluorescent probes, and moreover, the design of fluorescent dual-probe makes full use of the excellent fluorescence property of AgNCs and further improves the detection sensitivity. PMID:27295571

  1. Potential impact of viral load and genetic makeup of HIV type 1 on mother-to-child transmission: characterization of env-C2V3C3 and nef sequences.

    PubMed

    Pádua, Elizabeth; Parreira, Ricardo; Tendeiro, Rita; Nunes, Baltazar; Castela, João; Soares, Isabel; Mouzinho, Ana; Reis, Eduarda; Paixão, Maria Teresa

    2009-11-01

    HIV-1 mother-to-child transmission (MTCT) was evaluated in terms of the molecular characterization of the env and nef genomic regions and quantification of maternal RNA viral loads. Assignment of viral subtype was achieved by direct sequencing of PCR 1172 products amplified from proviral DNA in 45 HIV-1-nontransmitting mothers (NTM), along with 13 pairs of HIV-1-transmitting mothers (TM) and their infected children (C). Analysis of the env C2V3C3 and nef sequences revealed that subtypes G and B, and their genetic combinations (AG, BG), accounted for over 84.5% of all viruses identified. The genetic structure form envA-nefG was the most commonly observed, with a lower frequency in the NTM (13.3%) compared to the TM (23.1%) group. A greater number of genetic forms was observed among NTM, namely the presence of sequences assigned to subtypes D and F, as well as the intergenetic A/J, and C/U, recombinant forms, along with a mosaic provirus with a complex putative envA-nefEGE genetic structure. No significant differences were found when RNA viral loads were evaluated as a function of the viral subtypes. Nevertheless, a relatively high quantification of HIV-1 RNA was obtained in the NTM group, emphasizing the importance of the compliance and effectiveness of therapeutic schemes to control viral replication and reduce the risk of HIV vertical transmission. V3 sequences displaying features associated with the R5 phenotype dominated in both groups. Both C2V3C3 and Nef's functional domains were conserved during HIV-1 vertical transmission. PMID:19886833

  2. Quantitation of HIV-1 RNA viral load using nucleic acid sequence based amplification methodology and comparison with other surrogate markers for disease progression.

    PubMed

    Sitnik, R; Pinho, J R

    1998-01-01

    In this study, HIV-1 viral blood quantitation determined by Nucleic Acid Sequence Based Amplification (NASBA) was compared with other surrogate disease progression markers (antigen p24, CD4/CD8 cell counts and beta-2 microglobulin) in 540 patients followed up at São Paulo, SP, Brazil. HIV-1 RNA detection was statistically associated with the presence of antigen p24, but the viral RNA was also detected in 68% of the antigen p24 negative samples, confirming that NASBA is much more sensitive than the determination of antigen p24. Regarding other surrogate markers, no statistically significant association with the detection of viral RNA was found. The reproducibility of this viral load assay was assessed by 14 runs of the same sample, using different reagents batches. Viral load values in this sample ranged from 5.83 to 6.27 log (CV = 36%), less than the range (0.5 log) established to the determination of significant viral load changes. PMID:9698880

  3. Magic Angle Spinning NMR Reveals Sequence-Dependent Structural Plasticity, Dynamics, and the Spacer Peptide 1 Conformation in HIV-1 Capsid Protein Assemblies

    SciTech Connect

    Han, Yun; Hou, Guangjin; Suiter, Christopher L.; Ahn, Jinwoo; Byeon, In-Ja L.; Lipton, Andrew S.; Burton, Sarah D.; Hung, Ivan; Gorkov, Peter L.; Gan, Zhehong; Brey, William W.; Rice, David M.; Gronenborn, Angela M.; Polenova, Tatyana E.

    2013-11-27

    Maturation of HIV-1 virus into an infectious virion requires cleavage of the Gag polyprotein into its constituent domains and formation of a conical capsid core that encloses viral RNA and a small complement of proteins for replication. The final step of this process is the cleavage of the SP1 peptide from the CA-SP1 maturation intermediate, which triggers the condensation of the CA protein into a conical capsid. The mechanism of this step, including the conformation of the SP1 peptide in CA-SP1, is under intense debate. In this report, we examine the tubular assemblies of CA and the CA-SP1 maturation intermediate using Magic Angle Spinning NMR spectroscopy. At the magnetic fields of 19.9 T and above, tubular CA and CA-SP1 assemblies yield outstanding-quality 2D and 3D MAS NMR spectra, which are amenable to resonance assignments and detailed structural characterization. Dipolar- and scalar-based correlation experiments unequivocally indicate that SP1 peptide is in a random coil conformation and mobile in the assembled CA-SP1. Analysis of two sequence variants reveals that remarkably, the conformation of SP1 tail, of the functionally important CypA loop, and of the loop preceding helix 8 are sequence dependent and modulated by the residue variations at distal sites. These findings challenge the role of SP1 as a conformational switch in the maturation process and establish sequence-dependent conformational plasticity in CA.

  4. IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform

    PubMed Central

    Hepler, N. Lance; Scheffler, Konrad; Weaver, Steven; Murrell, Ben; Richman, Douglas D.; Burton, Dennis R.; Poignard, Pascal; Smith, Davey M.; Kosakovsky Pond, Sergei L.

    2014-01-01

    Since its identification in 1983, HIV-1 has been the focus of a research effort unprecedented in scope and difficulty, whose ultimate goals — a cure and a vaccine – remain elusive. One of the fundamental challenges in accomplishing these goals is the tremendous genetic variability of the virus, with some genes differing at as many as 40% of nucleotide positions among circulating strains. Because of this, the genetic bases of many viral phenotypes, most notably the susceptibility to neutralization by a particular antibody, are difficult to identify computationally. Drawing upon open-source general-purpose machine learning algorithms and libraries, we have developed a software package IDEPI (IDentify EPItopes) for learning genotype-to-phenotype predictive models from sequences with known phenotypes. IDEPI can apply learned models to classify sequences of unknown phenotypes, and also identify specific sequence features which contribute to a particular phenotype. We demonstrate that IDEPI achieves performance similar to or better than that of previously published approaches on four well-studied problems: finding the epitopes of broadly neutralizing antibodies (bNab), determining coreceptor tropism of the virus, identifying compartment-specific genetic signatures of the virus, and deducing drug-resistance associated mutations. The cross-platform Python source code (released under the GPL 3.0 license), documentation, issue tracking, and a pre-configured virtual machine for IDEPI can be found at https://github.com/veg/idepi. PMID:25254639

  5. Investigation by two-photon fluorescence correlation spectroscopy of the interaction of the nucleocapsid protein of HIV-1 with hairpin loop DNA sequences

    NASA Astrophysics Data System (ADS)

    Mely, Yves; Azoulay, Joel; Beltz, Herve; Clamme, Jean-Pierre; Bernacchi, Serena; Ficheux, Damien; Roques, Bernard P.; Darlix, Jean-Luc

    2004-09-01

    The nucleocapsid protein NCp7 of HIV-1 possesses nucleic acid chaperone properties that are critical for the two strand transfer reactions required during reverse transcription. The first DNA strand transfer relies on the destabilization by NCp7 of double-stranded segments of the transactivation response element, TAR sequence, at the 3' end of the genomic RNA and the complementary sequence cTAR at the 3" terminus of the early product of reverse transcription. To characterize NCp7-mediated nucleic acid destabilization, we investigated by steady-state and time-resolved fluorescence spectroscopy and two photon fluorescence correlation spectroscopy, the interaction of a doubly-labelled cTAR sequence with NCp7. The conformational fluctuations observed in the absence of NCp7 were associated with the rapid opening and closing (fraying) of the double stranded terminal segment of cTAR. NCp7 destabilizes cTAR mainly through a large increase of the opening rate constant. Additionally, the various destabilizing structures (bulges, internal loop, mismatches) spread all over cTAR secondary structure were found to be critical for NCp7 chaperone activity. Taken together, our data enabled us to propose a molecular mechanism for the destabilizing activity of NCp7 on cTAR which is crucial for the formation of the cTAR-TAR complex during the first strand transfer reaction.

  6. Phage randomization in a charybdotoxin scaffold leads to CD4-mimetic recognition motifs that bind HIV-1 envelope through non-aromatic sequences.

    PubMed

    Li, C; Dowd, C S; Zhang, W; Chaiken, I M

    2001-06-01

    Binding of HIV-1 gp120 to T-cell receptor CD4 initiates conformational changes in the viral envelope that trigger viral entry into host cells. Phage epitope randomization of a beta-turn loop of a charybdotoxin-based miniprotein scaffold was used to identify peptides that can bind gp120 and block the gp120-CD4 interaction. We describe here the display of the charybdotoxin scaffold on the filamentous phage fUSE5, its use to construct a beta-turn library, and miniprotein sequences identified through library panning with immobilized Env gp120. Competition enzyme-linked immunosorbent assay (ELISA) identified high-frequency phage selectants for which specific gp120 binding was competed by sCD4. Several of these selectants contain hydrophobic residues in place of the Phe that occurs in the gp120-binding beta-turns of both CD4 and previously identified scorpion toxin CD4 mimetics. One of these selectants, denoted TXM[24GQTL27], contains GQTL in place of the CD4 beta-turn sequence 40QGSF43. TXM[24GQTL27] peptide was prepared using solid-phase chemical synthesis, its binding to gp120 demonstrated by optical biosensor kinetics analysis and its affinity for the CD4 binding site of gp120 confirmed by competition ELISA. The results demonstrate that aromatic-less loop-containing CD4 recognition mimetics can be formed with detectable envelope protein binding within a beta-turn of the charybdotoxin miniprotein scaffold. The results of this work establish a methodology for phage display of a charybdotoxin miniprotein scaffold and point to the potential value of phage-based epitope randomization of this miniprotein for identifying novel CD4 mimetics. The latter are potentially useful in deconvoluting structural determinants of CD4-HIV envelope recognition and possibly in designing antagonists of viral entry. PMID:11437954

  7. Prevalence and Evolution of Low Frequency HIV Drug Resistance Mutations Detected by Ultra Deep Sequencing in Patients Experiencing First Line Antiretroviral Therapy Failure

    PubMed Central

    Recordon-Pinson, Patricia; Reigadas, Sandrine; Bidet, Yannick; Bruyand, Mathias; Bonnet, Fabrice; Lazaro, Estibaliz; Neau, Didier; Fleury, Hervé; Dabis, François; Morlat, Philippe; Masquelier, Bernard

    2014-01-01

    Objectives Clinical relevance of low-frequency HIV-1 variants carrying drug resistance associated mutations (DRMs) is still unclear. We aimed to study the prevalence of low-frequency DRMs, detected by Ultra-Deep Sequencing (UDS) before antiretroviral therapy (ART) and at virological failure (VF), in HIV-1 infected patients experiencing VF on first-line ART. Methods Twenty-nine ART-naive patients followed up in the ANRS-CO3 Aquitaine Cohort, having initiated ART between 2000 and 2009 and experiencing VF (2 plasma viral loads (VL) >500 copies/ml or one VL >1000 copies/ml) were included. Reverse transcriptase and protease DRMs were identified using Sanger sequencing (SS) and UDS at baseline (before ART initiation) and VF. Results Additional low-frequency variants with PI-, NNRTI- and NRTI-DRMs were found by UDS at baseline and VF, significantly increasing the number of detected DRMs by 1.35 fold (p<0.0001) compared to SS. These low-frequency DRMs modified ARV susceptibility predictions to the prescribed treatment for 1 patient at baseline, in whom low-frequency DRM was found at high frequency at VF, and 6 patients at VF. DRMs found at VF were rarely detected as low-frequency DRMs prior to treatment. The rare low-frequency NNRTI- and NRTI-DRMs detected at baseline that correlated with the prescribed treatment were most often found at high-frequency at VF. Conclusion Low frequency DRMs detected before ART initiation and at VF in patients experiencing VF on first-line ART can increase the overall burden of resistance to PI, NRTI and NNRTI. PMID:24475178

  8. Residue energy and mobility in sequence to global structure and dynamics of a HIV-1 protease (1DIFA) by a coarse-grained Monte Carlo simulation

    NASA Astrophysics Data System (ADS)

    Pandey, R. B.; Farmer, B. L.

    2009-01-01

    Energy, mobility, and structural profiles of residues in a specific sequence of human immunodeficiency virus (HIV)-1 protease chain and its global conformation and dynamics are studied by a coarse-grained computer simulation model on a cubic lattice. HIV-1 protease is described by a chain of 99 residues (nodes) in a specific sequence (1DIFA) with N- and C-terminals on the lattice, where empty lattice sites represent an effective solvent medium. Internal structures of the residues are ignored but their specificities are captured via an interaction (ɛij) matrix (residue-residue, residue-solvent) of the coefficient (fɛij) of the Lennard-Jones potential. Simulations are performed for a range of interaction strength (f ) with the solvent-residue interaction describing the quality of the solvent. Snapshots of the protein show considerable changes in the conformation of the protein on varying the interaction. From the mobility and energy profiles of the residues, it is possible to identify the active (and not so active) segments of the protein and consequently their role in proteolysis. Contrary to interaction thermodynamics, the hydrophobic residues possess higher configurational energy and lower mobility while the electrostatic and polar residues are more mobile despite their lower interaction energy. Segments of hydrophobic core residues, crucial for the structural evolution of the protein are identified—some of which are consistent with recent molecular dynamics simulation in context to possible clinical observations. Global energy and radius of gyration of the protein exhibit nonmonotonic dependence on the interaction strength (f) with opposite trends, e.g., rapid transition into globular structure with higher energy. Variations of the rms displacement of the protein and that of a tracer residue, Gly49, with the time steps show how they slow down on increasing the interaction strength.

  9. RFQ development at Los Alamos

    SciTech Connect

    Wangler, T.P.; Crandall, K.R.; Stokes, R.H.

    1982-01-01

    The basic principles of the radio-frequency quadrupole (RFQ) linac are reviewed and a summary of past and present Los Alamos work is presented. Some beam-dynamics effects, important for RFQ design, are discussed. A design example is shown for xenon and a brief discussion of low-frequency RFQ structures is given.

  10. Effects of sequence changes in the HIV-1 gp41 fusion peptide on CCR5 inhibitor resistance

    SciTech Connect

    Anastassopoulou, Cleo G.; Ketas, Thomas J.; Sanders, Rogier W.; Johan Klasse, Per; Moore, John P.

    2012-07-05

    A rare pathway of HIV-1 resistance to small molecule CCR5 inhibitors such as Vicriviroc (VCV) involves changes solely in the gp41 fusion peptide (FP). Here, we show that the G516V change is critical to VCV resistance in PBMC and TZM-bl cells, although it must be accompanied by either M518V or F519I to have a substantial impact. Modeling VCV inhibition data from the two cell types indicated that G516V allows both double mutants to use VCV-CCR5 complexes for entry. The model further identified F519I as an independent determinant of preference for the unoccupied, high-VCV affinity form of CCR5. From inhibitor-free reversion cultures, we also identified a substitution in the inner domain of gp120, T244A, which appears to counter the resistance phenotype created by the FP substitutions. Examining the interplay of these changes will enhance our understanding of Env complex interactions that influence both HIV-1 entry and resistance to CCR5 inhibitors.

  11. Longitudinal Antigenic Sequences and Sites from Intra-Host Evolution (LASSIE) identifies immune-selected HIV variants

    SciTech Connect

    Hraber, Peter; Korber, Bette; Wagh, Kshitij; Giorgi, Elena; Bhattacharya, Tanmoy; Gnanakaran, S.; Lapedes, Alan S.; Learn, Gerald H.; Kreider, Edward F.; Li, Yingying; Shaw, George M.; Hahn, Beatrice H.; Montefiori, David C.; Alam, S. Munir; Bonsignori, Mattia; Moody, M. Anthony; Liao, Hua-Xin; Gao, Feng; Haynes, Barton

    2015-10-21

    Within-host genetic sequencing from samples collected over time provides a dynamic view of how viruses evade host immunity. Immune-driven mutations might stimulate neutralization breadth by selecting antibodies adapted to cycles of immune escape that generate within-subject epitope diversity. Comprehensive identification of immune-escape mutations is experimentally and computationally challenging. With current technology, many more viral sequences can readily be obtained than can be tested for binding and neutralization, making down-selection necessary. Typically, this is done manually, by picking variants that represent different time-points and branches on a phylogenetic tree. Such strategies are likely to miss many relevant mutations and combinations of mutations, and to be redundant for other mutations. Longitudinal Antigenic Sequences and Sites from Intrahost Evolution (LASSIE) uses transmitted founder loss to identify virus “hot-spots” under putative immune selection and chooses sequences that represent recurrent mutations in selected sites. LASSIE favors earliest sequences in which mutations arise. Here, with well-characterized longitudinal Env sequences, we confirmed selected sites were concentrated in antibody contacts and selected sequences represented diverse antigenic phenotypes. Finally, practical applications include rapidly identifying immune targets under selective pressure within a subject, selecting minimal sets of reagents for immunological assays that characterize evolving antibody responses, and for immunogens in polyvalent “cocktail” vaccines.

  12. Longitudinal Antigenic Sequences and Sites from Intra-Host Evolution (LASSIE) Identifies Immune-Selected HIV Variants

    PubMed Central

    Hraber, Peter; Korber, Bette; Wagh, Kshitij; Giorgi, Elena E.; Bhattacharya, Tanmoy; Gnanakaran, S.; Lapedes, Alan S.; Learn, Gerald H.; Kreider, Edward F.; Li, Yingying; Shaw, George M.; Hahn, Beatrice H.; Montefiori, David C.; Alam, S. Munir; Bonsignori, Mattia; Moody, M. Anthony; Liao, Hua-Xin; Gao, Feng; Haynes, Barton F.

    2015-01-01

    Within-host genetic sequencing from samples collected over time provides a dynamic view of how viruses evade host immunity. Immune-driven mutations might stimulate neutralization breadth by selecting antibodies adapted to cycles of immune escape that generate within-subject epitope diversity. Comprehensive identification of immune-escape mutations is experimentally and computationally challenging. With current technology, many more viral sequences can readily be obtained than can be tested for binding and neutralization, making down-selection necessary. Typically, this is done manually, by picking variants that represent different time-points and branches on a phylogenetic tree. Such strategies are likely to miss many relevant mutations and combinations of mutations, and to be redundant for other mutations. Longitudinal Antigenic Sequences and Sites from Intrahost Evolution (LASSIE) uses transmitted founder loss to identify virus “hot-spots” under putative immune selection and chooses sequences that represent recurrent mutations in selected sites. LASSIE favors earliest sequences in which mutations arise. With well-characterized longitudinal Env sequences, we confirmed selected sites were concentrated in antibody contacts and selected sequences represented diverse antigenic phenotypes. Practical applications include rapidly identifying immune targets under selective pressure within a subject, selecting minimal sets of reagents for immunological assays that characterize evolving antibody responses, and for immunogens in polyvalent “cocktail” vaccines. PMID:26506369

  13. Longitudinal Antigenic Sequences and Sites from Intra-Host Evolution (LASSIE) identifies immune-selected HIV variants

    DOE PAGESBeta

    Hraber, Peter; Korber, Bette; Wagh, Kshitij; Giorgi, Elena; Bhattacharya, Tanmoy; Gnanakaran, S.; Lapedes, Alan S.; Learn, Gerald H.; Kreider, Edward F.; Li, Yingying; et al

    2015-10-21

    Within-host genetic sequencing from samples collected over time provides a dynamic view of how viruses evade host immunity. Immune-driven mutations might stimulate neutralization breadth by selecting antibodies adapted to cycles of immune escape that generate within-subject epitope diversity. Comprehensive identification of immune-escape mutations is experimentally and computationally challenging. With current technology, many more viral sequences can readily be obtained than can be tested for binding and neutralization, making down-selection necessary. Typically, this is done manually, by picking variants that represent different time-points and branches on a phylogenetic tree. Such strategies are likely to miss many relevant mutations and combinations ofmore » mutations, and to be redundant for other mutations. Longitudinal Antigenic Sequences and Sites from Intrahost Evolution (LASSIE) uses transmitted founder loss to identify virus “hot-spots” under putative immune selection and chooses sequences that represent recurrent mutations in selected sites. LASSIE favors earliest sequences in which mutations arise. Here, with well-characterized longitudinal Env sequences, we confirmed selected sites were concentrated in antibody contacts and selected sequences represented diverse antigenic phenotypes. Finally, practical applications include rapidly identifying immune targets under selective pressure within a subject, selecting minimal sets of reagents for immunological assays that characterize evolving antibody responses, and for immunogens in polyvalent “cocktail” vaccines.« less

  14. Drug Resistance Mutations in HIV pol Sequences from Argentinean Patients Under Antiretroviral Treatment: Subtype, Gender, and Age Issues

    PubMed Central

    Moretti, Franco; Calvo, Andrea Y.; Dilernia, Darío A.; Manrique, Julieta M.; Gómez-Carrillo, Manuel; Salomón, Horacio

    2012-01-01

    Abstract We studied drug resistance mutations (DRMs) in 2623 pol sequences. Out of 94,828 amino acid substitutions that were detected, 8749 corresponded to nucleoside reverse transcriptase inhibitor (NRTI), 3765 to nonnucleoside reverse transcriptase inhibitor (NNRTI), and 7141 to protease inhibitor (PI) resistance-associated mutations. The most common DRMs were L10I, I54V, L90M, V82A, A71V, L10V, M46I, M184V, M41L, T215Y, D67N, L210W, K70R, N348I, V118I, K103N, Y181C, G190A, K101E, V108I, L100I, V90I, K101Q, and A98G. As expected, DRMs frequencies depended on viral genotype. The amounts of NRTI and PI resistance mutations among B and BF sequences from children were higher than among sequences from adults. The frequencies of PI and NRTI resistance mutations among B and BF sequences from adult men were higher than among sequences from women. Some of these observations can be explained in light of the available epidemiological information, but some cannot, indicating that further studies are needed to understand the antiretroviral resistance epidemics in Argentina. PMID:21936717

  15. RFQ development at Los Alamos

    SciTech Connect

    Armstrong, D.D.; Cornelius, W.D.; Purser, F.O.; Jameson, R.A.; Wangler, T.P.

    1984-01-01

    We report recent progress on the two radio-frequency quadrupole (RFQ) structures being developed at Los Alamos. First, we report on the second 425-MHz RFQ for H/sup -/ acceleration, which is being built in a research effort to understand and further develop the RFQ. Second, we discuss progress on the 80-MHz cw RFQ for deuterons, which is being built for the Fusion Materials Irradiation Test (FMIT) facility.

  16. Deep sequencing analysis of HIV-1 reverse transcriptase at baseline and time of failure in patients receiving rilpivirine in the phase III studies ECHO and THRIVE.

    PubMed

    Van Eygen, Veerle; Thys, Kim; Van Hove, Carl; Rimsky, Laurence T; De Meyer, Sandra; Aerssens, Jeroen; Picchio, Gaston; Vingerhoets, Johan

    2016-05-01

    Minority variants (1.0-25.0%) were evaluated by deep sequencing (DS) at baseline and virological failure (VF) in a selection of antiretroviral treatment-naïve, HIV-1-infected patients from the rilpivirine ECHO/THRIVE phase III studies. Linkage between frequently emerging resistance-associated mutations (RAMs) was determined. DS (llIumina®) and population sequencing (PS) results were available at baseline for 47 VFs and time of failure for 48 VFs; and at baseline for 49 responders matched for baseline characteristics. Minority mutations were accurately detected at frequencies down to 1.2% of the HIV-1 quasispecies. No baseline minority rilpivirine RAMs were detected in VFs; one responder carried 1.9% F227C. Baseline minority mutations associated with resistance to other non-nucleoside reverse transcriptase inhibitors (NNRTIs) were detected in 8/47 VFs (17.0%) and 7/49 responders (14.3%). Baseline minority nucleoside/nucleotide reverse transcriptase inhibitor (NRTI) RAMs M184V and L210W were each detected in one VF (none in responders). At failure, two patients without NNRTI RAMs by PS carried minority rilpivirine RAMs K101E and/or E138K; and five additional patients carried other minority NNRTI RAMs V90I, V106I, V179I, V189I, and Y188H. Overall at failure, minority NNRTI RAMs and NRTI RAMs were found in 29/48 (60.4%) and 16/48 VFs (33.3%), respectively. Linkage analysis showed that E138K and K101E were usually not observed on the same viral genome. In conclusion, baseline minority rilpivirine RAMs and other NNRTI/NRTI RAMs were uncommon in the rilpivirine arm of the ECHO and THRIVE studies. DS at failure showed emerging NNRTI resistant minority variants in seven rilpivirine VFs who had no detectable NNRTI RAMs by PS. J. Med. Virol. 88:798-806, 2016. © 2015 Wiley Periodicals, Inc. PMID:26412111

  17. A zinc(II)-based two-dimensional MOF for sensitive and selective sensing of HIV-1 ds-DNA sequences.

    PubMed

    Zhao, Hai-Qing; Qiu, Gui-Hua; Liang, Zhen; Li, Min-Min; Sun, Bin; Qin, Liang; Yang, Shui-Ping; Chen, Wen-Hua; Chen, Jin-Xiang

    2016-05-30

    Coordination reaction of a known three-dimensional (3D) polymer precursor {Na3[Na9(Cbdcp)6(H2O)18]}n (A, Cbdcp = N-(4-carboxybenzyl)-(3,5-dicarboxyl)pyridinium) with Zn(NO3)2·6H2O in H2O or H2O/DMF at 100 °C and in the presence of aspirin, 5-fluorouracil (5-FU) as modulators, trans-1,2-bis(4-pyridyl)ethylene (bpe) or 1,2-bis(4-pyridyl)ethane (bpea) as ancillary ligands afforded six novel Zn(II)-based metal-organic frameworks (MOFs), that is, {[Zn(Cbdcp)(H2O)3]·H2O}n (1, 1D zigzag chain), {[Zn(HCbdcp)2]·H2O}n (2, 2D sheet), {[Zn(Cbdcp)(bpe)1/2]·2H2O}n (3, 3D polymer), {[Zn(Cbdcp)(bpe)1/2]·2H2O}n (4, 2D network), {[Zn(Cbdcp)(bpea)1/2]·2H2O}n (5, 3D polymer) and {[Zn(Cbdcp)(bpea)1/2]·2H2O}n (6, 2D network). Among them, compound 2 contains aromatic rings, positively charged pyridinium, Zn(2+) cation centers and carboxylic acid groups lined up on the 2D sheet structure with a certain extended surface exposure. The unique structure of 2 facilitates effective association with carboxyfluorescein (FAM) labeled probe single stranded DNA (probe ss-DNA, delineates as P-DNA) to yield a P-DNA@2 system, and leads to fluorescence quenching of FAM via a photoinduced electron transfer process. The P-DNA@2 system is effective and reliable for the detection of human immunodeficiency virus 1 ds-DNA (HIV ds-DNA) sequences and capable of distinguishing complementary HIV ds-DNA from mismatched target sequences with the detection limit as low as 10 pM (S/N = 3). PMID:27154832

  18. Simultaneous recognition of HIV-1 TAR RNA bulge and loop sequences by cyclic peptide mimics of Tat protein

    SciTech Connect

    Davidson, Amy; Leeper, Thomas C.; Athanassiou, Zafiria; Patora-Komisarska, Krystyna; Karn, Jonathan; Robinson, John A.; Varani, Gabriele

    2009-07-21

    The interaction of the HIV-1 transactivator protein Tat with its transactivation response (TAR) RNA is an essential step in viral replication and therefore an attractive target for developing antivirals with new mechanisms of action. Numerous compounds that bind to the 3-nt bulge responsible for binding Tat have been identified in the past, but none of these molecules had sufficient potency to warrant pharmaceutical development. We have discovered conformationally-constrained cyclic peptide mimetics of Tat that are specific nM inhibitors of the Tat-TAR interaction by using a structure-based approach. The lead peptides are nearly as active as the antiviral drug nevirapine against a variety of clinical isolates in human lymphocytes. The NMR structure of a peptide–RNA complex reveals that these molecules interfere with the recruitment to TAR of both Tat and the essential cellular cofactor transcription elongation factor-b (P-TEFb) by binding simultaneously at the RNA bulge and apical loop, forming an unusually deep pocket. This structure illustrates additional principles in RNA recognition: RNA-binding molecules can achieve specificity by interacting simultaneously with multiple secondary structure elements and by inducing the formation of deep binding pockets in their targets. It also provides insight into the P-TEFb binding site and a rational basis for optimizing the promising antiviral activity observed for these cyclic peptides.

  19. Long-range effects of tag sequence on marginally stabilized structure in HIV-1 p24 capsid protein monitored using NMR.

    PubMed

    Okazaki, Honoka; Kaneko, Chie; Hirahara, Miyuki; Watanabe, Satoru; Tochio, Naoya; Kigawa, Takanori; Nishimura, Chiaki

    2014-09-01

    N-terminal domain of HIV-1 p24 capsid protein is a globular fold composed of seven helices and two β-strands with a flexible structure including the α4-5 loop and both N- and C-terminal ends. However, the protein shows a high tendency (48%) for an intrinsically disordered structure based on the PONDR VL-XT prediction from the primary sequence. To assess the possibility of marginally stabilized structure under physiological conditions, the N-terminal domain of p24 was destabilized by the addition of an artificial flexible tag to either N- or C-terminal ends, and it was analyzed using T1, T2, hetero-nuclear NOE, and amide-proton exchange experiments. When the C-terminal tag (12 residues) was attached, the regions of the α3-4 loop and helix 6 as well as the α4-5 loop attained the flexible structures. Furthermore, in the protein containing the N-terminal tag (27 residues), helix 4 in addition to the above-mentioned area including α3-4 and α4-5 loops as well as helix 6 exhibited highly disordered structures. Thus, the long-range effects of the existence of tag sequence was observed in the stepwise manner of the appearance of disordered structures (step 1: α4-5 loop, step 2: α3-4 loop and helix 6, and step 3: helix 4). Furthermore, the disordered regions in tagged proteins were consistent with the PONDR VL-XT disordered prediction. The dynamic structure located in the middle part (α3-4 loop to helix 6) of the protein shown in this study may be related to the assembly of the viral particle. PMID:24960591

  20. Los Alamos Science: Number 16

    SciTech Connect

    Cooper, N.G.

    1988-01-01

    It was an unusually stimulating day and a half at Los Alamos when two Nobel Laureates in physiology, a leading paleontologist, and a leading bio-astrophysicist came together to discuss ''Unsolved Problems in the Science of Life,'' the topic of the second in a series of special meetings sponsored by the Fellows of the Laboratory. Just like the first one on ''Creativity in Science,'' this colloquium took us into a broader arena of ideas and viewpoints than is our usual daily fare. To contemplate the evolution and mysteries of intelligent life from the speakers' diverse points of view at one time, in one place was indeed a rare experience.

  1. Comparison of 454 Ultra-Deep Sequencing and Allele-Specific Real-Time PCR with Regard to the Detection of Emerging Drug-Resistant Minor HIV-1 Variants after Antiretroviral Prophylaxis for Vertical Transmission

    PubMed Central

    Hauser, Andrea; Kuecherer, Claudia; Kunz, Andrea; Dabrowski, Piotr Wojtek; Radonić, Aleksandar; Nitsche, Andreas; Theuring, Stefanie; Bannert, Norbert; Sewangi, Julius; Mbezi, Paulina; Dugange, Festo; Harms, Gundel; Meixenberger, Karolin

    2015-01-01

    Background Pregnant HIV-infected women were screened for the development of HIV-1 drug resistance after implementation of a triple-antiretroviral transmission prophylaxis as recommended by the WHO in 2006. The study offered the opportunity to compare amplicon-based 454 ultra-deep sequencing (UDS) and allele-specific real-time PCR (ASPCR) for the detection of drug-resistant minor variants in the HIV-1 reverse transcriptase (RT). Methods Plasma samples from 34 Tanzanian women were previously analysed by ASPCR for key resistance mutations in the viral RT selected by AZT, 3TC, and NVP (K70R, K103N, Y181C, M184V, T215Y/F). In this study, the RT region of the same samples was investigated by amplicon-based UDS for resistance mutations using the 454 GS FLX System. Results Drug-resistant HIV-variants were identified in 69% (20/29) of women by UDS and in 45% (13/29) by ASPCR. The absolute number of resistance mutations identified by UDS was twice that identified by ASPCR (45 vs 24). By UDS 14 of 24 ASPCR-detected resistance mutations were identified at the same position. The overall concordance between UDS and ASPCR was 61.0% (25/41). The proportions of variants quantified by UDS were approximately 2–3 times lower than by ASPCR. Amplicon generation from samples with viral loads below 20,000 copies/ml failed more frequently by UDS compared to ASPCR (limit of detection = 650 copies/ml), resulting in missing or insufficient sequence coverage. Conclusions Both methods can provide useful information about drug-resistant minor HIV-1 variants. ASPCR has a higher sensitivity than UDS, but is restricted to single resistance mutations. In contrast, UDS is limited by its requirement for high viral loads to achieve sufficient sequence coverage, but the sequence information reveals the complete resistance patterns within the genomic region analysed. Improvements to the UDS limit of detection are in progress, and UDS could then facilitate monitoring of drug-resistant minor variants in

  2. Genital HIV-1 RNA Quantity Predicts Risk of Heterosexual HIV-1 Transmission

    PubMed Central

    Baeten, Jared M.; Kahle, Erin; Lingappa, Jairam R.; Coombs, Robert W.; Delany-Moretlwe, Sinead; Nakku-Joloba, Edith; Mugo, Nelly R.; Wald, Anna; Corey, Lawrence; Donnell, Deborah; Campbell, Mary S.; Mullins, James I.; Celum, Connie

    2011-01-01

    High plasma HIV-1 RNA concentrations are associated with an increased risk of HIV-1 transmission. Although plasma and genital HIV-1 RNA concentrations are correlated, no study has evaluated the relationship between genital HIV-1 RNA and the risk of heterosexual HIV-1 transmission. In a prospective study of 2521 African HIV-1 serodiscordant couples, we assessed genital HIV-1 RNA quantity and HIV-1 transmission risk. HIV-1 transmission linkage was established within the partnership by viral sequence analysis. We tested endocervical samples from 1805 women, including 46 who transmitted HIV-1 to their partner, and semen samples from 716 men, including 32 who transmitted HIV-1 to their partner. Genital and plasma HIV-1 concentrations were correlated: For endocervical swabs, Spearman’s rank correlation coefficient rho was 0.56 (p<0.001), and for semen rho was 0.55 (p<0.001). Each 1 log10 increase in genital HIV-1 RNA was associated with a 2.20-fold (for endocervical swabs, 95% confidence interval 1.60–3.04, p<0.001) and a 1.79-fold (for semen, 95% confidence interval 1.30–2.47, p<0.001) increased risk of HIV-1 transmission. Genital HIV-1 RNA independently predicted HIV-1 transmission risk after adjusting for plasma HIV-1 quantity (hazard ratio 1.67 for endocervical swabs and 1.68 for semen). Seven female-to-male and four male-to-female HIV-1 transmissions (incidence <1% per year) occurred from persons with undetectable genital HIV-1 RNA, but in all eleven plasma HIV-1 RNA was detected. Thus, higher genital HIV-1 RNA concentrations are associated with greater risk of heterosexual HIV-1 transmission, and this effect was independent of plasma HIV-1 concentrations. These data suggest that HIV-1 RNA in genital secretions could be used as a marker of HIV-1 sexual transmission risk. PMID:21471433

  3. Analysis of sequences of hepatitis C virus NS5A genotype 1 in HIV-coinfected patients with a null response to nitazoxanide or peg-interferon plus ribavirin.

    PubMed

    Sede, M; Laufer, N; Ojeda, D; Gun, A; Cahn, P; Quarleri, J

    2013-09-01

    Even though new drugs have been approved for treatment of hepatitis C virus (HCV) infection, the risk of drug-drug interactions and concern about overlapping toxicities has hindered the development of studies in HIV/HCV-coinfected individuals. Traditional treatment with pegylated interferon plus ribavirin (peg-IFN + RBV) is very expensive and has a low rate of sustained virological response in coinfected patients, especially if they are infected with HCV genotype 1. Nitazoxanide (NTZ) is a drug that is being evaluated for the treatment of chronic HCV infection, both in HCV-monoinfected and HIV/HCV-coinfected patients. Understanding the NTZ resistance mechanism could allow the development of resistance to be minimized and would expand the treatment options, mainly in special populations such as HIV/HCV-coinfected patients. Similarly to IFN, NTZ increases the activity of the cellular protein kinase activated by double-stranded RNA (PKR), a key kinase in the innate antiviral response. In order to elucidate whether sequence heterogeneity in the PKR-binding domain of HCV NS5A genotype 1 could influence the antiviral activity of either NTZ monotherapy or peg-IFN + RBV, baseline and end-of-therapy plasma samples from two groups of eleven non-responder HIV/HCV-coinfected patients that had received NTZ or peg-IFN + RBV were studied. Most of the HCV NS5A sequences examined at the end of therapy did not change from the baseline, even after 30 days course of antiviral therapy. An extensive comparison of HCV NS5A genotype 1 and 4 sequences from the database with reported IFN therapy outcome was performed in order to infer their phylogenetic relationships. The HCV genotype 1 NS5A nucleotide sequences from therapy-non-responder patients were intermingled amongst those from the database, irrespective of their IFN-therapy outcome. When comparing NS5A-PKRBD amino acid sequences, significant differences were observed in genotype 4, but not in genotype 1 (p < 0.0001 and p

  4. HIV Molecular Immunology 2014

    SciTech Connect

    Yusim, Karina; Korber, Bette Tina Marie; Barouch, Dan; Koup, Richard; de Boer, Rob; Moore, John P.; Brander, Christian; Haynes, Barton F.; Walker, Bruce D.

    2015-02-03

    HIV Molecular Immunology is a companion volume to HIV Sequence Compendium. This publication, the 2014 edition, is the PDF version of the web-based HIV Immunology Database (http://www.hiv.lanl.gov/content/immunology/). The web interface for this relational database has many search options, as well as interactive tools to help immunologists design reagents and interpret their results. In the HIV Immunology Database, HIV-specific B-cell and T-cell responses are summarized and annotated. Immunological responses are divided into three parts, CTL, T helper, and antibody. Within these parts, defined epitopes are organized by protein and binding sites within each protein, moving from left to right through the coding regions spanning the HIV genome. We include human responses to natural HIV infections, as well as vaccine studies in a range of animal models and human trials. Responses that are not specifically defined, such as responses to whole proteins or monoclonal antibody responses to discontinuous epitopes, are summarized at the end of each protein section. Studies describing general HIV responses to the virus, but not to any specific protein, are included at the end of each part. The annotation includes information such as crossreactivity, escape mutations, antibody sequence, TCR usage, functional domains that overlap with an epitope, immune response associations with rates of progression and therapy, and how specific epitopes were experimentally defined. Basic information such as HLA specificities for T-cell epitopes, isotypes of monoclonal antibodies, and epitope sequences are included whenever possible. All studies that we can find that incorporate the use of a specific monoclonal antibody are included in the entry for that antibody. A single T-cell epitope can have multiple entries, generally one entry per study. Finally, maps of all defined linear epitopes relative to the HXB2 reference proteins are provided.

  5. HIV Symptoms

    MedlinePlus

    ... Submit Home > HIV/AIDS > What is HIV/AIDS? HIV/AIDS This information in Spanish ( en español ) HIV symptoms Photo courtesy of AIDS.gov More information ... and brain Return to top More information on HIV symptoms Explore other publications and websites Basic Information ...

  6. Los Alamos Science: The Human Genome Project. Number 20, 1992

    DOE R&D Accomplishments Database

    Cooper, N. G.; Shea, N. eds.

    1992-01-01

    This document provides a broad overview of the Human Genome Project, with particular emphasis on work being done at Los Alamos. It tries to emphasize the scientific aspects of the project, compared to the more speculative information presented in the popular press. There is a brief introduction to modern genetics, including a review of classic work. There is a broad overview of the Genome Project, describing what the project is, what are some of its major five-year goals, what are major technological challenges ahead of the project, and what can the field of biology, as well as society expect to see as benefits from this project. Specific results on the efforts directed at mapping chromosomes 16 and 5 are discussed. A brief introduction to DNA libraries is presented, bearing in mind that Los Alamos has housed such libraries for many years prior to the Genome Project. Information on efforts to do applied computational work related to the project are discussed, as well as experimental efforts to do rapid DNA sequencing by means of single-molecule detection using applied spectroscopic methods. The article introduces the Los Alamos staff which are working on the Genome Project, and concludes with brief discussions on ethical, legal, and social implications of this work; a brief glimpse of genetics as it may be practiced in the next century; and a glossary of relevant terms.

  7. Los Alamos Science: The Human Genome Project. Number 20, 1992

    SciTech Connect

    Cooper, N G; Shea, N

    1992-01-01

    This article provides a broad overview of the Human Genome Project, with particular emphasis on work being done at Los Alamos. It tries to emphasize the scientific aspects of the project, compared to the more speculative information presented in the popular press. There is a brief introduction to modern genetics, including a review of classic work. There is a broad overview of the Genome Project, describing what the project is, what are some of its major five-year goals, what are major technological challenges ahead of the project, and what can the field of biology, as well as society expect to see as benefits from this project. Specific results on the efforts directed at mapping chromosomes 16 and 5 are discussed. A brief introduction to DNA libraries is presented, bearing in mind that Los Alamos has housed such libraries for many years prior to the Genome Project. Information on efforts to do applied computational work related to the project are discussed, as well as experimental efforts to do rapid DNA sequencing by means of single-molecule detection using applied spectroscopic methods. The article introduces the Los Alamos staff which are working on the Genome Project, and concludes with brief discussions on ethical, legal, and social implications of this work; a brief glimpse of genetics as it may be practiced in the next century; and a glossary of relevant terms.

  8. HIV infections in otolaryngology

    PubMed Central

    Rzewnicki, Ireneusz; Olszewska, Ewa; Rogowska-Szadkowska, Dorota

    2012-01-01

    Summary HIV (human immunodeficiency virus) infection may produce no clinical symptoms for 10 years on average. However, after many years of infection most people develop symptoms that indicate progression of the disease. There are no regular characteristic symptoms or early stage, and no logical sequence of AIDS indicator disorders has been observed. People who are not aware of the infection are referred to physicians of various specializations, including otolaryngologists. It is on their knowledge about HIV infections, among other factors, that early diagnosis of the disease depends. Appropriate and quick introduction of anti-retroviral drugs may let a person with HIV live decades longer. PMID:22367140

  9. Multilocus Sequence Typing of Serially Collected Isolates of Cryptococcus from HIV-Infected Patients in South Africa

    PubMed Central

    Van Wyk, Marelize; Govender, Nelesh P.; Litvintseva, Anastasia P.

    2014-01-01

    Patients with cryptococcal meningitis in sub-Saharan Africa frequently relapse following treatment. The natural history and etiology of these recurrent episodes warrant investigation. Here, we used multilocus sequence typing (MLST) to compare the molecular genotypes of strains of Cryptococcus neoformans and Cryptococcus gattii isolated from serial episodes of cryptococcal meningitis that were separated by at least 110 days. The most common MLST genotypes among the isolates were the dominant global clinical genotypes (M5 and M4) of molecular type VNI, as well as the VNI genotypes apparently restricted to southern Africa. In addition, there was considerable genetic diversity among these South African isolates, as 15% of the patients had unique genotypes. Eleven percent of the patients were reinfected with a genetically different strain following their initial diagnosis and treatment. However, the majority of serial episodes (89%) were caused by strains with the same genotype as the original strain. These results indicate that serial episodes of cryptococcosis in South Africa are frequently associated with persistence or relapse of the original infection. Using a reference broth microdilution method, we found that the serial isolates of 11% of the patients infected with strains of C. neoformans var. grubii with identical genotypes exhibited ≥4-fold increases in the MICs to fluconazole. Therefore, these recurrent episodes may have been precipitated by inadequate induction or consolidation of antifungal treatment and occasionally may have been due to increased resistance to fluconazole, which may have developed during the chronic infection. PMID:24648562

  10. Sequence similarity between the erythrocyte binding domain 1 of the Plasmodium vivax Duffy binding protein and the V3 loop of HIV-1 strain MN reveals binding residues for the Duffy Antigen Receptor for Chemokines

    PubMed Central

    2011-01-01

    Background The surface glycoprotein (SU, gp120) of the human immunodeficiency virus (HIV) must bind to a chemokine receptor, CCR5 or CXCR4, to invade CD4+ cells. Plasmodium vivax uses the Duffy Binding Protein (DBP) to bind the Duffy Antigen Receptor for Chemokines (DARC) and invade reticulocytes. Results Variable loop 3 (V3) of HIV-1 SU and domain 1 of the Plasmodium vivax DBP share a sequence similarity. The site of amino acid sequence similarity was necessary, but not sufficient, for DARC binding and contained a consensus heparin binding site essential for DARC binding. Both HIV-1 and P. vivax can be blocked from binding to their chemokine receptors by the chemokine, RANTES and its analog AOP-RANTES. Site directed mutagenesis of the heparin binding motif in members of the DBP family, the P. knowlesi alpha, beta and gamma proteins abrogated their binding to erythrocytes. Positively charged residues within domain 1 are required for binding of P. vivax and P. knowlesi erythrocyte binding proteins. Conclusion A heparin binding site motif in members of the DBP family may form part of a conserved erythrocyte receptor binding pocket. PMID:21281498

  11. Molecular cloning and analysis of functional envelope genes from human immunodeficiency virus type 1 sequence subtypes A through G. The WHO and NIAID Networks for HIV Isolation and Characterization.

    PubMed Central

    Gao, F; Morrison, S G; Robertson, D L; Thornton, C L; Craig, S; Karlsson, G; Sodroski, J; Morgado, M; Galvao-Castro, B; von Briesen, H

    1996-01-01

    Present knowledge of human immunodeficiency virus type 1 (HIV-1) envelope immunobiology has been derived almost exclusively from analyses of subtype B viruses, yet such viruses represent only a minority of strains currently spreading worldwide. To generate a more representative panel of genetically diverse envelope genes, we PCR amplified, cloned, and sequenced complete gp160 coding regions of 35 primary (peripheral blood mononuclear cell-propagated) HIV-1 isolates collected at major epicenters of the current AIDS pandemic. Analysis of their deduced amino acid sequences revealed several important differences from prototypic subtype B strains, including changes in the number and distribution of cysteine residues, substantial length differences in hypervariable regions, and premature truncations in the gp41 domain. Moreover, transiently expressed glycoprotein precursor molecules varied considerably in both size and carbohydrate content. Phylogenetic analyses of full-length env sequences indicated that the panel included members of all major sequence subtypes of HIV-1 group M (clades A to G), as well as an intersubtype recombinant (F/B) from an infected individual in Brazil. In addition, all subtype E and three subtype G viruses initially classified on the basis of partial env sequences were found to cluster in subtype A in the 3' half of their gp41 coding region, suggesting that they are also recombinant. The biological activity of PCR-derived env genes was examined in a single-round virus infectivity assay. This analysis identified 20 clones, including 1 from each subtype (or recombinant), which expressed fully functional envelope glycoproteins. One of these, derived from a patient with rapid CD4 cell decline, contained an amino acid substitution in a highly conserved endocytosis signal (Y721C), as mediated virus entry with very poor efficiency, although they did not contain sequence changes predicted to alter protein function. These results indicate that the env

  12. HIV Prevention

    MedlinePlus

    ... to treat HIV infection (called antiretroviral therapy, or ART) the right way, every day and his or ... way, every day, the medicine to treat HIV (ART) reduces the amount of HIV (called “viral ...

  13. Los Alamos PC estimating system

    SciTech Connect

    Stutz, R.A.; Lemon, G.D.

    1987-01-01

    The Los Alamos Cost Estimating System (QUEST) is being converted to run on IBM personal computers. This very extensive estimating system is capable of supporting cost estimators from many different and varied fields. QUEST does not dictate any fixed method for estimating. QUEST supports many styles and levels of detail estimating. QUEST can be used with or without data bases. This system allows the estimator to provide reports based on levels of detail defined by combining work breakdown structures. QUEST provides a set of tools for doing any type of estimate without forcing the estimator to use any given method. The level of detail in the estimate can be mixed based on the amount of information known about different parts of the project. The system can support many different data bases simultaneously. Estimators can modify any cost in any data base.

  14. Study of antibody repertoires to the CD4 binding site of gp120 of a Chinese HIV-1-infected elite neutralizer, using 454 sequencing and single-cell sorting.

    PubMed

    Li, Dan; Wang, Zheng; Ren, Li; Zhang, Jing; Feng, Guangda; Hong, Kunxue; Hao, Yanling; Qi, Zhi; Liang, Hua; Shao, Yiming

    2016-04-01

    Broadly neutralizing antibodies (NAbs) against the CD4 binding site of HIV gp120 (CD4bs) have provided important information for vaccine design. In this study, we combined deep sequencing and single memory B cell sorting to isolate CD4bs-directed NAbs from a Chinese HIV-1-infected elite neutralizer. We first performed 454 pyrosequencing to capture the IGHV1, IGKV, and IGLV germline gene families. IGHV1-2*02, the heavy chain germline V gene (VH) of the CD4bs-directed bNAb VRC01, was found to have a relatively low somatic mutation rate. When an identity/divergence plot was used to interrogate the 454 sequencing data, no VRC01-like sequences were found within the dataset. We next used a pair of CD4bs-specific probes (RSC3/ΔRSC3) to sort the B cells from this Chinese donor and identified a CD4bs-directed Ab that showed limited neutralization capability. Interestingly, the VH gene of this weak NAb belongs to the IGHV5-51 lineage, with a somatic mutation rate of 7.99 %. Our study thus demonstrates that CD4bs-directed NAbs can be produced by rearrangement from other VH genes, such as IGHV5-51 in this donor, rather than IGHV1-2*02. The 454 sequencing data and NAb obtained from this study will provide useful insights into the CD4bs-directed B-cell response during HIV-1 infection as well as the diversity of neutralizing antibodies. PMID:26671829

  15. HIV-1 nucleocapsid protein activates transient melting of least stable parts of the secondary structure of TAR and its complementary sequence.

    PubMed

    Bernacchi, Serena; Stoylov, Stoyl; Piémont, Etienne; Ficheux, Damien; Roques, Bernard P; Darlix, Jean Luc; Mély, Yves

    2002-03-29

    The nucleocapsid protein NCp7 of HIV-1 possesses a nucleic acid chaperone activity that is critical in minus and plus strand transfer during reverse transcription. The minus strand transfer notably relies on the ability of NCp7 to destabilize the stable stem with five contiguous, double-stranded segments of both the TAR sequence at the 3' end of the viral genome and the complementary sequence, cTAR, in minus strong-stop DNA. In order to examine the nature and the extent of NCp7 destabilizing activity, we investigated, by absorbance and fluorescence spectroscopy, the interaction of TAR and cTAR with a (12-55)NCp7 peptide containing the zinc-finger motifs but lacking the ability to aggregate the oligonucleotides. The absorbance changes in the UV band of cTAR show that seven to eight base-pairs, on average, are melted per oligonucleotide at a ratio of one peptide to 7.5 nucleotides. In contrast, the melting of TAR does not exceed an average of one base-pair per oligonucleotide. This may be linked to the greater stability of TAR, since a strong correlation between NCp7 destabilizing effect and oligonucleotide stability was observed. The effect of (12-55)NCp7 on the stem terminus was investigated by using a cTAR molecule doubly labeled at the 3' and 5' ends by a donor/acceptor couple. In the absence of the peptide, about 80 % of the oligonucleotides are in a dark non-fluorescent state, having a close proximity of the two dyes. The remaining 20 % are distributed between three fluorescent species, having either the terminal segment, the two terminal segments or all segments of the stem melted. This is in line with a fraying mechanism wherein the stem terminus fluctuates rapidly between open and closed states. Addition of (12-55)NCp7 shifts the equilibrium toward the open species, suggesting that NC enhances fraying of the stem terminus. Taken together, our data suggest that NCp7 activates the transient opening of base-pairs in the least stable parts of the stem. Also

  16. The sequence of the CA-SP1 junction accounts for the differential sensitivity of HIV-1 and SIV to the small molecule maturation inhibitor 3-O-{3',3'-dimethylsuccinyl}-betulinic acid

    PubMed Central

    Zhou, Jing; Chen, Chin Ho; Aiken, Christopher

    2004-01-01

    Background Despite the effectiveness of currently available antiretroviral therapies in the treatment of HIV-1 infection, a continuing need exists for novel compounds that can be used in combination with existing drugs to slow the emergence of drug-resistant viruses. We previously reported that the small molecule 3-O-{3',3'-dimethylsuccinyl}-betulinic acid (DSB) specifically inhibits HIV-1 replication by delaying the processing of the CA-SP1 junction in Pr55Gag. By contrast, SIVmac239 replicates efficiently in the presence of high concentrations of DSB. To determine whether sequence differences in the CA-SP1 junction can fully account for the differential sensitivity of HIV-1 and SIV to DSB, we engineered mutations in this region of two viruses and tested their sensitivity to DSB in replication assays using activated human primary CD4+ T cells. Results Substitution of the P2 and P1 residues of HIV-1 by the corresponding amino acids of SIV resulted in strong resistance to DSB, but the mutant virus replicated with reduced efficiency. Conversely, replication of an SIV mutant containing three amino acid substitutions in the CA-SP1 cleavage site was highly sensitive to DSB, and the mutations resulted in delayed cleavage of the CA-SP1 junction in the presence of the drug. Conclusions These results demonstrate that the CA-SP1 junction in Pr55Gag represents the primary viral target of DSB. They further suggest that the therapeutic application of DSB will be accompanied by emergence of mutant viruses that are highly resistant to the drug but which exhibit reduced fitness relative to wild type HIV-1. PMID:15225375

  17. A Case of Seronegative HIV-1 Infection

    PubMed Central

    Spivak, Adam M.; Brennan, Tim; O'Connell, Karen; Sydnor, Emily; Williams, Thomas M.; Siliciano, Robert F.; Gallant, Joel E.; Blankson, Joel N.

    2009-01-01

    Patients infected with HIV-1 typically seroconvert within weeks of primary infection. In rare cases, patients do not develop antibodies against HIV-1 despite demonstrable infection. We describe an HLA-B*5802 positive individual who presented with AIDS despite repeatedly negative HIV-1 antibody screening tests. Phylogenetic analysis of env clones revealed little sequence diversity, and weak HIV-1 specific CD8+ T cell responses were present to Gag epitopes. The patient seroconverted after immune reconstitution on HAART. Lack of an antibody response to HIV-1 is rare and appears to be due to a defect in HIV-1-specific immunity rather than infection with attenuated virus. PMID:20039801

  18. Selection of an HLA-C*03:04-Restricted HIV-1 p24 Gag Sequence Variant Is Associated with Viral Escape from KIR2DL3+ Natural Killer Cells: Data from an Observational Cohort in South Africa

    PubMed Central

    Jimenez Cruz, Camilo A.; Garcia-Beltran, Wilfredo F.; Carlson, Jonathan M.; van Teijlingen, Nienke H.; Mann, Jaclyn K.; Jaggernath, Manjeetha; Kang, Seung-gu; Körner, Christian; Chung, Amy W.; Schafer, Jamie L.; Evans, David T.; Alter, Galit; Walker, Bruce D.; Goulder, Philip J.; Carrington, Mary; Hartmann, Pia; Pertel, Thomas; Zhou, Ruhong; Ndung’u, Thumbi; Altfeld, Marcus

    2015-01-01

    Background Viruses can evade immune surveillance, but the underlying mechanisms are insufficiently understood. Here, we sought to understand the mechanisms by which natural killer (NK) cells recognize HIV-1-infected cells and how this virus can evade NK-cell-mediated immune pressure. Methods and Findings Two sequence mutations in p24 Gag associated with the presence of specific KIR/HLA combined genotypes were identified in HIV-1 clade C viruses from a large cohort of infected, untreated individuals in South Africa (n = 392), suggesting viral escape from KIR+ NK cells through sequence variations within HLA class I—presented epitopes. One sequence polymorphism at position 303 of p24 Gag (TGag303V), selected for in infected individuals with both KIR2DL3 and HLA-C*03:04, enabled significantly better binding of the inhibitory KIR2DL3 receptor to HLA-C*03:04-expressing cells presenting this variant epitope compared to the wild-type epitope (wild-type mean 18.01 ± 10.45 standard deviation [SD] and variant mean 44.67 ± 14.42 SD, p = 0.002). Furthermore, activation of primary KIR2DL3+ NK cells from healthy donors in response to HLA-C*03:04+ target cells presenting the variant epitope was significantly reduced in comparison to cells presenting the wild-type sequence (wild-type mean 0.78 ± 0.07 standard error of the mean [SEM] and variant mean 0.63 ± 0.07 SEM, p = 0.012). Structural modeling and surface plasmon resonance of KIR/peptide/HLA interactions in the context of the different viral sequence variants studied supported these results. Future studies will be needed to assess processing and antigen presentation of the investigated HIV-1 epitope in natural infection, and the consequences for viral control. Conclusions These data provide novel insights into how viruses can evade NK cell immunity through the selection of mutations in HLA-presented epitopes that enhance binding to inhibitory NK cell receptors. Better understanding of the mechanisms by which HIV-1 evades

  19. Sunset at the ALaMO

    NASA Video Gallery

    A new color all-sky camera has opened its eyes at the ALaMO, or Automated Lunar and Meteor Observatory, at NASA's Marshall Space Flight Center in Huntsville, Ala. Watch its inaugural video below, s...

  20. Environmental surveillance at Los Alamos during 1994

    SciTech Connect

    1996-07-01

    This report describes environmental monitoring activities at Los Alamos National Laboratory for 1994. Data were collected to assess external penetrating radiation, airborne emissions, liquid effluents, radioactivity of environmental materials and food stuffs, and environmental compliance.

  1. New Rad Lab for Los Alamos

    ScienceCinema

    None

    2010-01-08

    The topping out ceremony for a key construction stage in the Los Alamos National Laboratory's newest facility, the Radiological Laboratory Utility & Office Building. This is part of the National Nu...  

  2. Publications of Los Alamos research 1988

    SciTech Connect

    Varjabedian, K.; Dussart, S.A.; McClary, W.J.; Rich, J.A.

    1989-12-01

    This bibliography lists unclassified publications of work done at the Los Alamos National Laboratory for 1988. The entries, which are subdivided by broad subject categories, are cross-referenced with an author index and a numeric index.

  3. New Rad Lab for Los Alamos

    SciTech Connect

    2008-08-06

    The topping out ceremony for a key construction stage in the Los Alamos National Laboratory's newest facility, the Radiological Laboratory Utility & Office Building. This is part of the National Nu...  

  4. Edward Teller Returns to LOS Alamos

    NASA Astrophysics Data System (ADS)

    Hecker, Siegfried S.

    2010-01-01

    I was asked to share some reflections of Edward Teller's return to Los Alamos during my directorship. I met Teller late in his life. My comments focus on that time and they will be mostly in the form of stories of my interactions and those of my colleagues with Teller. Although the focus of this symposium is on Teller's contributions to science, at Los Alamos it was never possible to separate Teller's science from policy and controversy ...

  5. Internship at Los Alamos National Laboratory

    SciTech Connect

    Dunham, Ryan Q.

    2012-07-11

    Los Alamos National Laboratory (LANL) is located in Los Alamos, New Mexico. It provides support for our country's nuclear weapon stockpile as well as many other scientific research projects. I am an Undergraduate Student Intern in the Systems Design and Analysis group within the Nuclear Nonproliferation division of the Global Security directorate at LANL. I have been tasked with data analysis and modeling of particles in a fluidized bed system for the capture of carbon dioxide from power plant flue gas.

  6. HIV-1 transmission linkage in an HIV-1 prevention clinical trial

    SciTech Connect

    Leitner, Thomas; Campbell, Mary S; Mullins, James I; Hughes, James P; Wong, Kim G; Raugi, Dana N; Scrensen, Stefanie

    2009-01-01

    HIV-1 sequencing has been used extensively in epidemiologic and forensic studies to investigate patterns of HIV-1 transmission. However, the criteria for establishing genetic linkage between HIV-1 strains in HIV-1 prevention trials have not been formalized. The Partners in Prevention HSV/HIV Transmission Study (ClinicaITrials.gov NCT00194519) enrolled 3408 HIV-1 serodiscordant heterosexual African couples to determine the efficacy of genital herpes suppression with acyclovir in reducing HIV-1 transmission. The trial analysis required laboratory confirmation of HIV-1 linkage between enrolled partners in couples in which seroconversion occurred. Here we describe the process and results from HIV-1 sequencing studies used to perform transmission linkage determination in this clinical trial. Consensus Sanger sequencing of env (C2-V3-C3) and gag (p17-p24) genes was performed on plasma HIV-1 RNA from both partners within 3 months of seroconversion; env single molecule or pyrosequencing was also performed in some cases. For linkage, we required monophyletic clustering between HIV-1 sequences in the transmitting and seroconverting partners, and developed a Bayesian algorithm using genetic distances to evaluate the posterior probability of linkage of participants sequences. Adjudicators classified transmissions as linked, unlinked, or indeterminate. Among 151 seroconversion events, we found 108 (71.5%) linked, 40 (26.5%) unlinked, and 3 (2.0%) to have indeterminate transmissions. Nine (8.3%) were linked by consensus gag sequencing only and 8 (7.4%) required deep sequencing of env. In this first use of HIV-1 sequencing to establish endpoints in a large clinical trial, more than one-fourth of transmissions were unlinked to the enrolled partner, illustrating the relevance of these methods in the design of future HIV-1 prevention trials in serodiscordant couples. A hierarchy of sequencing techniques, analysis methods, and expert adjudication contributed to the linkage

  7. Los Alamos Laser Eye Investigation.

    SciTech Connect

    Odom, C. R.

    2005-01-01

    A student working in a laser laboratory at Los Alamos National Laboratory sustained a serious retinal injury to her left eye when she attempted to view suspended particles in a partially evacuated target chamber. The principle investigator was using the white light from the flash lamp of a Class 4 Nd:YAG laser to illuminate the particles. Since the Q-switch was thought to be disabled at the time of the accident, the principal investigator assumed it would be safe to view the particles without wearing laser eye protection. The Laboratory Director appointed a team to investigate the accident and to report back to him the events and conditions leading up to the accident, equipment malfunctions, safety management causal factors, supervisory and management action/inaction, adequacy of institutional processes and procedures, emergency and notification response, effectiveness of corrective actions and lessons learned from previous similar events, and recommendations for human and institutional safety improvements. The team interviewed personnel, reviewed documents, and characterized systems and conditions in the laser laboratory during an intense six week investigation. The team determined that the direct and primary failures leading to this accident were, respectively, the principle investigator's unsafe work practices and the institution's inadequate monitoring of worker performance. This paper describes the details of the investigation, the human and institutional failures, and the recommendations for improving the laser safety program.

  8. Preexisting compensatory amino acids compromise fitness costs of a HIV-1 T cell escape mutation

    SciTech Connect

    Liu, Donglai; Zuo, Tao; Hora, Bhavna; Song, Hongshuo; Kong, Wei; Yu, Xianghui; Goonetilleke, Nilu; Bhattacharya, Tanmoy; Perelson, Alan S.; Haynes, Barton F.; McMichael, Andrew J.; Gao, Feng

    2014-01-01

    Background: Fitness costs and slower disease progression are associated with a cytolytic T lymphocyte (CTL) escape mutation T242N in Gag in HIV-1-infected individuals carrying HLA-B*57/5801 alleles. However, the impact of different context in diverse HIV-1 strains on the fitness costs due to the T242N mutation has not been well characterized. To better understand the extent of fitness costs of the T242N mutation and the repair of fitness loss through compensatory amino acids, we investigated its fitness impact in different transmitted/founder (T/F) viruses. Results: The T242N mutation resulted in various levels of fitness loss in four different T/F viruses. However, the fitness costs were significantly compromised by preexisting compensatory amino acids in (Isoleucine at position 247) or outside (glutamine at position 219) the CTL epitope. Moreover, the transmitted T242N escape mutant in subject CH131 was as fit as the revertant N242T mutant and the elimination of the compensatory amino acid I247 in the T/F viral genome resulted in significant fitness cost, suggesting the fitness loss caused by the T242N mutation had been fully repaired in the donor at transmission. Analysis of the global circulating HIV-1 sequences in the Los Alamos HIV Sequence Database showed a high prevalence of compensatory amino acids for the T242N mutation and other T cell escape mutations. Conclusions: Our results show that the preexisting compensatory amino acids in the majority of circulating HIV-1 strains could significantly compromise the fitness loss due to CTL escape mutations and thus increase challenges for T cell based vaccines.

  9. Preexisting compensatory amino acids compromise fitness costs of a HIV-1 T cell escape mutation

    DOE PAGESBeta

    Liu, Donglai; Zuo, Tao; Hora, Bhavna; Song, Hongshuo; Kong, Wei; Yu, Xianghui; Goonetilleke, Nilu; Bhattacharya, Tanmoy; Perelson, Alan S.; Haynes, Barton F.; et al

    2014-01-01

    Background: Fitness costs and slower disease progression are associated with a cytolytic T lymphocyte (CTL) escape mutation T242N in Gag in HIV-1-infected individuals carrying HLA-B*57/5801 alleles. However, the impact of different context in diverse HIV-1 strains on the fitness costs due to the T242N mutation has not been well characterized. To better understand the extent of fitness costs of the T242N mutation and the repair of fitness loss through compensatory amino acids, we investigated its fitness impact in different transmitted/founder (T/F) viruses. Results: The T242N mutation resulted in various levels of fitness loss in four different T/F viruses. However, themore » fitness costs were significantly compromised by preexisting compensatory amino acids in (Isoleucine at position 247) or outside (glutamine at position 219) the CTL epitope. Moreover, the transmitted T242N escape mutant in subject CH131 was as fit as the revertant N242T mutant and the elimination of the compensatory amino acid I247 in the T/F viral genome resulted in significant fitness cost, suggesting the fitness loss caused by the T242N mutation had been fully repaired in the donor at transmission. Analysis of the global circulating HIV-1 sequences in the Los Alamos HIV Sequence Database showed a high prevalence of compensatory amino acids for the T242N mutation and other T cell escape mutations. Conclusions: Our results show that the preexisting compensatory amino acids in the majority of circulating HIV-1 strains could significantly compromise the fitness loss due to CTL escape mutations and thus increase challenges for T cell based vaccines.« less

  10. Dispersion of the HIV-1 Epidemic in Men Who Have Sex with Men in the Netherlands: A Combined Mathematical Model and Phylogenetic Analysis

    PubMed Central

    Ratmann, Oliver; van Sighem, Ard; Hermanides, Hillegonda S.; Dutilh, Bas E.; Gras, Luuk; Rodrigues Faria, Nuno; van den Hengel, Rob; Duits, Ashley J.; Reiss, Peter; de Wolf, Frank; Fraser, Christophe

    2015-01-01

    Background The HIV-1 subtype B epidemic amongst men who have sex with men (MSM) is resurgent in many countries despite the widespread use of effective combination antiretroviral therapy (cART). In this combined mathematical and phylogenetic study of observational data, we aimed to find out the extent to which the resurgent epidemic is the result of newly introduced strains or of growth of already circulating strains. Methods and Findings As of November 2011, the ATHENA observational HIV cohort of all patients in care in the Netherlands since 1996 included HIV-1 subtype B polymerase sequences from 5,852 patients. Patients who were diagnosed between 1981 and 1995 were included in the cohort if they were still alive in 1996. The ten most similar sequences to each ATHENA sequence were selected from the Los Alamos HIV Sequence Database, and a phylogenetic tree was created of a total of 8,320 sequences. Large transmission clusters that included ≥10 ATHENA sequences were selected, with a local support value ≥ 0.9 and median pairwise patristic distance below the fifth percentile of distances in the whole tree. Time-varying reproduction numbers of the large MSM-majority clusters were estimated through mathematical modeling. We identified 106 large transmission clusters, including 3,061 (52%) ATHENA and 652 Los Alamos sequences. Half of the HIV sequences from MSM registered in the cohort in the Netherlands (2,128 of 4,288) were included in 91 large MSM-majority clusters. Strikingly, at least 54 (59%) of these 91 MSM-majority clusters were already circulating before 1996, when cART was introduced, and have persisted to the present. Overall, 1,226 (35%) of the 3,460 diagnoses among MSM since 1996 were found in these 54 long-standing clusters. The reproduction numbers of all large MSM-majority clusters were around the epidemic threshold value of one over the whole study period. A tendency towards higher numbers was visible in recent years, especially in the more recently

  11. Women and HIV

    MedlinePlus

    ... Consumer Information by Audience For Women Women and HIV Share Tweet Linkedin Pin it More sharing options ... HIV? What should pregnant women know about HIV? HIV Quick Facts What is HIV? HIV is the ...

  12. The C-terminal tail of the gp41 transmembrane envelope glycoprotein of HIV-1 clades A, B, C, and D may exist in two conformations: an analysis of sequence, structure, and function

    SciTech Connect

    Hollier, Mark J.; Dimmock, Nigel J. . E-mail: n.j.dimmock@warwick.ac.uk

    2005-07-05

    In addition to the major ectodomain, the gp41 transmembrane glycoprotein of HIV-1 is now known to have a minor ectodomain that is part of the long C-terminal tail. Both ectodomains are highly antigenic, carry neutralizing and non-neutralizing epitopes, and are involved in virus-mediated fusion activity. However, data have so far been biologically based, and derived solely from T cell line-adapted (TCLA), B clade viruses. Here we have carried out sequence and theoretically based structural analyses of 357 gp41 C-terminal sequences of mainly primary isolates of HIV-1 clades A, B, C, and D. Data show that all these viruses have the potential to form a tail loop structure (the minor ectodomain) supported by three, {beta}-sheet, membrane-spanning domains (MSDs). This means that the first (N-terminal) tyrosine-based sorting signal of the gp41 tail is situated outside the cell membrane and is non-functional, and that gp41 that reaches the cell surface may be recycled back into the cytoplasm through the activity of the second tyrosine-sorting signal. However, we suggest that only a minority of cell-associated gp41 molecules - those destined for incorporation into virions - has 3 MSDs and the minor ectodomain. Most intracellular gp41 has the conventional single MSD, no minor ectodomain, a functional first tyrosine-based sorting signal, and in line with current thinking is degraded intracellularly. The gp41 structural diversity suggested here can be viewed as an evolutionary strategy to minimize HIV-1 envelope glycoprotein expression on the cell surface, and hence possible cytotoxicity and immune attack on the infected cell.

  13. Genome Sequence of a Complex HIV-1 Unique Recombinant Form Involving CRF01_AE, Subtype B, and Subtype B' Identified in Malaysia.

    PubMed

    Chow, Wei Zhen; Nizam, Sarimie; Ong, Lai Yee; Ng, Kim Tien; Chan, Kok Gan; Takebe, Yutaka; Koh, Clayton; Kamarulzaman, Adeeba; Tee, Kok Keng

    2014-01-01

    A complex HIV-1 unique recombinant form involving subtypes CRF01_AE, B, and B' was recently identified from an injecting drug user in Malaysia. A total of 13 recombination breakpoints were mapped across the near-full-length genome of isolate 10MYPR226, indicating the increasingly diverse molecular epidemiology and frequent linkage among various high-risk groups. PMID:24675847

  14. Long-Range HIV Genotyping Using Viral RNA and Proviral DNA for Analysis of HIV Drug Resistance and HIV Clustering.

    PubMed

    Novitsky, Vlad; Zahralban-Steele, Melissa; McLane, Mary Fran; Moyo, Sikhulile; van Widenfelt, Erik; Gaseitsiwe, Simani; Makhema, Joseph; Essex, M

    2015-08-01

    The goal of the study was to improve the methodology of HIV genotyping for analysis of HIV drug resistance and HIV clustering. Using the protocol of Gall et al. (A. Gall, B. Ferns, C. Morris, S. Watson, M. Cotten, M. Robinson, N. Berry, D. Pillay, and P. Kellam, J Clin Microbiol 50:3838-3844, 2012, doi:10.1128/JCM.01516-12), we developed a robust methodology for amplification of two large fragments of viral genome covering about 80% of the unique HIV-1 genome sequence. Importantly, this method can be applied to both viral RNA and proviral DNA amplification templates, allowing genotyping in HIV-infected subjects with suppressed viral loads (e.g., subjects on antiretroviral therapy [ART]). The two amplicons cover critical regions across the HIV-1 genome (including pol and env), allowing analysis of mutations associated with resistance to protease inhibitors, reverse transcriptase inhibitors (nucleoside reverse transcriptase inhibitors [NRTIs] and nonnucleoside reverse transcriptase inhibitors [NNRTIs]), integrase strand transfer inhibitors, and virus entry inhibitors. The two amplicons generated span 7,124 bp, providing substantial sequence length and numbers of informative sites for comprehensive phylogenic analysis and greater refinement of viral linkage analyses in HIV prevention studies. The long-range HIV genotyping from proviral DNA was successful in about 90% of 212 targeted blood specimens collected in a cohort where the majority of patients had suppressed viral loads, including 65% of patients with undetectable levels of HIV-1 RNA loads. The generated amplicons could be sequenced by different methods, such as population Sanger sequencing, single-genome sequencing, or next-generation ultradeep sequencing. The developed method is cost-effective-the cost of the long-range HIV genotyping is under $140 per subject (by Sanger sequencing)-and has the potential to enable the scale up of public health HIV prevention interventions. PMID:26041893

  15. New Generation of Los Alamos Opacity Tables

    NASA Astrophysics Data System (ADS)

    Colgan, James; Kilcrease, D. P.; Magee, N. H.; Sherrill, M. E.; Abdallah, J.; Hakel, P.; Fontes, C. J.; Guzik, J. A.; Mussack, K. A.

    2016-05-01

    We present a new generation of Los Alamos OPLIB opacity tables that have been computed using the ATOMIC code. Our tables have been calculated for all 30 elements from hydrogen through zinc and are publicly available through our website. In this poster we discuss the details of the calculations that underpin the new opacity tables. We also show several recent applications of the use of our opacity tables to solar modeling and other astrophysical applications. In particular, we demonstrate that use of the new opacities improves the agreement between solar models and helioseismology, but does not fully resolve the long-standing `solar abundance' problem. The Los Alamos National Laboratory is operated by Los Alamos National Security, LLC for the National Nuclear Security Administration of the U.S. Department of Energy under Contract No. DE-AC5206NA25396.

  16. Status of Monte Carlo at Los Alamos

    SciTech Connect

    Thompson, W.L.; Cashwell, E.D.

    1980-01-01

    At Los Alamos the early work of Fermi, von Neumann, and Ulam has been developed and supplemented by many followers, notably Cashwell and Everett, and the main product today is the continuous-energy, general-purpose, generalized-geometry, time-dependent, coupled neutron-photon transport code called MCNP. The Los Alamos Monte Carlo research and development effort is concentrated in Group X-6. MCNP treats an arbitrary three-dimensional configuration of arbitrary materials in geometric cells bounded by first- and second-degree surfaces and some fourth-degree surfaces (elliptical tori). Monte Carlo has evolved into perhaps the main method for radiation transport calculations at Los Alamos. MCNP is used in every technical division at the Laboratory by over 130 users about 600 times a month accounting for nearly 200 hours of CDC-7600 time.

  17. Publications of Los Alamos Research, 1983

    SciTech Connect

    Sheridan, C.J.; McClary, W.J.; Rich, J.A.; Rodriguez, L.L.

    1984-10-01

    This bibliography is a compilation of unclassified publications of work done at the Los Alamos National Laboratory for 1983. Papers published in 1982 are included regardless of when they were actually written. Publications received too late for inclusion in earlier compilations have also been listed. Declassification of previously classified reports is considered to constitute publication. All classified issuances are omitted - even those papers, themselves unclassified, which were published only as part of a classified document. If a paper was published more than once, all places of publication are included. The bibliography includes Los Alamos National Laboratory reports, papers released as non-Laboratory reports, journal articles, books, chapters of books, conference papers either published separately or as part of conference proceedings issued as books or reports, papers publishd in congressional hearings, theses, and US patents. Publications by Los Alamos authors that are not records of Laboratory-sponsored work are included when the Library becomes aware of them.

  18. Publications of Los Alamos research 1980

    SciTech Connect

    Salazar, C.A.; Willis, J.K.

    1981-09-01

    This bibliography is a compilation of unclassified publications of work done at the Los Alamos National Laboratory for 1980. Papers published in 1980 are included regardless of when they were actually written. Publications received too late for inclusion in earlier compilations have also been listed. Declassification of previously classified reports is considered to constitute publication. All classified issuances are omitted-even those papers, themselves unclassified, which were published only as part of a classified document. If a paper was pubished more than once, all places of publication are included. The bibliography includes Los Alamos National Laboratory reports, papers released as non-laboratory reports, journal articles, books, chapters of books, conference papers published either separately or as part of conference proceedings issued as books or reports, papers published in congressional hearings, theses, and US patents. Publications by Los Alamos authors that are not records of Laboratory-sponsored work are included when the Library becomes aware of them.

  19. SEDs at Los Alamos: A Personal Memoir

    NASA Astrophysics Data System (ADS)

    Bederson, Benjamin

    2001-03-01

    I have written this personal memoir approximately 55 years after the events I describe. It is based almost exclusively on memory, since apart from the diary I kept while on Tinian, I have few documents concerning it. It covers my service in the U.S. Army's Special Engineering Detachment (SED) in Oak Ridge and Los Alamos in 1944-45, on Tinian island, the launching pad for the bombing raids on Japan, in the summer and fall of 1945, and my return to Los Alamos until my discharge in January 1946.

  20. Upper Los Alamos canyon fact sheet

    SciTech Connect

    Berger, Jeffrey H

    2007-01-01

    Los Alamos National Laboratory is planning to make environmental assessments in portions of Upper Los Alamos Canyon. Upper Los Alamos Canyon is one of the areas included in the 2005 Consent Order agreed to by Los Alamos National Laboratory, the National Nuclear Security Administration, and the New Mexico Environment Department. As such, it must be evaluated for potential contamination. The area is located within and south of the Los Alamos townsite in Technical Areas 00, 01, 03, 32, 41, 43, and 61 of Los Alamos National Laboratory and includes a total of 115 solid waste management units and areas of concern. This area was home to some of the earliest operations at Los Alamos, dating from the 1940s. Of the 115 solid-waste management units and areas of concern, 54 have been addressed previously. The remaining 61 are the focus of this project. These include septic tanks and outfalls, sanitary and industrial waste lines, storm drains, soil contamination areas, landfill and surface disposal areas, transformer sites, and incinerators. The Consent Order requires the Laboratory to evaluate historical work sites for the potential presence of residual contamination. It also requires the Laboratory to identify and implement corrective actions should contamination be found. The Laboratory began performing these types of activities in the 1990s. The Upper Los Alamos Canyon project entails: (1) collecting soil and rock samples using the most efficient and least-invasive methods practicable; (2) defining the nature and extent of any residual contamination associated with each solid waste management unit or area of concern; and (3) gathering additional data if needed to evaluate potential remedial alternatives. A variety of methods, including studies of engineering drawings, nonintrusive geophysical surveys, and trenching, may be used to identify the final sampling locations. The field team then determines which collection method to use at each location, based on such site

  1. Plutonium 238 facilities at Los Alamos

    NASA Astrophysics Data System (ADS)

    Rinehart, Gary H.

    1991-01-01

    Plutonium 238 operations at Los Alamos are performed at the Plutonium Facility (TA-55), the Chemistry and Metallurgy Research (CMR) Building, and the Radioisotope Fuels Impact Test Facility. The plutonium 238 facilities at Los Alamos support a wide variety of heat source activities including development of new fuel forms and containment materials, research on the high temperature properties of containment materials, investigation of the high temperature compatibility of fuels with potential container materials, processing plutonium 238 fuel forms, manufacture of heat sources under quality assurance surveillance, and performing safety testing on heat sources and radioisotope thermoelectric generators.

  2. Plutonium-238 facilities at Los Alamos

    NASA Astrophysics Data System (ADS)

    Rinehart, Gary H.

    Plutonium-238 operations at Los Alamos are performed at the Plutonium Facility (TA-55), the Chemistry and Metallurgy Research (CMR) Building, and the Radioisotope Fuels Impact Test Facility. The plutonium-238 facilities at Los Alamos support a wide variety of heat source activities including development of new fuel forms and containment materials, research on the high temperature properties of containment materials, investigation of the high temperature compatibility of fuels with potential container materials, processing plutonium-238 fuel forms, manufacture of heat sources under quality assurance surveillance, and performing safety testing on heat sources and radioisotope thermoelectric generators.

  3. Temporal analysis of HIV envelope sequence evolution and antibody escape in a subtype A-infected individual with a broad neutralizing antibody response

    PubMed Central

    Bosch, Katherine A.; Rainwater, Stephanie; Jaoko, Walter; Overbaugh, Julie

    2010-01-01

    The origin of broadly neutralizing HIV-specific antibodies and their relation to HIV evolution are not well defined. Here we examined virus evolution and neutralizing antibody escape in a subtype A infected individual with a broad, cross subtype, antibody response. The majority of envelope variants isolated over the first ~ 5 years post-infection were poorly neutralized by contemporaneous plasma that neutralized variants from earlier in infection, consistent with a dynamic process of escape. The majority of variants could be neutralized by later plasma, suggesting these evolving variants may have contributed to the elicitation of new antibody responses. However, some variants from later in infection were recognized by plasma from earlier in infection, including one notably neutralization-sensitive variant that was sensitive due to a proline at position 199 in V2. These studies suggest a complex pattern of virus evolution in this individual with a broad NAb response, including persistence of neutralization-sensitive viruses. PMID:20034648

  4. Proceedings of the Los Alamos neutrino workshop

    SciTech Connect

    Boehm, F.; Stephenson, G.J. Jr.

    1982-08-01

    A workshop on neutrino physics was held at Los Alamos from June 8 to 12, 1981. The material presented has been provided in part by the organizers, in part by the chairmen of the working sessions. Closing date for contributions was October 1981.

  5. Induction inserts at the Los Alamos PSR

    SciTech Connect

    King-Yuen Ng

    2002-09-30

    Ferrite-loaded induction tuners installed in the Los Alamos Proton Storage Ring have been successful in compensating space-charge effects. However, the resistive part of the ferrite introduces unacceptable microwave instability and severe bunch lengthening. An effective cure was found by heating the ferrite cores up to {approx} 130 C. An understanding of the instability and cure is presented.

  6. Los Alamos waste drum shufflers users manual

    SciTech Connect

    Rinard, P.M.; Adams, E.L.; Painter, J.

    1993-08-24

    This user manual describes the Los Alamos waste drum shufflers. The primary purpose of the instruments is to assay the mass of {sup 235}U (or other fissile materials) in drums of assorted waste. It can perform passive assays for isotopes that spontaneously emit neutrons or active assays using the shuffler technique as described on this manual.

  7. Los Alamos Fires From Landsat 7

    NASA Technical Reports Server (NTRS)

    2002-01-01

    On May 9, 2000, the Landsat 7 satellite acquired an image of the area around Los Alamos, New Mexico. The Landsat 7 satellite acquired this image from 427 miles in space through its sensor called the Enhanced Thematic Mapper Plus (ETM+). Evident within the imagery is a view of the ongoing Cerro Grande fire near the town of Los Alamos and the Los Alamos National Laboratory. Combining the high-resolution (30 meters per pixel in this scene) imaging capacity of ETM+ with its multi-spectral capabilities allows scientists to penetrate the smoke plume and see the structure of the fire on the surface. Notice the high-level of detail in the infrared image (bottom), in which burn scars are clearly distinguished from the hotter smoldering and flaming parts of the fire. Within this image pair several features are clearly visible, including the Cerro Grande fire and smoke plume, the town of Los Alamos, the Los Alamos National Laboratory and associated property, and Cerro Grande peak. Combining ETM+ channels 7, 4, and 2 (one visible and two infrared channels) results in a false color image where vegetation appears as bright to dark green (bottom image). Forested areas are generally dark green while herbaceous vegetation is light green. Rangeland or more open areas appear pink to light purple. Areas with extensive pavement or urban development appear light blue or white to purple. Less densely-developed residential areas appear light green and golf courses are very bright green. The areas recently burned appear black. Dark red to bright red patches, or linear features within the burned area, are the hottest and possibly actively burning areas of the fire. The fire is spreading downslope and the front of the fire is readily detectable about 2 kilometers to the west and south of Los Alamos. Combining ETM+ channels 3, 2, and 1 provides a true-color image of the greater Los Alamos region (top image). Vegetation is generally dark to medium green. Forested areas are very dark green

  8. HIV transmission biology: translation for HIV prevention.

    PubMed

    Ronen, Keshet; Sharma, Amit; Overbaugh, Julie

    2015-11-01

    Rigorous testing of new HIV-prevention strategies is a time-consuming and expensive undertaking. Thus, making well informed decisions on which candidate-prevention approaches are most likely to provide the most benefit is critical to appropriately prioritizing clinical testing. In the case of biological interventions, the decision to test a given prevention approach in human trials rests largely on evidence of protection in preclinical studies. The ability of preclinical studies to predict efficacy in humans may depend on how well the model recapitulates key biological features of HIV transmission relevant to the question at hand. Here, we review our current understanding of the biology of HIV transmission based on data from animal models, cell culture, and viral sequence analysis from human infection. We summarize studies of the bottleneck in viral transmission; the characteristics of transmitted viruses; the establishment of infection; and the contribution of cell-free and cell-associated virus. We seek to highlight the implications of HIV-transmission biology for development of prevention interventions, and to discuss the limitations of existing preclinical models. PMID:26418086

  9. Spatio-Temporal History of HIV-1 CRF35_AD in Afghanistan and Iran

    PubMed Central

    Eybpoosh, Sana; Bahrampour, Abbas; Karamouzian, Mohammad; Azadmanesh, Kayhan; Jahanbakhsh, Fatemeh; Mostafavi, Ehsan; Zolala, Farzaneh; Haghdoost, Ali Akbar

    2016-01-01

    HIV-1 Circulating Recombinant Form 35_AD (CRF35_AD) has an important position in the epidemiological profile of Afghanistan and Iran. Despite the presence of this clade in Afghanistan and Iran for over a decade, our understanding of its origin and dissemination patterns is limited. In this study, we performed a Bayesian phylogeographic analysis to reconstruct the spatio-temporal dispersion pattern of this clade using eligible CRF35_AD gag and pol sequences available in the Los Alamos HIV database (432 sequences available from Iran, 16 sequences available from Afghanistan, and a single CRF35_AD-like pol sequence available from USA). Bayesian Markov Chain Monte Carlo algorithm was implemented in BEAST v1.8.1. Between-country dispersion rates were tested with Bayesian stochastic search variable selection method and were considered significant where Bayes factor values were greater than three. The findings suggested that CRF35_AD sequences were genetically similar to parental sequences from Kenya and Uganda, and to a set of subtype A1 sequences available from Afghan refugees living in Pakistan. Our results also showed that across all phylogenies, Afghan and Iranian CRF35_AD sequences formed a monophyletic cluster (posterior clade credibility> 0.7). The divergence date of this cluster was estimated to be between 1990 and 1992. Within this cluster, a bidirectional dispersion of the virus was observed across Afghanistan and Iran. We could not clearly identify if Afghanistan or Iran first established or received this epidemic, as the root location of this cluster could not be robustly estimated. Three CRF35_AD sequences from Afghan refugees living in Pakistan nested among Afghan and Iranian CRF35_AD branches. However, the CRF35_AD-like sequence available from USA diverged independently from Kenyan subtype A1 sequences, suggesting it not to be a true CRF35_AD lineage. Potential factors contributing to viral exchange between Afghanistan and Iran could be injection drug

  10. Spatio-Temporal History of HIV-1 CRF35_AD in Afghanistan and Iran.

    PubMed

    Eybpoosh, Sana; Bahrampour, Abbas; Karamouzian, Mohammad; Azadmanesh, Kayhan; Jahanbakhsh, Fatemeh; Mostafavi, Ehsan; Zolala, Farzaneh; Haghdoost, Ali Akbar

    2016-01-01

    HIV-1 Circulating Recombinant Form 35_AD (CRF35_AD) has an important position in the epidemiological profile of Afghanistan and Iran. Despite the presence of this clade in Afghanistan and Iran for over a decade, our understanding of its origin and dissemination patterns is limited. In this study, we performed a Bayesian phylogeographic analysis to reconstruct the spatio-temporal dispersion pattern of this clade using eligible CRF35_AD gag and pol sequences available in the Los Alamos HIV database (432 sequences available from Iran, 16 sequences available from Afghanistan, and a single CRF35_AD-like pol sequence available from USA). Bayesian Markov Chain Monte Carlo algorithm was implemented in BEAST v1.8.1. Between-country dispersion rates were tested with Bayesian stochastic search variable selection method and were considered significant where Bayes factor values were greater than three. The findings suggested that CRF35_AD sequences were genetically similar to parental sequences from Kenya and Uganda, and to a set of subtype A1 sequences available from Afghan refugees living in Pakistan. Our results also showed that across all phylogenies, Afghan and Iranian CRF35_AD sequences formed a monophyletic cluster (posterior clade credibility> 0.7). The divergence date of this cluster was estimated to be between 1990 and 1992. Within this cluster, a bidirectional dispersion of the virus was observed across Afghanistan and Iran. We could not clearly identify if Afghanistan or Iran first established or received this epidemic, as the root location of this cluster could not be robustly estimated. Three CRF35_AD sequences from Afghan refugees living in Pakistan nested among Afghan and Iranian CRF35_AD branches. However, the CRF35_AD-like sequence available from USA diverged independently from Kenyan subtype A1 sequences, suggesting it not to be a true CRF35_AD lineage. Potential factors contributing to viral exchange between Afghanistan and Iran could be injection drug

  11. Get Tested for HIV

    MedlinePlus

    ... Print This Topic En español Get Tested for HIV Browse Sections The Basics Overview What Is HIV? ... 1 of 7 sections The Basics: What Is HIV? What is HIV? HIV stands for human immunodeficiency ...

  12. HIV Treatment: The Basics

    MedlinePlus

    HIV Treatment HIV Treatment: The Basics (Last updated 3/1/2016; last reviewed 3/1/2016) Key Points Antiretroviral therapy (ART) ... reduces the risk of HIV transmission . How do HIV medicines work? HIV attacks and destroys the infection- ...

  13. Sequence similarity between the erythrocyte binding domain of the Plasmodium vivax Duffy binding protein and the V3 loop of HIV-1 strain MN reveals a functional heparin binding motif involved in binding to the Duffy antigen receptor for chemokines

    PubMed Central

    2011-01-01

    Background The HIV surface glycoprotein gp120 (SU, gp120) and the Plasmodium vivax Duffy binding protein (PvDBP) bind to chemokine receptors during infection and have a site of amino acid sequence similarity in their binding domains that often includes a heparin binding motif (HBM). Infection by either pathogen has been found to be inhibited by polyanions. Results Specific polyanions that inhibit HIV infection and bind to the V3 loop of X4 strains also inhibited DBP-mediated infection of erythrocytes and DBP binding to the Duffy Antigen Receptor for Chemokines (DARC). A peptide including the HBM of PvDBP had similar affinity for heparin as RANTES and V3 loop peptides, and could be specifically inhibited from heparin binding by the same polyanions that inhibit DBP binding to DARC. However, some V3 peptides can competitively inhibit RANTES binding to heparin, but not the PvDBP HBM peptide. Three other members of the DBP family have an HBM sequence that is necessary for erythrocyte binding, however only the protein which binds to DARC, the P. knowlesi alpha protein, is inhibited by heparin from binding to erythrocytes. Heparitinase digestion does not affect the binding of DBP to erythrocytes. Conclusion The HBMs of DBPs that bind to DARC have similar heparin binding affinities as some V3 loop peptides and chemokines, are responsible for specific sulfated polysaccharide inhibition of parasite binding and invasion of red blood cells, and are more likely to bind to negative charges on the receptor than cell surface glycosaminoglycans. PMID:22122911

  14. The sequence complementarity between HIV-1 5' splice site SD4 and U1 snRNA determines the steady-state level of an unstable env pre-mRNA.

    PubMed Central

    Kammler, S; Leurs, C; Freund, M; Krummheuer, J; Seidel, K; Tange, T O; Lund, M K; Kjems, J; Scheid, A; Schaal, H

    2001-01-01

    HIV-1 env expression from certain subgenomic vectors requires the viral regulatory protein Rev, its target sequence RRE, and a 5' splice site upstream of the env open reading frame. To determine the role of this splice site in the 5'-splice-site-dependent Rev-mediated env gene expression, we have subjected the HIV-1 5' splice site, SD4, to a mutational analysis and have analyzed the effect of those mutations on env expression. The results demonstrate that the overall strength of hydrogen bonding between the 5' splice site, SD4, and the free 5' end of the U1 snRNA correlates with env expression efficiency, as long as env expression is suboptimal, and that a continuous stretch of 14 hydrogen bonds can lead to full env expression, as a result of stabilizing the pre-mRNA. The U1 snRNA-mediated stabilization is independent of functional splicing, as a mismatch in position +1 of the 5' splice site that led to loss of detectable amounts of spliced transcripts did not preclude stabilization and expression of the unspliced env mRNA, provided that Rev enables its nuclear export. The nucleotides capable of participating in U1 snRNA:pre-mRNA interaction include positions -3 to +8 of the 5' splice site and all 11 nt constituting the single-stranded 5' end of U1 snRNA. Moreover, env gene expression is significantly decreased upon the introduction of point mutations in several upstream GAR nucleotide motifs, which are mediating SF2/ASF responsiveness in an in vitro splicing assay. This suggests that the GAR sequences may play a role in stabilizing the pre-mRNA by sequestering U1 snRNP to SD4. PMID:11333022

  15. Probing the influence of hypermodified residues within the tRNA3(Lys) anticodon stem loop interacting with the A-loop primer sequence from HIV-1.

    PubMed

    Galindo-Murillo, Rodrigo; Davis, Darrell R; Cheatham, Thomas E

    2016-03-01

    Replication of the HIV-1 virus requires reverse transcription of the viral RNA genome, a process that is specifically initiated by human tRNA3(Lys) packaged within the infectious virion. The primary binding site for the tRNA involves the 3' 18 nucleotides with an additional interaction between an adenine rich loop (A-loop) in the template and the anticodon stem-loop region of the tRNA3(Lys). The loop of the tRNA primer contains two hypermodified base residues and a pseudouridine that are required for a proper binding and activity. Here, we investigate the influence on the structure, dynamics and binding stability of the three modified residues (mnm(5)s(2)U34, t(6)A37 and Ψ39) using extensive molecular dynamics and Quantum Theory of Atoms in Molecules (QTAIM) analysis. Consistent with experiment, the results suggest that the three modified residues are required for faithful binding. Residues mnm(5)s(2)U34 and Ψ39 have a major influence in stabilizing the anticodon loop whereas mnm(5)s(2)U34 and t(6)A37 appear to stabilize the formation of the complex of tRNA3(Lys) with the HIV-1 A-loop. PMID:26655694

  16. Nuclear Forensics at Los Alamos National Laboratory

    SciTech Connect

    Podlesak, David W; Steiner, Robert E.; Burns, Carol J.; LaMont, Stephen P.; Tandon, Lav

    2012-08-09

    The overview of this presentation is: (1) Introduction to nonproliferation efforts; (2) Scope of activities at Los Alamos National Laboratory; (3) Facilities for radioanalytical work at LANL; (4) Radiochemical characterization capabilities; and (5) Bulk chemical and materials analysis capabilities. Some conclusions are: (1) Analytical chemistry measurements on plutonium and uranium matrices are critical to numerous defense and non-defense programs including safeguards accountancy verification measurements; (2) Los Alamos National Laboratory operates capable actinide analytical chemistry and material science laboratories suitable for nuclear material forensic characterization; (3) Actinide analytical chemistry uses numerous means to validate and independently verify that measurement data quality objectives are met; and (4) Numerous LANL nuclear facilities support the nuclear material handling, preparation, and analysis capabilities necessary to evaluate samples containing nearly any mass of an actinide (attogram to kilogram levels).

  17. Amphibians and Reptiles of Los Alamos County

    SciTech Connect

    Teralene S. Foxx; Timothy K. Haarmann; David C. Keller

    1999-10-01

    Recent studies have shown that amphibians and reptiles are good indicators of environmental health. They live in terrestrial and aquatic environments and are often the first animals to be affected by environmental change. This publication provides baseline information about amphibians and reptiles that are present on the Pajarito Plateau. Ten years of data collection and observations by researchers at Los Alamos National Laboratory, the University of New Mexico, the New Mexico Department of Game and Fish, and hobbyists are represented.

  18. Los Alamos Novel Rocket Design Flight Tested

    ScienceCinema

    Tappan, Bryce

    2015-01-05

    Los Alamos National Laboratory scientists recently flight tested a new rocket design that includes a high-energy fuel and a motor design that also delivers a high degree of safety. Researchers will now work to scale-up the design, as well as explore miniaturization of the system, in order to exploit all potential applications that would require high-energy, high-velocity, and correspondingly high safety margins.

  19. Los Alamos Novel Rocket Design Flight Tested

    SciTech Connect

    Tappan, Bryce

    2014-10-23

    Los Alamos National Laboratory scientists recently flight tested a new rocket design that includes a high-energy fuel and a motor design that also delivers a high degree of safety. Researchers will now work to scale-up the design, as well as explore miniaturization of the system, in order to exploit all potential applications that would require high-energy, high-velocity, and correspondingly high safety margins.

  20. Los Alamos Team Demonstrates Bottle Scanner Technology

    SciTech Connect

    Espy, Michelle; Schultz, Larry

    2014-05-06

    Los Alamos scientists are demonstrating a Nuclear Magnetic Resonance Imaging (NMR) technology that may provide a breakthrough for screening liquids at airport security. By adding low-power X-ray data to the NMR mix, scientists believe they have unlocked a new detection technology. Funded in part by the Department of Homeland Security's Science and Technology Directorate, the new technology is called MagRay.

  1. The Los Alamos accelerator code group

    SciTech Connect

    Krawczyk, F.L.; Billen, J.H.; Ryne, R.D.; Takeda, Harunori; Young, L.M.

    1995-05-01

    The Los Alamos Accelerator Code Group (LAACG) is a national resource for members of the accelerator community who use and/or develop software for the design and analysis of particle accelerators, beam transport systems, light sources, storage rings, and components of these systems. Below the authors describe the LAACG`s activities in high performance computing, maintenance and enhancement of POISSON/SUPERFISH and related codes and the dissemination of information on the INTERNET.

  2. Los Alamos Team Demonstrates Bottle Scanner Technology

    ScienceCinema

    Espy, Michelle; Schultz, Larry

    2014-06-02

    Los Alamos scientists are demonstrating a Nuclear Magnetic Resonance Imaging (NMR) technology that may provide a breakthrough for screening liquids at airport security. By adding low-power X-ray data to the NMR mix, scientists believe they have unlocked a new detection technology. Funded in part by the Department of Homeland Security's Science and Technology Directorate, the new technology is called MagRay.

  3. Los Alamos National Laboratory Facility Review

    SciTech Connect

    Nelson, Ronald Owen

    2015-06-05

    This series of slides depicts the Los Alamos Neutron Science Center (LANSCE). The Center's 800-MeV linac produces H+ and H- beams as well as beams of moderated (cold to 1 MeV) and unmoderated (0.1 to 600 MeV) neutrons. Experimental facilities and their capabilities and characteristics are outlined. Among these are LENZ, SPIDER, and DANCE.

  4. Los Alamos synchronous orbit data set

    SciTech Connect

    Baker, D.N.; Higbie, P.R.; Belian, R.D.; Hones, E.W.; Klebesadel, R.W.

    1981-01-01

    Energetic electron (30-15000 keV) and proton 145 keV to 150 MeV) measurements made by Los Alamos National Laboratory sensors at geostationary orbit (6.6 R/sub E/) are summarized. The instrumentation employed and the satellite positions are described. The spacecraft have been variously located, but in their present configuration the Los Alamos satellites designated 1976-059, 1977-007, and 1979-053 are located, respectively, at approx. 70/sup 0/W, approx. 70/sup 0/E, and approx. 135/sup 0/W longitude. Several examples of the high temporal and full three-dimensional spatial measurement capabilities of these instruments are illustrated by examples from the published literature. Discussion is also given for the Los Alamos Synoptic Data Set (SDS) which gives a broad overview of the Los Alamos geostationary orbit measurements. The SDS data are plotted in terms of daily average spectra, 3-hour local time averages, and in a variety of statistical formats. The data summarize conditions from mid-1976 through 1978 (S/C 1976-059) and from early 1977 through 1978 (S/C 1977-007). The SDS compilations presented correspond to measurements at 35/sup 0/W, 70/sup 0/W, and 135/sup 0/W geographic longitude and thus are indicative of conditions at 9/sup 0/, 11/sup 0/, and 4.8/sup 0/ geomagnetic latitude, respectively. The bulk of the SDS report presents data plots which are organized according to Carrington solar rotations and, as such, the data are readily comparable to solar rotation-dependent interplanetary conditions. Potential applications of the Synoptic Data Set (available to all interested users in June 1981) are discussed.

  5. Status of the Los Alamos Anger camera

    SciTech Connect

    Seeger, P.A.; Nutter, M.J.

    1985-01-01

    Results of preliminary tests of the neutron Anger camera being developed at Los Alamos are presented. This detector uses a unique encoding scheme involving parellel processing of multiple receptive fields. Design goals have not yet been met, but the results are very encouraging and improvements in the test procedures are expected to show that the detector will be ready for use on a small-angle scattering instrument next year. 3 refs., 4 figs.

  6. Critical partnerships: Los Alamos, universities, and industry

    SciTech Connect

    Berger, C.L.

    1997-04-01

    Los Alamos National Laboratory, situated 35 miles northwest of Santa Fe, NM, is one of the Department of Energy`s three Defense Programs laboratories. It encompasses 43 square miles, employees approximately 10,000 people, and has a budget of approximately $1.1B in FY97. Los Alamos has a strong post-cold war mission, that of reducing the nuclear danger. But even with that key role in maintaining the nation`s security, Los Alamos views partnerships with universities and industry as critical to its future well being. Why is that? As the federal budget for R&D comes under continued scrutiny and certain reduction, we believe that the triad of science and technology contributors to the national system of R&D must rely on and leverage each others capabilities. For us this means that we will rely on these partners to help us in 5 key ways: We expect that partnerships will help us maintain and enhance our core competencies. In doing so, we will be able to attract the best scientists and engineers. To keep on the cutting edge of research and development, we have found that partnerships maintain the excellence of staff through new and exciting challenges. Additionally, we find that from our university and corporate partners we often learn and incorporate {open_quotes}best practices{close_quotes} in organizational management and operations. Finally, we believe that a strong national system of R&D will ensure and enhance our ability to generate revenues.

  7. Los Alamos National Laboratory Building Cost Index

    SciTech Connect

    Orr, H.D.; Lemon, G.D.

    1983-01-01

    The Los Alamos National Laboratory Building Cost Index indicates that actual escalation since 1970 is near 10% per year. Therefore, the Laboratory will continue using a 10% per year escalation rate for construction estimates through 1985 and a slightly lower rate of 8% per year from 1986 through 1990. The computerized program compares the different elements involved in the cost of a typical construction project, which for our purposes, is a complex of office buildings and experimental laboratores. The input data used in the program consist primarily of labor costs and material and equipment costs. The labor costs are the contractural rates of the crafts workers in the Los Alamos area. For the analysis, 12 field-labor draft categories are used; each is weighted corresponding to the labor craft distribution associated with the typical construction project. The materials costs are current Los Alamos prices. Additional information sources include material and equipment quotes obtained through conversations with vendors and from trade publications. The material and equipment items separate into 17 categories for the analysis and are weighted corresponding to the material and equipment distribution associated with the typical construction project. The building cost index is compared to other national building cost indexes.

  8. Los Alamos National Laboratory building cost index

    SciTech Connect

    Orr, H.D.; Lemon, G.D.

    1982-10-01

    The Los Alamos National Laboratory Building Cost Index indicates that actual escalation since 1970 is near 10% per year. Therefore, the Laboratory will continue using a 10% per year escalation rate for construction estimates through 1985 and a slightly lower rate of 8% per year from 1986 through 1990. The computerized program compares the different elements involved in the cost of a typical construction project, which for our purposes, is a complex of office buildings and experimental laboratories. The input data used in the program consist primarily of labor costs and material and equipment costs. The labor costs are the contractual rates of the crafts workers in the Los Alamos area. For the analysis, 12 field-labor craft categories are used; each is weighted corresponding to the labor craft distribution associated with the typical construction project. The materials costs are current Los Alamos prices. Additional information sources include material and equipment quotes obtained through conversations with vendors and from trade publications. The material and equipment items separate into 17 categories for the analysis and are weighted corresponding to the material and equipment distribution associated with the typical construction project. The building cost index is compared to other national building cost indexes.

  9. Exploration geochemistry: The Los Alamos experience

    SciTech Connect

    Maassen, L.W.; Bolivar, S.L.

    1989-01-01

    Los Alamos National Laboratory became actively involved in geochemical exploration in 1975 by conducting a reconnaissance-scale exploration program for uranium as part of the National Uranium Resource Evaluation program. Initially, only uranium and thorium were analyzed. By 1979 Los Alamos was analyzing a multielement suite. The data were presented in histograms and as black and white concentration plots for uranium and thorium only. Data for the remaining elements were presented as hard copy data listings in an appendix to the report. In 1983 Los Alamos began using exploration geochemistry for the purpose of finding economic mineral deposits to help stimulate the economies of underdeveloped countries. Stream-sediment samples were collected on the Caribbean island of St. Lucia and a geochemical atlas of that island was produced. The data were statistically smoothed and presented as computer-generated color plots of each element of the multielement suite. Studies for the US Bureau of Land Management in 1984 consisted of development of techniques for the integration of several large data sets, which could then be used for computer-assisted mineral resource assessments. A supervised classification technique was developed which compares the attributes of grid cells containing mines or mineral occurrences with attributes of unclassified cells not known to contain mines or occurrences. Color maps indicate how closely unclassified cells match in attributes the cells with mines or occurrences. 20 refs., 1 fig., 1 tab.

  10. The Role of HIV-1 gp41 Glycoprotein in Infectious Tropism Inferred from Physico-Chemical Properties of its Amino Acid Sequence

    NASA Astrophysics Data System (ADS)

    Figueroa, E.; Villarreal, C.; Huerta, L.; Cocho, G.

    2006-09-01

    We performed a statistical analysis of the amino acid sequence of the gp41 ectodomain of the Human Immunodeficiency Virus type 1. We found strong correlations between physicochemical properties of highly variable residues and the viral infectious tropism.

  11. Defective HIV-1 proviruses produce novel protein-coding RNA species in HIV-infected patients on combination antiretroviral therapy.

    PubMed

    Imamichi, Hiromi; Dewar, Robin L; Adelsberger, Joseph W; Rehm, Catherine A; O'Doherty, Una; Paxinos, Ellen E; Fauci, Anthony S; Lane, H Clifford

    2016-08-01

    Despite years of plasma HIV-RNA levels <40 copies per milliliter during combination antiretroviral therapy (cART), the majority of HIV-infected patients exhibit persistent seropositivity to HIV-1 and evidence of immune activation. These patients also show persistence of proviruses of HIV-1 in circulating peripheral blood mononuclear cells. Many of these proviruses have been characterized as defective and thus thought to contribute little to HIV-1 pathogenesis. By combining 5'LTR-to-3'LTR single-genome amplification and direct amplicon sequencing, we have identified the presence of "defective" proviruses capable of transcribing novel unspliced HIV-RNA (usHIV-RNA) species in patients at all stages of HIV-1 infection. Although these novel usHIV-RNA transcripts had exon structures that were different from those of the known spliced HIV-RNA variants, they maintained translationally competent ORFs, involving elements of gag, pol, env, rev, and nef to encode a series of novel HIV-1 chimeric proteins. These novel usHIV-RNAs were detected in five of five patients, including four of four patients with prolonged viral suppression of HIV-RNA levels <40 copies per milliliter for more than 6 y. Our findings suggest that the persistent defective proviruses of HIV-1 are not "silent," but rather may contribute to HIV-1 pathogenesis by stimulating host-defense pathways that target foreign nucleic acids and proteins. PMID:27432972

  12. HIV Transmission

    MedlinePlus

    ... pre-chewed by an HIV-infected person. The contamination occurs when infected blood from a caregiver’s mouth ... pre-chewed by an HIV-infected person. The contamination occurs when infected blood from a caregiver’s mouth ...

  13. DETERMINISTIC TRANSPORT METHODS AND CODES AT LOS ALAMOS

    SciTech Connect

    J. E. MOREL

    1999-06-01

    The purposes of this paper are to: Present a brief history of deterministic transport methods development at Los Alamos National Laboratory from the 1950's to the present; Discuss the current status and capabilities of deterministic transport codes at Los Alamos; and Discuss future transport needs and possible future research directions. Our discussion of methods research necessarily includes only a small fraction of the total research actually done. The works that have been included represent a very subjective choice on the part of the author that was strongly influenced by his personal knowledge and experience. The remainder of this paper is organized in four sections: the first relates to deterministic methods research performed at Los Alamos, the second relates to production codes developed at Los Alamos, the third relates to the current status of transport codes at Los Alamos, and the fourth relates to future research directions at Los Alamos.

  14. Rational development of radiopharmaceuticals for HIV-1.

    PubMed

    Lau, Chuen-Yen; Maldarelli, Frank; Eckelman, William C; Neumann, Ronald D

    2014-04-01

    The global battle against HIV-1 would benefit from a sensitive and specific radiopharmaceutical to localize HIV-infected cells. Ideally, this probe would be able to identify latently infected host cells containing replication competent HIV sequences. Clinical and research applications would include assessment of reservoirs, informing clinical management by facilitating assessment of burden of infection in different compartments, monitoring disease progression and monitoring response to therapy. A "rational" development approach could facilitate efficient identification of an appropriate targeted radiopharmaceutical. Rational development starts with understanding characteristics of the disease that can be effectively targeted and then engineering radiopharmaceuticals to hone in on an appropriate target, which in the case of HIV-1 (HIV) might be an HIV-specific product on or in the host cell, a differentially expressed gene product, an integrated DNA sequence specific enzymatic activity, part of the inflammatory response, or a combination of these. This is different from the current approach that starts with a radiopharmaceutical for a target associated with a disease, mostly from autopsy studies, without a strong rationale for the potential to impact patient care. At present, no targeted therapies are available for HIV latency, although a number of approaches are under study. Here we discuss requirements for a radiopharmaceutical useful in strategies targeting persistently infected cells. The radiopharmaceutical for HIV should be developed based on HIV biology, studied in an animal model and then in humans, and ultimately used in clinical and research settings. PMID:24607432

  15. Heterogeneous Evolution of HIV-1 CRF01_AE in Men Who Have Sex with Men (MSM) and Other Populations in China

    PubMed Central

    Peng, Xiaorong; Wu, Haibo; Peng, Xiuming; Jin, Changzhong; Wu, Nanping

    2015-01-01

    Introduction The HIV epidemic in men who have sex with men (MSM) continues to grow in most countries. However, the phylodynamic and virological differences among HIV-1 strains circulating in MSM and other populations are not well characterized. Methods Nearly full-length genomes (NFLGs) of the HIV-1 CRF01_AE were obtained from the Los Alamos HIV database. Phylogenetic analyses were conducted using the NFLG, gag, pol and env genes, using the maximum likelihood method. Selection pressure analyses at the codon level were performed for each gene in the phylogenetic clusters using PAML. Results Sequences isolated from MSM in China clustered in Clusters 1 (92.5%) and 2 (85.71%). The major risk factor for Cluster 3 was heterosexual transmission (62.16%). The ratio of non-synonymous to synonymous substitutions in the env gene (0.7–0.75) was higher than the gag (0.26–0.34) or pol (0.21–0.26) genes. In env gene, Cluster 1 (4.56×10-3subs/site/year) and 2 (6.01×10-3subs/site/year) had higher evolutionary rates than Cluster 3 (1.14×10-3subs/site/year). Positive selection affected 4.2–6.58% of the amino acid sites in the env gene. Two sites (HXB2:136 and 316) evolved similarly in Clusters 1 and 2, but not Cluster 3. Conclusion The HIV-1 CRF01_AE in MSM is evolving differently than in other populations. PMID:26623642

  16. The Epidemic Dynamics of Four Major Lineages of HIV-1 CRF01_AE Strains After Their Introduction into China.

    PubMed

    Zeng, Haiyan; Li, Tingting; Wang, Yan; Sun, Binlian; Yang, Rongge

    2016-05-01

    The epidemic of HIV-1 CRF01_AE in China was driven by multiple lineages of HIV-1 viruses introduced in the 1990s and increasing; it is important to investigate their epidemic status in China. In this study, we download all available CRF01_AE sequences (n = 2,931) from China and their associated epidemiological information in the Los Alamos HIV database for our analysis to explore their epidemic status in China. The results showed there were 11 distinct clusters of CRF01_AE strains in China, and 4 major clusters that accounted for 80.0% (1,793/2,241) of Chinese CRF01_AE strains in total had led a real epidemic. Clusters 1 and 2 were epidemic among heterosexuals and injecting drug users in southern and southwestern China, while Clusters 3 and 4 were predominant among homosexuals in eastern and central China and northeastern China, respectively. HIV-1 CRF01_AE strains detected in heterosexuals had the most complex characteristic, underscoring its important role in the occurrence of multiple CRF01_AE lineages. Furthermore, epidemic history reconstruction analysis using the birth-death susceptible-infected-removed package revealed that the four clusters had gone through varying epidemic stages. Clusters 2 and 3 were near the peak of the local epidemic, while Clusters 1 and 4 were just in the very early stage of their epidemic. The epidemic status of CRF01_AE clusters in the future is mainly determined by the effect of prevention and control. Our study provides new insights into the understanding of the epidemic dynamics of CRF01_AE in China. PMID:26830205

  17. Natural polymorphisms of HIV-1 CRF01_AE integrase coding region in ARV-naïve individuals in Cambodia, Thailand and Vietnam: an ANRS AC12 working group study.

    PubMed

    Nouhin, Janin; Donchai, Tawee; Hoang, Khanh Thu Huynh; Ken, Sreymom; Kamkorn, Jiraporn; Tran, Ton; Ayouba, Ahidjo; Peeters, Martine; Chaix, Marie-Laure; Lien, Truong Xuan; Nerrienet, Eric; Ngo-Giang-Huong, Nicole

    2011-01-01

    The HIV integrase enzyme is essential for the HIV life cycle as it mediates integration of HIV-1 proviral DNA into the infected cell's genome. Recently, the development of drugs capable of inhibiting integrase has provided major new options for HIV-infected, treatment-experienced patients with multidrug resistant virus, as well treatment-naïve patients. More than 40 amino acid substitutions within integrase have been described as associated mostly with resistance of HIV B-subtypes to currently available integrase inhibitors (INIs). We have analyzed the natural polymorphisms of the integrase coding region in 87 antiretroviral-naïve subjects (32 from Cambodia, 37 from Thailand and 18 from Vietnam) infected with CRF01_AE virus, the predominant HIV-1 strain circulating in Southeast Asia. The 864bp integrase coding region was sequenced using the ANRS consensus sequencing technique from plasma samples, and amino acid results were interpreted for drug resistance according to the ANRS (Updated July 2009, version 18) and Stanford algorithms (Version November 6, 2009). Alignment of the 87 amino acid sequences against the 2004 Los Alamos HIV-1 clade B consensus sequence showed that overall, 119 of 288 (41.3%) amino acid positions presented at least one polymorphism each. Substitutions found in >60% of study subjects occurred at: K14, A21, V31, S39, I72, T112, T124, T125, G134, I135, K136, D167, V201, L234 and S283. Also, new amino acid substitutions of as yet unknown significance were identified: E152K/H, S153F/L, N155I and E157G. None of the known integrase resistance mutations were observed, except E157Q found in one Cambodian subject (1.1%, CI 95% 0.02-6.3%). The clinical impact of this substitution on resistance of B and nonB-viruses to the licensed INI raltegravir is unclear. If this substitution is confirmed to compromise the virologic response to raltegravir, further studies will be needed to better assess the prevalence of this substitution among CRF01_AE virus

  18. Los Alamos Before and After the Fire

    NASA Technical Reports Server (NTRS)

    2002-01-01

    On May 4, 2000, a prescribed fire was set at Bandelier National Monument, New Mexico, to clear brush and dead and dying undergrowth to prevent a larger, subsequent wildfire. Unfortunately, due to high winds and extremely dry conditions in the surrounding area, the prescribed fire quickly raged out of control and, by May 10, the blaze had spread into the nearby town of Los Alamos. In all, more than 20,000 people were evacuated from their homes and more than 200 houses were destroyed as the flames consumed about 48,000 acres in and around the Los Alamos area. The pair of images above were acquired by the Enhanced Thematic Mapper Plus (ETM+) sensor, flying aboard NASA's Landsat 7 satellite, shortly before the Los Alamos fire (top image, acquired April 14) and shortly after the fire was extinguished (lower image, June 17). The images reveal the extent of the damage caused by the fire. Combining ETM+ channels 7, 4, and 2 (one visible and two infrared channels) results in a false-color image where vegetation appears as bright to dark green. Forested areas are generally dark green while herbaceous vegetation is light green. Rangeland or more open areas appear pink to light purple. Areas with extensive pavement or urban development appear light blue or white to purple. Less densely-developed residential areas appear light green and golf courses are very bright green. In the lower image, the areas recently burned appear bright red. Landsat 7 data courtesy United States Geological Survey EROS DataCenter. Images by Robert Simmon, NASA GSFC.

  19. HIV Medication Adherence

    MedlinePlus

    HIV Treatment HIV Medication Adherence (Last updated 3/1/2016; last reviewed 3/1/2016) Key Points Medication adherence means sticking ... exactly as prescribed. Why is adherence to an HIV regimen important? Adherence to an HIV regimen gives ...

  20. HIV among Transgender People

    MedlinePlus

    ... of transgender Virginians . Richmond, VA: Virginia HIV Community Planning Committee and Virginia Department of Health; 2007. Accessed April 14, 2016. Additional ... HIV/AIDS CDC HIV CDC HIV/AIDS ...

  1. LAMPF II workshop, Los Alamos National Laboratory, Los Alamos, New Mexico, February 1-4, 1982

    SciTech Connect

    Thiessen, H.A.

    1982-01-01

    This report contains the proceedings of the first LAMPF II Workshop held at Los Alamos February 1 to 4, 1982. Included are the talks that were available in written form. The conclusion of the participants was that there are many exciting areas of physics that will be addressed by such a machine.

  2. Biological assessment for the effluent reduction program, Los Alamos National Laboratory, Los Alamos, New Mexico

    SciTech Connect

    Cross, S.P.

    1996-08-01

    This report describes the biological assessment for the effluent recution program proposed to occur within the boundaries of Los Alamos National Laboratory. Potential effects on wetland plants and on threatened and endangered species are discussed, along with a detailed description of the individual outfalls resulting from the effluent reduction program.

  3. Los Alamos National Laboratory computer benchmarking 1982

    SciTech Connect

    Martin, J.L.

    1983-06-01

    Evaluating the performance of computing machinery is a continual effort of the Computer Research and Applications Group of the Los Alamos National Laboratory. This report summarizes the results of the group's benchmarking activities performed between October 1981 and September 1982, presenting compilation and execution times as well as megaflop rates for a set of benchmark codes. Tests were performed on the following computers: Cray Research, Inc. (CRI) Cray-1S; Control Data Corporation (CDC) 7600, 6600, Cyber 73, Cyber 825, Cyber 835, Cyber 855, and Cyber 205; Digital Equipment Corporation (DEC) VAX 11/780 and VAX 11/782; and Apollo Computer, Inc., Apollo.

  4. Ultraprecision machining of optics at Los Alamos

    SciTech Connect

    Rhorer, R.L.; Gauler, A.L.; Colston, E.W.; Ruhe, J.R.

    1982-01-01

    Ultraprecision machine tools are used at the Los Alamos National Laboratory for single-point diamond turning of optics and other precision parts. Measurements of a 50-mm-diam copper flat illustrate the quality of a part that can be machined on the Moore No. 3 lathe. Measurements of a 0.4-m-diam aluminum mirror with a 20-m radius of curvature are presented as an example of a part machined on the Moore No. 5 lathe. A varying frequency sine wave grating shows a type of special optical grating that can be produced using the Pneumo lathe.

  5. Ultraprecision machining of optics at Los Alamos

    SciTech Connect

    Rhorer, R.L.; Gauler, A.L.; Colston, E.W.; Ruhe, J.R.

    1981-01-01

    Ultraprecision machine tools are used at Los Alamos for single point diamond turning of optics and other precision parts. Measurements of a 50-mm-dia copper flat are used to illustrate the quality of a part which can be machined on the Moore No. 3 lathe. Measurements of a 0.4-m-dia aluminum mirror with a 20-m radius-of-curvature are presented as an example of a part machined on the Moore No. 5 lathe. A varying frequency sine wave grating is used to show a type of special optical grating which can be produced using the Pneumo lathe.

  6. Environmental Programs at Los Alamos National Laboratory

    SciTech Connect

    Jones, Patricia

    2012-07-11

    Summary of this project is: (1) Teamwork, partnering to meet goals - (a) Building on cleanup successes, (b) Solving legacy waste problems, (c) Protecting the area's environment; (2) Strong performance over the past three years - (a) Credibility from four successful Recovery Act Projects, (b) Met all Consent Order milestones, (c) Successful ramp-up of TRU program; (3) Partnership between the National Nuclear Security Administration's Los Alamos Site Office, DOE Carlsbad Field Office, New Mexico Environment Department, and contractor staff enables unprecedented cleanup progress; (4) Continued focus on protecting water resources; and (5) All consent order commitments delivered on time or ahead of schedule.

  7. Los Alamos National Laboratory strategic directions

    SciTech Connect

    Hecker, S.

    1995-10-01

    It is my pleasure to welcome you to Los Alamos. I like the idea of bringing together all aspects of the research community-defense, basic science, and industrial. It is particularly important in today`s times of constrained budgets and in fields such as neutron research because I am convinced that the best science and the best applications will come from their interplay. If we do the science well, then we will do good applications. Keeping our eye focused on interesting applications will spawn new areas of science. This interplay is especially critical, and it is good to have these communities represented here today.

  8. Detection of human papillomavirus and Epstein-Barr virus DNA sequences in oral mucosa of HIV-infected patients by the polymerase chain reaction.

    PubMed Central

    Snijders, P. J.; Schulten, E. A.; Mullink, H.; ten Kate, R. W.; Jiwa, M.; van der Waal, I.; Meijer, C. J.; Walboomers, J. M.

    1990-01-01

    The presence of human papillomavirus (HPV) and Epstein-Barr virus (EBV) was analyzed in 21 oral biopsy specimens of HIV-infected patients using the polymerase chain reaction (PCR) method. Biopsies were categorized as hairy leukoplakia (HL) (n = 12), candidiasis (n = 3), oral warts (n = 2), and clinically normal epithelium (n = 4). For HPV detection a modified general primer-mediated PCR method (GP-PCR), which detects a broad spectrum of HPV genotypes at sub-picogram levels, was used. Human papillomavirus DNA was only found in two oral warts and was identified as HPV type 32. Epstein-Barr virus DNA was detected in 16 biopsy specimens, including the 12 HLs, 2 cases of candidiasis, and 2 samples of normal epithelium. Epstein-Barr virus positivity in HL could be confirmed by Southern blot analysis and DNA in situ hybridization using biotinylated DNA probes (bio-DISH). Epstein-Barr virus bio-DISH was also positive in one sample of normal epithelium from a patient with HL. The results indicate that HL is strongly associated with EBV and not with any of the common HPV types that react with general HPV primers in the PCR. However the detection of EBV in normal oral epithelium by PCR and bio-DISH suggests that the presence of this virus is not exclusively related to HL. Images Figure 1 Figure 2 Figure 3 Figure 4 PMID:2169191

  9. Direct Interrogation of Viral Peptides Presented by the Class I HLA of HIV-Infected T Cells

    PubMed Central

    Yaciuk, Jane C.; Skaley, Matthew; Bardet, Wilfried; Schafer, Fredda; Mojsilovic, Danijela; Cate, Steven; Stewart, Christopher J.; McMurtrey, Curtis; Jackson, Kenneth W.; Buchli, Rico; Olvera, Alex; Cedeño, Samandhy; Plana, Montserrat; Mothe, Beatriz; Brander, Christian; West, John T.

    2014-01-01

    ABSTRACT Identification of CD8+ cytotoxic T lymphocyte (CTL) epitopes has traditionally relied upon testing of overlapping peptide libraries for their reactivity with T cells in vitro. Here, we pursued deep ligand sequencing (DLS) as an alternative method of directly identifying those ligands that are epitopes presented to CTLs by the class I human leukocyte antigens (HLA) of infected cells. Soluble class I HLA-A*11:01 (sHLA) was gathered from HIV-1 NL4-3-infected human CD4+ SUP-T1 cells. HLA-A*11:01 harvested from infected cells was immunoaffinity purified and acid boiled to release heavy and light chains from peptide ligands that were then recovered by size-exclusion filtration. The ligands were first fractionated by high-pH high-pressure liquid chromatography and then subjected to separation by nano-liquid chromatography (nano-LC)–mass spectrometry (MS) at low pH. Approximately 10 million ions were selected for sequencing by tandem mass spectrometry (MS/MS). HLA-A*11:01 ligand sequences were determined with PEAKS software and confirmed by comparison to spectra generated from synthetic peptides. DLS identified 42 viral ligands presented by HLA-A*11:01, and 37 of these were previously undetected. These data demonstrate that (i) HIV-1 Gag and Nef are extensively sampled, (ii) ligand length variants are prevalent, particularly within Gag and Nef hot spots where ligand sequences overlap, (iii) noncanonical ligands are T cell reactive, and (iv) HIV-1 ligands are derived from de novo synthesis rather than endocytic sampling. Next-generation immunotherapies must factor these nascent HIV-1 ligand length variants and the finding that CTL-reactive epitopes may be absent during infection of CD4+ T cells into strategies designed to enhance T cell immunity. IMPORTANCE HIV-1 epitopes catalogued by the Los Alamos National Laboratory (LANL) have yielded limited success in vaccine trials. Because the HLA of infected cells have not previously been assessed for HIV-1 ligands, the

  10. Screening and diagnosis for HIV

    MedlinePlus

    HIV testing; HIV screening; HIV screening test; HIV confirmatory test ... A positive result on a screening test does not confirm that the person has HIV infection. More tests are needed to confirm HIV infection. A negative test ...

  11. HIV among Women

    MedlinePlus

    ... testing site near you. Enter ZIP code or city Follow HIV/AIDS CDC HIV CDC HIV/AIDS ... HIV infection—National HIV Behavioral Surveillance, 20 U.S. cities, 2013 . HIV Surveillance Special Report 13 . Accessed January ...

  12. HIV Drug Resistance Surveillance Among Jamaican Men Who Have Sex with Men Should Be Prioritized for Reducing HIV Transmission.

    PubMed

    Collins-Fairclough, Aneisha M; Dennis, Ann M; Nelson, Julie A E; Weir, Sharon S; Figueroa, J Peter

    2015-08-01

    The prevalence of human immunodeficiency virus type 1 (HIV-1) is highest among men who have sex with men (MSM) in Jamaica but no genotypic data are available on the virus strains that are responsible for the epidemic among this key population. HIV-1 polymerase (pol) genes from 65 MSM were sequenced and used to predict drug resistance mutations. An HIV drug resistance prevalence of 28% (minimum 13%) was observed among this cohort, with the most frequent mutations conferring resistance to efavirenz, nevirapine, and lamivudine. Phylogenetic analysis of the sequences revealed 10 times the number of linked HIV infections among this cohort than respondent reporting. HIV treatment and prevention efforts in Jamaica could benefit significantly from Pol genotyping of the HIV strains infecting socially vulnerable MSM prior to initiating antiretroviral therapy (ART), as this would guide suppressive ART and unearth HIV transmission clusters to enable more effective delivery of treatment and prevention programs. PMID:26133540

  13. HIV Drug Resistance Surveillance Among Jamaican Men Who Have Sex with Men Should Be Prioritized for Reducing HIV Transmission

    PubMed Central

    Dennis, Ann M.; Nelson, Julie A.E.; Weir, Sharon S.; Figueroa, J. Peter

    2015-01-01

    Abstract The prevalence of human immunodeficiency virus type 1 (HIV-1) is highest among men who have sex with men (MSM) in Jamaica but no genotypic data are available on the virus strains that are responsible for the epidemic among this key population. HIV-1 polymerase (pol) genes from 65 MSM were sequenced and used to predict drug resistance mutations. An HIV drug resistance prevalence of 28% (minimum 13%) was observed among this cohort, with the most frequent mutations conferring resistance to efavirenz, nevirapine, and lamivudine. Phylogenetic analysis of the sequences revealed 10 times the number of linked HIV infections among this cohort than respondent reporting. HIV treatment and prevention efforts in Jamaica could benefit significantly from Pol genotyping of the HIV strains infecting socially vulnerable MSM prior to initiating antiretroviral therapy (ART), as this would guide suppressive ART and unearth HIV transmission clusters to enable more effective delivery of treatment and prevention programs. PMID:26133540

  14. Helical structure determined by NMR of the HIV-1 (345–392)Gag sequence, surrounding p2: Implications for particle assembly and RNA packaging

    PubMed Central

    Morellet, Nelly; Druillennec, Sabine; Lenoir, Christine; Bouaziz, Serge; Roques, Bernard P.

    2005-01-01

    Gag protein oligomerization, an essential step during virus assembly, results in budding of spherical virus particles. This process is critically dependent on the spacer p2, located between the capsid and the nucleocapsid proteins. P2 contributes also, in association with NCp7, to specific recognition of the HIV-1 packaging signal resulting in viral genome encapsidation. There is no structural information about the 20 last amino acids of the C-terminal part of capsid (CA[CTD]) and p2, in the molecular mechanism of Gag assembly. In this study the structure of a peptide encompassing the 14 residues of p2 with the upstream 21 residues and the downstream 13 residues was determined by 1H NMR in 30% trifluoroethanol (TFE). The main structural motif is a well-defined amphipathic α-helix including p2, the seven last residues of the CA(CTD), and the two first residues of NCp7. Peptides containing the p2 domain have a strong tendency to aggregate in solution, as shown by gel filtration analyses in pure H2O. To take into account the aggregation phenomena, models of dimer and trimer formed through hydrophobic or hydrophilic interfaces were constructed by molecular dynamic simulations. Gel shift experiments demonstrate that the presence of at least p2 and the 13 first residues of NCp7 is required for RNA binding. A computer-generated model of the Gag polyprotein segment (282–434)Gag interacting with the packaging element SL3 is proposed, illustrating the importance of p2 and NCp7 in genomic encapsidation. PMID:15659370

  15. HIV / AIDS

    MedlinePlus

    ... Marketing Share this: Main Content Area Understanding HIV/AIDS AIDS was first reported in the United States in ... and has since become a major worldwide epidemic. AIDS is caused by the human immunodeficiency virus, or ...

  16. Audit of personal property management at Los Alamos National Laboratory

    SciTech Connect

    Not Available

    1993-12-07

    The Department of Energy`s (Department) Albuquerque Operations Office (Albuquerque) and the Los Alamos National Laboratory (Los Alamos) are responsible for ensuring that Los Alamos maintains an efficient and effective personal property management system that protects, identifies, and controls Government-owned personal property in accordance with applicable regulations. Albuquerque is responsible for reviewing and approving Los Alamos` personal property management system. Los Alamos is responsible for ensuring that personal property is properly protected, identified, and controlled. The audit disclosed that Los Alamos did not have an efficient and effective personal property management system to ensure that personal property was adequately protected, identified, and controlled. In addition, Albuquerque did not approve or disapprove Los Alamos` personal property management system consistent with Federal and Department regulations. Specifically, the audit showed that Los Alamos did not account for $11.6 million of personal property. In addition, $22.2 million of personal property was not properly recorded in the database, $61.7 million of personal property could not be inventoried, and loans to employees and other entities were not adequately justified. As a result, from a total personal property inventory of approximately $1 billion, it is estimated that $100 million of personal property may not be accounted for, and $207 million may not be correctly recorded in the database. Moreover, substantial amounts of personal property on loan to employees and other entities were at risk of unauthorized use. Albuquerque concurred with the finding and agreed to implement the corrective actions recommended in the report.

  17. The Climate at Los Alamos; Are we measurement changes?

    SciTech Connect

    Dewart, Jean Marie

    2015-04-16

    A new report shows new graphic displays of the weather trends in Los Alamos, New Mexico, and at the Los Alamos National Laboratory (LANL). The graphs show trends of average, minimum average, and maximum average temperature for summer and winter months going back decades. Records of summer and winter precipitation are also included in the report.

  18. Los Alamos personnel and area criticality dosimeter systems

    SciTech Connect

    Vasilik, D.G.; Martin, R.W.

    1981-06-01

    Fissionable materials are handled and processed at the Los Alamos National Laboratory. Although the probability of a nuclear criticality accident is very remote, it must be considered. Los Alamos maintains a broad spectrum of dose assessment capabilities. This report describes the methods employed for personnel neutron, area neutron, and photon dose evaluations with passive dosimetry systems.

  19. Carbon isotope chemostratigraphy and precise dating of middle Frasnian (lower Upper Devonian) Alamo Breccia, Nevada, USA

    USGS Publications Warehouse

    Morrow, J.R.; Sandberg, C.A.; Malkowski, K.; Joachimski, M.M.

    2009-01-01

    At Hancock Summit West, Nevada, western USA, uppermost Givetian (upper Middle Devonian) and lower and middle Frasnian (lower Upper Devonian) rocks of the lower Guilmette Formation include, in stratigraphic sequence, carbonate-platform facies of the conodont falsiovalis, transitans, and punctata Zones; the type Alamo Breccia Member of the middle punctata Zone; and slope facies of the punctata and hassi Zones. The catastrophically deposited Alamo Breccia and related phenomena record the ~ 382??Ma Alamo event, produced by a km-scale bolide impact into a marine setting seaward of an extensive carbonate platform fringing western North America. Re-evaluation of conodonts from the lower Guilmette Formation and Alamo Breccia Member, together with regional sedimentologic and conodont biofacies comparisons, now firmly locates the onset of the Johnson et al. (1985) transgressive-regressive (T-R) cycle IIc, which occurred after the start of the punctata Zone, within a parautochthonous megablock low in the Alamo Breccia. Whole-rock carbon isotope analyses through the lower Guilmette Formation and Alamo Breccia Member reveal two positive ??13Ccarb excursions: (1) a small, 3??? excursion, which is possibly correlative with the falsiovalis Event previously identified from sections in Western Europe and Australia, occurs below the breccia in the Upper falsiovalis Zone to early part of the transitans Zone; and (2) a large, multi-part excursion, dominated by a 6??? positive shift, begins above the start of the punctata Zone and onset of T-R cycle IIc and continues above the Alamo Breccia, ending near the punctata- hassi zonal boundary. This large excursion correlates with the punctata Event, a major positive ??13C excursion previously recognized in eastern Laurussia and northern Gondwana. Consistent with previous studies, at Hancock Summit West the punctata Event is apparently not associated with any regional extinctions or ecosystem reorganizations. In the study area, onset of the

  20. HIV-1 RNA quantification in CRF02_AG HIV-1 infection: too easy to make mistakes.

    PubMed

    Tatarelli, Paola; Taramasso, Lucia; Di Biagio, Antonio; Sticchi, Laura; Nigro, Nicola; Barresi, Renata; Viscoli, Claudio; Bruzzone, Bianca

    2016-04-01

    The number of patients newly infected by HIV-1 non-B subtypes and circulating recombinant forms (CRFs) is increasing worldwide, including in the western countries. We report on a primary HIV-1 infection in a Caucasian patient. A routine quantitative assay (Nuclisens EasyQ HIV-1 2.0, BioMérieux SA) showed 6,700 HIV-1 RNA copies/ml. A combined antiretroviral therapy (cART) consistent with low baseline HIV-1 RNA was started. Few days later, the analysis performed with REGA HIV-1 Subtyping Tool - Version 3.0 attributed the HIV-1 sequence to the CRF02_AG recombinant form. Therefore, a second real-time PCR assay was performed, using the Versant HIV-1 RNA 1.0 Assay (kPCR) (Siemens HealthCare Diagnostics) which revealed a HIV-1 RNA of 230,000 copies/ml. Consequently, the ongoing cART was potentiated. This case suggests that the wide genetic variability of HIV-1 subtypes may affect the capability of the commonly used assays to detect and accurately quantify HIV-1 RNA in non-B subtypes and CRFs. In presence of CRFs different commercial HIV-1 RNA tests should be performed to find the most reliable for viral load quantification at the diagnosis, because it influences the choice of cART, and during the follow-up. Indeed, international guidelines for HIV-1 infection management suggest to monitor patient' HIV-RNA with the same assay over the course of treatment. As different commercial tests can be performed in the same laboratory with considerable difficulty, the laboratory should select an assay that is suitable not only for the more prevalent strain, but also for less frequent ones that, nevertheless, can occur. Then, knowing and investigating the spread of non-B strains has essential clinical and laboratory implications. PMID:27196556

  1. Portable MRI developed at Los Alamos

    SciTech Connect

    Espy, Michelle

    2015-04-22

    Scientists at Los Alamos National Laboratory are developing an ultra-low-field Magnetic Resonance Imaging (MRI) system that could be low-power and lightweight enough for forward deployment on the battlefield and to field hospitals in the World's poorest regions. "MRI technology is a powerful medical diagnostic tool," said Michelle Espy, the Battlefield MRI (bMRI) project leader, "ideally suited for imaging soft-tissue injury, particularly to the brain." But hospital-based MRI devices are big and expensive, and require considerable infrastructure, such as large quantities of cryogens like liquid nitrogen and helium, and they typically use a large amount of energy. "Standard MRI machines just can't go everywhere," said Espy. "Soldiers wounded in battle usually have to be flown to a large hospital and people in emerging nations just don't have access to MRI at all. We've been in contact with doctors who routinely work in the Third World and report that MRI would be extremely valuable in treating pediatric encephalopathy, and other serious diseases in children." So the Los Alamos team started thinking about a way to make an MRI device that could be relatively easy to transport, set up, and use in an unconventional setting. Conventional MRI machines use very large magnetic fields that align the protons in water molecules to then create magnetic resonance signals, which are detected by the machine and turned into images. The large magnetic fields create exceptionally detailed images, but they are difficult and expensive to make. Espy and her team wanted to see if images of sufficient quality could be made with ultra-low-magnetic fields, similar in strength to the Earth's magnetic field. To achieve images at such low fields they use exquisitely sensitive detectors called Superconducting Quantum Interference Devices, or SQUIDs. SQUIDs are among the most sensitive magnetic field detectors available, so interference with the signal is the primary stumbling block. "SQUIDs are

  2. HIV-1 Envelope Resistance to Proteasomal Cleavage: Implications for Vaccine Induced Immune Responses

    PubMed Central

    Steers, Nicholas J.; Ratto-Kim, Silvia; de Souza, Mark S.; Currier, Jeffrey R.; Kim, Jerome H.; Michael, Nelson L.; Alving, Carl R.; Rao, Mangala

    2012-01-01

    Background Antigen processing involves many proteolytic enzymes such as proteasomes and cathepsins. The processed antigen is then presented on the cell surface bound to either MHC class I or class II molecules and induces/interacts with antigen-specific CD8+ and CD4+ T-cells, respectively. Preliminary immunological data from the RV144 phase III trial indicated that the immune responses were biased towards the Env antigen with a dominant CD4+ T-cell response. Methods In this study, we examined the susceptibility of HIV-1 Env-A244 gp120 protein, one of the protein boost subunits of the RV144 Phase III vaccine trial, to proteasomes and cathepsins and identified the generated peptide epitope repertoire by mass spectrometry. The peptide fragments were tested for cytokine production in CD4+ T-cell lines derived from RV144 volunteers. Results Env-A244 was resistant to proteasomes, thus diminishing the possibility of the generation of class I epitopes by the classical MHC class I pathway. However, Env-A244 was efficiently cleaved by cathepsins generating peptide arrays identified by mass spectrometry that contained both MHC class I and class II epitopes as reported in the Los Alamos database. Each of the cathepsins generated distinct degradation patterns containing regions of light and dense epitope clusters. The sequence DKKQKVHALF that is part of the V2 loop of gp120 produced by cathepsins induced a polyfunctional cytokine response including the generation of IFN-γ from CD4+ T-cell lines-derived from RV144 vaccinees. This sequence is significant since antibodies to the V1/V2-loop region correlated inversely with HIV-1 infection in the RV144 trial. Conclusions Based on our results, the susceptibility of Env-A244 to cathepsins and not to proteasomes suggests a possible mechanism for the generation of Env-specific CD4+T cell and antibody responses in the RV144 vaccinees. PMID:22880042

  3. Mutagenicity and pausing of HIV reverse transcriptase during HIV plus-strand DNA synthesis.

    PubMed Central

    Ji, J; Hoffmann, J S; Loeb, L

    1994-01-01

    The unusually high frequency of misincorporation by HIV-1 reverse transcriptase (HIV RT) is likely to be the major factor in the rapid accumulation of viral mutations in AIDS, especially in the env gene. To investigate the ability of HIV RT to copy the env gene, we subcloned an HIV env gene fragment into a single-stranded DNA vector and measured the progression of synthesis by HIV RT. We observed that HIV RT, but not RT from avian myeloblastosis virus, DNA polymerase-alpha or T7 DNA polymerase, pauses specifically at poly-deoxyadenosine stretches within the env gene. The frequency of bypassing the polyadenosine stretches by HIV RT is enhanced by increasing the ratio of enzyme to template. We measured the fidelity of DNA synthesis within a segment of the hypervariable region 1 of the env gene (V-1) containing a poly-deoxyadenosine sequence by repetitively copying the DNA by HIV RT, and then cloning and sequencing the copied fragments. We found that 27% of the errors identified in V-1 sequence were frameshift mutations opposite the poly-adenosine tract, a site where strong pausing was observed. Pausing of HIV RT at the polyadenosine tract could be enhanced by either distamycin A or netropsin, (A-T)-rich minor groove binding peptides. Moreover, netropsin increases the frequency of frameshift mutations in experiments in which HIV RT catalyzes gap filling synthesis within the lacZ gene in double-stranded circular M13mp2 DNA. These combined results suggest that the enhanced mutation frequency may be due to increased pausing at netropsin-modified polyadenosine tracts. Therefore, netropsin and related A-T binding chemicals may selectively enhance frameshift mutagenesis induced by HIV RT and yield predominantly non-viable virus. Images PMID:7510388

  4. Envelope gene evolution and HIV-1 neuropathogenesis

    PubMed Central

    Vázquez-Santiago, Fabián J.; Rivera-Amill, Vanessa

    2016-01-01

    In the era of combined antiretroviral therapy (cART), HIV-associated neurocognitive disorders (HAND) account for 40 to 56% of all HIV+ cases. During the acute stage of HIV-1 infection (<6 months), the virus invades and replicates within the central nervous system (CNS). Compared to peripheral tissues, the local CNS cell population expresses distinct levels of chemokine receptors, which levels exert selective pressure on the invading virus. HIV-1 envelope (env) sequences recovered from the brains and cerebrospinal fluid (CSF) of neurocognitively impaired HIV+ subjects often display higher nucleotide variability as compared to non-impaired HIV+ subjects. Specifically, env evolution provides HIV-1 with the strategies to evade host immune response, to reduce chemokine receptor dependence, to increase co-receptor binding efficiency, and to potentiate neurotoxicity. The evolution of env within the CNS leads to changes that may result in the emergence of novel isolates with neurotoxic and neurovirulent features. However, whether specific factors of HIV-1 evolution lead to the emergence of neurovirulent and neurotropic isolates remains ill-defined. HIV-1 env evolution is an ongoing phenomenon that occurs independently of neurological and neurocognitive disease severity; thus HIV env evolution may play a pivotal and reciprocal role in the etiology of HAND. Despite the use of cART, the reactivation of latent viral reservoirs represents a clinical challenge because of the replenishment of the viral pool that may subsequently lead to persistent infection. Therefore, gaining a more complete understanding of how HIV-1 env evolves over the course of the disease should be considered for the development of future therapies aimed at controlling CNS burden, diminishing persistent viremia, and eradicating viral reservoirs. Here we review the current literature on the role of HIV-1 env evolution in the setting of HAND disease progression and on the impact of cART on the dynamics of

  5. Environmental surveillance at Los Alamos during 1979

    SciTech Connect

    Not Available

    1980-04-01

    This report documents the environmental surveillance program conducted by the Los Alamos Scientific Laboratory (LASL) in 1979. Routine monitoring for radiation and radioactive or chemical substances was conducted on the Laboratory site and in the surrounding region to determine compliance with appropriate standards and permit early identification of possible undesirable trends. Results and interpretation of the data for 1979 on penetrating radiation, chemical and radiochemical quality of ambient air, surface and ground water, municipal water supply, soils and sediments, food, and airborne and liquid effluents are included. Comparisons with appropriate standards and regulations or with background levels from natural or other non-LASL sources provide a basis for concluding that environmental effects attributable to LASL operations are minor and cannot be considered likely to result in any hazard to the population of the area. Results of several special studies provide documentation of some unique environmental conditions in the LASL environs.

  6. Environmental surveillance at Los Alamos during 1992

    SciTech Connect

    Kohen, K.; Stoker, A.; Stone, G.

    1994-07-01

    This report describes the environmental surveillance program at Los Alamos National Laboratory during 1992. The Laboratory routinely monitors for radiation and for radioactive and nonradioactive materials at (or on) Laboratory sites as well as in the surrounding region. LANL uses the monitoring results to determine compliance with appropriate standards and to identify potentially undesirable trends. Data were collected in 1992 to assess external penetrating radiation; quantities of airborne emissions and liquid effluents; concentrations of chemicals and radionuclides in ambient air, surface waters and groundwaters, municipal water supply, soils and sediments, and foodstuffs; and environmental compliance. Using comparisons with standards, regulations, and background levels, this report concludes that environmental effects from Laboratory operations are small and do not pose a demonstrable threat to the public, laboratory employees, or the environment.

  7. Foreign National Involvement at Los Alamos

    NASA Astrophysics Data System (ADS)

    Wilhelmy, Jerry

    2000-04-01

    Since the beginning of the spring of 1999 there has been an intense national media focus on alleged security breaches by a foreign born scientist employed at LANL. Alarmed by an apparent growing sense of xenophobia, the Fellows of the Los Alamos National Laboratory addressed this issue by preparing a white paper on Foreign National Involvement at LANL (www.fellows.lanl.gov). Its purpose was to recognize and acknowledge the vital role that foreign scientists have played and continue to play in making LANL a forefront scientific institution. This legacy will be discussed, as well as concerns that constraining regulations triggered by this episode and subsequent reactions to this by our scientific peer community could have long term consequences on the vitality of the Laboratory.

  8. Environmental surveillance at Los Alamos during 1989

    SciTech Connect

    Not Available

    1990-12-01

    This report describes the environmental surveillance program conducted by Los Alamos National Laboratory during 1989. Routine monitoring for radiation and radioactive or chemical materials is conducted on the Laboratory site as well as in the surrounding region. Monitoring results are used to determine compliance with appropriate standards and to permit early identification of potentially undesirable trends. Results and interpretation of data for 1989 cover external penetrating radiation; quantities of airborne emissions and effluents; concentrations of chemicals and radionuclides in ambient air, surface and ground waters, municipal water supply, soils and sediments, and foodstuffs; and environmental compliance. Comparisons with appropriate standards, regulations, and background levels provide the basis for concluding that environmental effects from Laboratory operations are small and do not pose a threat to the public, Laboratory employees, or the environment. 58 refs., 31 figs., 39 tabs.

  9. Environmental surveillance at Los Alamos during 1995

    SciTech Connect

    1996-10-01

    This report describes the environmental surveillance program at Los Alamos National Laboratory (LANL or the Laboratory) during 1995. The Laboratory routinely monitors for radiation and for radioactive and nonradioactive materials at (or on) Laboratory sites as well as in the surrounding region. LANL uses the monitoring result to determine compliance with appropriate standards and to identify potentially undesirable trends. Data were collected in 1995 to assess external penetrating radiation; quantities of airborne emissions and liquid effluents; concentrations of chemicals and radionuclides in ambient air, surface waters and groundwaters, municipal water supply, soils and sediments, and foodstuffs; and environmental compliance. Using comparisons with standards, regulations, and background levels, this report concludes that environmental effects from Laboratory operations are small and do not pose a demonstrable threat to the public, Laboratory employees, or the environment.

  10. Environmental surveillance at Los Alamos during 1987

    SciTech Connect

    Not Available

    1988-05-01

    This report describes the environmental surveillance program conducted by Los Alamos National Laboratory during 1987. Routine monitoring for radiation and radioactive or chemical materials is conducted on the Laboratory site as well as in the surrounding region. Monitoring results are used to determine compliance with appropriate standards and to permit early identification of potentially undesirable trends. Results and interpretation of data for 1987 cover: external penetrating radiation; quantities of airborne emissions and liquid effluents; concentrations of chemicals and radionuclides in ambient air, surface and ground waters, municipal water supply, soils and sediments, and foodstuffs; and environmental compliance. Comparisons with appropriate standards, regulations, and background levels provide the basis for concluding that environmental effects from Laboratory operations are insignificant and do not pose a threat to the public, Laboratory employees, or the environment. 113 refs., 33 figs., 120 tabs.

  11. Los Alamos National Laboratory transuranic database analysis

    SciTech Connect

    Christensen, D.V.; Rogers, P.S.Z.; Kosiewicz, S.T.; LeBrun, D.B.

    1997-02-01

    This paper represents an overview of analyses conducted on the TRU database maintained by the Los Alamos National Laboratory (LANL). This evaluation was conducted to support the ``TRU Waste Workoff Strategies`` document and provides an estimation of the waste volume that potentially could be certified and ready for shipment to (WIPP) in April of 1998. Criteria defined in the WIPP WAC, including container type, weight limits, plutonium fissile gram equivalents and decay heat, were used to evaluated the waste for compliance. LANL evaluated the containers by facility and by waste stream to determining the most efficient plan for characterization and certification of the waste. Evaluation of the waste presently in storage suggested that 40- 60% potentially meets the WIPP WAC Rev. 5 criteria.

  12. Information about Practicums at Los Alamos

    SciTech Connect

    Bradley, Paul A.

    2012-07-24

    The Los Alamos Neutron Science Center is the premier facility for neutron science experiments ranging from cross section measurements, neutron scattering experiments, proton radiography, cold neutrons, actinide neutronic properties, and many other exciting topics. The National High Magnetic Field Laboratory is home to several powerful magnets, including the one that created the first non-destructive 100 Tesla field in March 2012. They probe the electronic structure of superconductors, magnetic properties of materials (including magneto-quantum effects). Research is also conducted in correlated materials, thermoacoustics, and magnetic properties of actinides. The Trident Laser has a unique niche with very high power, short pulse experiments, with a peak power of 10{sup 20} W in short pulse mode. Discoveries range from production of monoenergetic MeV ion beam, nonlinear kinetic plasma waves, the transition between kinetic and fluid nonlinear behavior and other laser-plasma interaction processes.

  13. Environmental analysis of Lower Pueblo/Lower Los Alamos Canyon, Los Alamos, New Mexico

    SciTech Connect

    Ferenbaugh, R.W.; Buhl, T.E.; Stoker, A.K.; Becker, N.M.; Rodgers, J.C.; Hansen, W.R.

    1994-12-01

    The radiological survey of the former radioactive waste treatment plant site (TA-45), Acid Canyon, Pueblo Canyon, and Los Alamos Canyon found residual contamination at the site itself and in the channel and banks of Acid, Pueblo, and lower Los Alamos Canyons all the way to the Rio Grande. The largest reservoir of residual radioactivity is in lower Pueblo Canyon, which is on DOE property. However, residual radioactivity does not exceed proposed cleanup criteria in either lower Pueblo or lower Los Alamos Canyons. The three alternatives proposed are (1) to take no action, (2) to construct a sediment trap in lower Pueblo Canyon to prevent further transport of residual radioactivity onto San Ildefonso Indian Pueblo land, and (3) to clean the residual radioactivity from the canyon system. Alternative 2, to cleanup the canyon system, is rejected as a viable alternative. Thousands of truckloads of sediment would have to be removed and disposed of, and this effort is unwarranted by the low levels of contamination present. Residual radioactivity levels, under either present conditions or projected future conditions, will not result in significant radiation doses to persons exposed. Modeling efforts show that future transport activity will not result in any residual radioactivity concentrations higher than those already existing. Thus, although construction of a sediment trap in lower Pueblo Canyon is a viable alternative, this effort also is unwarranted, and the no-action alternative is the preferred alternative.

  14. Environmental surveillance at Los Alamos during 2008

    SciTech Connect

    Fuehne, David; Gallagher, Pat; Hjeresen, Denny; Isaacson, John; Johson, Scot; Morgan, Terry; Paulson, David; Rogers, David

    2009-09-30

    Environmental Surveillance at Los Alamos reports are prepared annually by the Los Alamos National Laboratory (the Laboratory) Environmental Programs Directorate, as required by US Department of Energy Order 450.1, General Environmental Protection Program, and US Department of Energy Order 231.1A, Environment, Safety, and Health Reporting. These annual reports summarize environmental data that are used to determine compliance with applicable federal, state, and local environmental laws and regulations, executive orders, and departmental policies. Additional data, beyond the minimum required, are also gathered and reported as part of the Laboratory’s efforts to ensure public safety and to monitor environmental quality at and near the Laboratory. Chapter 1 provides an overview of the Laboratory’s major environmental programs and explains the risks and the actions taken to reduce risks at the Laboratory from environmental legacies and waste management operations. Chapter 2 reports the Laboratory’s compliance status for 2007. Chapter 3 provides a summary of the maximum radiological dose the public and biota populations could have potentially received from Laboratory operations and discusses chemical exposures. The environmental surveillance and monitoring data are organized by environmental media (Chapter 4, air; Chapters 5 and 6, water and sediments; Chapter 7, soils; and Chapter 8, foodstuffs and biota) in a format to meet the needs of a general and scientific audience. Chapter 9 provides a summary of the status of environmental restoration work around LANL. A glossary and a list of acronyms and abbreviations are in the back of the report. Appendix A explains the standards for environmental contaminants, Appendix B explains the units of measurements used in this report, Appendix C describes the Laboratory’s technical areas and their associated programs, and Appendix D provides web links to more information.

  15. Environmental surveillance at Los Alamos during 2005

    SciTech Connect

    2006-09-30

    Environmental Surveillance at Los Alamos reports are prepared annually by the Los Alamos National Laboratory (LANL or the Laboratory) environmental organization, as required by US Department of Energy Order 5400.1, General Environmental Protection Program, and US Department of Energy Order 231.IA, Environment, Safety, and Health Reporting. These annual reports summarize environmental data that are used to determine compliance with applicable federal, state, and local environmental laws and regulations, executive orders, and departmental policies. Additional data, beyond the minimum required, are also gathered and reported as part of the Laboratory's efforts to ensure public safety and to monitor environmental quality at and near the Laboratory. Chapter 1 provides an overview of the Laboratory's major environmental programs. Chapter 2 reports the Laboratory's compliance status for 2005. Chapter 3 provides a summary of the maximum radiological dose the public and biota populations could have potentially received from Laboratory operations. The environmental surveillance and monitoring data are organized by environmental media (Chapter 4, Air; Chapters 5 and 6, Water and Sediments; Chapter 7, Soils; and Chapter 8, Foodstuffs and Biota) in a format to meet the needs of a general and scientific audience. Chapter 9, new for this year, provides a summary of the status of environmental restoration work around LANL. A glossary and a list ofacronyms and abbreviations are in the back of the report. Appendix A explains the standards for environmental contaminants, Appendix B explains the units of measurements used in this report, Appendix C describes the Laboratory's technical areas and their associated programs, and Appendix D provides web links to more information.

  16. Environmental surveillance at Los Alamos during 2009

    SciTech Connect

    Fuehne, David; Poff, Ben; Hjeresen, Denny; Isaacson, John; Johnson, Scot; Morgan, Terry; Paulson, David; Salzman, Sonja; Rogers, David

    2010-09-30

    Environmental Surveillance at Los Alamos reports are prepared annually by the Los Alamos National Laboratory (the Laboratory) environmental organization, as required by US Department of Energy Order 5400.1, General Environmental Protection Program, and US Department of Energy Order 231.1A, Environment, Safety, and Health Reporting. These annual reports summarize environmental data that are used to determine compliance with applicable federal, state, and local environmental laws and regulations, executive orders, and departmental policies. Additional data, beyond the minimum required, are also gathered and reported as part of the Laboratory’s efforts to ensure public safety and to monitor environmental quality at and near the Laboratory. Chapter 1 provides an overview of the Laboratory’s major environmental programs and explains the risks and the actions taken to reduce risks at the Laboratory from environmental legacies and waste management operations. Chapter 2 reports the Laboratory’s compliance status for 2009. Chapter 3 provides a summary of the maximum radiological dose the public and biota populations could have potentially received from Laboratory operations and discusses chemical exposures. The environmental surveillance and monitoring data are organized by environmental media (air in Chapter 4; water and sediments in Chapters 5 and 6; soils in Chapter 7; and foodstuffs and biota in Chapter 8) in a format to meet the needs of a general and scientific audience. Chapter 9 provides a summary of the status of environmental restoration work around LANL. The new Chapter 10 describes the Laboratory’s environmental stewardship efforts and provides an overview of the health of the Rio Grande. A glossary and a list of acronyms and abbreviations are in the back of the report. Appendix A explains the standards for environmental contaminants, Appendix B explains the units of measurements used in this report, Appendix C describes the Laboratory’s technical

  17. Comparative Fitness of Multi-Dideoxynucleoside-Resistant Human Immunodeficiency Virus Type 1 (HIV-1) in an In Vitro Competitive HIV-1 Replication Assay

    PubMed Central

    Kosalaraksa, Pope; Kavlick, Mark F.; Maroun, Victor; Le, Richard; Mitsuya, Hiroaki

    1999-01-01

    We examined whether human immunodeficiency virus type 1 (HIV-1) fitness was altered upon the acquisition of a set or subset of five mutations (A62V, V75I, F77L, F116Y, and Q151M) in the pol gene, which confers resistance to multiple dideoxynucleosides (MDR), as well as the zidovudine resistance-associated mutation T215Y, using a competitive HIV-1 replication assay in a setting of an HXB2D genetic background. Target H9 cells were exposed to a 50:50 mixture of paired infectious molecular clones, and HIV-1 in the culture supernatant was transmitted to new cultures every 7 to 10 days. The polymerase-encoding region of the virus was sequenced at various time points, and the relative proportion of the two viral populations was determined. In the absence of drugs, the comparative order for replicative fitness was HIV-162/75/77/116/151 > HIV-177/116/151 > HIV-1151 > wild-type HIV-1 (HIV-1wt) > HIV-175/77/116/151 > HIV-1151/215 > HIV-1215. In the presence of zidovudine or didanosine, the order was HIV-162/75/77/116/151 > HIV-177/116/151 > HIV-175/77/116/151 > HIV-1151 > HIV-1215. HIV-1215S(TCC), a putative intermediate infectious clone for HIV-1215, replicated comparably to HIV-1wt, while two putative intermediates for HIV-1151 [HIV-1151L(CTG) and HIV-1151K(AAG)] replicated much less efficiently than HIV-1wt and HIV-1151, suggesting that for HIV-1151 to develop, two base substitutions are likely to occur concurrently or within a short interval. These data may illustrate the molecular basis by which HIV-1151 emerges much less frequently than HIV-1215. The present data also demonstrate that several MDR HIV-1 variants are more fit than HIV-1wt in the absence of drugs and that resistance-associated mutations and drug pressure are critical variates for HIV-1 fitness. PMID:10364282

  18. Signature Peptide-Enabled Metagenomics (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema

    McMahon, Ben [LANL

    2013-01-25

    Ben McMahon of Los Alamos National Laboratory (LANL) presents "Signature Peptide-Enabled Metagenomics" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  19. Signature Peptide-Enabled Metagenomics (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    SciTech Connect

    McMahon, Ben

    2012-06-01

    Ben McMahon of Los Alamos National Laboratory (LANL) presents "Signature Peptide-Enabled Metagenomics" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  20. Mutations Related to Antiretroviral Resistance Identified by Ultra-Deep Sequencing in HIV-1 Infected Children under Structured Interruptions of HAART.

    PubMed

    Vazquez-Guillen, Jose Manuel; Palacios-Saucedo, Gerardo C; Rivera-Morales, Lydia G; Garcia-Campos, Jorge; Ortiz-Lopez, Rocio; Noguera-Julian, Marc; Paredes, Roger; Vielma-Ramirez, Herlinda J; Ramirez, Teresa J; Chavez-Garcia, Marcelino; Lopez-Guillen, Paulo; Briones-Lara, Evangelina; Sanchez-Sanchez, Luz M; Vazquez-Martinez, Carlos A; Rodriguez-Padilla, Cristina

    2016-01-01

    Although Structured Treatment Interruptions (STI) are currently not considered an alternative strategy for antiretroviral treatment, their true benefits and limitations have not been fully established. Some studies suggest the possibility of improving the quality of life of patients with this strategy; however, the information that has been obtained corresponds mostly to studies conducted in adults, with a lack of knowledge about its impact on children. Furthermore, mutations associated with antiretroviral resistance could be selected due to sub-therapeutic levels of HAART at each interruption period. Genotyping methods to determine the resistance profiles of the infecting viruses have become increasingly important for the management of patients under STI, thus low-abundance antiretroviral drug-resistant mutations (DRM's) at levels under limit of detection of conventional genotyping (<20% of quasispecies) could increase the risk of virologic failure. In this work, we analyzed the protease and reverse transcriptase regions of the pol gene by ultra-deep sequencing in pediatric patients under STI with the aim of determining the presence of high- and low-abundance DRM's in the viral rebounds generated by the STI. High-abundance mutations in protease and high- and low-abundance mutations in reverse transcriptase were detected but no one of these are directly associated with resistance to antiretroviral drugs. The results could suggest that the evaluated STI program is virologically safe, but strict and carefully planned studies, with greater numbers of patients and interruption/restart cycles, are still needed to evaluate the selection of DRM's during STI. PMID:26807922

  1. HIV Life Cycle

    MedlinePlus

    HIV Overview The HIV Life Cycle (Last updated 9/8/2016; last reviewed 9/8/2016) Key Points HIV gradually destroys the immune ... life cycle. What is the connection between the HIV life cycle and HIV medicines? Antiretroviral therapy (ART) ...

  2. HIV-Induced Epigenetic Alterations in Host Cells.

    PubMed

    Abdel-Hameed, Enass A; Ji, Hong; Shata, Mohamed Tarek

    2016-01-01

    Human immunodeficiency virus (HIV), a member of the Retroviridae family, is a positive-sense, enveloped RNA virus. HIV, the causative agent of acquired immunodeficiency syndrome (AIDS) has two major types, HIV-1 and HIV-2 In HIV-infected cells the single stranded viral RNA genome is reverse transcribed and the double-stranded viral DNA integrates into the cellular DNA, forming a provirus. The proviral HIV genome is controlled by the host epigenetic regulatory machinery. Cellular epigenetic regulators control HIV latency and reactivation by affecting the chromatin state in the vicinity of the viral promoter located to the 5' long terminal repeat (LTR) sequence. In turn, distinct HIV proteins affect the epigenotype and gene expression pattern of the host cells. HIV-1 infection of CD4(+) T cells in vitro upregulated DNMT activity and induced hypermethylation of distinct cellular promoters. In contrast, in the colon mucosa and peripheral blood mononuclear cells from HIV-infected patients demethylation of the FOXP3 promoter was observed, possibly due to the downregulation of DNA methyltransferase 1. For a curative therapy of HIV infected individuals and AIDS patients, a combination of antiretroviral drugs with epigenetic modifying compounds have been suggested for the reactivation of latent HIV-1 genomes. These epigenetic drugs include histone deacetylase inhibitors (HDACI), histone methyltransferase inhibitors (HMTI), histone demethylase inhibitors, and DNA methyltransferase inhibitors (DNMTI). PMID:26659262

  3. Mutations Related to Antiretroviral Resistance Identified by Ultra-Deep Sequencing in HIV-1 Infected Children under Structured Interruptions of HAART

    PubMed Central

    Vazquez-Guillen, Jose Manuel; Palacios-Saucedo, Gerardo C.; Rivera-Morales, Lydia G.; Garcia-Campos, Jorge; Ortiz-Lopez, Rocio; Noguera-Julian, Marc; Paredes, Roger; Vielma-Ramirez, Herlinda J.; Ramirez, Teresa J.; Chavez-Garcia, Marcelino; Lopez-Guillen, Paulo; Briones-Lara, Evangelina; Sanchez-Sanchez, Luz M.; Vazquez-Martinez, Carlos A.; Rodriguez-Padilla, Cristina

    2016-01-01

    Although Structured Treatment Interruptions (STI) are currently not considered an alternative strategy for antiretroviral treatment, their true benefits and limitations have not been fully established. Some studies suggest the possibility of improving the quality of life of patients with this strategy; however, the information that has been obtained corresponds mostly to studies conducted in adults, with a lack of knowledge about its impact on children. Furthermore, mutations associated with antiretroviral resistance could be selected due to sub-therapeutic levels of HAART at each interruption period. Genotyping methods to determine the resistance profiles of the infecting viruses have become increasingly important for the management of patients under STI, thus low-abundance antiretroviral drug-resistant mutations (DRM’s) at levels under limit of detection of conventional genotyping (<20% of quasispecies) could increase the risk of virologic failure. In this work, we analyzed the protease and reverse transcriptase regions of the pol gene by ultra-deep sequencing in pediatric patients under STI with the aim of determining the presence of high- and low-abundance DRM’s in the viral rebounds generated by the STI. High-abundance mutations in protease and high- and low-abundance mutations in reverse transcriptase were detected but no one of these are directly associated with resistance to antiretroviral drugs. The results could suggest that the evaluated STI program is virologically safe, but strict and carefully planned studies, with greater numbers of patients and interruption/restart cycles, are still needed to evaluate the selection of DRM’s during STI. PMID:26807922

  4. Near full-length genome sequence of a novel HIV-1 recombinant form (CRF01_AE/B) detected among men who have sex with men in Jilin Province, China.

    PubMed

    Li, Xingguang; Feng, Yi; Yang, Yao; Chen, Yanli; Guo, Qi; Sun, Liuyan; Zang, Xihui; Xing, Hui; Shao, Yiming

    2014-07-01

    We report here a novel HIV-1 recombinant form (CRF01_AE/B) detected from a comprehensive HIV-1 molecular epidemiologic study among men who have sex with men (MSM) in Jilin province of northeastern China. The near full-length genome (NFLG) analyses showed that the novel HIV-1 recombinant isolate (JL.RF07) was composed of CRF01_AE cluster 5 (northeastern China origin) and subtype B (U.S. and European origin), with six recombinant breakpoints observed in the pol, vif, tat, rev, and env gene regions. To the best of our knowledge, this is the first detection of a novel HIV-1 recombinant form (CRF01_AE/B) in Jilin, which may indicate an active transmission network of HIV-1 infection among MSM in the region. Further studies of the molecular epidemiology of the HIV-1 epidemic among MSM in northeastern China are necessary to gain a fuller understanding of the transmission network and potential public health impact of HIV-1 among MSM in this region. PMID:24521207

  5. HIV classification using coalescent theory

    SciTech Connect

    Zhang, Ming; Letiner, Thomas K; Korber, Bette T

    2008-01-01

    Algorithms for subtype classification and breakpoint detection of HIV-I sequences are based on a classification system of HIV-l. Hence, their quality highly depend on this system. Due to the history of creation of the current HIV-I nomenclature, the current one contains inconsistencies like: The phylogenetic distance between the subtype B and D is remarkably small compared with other pairs of subtypes. In fact, it is more like the distance of a pair of subsubtypes Robertson et al. (2000); Subtypes E and I do not exist any more since they were discovered to be composed of recombinants Robertson et al. (2000); It is currently discussed whether -- instead of CRF02 being a recombinant of subtype A and G -- subtype G should be designated as a circulating recombination form (CRF) nd CRF02 as a subtype Abecasis et al. (2007); There are 8 complete and over 400 partial HIV genomes in the LANL-database which belong neither to a subtype nor to a CRF (denoted by U). Moreover, the current classification system is somehow arbitrary like all complex classification systems that were created manually. To this end, it is desirable to deduce the classification system of HIV systematically by an algorithm. Of course, this problem is not restricted to HIV, but applies to all fast mutating and recombining viruses. Our work addresses the simpler subproblem to score classifications of given input sequences of some virus species (classification denotes a partition of the input sequences in several subtypes and CRFs). To this end, we reconstruct ancestral recombination graphs (ARG) of the input sequences under restrictions determined by the given classification. These restritions are imposed in order to ensure that the reconstructed ARGs do not contradict the classification under consideration. Then, we find the ARG with maximal probability by means of Markov Chain Monte Carlo methods. The probability of the most probable ARG is interpreted as a score for the classification. To our

  6. Review of liquid metal heat pipe work at Los Alamos

    SciTech Connect

    Reid, R.S.; Merrigan, M.A.; Sena, J.T.

    1990-01-01

    A survey of space-power related liquid metal heat pipe work at Los Alamos National Laboratory is presented. Heat pipe development at Los Alamos has been on-going since 1963. Heat pipes were initially developed for thermionic nuclear-electrical power production in space. Since then Los Alamos has developed liquid metal heat pipes for numerous applications related to high temperature systems in both the space and terrestrial environments. Some of these applications include thermionic electrical generators, thermoelectric energy conversion (both in-core and direct radiation), thermal energy storage, hypersonic vehicle leading edge cooling, and heat pipe vapor laser cells. Some of the work performed at Los Alamos has been documented in internal reports that are often little-known. A representative description and summary of progress in space-related liquid metal heat pipe technology is provided followed by a reference section citing sources where these works may be found. 53 refs.

  7. Explosive Flux Compression: 50 Years of Los Alamos Activities

    SciTech Connect

    Fowler, C.M.; Thomson, D.B.; Garn, W.B.

    1998-10-18

    Los Alamos flux compression activities are surveyed, mainly through references in view of space limitations. However, two plasma physics programs done with Sandia National Laboratory are discussed in more detail.

  8. Environmental Surveillance at Los Alamos during 2007

    SciTech Connect

    2008-09-30

    Environmental Surveillance at Los Alamos reports are prepared annually by the Los Alamos National Laboratory (the Laboratory) Environmental Directorate, as required by US Department of Energy Order 450.1, General Environmental Protection Program, and US Department of Energy Order 231.1A, Environment, Safety, and Health Reporting. These annual reports summarize environmental data that are used to determine compliance with applicable federal, state, and local environmental laws and regulations, executive orders, and departmental policies. Additional data, beyond the minimum required, are also gathered and reported as part of the Laboratory’s efforts to ensure public safety and to monitor environmental quality at and near the Laboratory. Chapter 1 provides an overview of the Laboratory’s major environmental programs and explains the risks and the actions taken to reduce risks at the Laboratory from environmental legacies and waste management operations. Chapter 2 reports the Laboratory’s compliance status for 2007. Chapter 3 provides a summary of the maximum radiological dose the public and biota populations could have potentially received from Laboratory operations and discusses chemical exposures. The environmental surveillance and monitoring data are organized by environmental media (Chapter 4, air; Chapters 5 and 6, water and sediments; Chapter 7, soils; and Chapter 8, foodstuffs and biota) in a format to meet the needs of a general and scientific audience. Chapter 9 provides a summary of the status of environmental restoration work around LANL. A glossary and a list of acronyms and abbreviations are in the back of the report. Appendix A explains the standards for environmental contaminants, Appendix B explains the units of measurements used in this report, Appendix C describes the laboratory’s technical areas and their associated programs, and Appendix D provides web links to more information. In printed copies of this report or Executive Summary, we have

  9. Towards modeling DNA sequences as automata

    NASA Astrophysics Data System (ADS)

    Burks, Christian; Farmer, Doyne

    1984-01-01

    We seek to describe a starting point for modeling the evolution and role of DNA sequences within the framework of cellular automata by discussing the current understanding of genetic information storage in DNA sequences. This includes alternately viewing the role of DNA in living organisms as a simple scheme and as a complex scheme; a brief review of strategies for identifying and classifying patterns in DNA sequences; and finally, notes towards establishing DNA-like automata models, including a discussion of the extent of experimentally determined DNA sequence data present in the database at Los Alamos.

  10. HIV Testing

    MedlinePlus

    ... the right way, every day. If you have health insurance, your insurer is required to cover some medicines ... to treat HIV. If you don’t have health insurance, or you’re unable to afford your co- ...

  11. HIV migration between blood plasma and cellular subsets before and after HIV therapy.

    PubMed

    Choi, Jun Yong; Chaillon, Antoine; Oh, Jin Ok; Ahn, Jin Young; Ann, Hae Won; Jung, In Young; Ahn, Mi-Young; Jeon, Yong Duk; Ku, Nam Su; Smith, Davey M; Kim, June Myung

    2016-04-01

    The cellular source of HIV RNA circulating in blood plasma remains unclear. Here, we investigated whether sequence analysis of HIV RNA populations circulating before combination antiretroviral therapy (cART) and HIV DNA populations in cellular subsets (CS) after cART could identify the cellular sources of circulating HIV RNA. Blood was collected from five subjects at cART initiation and again 6 months later. Naïve CD4+ T cells, resting central memory and effector memory CD4+ T cells, activated CD4+ T cells, monocytes, and natural killer cells were sorted using a fluorescence-activated cell sorter. HIV-1 env C2V3 sequences from HIV RNA in blood plasma and HIV DNA in CSs were generated using single genome sequencing. Sequences were evaluated for viral compartmentalization (Fst test) and migration events (MEs; Slatkin Maddison and cladistic measures) between blood plasma and each CS. Viral compartmentalization was observed in 88% of all cellular subset comparisons (range: 77-100% for each subject). Most observed MEs were directed from blood plasma to CSs (52 MEs, 85.2%). In particular, there was only viral movement from plasma to NK cells (15 MEs), monocytes (seven MEs), and naïve cells (five ME). We observed a total of nine MEs from activated CD4 cells (2/9 MEs), central memory T cells (3/9 MEs), and effector memory T cells (4/9 MEs) to blood plasma. Our results revealed that the HIV RNA population in blood plasma plays an important role in seeding various cellular reservoirs and that the cellular source of the HIV RNA population is activated central memory and effector memory T cells. J. Med. Virol. 88:606-613, 2016. © 2015 Wiley Periodicals, Inc. PMID:26348372

  12. HIV/AIDS

    MedlinePlus

    ... at risk for serious infections and certain cancers. AIDS stands for acquired immunodeficiency syndrome. It is the final stage of infection with HIV. Not everyone with HIV develops AIDS. HIV most often spreads through unprotected sex with ...

  13. Preventing HIV with Medicine

    MedlinePlus

    ... information in Spanish ( en español ) Preventing HIV with medicine Get medicine right after you are exposed to ... to top More information on Preventing HIV with medicine Explore other publications and websites National HIV and ...

  14. HIV/AIDS

    MedlinePlus

    HIV stands for human immunodeficiency virus. It kills or damages the body's immune system cells. AIDS stands for acquired immunodeficiency syndrome. It is the most advanced stage of infection with HIV. HIV most ...

  15. How HIV Causes AIDS

    MedlinePlus

    ... Share this: Main Content Area How HIV Causes AIDS HIV destroys CD4 positive (CD4+) T cells, which ... and disease, ultimately resulting in the development of AIDS. Most people who are infected with HIV can ...

  16. HIV/AIDS Basics

    MedlinePlus

    ... Enter ZIP code or city Follow Act Against AIDS Act Against AIDS @talkHIV Act Against AIDS Get Email Updates on AAA Anonymous Feedback HIV/AIDS Media Infographics Syndicated Content Podcasts Slide Sets HIV/ ...

  17. HIV-AIDS Connection

    MedlinePlus

    ... Marketing Share this: Main Content Area The HIV-AIDS Connection AIDS was first recognized in 1981 and ... is there overwhelming scientific consensus that HIV causes AIDS? Before HIV infection became widespread in the human ...

  18. HIV/AIDS

    MedlinePlus

    ... HIV infections. HIV infection is often diagnosed through rapid diagnostic tests (RDTs), which detect the presence or absence of ... accuracy. It is important to note that serological tests detect antibodies produced ... pathogens, rather than direct detection of HIV itself. Most ...

  19. Older People and HIV

    MedlinePlus

    ... common than they were before the use of anti-HIV drugs. It is difficult to know what is causing mental problems in older people with HIV. Is it normal aging, or is it HIV disease? Research studies have ...

  20. Broad activation of latent HIV-1 in vivo.

    PubMed

    Barton, Kirston; Hiener, Bonnie; Winckelmann, Anni; Rasmussen, Thomas Aagaard; Shao, Wei; Byth, Karen; Lanfear, Robert; Solomon, Ajantha; McMahon, James; Harrington, Sean; Buzon, Maria; Lichterfeld, Mathias; Denton, Paul W; Olesen, Rikke; Østergaard, Lars; Tolstrup, Martin; Lewin, Sharon R; Søgaard, Ole Schmeltz; Palmer, Sarah

    2016-01-01

    The 'shock and kill' approach to cure human immunodeficiency virus (HIV) includes transcriptional induction of latent HIV-1 proviruses using latency-reversing agents (LRAs) with targeted immunotherapy to purge infected cells. The administration of LRAs (panobinostat or vorinostat) to HIV-1-infected individuals on antiretroviral therapy induces a significant increase in cell-associated unspliced (CA-US) HIV-1 RNA from CD4(+) T cells. However, it is important to discern whether the increases in CA-US HIV-1 RNA are due to limited or broad activation of HIV-1 proviruses. Here we use single-genome sequencing to find that the RNA transcripts observed following LRA administration are genetically diverse, indicating activation of transcription from an extensive range of proviruses. Defective sequences are more frequently found in CA HIV-1 RNA than in HIV-1 DNA, which has implications for developing an accurate measure of HIV-1 reservoir size. Our findings provide insights into the effects of panobinostat and vorinostat as LRAs for latent HIV-1. PMID:27605062

  1. Los Alamos low-level waste performance assessment status

    SciTech Connect

    Wenzel, W.J.; Purtymun, W.D.; Dewart, J.M.; Rodgers, J.E.

    1986-06-01

    This report reviews the documented Los Alamos studies done to assess the containment of buried hazardous wastes. Five sections logically present the environmental studies, operational source terms, transport pathways, environmental dosimetry, and computer model development and use. This review gives a general picture of the Los Alamos solid waste disposal and liquid effluent sites and is intended for technical readers with waste management and environmental science backgrounds but without a detailed familiarization with Los Alamos. The review begins with a wide perspective on environmental studies at Los Alamos. Hydrology, geology, and meteorology are described for the site and region. The ongoing Laboratory-wide environmental surveillance and waste management environmental studies are presented. The next section describes the waste disposal sites and summarizes the current source terms for these sites. Hazardous chemical wastes and liquid effluents are also addressed by describing the sites and canyons that are impacted. The review then focuses on the transport pathways addressed mainly in reports by Healy and Formerly Utilized Sites Remedial Action Program. Once the source terms and potential transport pathways are described, the dose assessment methods are addressed. Three major studies, the waste alternatives, Hansen and Rogers, and the Pantex Environmental Impact Statement, contributed to the current Los Alamos dose assessment methodology. Finally, the current Los Alamos groundwater, surface water, and environmental assessment models for these mesa top and canyon sites are described.

  2. Expanded recycling at Los Alamos National Laboratory

    SciTech Connect

    Betschart, J.F.; Malinauskas, L.; Burns, M.

    1996-07-01

    The Pollution Prevention Program Office has increased recycling activities, reuse, and options to reduce the solid waste streams through streamlining efforts that applied best management practices. The program has prioritized efforts based on volume and economic considerations and has greatly increased Los Alamos National Laboratory`s (LANL`s) recycle volumes. The Pollution Prevention Program established and chairs a Solid Waste Management Solutions Group to specifically address and solve problems in nonradioactive, Resource Conservation and Recovery Act (RCRA), state-regulated, and sanitary and industrial waste streams (henceforth referred to as sanitary waste in this paper). By identifying materials with recycling potential, identifying best management practices and pathways to return materials for reuse, and introducing the concept and practice of {open_quotes}asset management,{open_quotes} the Group will divert much of the current waste stream from disposal. This Group is developing procedures, agreements, and contracts to stage, collect, sort, segregate, transport and process materials, and is also garnering support for the program through the involvement of upper management, facility managers, and generators.

  3. Saving Water at Los Alamos National Laboratory

    SciTech Connect

    Erickson, Andy

    2015-03-16

    Los Alamos National Laboratory decreased its water usage by 26 percent in 2014, with about one-third of the reduction attributable to using reclaimed water to cool a supercomputing center. The Laboratory's goal during 2014 was to use only re-purposed water to support the mission at the Strategic Computing Complex. Using reclaimed water from the Sanitary Effluent Reclamation Facility, or SERF, substantially decreased water usage and supported the overall mission. SERF collects industrial wastewater and treats it for reuse. The reclamation facility contributed more than 27 million gallons of re-purposed water to the Laboratory's computing center, a secured supercomputing facility that supports the Laboratory’s national security mission and is one of the institution’s larger water users. In addition to the strategic water reuse program at SERF, the Laboratory reduced water use in 2014 by focusing conservation efforts on areas that use the most water, upgrading to water-conserving fixtures, and repairing leaks identified in a biennial survey.

  4. Historic Manhattan Project Sites at Los Alamos

    ScienceCinema

    McGehee, Ellen

    2014-05-22

    The Manhattan Project laboratory constructed at Los Alamos, New Mexico, beginning in 1943, was intended from the start to be temporary and to go up with amazing speed. Because most of those WWII-era facilities were built with minimal materials and so quickly, much of the original infrastructure was torn down in the late '40s and early '50s and replaced by more permanent facilities. However, a few key facilities remained, and are being preserved and maintained for historic significance. Four such sites are visited briefly in this video, taking viewers to V-Site, the buildings where the first nuclear explosive device was pre-assembled in preparation for the Trinity Test in Southern New Mexico. Included is another WWII area, Gun Site. So named because it was the area where scientists and engineers tested the so-called "gun method" of assembling nuclear materials -- the fundamental design of the Little Boy weapon that was eventually dropped on Hiroshima. The video also goes to Pajarito Site, home of the "Slotin Building" and "Pond Cabin." The Slotin Building is the place where scientist Louis Slotin conducted a criticality experiment that went awry in early 1946, leading to his unfortunate death, and the Pond Cabin served the team of eminent scientist Emilio Segre who did early chemistry work on plutonium that ultimately led to the Fat Man weapon.

  5. Population genomics of intrapatient HIV-1 evolution.

    PubMed

    Zanini, Fabio; Brodin, Johanna; Thebo, Lina; Lanz, Christa; Bratt, Göran; Albert, Jan; Neher, Richard A

    2015-01-01

    Many microbial populations rapidly adapt to changing environments with multiple variants competing for survival. To quantify such complex evolutionary dynamics in vivo, time resolved and genome wide data including rare variants are essential. We performed whole-genome deep sequencing of HIV-1 populations in 9 untreated patients, with 6-12 longitudinal samples per patient spanning 5-8 years of infection. The data can be accessed and explored via an interactive web application. We show that patterns of minor diversity are reproducible between patients and mirror global HIV-1 diversity, suggesting a universal landscape of fitness costs that control diversity. Reversions towards the ancestral HIV-1 sequence are observed throughout infection and account for almost one third of all sequence changes. Reversion rates depend strongly on conservation. Frequent recombination limits linkage disequilibrium to about 100 bp in most of the genome, but strong hitch-hiking due to short range linkage limits diversity. PMID:26652000

  6. HIV-1 subtype C is not associated with higher risk of heterosexual HIV-1 transmission: a multinational study among African HIV-1 serodiscordant couples

    PubMed Central

    Kahle, Erin; Campbell, Mary; Lingappa, Jairam; Donnell, Deborah; Celum, Connie; Ondondo, Raphael; Mujugira, Andrew; Fife, Kenneth; Mugo, Nelly; Kapiga, Saidi; Mullins, James I.; Baeten, Jared M.

    2014-01-01

    Background HIV-1 subtype C has emerged as the most prevalent strain of HIV-1 worldwide, leading to speculation that subtype C may be more transmissible than other subtypes. We compared the risk of HIV-1 transmission for subtype C versus non-C subtypes (A, D, G and recombinant forms) among heterosexual African HIV-1 serodiscordant couples. Methods We conducted a nested case-control analysis using data from two prospective cohort studies of heterosexual HIV-1 serodiscordant couples from 6 countries in eastern and southern Africa. Cases (N=121) included incident HIV-1 transmissions that were established as linked within the serodiscordant partnership by viral sequencing; controls (N=501) were non-transmitting HIV-1 infected partners. Subtype was determined for partial env and gag genes. Multiple logistic regression controlled for age and gender of the HIV-1 infected partner and self-reported unprotected sex. Plasma and genital HIV-1 RNA concentrations were compared between subtype C and non-C subtypes using generalized estimating equations. Results HIV-1 subtype C was not associated with increased risk of HIV-1 transmission compared to non-C subtypes: env adjusted odds ratio (adjOR) 1.14 (95% confidence interval [CI] 0.74–1.75, p=0.6) and gag adjOR 0.98 (95% CI 0.63–1.52, p=0.9). Plasma and genital HIV-1 RNA levels did not differ significantly for subtype C versus non-C. Conclusion In a geographically diverse population of heterosexual African HIV-1 serodiscordant couples, subtype C was not associated with greater risk of HIV-1 transmission compared to non-C subtypes, arguing against the hypothesis that subtype C is more transmissible compared to other common subtypes. PMID:24413311

  7. Uneven Genetic Robustness of HIV-1 Integrase

    PubMed Central

    Rihn, Suzannah J.; Hughes, Joseph; Wilson, Sam J.

    2014-01-01

    ABSTRACT Genetic robustness (tolerance of mutation) may be a naturally selected property in some viruses, because it should enhance adaptability. Robustness should be especially beneficial to viruses like HIV-1 that exhibit high mutation rates and exist in immunologically hostile environments. Surprisingly, however, the HIV-1 capsid protein (CA) exhibits extreme fragility. To determine whether fragility is a general property of HIV-1 proteins, we created a large library of random, single-amino-acid mutants in HIV-1 integrase (IN), covering >40% of amino acid positions. Despite similar degrees of sequence variation in naturally occurring IN and CA sequences, we found that HIV-1 IN was significantly more robust than CA, with random nonsilent IN mutations only half as likely to cause lethal defects. Interestingly, IN and CA were similar in that a subset of mutations with high in vitro fitness were rare in natural populations. IN mutations of this type were more likely to occur in the buried interior of the modeled HIV-1 intasome, suggesting that even very subtle fitness effects suppress variation in natural HIV-1 populations. Lethal mutations, in particular those that perturbed particle production, proteolytic processing, and particle-associated IN levels, were strikingly localized at specific IN subunit interfaces. This observation strongly suggests that binding interactions between particular IN subunits regulate proteolysis during HIV-1 virion morphogenesis. Overall, use of the IN mutant library in conjunction with structural models demonstrates the overall robustness of IN and highlights particular regions of vulnerability that may be targeted in therapeutic interventions. IMPORTANCE The HIV-1 integrase (IN) protein is responsible for the integration of the viral genome into the host cell chromosome. To measure the capacity of IN to maintain function in the face of mutation, and to probe structure/function relationships, we created a library of random single

  8. HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations.

    PubMed

    Faria, Nuno R; Rambaut, Andrew; Suchard, Marc A; Baele, Guy; Bedford, Trevor; Ward, Melissa J; Tatem, Andrew J; Sousa, João D; Arinaminpathy, Nimalan; Pépin, Jacques; Posada, David; Peeters, Martine; Pybus, Oliver G; Lemey, Philippe

    2014-10-01

    Thirty years after the discovery of HIV-1, the early transmission, dissemination, and establishment of the virus in human populations remain unclear. Using statistical approaches applied to HIV-1 sequence data from central Africa, we show that from the 1920s Kinshasa (in what is now the Democratic Republic of Congo) was the focus of early transmission and the source of pre-1960 pandemic viruses elsewhere. Location and dating estimates were validated using the earliest HIV-1 archival sample, also from Kinshasa. The epidemic histories of HIV-1 group M and nonpandemic group O were similar until ~1960, after which group M underwent an epidemiological transition and outpaced regional population growth. Our results reconstruct the early dynamics of HIV-1 and emphasize the role of social changes and transport networks in the establishment of this virus in human populations. PMID:25278604

  9. Contrasting HIV phylogenetic relationships and V3 loop protein similarities

    SciTech Connect

    Korber, B. |; Myers, G.

    1992-12-31

    At least five distinct sequence subtypes of HIV-I can be identified from the major centers of the AMS pandemic. While it is too early to tell whether these subtypes are serologically or phenotypically similar or distinct in terms of properties such as pathogenicity and transmissibility, we can begin to investigate their potential for phenotypic divergence at the protein sequence level. Phylogenetic analysis of HIV DNA sequences is being widely used to examine lineages of different viral strains as they evolve and spread throughout the globe. We have identified five distinct HIV-1 subtypes (designated A-E), or clades, based on phylogenetic clustering patterns generated from genetic information from both the gag and envelope (env) genes from a spectrum of international isolates. Our initial observations concerning both HIV-1 and HIV-2 sequences indicate that conserved patterns in protein chemistry may indeed exist across distant lineages. Such patterns in V3 loop amino acid chemistry may be indicative of stable lineages or convergence within this highly variable, though functionally and immunologically critical, region. We think that there may be parallels between the apparently stable HIV-2 V3 lineage and the previously mentioned HIV-1 V3 loops which are very similar at the protein level despite being distant by cladistic analysis, and which do not possess the distinctive positively charged residues. Highly conserved V3 loop protein sequences are also encountered in SIVAGMs and CIVs (chimpanzee viral strains), which do not appear to be pathogenic in their wild-caught natural hosts.

  10. Contrasting HIV phylogenetic relationships and V3 loop protein similarities

    SciTech Connect

    Korber, B. Santa Fe Inst., NM ); Myers, G. )

    1992-01-01

    At least five distinct sequence subtypes of HIV-I can be identified from the major centers of the AMS pandemic. While it is too early to tell whether these subtypes are serologically or phenotypically similar or distinct in terms of properties such as pathogenicity and transmissibility, we can begin to investigate their potential for phenotypic divergence at the protein sequence level. Phylogenetic analysis of HIV DNA sequences is being widely used to examine lineages of different viral strains as they evolve and spread throughout the globe. We have identified five distinct HIV-1 subtypes (designated A-E), or clades, based on phylogenetic clustering patterns generated from genetic information from both the gag and envelope (env) genes from a spectrum of international isolates. Our initial observations concerning both HIV-1 and HIV-2 sequences indicate that conserved patterns in protein chemistry may indeed exist across distant lineages. Such patterns in V3 loop amino acid chemistry may be indicative of stable lineages or convergence within this highly variable, though functionally and immunologically critical, region. We think that there may be parallels between the apparently stable HIV-2 V3 lineage and the previously mentioned HIV-1 V3 loops which are very similar at the protein level despite being distant by cladistic analysis, and which do not possess the distinctive positively charged residues. Highly conserved V3 loop protein sequences are also encountered in SIVAGMs and CIVs (chimpanzee viral strains), which do not appear to be pathogenic in their wild-caught natural hosts.

  11. Recent UCN source developments at Los Alamos

    SciTech Connect

    Seestrom, S.J.; Anaya, J.M.; Bowles, T.J.

    1998-12-01

    The most intense sources of ultra cold neutrons (UCN) have bee built at reactors where the high average thermal neutron flux can overcome the low UCN production rate to achieve usable densities of UCN. At spallation neutron sources the average flux available is much lower than at a reactor, though the peak flux can be comparable or higher. The authors have built a UCN source that attempts to take advantage of the high peak flux available at the short pulse spallation neutron source at the Los Alamos Neutron Science Center (LANSCE) to generate a useful number of UCN. In the source UCN are produced by Doppler-shifted Bragg scattering of neutrons to convert 400-m/s neutrons down into the UCN regime. This source was initially tested in 1996 and various improvements were made based on the results of the 1996 running. These improvements were implemented and tested in 1997. In sections 2 and 3 they discuss the improvements that have been made and the resulting source performance. Recently an even more interesting concept was put forward by Serebrov et al. This involves combining a solid Deuterium UCN source, previously studied by Serebrov et al., with a pulsed spallation source to achieve world record UCN densities. They have initiated a program of calculations and measurements aimed at verifying the solid Deuterium UCN source concept. The approach has been to develop an analytical capability, combine with Monte Carlo calculations of neutron production, and perform benchmark experiments to verify the validity of the calculations. Based on the calculations and measurements they plan to test a modified version of the Serebrov UCN factory. They estimate that they could produce over 1,000 UCN/cc in a 15 liter volume, using 1 {micro}amp of 800 MeV protons for two seconds every 500 seconds. They will discuss the result UCN production measurements in section 4.

  12. Beam funneling studies at Los Alamos

    SciTech Connect

    Stovall, J.E.; Guy, F.W.; Stokes, R.H.; Wangler, T.P.

    1988-01-01

    Funneling two ion beams by interlacing their bunches can reduce the cost and complexity of systems producing intense beams. Applications of funneling could include accelerators for heavy ion inertial fusion, electronuclear breeding, and fusion materials irradiation. Funneling in an RFQ-like structure is an elegant solution at low energy where electric fields are needed to provide strong focusing. Discrete-element funnels, with separate focusing elements, bending magnets, rebunchers and if deflectors, are more flexible. At sufficiently high energies, magnetic-quadrupole lenses can provide strong focusing in a discrete-element funnel. Such a funnel has been designed as a preliminary example of a second funnel in the HIBALL-II accelerator system. In a simulation, two Bi/sup +1/ (mass = 209 amu) beams at 0.5 MeV/A, 20 MHz, 40-mA, separated by 55 cm and angled at +-6/degree/ were combined into a single 80-mA beam at 40 MHz. Emittance growth was calculated, by a modified version of the PIC (particle-in-cell) code PARMILA, to be about 1%. Funnel design experience at Los Alamos has evolved rules-of-thumb that reduce emittance growth. Some of these are to maintain focusing periodicity and strength in both transverse and longitudinal directions; use strong focusing so that the bunch will be small; minimize angles of bend and rf deflection; adjust longitudinal focusing to produce a short bunch at the rf deflector; and design rf deflectors for a uniform electrical field. 4 refs., 3 figs., 2 tabs.

  13. Restricting HIV-1 pathways for escape using rationally designed anti–HIV-1 antibodies

    PubMed Central

    Klein, Florian; Horwitz, Joshua A.; Halper-Stromberg, Ariel; Sather, D. Noah; Marcovecchio, Paola M.; Lee, Terri; West, Anthony P.; Gao, Han; Seaman, Michael S.; Stamatatos, Leonidas; Nussenzweig, Michel C.; Bjorkman, Pamela J.

    2013-01-01

    Recently identified broadly neutralizing antibodies (bNAbs) that potently neutralize most HIV-1 strains are key to potential antibody-based therapeutic approaches to combat HIV/AIDS in the absence of an effective vaccine. Increasing bNAb potencies and resistance to common routes of HIV-1 escape through mutation would facilitate their use as therapeutics. We previously used structure-based design to create the bNAb NIH45-46G54W, which exhibits superior potency and/or breadth compared with other bNAbs. We report new, more effective NIH45-46G54W variants designed using analyses of the NIH45-46–gp120 complex structure and sequences of NIH45-46G54W–resistant HIV-1 strains. One variant, 45-46m2, neutralizes 96% of HIV-1 strains in a cross-clade panel and viruses isolated from an HIV-infected individual that are resistant to all other known bNAbs, making it the single most broad and potent anti–HIV-1 antibody to date. A description of its mechanism is presented based on a 45-46m2–gp120 crystal structure. A second variant, 45-46m7, designed to thwart HIV-1 resistance to NIH45-46G54W arising from mutations in a gp120 consensus sequence, targets a common route of HIV-1 escape. In combination, 45-46m2 and 45-46m7 reduce the possible routes for the evolution of fit viral escape mutants in HIV-1YU-2–infected humanized mice, with viremic control exhibited when a third antibody, 10–1074, was added to the combination. PMID:23712429

  14. High Degree of HIV-1 Group M (HIV-1M) Genetic Diversity within Circulating Recombinant Forms: Insight into the Early Events of HIV-1M Evolution.

    PubMed

    Tongo, Marcel; Dorfman, Jeffrey R; Martin, Darren P

    2016-03-01

    The existence of various highly divergent HIV-1 lineages and of recombination-derived sequence tracts of indeterminate origin within established circulating recombinant forms (CRFs) strongly suggests that HIV-1 group M (HIV-1M) diversity is not fully represented under the current classification system. Here we used a fully exploratory screen for recombination on a set of 480 near-full-length genomes representing the full known diversity of HIV-1M. We decomposed recombinant sequences into their constituent parts and then used maximum-likelihood phylogenetic analyses of this mostly recombination-free data set to identify rare divergent sequence lineages that fall outside the major named HIV-1M taxonomic groupings. We found that many of the sequence fragments occurring within CRFs (including CRF04_cpx, CRF06_cpx, CRF11_cpx, CRF18_cpx, CRF25_cpx, CRF27_cpx, and CRF49_cpx) are in fact likely derived from divergent unclassified parental lineages that may predate the current subtypes, even though they are presently identified as derived from currently defined HIV-1M subtypes. Our evidence suggests that some of these CRFs are descended predominantly from what were or are major previously unidentified HIV-1M lineages that were likely epidemiologically relevant during the early stages of the HIV-1M epidemic. The restriction of these divergent lineages to the Congo basin suggests that they were less infectious and/or simply not present at the time and place of the initial migratory wave that triggered the global epidemic.IMPORTANCE HIV-1 group M (HIV-1M) likely spread to the rest of the world from the Congo basin in the mid-1900s (N. R. Faria et al., Science 346:56-61, 2014, http://dx.doi.org/10.1126/science.1256739) and is today the principal cause of the AIDS pandemic. Here, we show that large sequence fragments from several HIV-1M circulating recombinant forms (CRFs) are derived from divergent parental lineages that cannot reasonably be classified within the nine

  15. Recognition of HIV-1 Peptides by Host CTL Is Related to HIV-1 Similarity to Human Proteins

    PubMed Central

    Rolland, Morgane; Nickle, David C.; Deng, Wenjie; Frahm, Nicole; Brander, Christian; Learn, Gerald H.; Heckerman, David; Jojic, Nebosja; Jojic, Vladimir; Walker, Bruce D.; Mullins, James I.

    2007-01-01

    Background While human immunodeficiency virus type 1 (HIV-1)-specific cytotoxic T lymphocytes preferentially target specific regions of the viral proteome, HIV-1 features that contribute to immune recognition are not well understood. One hypothesis is that similarities between HIV and human proteins influence the host immune response, i.e., resemblance between viral and host peptides could preclude reactivity against certain HIV epitopes. Methodology/Principal Findings We analyzed the extent of similarity between HIV-1 and the human proteome. Proteins from the HIV-1 B consensus sequence from 2001 were dissected into overlapping k-mers, which were then probed against a non-redundant database of the human proteome in order to identify segments of high similarity. We tested the relationship between HIV-1 similarity to host encoded peptides and immune recognition in HIV-infected individuals, and found that HIV immunogenicity could be partially modulated by the sequence similarity to the host proteome. ELISpot responses to peptides spanning the entire viral proteome evaluated in 314 individuals showed a trend indicating an inverse relationship between the similarity to the host proteome and the frequency of recognition. In addition, analysis of responses by a group of 30 HIV-infected individuals against 944 overlapping peptides representing a broad range of individual HIV-1B Nef variants, affirmed that the degree of similarity to the host was significantly lower for peptides with reactive epitopes than for those that were not recognized. Conclusions/Significance Our results suggest that antigenic motifs that are scarcely represented in human proteins might represent more immunogenic CTL targets not selected against in the host. This observation could provide guidance in the design of more effective HIV immunogens, as sequences devoid of host-like features might afford superior immune reactivity. PMID:17786195

  16. Nearly Finished Genomes Produced Using Gel Microdroplet Culturing (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema

    Fitzsimmons, Michael [LANL

    2013-01-25

    Michael Fitzsimmons from Los Alamos National Laboratory gives a talk titled "Nearly Finished Genomes Produced Using Gel Microdroplet Culturing" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  17. HIV and AIDS

    MedlinePlus

    ... I Help a Friend Who Cuts? HIV and AIDS KidsHealth > For Teens > HIV and AIDS Print A A A Text Size What's in ... in human history. HIV causes a condition called acquired immunodeficiency syndrome — better known as AIDS . HIV destroys a type ...

  18. HIV Structural Database

    National Institute of Standards and Technology Data Gateway

    SRD 102 HIV Structural Database (Web, free access)   The HIV Protease Structural Database is an archive of experimentally determined 3-D structures of Human Immunodeficiency Virus 1 (HIV-1), Human Immunodeficiency Virus 2 (HIV-2) and Simian Immunodeficiency Virus (SIV) Proteases and their complexes with inhibitors or products of substrate cleavage.

  19. Near full-length genome sequence of a novel HIV type 1 second-generation recombinant form (CRF01_AE/CRF07_BC) identified among men who have sex with men in Jilin, China.

    PubMed

    Li, Xingguang; Ning, Chuanyi; He, Xiang; Yang, Yao; Xing, Hui; Hong, Kunxue; Shao, Yiming; Yang, Rongge

    2013-12-01

    We report here a novel HIV-1 second-generation recombinant form (CRF01_AE/CRF07_BC) composed of CRF01_AE and CRF07_BC, identified among men who have sex with men (MSM) in Jilin, with four breakpoints observed in the pol, vif, and vpr genes. The CRF01_AE regions of the recombinant were clustered with the CRF01_AE lineage, which is mainly circulating among MSM in northern China, with the support of 100% bootstrap value, indicating that the parental origin of the CRF01_AE regions was from MSM, in which recombination events may be more likely to occur. To the best of our knowledge, this is the first detection of a novel HIV-1 second-generation recombinant form (CRF01AE/CRF07_BC) in Jilin, which indicates active transmission networks of HIV-1 infection among MSM in the region. Therefore, it is necessary to continue monitoring the molecular epidemiology of HIV-1 among MSM in Jilin to obtain a better understanding of the transmission and potential public health impact of HIV-1 among MSM in the region. PMID:23809010

  20. 1993 Northern goshawk inventory on portions of Los Alamos National Laboratory, Los Alamos, NM. Final report

    SciTech Connect

    Sinton, D.T.; Kennedy, P.L.

    1994-06-01

    Northern goshawks (Accipiter gentilis) (hereafter referred to as goshawk) is a large forest dwelling hawk. Goshawks may be declining in population and reproduction in the southwestern United States. Reasons for the possible decline in goshawk populations include timber harvesting resulting in the loss of nesting habitat, toxic chemicals, and the effects of drought, fire, and disease. Thus, there is a need to determine their population status and assess impacts of management activities in potential goshawk habitat. Inventory for the goshawk was conducted on 2,254 ha of Los Alamos National Laboratory (LANL) to determine the presence of nesting goshawks on LANL lands. This information can be incorporated into LANL`s environmental management program. The inventory was conducted by Colorado State University personnel from May 12 to July 30, 1993. This report summarizes the results of this inventory.

  1. HIV-1 RNAs are Not Part of the Argonaute 2 Associated RNA Interference Pathway in Macrophages

    PubMed Central

    Kishore, Shivendra; Jaskiewicz, Lukasz; Hall, Jonathan; Günthard, Huldrych F.; Beerenwinkel, Niko; Metzner, Karin J.

    2015-01-01

    Background MiRNAs and other small noncoding RNAs (sncRNAs) are key players in post-transcriptional gene regulation. HIV-1 derived small noncoding RNAs (sncRNAs) have been described in HIV-1 infected cells, but their biological functions still remain to be elucidated. Here, we approached the question whether viral sncRNAs may play a role in the RNA interference (RNAi) pathway or whether viral mRNAs are targeted by cellular miRNAs in human monocyte derived macrophages (MDM). Methods The incorporation of viral sncRNAs and/or their target RNAs into RNA-induced silencing complex was investigated using photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP) as well as high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP), which capture Argonaute2-bound miRNAs and their target RNAs. HIV-1 infected monocyte-derived macrophages (MDM) were chosen as target cells, as they have previously been shown to express HIV-1 sncRNAs. In addition, we applied small RNA deep sequencing to study differential cellular miRNA expression in HIV-1 infected versus non-infected MDMs. Results and Conclusion PAR-CLIP and HITS-CLIP data demonstrated the absence of HIV-1 RNAs in Ago2-RISC, although the presence of a multitude of HIV-1 sncRNAs in HIV-1 infected MDMs was confirmed by small RNA sequencing. Small RNA sequencing revealed that 1.4% of all sncRNAs were of HIV-1 origin. However, neither HIV-1 derived sncRNAs nor putative HIV-1 target sequences incorporated into Ago2-RISC were identified suggesting that HIV-1 sncRNAs are not involved in the canonical RNAi pathway nor is HIV-1 targeted by this pathway in HIV-1 infected macrophages. PMID:26226348

  2. Doctors Report Groundbreaking HIV-To-HIV Organ Transplants

    MedlinePlus

    ... medlineplus/news/fullstory_158039.html Doctors Report Groundbreaking HIV-to-HIV Organ Transplants One donor supplied a kidney to ... News) -- Trailblazing liver and kidney transplants from an HIV-positive donor to HIV-positive recipients were announced ...

  3. Side Effects of HIV Medicines: HIV and Lactic Acidosis

    MedlinePlus

    ... HIV medicines. All HIV medicines in the nucleoside reverse transcriptase inhibitor (NRTI) drug class may cause lactic acidosis, but ... some HIV medicines. HIV medicines in the nucleoside reverse transcriptase inhibitor (NRTI) drug class can cause the body to ...

  4. Publications of Los Alamos research, 1977-1981

    SciTech Connect

    Sheridan, C.J.; Garcia, C.A.

    1983-03-01

    This bibliography is a compilation of unclassified publications of work done at the Los Alamos National Laboratory for 1977-1981. Papers published in those years are included regardless of when they were actually written. Publications received too late for inclusion in earlier compilations have also been listed. Declassification of previously classified reports is considered to constitute publication. All classified issuances are omitted - even those papers, themselves unclassified, which were published only as part of a classified document. If a paper was published more than once, all places of publication are included. The bibliography includes Los Alamos National Laboratory reports, papers released as non-Laboratory reports, journal articles, books, chapters of books, conference papers either published separately or as part of conference proceedings issued as books or reports, papers published in congressional hearings, theses, and US patents. Publications by Los Alamos authors that are not records of Laboratory-sponsored work are included when the Library becomes aware of them.

  5. Water Supply at Los Alamos 1998-2001

    SciTech Connect

    Richard J. Koch; David B. Rogers

    2003-03-01

    For the period 1998 through 2001, the total water used at Los Alamos from all sources ranged from 1325 million gallons (Mg) in 1999 to 1515 Mg in 2000. Groundwater production ranged from 1323 Mg in 1999 to 1506 Mg in 2000 from the Guaje, Pajarito, and Otowi fields. Nonpotable surface water used from Los Alamos reservoir ranged from zero gallons in 2001 to 9.3 Mg in 2000. For years 1998 through 2001, over 99% of all water used at Los Alamos was groundwater. Water use by Los Alamos National Laboratory (LANL) between 1998 and 2001 ranged from 379 Mg in 2000 to 461 Mg in 1998. The LANL water use in 2001 was 393 Mg or 27% of the total water use at Los Alamos. Water use by Los Alamos County ranged from 872 Mg in 1999 to 1137 Mg in 2000, and averaged 1006 Mg/yr. Four new replacement wells in the Guaje field (G-2A, G-3A, G-4A, and G-5A) were drilled in 1998 and began production in 1999; with existing well G-1A, the Guaje field currently has five producing wells. Five of the old Guaje wells (G-1, G-2, G-4, G-5, and G-6) were plugged and abandoned in 1999, and one well (G-3) was abandoned but remains as an observation well for the Guaje field. The long-term water level observations in production and observation (test) wells at Los Alamos are consistent with the formation of a cone of depression in response to water production. The water level decline is gradual and at most has been about 0.7 to 2 ft per year for production wells and from 0.4 to 0.9 ft/yr for observation (test) wells. The largest water level declines have been in the Guaje field where nonpumping water levels were about 91 ft lower in 2001 than in 1951. The initial water levels of the Guaje replacement wells were 32 to 57 ft lower than the initial water levels of adjacent original Guaje wells. When production wells are taken off-line for pump replacement or repair, water levels have returned to within about 25 ft of initial static levels within 6 to 12 months. Thus, the water-level trends suggest no adverse

  6. A progress report on UNICOS misuse detection at Los Alamos

    SciTech Connect

    Thompson, J.L.; Jackson, K.A.; Stallings, C.A.; Simmonds, D.D.; Siciliano, C.L.B.; Pedicini, G.A.

    1995-10-01

    An effective method for detecting computer misuse is the automatic monitoring and analysis of on-line user activity. During the past year, Los Alamos enhanced its Network Anomaly Detection and Intrusion Reporter (NADIR) to include analysis of user activity on Los Alamos` UNICOS Crays. In near real-time, NADIR compares user activity to historical profiles and tests activity against expert rules. The expert rules express Los Alamos` security policy and define improper or suspicious behavior. NADIR reports suspicious behavior to security auditors and provides tools to aid in follow-up investigations. This paper describes the implementation to date of the UNICOS component of NADIR, along with the operational experiences and future plans for the system.

  7. Molecular Characterization of HIV-1 CRF01_AE in Mekong Delta, Vietnam, and Impact of T-Cell Epitope Mutations on HLA Recognition (ANRS 12159)

    PubMed Central

    Bellecave, Pantxika; Guidicelli, Gwenda-Line; Anies, Guerric; Hoang Khanh Thu, Huynh; Pillot Debelleix, Marie; Vray, Muriel; Recordon-Pinson, Patricia; Taupin, Jean-Luc; Thi Xuan Lien, Truong; Fleury, Herve

    2011-01-01

    Background To date, 11 HIV-1 subtypes and 48 circulating recombinant forms have been described worldwide. The underlying reason why their distribution is so heterogeneous is not clear. Host genetic factors could partly explain this distribution. The aim of this study was to describe HIV-1 strains circulating in an unexplored area of Mekong Delta, Vietnam, and to assess the impact of optimal epitope mutations on HLA binding. Methods We recruited 125 chronically antiretroviral-naive HIV-1-infected subjects from five cities in the Mekong Delta. We performed high-resolution DNA typing of HLA class I alleles, sequencing of Gag and RT-Prot genes and phylogenetic analysis of the strains. Epitope mutations were analyzed in patients bearing the HLA allele restricting the studied epitope. Optimal wild-type epitopes from the Los Alamos database were used as reference. T-cell epitope recognition was predicted using the immune epitope database tool according to three different scores involved in antigen processing (TAP and proteasome scores) and HLA binding (MHC score). Results All sequences clustered with CRF01_AE. HLA class I genotyping showed the predominance of Asian alleles as A*11:01 and B*46:01 with a Vietnamese specificity held by two different haplotypes. The percentage of homology between Mekong and B consensus HIV-1 sequences was above 85%. Divergent epitopes had TAP and proteasome scores comparable with wild-type epitopes. MHC scores were significantly lower in divergent epitopes with a mean of 2.4 (±0.9) versus 2 (±0.7) in non-divergent ones (p<0.0001). Conclusions Our study confirms the wide predominance of CRF01_AE in the Mekong Delta where patients harbor a specific HLA pattern. Moreover, it demonstrates the lower MHC binding affinity among divergent epitopes. This weak immune pressure combined with a narrow genetic diversity favors immune escape and could explain why CRF01_AE is still predominant in Vietnam, particularly in the Mekong area. PMID:22039450

  8. HIV-1 propagates in human neuroblastoma cells.

    PubMed

    Shapshak, P; Sun, N C; Resnick, L; Thornthwaite, J T; Schiller, P; Yoshioka, M; Svenningsson, A; Tourtellotte, W W; Imagawa, D T

    1991-01-01

    A major question in the pathogenesis of AIDS encephalopathy and dementia is whether HIV-1 directly infects cells of the central nervous system (CNS). The propagation of HIV was attempted in six cell lines: three related and three unrelated to the nervous system. HIV was able to propagate in two human neuroblastoma cell lines and a lymphocytic cell line control but did not result in infections of African green monkey kidney cells, human cervix carcinoma cells, and one human brain astrocytoma cell line. Neuroblastoma cell lines infected with HIV showed peaks of reverse transcriptase activity at 10-14 days postinfection. After prolonged growth in cell cultures, one of the neuroblastoma cell lines showed multiphasic virus production, additional high peaks of reverse transcriptase activity, 20-fold greater than the first, lasting from 36 to 74 days and 110 to 140 days postinfection. The presence of HIV was confirmed by p24 antigen capture. The neuroblastoma cell lines had weak but detectable levels of CD4 immunoreactivity by immunoperoxidase and flow immunocytometric analysis. Although no T4-specific RNA sequences were detected by hybridization of Northern blots of total and poly A-selected RNA extracted from the two neuroblastoma cell lines by using a T4 specific complimentary DNA probe, monoclonal antibodies to the CD4 receptor blocked HIV infection in both neuroblastoma cell lines. Thus, the infection of neuroblastoma cells by HIV occurs in part by a CD4-dependent mechanism. Passaging the neuroblastoma cell lines weekly and bimonthly resulted in similar cell cycle-DNA content patterns for the more permissive cell line and with significant numbers of cells in the S phase. HIV-infected neuroblastoma cell lines provide an in vitro model for the evaluation of virus-host cell interactions and may be useful in addressing the issue of the persistence of HIV in the human CNS. PMID:1704060

  9. Los Alamos Using Neutrons to Stop Nuclear Smugglers

    ScienceCinema

    Favalli, Andrea; Swinhoe, Martyn

    2014-06-02

    Los Alamos National Laboratory researchers have successfully demonstrated for the first time that laser-generated neutrons can be enlisted as a useful tool in the War on Terror. The international research team used the short-pulse laser at Los Alamos's TRIDENT facility to generate a neutron beam with novel characteristics that interrogated a closed container to confirm the presence and quantity of nuclear material inside. The successful experiment paves the way for creation of a table-top-sized or truck-mounted neutron generator that could be installed at strategic locations worldwide to thwart smugglers trafficking in nuclear materials.

  10. The development of the atomic bomb, Los Alamos

    SciTech Connect

    Seidel, R.W.

    1993-11-01

    The historical presentation begins with details of the selection of Los Alamos as the site of the Army installation. Wartime efforts of the Army Corps of Engineers, and scientists to include the leader of Los Alamos, Robert Oppenheimer are presented. The layout and construction of the facilities are discussed. The monumental design requirements of the bombs are discussed, including but not limited to the utilization of the second choice implosion method of detonation, and the production of bomb-grade nuclear explosives. The paper ends with a philosophical discussion on the use of nuclear weapons.

  11. Fifty-one years of Los Alamos Spacecraft

    SciTech Connect

    Fenimore, Edward E.

    2014-09-04

    From 1963 to 2014, the Los Alamos National Laboratory was involved in at least 233 spacecraft. There are probably only one or two institutions in the world that have been involved in so many spacecraft. Los Alamos space exploration started with the Vela satellites for nuclear test detection, but soon expanded to ionospheric research (mostly barium releases), radioisotope thermoelectric generators, solar physics, solar wind, magnetospheres, astrophysics, national security, planetary physics, earth resources, radio propagation in the ionosphere, and cubesats. Here, we present a list of the spacecraft, their purpose, and their launch dates for use during RocketFest

  12. Los Alamos Using Neutrons to Stop Nuclear Smugglers

    SciTech Connect

    Favalli, Andrea; Swinhoe, Martyn

    2013-06-03

    Los Alamos National Laboratory researchers have successfully demonstrated for the first time that laser-generated neutrons can be enlisted as a useful tool in the War on Terror. The international research team used the short-pulse laser at Los Alamos's TRIDENT facility to generate a neutron beam with novel characteristics that interrogated a closed container to confirm the presence and quantity of nuclear material inside. The successful experiment paves the way for creation of a table-top-sized or truck-mounted neutron generator that could be installed at strategic locations worldwide to thwart smugglers trafficking in nuclear materials.

  13. Needs assessment for fire department services and resources for the Los Alamos National Laboratory, Los Alamos, New Mexico. Final report

    SciTech Connect

    1995-11-15

    This report has been developed in response to a request from the Los Alamos National Laboratory (LANL) to evaluate the need for fire department services so as to enable the Laboratory to plan effective fire protection and thereby: meet LANL`s regulatory and contractual obligations; interface with the Department of Energy (DOE) and other agencies on matters relating to fire and emergency services; and ensure appropriate protection of the community and environment. This study is an outgrowth of the 1993 Fire Department Needs Assessment (prepared for DOE) but is developed from the LANL perspective. Input has been received from cognizant and responsible representatives at LANL, DOE, Los Alamos County (LAC) and the Los Alamos Fire Department (LAFD).

  14. Human immunodeficiency virus type 1 and 2 envelope glycoproteins oligomerize through conserved sequences.

    PubMed Central

    Center, R J; Kemp, B E; Poumbourios, P

    1997-01-01

    Hetero-oligomerization between human immunodeficiency virus type 2 (HIV-2) envelope glycoprotein (Env) truncation mutants and epitope-tagged gp160 is dependent on the presence of gp41 transmembrane protein (TM) amino acids 552 to 589, a putative amphipathic alpha-helical sequence. HIV-2 Env truncation mutants containing this sequence were also able to form cross-type hetero-oligomers with HIV-1 Env. HIV-2/HIV-1 hetero-oligomerization was, however, more sensitive to disruption by mutagenesis or increased temperature. The conservation of the Env oligomerization function of the HIV-1 and HIV-2 alpha-helical sequences suggests that retroviral TM alpha-helical motifs may have a universal role in oligomerization. PMID:9188654

  15. Monitoring Sensitive Bat Species at Los Alamos National Laboratory

    SciTech Connect

    Schoenberg, Kari M.

    2014-01-15

    Bats play a critical role in ecosystems and are vulnerable to disturbance and disruption by human activities. In recent decades, bat populations in the United States and elsewhere have decreased tremendously. There are 47 different species of bat in the United States and 28 of these occur in New Mexico with 15 different species documented at the Los Alamos National Laboratory (LANL) and surrounding areas. Euderma maculatum(the spotted bat) is listed as “threatened” by the state of New Mexico and is known to occur at LANL. Four other species of bats are listed as “sensitive” and also occur here. In 1995, a four year study was initiated at LANL to assess the status of bat species of concern, elucidate distribution and relative abundance, and obtain information on roosting sites. There have been no definitive studies since then. Biologists in the Environmental Protection Division at LANL initiated a multi-year monitoring program for bats in May 2013 to implement the Biological Resources Management Plan. The objective of this ongoing study is to monitor bat species diversity and seasonal activity over time at LANL. Bat species diversity and seasonal activity were measured using an acoustic bat detector, the Pettersson D500X. This ultrasound recording unit is intended for long-term, unattended recording of bat and other high frequency animal calls. During 2013, the detector was deployed at two locations around LANL. Study sites were selected based on proximity to water where bats may be foraging. Recorded bat calls were analyzed using Sonobat, software that can help determine specific species of bat through their calls. A list of bat species at the two sites was developed and compared to lists from previous studies. Species diversity and seasonal activity, measured as the number of call sequences recorded each month, were compared between sites and among months. A total of 17,923 bat calls were recorded representing 15 species. Results indicate that there is a

  16. A survey of macromycete diversity at Los Alamos National Laboratory, Bandelier National Monument, and Los Alamos County; A preliminary report

    SciTech Connect

    Jarmie, N.; Rogers, F.J.

    1997-11-01

    The authors have completed a 5-year survey (1991--1995) of macromycetes found in Los Alamos County, Los Alamos National Laboratory, and Bandelier National Monument. The authors have compiled a database of 1,048 collections, their characteristics, and identifications. The database represents 123 (98%) genera and 175 (73%) species reliably identified. Issues of habitat loss, species extinction, and ecological relationships are addressed, and comparisons with other surveys are made. With this baseline information and modeling of this baseline data, one can begin to understand more about the fungal flora of the area.

  17. Airport-Noise Levels and Annoyance Model (ALAMO) system's reference manual

    NASA Technical Reports Server (NTRS)

    Deloach, R.; Donaldson, J. L.; Johnson, M. J.

    1986-01-01

    The airport-noise levels and annoyance model (ALAMO) is described in terms of the constituent modules, the execution of ALAMO procedure files, necessary for system execution, and the source code documentation associated with code development at Langley Research Center. The modules constituting ALAMO are presented both in flow graph form, and through a description of the subroutines and functions that comprise them.

  18. Molecular mechanisms of HIV-1 mother-to-child transmission and infection in neonatal target cells

    PubMed Central

    Ahmad, Nafees

    2010-01-01

    HIV-1 mother-to-child transmission (MTCT) occurs mainly at three stages, including prepartum, intrapartum and postpartum. Several maternal factors, including low CD4+ lymphocyte counts, high viral load, immune response, advanced disease status, smoking and abusing drugs have been implicated in an increased risk of HIV-1 MTCT. While use of antiretroviral therapy (ART) during pregnancy has significantly reduced the rate of MTCT, selective transmission of ART resistant mutants has been reported. Based on HIV-1 sequence comparison, the maternal HIV-1 minor genotypes with R5 phenotypes are predominantly transmitted to their infants and initially maintained in the infants with the same properties. Several HIV-1 structural, regulatory and accessory genes were highly conserved following MTCT. In addition, HIV-1 sequences from non-transmitting mothers are less heterogeneous compared with transmitting mothers, suggesting that a higher level of viral heterogeneity influences MTCT. Analysis of the immunologically relevant epitopes showed that variants evolved to escape the immune response that influenced HIV-1 MTCT. Several cytotoxic T lymphocyte (CTL) epitopes were identified in various HIV-1 genes that were conserved in HIV-1 mother-infant sequences, suggesting a role in MTCT. We have shown that HIV-1 replicates more efficiently in neonatal T-lymphocytes and monocytes/macrophages compared with adult cells, and this differential replication is influenced at the level of HIV-1 gene expression, which was due to differential expression of host factors, including transcriptional activators, signal transducers and cytokines in neonatal than adult cells. In addition, HIV-1 integration occurs in more actively transcribed genes in neonatal compared with adult cells, which may influence HIV-1 gene expression. The increased HIV-1 gene expression and replication in neonatal target cells contribute to a higher viral load and more rapid disease progression in neonates/infants than adults

  19. Identification of unique reciprocal and non reciprocal cross packaging relationships between HIV-1, HIV-2 and SIV reveals an efficient SIV/HIV-2 lentiviral vector system with highly favourable features for in vivo testing and clinical usage

    PubMed Central

    Strappe, Padraig M; Hampton, David W; Brown, Douglas; Cachon-Gonzalez, Begona; Caldwell, Maeve; Fawcett, James W; Lever, Andrew ML

    2005-01-01

    Background Lentiviral vectors have shown immense promise as vehicles for gene delivery to non-dividing cells particularly to cells of the central nervous system (CNS). Improvements in the biosafety of viral vectors are paramount as lentiviral vectors move into human clinical trials. This study investigates the packaging relationship between gene transfer (vector) and Gag-Pol expression constructs of HIV-1, HIV-2 and SIV. Cross-packaged vectors expressing GFP were assessed for RNA packaging, viral vector titre and their ability to transduce rat primary glial cell cultures and human neural stem cells. Results HIV-1 Gag-Pol demonstrated the ability to cross package both HIV-2 and SIV gene transfer vectors. However both HIV-2 and SIV Gag-Pol showed a reduced ability to package HIV-1 vector RNA with no significant gene transfer to target cells. An unexpected packaging relationship was found to exist between HIV-2 and SIV with SIV Gag-Pol able to package HIV-2 vector RNA and transduce dividing SV2T cells and CNS cell cultures with an efficiency equivalent to the homologous HIV-1 vector however HIV-2 was unable to deliver SIV based vectors. Conclusion This new non-reciprocal cross packaging relationship between SIV and HIV-2 provides a novel way of significantly increasing bio-safety with a reduced sequence homology between the HIV-2 gene transfer vector and the SIV Gag-Pol construct thus ensuring that vector RNA packaging is unidirectional. PMID:16168051

  20. Inertial confinement fusion at the Los Alamos National Laboratory

    SciTech Connect

    Lindman, E.; Baker, D.; Barnes, C.; Bauer, B.; Beck, J.B.

    1997-11-01

    The Los Alamos National Laboratory is contributing to the resolution of key issues in the US Inertial-Confinement-Fusion Program and plans to play a strong role in the experimental program at the National Ignition Facility when it is completed.

  1. The Los Alamos Space Science Outreach (LASSO) Program

    NASA Astrophysics Data System (ADS)

    Barker, P. L.; Skoug, R. M.; Alexander, R. J.; Thomsen, M. F.; Gary, S. P.

    2002-12-01

    The Los Alamos Space Science Outreach (LASSO) program features summer workshops in which K-14 teachers spend several weeks at LANL learning space science from Los Alamos scientists and developing methods and materials for teaching this science to their students. The program is designed to provide hands-on space science training to teachers as well as assistance in developing lesson plans for use in their classrooms. The program supports an instructional model based on education research and cognitive theory. Students and teachers engage in activities that encourage critical thinking and a constructivist approach to learning. LASSO is run through the Los Alamos Science Education Team (SET). SET personnel have many years of experience in teaching, education research, and science education programs. Their involvement ensures that the teacher workshop program is grounded in sound pedagogical methods and meets current educational standards. Lesson plans focus on current LANL satellite projects to study the solar wind and the Earth's magnetosphere. LASSO is an umbrella program for space science education activities at Los Alamos National Laboratory (LANL) that was created to enhance the science and math interests and skills of students from New Mexico and the nation. The LASSO umbrella allows maximum leveraging of EPO funding from a number of projects (and thus maximum educational benefits to both students and teachers), while providing a format for the expression of the unique science perspective of each project.

  2. Direct-current proton-beam measurements at Los Alamos

    SciTech Connect

    Sherman, Joseph; Stevens, Ralph R.; Schneider, J. David; Zaugg, Thomas

    1995-09-15

    Recently, a CW proton accelerator complex was moved from Chalk River Laboratories (CRL) to Los Alamos National Laboratory. This includes a 50-keV dc proton injector with a single-solenoid low-energy beam transport system (LEBT) and a CW 1.25-MeV, 267-MHz radiofrequency quadrupole (RFQ). The move was completed after CRL had achieved 55-mA CW operation at 1.25 MeV using 250-kW klystrode tubes to power the RFQ. These accelerator components are prototypes for the front end of a CW linac required for an accelerator-driven transmutation linac, and they provide early confirmation of some CW accelerator components. The injector (ion source and LEBT) and emittance measuring unit are installed and operational at Los Alamos. The dc microwave ion source has been operated routinely at 50-keV, 75-mA hydrogen-ion current. This ion source has demonstrated very good discharge and H2 gas efficiencies, and sufficient reliability to complete CW RFQ measurements at CRL. Proton fraction of 75% has been measured with 550-W discharge power. This high proton fraction removes the need for an analyzing magnet. Proton LEBT emittance measurements completed at Los Alamos suggest that improved transmission through the RFQ may be achieved by increasing the solenoid focusing current. Status of the final CW RFQ operation at CRL and the installation of the RFQ at Los Alamos will be given.

  3. Direct-current proton-beam measurements at Los Alamos

    SciTech Connect

    Sherman, J.; Stevens, R.R.; Schneider, J.D.; Zaugg, T.

    1994-08-01

    Recently, a CW proton accelerator complex was moved from Chalk River Laboratories (CRL) to Los Alamos National Laboratory. This includes a 50-keV dc proton injector with a single-solenoid low-energy beam transport system (LEBT) and a CW 1.25-MeV, 267-MHz radiofrequency quadrupole (RFQ). The move was completed after CRL had achieved 55-mA CW operation at 1.25 MeV using 250-kW klystrode tubes to power the RFQ. These accelerator components are prototypes for the front end of a CW linac required for an accelerator-driven transmutation linac, and they provide early confirmation of some CW accelerator components. The injector (ion source and LEBT) and emittance measuring unit are installed and operational at Los Alamos. The dc microwave ion source has been operated routinely at 50-keV, 75-mA hydrogen-ion current. This ion source has demonstrated very good discharge and H{sub 2} gas efficiencies, and sufficient reliability to complete CW RFQ measurements at CRL. Proton fraction of 75% has been measured with 550-W discharge power. This high proton fraction removes the need for an analyzing magnet. Proton LEBT emittance measurements completed at Los Alamos suggest that improved transmission through the RFQ may be achieved by increasing the solenoid focusing current. Status of the final CW RFQ operation at CRL and the installation of the RFQ at Los Alamos is given.

  4. High-energy density physics at Los Alamos

    NASA Astrophysics Data System (ADS)

    Byrnes, P.

    1993-03-01

    This brochure describes the facilities of the Above Ground Experiments 2 (AGEX 2) and the Inertial Confinement Fusion (ICF) programs at Los Alamo. Combined, these programs represent, an unparalleled capability to address important issues in high-energy density physics that are critical to the future defense, energy, and research needs of the United States. The mission of the AGEX 2 program at Los Alamos is to provide additional experimental opportunities for the nuclear weapons program. For this purpose we have assembled at Los Alamos the broadest array of high-energy density physics facilities of any laboratory in the world. Inertial confinement fusion seeks to achieve thermonuclear burn on a laboratory scale through the implosion of a small quantity of deuterium and tritium fuel to very high pressure and temperature. The Los Alamos ICF program is focused on target physics. With the largest scientific computing center in the world, We can perform calculations of unprecedented sophistication and precision. We field experiments at facilities worldwide--including our own Trident and Mercury lasers--to confirm our understanding and to provide the necessary data base to proceed toward the historic goal of controlled fusion in the laboratory. The ultrahigh magnetic fields produced in our high explosive pulsed-power generators can be used in a wide variety of solid state physics and temperature superconductor studies. The structure and dynamics of planetary atmospheres can be simulated through the compression of gas mixtures.

  5. The Los Alamos nuclear safeguards and nonproliferation technology development program

    SciTech Connect

    Smith, H.A. Jr.; Menlove, H.O.; Reilly, T.D.; Bosler, G.E.; Hakkila, E.A.; Eccleston, G.W.

    1994-04-01

    For nearly three decades, Los Alamos National Laboratory has developed and implemented nuclear measurement technology and training in support of national and international nuclear safeguards. This paper outlines the major elements of those technologies and highlights some of the latest developments.

  6. Working with Fermi at Chicago and Los Alamos

    NASA Astrophysics Data System (ADS)

    Garwin, Richard L.

    2010-02-01

    I discuss my experience with Enrico Fermi as student and fellow faculty member at Chicago and with him as consultants to the Los Alamos Scientific Laboratory in 1950-1952. The talk shares observations about this great physicist and exemplary human being. )

  7. Optical velocimetry at the Los Alamos Proton Radiography Facility

    NASA Astrophysics Data System (ADS)

    Tupa, Dale; Tainter, Amy; Neukirch, Levi; Hollander, Brian; Buttler, William; Holtkamp, David; The Los Alamos Proton Radiography Team Team

    2016-05-01

    The Los Alamos Proton Radiography Facility (pRad) employs a high-energy proton beam to image the properties and behavior of materials driven by high explosives. We will discuss features of pRad and describe some recent experiments, highlighting optical diagnostics for surface velocity measurements.

  8. Technical manpower needs and resources at Los Alamos National Laboratory

    SciTech Connect

    Freese, K.B.

    1984-01-01

    The Los Alamos National Laboratory has begun a program to share its scientific and technological expertise with students and teachers in the surrounding area. The goal of the Laboratory's Educational Outreach Program is to stimulate an awareness of professional opportunities in the sciences and engineering.

  9. The Controlled-Air Incinerator at Los Alamos

    SciTech Connect

    Newmyer, J.N.

    1994-04-01

    The Controlled-Air Incinerator (CAI) at Los Alamos is being modified and upgraded to begin routine operations treating low-level mixed waste (LLMW), radioactively contaminated polychlorinated biphenyl (PCB) wastes, low-level liquid wastes, and possibly transuranic (TRU) wastes. This paper describes those modifications. Routine waste operations should begin in late FY95.

  10. [Los Alamos National Laboratory industrial applications and technology transfer

    SciTech Connect

    Not Available

    1992-09-30

    In October 1989, the Los Alamos Economic Development Corporation (LAEDC) entered into a contract with the Industrial Applications office (IAO) of Los Alamos National Laboratory (LANL) whereby the LAEDC was to provide support services to IAO. More specifically, according to the Statement of Work in this contract The Los Alamos Economic Development Corporation shall assist the Los Alamos National Laboratory Industrial Applications Office in establishing and strengthening connections between potential entrepreneurs at the Laboratory and the business assistance community throughout New Mexico, directed toward enhancing the number, of successful start up businesses spinning off the Laboratory's technology base.'' As part of this contract and subsequent modifications thereof, the LAEDC was to perform seven tasks: 1. Provide business planning assistance to potential entrepreneurs. 2. (Assist IAO in preparing and distributing) informational materials on technology transfer. 3. (Organize and manage) meetings and seminars on technology transfer and entrepreneurship. 4. Identify new opportunities for technology transfer. 5. (Identify and implement programs for the) recognition of Laboratory Entrepreneurs. 6. Training Lab personnel, in the area of technology transfer and Laboratory industrial interactions. 7. Review and summarize prior New Mexico economic development studies. The purpose of this report, is to summarize the accomplishments of the LAEDC under its contract with IAO, and to fulfill its reporting requirements. This report covers the period from October 1989 to September 1992.

  11. Brief review of Rover fuel development at Los Alamos

    NASA Technical Reports Server (NTRS)

    Davidson, Keith V.

    1991-01-01

    A brief review of the graphite matrix uranium fuel development efforts at Los Alamos from 1955 through 1972 is presented. The uses of graphite flour carbon black, various binders, uranium dioxide, coated UC2 particles, and zirconium carbide in this development are described.

  12. HIV Transmission at a Saudi Arabia Hemodialysis Unit

    PubMed Central

    Mashragi, Faisal; Bernstein, Robert S.; Al-Mazroa, Mohammad; Al-Tawfiq, Jaffar A.; Filemban, Sanaa; Assiri, Abdullah; Furukawa, Elaine; Al Hazmi, Mohammad; Alzahrani, Abdullah; Stephens, Gwen; Memish, Ziad A.

    2014-01-01

    Background. Hemodialysis is associated with increased risk of healthcare-associated infections but considered a low-risk setting for human immunodeficiency virus (HIV) transmission. We investigated 3 hemodialysis unit (HDU) patients with new HIV infections to determine whether transmission was hemodialysis-associated and to correct factors that contributed to transmission. Methods. Each patient was evaluated for HIV risk factors. Blood samples were tested to determine relatedness of HIV strains. Clinical data (gathered over 18 months) was reviewed to identify seroconversions at 12 HDUs. Infection prevention and control practices were evaluated at 14 HDUs. Findings. No other HIV seroconversions were identified during the study. HIV gag, pol, and env gene sequences were consistent with a clonal relationship. HIV and hepatitis C virus prevalence rates at one HDU 1 (5.7% and 6.5%, respectively) were higher than for 11 other HDUs (0% and 0.15%, respectively). Conclusions. Sequencing supports either patient-to-patient or common-source transmission. Infections occurred despite Saudi Arabia's low HIV prevalence and national dialysis policies that emphasize stringent infection prevention and control practices. PMID:24846636

  13. Audit Report, "Fire Protection Deficiencies at Los Alamos National Laboratory"

    SciTech Connect

    2009-06-01

    The Department of Energy's Los Alamos National Laboratory (Los Alamos) maintains some of the Nation's most important national security assets, including nuclear materials. Many of Los Alamos' facilities are located in close proximity to one another, are occupied by large numbers of contract and Federal employees, and support activities ranging from nuclear weapons design to science-related activities. Safeguarding against fires, regardless of origin, is essential to protecting employees, surrounding communities, and national security assets. On June 1, 2006, Los Alamos National Security, LLC (LANS), became the managing and operating contractor for Los Alamos, under contract with the Department's National Nuclear Security Administration (NNSA). In preparation for assuming its management responsibilities at Los Alamos, LANS conducted walk-downs of the Laboratory's facilities to identify pre-existing deficiencies that could give rise to liability, obligation, loss or damage. The walk-downs, which identified 812 pre-existing fire protection deficiencies, were conducted by subject matter professionals, including fire protection experts. While the Los Alamos Site Office has overall responsibility for the effectiveness of the fire protection program, LANS, as the Laboratory's operating contractor, has a major, day-to-day role in minimizing fire-related risks. The issue of fire protection at Los Alamos is more than theoretical. In May 2000, the 'Cerro Grande' fire burned about 43,000 acres, including 7,700 acres of Laboratory property. Due to the risk posed by fire to the Laboratory's facilities, workforce, and surrounding communities, we initiated this audit to determine whether pre-existing fire protection deficiencies had been addressed. Our review disclosed that LANS had not resolved many of the fire protection deficiencies that had been identified in early 2006: (1) Of the 296 pre-existing deficiencies we selected for audit, 174 (59 percent) had not been corrected

  14. Cyclophilin B enhances HIV-1 infection.

    PubMed

    DeBoer, Jason; Madson, Christian J; Belshan, Michael

    2016-02-01

    Cyclophilin B (CypB) is a member of the immunophilin family and intracellular chaperone. It predominantly localizes to the ER, but also contains a nuclear localization signal and is secreted from cells. CypB has been shown to interact with the Gag protein of human immunodeficiency type 1 (HIV-1). Several proteomic and genetic studies identified it as a potential factor involved in HIV replication. Herein, we show that over-expression of CypB enhances HIV infection by increasing nuclear import of viral DNA. This enhancement was unaffected by cyclosporine treatment and requires the N-terminus of the protein. The N-terminus contains an ER leader sequence, putative nuclear localization signal, and is required for secretion. Deletion of the N-terminus resulted in mislocalization from the ER and suppression of HIV infection. Passive transfer experiments showed that secreted CypB did not impact HIV infection. Combined, these experiments show that intracellular CypB modulates a pathway of HIV nuclear import. PMID:26774171

  15. Inhibition of the HIV-1 and HIV-2 proteases by a monoclonal antibody.

    PubMed Central

    Lescar, J.; Brynda, J.; Rezacova, P.; Stouracova, R.; Riottot, M. M.; Chitarra, V.; Fabry, M.; Horejsi, M.; Sedlacek, J.; Bentley, G. A.

    1999-01-01

    The monoclonal antibody 1696, directed against the HIV-1 protease, displays strong inhibitory effects toward the catalytic activity of the enzyme of both the HIV-1 and HIV-2 isolates. This antibody cross-reacts with peptides that include the N-terminus of the enzyme, a region that is well conserved in sequence among different viral strains and which, furthermore, is crucial for homodimerization to the active enzymatic form. This observation, as well as antigen-binding studies in the presence of an active site inhibitor, suggest that 1696 inhibits the HIV protease by destabilizing its active homodimeric form. To characterize further how the antibody 1696 inhibits the HIV-1 and HIV-2 proteases, we have solved the crystal structure of its Fab fragment by molecular replacement and refined it at 3.0 A resolution. The antigen binding site has a deep cavity at its center, which is lined mainly by acidic and hydrophobic residues, and is large enough to accommodate several antigen residues. The structure of the Fab 1696 could form a starting basis for the design of alternative HIV protease-inhibiting molecules of broad specificity. PMID:10631984

  16. A Novel HIV-1 Reporter Virus with a Membrane-Bound Gaussia princeps Luciferase

    PubMed Central

    Suree, Nuttee; Koizumi, Naoya; Sahakyan, Anna; Shimizu, Saki; An, Dong Sung

    2014-01-01

    Summary HIV-1 reporter viruses are a critical tool for investigating HIV-1 infection. By having a reporter gene incorporated into the HIV-1 genome, the expressed reporter protein acts as a specific tag, thus enabling specific detection of HIV-1 infected cells. Currently existing HIV-1 reporter viruses utilize reporters for the detection of HIV-1 infected cells by a single assay. A reporter virus enabling the detection of viral particles as well as HIV-1 infected cells by two assays can be more versatile for many applications. In this report, a novel reporter HIV-1 was generated by introducing a membrane-anchored form of the Gaussia princeps luciferase gene (mGluc) upstream of the nef gene in the HIV-1NL4-3 genome using a picornaviral 2A-like sequence. The resulting HIV-1NL4-3mGluc virus expresses Gaussia princeps luciferase efficiently on viral membrane and the cell surface of infected human T cell lines and primary peripheral blood mononuclear cells. This HIV-1 reporter is replication competent and the reporter gene mGluc is expressed during multiple rounds of infection. Importantly, viral particles can be detected by bioluminescence and infected cells can be detected simultaneously by bioluminescence and flow cytometric assays. With the versatility of two sensitive detection methods, this novel luciferase reporter has many applications such as cell-based screening for anti-HIV-1 agents or studies of HIV-1 pathogenicity. PMID:22483780

  17. Environmental Survey preliminary report, Los Alamos National Laboratory, Los Alamos, New Mexico

    SciTech Connect

    Not Available

    1988-01-01

    This report presents the preliminary findings from the first phase of the Environmental Survey of the United States Department of Energy's (DOE) Los Alamos National Laboratory (LANL), conducted March 29, 1987 through April 17, 1987. The Survey is being conducted by an interdisciplinary team of environmental specialists, led and managed by the Office of Environment, Safety and Health's Office of Environmental Audit. Individual team components are outside experts being supplied by a private contractor. The objective of the Survey is to identify environmental problems and areas of environmental risk associated with the LANL. The Survey covers all environmental media and all areas of environmental regulation. It is being performed in accordance with the DOE Environmental Survey Manual. The on-site phase of the Survey involves the review of existing site environmental data, observations of the operations carried on at the LANL, and interviews with site personnel. The Survey team developed Sampling and Analysis Plan to assist in further assessing certain of the environmental problems identified during its on-site activities. The Sampling and Analysis Plan will be executed by the Idaho National Engineering Laboratory. When completed, the results will be incorporated into the LANL Environmental Survey Interim Report. The Interim Report will reflect the final determinations of the Survey for the LANL. 65 refs., 68 figs., 73 tabs.

  18. Environmental assessment for effluent reduction, Los Alamos National Laboratory, Los Alamos, New Mexico

    SciTech Connect

    1996-09-11

    The Department of Energy (DOE) proposes to eliminate industrial effluent from 27 outfalls at Los Alamos National Laboratory (LANL). The Proposed Action includes both simple and extensive plumbing modifications, which would result in the elimination of industrial effluent being released to the environment through 27 outfalls. The industrial effluent currently going to about half of the 27 outfalls under consideration would be rerouted to LANL`s sanitary sewer system. Industrial effluent from other outfalls would be eliminated by replacing once-through cooling water systems with recirculation systems, or, in a few instances, operational changes would result in no generation of industrial effluent. After the industrial effluents have been discontinued, the affected outfalls would be removed from the NPDES Permit. The pipes from the source building or structure to the discharge point for the outfalls may be plugged, or excavated and removed. Other outfalls would remain intact and would continue to discharge stormwater. The No Action alternative, which would maintain the status quo for LANL`s outfalls, was also analyzed. An alternative in which industrial effluent would be treated at the source facilities was considered but dismissed from further analysis because it would not reasonably meet the DOE`s purpose for action, and its potential environmental effects were bounded by the analysis of the Proposed Action and the No Action alternatives.

  19. Probabilistic risk assessment for the Los Alamos Meson Physics Facility worst-case design-basis accident

    SciTech Connect

    Sharirli, M.; Butner, J.M.; Rand, J.L.; Macek, R.J.; McKinney, S.J.; Roush, M.L.

    1992-12-01

    This paper presents results from a Los Alamos National Laboratory Engineering and Safety Analysis Group assessment of the worse-case design-basis accident associated with the Clinton P. Anderson Meson Physics Facility (LAMPF)/Weapons Neutron Research (WNR) Facility. The primary goal of the analysis was to quantify the accident sequences that result in personnel radiation exposure in the WNR Experimental Hall following the worst-case design-basis accident, a complete spill of the LAMPF accelerator 1L beam. This study also provides information regarding the roles of hardware systems and operators in these sequences, and insights regarding the areas where improvements can increase facility-operation safety. Results also include confidence ranges to incorporate combined effects of uncertainties in probability estimates and importance measures to determine how variations in individual events affect the frequencies in accident sequences.

  20. Probabilistic risk assessment for the Los Alamos Meson Physics Facility worst-case design-basis accident

    SciTech Connect

    Sharirli, M.; Butner, J.M.; Rand, J.L.; Macek, R.J. ); McKinney, S.J. ); Roush, M.L. . Center for Reliability Engineering)

    1992-01-01

    This paper presents results from a Los Alamos National Laboratory Engineering and Safety Analysis Group assessment of the worse-case design-basis accident associated with the Clinton P. Anderson Meson Physics Facility (LAMPF)/Weapons Neutron Research (WNR) Facility. The primary goal of the analysis was to quantify the accident sequences that result in personnel radiation exposure in the WNR Experimental Hall following the worst-case design-basis accident, a complete spill of the LAMPF accelerator 1L beam. This study also provides information regarding the roles of hardware systems and operators in these sequences, and insights regarding the areas where improvements can increase facility-operation safety. Results also include confidence ranges to incorporate combined effects of uncertainties in probability estimates and importance measures to determine how variations in individual events affect the frequencies in accident sequences.

  1. Conserved epitopes on HIV-1, FIV and SIV p24 proteins are recognized by HIV-1 infected subjects

    PubMed Central

    Roff, Shannon R; Sanou, Missa P; Rathore, Mobeen H; Levy, Jay A; Yamamoto, Janet K

    2015-01-01

    Cross-reactive peptides on HIV-1 and FIV p24 protein sequences were studied using peripheral blood mononuclear cells (PBMC) from untreated HIV-1-infected long-term survivors (LTS; >10 y of infection without antiretroviral therapy, ART), short-term HIV-1 infected subjects not on ART, and ART-treated HIV-1 infected subjects. IFNγ-ELISpot and CFSE-proliferation analyses were performed with PBMC using overlapping HIV-1 and FIV p24 peptides. Over half of the HIV-1 infected subjects tested (22/31 or 71%) responded to one or more FIV p24 peptide pools by either IFNγ or T-cell proliferation analysis. PBMC and T cells from infected subjects in all 3 HIV+ groups predominantly recognized one FIV p24 peptide pool (Fp14) by IFNγ production and one additional FIV p24 peptide pool (Fp9) by T-cell proliferation analysis. Furthermore, evaluation of overlapping SIV p24 peptide sequences identified conserved epitope(s) on the Fp14/Hp15-counterpart of SIV, Sp14, but none on Fp9-counterpart of SIV, Sp9. The responses to these FIV peptide pools were highly reproducible and persisted throughout 2–4 y of monitoring. Intracellular staining analysis for cytotoxins and phenotyping for CD107a determined that peptide epitopes from Fp9 and Fp14 pools induced cytotoxic T lymphocyte-associated molecules including perforin, granzyme B, granzyme A, and/or expression of CD107a. Selected FIV and corresponding SIV epitopes recognized by HIV-1 infected patients indicate that these protein sequences are evolutionarily conserved on both SIV and HIV-1 (e.g., Hp15:Fp14:Sp14). These studies demonstrate that comparative immunogenicity analysis of HIV-1, FIV, and SIV can identify evolutionarily-conserved T cell-associated lentiviral epitopes, which could be used as a vaccine for prophylaxis or immunotherapy. PMID:25844718

  2. Testing for HIV

    MedlinePlus

    ... Medical Devices Radiation-Emitting Products Vaccines, Blood & Biologics Animal & Veterinary Cosmetics Tobacco Products Vaccines, Blood & Biologics Home Vaccines, Blood & Biologics Safety & Availability (Biologics) HIV Home Test Kits Testing for HIV Share Tweet Linkedin Pin it More ...

  3. HIV/AIDS

    MedlinePlus

    ... immunodeficiency virus (HIV) is the virus that causes AIDS. When a person becomes infected with HIV, the ... cancers. When that happens, the illness is called AIDS. Once a person has the virus, it stays ...

  4. HIV and AIDS

    MedlinePlus

    ... that causes the disease AIDS. HIV Hurts the Immune System People who are HIV positive have been tested ... to everyone in the world. When the person's immune system has weakened and more of the blood's T ...

  5. HIV and Cardiovascular Disease

    MedlinePlus

    ... CVD. ART can increase blood fats (cholesterol and triglycerides, see fact sheet 123.) It can also help ... disease. HIV infection decreases good cholesterol and increases triglycerides. HIV causes inflammation. This can also contribute to ...

  6. Older People and HIV

    MedlinePlus

    ... Many older people believe that HIV only affects younger people Most older people get little training in ... diseases among older people, as they do for younger people. Physicians may not diagnose HIV infection in ...

  7. Smoking and HIV

    MedlinePlus

    ... 28, 2014 Select a Language: Fact Sheet 803 Smoking and HIV WHY IS SMOKING MORE DANGEROUS FOR ... It can also worsen liver problems like hepatitis. Smoking and Side Effects People with HIV who smoke ...

  8. HIV and Pregnancy

    MedlinePlus

    ... Pregnancy Patient Education FAQs HIV and Pregnancy Patient Education Pamphlets - Spanish HIV and Pregnancy FAQ113, December 2012 PDF Format ... Your Practice Patient Safety & Quality Payment Reform (MACRA) Education & Events Annual ... Pamphlets Teen Health About ACOG About Us Leadership & ...

  9. Commercialization of Los Alamos National Laboratory technologies via small businesses. Final report

    SciTech Connect

    Brice, R.; Carton, D.; Rhyne, T.

    1997-06-01

    Appendices are presented from a study performed on a concept model system for the commercialization of Los Alamos National Laboratory technologies via small businesses. Topics include a summary of information from the joint MCC/Los Alamos technology conference; a comparison of New Mexico infrastructure to other areas; a typical licensing agreement; technology screening guides; summaries of specific DOE/UC/Los Alamos documents; a bibliography; the Oak Ridge National Laboratory TCRD; The Ames Center for Advanced Technology Development; Los Alamos licensing procedures; presentation of slides from monthly MCC/Los Alamos review meetings; generalized entrepreneurship model; and a discussion on receiving equity for technology.

  10. When phylogenetic analysis complements the epidemiological investigation: a case of HIV-2 infection, Italy.

    PubMed

    Ciccozzi, Massimo; Callegaro, Annapaola; Lo Presti, Alessandra; Cella, Eleonora; Giovanetti, Marta; Salpini, Romina; Babakir-Mina, Muhammed; Farina, Claudio; Maggiolo, Franco; Perno, Carlo Federico; Ciotti, Marco

    2013-01-01

    Human immunodeficiency virus type 2 (HIV-2) infection is geographically restricted, affecting West African countries such as Guinea- Bissau and Cape Verde. We describe a recent case of HIV-2 infection in an Italian patient. Phylogenetic analysis of the V3 region of HIV-2 indicated that the Italian patient was infected by HIV-2 subtype A2. The sequence obtained from the Italian patient clustered significantly with a sequence isolated from Senegal. A phylogenetic doubt may arise from a Guinea Bissau sequence because it was in a major clade with the Italian and Senegal sequences, but was not statistically significant. The discovery of another Italian case over a short time frame stresses the importance of strengthening the surveillance system for HIV-2 because of the increase in migration from endemic areas to Italy. PMID:23435822

  11. Novel anti-HIV peptides containing multiple copies of artificially designed heptad repeat motifs

    SciTech Connect

    Shi Weiguo; Qi Zhi; Pan Chungen; Xue Na; Debnath, Asim K.; Qie Jiankun; Jiang Shibo Liu Keliang

    2008-10-03

    The peptidic anti-HIV drug T20 (Fuzeon) and its analog C34 share a common heptad repeat (HR) sequence, but they have different functional domains, i.e., pocket- and lipid-binding domains (PBD and LBD, respectively). We hypothesize that novel anti-HIV peptides may be designed by using artificial sequences containing multiple copies of HR motifs plus zero, one or two functional domains. Surprisingly, we found that the peptides containing only the non-natural HR sequences could significantly inhibit HIV-1 infection, while addition of PBD and/or LBD to the peptides resulted in significant improvement of anti-HIV-1 activity. These results suggest that these artificial HR sequences, which may serve as structural domains, could be used as templates for the design of novel antiviral peptides against HIV and other viruses with class I fusion proteins.

  12. Aptamer-siRNA chimeras for HIV.

    PubMed

    Takahashi, Mayumi; Burnett, John C; Rossi, John J

    2015-01-01

    Since 1980s, HIV/AIDS has escalated into a global pandemic. Although combinatorial antiretroviral therapy (cART) regimens can suppress plasma virus levels to below the detection limit and the survival rate of HIV-1 infected patients has been improving, long-term cART holds the potential to cause a number of chronic diseases. RNA interference (RNAi) is considered as a powerful method for developing new generation of therapeutics. Discovery of small interfering RNAs (siRNAs) shed light on limitations of targets that are "undruggable" with current technologies. However, delivery remains a major hurdle of siRNA-based therapy. Recent progress in technology of engineering nucleic acid enables a targeted delivery of siRNAs using aptamers, which, as often regarded as nucleic acid "antibodies," can recognize/bind to multiple different proteins and small-molecule targets by forming scaffolds for molecular interactions. SELEX technology enabled to isolate highly target specific aptamers from a random sequence oligonucleotide library. A number of aptamers for HIV-1 proteins as well as host proteins that interact with HIV-1 have been developed and some of them have potent viral neutralization ability and inhibition of HIV-1 infectivity. The availability of these aptamers has given an idea of using aptamers for targeting delivery of siRNAs. So far, aptamers against either HIV-1 gp120 or CD4 have been eagerly evaluated as the aptamer portion of the aptamer-siRNA chimeras for the treatment or prevention of HIV-1. In this chapter, we highlight the development and therapeutic potential of aptamer-siRNA chimeras for HIV-1. PMID:25757623

  13. Discrepant amplification results during the development of an assay leads to reclassification of two AIDS reagent repository HIV-2 isolates as HIV-1.

    PubMed

    Jagodzinski, Linda L; Liu, Ying; Hack, Holly R; Kibirige, Catherine; Peel, Sheila A; Manak, Mark M

    2014-01-01

    The development and verification of HIV-2 assays depends in part on the availability of well-characterized samples, including those from reagent repositories. During the development of an HIV-2 RNA quantification assay, two HIV-2 viral isolates (CDC 301340 and CDC 301342) obtained from the NIAID AIDS Reagent and Reference Repository were not detected leading to an investigation. Two HIV-2 primers/probe sets of known performance in real-time viral RNA quantification assays, targeting different regions of the virus, also failed to generate RT-PCR products for these two isolates. These isolates were tested in the HIV-1 specific COBAS AmpliPrep/COBAS TaqMan HIV-1 Test v2.0 (Roche Molecular Diagnostics) and were quantified at high copy number. Other HIV-2 isolates tested were not amplified in the COBAS HIV-1 TaqMan assay. Furthermore, the discrepant isolates were highly reactive in an HIV-1 p24 antigen test while the other HIV-2 isolates showed very weak, if any, cross-reactivity with the HIV-1 p24 assay. Phylogenetic tree analysis of sequences from the protease-reverse transcriptase regions of the discrepant HIV-2 isolates mapped with HIV-1 Group M, Subtype CRF02_AG confirming these isolates were of HIV-1 origin and had been misclassified as HIV-2. The use of misclassified isolates in the verification of molecular and immunological assays can lead to misinterpretation of test results, misdirection of efforts into assay redesign and increased development costs. The results of this study were shared with the NIAID AIDS Reagent Program, leading to the reclassification of the two discrepant isolates as HIV-1. PMID:24797800

  14. Thermodynamic and phylogenetic insights into hnRNP A1 recognition of the HIV-1 exon splicing silencer 3 element.

    PubMed

    Rollins, Carrie; Levengood, Jeffrey D; Rife, Brittany D; Salemi, Marco; Tolbert, Blanton S

    2014-04-01

    Complete expression of the HIV-1 genome requires balanced usage of suboptimal splice sites. The 3' acceptor site A7 (ssA7) is negatively regulated in part by an interaction between the host hnRNP A1 protein and a viral splicing silencer (ESS3). Binding of hnRNP A1 to ESS3 and other upstream silencers is sufficient to occlude spliceosome assembly. Efforts to understand the splicing repressive properties of hnRNP A1 on ssA7 have revealed hnRNP A1 binds specific sites within the context of a highly folded RNA structure; however, biochemical models assert hnRNP A1 disrupts RNA structure through cooperative spreading. In an effort to improve our understanding of the ssA7 binding properties of hnRNP A1, herein we have performed a combined phylogenetic and biophysical study of the interaction of its UP1 domain with ESS3. Phylogenetic analyses of group M sequences (x̅ = 2860) taken from the Los Alamos HIV database reveal the ESS3 stem loop (SL3(ESS3)) structure has been conserved throughout HIV-1 evolution, despite variations in primary sequence. Calorimetric titrations with UP1 clearly show the SL3(ESS3) structure is a critical binding determinant because deletion of the base-paired region reduces the affinity by ∼150-fold (Kd values of 27.8 nM and 4.2 μM). Cytosine substitutions of conserved apical loop nucleobases show UP1 preferentially binds purines over pyrimidines, where site-specific interactions were detected via saturation transfer difference nuclear magnetic resonance. Chemical shift mapping of the UP1-SL3(ESS3) interface by (1)H-(15)N heteronuclear single-quantum coherence spectroscopy titrations reveals a broad interaction surface on UP1 that encompasses both RRM domains and the inter-RRM linker. Collectively, our results describe a UP1 binding mechanism that is likely different from current models used to explain the alternative splicing properties of hnRNP A1. PMID:24628426

  15. Polyclonal B-cell activation reveals antibodies against human immunodeficiency virus type 1 (HIV-1) in HIV-1-seronegative individuals.

    PubMed Central

    Jehuda-Cohen, T; Slade, B A; Powell, J D; Villinger, F; De, B; Folks, T M; McClure, H M; Sell, K W; Ahmed-Ansari, A

    1990-01-01

    Identification of human immunodeficiency virus type 1 (HIV-1)-infected individuals is of paramount importance for the control of the spread of AIDS worldwide. Currently, the vast majority of screening centers throughout the world rely on serological techniques. As such, clinically asymptomatic but HIV-infected, seronegative individuals are rarely identified. In this report we show that 18% (30/165) of seronegative individuals who were considered to be a unique cohort of patients at high risk for HIV infection had circulating B cells that, upon in vitro polyclonal activation with pokeweed mitogen, produced antibodies reactive with HIV. Furthermore, polymerase chain reaction analysis of DNA obtained from aliquots of the peripheral blood mononuclear cells from these seronegative but pokeweed mitogen assay-positive individuals tested revealed the presence of HIV-specific sequences in a significant number of samples. In addition, depletion of CD8+ T cells from peripheral blood mononuclear cells of HIV-1-seronegative individuals prior to in vitro culture with pokeweed mitogen resulted in increased sensitivity for detecting HIV-reactive antibodies. This assay has obvious epidemiological implications, especially in the case of high-risk groups, and also provides a simple technique to enhance detection of HIV-infected individuals. Of further interest is the determination of the mechanisms related to the lack of HIV-specific antibodies in the serum of these infected individuals. Images PMID:2111024

  16. Immunogenetics of HIV and HIV associated tuberculosis.

    PubMed

    Raghavan, S; Alagarasu, K; Selvaraj, P

    2012-01-01

    Tuberculosis (TB) is the frequent major opportunistic infection in HIV-infected patients, and is the leading cause of mortality among HIV-infected patients. Genetic susceptibility to TB in HIV negative subjects is well documented. Since coinfections can influence the way in which immune system respond to different pathogens, genetic susceptibility to TB in HIV patients might also change. Studies from India and other parts of the world have shown that genetic susceptibility to TB is influenced by HIV infection. In the present review, we emphasize the role of genetic factors in determining susceptibility to HIV infection, disease progression and development of TB in HIV-infected patients. Polymorphisms in human leukocyte antigen (HLA), MBL2, CD209, vitamin D receptor, cytokine, chemokine and chemokine receptor genes have been shown to be associated with development of TB in HIV patients. However, the results are inconclusive and larger well-defined studies with precise clinical data are required to validate these associations. Apart from candidate gene approach, genome-wide association studies are also needed to unravel the unknown or to establish the previously reported genetic associations with HIV associated TB. Despite the preliminary status of the reported associations, it is becoming clear that susceptibility to development of TB in HIV patients is influenced by both environmental and genetic components. Understanding the genetic and immunologic factors that influence susceptibility to TB in HIV patients could lead to novel insights for vaccine development as well as diagnostic advances to target treatment to those who are at risk for developing active disease. PMID:21943869

  17. Low-Frequency Drug Resistance in HIV-Infected Ugandans on Antiretroviral Treatment Is Associated with Regimen Failure.

    PubMed

    Kyeyune, Fred; Gibson, Richard M; Nankya, Immaculate; Venner, Colin; Metha, Samar; Akao, Juliet; Ndashimye, Emmanuel; Kityo, Cissy M; Salata, Robert A; Mugyenyi, Peter; Arts, Eric J; Quiñones-Mateu, Miguel E

    2016-06-01

    Most patients failing antiretroviral treatment in Uganda continue to fail their treatment regimen even if a dominant drug-resistant HIV-1 genotype is not detected. In a recent retrospective study, we observed that approximately 30% of HIV-infected individuals in the Joint Clinical Research Centre (Kampala, Uganda) experienced virologic failure with a susceptible HIV-1 genotype based on standard Sanger sequencing. Selection of minority drug-resistant HIV-1 variants (not detectable by Sanger sequencing) under antiretroviral therapy pressure can lead to a shift in the viral quasispecies distribution, becoming dominant members of the virus population and eventually causing treatment failure. Here, we used a novel HIV-1 genotyping assay based on deep sequencing (DeepGen) to quantify low-level drug-resistant HIV-1 variants in 33 patients failing a first-line antiretroviral treatment regimen in the absence of drug-resistant mutations, as screened by standard population-based Sanger sequencing. Using this sensitive assay, we observed that 64% (21/33) of these individuals had low-frequency (or minority) drug-resistant variants in the intrapatient HIV-1 population, which correlated with treatment failure. Moreover, the presence of these minority HIV-1 variants was associated with higher intrapatient HIV-1 diversity, suggesting a dynamic selection or fading of drug-resistant HIV-1 variants from the viral quasispecies in the presence or absence of drug pressure, respectively. This study identified low-frequency HIV drug resistance mutations by deep sequencing in Ugandan patients failing antiretroviral treatment but lacking dominant drug resistance mutations as determined by Sanger sequencing methods. We showed that these low-abundance drug-resistant viruses could have significant consequences for clinical outcomes, especially if treatment is not modified based on a susceptible HIV-1 genotype by Sanger sequencing. Therefore, we propose to make clinical decisions using more

  18. Reduce HIV Risk

    MedlinePlus

    ... are increasing among younger people from 13 to 30 years of age. The key to defeating HIV lies ... Control and Prevention (CDC) has used them as models, and Dr. Jemmott was invited to South Africa to help decrease HIV/AIDS there. "For the past 15 years, I have observed how the HIV/AIDS epidemic ...

  19. HIV and the menopause.

    PubMed

    Fan, Maria D; Maslow, Bat-Sheva; Santoro, Nanette; Schoenbaum, Ellie

    2008-12-01

    Dramatic improvement in the survival of the HIV population has occurred with the ascendance of highly active antiretroviral therapy (HAART). In the foreseeable future, HIV-infected women who acquired disease during the peak years of the epidemic are expected to survive to experience menopause and even years beyond. The HIV epidemic may be viewed as 'mature', as its earlier victims become part of the geriatric population. Research about the process of menopause in HIV-infected women and, conversely, about HIV infection in women undergoing menopause is currently limited. Existing research suggests that the process of menopause is affected by HIV infection, inasmuch as infected women appear to experience menopause at an earlier age, with greater symptomatology, and with different reproductive hormone profiles compared with HIV-uninfected women. HIV infection also appears to affect bone mineral density, cardiovascular disease and cognition, with some age-related interactions. Lifestyle and demographic factors have pervasive importance for both HIV infection and the menopause in women. This article reviews the current state of knowledge about the menopausal process in HIV-infected women, and the common conditions in postmenopausal women that are likely to be affected by HIV infection. Clinicians should appreciate the potential role of HIV infection in caring for menopause-aged women. PMID:19037065

  20. HIV Disease: Current Concepts.

    ERIC Educational Resources Information Center

    Keeling, Richard P.

    1993-01-01

    Describes human immunodeficiency virus (HIV), newly characterized human retrovirus which causes chronic, progressive, immune deficiency disease, the most severe phase of which is Acquired Immune Deficiency Syndrome (AIDS). Reviews most important current epidemiologic, clinical, and virologic information about HIV and HIV disease and provides…

  1. 75 FR 24957 - Decision to Evaluate a Petition to Designate a Class of Employees From the Los Alamos National...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-06

    ... HUMAN SERVICES Decision to Evaluate a Petition to Designate a Class of Employees From the Los Alamos National Laboratory, Los Alamos, NM, To Be Included in the Special Exposure Cohort AGENCY: National... designate a class of employees from the Los Alamos National Laboratory, Los Alamos, New Mexico, to...

  2. Neuropsychological abnormalities in AIDS and asymptomatic HIV seropositive patients.

    PubMed Central

    Villa, G; Monteleone, D; Marra, C; Bartoli, A; Antinori, A; Pallavicini, F; Tamburrini, E; Izzi, I

    1993-01-01

    Neuropsychological and immunological parameters were studied in 36 AIDS patients with early disease and without clinical, laboratory, and neuroradiological signs of CNS impairment, and also in 33 asymptomatic HIV seropositive subjects. Many AIDS patients performed abnormally on timed psychomotor tasks, tasks involving sequencing and "set-shifting", and memory tasks stressing attention, learning, active retrieval, and monitoring of information. Asymptomatic HIV seropositive subjects as a group did not perform significantly worse than controls. However, on the basis of a cut off number of pathological performances on neuropsychological tasks, 52.8% of AIDS and 30.3% of asymptomatic HIV seropositive subjects had cognitive impairment, compared with 3.9% of HIV seronegative controls. Low values of CD4+ cells and of CD4+/CD8+ ratio and high titres of P-24 antigen in the blood prevailed among subjects with cognitive impairment, especially in the asymptomatic HIV seropositive group. PMID:8350104

  3. The engineering institute of Los Alamos National Laboratory

    SciTech Connect

    Farrar, Charles R; Park, Gyuhae; Cornwell, Phillip J; Todd, Michael D

    2008-01-01

    Los Alamos National Laboratory (LANL) and the University of California, San Diego (UCSD) have taken the unprecedented step of creating a collaborative, multi-disciplinary graduate education program and associated research agenda called the Engineering Institute. The mission of the Engineering Institute is to develop a comprehensive approach for conducting LANL mission-driven, multidisciplinary engineering research and to improve recruiting, revitalization, and retention of the current and future staff necessary to support the LANL' s national security responsibilities. The components of the Engineering Institute are (1) a joint LANL/UCSD degree program, (2) joint LANL/UCSD research projects, (3) the Los Alamos Dynamic Summer School, (4) an annual workshop, and (5) industry short courses. This program is a possible model for future industry/government interactions with university partners.

  4. Airport-Noise Levels and Annoyance Model (ALAMO) user's guide

    NASA Technical Reports Server (NTRS)

    Deloach, R.; Donaldson, J. L.; Johnson, M. J.

    1986-01-01

    A guide for the use of the Airport-Noise Level and Annoyance MOdel (ALAMO) at the Langley Research Center computer complex is provided. This document is divided into 5 primary sections, the introduction, the purpose of the model, and an in-depth description of the following subsystems: baseline, noise reduction simulation and track analysis. For each subsystem, the user is provided with a description of architecture, an explanation of subsystem use, sample results, and a case runner's check list. It is assumed that the user is familiar with the operations at the Langley Research Center (LaRC) computer complex, the Network Operating System (NOS 1.4) and CYBER Control Language. Incorporated within the ALAMO model is a census database system called SITE II.

  5. Tiger Team Assessment of the Los Alamos National Laboratory

    SciTech Connect

    Not Available

    1991-11-01

    This report documents the Tiger Team Assessment of the Los Alamos National Laboratory (LANL) located in Los Alamos, New Mexico. LANL is operated for the US Department of Energy (DOE) by the University of California. The Tiger Team Assessment was conducted from September 23 to November 8, 1991, under the auspices of the DOE Office of Special Projects, Office of Assistant Secretary for Environment, Safety and Health. The assessment was comprehensive, encompassing environmental, safety, and health (ES H) disciplines; management; and contractor and DOE self-assessments. Compliance with applicable Federal, state, and local regulations; applicable DOE Orders; best management practices; and internal LANL site requirements was assessed. In addition, an evaluation of the adequacy and effectiveness of the DOE and the site contractors' management of ES H/quality assurance programs was conducted. This volume discusses findings concerning the environmental assessment.

  6. Penetrating radiation: applications at Los Alamos National Laboratory

    NASA Astrophysics Data System (ADS)

    Watson, Scott; Hunter, James; Morris, Christopher

    2013-09-01

    Los Alamos has used penetrating radiography extensively throughout its history dating back to the Manhattan Project where imaging dense, imploding objects was the subject of intense interest. This interest continues today as major facilities like DARHT1 have become the mainstay of the US Stockpile Stewardship Program2 and the cornerstone of nuclear weapons certification. Meanwhile, emerging threats to national security from cargo containers and improvised explosive devices (IEDs) have invigorated inspection efforts using muon tomography, and compact x-ray radiography. Additionally, unusual environmental threats, like those from underwater oil spills and nuclear power plant accidents, have caused renewed interest in fielding radiography in severe operating conditions. We review the history of penetrating radiography at Los Alamos and survey technologies as presently applied to these important problems.

  7. Status of optical model activities at Los Alamos National Laboratory

    SciTech Connect

    Young, P.G.

    1995-12-01

    An update will be given of activities at Los Alamos National Laboratory aimed at developing optical model potentials for applied calculations. Recent work on a coupled-channels potential for neutron reactions on {sup 241,243}Am and spherical neutron potential updates for {sup 56}Fe and {sup 59}Co will be presented, together with examples of their application in nuclear reaction calculations with the GNASH code system. New potentials utilized in evaluations at Livermore for {sup 12}C, {sup 14}N and {sup 16}O are described and additional potentials from earlier analyses at Los Alamos of Ti, V, and Ni data are made available for possible inclusion in the Reference Input Parameter Library (RIPL) for nuclear model calculations of nuclear data. Specific activities directed at development of the optical potential segment of the RIPL will be summarized.

  8. A New Generation of Los Alamos Opacity Tables

    NASA Astrophysics Data System (ADS)

    Colgan, J.; Kilcrease, D. P.; Magee, N. H.; Sherrill, M. E.; Abdallah, J., Jr.; Hakel, P.; Fontes, C. J.; Guzik, J. A.; Mussack, K. A.

    2016-02-01

    We present a new, publicly available set of Los Alamos OPLIB opacity tables for the elements hydrogen through zinc. Our tables are computed using the Los Alamos ATOMIC opacity and plasma modeling code, and make use of atomic structure calculations that use fine-structure detail for all the elements considered. Our equation of state model, known as ChemEOS, is based on the minimization of free energy in a chemical picture and appears to be a reasonable and robust approach to determining atomic state populations over a wide range of temperatures and densities. In this paper we discuss in detail the calculations that we have performed for the 30 elements considered, and present some comparisons of our monochromatic opacities with measurements and other opacity codes. We also use our new opacity tables in solar modeling calculations and compare and contrast such modeling with previous work.

  9. Tuberculosis and HIV Coinfection.

    PubMed

    Bruchfeld, Judith; Correia-Neves, Margarida; Källenius, Gunilla

    2015-07-01

    Tuberculosis (TB) and human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) constitute the main burden of infectious disease in resource-limited countries. In the individual host, the two pathogens, Mycobacterium tuberculosis and HIV, potentiate one another, accelerating the deterioration of immunological functions. In high-burden settings, HIV coinfection is the most important risk factor for developing active TB, which increases the susceptibility to primary infection or reinfection and also the risk of TB reactivation for patients with latent TB. M. tuberculosis infection also has a negative impact on the immune response to HIV, accelerating the progression from HIV infection to AIDS. The clinical management of HIV-associated TB includes the integration of effective anti-TB treatment, use of concurrent antiretroviral therapy (ART), prevention of HIV-related comorbidities, management of drug cytotoxicity, and prevention/treatment of immune reconstitution inflammatory syndrome (IRIS). PMID:25722472

  10. Basic HIV/AIDS Statistics

    MedlinePlus

    ... Abroad Treatment Basic Statistics Get Tested Find an HIV testing site near you. Enter ZIP code or city Follow HIV/AIDS CDC HIV CDC HIV/AIDS See RSS | ... Collapse All How many people are diagnosed with HIV each year in the United States? In 2014, ...

  11. HIV Medicines and Side Effects

    MedlinePlus

    Side Effects of HIV Medicines HIV Medicines and Side Effects (Last updated 1/7/2016; last reviewed 1/7/2016) Key Points HIV medicines help people with ... will depend on a person’s individual needs. Can HIV medicines cause side effects? HIV medicines help people ...

  12. Evolution of some Los Alamos flux compression programs

    SciTech Connect

    Fowler, C.M.; Goforth, J.H.

    1996-12-31

    When we were approached to give a general discussion of some aspects of the Los Alamos flux compression program, we decided to present historical backgrounds of a few topics that have some relevance to programs that we very much In the forefront of activities going on today. Of some thirty abstracts collected at Los Alamos for this conference, ten of them dealt with electromagnetic acceleration of materials, notably the compression of heavy liners, and five dealt with plasma compression. Both of these topics have been under investigation, off and on, from the time a formal flux compression program was organized at Los Alamos. We decided that a short overview of work done In these areas would be of some interest. Some of the work described below has been discussed in Laboratory reports that, while referenced and available, are not readily accessible. For completeness, some previously published, accessible work Is also discussed but much more briefly. Perhaps the most striking thing about the early work In these two areas is how primitive much of it was when compared to the far more sophisticated, related activities of today. Another feature of these programs, actually for most programs, Is their cyclic nature. Their relevance and/or funding seems to come land go. Eventually, many of the older programs come back into favor. Activities Involving the dense plasma focus (DPF), about which some discussions will be given later, furnish a classic example of this kind, coming Into and then out of periods of heightened interest. We devote the next two sections of this paper to a review of our work In magnetic acceleration of solids and of plasma compression. A final section gives a survey of our work In which thin foils are imploded to produce intense quantities of son x-rays. The authors are well aware of much excellent work done elsewhere In all of these topics, but partly because of space limitations, have confined this discussion to work done at Los Alamos.

  13. Los Alamos National Laboratory's high-performance data system

    SciTech Connect

    Mercier, C.; Chorn, G.; Christman, R.; Collins, B.

    1991-01-01

    Los Alamos National Laboratory is designing a High-Performance Data System (HPDS) that will provide storage for supercomputers requiring large files and fast transfer speeds. The HPDS will meet the performance requirements by managing data transfers from high-speed storage systems connected directly to a high-speed network. File and storage management software will be distributed in workstations. Network protocols will ensure reliable, wide-area network data delivery to support long-distance distributed processing. 3 refs., 2 figs.

  14. [Los Alamos National Laboratory industrial applications and technology transfer

    SciTech Connect

    Not Available

    1991-10-31

    This report summarizes the accomplishments of the Los Alamos Economic Development Corporation (LAEDC) under its contract with the Industrial Applications Office (IAO). The LAEDC has: provided business planning assistance to potential entrepreneurs, assisted IAO in preparing and distributing informational materials on technology, organized and managed meetings and seminars on technology transfer and entrepreneurship, identified new opportunities for technology transfer, and identified and implemented programs for the recognition of Laboratory entrepreneurs.

  15. Tat-dependent occlusion of the HIV poly(A) site.

    PubMed Central

    Weichs an der Glon, C; Ashe, M; Eggermont, J; Proudfoot, N J

    1993-01-01

    Retroviruses must ensure that poly(A) signals in the 3' LTR are highly active, while identical signals in the 5' LTR are inactive (occluded). In the case of HIV-1, both promoter proximity in the 5' LTR and U3 sequences in the 3' LTR may contribute to this regulation. We have discovered a novel regulatory mechanism for poly(A) site occlusion in HIV-1. When transcription initiation from the HIV promoter is activated by Tat, the HIV poly(A) site is specifically occluded, while other poly(A) sites are unaffected by Tat. Nucleotide signals associated with this Tat effect are immediately adjacent to the AAUAAA sequence of the HIV-1 poly(A) signal. These data suggest that elongating RNA polymerase II, activated by Tat specifically occludes the HIV poly(A) site. Images PMID:8491200

  16. Using the Internet in Middle Schools: A Model for Success. A Collaborative Effort between Los Alamos National Laboratory (LANL) and Los Alamos Middle School (LAMS).

    ERIC Educational Resources Information Center

    Addessio, Barbara K.; And Others

    Los Alamos National Laboratory (LANL) developed a model for school networking using Los Alamos Middle School as a testbed. The project was a collaborative effort between the school and the laboratory. The school secured administrative funding for hardware and software; and LANL provided the network architecture, installation, consulting, and…

  17. Overview of laser technology at Los Alamos National Laboratory

    NASA Astrophysics Data System (ADS)

    Lewis, G. K.; Cremers, D. A.

    Los Alamos National Laboratory has had a long history of involvement in laser sciences and has been recognized both for its large laser programs and smaller scale developments in laser technology and applications. The first significant program was with the Rover nuclear-based rocket propulsion system in 1968 to study laser initiated fusion. From here applications spread to programs in laser isotope separation and development of large lasers for fusion. These programs established the technological human resource base of highly trained laser physicists, engineers, and chemists that remain at the Laboratory today. Almost every technical division at Los Alamos now has some laser capability ranging from laser development, applications, studies on nonlinear processes, modeling and materials processing. During the past six years over eight R&D-100 Awards have been received by Los Alamos for development of laser-based techniques and instrumentation. Outstanding examples of technology developed include LIDAR applications to environmental monitoring, single molecule detection using fluorescence spectroscopy, a laser-based high kinetic energy source of oxygen atoms produced by a laser-sustained plasma, laser-induced breakdown spectroscopy (LIBS) for compositional, analysis, thin film high temperature superconductor deposition, multi-station laser welding, and direct metal deposition and build-up of components by fusing powder particles with a laser beam.

  18. Los Alamos, Toshiba probing Fukushima with cosmic rays

    ScienceCinema

    Morris, Christopher

    2014-06-25

    Los Alamos National Laboratory has announced an impending partnership with Toshiba Corporation to use a Los Alamos technique called muon tomography to safely peer inside the cores of the Fukushima Daiichi reactors and create high-resolution images of the damaged nuclear material inside without ever breaching the cores themselves. The initiative could reduce the time required to clean up the disabled complex by at least a decade and greatly reduce radiation exposure to personnel working at the plant. Muon radiography (also called cosmic-ray radiography) uses secondary particles generated when cosmic rays collide with upper regions of Earth's atmosphere to create images of the objects that the particles, called muons, penetrate. The process is analogous to an X-ray image, except muons are produced naturally and do not damage the materials they contact. Muon radiography has been used before in imaginative applications such as mapping the interior of the Great Pyramid at Giza, but Los Alamos's muon tomography technique represents a vast improvement over earlier technology.

  19. Los Alamos, Toshiba probing Fukushima with cosmic rays

    SciTech Connect

    Morris, Christopher

    2014-06-16

    Los Alamos National Laboratory has announced an impending partnership with Toshiba Corporation to use a Los Alamos technique called muon tomography to safely peer inside the cores of the Fukushima Daiichi reactors and create high-resolution images of the damaged nuclear material inside without ever breaching the cores themselves. The initiative could reduce the time required to clean up the disabled complex by at least a decade and greatly reduce radiation exposure to personnel working at the plant. Muon radiography (also called cosmic-ray radiography) uses secondary particles generated when cosmic rays collide with upper regions of Earth's atmosphere to create images of the objects that the particles, called muons, penetrate. The process is analogous to an X-ray image, except muons are produced naturally and do not damage the materials they contact. Muon radiography has been used before in imaginative applications such as mapping the interior of the Great Pyramid at Giza, but Los Alamos's muon tomography technique represents a vast improvement over earlier technology.

  20. Overview of laser technology at Los Alamos National Laboratory

    SciTech Connect

    Lewis, G.K.; Cremers, D.A.

    1994-09-01

    Los Alamos National Laboratory has had a long history of involvement in laser sciences and has been recognized both for its large laser programs and smaller scale developments in laser technology and applications. The first significant program was with the Rover nuclear-based rocket propulsion system in 1968 to study laser initiated fusion. From here applications spread to programs in laser isotope separation and development of large lasers for fusion. These programs established the technological human resource base of highly trained laser physicists, engineers, and chemists that remain at the Laboratory today. Almost every technical division at Los Alamos now has some laser capability ranging from laser development, applications, studies on nonlinear processes, modeling and materials processing. During the past six years over eight R&D-100 Awards have been received by Los Alamos for development of laser-based techniques and instrumentation. Outstanding examples of technology developed include LIDAR applications to environmental monitoring, single molecule detection using fluorescence spectroscopy, a laser-based high kinetic energy source of oxygen atoms produced by a laser-sustained plasma, laser-induced breakdown spectroscopy (LIBS) for compositional, analysis, thin film high temperature superconductor deposition, multi-station laser welding, and direct metal deposition and build-up of components by fusing powder particles with a laser beam.

  1. James L. Tuck Los Alamos ball lightning pioneer

    SciTech Connect

    Baker, D.A.

    1999-07-01

    James Tuck was well known for starting the Project Sherwood group at Los Alamos Scientific Laboratory in 1952. This group was formed to study and develop concepts for controlled fusion energy. In his later years after retiring from Controlled Fusion Division, he continued research at Los Alamos on the topic of ball lightning. He traveled widely giving lectures on both observations of others and his own experimental efforts. He collected anecdotal observations obtained from those in his lecture audiences during his travels and from responses from newspaper articles where he asked for specific information from ball lightning observers. He finally cut off this collection of data when the number of responses became overwhelming. The author's primary publication on ball lightning was a short laboratory report. He planned on publishing a book on the subject but this was never completed before his death. Tuck focused his experimental effort on attempting to duplicate the production of plasma balls claimed to be observed in US Navy submarines when a switch was opened under overload conditions with battery power. During lunch breaks he made use of a Los Alamos N-division battery bank facility to mock up a submarine power pack and switch gear. This non-funded effort was abruptly terminated when an explosion occurred in the facility. An overview of Tuck's research and views will be given. The flavor Jim's personality as well as a ball produced with his experimental apparatus will be shown using video chips.

  2. Quasispecies Analyses of the HIV-1 Near-full-length Genome With Illumina MiSeq.

    PubMed

    Ode, Hirotaka; Matsuda, Masakazu; Matsuoka, Kazuhiro; Hachiya, Atsuko; Hattori, Junko; Kito, Yumiko; Yokomaku, Yoshiyuki; Iwatani, Yasumasa; Sugiura, Wataru

    2015-01-01

    Human immunodeficiency virus type-1 (HIV-1) exhibits high between-host genetic diversity and within-host heterogeneity, recognized as quasispecies. Because HIV-1 quasispecies fluctuate in terms of multiple factors, such as antiretroviral exposure and host immunity, analyzing the HIV-1 genome is critical for selecting effective antiretroviral therapy and understanding within-host viral coevolution mechanisms. Here, to obtain HIV-1 genome sequence information that includes minority variants, we sought to develop a method for evaluating quasispecies throughout the HIV-1 near-full-length genome using the Illumina MiSeq benchtop deep sequencer. To ensure the reliability of minority mutation detection, we applied an analysis method of sequence read mapping onto a consensus sequence derived from de novo assembly followed by iterative mapping and subsequent unique error correction. Deep sequencing analyses of aHIV-1 clone showed that the analysis method reduced erroneous base prevalence below 1% in each sequence position and discarded only < 1% of all collected nucleotides, maximizing the usage of the collected genome sequences. Further, we designed primer sets to amplify the HIV-1 near-full-length genome from clinical plasma samples. Deep sequencing of 92 samples in combination with the primer sets and our analysis method provided sufficient coverage to identify >1%-frequency sequences throughout the genome. When we evaluated sequences of pol genes from 18 treatment-naïve patients' samples, the deep sequencing results were in agreement with Sanger sequencing and identified numerous additional minority mutations. The results suggest that our deep sequencing method would be suitable for identifying within-host viral population dynamics throughout the genome. PMID:26617593

  3. Quasispecies Analyses of the HIV-1 Near-full-length Genome With Illumina MiSeq

    PubMed Central

    Ode, Hirotaka; Matsuda, Masakazu; Matsuoka, Kazuhiro; Hachiya, Atsuko; Hattori, Junko; Kito, Yumiko; Yokomaku, Yoshiyuki; Iwatani, Yasumasa; Sugiura, Wataru

    2015-01-01

    Human immunodeficiency virus type-1 (HIV-1) exhibits high between-host genetic diversity and within-host heterogeneity, recognized as quasispecies. Because HIV-1 quasispecies fluctuate in terms of multiple factors, such as antiretroviral exposure and host immunity, analyzing the HIV-1 genome is critical for selecting effective antiretroviral therapy and understanding within-host viral coevolution mechanisms. Here, to obtain HIV-1 genome sequence information that includes minority variants, we sought to develop a method for evaluating quasispecies throughout the HIV-1 near-full-length genome using the Illumina MiSeq benchtop deep sequencer. To ensure the reliability of minority mutation detection, we applied an analysis method of sequence read mapping onto a consensus sequence derived from de novo assembly followed by iterative mapping and subsequent unique error correction. Deep sequencing analyses of aHIV-1 clone showed that the analysis method reduced erroneous base prevalence below 1% in each sequence position and discarded only < 1% of all collected nucleotides, maximizing the usage of the collected genome sequences. Further, we designed primer sets to amplify the HIV-1 near-full-length genome from clinical plasma samples. Deep sequencing of 92 samples in combination with the primer sets and our analysis method provided sufficient coverage to identify >1%-frequency sequences throughout the genome. When we evaluated sequences of pol genes from 18 treatment-naïve patients' samples, the deep sequencing results were in agreement with Sanger sequencing and identified numerous additional minority mutations. The results suggest that our deep sequencing method would be suitable for identifying within-host viral population dynamics throughout the genome. PMID:26617593

  4. Long antibody HCDR3s from HIV-naïve donors presented on a PG9 neutralizing antibody background mediate HIV neutralization.

    PubMed

    Willis, Jordan R; Finn, Jessica A; Briney, Bryan; Sapparapu, Gopal; Singh, Vidisha; King, Hannah; LaBranche, Celia C; Montefiori, David C; Meiler, Jens; Crowe, James E

    2016-04-19

    Development of broadly neutralizing antibodies (bnAbs) against HIV-1 usually requires prolonged infection and induction of Abs with unusual features, such as long heavy-chain complementarity-determining region 3 (HCDR3) loops. Here we sought to determine whether the repertoires of HIV-1-naïve individuals contain Abs with long HCDR3 loops that could mediate HIV-1 neutralization. We interrogated at massive scale the structural properties of long Ab HCDR3 loops in HIV-1-naïve donors, searching for structured HCDR3s similar to those of the HIV-1 bnAb PG9. We determined the nucleotide sequences encoding 2.3 × 10(7)unique HCDR3 amino acid regions from 70 different HIV-1-naïve donors. Of the 26,917 HCDR3 loops with 30-amino acid length identified, we tested 30 for further study that were predicted to have PG9-like structure when chimerized onto PG9. Three of these 30 PG9 chimeras bound to the HIV-1 gp120 monomer, and two were neutralizing. In addition, we found 14 naturally occurring HCDR3 sequences that acquired the ability to bind to the HIV-1 gp120 monomer when adding 2- to 7-amino acid mutations via computational design. Of those 14 designed Abs, 8 neutralized HIV-1, with IC50values ranging from 0.7 to 98 µg/mL. These data suggest that the repertoire of HIV-1-naïve individuals contains rare B cells that encode HCDR3 loops that bind or neutralize HIV-1 when presented on a PG9 background with relatively few or no additional mutations. Long HCDR3 sequences are present in the HIV-naïve B-cell repertoire, suggesting that this class of bnAbs is a favorable target for rationally designed preventative vaccine efforts. PMID:27044078

  5. Types of HIV/AIDS Antiretroviral Drugs

    MedlinePlus

    ... reverse transcriptase (RT) from converting single-stranded HIV RNA into double-stranded HIV DNA―a process called ... RT, interfering with its ability to convert HIV RNA into HIV DNA Integrase Inhibitors block the HIV ...

  6. Side Effects of HIV Medicines: HIV and Osteoporosis

    MedlinePlus

    Side Effects of HIV Medicines HIV and Osteoporosis (Last updated 1/11/2016; last reviewed 1/11/2016) Key ... in HIV-1-Infected Adults and Adolescents: Adverse Effects of Antiretroviral Agents From the National Institutes of ...

  7. Impact of Human Immunodeficiency Virus Type 1 (HIV-1) Genetic Diversity on Performance of Four Commercial Viral Load Assays: LCx HIV RNA Quantitative, AMPLICOR HIV-1 MONITOR v1.5, VERSANT HIV-1 RNA 3.0, and NucliSens HIV-1 QT

    PubMed Central

    Swanson, Priscilla; de Mendoza, Carmen; Joshi, Yagnya; Golden, Alan; Hodinka, Richard L.; Soriano, Vincent; Devare, Sushil G.; Hackett, John

    2005-01-01

    Human immunodeficiency virus type 1 (HIV-1) evolution and changing strain distribution present a challenge to nucleic acid-based assays. Reliable patient monitoring of viral loads requires the detection and accurate quantification of genetically diverse HIV-1. A panel of 97 HIV-1-seropositive plasma samples collected from Cameroon, Brazil, and South Africa was used to compare the performance of four commercially available HIV RNA quantitative tests: Abbott LCx HIV RNA Quantitative assay (LCx), Bayer Versant HIV-1 RNA 3.0 (bDNA), Roche AMPLICOR HIV-1 MONITOR v1.5 (Monitor v1.5), and bioMérieux NucliSens HIV-1 QT (NucliSens). The panel included group M, group O, and recombinant viruses based on sequence analysis of gag p24, pol integrase, and env gp41. The LCx HIV assay quantified viral RNA in 97 (100%) of the samples. In comparison, bDNA, Monitor v1.5, and NucliSens quantified viral RNA in 96.9%, 94.8%, and 88.6% of the samples, respectively. The two group O specimens were quantified only by the LCx HIV assay. Analysis of nucleotide mismatches at the primer/probe binding sites for Monitor v1.5, NucliSens, and LCx assays revealed that performance characteristics reflected differences in the level of genetic conservation within the target regions. PMID:16081923

  8. Analysis of human immunodeficiency virus type 1 nef gene sequences present in vivo.

    PubMed Central

    Shugars, D C; Smith, M S; Glueck, D H; Nantermet, P V; Seillier-Moiseiwitsch, F; Swanstrom, R

    1993-01-01

    The nef genes of the human immunodeficiency viruses type 1 and 2 (HIV-1 and HIV-2) and the related simian immunodeficiency viruses (SIVs) encode a protein (Nef) whose role in virus replication and cytopathicity remains uncertain. As an attempt to elucidate the function of nef, we characterized the nucleotide and corresponding protein sequences of naturally occurring nef genes obtained from several HIV-1-infected individuals. A consensus Nef sequence was derived and used to identify several features that were highly conserved among the Nef sequences. These features included a nearly invariant myristylation signal, regions of sequence polymorphism and variable duplication, a region with an acidic charge, a (Pxx)4 repeat sequence, and a potential protein kinase C phosphorylation site. Clustering of premature stop codons at position 124 was noted in 6 of the 54 Nef sequences. Further analysis revealed four stretches of residues that were highly conserved not only among the patient-derived HIV-1 Nef sequences, but also among the Nef sequences of HIV-2 and the SIVs, suggesting that Nef proteins expressed by these retroviruses are functionally equivalent. The "Nef-defining" sequences were used to evaluate the sequence alignments of known proteins reported to share sequence similarity with Nef sequences and to conduct additional computer-based searches for similar protein sequences. A gene encoding the consensus Nef sequence was also generated. This gene encodes a full-length Nef protein that should be a valuable tool in further studies of Nef function. Images PMID:8043040

  9. Detecting primary drug-resistant mutations in Korean HIV patients using ultradeep pyrosequencing.

    PubMed

    Cho, Min-Chul; Park, Chang-Wook; Park, Borae G; Oh, Heung-Bum; Choi, Sang-Ho; Choi, Sung-Eun; Cho, Nam-Sun

    2016-08-01

    HIV primary resistance, drug resistance in treatment-naïve patients, is an emerging public health issue. The prevalence of HIV primary resistance mutations down to the level of 1% minor variants was investigated using ultradeep pyrosequencing (UDPS) in HIV-positive Korean blood donors and in treatment naïve chronic patients for the comparison. The entire pol region was sequenced from 25 HIV-positive blood donors, and 18 treatment-naïve chronic HIV patients. UDPS was successful in 19 blood donors and 18 chronic patients. In total, 1,011,338 sequence reads were aligned, and 28,093 sequence reads were aligned on average per sample. The prevalence of HIV primary resistance mutations in the HIV-positive blood donors and chronic HIV patients were 63.2% and 44.4% according to UDPS, respectively. Protease inhibitor (PI) drugs demonstrated different patterns in HIV-positive blood donors and chronic HIV patients, whereas non-nucleoside reverse transcriptase inhibitors (NNRTI), nucleoside reverse transcriptase inhibitors (NRTI), and integrase inhibitor (INI) drugs showed similar patterns between the two groups. Higher level of primary resistance prevalence was observed mainly because UDPS method could detect mutations in minor variants with 1-10% frequency. The higher resistance prevalence was observed in HIV-positive blood donors than in chronic patients. Considering that treatments for HIV-infected patients were recently amended to start at an earlier stage, information about degree of drug resistance to each drug between the two groups would help to establish future policies, design additional clinical trials, assess HIV patient care in Korea. PMID:27109046

  10. Retroviral DNA Integration Directed by HIV Integration Protein in Vitro

    NASA Astrophysics Data System (ADS)

    Bushman, Frederic D.; Fujiwara, Tamio; Craigie, Robert

    1990-09-01

    Efficient retroviral growth requires integration of a DNA copy of the viral RNA genome into a chromosome of the host. As a first step in analyzing the mechanism of integration of human immunodeficiency virus (HIV) DNA, a cell-free system was established that models the integration reaction. The in vitro system depends on the HIV integration (IN) protein, which was partially purified from insect cells engineered to express IN protein in large quantities. Integration was detected in a biological assay that scores the insertion of a linear DNA containing HIV terminal sequences into a λ DNA target. Some integration products generated in this assay contained five-base pair duplications of the target DNA at the recombination junctions, a characteristic of HIV integration in vivo; the remaining products contained aberrant junctional sequences that may have been produced in a variation of the normal reaction. These results indicate that HIV IN protein is the only viral protein required to insert model HIV DNA sequences into a target DNA in vitro.

  11. Prospects for a Globally Effective HIV-1 Vaccine.

    PubMed

    Excler, Jean-Louis; Robb, Merlin L; Kim, Jerome H

    2015-12-01

    A globally effective vaccine strategy must cope with the broad genetic diversity of HIV and contend with multiple transmission modalities. Understanding correlates of protection and the role of diversity in limiting protective vaccines with those correlates is key. RV144 was the first HIV-1 vaccine trial to demonstrate efficacy against HIV-1 infection. A correlates analysis comparing vaccine-induced immune responses in vaccinated-infected and vaccinated-uninfected volunteers suggested that IgG specific for the V1V2 region of gp120 was associated with reduced risk of HIV-1 infection and that plasma Env IgA was directly correlated with infection risk. RV144 and recent non-human primate (NHP) challenge studies suggest that Env is essential and perhaps sufficient to induce protective antibody responses against mucosally acquired HIV-1. Whether RV144 immune correlates can apply to different HIV vaccines, to populations with different modes and intensity of transmission, or to divergent HIV-1 subtypes remains unknown. Newer prime-boost mosaic and conserved sequence immunization strategies aiming at inducing immune responses of greater breadth and depth as well as the development of immunogens inducing broadly neutralizing antibodies should be actively pursued. Efficacy trials are now planned in heterosexual populations in southern Africa and men who have sex with men in Thailand. Although NHP challenge studies may guide vaccine development, human efficacy trials remain key to answer the critical questions leading to the development of a global HIV-1 vaccine for licensure. PMID:26590431

  12. Prospects for a globally effective HIV-1 vaccine.

    PubMed

    Excler, Jean-Louis; Robb, Merlin L; Kim, Jerome H

    2015-11-27

    A globally effective vaccine strategy must cope with the broad genetic diversity of HIV and contend with multiple transmission modalities. Understanding correlates of protection and the role of diversity in limiting protective vaccines with those correlates is key. RV144 was the first HIV-1 vaccine trial to demonstrate efficacy against HIV-1 infection. A correlates analysis compared vaccine-induced immune responses in vaccinated-infected and vaccinated-uninfected volunteers suggested that IgG specific for the V1V2 region of gp120 was associated with reduced risk of HIV-1 infection and that plasma Env IgA was directly correlated with infection risk. RV144 and recent NHP challenge studies suggest that Env is essential and perhaps sufficient to induce protective antibody responses against mucosally acquired HIV-1. Whether RV144 immune correlates can apply to different HIV vaccines, to populations with different modes and intensity of transmission, or to divergent HIV-1 subtypes remains unknown. Newer prime-boost mosaic and conserved sequence immunization strategies aiming at inducing immune responses of greater breadth and depth as well as the development of immunogens inducing broadly neutralizing antibodies should be actively pursued. Efficacy trials are now planned in heterosexual populations in southern Africa and MSM in Thailand. Although NHP challenge studies may guide vaccine development, human efficacy trials remain key to answer the critical questions leading to the development of a global HIV-1 vaccine for licensure. PMID:26100921

  13. [A new unique HIV-1 recombinant form detected in Belarus].

    PubMed

    Eremin, V F; Gasich, E L; Sosinovich, S V

    2012-01-01

    Republican Research-and-Practical Center for Epidemiology and Microbiology, Ministry of Health of Belarus, Minsk The paper presents data on the molecular genetic characteristics of a new HIV-1 recombinant form. The study has shown that the virus is referred to as HIV-1 subtype B in terms of the gag gene and HIV-1 subtype A in terms of the pol and env genes. At the same time the new isolate is closer, in terms of the gag gene, to the HIV-1 DQ207943 strain isolated in Georgia, in terms of the pol gene, to the HIV-1 AF413987.1 strain isolated in Ukraine and, in terms of the env gene to the HIV-1 AY500393 strain isolated in Russia. Thus, the described new HIV-1 recombinant form has the following structure: BgagApolAenv. The gag, pol, and env gene sequences from the new unique HIV-1 recombinant form have been registered in the international database EMBL/Genbank/DDBJ under accession numbers FR775442.1, FN995656.1, and FR775443.1. PMID:22905420

  14. TALEN gene editing takes aim on HIV.

    PubMed

    Benjamin, Ronald; Berges, Bradford K; Solis-Leal, Antonio; Igbinedion, Omoyemwen; Strong, Christy L; Schiller, Martin R

    2016-09-01

    Transcription activator-like effector nucleases (TALENs) are one of several types of programmable, engineered nucleases that bind and cleave specific DNA sequences. Cellular machinery repairs the cleaved DNA by introducing indels. In this review, we emphasize the potential, explore progress, and identify challenges in using TALENs as a therapeutic tool to treat HIV infection. TALENs have less off-target editing and can be more effective at tolerating HIV escape mutations than CRISPR/Cas-9. Scientists have explored TALEN-mediated editing of host genes such as viral entry receptors (CCR5 and CXCR4) and a protein involved in proviral integration (LEDGF/p75). Viral targets include the proviral DNA, particularly focused on the long terminal repeats. Major challenges with translating gene therapy from bench to bedside are improving cleavage efficiency and delivery, while minimizing off-target editing, cytotoxicity, and immunogenicity. However, rapid improvements in TALEN technology are enhancing cleavage efficiency and specificity. Therapeutic testing in animal models of HIV infection will help determine whether TALENs are a viable HIV treatment therapy. TALENs or other engineered nucleases could shift the therapeutic paradigm from life-long antiretroviral therapy toward eradication of HIV infection. PMID:27170155

  15. HIV Type 1 Transmission Networks Among Men Having Sex with Men and Heterosexuals in Kenya

    PubMed Central

    Faria, Nuno Rodrigues; Hassan, Amin; Hamers, Raph L.; Mutua, Gaudensia; Anzala, Omu; Mandaliya, Kishor; Cane, Patricia; Berkley, James A.; Rinke de Wit, Tobias F.; Wallis, Carole; Graham, Susan M.; Price, Matthew A.; Coutinho, Roel A.; Sanders, Eduard J.

    2014-01-01

    Abstract We performed a molecular phylogenetic study on HIV-1 polymerase sequences of men who have sex with men (MSM) and heterosexual patient samples in Kenya to characterize any observed HIV-1 transmission networks. HIV-1 polymerase sequences were obtained from samples in Nairobi and coastal Kenya from 84 MSM, 226 other men, and 364 women from 2005 to 2010. Using Bayesian phylogenetics, we tested whether sequences clustered by sexual orientation and geographic location. In addition, we used trait diffusion analyses to identify significant epidemiological links and to quantify the number of transmissions between risk groups. Finally, we compared 84 MSM sequences with all HIV-1 sequences available online at GenBank. Significant clustering of sequences from MSM at both coastal Kenya and Nairobi was found, with evidence of HIV-1 transmission between both locations. Although a transmission pair between a coastal MSM and woman was confirmed, no significant HIV-1 transmission was evident between MSM and the comparison population for the predominant subtype A (60%). However, a weak but significant link was evident when studying all subtypes together. GenBank comparison did not reveal other important transmission links. Our data suggest infrequent intermingling of MSM and heterosexual HIV-1 epidemics in Kenya. PMID:23947948

  16. HIV Type 1 transmission networks among men having sex with men and heterosexuals in Kenya.

    PubMed

    Bezemer, Daniela; Faria, Nuno Rodrigues; Hassan, Amin; Hamers, Raph L; Mutua, Gaudensia; Anzala, Omu; Mandaliya, Kishor; Cane, Patricia; Berkley, James A; Rinke de Wit, Tobias F; Wallis, Carole; Graham, Susan M; Price, Matthew A; Coutinho, Roel A; Sanders, Eduard J

    2014-02-01

    We performed a molecular phylogenetic study on HIV-1 polymerase sequences of men who have sex with men (MSM) and heterosexual patient samples in Kenya to characterize any observed HIV-1 transmission networks. HIV-1 polymerase sequences were obtained from samples in Nairobi and coastal Kenya from 84 MSM, 226 other men, and 364 women from 2005 to 2010. Using Bayesian phylogenetics, we tested whether sequences clustered by sexual orientation and geographic location. In addition, we used trait diffusion analyses to identify significant epidemiological links and to quantify the number of transmissions between risk groups. Finally, we compared 84 MSM sequences with all HIV-1 sequences available online at GenBank. Significant clustering of sequences from MSM at both coastal Kenya and Nairobi was found, with evidence of HIV-1 transmission between both locations. Although a transmission pair between a coastal MSM and woman was confirmed, no significant HIV-1 transmission was evident between MSM and the comparison population for the predominant subtype A (60%). However, a weak but significant link was evident when studying all subtypes together. GenBank comparison did not reveal other important transmission links. Our data suggest infrequent intermingling of MSM and heterosexual HIV-1 epidemics in Kenya. PMID:23947948

  17. HIV, AIDS, and the Future

    MedlinePlus

    ... Navigation Bar Home Current Issue Past Issues HIV / AIDS HIV, AIDS, and the Future Past Issues / Summer 2009 Table ... and your loved ones from HIV/AIDS. The AIDS Memorial Quilt In 1987, a total of 1, ...

  18. HIV / AIDS: An Unequal Burden

    MedlinePlus

    ... Navigation Bar Home Current Issue Past Issues HIV / AIDS HIV / AIDS: An Unequal Burden Past Issues / Summer 2009 Table ... Victoria Cargill talks to students about HIV and AIDS at the opening of a National Library of ...

  19. HIV/AIDS and Alcohol

    MedlinePlus

    ... Psychiatric Disorders Other Substance Abuse HIV/AIDS HIV/AIDS Human immunodeficiency virus (HIV) targets the body’s immune ... and often leads to acquired immune deficiency syndrome (AIDS). Each year in the United States, between 55, ...

  20. HIV, AIDS, and the Future

    MedlinePlus

    Skip Navigation Bar Home Current Issue Past Issues HIV / AIDS HIV, AIDS, and the Future Past Issues / Summer 2009 ... turn Javascript on. Photo: The NAMES Project Foundation HIV and AIDS are a global catastrophe. While advances ...

  1. Women and HIV/AIDS

    MedlinePlus

    ... action on HIV/AIDS National Women and Girls HIV/AIDS Awareness Day – March 10 Programs Share your story Anonymous from Illinois says... Although I am HIV negative, I would like to share my story. ...

  2. HIV/AIDS in Women

    MedlinePlus

    HIV, the human immunodeficiency virus, kills or damages cells of the body's immune system. The most advanced stage of infection with HIV is AIDS, which stands for acquired immunodeficiency syndrome. HIV often ...

  3. HIV-Positive-to-HIV-Positive Liver Transplantation.

    PubMed

    Calmy, A; van Delden, C; Giostra, E; Junet, C; Rubbia Brandt, L; Yerly, S; Chave, J-P; Samer, C; Elkrief, L; Vionnet, J; Berney, T

    2016-08-01

    Most countries exclude human immunodeficiency virus (HIV)-positive patients from organ donation because of concerns regarding donor-derived HIV transmission. The Swiss Federal Act on Transplantation has allowed organ transplantation between HIV-positive donors and recipients since 2007. We report the successful liver transplantation from an HIV-positive donor to an HIV-positive recipient. Both donor and recipient had been treated for many years with antiretroviral therapy and harbored multidrug-resistant viruses. Five months after transplantation, HIV viremia remains undetectable. This observation supports the inclusion of appropriate HIV-positive donors for transplants specifically allocated to HIV-positive recipients. PMID:27109874

  4. Potent and broad neutralization of HIV-1 by a llama antibody elicited by immunization

    PubMed Central

    McCoy, Laura E.; Quigley, Anna Forsman; Strokappe, Nika M.; Bulmer-Thomas, Bianca; Seaman, Michael S.; Mortier, Daniella; Rutten, Lucy; Chander, Nikita; Edwards, Carolyn J.; Ketteler, Robin; Davis, David; Verrips, Theo

    2012-01-01

    Llamas (Lama glama) naturally produce heavy chain–only antibodies (Abs) in addition to conventional Abs. The variable regions (VHH) in these heavy chain–only Abs demonstrate comparable affinity and specificity for antigens to conventional immunoglobulins despite their much smaller size. To date, immunizations in humans and animal models have yielded only Abs with limited ability to neutralize HIV-1. In this study, a VHH phagemid library generated from a llama that was multiply immunized with recombinant trimeric HIV-1 envelope proteins (Envs) was screened directly for HIV-1 neutralization. One VHH, L8CJ3 (J3), neutralized 96 of 100 tested HIV-1 strains, encompassing subtypes A, B, C, D, BC, AE, AG, AC, ACD, CD, and G. J3 also potently neutralized chimeric simian-HIV strains with HIV subtypes B and C Env. The sequence of J3 is highly divergent from previous anti–HIV-1 VHH and its own germline sequence. J3 achieves broad and potent neutralization of HIV-1 via interaction with the CD4-binding site of HIV-1 Env. This study may represent a new benchmark for immunogens to be included in B cell–based vaccines and supports the development of VHH as anti–HIV-1 microbicides. PMID:22641382

  5. Analysis results from the Los Alamos 2D/3D program

    SciTech Connect

    Boyack, B.E.; Cappiello, M.W.; Harmony, S.C.; Shire, P.R.; Siebe, D.A.

    1987-01-01

    Los Alamos National Laboratory is a participant in the 2D/3D program. Activities conducted at Los Alamos National Laboratory in support of 2D/3D program goals include analysis support of facility design, construction, and operation; provision of boundary and initial conditions for test-facility operations based on analysis of pressurized water reactors; performance of pretest and posttest predictions and analyses; and use of experimental results to validate and assess the single- and multi-dimensional, nonequilibrium features in the Transient Reactor Analysis Code (TRAC). During fiscal year 1987, Los Alamos conducted analytical assessment activities using data from the Slab Core Test Facility, The Cylindrical Core Test Facility, and the Upper Plenum Test Facility. Finally, Los Alamos continued work to provide TRAC improvements. In this paper, Los Alamos activities during fiscal year 1987 will be summarized; several significant accomplishments will be described in more detail to illustrate the work activities at Los Alamos.

  6. A discrete element 3' of human immunodeficiency virus 1 (HIV-1) and HIV-2 mRNA initiation sites mediates transcriptional activation by an HIV trans activator

    SciTech Connect

    Jakobovits, A.; Smith, D.H.; Jakobovits, E.B.; Capon, D.J.

    1988-06-01

    An important point of regulation in the reproductive growth and latency of the human and simian immunodeficiency viruses (HIV and SIV, respectively) is provided by virally encoded trans-activators (tat), proteins capable of dramatically increasing viral gene expression. The mechanism of this autostimulatory pathway has remained unclear, however, with substantial effects having been reported at the level of either mRNA accumulation, translational efficiency, or both. The authors' previous findings indicated that trans-activation results primarily from induction of RNA levels but could not distinguish between the roles of transcriptional rate, RNA stabilization, and RNA transport in this event. In addition, the boundaries of tat-responding elements, which would be valuable in elucidating the mode of tat action, are not precisely known. In this study, HIV-1 and HIV-2 long terminal repeat-directed expression was characterized by using in an vitro nuclear transcription assay to clarify this mechanism, and a detailed mutational analysis was undertaken to localize precisely the sequences participating in this process. Two key findings were revealed: an increased transcription rate was the primary event in tat-mediated activation of HIV-1 and HIV-2, and trans-activation was impaired by mutations in two regions, the TATA box and sequences between +19 to +42, a region lacking enhancer activity. These results implicate a discrete 3' regulatory element in the transcriptional activation of the HIVs.

  7. Epstein-Barr virus and HIV play no direct role in persistent generalized lymphadenopathy syndrome.

    PubMed

    Boyle, M J; Sculley, T B; Cooper, D A; Turner, J J; Penny, R; Sewell, W A

    1992-03-01

    Persistent generalized lymphadenopathy (PGL) and polyclonal B cell activation are features of infection with HIV. Epstein-Barr virus (EBV) and HIV are known to activate B cells in vitro, but whether they are important B cell activators in patients infected with HIV is less clear. In this study, lymph node tissue was obtained from 10 patients with PGL and assessed for evidence of EBV and HIV gene sequences. DNA was extracted and specific viral gene sequences identified using the polymerase chain reaction (PCR). EBV sequences were difficult to detect in the PGL tissue, with a signal intensity similar to that of other benign and malignant lymphoid conditions not associated with EBV. HIV sequences were also rare in the PGL tissue, consistent with HIV infection of the small number of peripheral blood cells and nodal T cells likely to be present in such a sample. These findings suggest that the polyclonal B cell activation typical of HIV is not driven by direct EBV or HIV infection of B cells. PMID:1311993

  8. Barriers to HIV Cure.

    PubMed

    Stein, J; Storcksdieck Genannt Bonsmann, M; Streeck, H

    2016-10-01

    Since the beginning of the epidemic, more than 70 million people have been infected with human immunodeficiency virus (HIV) and about 38 million have died from acquired immune deficiency syndrome (AIDS)-related illnesses. While the discovery of highly active antiretroviral therapy (HAART) in the mid 90's has saved millions of lives, a complete eradication of HIV is still not possible as HIV can persist for decades in a small reservoir of latently infected cells. Once reactivated, these latently infected cells can actively produce viral particles. Recent studies suggest that several sanctuaries exist within infected individuals where HIV can remain undetected by the immune system. These cellular, anatomical and microanatomical viral reservoirs represent a major obstacle for the eradication of HIV. Here we review recent findings on potential sanctuaries of HIV and address potential avenues to overcome these immunological barriers. PMID:27620852

  9. Molecular epidemiology of recent HIV-1 infections in southern Poland.

    PubMed

    Smoleń-Dzirba, Joanna; Rosińska, Magdalena; Kruszyński, Piotr; Bratosiewicz-Wąsik, Jolanta; Janiec, Janusz; Beniowski, Marek; Bociąga-Jasik, Monika; Jabłonowska, Elżbieta; Szetela, Bartosz; Porter, Kholoud; Wąsik, Tomasz J

    2012-12-01

    The genetic diversity of human immunodeficiency virus type 1 (HIV-1) offers an opportunity to track the development of the epidemic across different populations. Viral pol gene fragments from 55 individuals of Polish origin with recent HIV-1 infection identified in 2008-2010 in four Polish cities were analyzed. Viral sequences were compared with sequences from 100 individuals (reference group) infected before 2004. Viral spread among groups with different HIV transmission categories was compared using a phylogenetic approach. The majority of sequences from individuals with recent infection were subtype B (93%) within which four transmission clusters (18% of samples) were detected. Samples from men infected through sex between men and from persons infected through injecting drugs were broadly separated (P < 0.0001), while samples from individuals infected by heterosexual contacts were dispersed uniformly within phylogenetic tree (P = 0.244) inferred from viral sequences derived from individuals infected recently and the reference group. The percentage of samples from persons infected by heterosexual contacts which clustered with samples from men infected through sex between men was not significantly higher for those with recent infection (47%), compared to the reference group (36%). In conclusion, men infected by sex between men and individuals infected through injecting drugs appear to form separate HIV transmission networks in Poland. The recent spread of HIV-1 among persons infected with subtype B by heterosexual contacts appears to be linked to both these groups. PMID:23080488

  10. HIV Evolution and Escape.

    PubMed Central

    Richman, Douglas D.; Little, Susan J.; Smith, Davey M.; Wrin, Terri; Petropoulos, Christos; Wong, Joseph K.

    2004-01-01

    Human immunodeficiency virus (HIV) exemplifies the principles of Darwinian evolution with a telescoped chronology. Because of its high mutation rate and remarkably high rates of replication, evolution can be appreciated over periods of days in contrast to the durations conceived of by Darwin. Certain selective pressures that drive the evolution of HIV include chemotherapy, anatomic compartmentalization and the immune response. Examples of these selective forces on HIV evolution are described. Images Fig. 5 PMID:17060974

  11. HIV Associated Opportunistic Pneumonias.

    PubMed

    Ismail, T; Lee, C

    2011-03-01

    Opportunistic pneumonias are major causes of morbidity and mortality in HIV infected individuals. The majority of new HIV infections in Malaysia are adults aged 20 to 39 years old and many are unaware of their HIV status until they present with an opportunistic infection. HIV associated opportunistic pneumonias can progress rapidly without appropriate therapy. Therefore a proper diagnostic evaluation is vital and prompt empiric treatment of the suspected diagnosis should be commenced while waiting for the results of the diagnostic studies. Tuberculosis, Pneumocystis pneumonia (PCP) and recurrent bacterial pneumonias are common causes of AIDS-defining diseases and are discussed in this article. PMID:23765154

  12. Population-Level Immune-Mediated Adaptation in HIV-1 Polymerase during the North American Epidemic

    PubMed Central

    Kinloch, Natalie N.; MacMillan, Daniel R.; Le, Anh Q.; Cotton, Laura A.; Bangsberg, David R.; Buchbinder, Susan; Carrington, Mary; Fuchs, Jonathan; Harrigan, P. Richard; Koblin, Beryl; Kushel, Margot; Markowitz, Martin; Mayer, Kenneth; Milloy, M. J.; Schechter, Martin T.; Wagner, Theresa; Walker, Bruce D.; Carlson, Jonathan M.; Poon, Art F. Y.

    2015-01-01

    ABSTRACT Human leukocyte antigen (HLA) class I-associated polymorphisms in HIV-1 that persist upon transmission to HLA-mismatched hosts may spread in the population as the epidemic progresses. Transmission of HIV-1 sequences containing such adaptations may undermine cellular immune responses to the incoming virus in future hosts. Building upon previous work, we investigated the extent of HLA-associated polymorphism accumulation in HIV-1 polymerase (Pol) through comparative analysis of linked HIV-1/HLA class I genotypes sampled during historic (1979 to 1989; n = 338) and modern (2001 to 2011; n = 278) eras from across North America (Vancouver, BC, Canada; Boston, MA; New York, NY; and San Francisco, CA). Phylogenies inferred from historic and modern HIV-1 Pol sequences were star-like in shape, with an inferred most recent common ancestor (epidemic founder virus) sequence nearly identical to the modern North American subtype B consensus sequence. Nevertheless, modern HIV-1 Pol sequences exhibited roughly 2-fold-higher patristic (tip-to-tip) genetic distances than historic sequences, with HLA pressures likely driving ongoing diversification. Moreover, the frequencies of published HLA-associated polymorphisms in individuals lacking the selecting HLA class I allele was on average ∼2.5-fold higher in the modern than in the historic era, supporting their spread in circulation, though some remained stable in frequency during this time. Notably, polymorphisms restricted by protective HLA alleles appear to be spreading to a greater relative extent than others, though these increases are generally of modest absolute magnitude. However, despite evidence of polymorphism spread, North American hosts generally remain at relatively low risk of acquiring an HIV-1 polymerase sequence substantially preadapted to their HLA profiles, even in the present era. IMPORTANCE HLA class I-restricted cytotoxic T-lymphocyte (CTL) escape mutations in HIV-1 that persist upon transmission may

  13. Repetitive Sequences

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Repetitive sequences, or repeats, account for a substantial portion of the eukaryotic genomes. These sequences include very different types of DNA with respect to mode of origin, function, structure, and genomic distribution. Two large families of repetitive sequences can be readily recognized, ta...

  14. HIV drug resistance interpreted by cumulative versus last genotypes in HIV-infected patients with multiple treatment failures.

    PubMed

    Punyacam, Punthiya; Iemwimangsa, Nareenart; Chantratita, Wasun; Sukasem, Chonlaphat; Sungkanuparph, Somnuek

    2012-04-01

    Genotypic resistance test has been recommended to evaluate HIV drug resistance and guide the effective regimens of antiretroviral therapy (ART) in HIV-infected patients with treatment failure. In patients with multiple treatment failures, drug resistance-associated mutations may disappear due to the loss of selective drug pressure after switching regimens. A cohort study was conducted among HIV-infected patients who had ≥2 genotypic resistance tests during 2003-2011. HIV-1 pol nucleotide sequencing of reverse transcriptase and protease region was carried out using TRUGENE HIV-1 Genotypic Assay. Sequencing data was analyzed using Stanford rule-based interpretation algorithms. Of 54 patients with mean age of 30.1 years, 46.3% were males. HIV-1 subtype A/E was observed in 88.9% of patients. At the latest failure, 55.3% were receiving protease inhibitor-based regimens. Median CD4 and HIV RNA were 167 cells/mm(3) and 22,359 copies/mL. During a median duration of ART of 38.6 months, 72.2%, 22.2%, and 5.6% had 5, 3, and 2 genotype tests, respectively. When compared between using cumulative (CG) and last genotypes (LG), CG interpreted resistance to any drug 59.3% higher than LG did. For NRTI, NNRTI, and PI drug classes, CG interpreted as resistance 42.6%, 27.8%, and 7.4% higher than LG, respectively. The most common drugs that CG interpreted resistance with the higher rate than LG were lamivudine/emtricitabine, nevirapine, efavirenz, etravirine and abacavir. In conclusion, CG interprets HIV drug resistance at a higher rate than LG and may be more accurate to use for selecting the next effective regimen of ART among HIV-infected patients with multiple treatment failures. PMID:22497699

  15. Natural Attenuation of Anthropogenic Chromium in Selected Puye Formation in Regional Aquifer System of LOS Alamos, New Mexico

    NASA Astrophysics Data System (ADS)

    Brown, D. B.; Ding, M.; WoldeGabriel, G. W.; Cheshire, M.; Rearick, M.; Conradson, S.; Kluk, E.; Katzman, D.

    2014-12-01

    Routine groundwater monitoring conducted in 2005 revealed significant chromium (Cr) contamination in regional groundwater in Los Alamos, New Mexico. Previous use of potassium dichromate (K2Cr2O7) in cooling towers at Los Alamos National Laboratory's main power plant is believed to be the source of the elevated chromium levels. From 1956 to 1972 between 31,000 and 72,000 Kg of toxic Cr(IV) was released into Sandia Canyon. Initial investigations of the vadose zone using chromium isotopes indicated that reduction of anthropogenic Cr(IV) had occurred. However, to justify the use of Monitoring Natural Attenuation (MNA) as a valid remediation strategy, the Cr attenuation mechanism and the reduction capacity of the regional aquifer needs to be determined. Conventional batch sorption and synchrotron-based X-ray absorption spectroscopy studies were performed. Two samples were selected from the Puye formation, a silicoclastic sedimentary rock sequence located within the contaminated aquifer. Additionally, two Los Alamos Puye outcrop samples with no chromium exposure were selected for comparison. Each sample was subsequently sorted based on grain size, magnetic, and clay fractions. Groundwater with a known concentration of Cr(IV) was used in the batch experiments. Spectroscopy measurements of Puye samples before and after exposure to the same contaminated groundwater were conducted at the Stanford Synchrotron Radiation Lightsource (SSRL). Batch sorption results indicated little to no attenuation, as indicated by the small measured sorption coefficient (Kd < 5 Kg/L). Spectroscopic measurements suggest that attenuation of hexavalent chromium in groundwater is due to reduction of Cr(VI) to Cr(III) in the Puye and may be attributed almost exclusively to the clay fraction. These results indicate that the tested Puye sediments occurring in the regional aquifer have minor ability to naturally attenuate anthropogenic Cr(IV), with the clay fraction dominating the reduction process

  16. BioAfrica's HIV-1 proteomics resource: combining protein data with bioinformatics tools.

    PubMed

    Doherty, Ryan S; De Oliveira, Tulio; Seebregts, Chris; Danaviah, Sivapragashini; Gordon, Michelle; Cassol, Sharon

    2005-01-01

    Most Internet online resources for investigating HIV biology contain either bioinformatics tools, protein information or sequence data. The objective of this study was to develop a comprehensive online proteomics resource that integrates bioinformatics with the latest information on HIV-1 protein structure, gene expression, post-transcriptional/post-translational modification, functional activity, and protein-macromolecule interactions. The BioAfrica HIV-1 Proteomics Resource http://bioafrica.mrc.ac.za/proteomics/index.html is a website that contains detailed information about the HIV-1 proteome and protease cleavage sites, as well as data-mining tools that can be used to manipulate and query protein sequence data, a BLAST tool for initiating structural analyses of HIV-1 proteins, and a proteomics tools directory. The Proteome section contains extensive data on each of 19 HIV-1 proteins, including their functional properties, a sample analysis of HIV-1HXB2, structural models and links to other online resources. The HIV-1 Protease Cleavage Sites section provides information on the position, subtype variation and genetic evolution of Gag, Gag-Pol and Nef cleavage sites. The HIV-1 Protein Data-mining Tool includes a set of 27 group M (subtypes A through K) reference sequences that can be used to assess the influence of genetic variation on immunological and functional domains of the protein. The BLAST Structure Tool identifies proteins with similar, experimentally determined topologies, and the Tools Directory provides a categorized list of websites and relevant software programs. This combined database and software repository is designed to facilitate the capture, retrieval and analysis of HIV-1 protein data, and to convert it into clinically useful information relating to the pathogenesis, transmission and therapeutic response of different HIV-1 variants. The HIV-1 Proteomics Resource is readily accessible through the BioAfrica website at: http

  17. Towards an advanced hadron facility at Los Alamos

    NASA Astrophysics Data System (ADS)

    Thiessen, Henry A.

    1988-11-01

    In the 1987 AHF Workshop, it was pointed out that activation of the accelerator is a serious problem. At this workshop, it was suggested that a new type of slow extraction system is needed to reduce the activation. We report on the response to this need. The Los Alamos plan is reviewed including as elements the long lead-time R&D in preparation for a 1993 construction start, a menu of accelerator designs, improved losses at injection and extraction time, active participation in the development of PSR, an accelerated hardware R&D program, and close collaboration with TRIUMF. We review progress on magnets and power supplies, on ceramic vacuum chambers, and on ferrite-tuned rf systems. We report on the plan for a joint TRIUMF-Los Alamos main-ring cavity to be tested in PSR in 1989. The problem of beam losses is discussed in detail and a recommendation for a design procedure for the injection system is made. This recommendation includes taking account of single Coulomb scattering, a painting scheme for minimizing foil hits, and a collimator and dump system for containing the expected spills. The slow extraction problem is reviewed and progress on an improved design is discussed. The problem of designing the accelerators for minimum operation and maintenance cost is briefly discussed. The question of the specifications for an advanced hadron facility is raised and it is suggested that the Los Alamos Proposal of a dual energy machine—1.6 GeV and 60 GeV—is a better match to the needs of the science program than the single-energy proposals made elsewhere. It is suggested that design changes need be made in all of the world's hadron facility proposals to prepare for high-intensity operation.

  18. Los Alamos safeguards program overview and NDA in safeguards

    SciTech Connect

    Keepin, G.R.

    1988-01-01

    Over the years the Los Alamos safeguards program has developed, tested, and implemented a broad range of passive and active nondestructive analysis (NDA) instruments (based on gamma and x-ray detection and neutron counting) that are now widely employed in safeguarding nuclear materials of all forms. Here very briefly, the major categories of gamma ray and neutron based NDA techniques, give some representative examples of NDA instruments currently in use, and cite a few notable instances of state-of-the-art NDA technique development. Historical aspects and a broad overview of the safeguards program are also presented.

  19. Groundwater Level Status Report for 2005 Los Alamos National Laboratory

    SciTech Connect

    S.P. Allen; R.J. Koch

    2006-05-15

    The status of groundwater level monitoring at Los Alamos National Laboratory (LANL) in 2005 is provided in this report. The Groundwater Level Monitoring Project was instituted in 2005 to provide a framework for the collection and processing of quality controlled groundwater level data. This report summarizes groundwater level data for 137 monitoring wells, including 41 regional aquifer wells, 22 intermediate wells, and 74 alluvial wells. Pressure transducers were installed in 118 monitoring wells for continuous monitoring of groundwater levels. Time-series hydrographs of groundwater level data are presented along with pertinent construction and location information for each well.

  20. The Los Alamos National Laboratory Nuclear Vision Project

    SciTech Connect

    Arthur, E.D.; Wagner, R.L. Jr.

    1996-09-01

    Los Alamos National Laboratory has initiated a project to examine possible futures associated with the global nuclear enterprise over the course of the next 50 years. All major components are included in this study--weapons, nonproliferation, nuclear power, nuclear materials, and institutional and public factors. To examine key issues, the project has been organized around three main activity areas--workshops, research and analyses, and development of linkages with other synergistic world efforts. This paper describes the effort--its current and planned activities--as well as provides discussion of project perspectives on nuclear weapons, nonproliferation, nuclear energy, and nuclear materials focus areas.

  1. Los Alamos Science, Number 25 -- 1997: Celebrating the Neutrino

    DOE R&D Accomplishments Database

    Cooper, N. G. ed.

    1997-01-01

    This issue is devoted to the neutrino and its remaining mysteries. It is divided into the following areas: (1) The Reines-Cowan experiment -- detecting the poltergeist; (2) The oscillating neutrino -- an introduction to neutrino masses and mixing; (3) A brief history of neutrino experiments at LAMPF; (4) A thousand eyes -- the story of LSND (Los Alamos neutrino oscillation experiment); (5) The evidence for oscillations; (6) The nature of neutrinos in muon decay and physics beyond the Standard Model; (7) Exorcising ghosts -- in pursuit of the missing solar neutrinos; (8) MSW -- a possible solution to the solar neutrino problem; (8) Neutrinos and supernovae; and (9) Dark matter and massive neutrinos.

  2. Recent developments in the Los Alamos radiation transport code system

    SciTech Connect

    Forster, R.A.; Parsons, K.

    1997-06-01

    A brief progress report on updates to the Los Alamos Radiation Transport Code System (LARTCS) for solving criticality and fixed-source problems is provided. LARTCS integrates the Diffusion Accelerated Neutral Transport (DANT) discrete ordinates codes with the Monte Carlo N-Particle (MCNP) code. The LARCTS code is being developed with a graphical user interface for problem setup and analysis. Progress in the DANT system for criticality applications include a two-dimensional module which can be linked to a mesh-generation code and a faster iteration scheme. Updates to MCNP Version 4A allow statistical checks of calculated Monte Carlo results.

  3. Laser protective eyewear program at the Los Alamos Scientific Laboratory

    SciTech Connect

    Winburn, D.C.

    1980-01-01

    The proliferation of lasers at Los Alamos focused considerable attention on providing adequate eye protection for experimenters involved in the use of a wide variety of nonionizing radiation. Experiments with fast-pulsed lasers (Nd:YAG, HF, and CO/sub 2/) were performed to gain biological threshold data on ocular damage. In parallel, eye protection devices were evaluated, which resulted in the development of lightweight, comfortable spectacles of colored glass filters that can be ground to prescription specifications. Goggle styles are employed in specific applications.

  4. Mac configuration management at the Los Alamos National Laboratory

    SciTech Connect

    Marcus, Allan B

    2010-01-01

    The Los Alamos National Laboratory (LANL) had a need for central configuration management of non-Windows computers. LANL has three to five thousand Macs and an equal number of Linux based systems. The primary goal was to be able to inventory all non-windows systems and patch Mc OS X systems. LANL examined a number of commercial and open source solutions and ultimately selected Puppet. This paper will discuss why we chose Puppet, how we implemented it, and some lessons we learned along the way.

  5. Los Alamos Science, Number 25 -- 1997: Celebrating the neutrino

    SciTech Connect

    Cooper, N.G.

    1997-12-31

    This issue is devoted to the neutrino and its remaining mysteries. It is divided into the following areas: (1) The Reines-Cowan experiment -- detecting the poltergeist; (2) The oscillating neutrino -- an introduction to neutrino masses and mixing; (3) A brief history of neutrino experiments at LAMPF; (4) A thousand eyes -- the story of LSND (Los Alamos neutrino oscillation experiment); (5) The evidence for oscillations; (6) The nature of neutrinos in muon decay and physics beyond the Standard Model; (7) Exorcising ghosts -- in pursuit of the missing solar neutrinos; (8) MSW -- a possible solution to the solar neutrino problem; (8) Neutrinos and supernovae; and (9) Dark matter and massive neutrinos.

  6. Auditing nuclear weapons quality programs at Los Alamos

    SciTech Connect

    Davis, A.H.

    1988-01-01

    Some of the problems involved in introducing quality assurance on a broad scale in a national laboratory are discussed. A philosophy of how QA can be utilized beneficially in research and development activities is described briefly, and our experiences at Los Alamos in applying QA to nuclear weapons activities are outlines. The important role of audits is emphasized; audits are used not merely to determine the effectiveness of QA programs but also to explain and demonstrate the usefulness of QA to a generally sceptical body of engineers and scientists. Finally, some ways of easing the application of QA in the future are proposed. 1 ref.

  7. Gamma-ray isotopic analysis development at Los Alamos

    SciTech Connect

    Thomas E. Sampson

    1999-11-01

    This report describes the development history and characteristics of software developed in the Safeguards Science and Technology group at Los Alamos for gamma-ray isotopic analysis. This software analyzes the gamma-ray spectrum from measurements performed on actinide samples (principally plutonium and uranium) of arbitrary size, geometry, and physical and chemical composition. The results are obtained without calibration using only fundamental tabulated nuclear constants. Characteristics of the current software versions are discussed in some detail and many examples of implemented measurement systems are shown.

  8. Groundwater level status report for 2010, Los Alamos National Laboratory

    SciTech Connect

    Koch, Richard J.; Schmeer, Sarah

    2011-03-01

    The status of groundwater level monitoring at Los Alamos National Laboratory in 2010 is provided in this report. This report summarizes groundwater level data for 194 monitoring wells, including 63 regional aquifer wells (including 10 regional/intermediate wells), 34 intermediate wells, 97 alluvial wells, and 12 water supply wells. Pressure transducers were installed in 162 monitoring wells for continuous monitoring of groundwater levels. Time-series hydrographs of groundwater level data are presented along with pertinent construction and location information for each well. The report also summarizes the groundwater temperatures recorded in intermediate and regional aquifer monitoring wells and seasonal responses to snowmelt runoff observed in intermediate wells.

  9. Industrial applications of computed tomography at Los Alamos Scientific Laboratory

    SciTech Connect

    Kruger, R.P.; Morris, R.A.; Wecksung, G.W.; Wonn, G.; London, R.

    1980-06-01

    A research and development program was begun two years ago at the Los Alamos Scientific Laboratory (LASL) to study nonmedical applications of computed tomography. This program had several goals. The first goal was to develop the necessary reconstruction algorithms to accurately reconstruct cross sections of nonmedical industrial objects. The second goal was to be able to perform extensive tomographic simulations to determine the efficacy of tomographic reconstruction with a variety of hardware configurations. The final goal was to construct an inexpensive industrial prototype scanner with a high degree of design flexibility. The implementation of these program goals is described.

  10. Water supply at Los Alamos during 1985: Progress report

    SciTech Connect

    Purtymun, W.D.; Becker, N.M.; Maes, M.N.

    1986-10-01

    Well field operations during 1985 were satisfactory with municipal and industrial supplies consisting of 1587 x 10/sup 6/ gal from wells in three well fields and 37 x 10/sup 6/ gal from the gallery in Water Canyon. About 2.8 x 10/sup 6/ gal of water from Guaje Reservoir and 0.9 x 10/sup 6/ gal from Los Alamos Reservoir were used for irrigation; thus the total water usage in 1985 was about 1628 x 10/sup 6/ gal. Primary and secondary chemical quality of water in the distribution system is in compliance with federal regulations.

  11. Upgrade of the Los Alamos Plutonium Facility control system

    SciTech Connect

    Pope, N.G.; Turner, W.J.; Brown, R.E.; Bibeau, R.A.; Davis, R.R.; Hogan, K.

    1996-05-01

    After 20 yrs service, the Los Alamos Plutonium Facility is undergoing an upgrade to its aging Facility Control System. The new system design includes a network of redundantly-paired programmable logic controllers that will interface with about 2200 field data points. The data communications network that has been designed includes a redundant, self-healing fiber optic data highway as well as a fiber optic ethernet. Commercially available human-machine interface software running on a UNIX-based system displays facility subsystem status operator X-terminals. Project design features, methods, costs, and schedule are discussed.

  12. Tiger Team Assessment of the Los Alamos National Laboratory

    SciTech Connect

    Not Available

    1991-11-01

    The purpose of the safety and health assessment was to determine the effectiveness of representative safety and health programs at the Los Alamos National Laboratory (LANL). Within the safety and health programs at LANL, performance was assessed in the following technical areas: Organization and Administration, Quality Verification, Operations, Maintenance, Training and Certification, Auxiliary Systems, Emergency Preparedness, Technical Support, Packaging and Transportation, Nuclear Criticality Safety, Security/Safety Interface, Experimental Activities, Site/Facility Safety Review, Radiological Protection, Personnel Protection, Worker Safety and Health (OSHA) Compliance, Fire Protection, Aviation Safety, Explosives Safety, Natural Phenomena, and Medical Services.

  13. Polyomavirus JCV excretion and genotype analysis in HIV-infected patients receiving highly active antiretroviral therapy

    NASA Technical Reports Server (NTRS)

    Lednicky, John A.; Vilchez, Regis A.; Keitel, Wendy A.; Visnegarwala, Fehmida; White, Zoe S.; Kozinetz, Claudia A.; Lewis, Dorothy E.; Butel, Janet S.

    2003-01-01

    OBJECTIVE: To assess the frequency of shedding of polyomavirus JC virus (JCV) genotypes in urine of HIV-infected patients receiving highly active antiretroviral therapy (HAART). METHODS: Single samples of urine and blood were collected prospectively from 70 adult HIV-infected patients and 68 uninfected volunteers. Inclusion criteria for HIV-infected patients included an HIV RNA viral load < 1000 copies, CD4 cell count of 200-700 x 106 cells/l, and stable HAART regimen. PCR assays and sequence analysis were carried out using JCV-specific primers against different regions of the virus genome. RESULTS: JCV excretion in urine was more common in HIV-positive patients but not significantly different from that of the HIV-negative group [22/70 (31%) versus 13/68 (19%); P = 0.09]. HIV-positive patients lost the age-related pattern of JCV shedding (P = 0.13) displayed by uninfected subjects (P = 0.01). Among HIV-infected patients significant differences in JCV shedding were related to CD4 cell counts (P = 0.03). Sequence analysis of the JCV regulatory region from both HIV-infected patients and uninfected volunteers revealed all to be JCV archetypal strains. JCV genotypes 1 (36%) and 4 (36%) were the most common among HIV-infected patients, whereas type 2 (77%) was the most frequently detected among HIV-uninfected volunteers. CONCLUSION: These results suggest that JCV shedding is enhanced by modest depressions in immune function during HIV infection. JCV shedding occurred in younger HIV-positive persons than in the healthy controls. As the common types of JCV excreted varied among ethnic groups, JCV genotypes associated with progressive multifocal leukoencephalopathy may reflect demographics of those infected patient populations.

  14. Side Effects of HIV Medicines: HIV and Hepatotoxicity

    MedlinePlus

    Side Effects of HIV Medicines HIV and Hepatotoxicity (Last updated 1/7/2016; last reviewed 1/7/2016) Key Points Hepatotoxicity means damage to the ... the liver can be life-threatening. What HIV medicines can cause hepatotoxicity? HIV medicines in the following ...

  15. [HIV and reproductive choices].

    PubMed

    Boer, K; de Vries, J W; de Beaufort, I E

    1995-05-13

    It is estimated that there are about 120-150 hemophilic men infected with HIV in the Netherlands as well as 1000 men infected via intravenous drug use. The majority of them are in reproductive age with relationships with seronegative women. In the event they want to have a child, artificial insemination with donor sperm (KID) is an option. In 1994 there were 147 instances of insemination of 66 women with the processed semen of HIV-positive men and no infection resulted. The annual risk of HIV infection was 7.2% of a woman engaging in unprotected intercourse, according to a prospective Italian study. The risk of HIV infection per contact was estimated at 0.1-5.6%. However, it is not yet proven that processed sperm of an HIV-seropositive man can produce a pregnancy without the risk of infecting the woman. The risk of transmission of HIV to the fetus is higher in artificial insemination of a seropositive woman with the sperm of her partner. In vitro fertilization is not a sure method either for the prevention of HIV infection of the mother because of the possibility of an egg cell being infected before fertilization. HIV-infected pregnant women face the problems of caring for HIV-infected offspring. For HIV discordant couples the advice is to use both condoms for the prevention of infection and oral contraceptives for the prevention of pregnancy. In the case of a lesbian relationship, if the partners want to have a child, HIV infection is still a factor because of previous heterosexual contacts. PMID:7753239

  16. Demonstration of de novo HIV type 1 production by detection of multiply spliced and unspliced HIV type 1 RNA in paraffin-embedded tonsils.

    PubMed

    Brachtel, Elena F; Mascola, John R; Wear, Douglas J; Ehrenberg, Philip K; Dayhoff, Deborah E; Sanders-Buell, Eric; Michael, Nelson L; Frankel, Sarah Schlesinger

    2002-07-20

    HIV-1 infection of tonsils takes place when virus spreads systemically, and may occur when tonsillar tissue serves as the initial portal of HIV-1 entry. The HIV replication cycle includes the production of regulatory and accessory gene mRNAs, produced by splicing of genomic mRNA, that are hallmarks of de novo virus production. We sought to demonstrate, for the first time, the presence of multiply spliced viral RNA transcripts in archival tissue as a marker for active virus replication. Further, amplified cDNA sequences from unspliced pol gene mRNA were used to define the genetic subtype of HIV-1 within these tissues. RNA was extracted from surgical pathological, formalin-fixed, paraffin-embedded specimens, and RT-PCR was performed with primers for unspliced and multiply spliced HIV-1 transcripts. Amplification products were analyzed by agarose gel electrophoresis and their specificity was confirmed by sequencing and Southern blot hybridization. Unspliced HIV-1 pol transcripts yielded cDNA amplicons of 184 base pairs (bp) that were cloned and sequenced. Phylogenetic analysis revealed these sequences to be of HIV-1 subtype B. Multiply spliced transcripts specific for the tat/rev (173 bp), tat (268 bp), and tat/rev/nef (146 bp) regulatory gene mRNAs could be demonstrated in all cases. These results support the demonstration of active replication of HIV-1 in archival tonsillar tissues previously shown by p24 antigen staining. They also show the feasibility of performing molecular epidemiologic studies on HIV-1 cDNA sequences from archived pathologic specimens. PMID:12167270

  17. HIV-1 VACCINES. HIV-1 neutralizing antibodies induced by native-like envelope trimers.

    PubMed

    Sanders, Rogier W; van Gils, Marit J; Derking, Ronald; Sok, Devin; Ketas, Thomas J; Burger, Judith A; Ozorowski, Gabriel; Cupo, Albert; Simonich, Cassandra; Goo, Leslie; Arendt, Heather; Kim, Helen J; Lee, Jeong Hyun; Pugach, Pavel; Williams, Melissa; Debnath, Gargi; Moldt, Brian; van Breemen, Mariëlle J; Isik, Gözde; Medina-Ramírez, Max; Back, Jaap Willem; Koff, Wayne C; Julien, Jean-Philippe; Rakasz, Eva G; Seaman, Michael S; Guttman, Miklos; Lee, Kelly K; Klasse, Per Johan; LaBranche, Celia; Schief, William R; Wilson, Ian A; Overbaugh, Julie; Burton, Dennis R; Ward, Andrew B; Montefiori, David C; Dean, Hansi; Moore, John P

    2015-07-10

    A challenge for HIV-1 immunogen design is the difficulty of inducing neutralizing antibodies (NAbs) against neutralization-resistant (tier 2) viruses that dominate human transmissions. We show that a soluble recombinant HIV-1 envelope glycoprotein trimer that adopts a native conformation, BG505 SOSIP.664, induced NAbs potently against the sequence-matched tier 2 virus in rabbits and similar but weaker responses in macaques. The trimer also consistently induced cross-reactive NAbs against more sensitive (tier 1) viruses. Tier 2 NAbs recognized conformational epitopes that differed between animals and in some cases overlapped with those recognized by broadly neutralizing antibodies (bNAbs), whereas tier 1 responses targeted linear V3 epitopes. A second trimer, B41 SOSIP.664, also induced a strong autologous tier 2 NAb response in rabbits. Thus, native-like trimers represent a promising starting point for the development of HIV-1 vaccines aimed at inducing bNAbs. PMID:26089353

  18. Living with HIV/AIDS

    MedlinePlus

    Infection with HIV is serious. But the outlook for people with HIV/AIDS is improving. If you are infected with HIV, there are many things you can do to ... health care provider who knows how to treat HIV. You may want to join a support group. ...

  19. Positive: HIV Affirmative Counseling.

    ERIC Educational Resources Information Center

    Kain, Craig D.

    At the end of the 1980s, counselors largely lacked an integrated approach to counseling people living with HIV disease. This book describes the experience of counseling this group of persons. The major premise here is that counselors who counsel HIV-positive clients must come to understand and affirm their clients' experiences. The text defines a…

  20. Psychoneuroimmunology and HIV-1.

    ERIC Educational Resources Information Center

    Antoni, Michael H.; And Others

    1990-01-01

    Presents evidence describing benefits of behavioral interventions such as aerobic exercise training on both psychological and immunological functioning among high risk human immunodeficiency virus-Type 1 (HIV-1) seronegative and very early stage seropositive homosexual men. HIV-1 infection is cast as chronic disease for which early…

  1. HIV and Communication

    ERIC Educational Resources Information Center

    McNeilly, L.G.

    2005-01-01

    The human immunodeficiency virus (HIV) continues to plague many countries across the globe, including the United States, Africa, China and India. Children and adults have been infected with HIV, and both populations can present with communication disorders that coexist with the presence of the virus. The purpose of this paper is to present an…

  2. Overview of HIV.

    PubMed

    Klimas, Nancy; Koneru, Anne O'Brien; Fletcher, Mary Ann

    2008-06-01

    This article provides an overview and reviews the HIV pandemic, the basic biology and immunology of the virus (e.g., genetic diversity of HIV and the viral life cycle), the phases of disease progression, modes of HIV transmission, HIV testing, immune response to the infection, and current therapeutic strategies. HIV is occurring in epidemic proportions, especially in Sub-Saharan Africa. In the US, men who have sex with men account for over half of AIDS diagnoses; racial and ethnic minorities are disproportionally affected. Factors influencing the progression and severity of HIV infection include type of immune response, coinfection (e.g., another sexually transmitted infection, including hepatitis B or C), age and behavioral and psychosocial factors. Antiretroviral therapies can achieve reduction in blood levels of the HIV virus below the limits of detection by current technology. However, effective treatment requires adherence to therapy. Patient failure to adhere to treatment regimens results in detectible circulating virus and in HIV disease progression, and is the primary cause of drug resistance. In addition to research on the immunology and virology of the disease, other studies focus on behavioral and psychosocial factors that may affect medication adherence and risk behaviors. PMID:18541903

  3. Smart HIV testing system.

    PubMed

    El Kateeb, Ali; Law, Peter; Chan, King

    2005-06-01

    The quick HIV testing method called "MiraWell Rapid HIV Test" uses a specialized testing kit to determine whether an individual's blood is contaminated with the HIV virus or not. When a drop of blood is placed on the center of the testing kit, a simple pattern will appear in the middle of the kit to indicate the test status, i.e., positive or negative. This HIV test should be done in a small clinic or in a lab and the test must be conducted by a trained technician. A smart HIV testing system was developed through this research to eliminate the human error that is associated with the use of the quick HIV testing kits. Also, the smart HIV system will improve the testing productivity in comparison to those achieved by the trained technicians. In this research, we have developed a cost-effective system that analyzes the image produced by the HIV kits. We have used a System-On-Chip (SOC) design approach based on the Field Programmable Gate Array (FPGA) technology and the Xilinx Virtex SOC chip in building the system's prototype. The system used a CMOS digital camera to capture the image and an FPGA chip to process the captured image and send the testing results to the display unit. The system can be used in small clinics and pharmacies and eliminates the need for trained technicians. The system has been tested successfully and 98% of the tests were correct. PMID:16078623

  4. Women and HIV

    MedlinePlus

    ... The impact of HIV is especially great among young women of color. More than one third of new ... legs. Abnormal pre-cancerous cell types related to cervical cancer are more frequent and severe in women who are HIV-positive. See fact sheet 510 ...

  5. Identification of potent maturation inhibitors against HIV-1 clade C.

    PubMed

    Timilsina, Uddhav; Ghimire, Dibya; Timalsina, Bivek; Nitz, Theodore J; Wild, Carl T; Freed, Eric O; Gaur, Ritu

    2016-01-01

    Antiretroviral therapy has led to a profound improvement in the clinical care of HIV-infected patients. However, drug tolerability and the evolution of drug resistance have limited treatment options for many patients. Maturation inhibitors are a new class of antiretroviral agents for treatment of HIV-1. They act by interfering with the maturation of the virus by blocking the last step in Gag processing: the cleavage of the capsid-spacer peptide 1 (CA-SP1) intermediate to mature CA by the viral protease (PR). The first-in-class maturation inhibitor bevirimat (BVM) failed against a subset of HIV-1 isolates in clinical trials due to polymorphisms present in the CA-SP1 region of the Gag protein. Sequence analysis indicated that these polymorphisms are more common in non-clade B strains of HIV-1 such as HIV-1 clade C. Indeed, BVM was found to be ineffective against HIV-1 clade C molecular clones tested in this study. A number of BVM analogs were synthesized by chemical modifications at the C-28 position to improve its activity. The new BVM analogs displayed potent activity against HIV-1 clade B and C and also reduced infectivity of the virus. This study identifies novel and broadly active BVM analogs that may ultimately demonstrate efficacy in the clinic. PMID:27264714

  6. Identification of potent maturation inhibitors against HIV-1 clade C

    PubMed Central

    Timilsina, Uddhav; Ghimire, Dibya; Timalsina, Bivek; Nitz, Theodore J.; Wild, Carl T.; Freed, Eric O.; Gaur, Ritu

    2016-01-01

    Antiretroviral therapy has led to a profound improvement in the clinical care of HIV-infected patients. However, drug tolerability and the evolution of drug resistance have limited treatment options for many patients. Maturation inhibitors are a new class of antiretroviral agents for treatment of HIV-1. They act by interfering with the maturation of the virus by blocking the last step in Gag processing: the cleavage of the capsid-spacer peptide 1 (CA-SP1) intermediate to mature CA by the viral protease (PR). The first-in-class maturation inhibitor bevirimat (BVM) failed against a subset of HIV-1 isolates in clinical trials due to polymorphisms present in the CA-SP1 region of the Gag protein. Sequence analysis indicated that these polymorphisms are more common in non-clade B strains of HIV-1 such as HIV-1 clade C. Indeed, BVM was found to be ineffective against HIV-1 clade C molecular clones tested in this study. A number of BVM analogs were synthesized by chemical modifications at the C-28 position to improve its activity. The new BVM analogs displayed potent activity against HIV-1 clade B and C and also reduced infectivity of the virus. This study identifies novel and broadly active BVM analogs that may ultimately demonstrate efficacy in the clinic. PMID:27264714

  7. Defining the roles for Vpr in HIV-1-associated neuropathogenesis.

    PubMed

    James, Tony; Nonnemacher, Michael R; Wigdahl, Brian; Krebs, Fred C

    2016-08-01

    It is increasingly evident that the human immunodeficiency virus type 1 (HIV-1) viral protein R (Vpr) has a unique role in neuropathogenesis. Its ability to induce G2/M arrest coupled with its capacity to increase viral gene transcription gives it a unique role in sustaining viral replication and aiding in the establishment and maintenance of a systemic infection. The requirement of Vpr for HIV-1 infection and replication in cells of monocytic origin (a key lineage of cells involved in HIV-1 neuroinvasion) suggests an important role in establishing and sustaining infection in the central nervous system (CNS). Contributions of Vpr to neuropathogenesis can be expanded further through (i) naturally occurring HIV-1 sequence variation that results in functionally divergent Vpr variants; (ii) the dual activities of Vpr as a intracellular protein delivered and expressed during HIV-1 infection and as an extracellular protein that can act on neighboring, uninfected cells; (iii) cell type-dependent consequences of Vpr expression and exposure, including cell cycle arrest, metabolic dysregulation, and cytotoxicity; and (iv) the effects of Vpr on exosome-based intercellular communication in the CNS. Revealing that the effects of this pleiotropic viral protein is an essential part of a greater understanding of HIV-1-associated pathogenesis and potential approaches to treating and preventing disease caused by HIV-1 infection. PMID:27056720

  8. Investigation of excess thyroid cancer incidence in Los Alamos County

    SciTech Connect

    Athas, W.F.

    1996-04-01

    Los Alamos County (LAC) is home to the Los Alamos National Laboratory, a U.S. Department of Energy (DOE) nuclear research and design facility. In 1991, the DOE funded the New Mexico Department of Health to conduct a review of cancer incidence rates in LAC in response to citizen concerns over what was perceived as a large excess of brain tumors and a possible relationship to radiological contaminants from the Laboratory. The study found no unusual or alarming pattern in the incidence of brain cancer, however, a fourfold excess of thyroid cancer was observed during the late-1980`s. A rapid review of the medical records for cases diagnosed between 1986 and 1990 failed to demonstrate that the thyroid cancer excess had resulted from enhanced detection. Surveillance activities subsequently undertaken to monitor the trend revealed that the excess persisted into 1993. A feasibility assessment of further studies was made, and ultimately, an investigation was conducted to document the epidemiologic characteristics of the excess in detail and to explore possible causes through a case-series records review. Findings from the investigation are the subject of this report.

  9. Electronic full-image reports at Los Alamos National Laboratory

    SciTech Connect

    Mosier, M.L.

    1998-03-02

    Los Alamos National Laboratory is a Department of Energy laboratory operated by the University of California. There are over 10,000 laboratory employees and contractors, many engaged in a variety of scientific and technical research. The laboratory covers forty-three square miles in northern New Mexico, one hundred miles from the nearest city which might reasonably be expected to meet the needs of the researchers. Because of the remoteness of the institution, the Research Library is a vital source for scientific and technical information. Due to the size of the institution, access to the physical library is difficult. These barriers, along with advances in technology, have led the Research Library to provide desktop access to all formal, unlimited Los Alamos reports. Older reports have been scanned and newer ones are received in electronic format. Currently over 10,000 reports are available in portable document format (PDF) via the World Wide Web (http://lib-www.lanl.gov). Researchers can search the library Web catalog (on a Z39.50 server), find a report, and click on a link to automatically bring up the report. This has been an extremely successful project as shown by the high usage, over 3,000 files retrieved per month in 1997 compared with around 100 for the hardcopy. This paper will discuss the reasons for, and the mechanics of, digitizing the reports, the results that have been observed, and plans for the future.

  10. Cleanup at Los Alamos National Laboratory - the challenges - 9493

    SciTech Connect

    Stiger, Susan G; Hargis, Kenneth M; Graham, Michael J; Rael, George J

    2008-01-01

    This paper provides an overview of environmental cleanup at the Los Alamos National Laboratory (LANL) and some of the unique aspects and challenges. Cleanup of the 65-year old Department of Energy Laboratory is being conducted under a RCRA Consent Order with the State of New Mexico. This agreement is one of the most recent cleanup agreements signed in the DOE complex and was based on lessons learned at other DOE sites. A number of attributes create unique challenges for LANL cleanup -- the proximity to the community and pueblos, the site's topography and geology, and the nature of LANL's on-going missions. This overview paper will set the stage for other papers in this session, including papers that present: Plans to retrieve buried waste at Material Disposal Area B, across the street from oen of Los Alamos' commercial districts and the local newspaper; Progress to date and joint plans with WIPP for disposal of the remaining inventory of legacy transuranic waste; Reviews of both groundwater and surface water contamination and the factors complicating both characterization and remediation; Optimizing the disposal of low-level radioactive waste from ongoing LANL missions; A stakeholder environmental data transparency project (RACER), with full public access to all available information on contamination at LANL, and A description of the approach to waste processing cost recovery from the programs that generate hazardous and radioactive waste at LANL.

  11. Summary of safeguards interactions between Los Alamos and Chinese scientists

    SciTech Connect

    Eccleston, G.W.

    1994-04-20

    Los Alamos has been collaborating since 1984 with scientists from the Chinese Institute of Atomic Energy (CIAE) to develop nuclear measurement instrumentation and safeguards systems technologies that will help China support implementation of the nonproliferation treaty (NPT). To date, four Chinese scientists have visited Los Alamos, for periods of six months to two years, where they have studied nondestructive assay instrumentation and learned about safeguards systems and inspection techniques that are used by International Atomic Energy Agency (IAEA) inspectors. Part of this collaboration involves invitations from the CIAE to US personnel to visit China and interact with a larger number of Institute staff and to provide a series of presentations on safeguards to a wider audience. Typically, CIAE scientists, Beijing Institute of Nuclear Engineering (BINE) staff, and officials from the Government Safeguards Office attend the lectures. The BINE has an important role in developing the civilian nuclear power fuel cycle. BINE is designing a reprocessing plant for spent nuclear fuel from Chinese nuclear Power reactors. China signed the nonproliferation treaty in 1992 and is significantly expanding its safeguards expertise and activities. This paper describes the following: DOE support for US and Chinese interactions on safeguards; Chinese safeguards; impacts of US-China safeguards interactions; and possible future safeguards interactions.

  12. Los Alamos Center for Computer Security formal computer security model

    SciTech Connect

    Dreicer, J.S.; Hunteman, W.J.; Markin, J.T.

    1989-01-01

    This paper provides a brief presentation of the formal computer security model currently being developed at the Los Alamos Department of Energy (DOE) Center for Computer Security (CCS). The need to test and verify DOE computer security policy implementation first motivated this effort. The actual analytical model was a result of the integration of current research in computer security and previous modeling and research experiences. The model is being developed to define a generic view of the computer and network security domains, to provide a theoretical basis for the design of a security model, and to address the limitations of present formal mathematical models for computer security. The fundamental objective of computer security is to prevent the unauthorized and unaccountable access to a system. The inherent vulnerabilities of computer systems result in various threats from unauthorized access. The foundation of the Los Alamos DOE CCS model is a series of functionally dependent probability equations, relations, and expressions. The model is undergoing continued discrimination and evolution. We expect to apply the model to the discipline of the Bell and LaPadula abstract sets of objects and subjects. 6 refs.

  13. The Los Alamos universe: Using multimedia to promote laboratory capabilities

    SciTech Connect

    Kindel, J.

    2000-03-01

    This project consists of a multimedia presentation that explains the technological capabilities of Los Alamos National Laboratory. It takes the form of a human-computer interface built around the metaphor of the universe. The project is intended promote Laboratory capabilities to a wide audience. Multimedia is simply a means of communicating information through a diverse set of tools--be they text, sound, animation, video, etc. Likewise, Los Alamos National Laboratory is a collection of diverse technologies, projects, and people. Given the ample material available at the Laboratory, there are tangible benefits to be gained by communicating across media. This paper consists of three parts. The first section provides some basic information about the Laboratory, its mission, and its needs. The second section introduces this multimedia presentation and the metaphor it is based on along with some basic concepts of color and user interaction used in the building of this project. The final section covers construction of the project, pitfalls, and future improvements.

  14. Seismic vulnerability study Los Alamos Meson Physics Facility (LAMPF)

    SciTech Connect

    Salmon, M.; Goen, L.K.

    1995-12-01

    The Los Alamos Meson Physics Facility (LAMPF), located at TA-53 of Los Alamos National Laboratory (LANL), features an 800 MeV proton accelerator used for nuclear physics and materials science research. As part of the implementation of DOE Order 5480.25 and in preparation for DOE Order 5480.28, a seismic vulnerability study of the structures, systems, and components (SSCs) supporting the beam line from the accelerator building through to the ends of die various beam stops at LAMPF has been performed. The study was accomplished using the SQUG GIP methodology to assess the capability of the various SSCs to resist an evaluation basis earthquake. The evaluation basis earthquake was selected from site specific seismic hazard studies. The goals for the study were as follows: (1) identify SSCs which are vulnerable to seismic loads; and (2) ensure that those SSCs screened during die evaluation met the performance goals required for DOE Order 5480.28. The first goal was obtained by applying the SQUG GIP methodology to those SSCS represented in the experience data base. For those SSCs not represented in the data base, information was gathered and a significant amount of engineering judgment applied to determine whether to screen the SSC or to classify it as an outlier. To assure the performance goals required by DOE Order 5480.28 are met, modifications to the SQUG GIP methodology proposed by Salmon and Kennedy were used. The results of this study ire presented in this paper.

  15. Recent progress in the Los Alamos KrF Program

    SciTech Connect

    McDonald, T.E.; Cartwright, D.C.; Coggeshall, S.V.; Fenstermacher, C.A.; Figueira, J.F.; Foreman, L.R.; Goldstone, P.D.; Hanson, D.E.; Harris, D.B.; Hauer, A.A.

    1988-01-01

    The goal of the Inertial Confinement Fusion Program (ICF) is to develop the ability to ignite and burn small masses of thermonuclear fuel. Although the present near-term objectives of the program are directed toward defense applications, ICF research continues to be carried out with a view to the longer term goal of commercial power production. The characteristics of a KrF laser make it an attractive candidate as an ICF driver. The KrF wavelength of 248 nm provides a target coupling that is very high at intensities of 10/sup 14/w/cm/sup 2/. In addition, the KrF laser can be repetitively operated at frequencies appropriate for a power reactor and has an intrinsically high efficiency, which allows projections to the long-term goal of energy production. The ICF program at Los Alamos consists of driver development, target design and fabrication, and target experimentation. The major effort at present is the investigation and development of KrF technology to determine its applicability for use in a laboratory driver at Los Alamos. Such a driver would be used in defense related technology studies and in areas of scientific study such as highly ionized materials and high-energy-density physics.

  16. Water supply at Los Alamos during 1987: Progress report

    SciTech Connect

    Purtymun, W.D.; Stoker, A.K.; Maes, M.N.

    1989-01-01

    Municipal and industrial water supply during 1987 was 1594 /times/ 10W gal from wells in three fields and 34 /times/ 10W gal from the spring gallery in Water Canyon. About 2.8 /times/ 10W gal of nonpotable water from the Guaje Reservoir and 3.2 /times/ 10W gal from the Los Alamos Reservoir were used for irrigation; thus, the total water usage in 1987 was about 1634 /times/ 10W gal. Water supply was satisfactory in that the production met demand and water quality in the distribution system was in compliance with state and federal regulations. However, in 1987 two wells were lost because of deterioration of the casing and screen. In spite of rehabilitation attempts to maintain the yield, production from the older wells continued to decline. A comprehensive evaluation of the wells and well fields made in late 1987 concluded that replacement wells and new wells were needed soon to ensure a reliable water supply for the Laboratory and the county of Los Alamos. 25 refs., 6 figs., 7 tabs.

  17. Solar pond research at the Los Alamos National Laboratory

    SciTech Connect

    Jones, G.F.; Meyer, K.A.; Hedstrom, J.C.; Grimmer, D.P.

    1984-01-01

    A description of solar pond research at Los Alamos National Laboratory is presented. The main issues in the theory of solar ponds are discussed. Among these are the interfacial-boundary-layer model, models for interface motion and pond performance, heat extraction, and ground heat loss. The core of the research effort at Los Alamos was the development of a one-dimensional computer program to accurately predict dynamic performance of a solar pond. The computer model and the experiments that were designed and performed to validate it are described. The experiments include two laboratory tanks wherein temperature, salinity, and flow visualization data were obtained and a 232 m/sup 2/ outdoor solar pond. Results from preliminary validation show good agreement between the pond's predicted dynamic behavior and that which actually occurred in the experiments. More validation using data from full-sized solar ponds is needed. A new correlation for the ratio of interfacial salt-flux to heat-flux is proposed which agrees well with our data. Recommendations for future research are given.

  18. An organizational survey of the Los Alamos Site

    SciTech Connect

    Shurberg, D.A.; Haber, S.B.

    1991-11-01

    An Organizational Survey (OS) was administered at the Los Alamos Site that queried employees on the subjects of organizational culture, various aspects of communications, employee commitment, work group cohesion, coordination of work, environmental, safety, and health concern, hazardous nature of work, safety and overall job satisfaction. The purpose of the OS is to measure in a quantitative and objective way the notion of ``culture;`` that is, the values, attitudes, and beliefs of the individuals working within the organization. In addition, through the OS, a broad sample of individuals can be reached that would probably not be interviewed or observed during the course of a typical assessment. The OS also provides a descriptive profile of the organization at one point in time that can then be compared to a profile taken at a different point in time to assess changes in the culture of the organization. While comparisons among groups are made, it is not the purpose of this report to make evaluative statements of which profile may be positive or negative. However, using the data presented in this report in conjunction with other evaluative activities, may provide useful insight into the organization. The OS administration at the Los Alamos Site was the ninth to occur at a Department of Energy (DOE) facility. All data from the OS is presented in group summaries, by organization, department or directorate within organization, supervisory level both overall and within organization, and staff classification within organization. Statistically significant differences between groups are identified and discussed. 9 refs., 94 figs., 11 tabs.

  19. An organizational survey of the Los Alamos Site

    SciTech Connect

    Shurberg, D.A.; Haber, S.B.

    1991-11-01

    An Organizational Survey (OS) was administered at the Los Alamos Site that queried employees on the subjects of organizational culture, various aspects of communications, employee commitment, work group cohesion, coordination of work, environmental, safety, and health concern, hazardous nature of work, safety and overall job satisfaction. The purpose of the OS is to measure in a quantitative and objective way the notion of culture;'' that is, the values, attitudes, and beliefs of the individuals working within the organization. In addition, through the OS, a broad sample of individuals can be reached that would probably not be interviewed or observed during the course of a typical assessment. The OS also provides a descriptive profile of the organization at one point in time that can then be compared to a profile taken at a different point in time to assess changes in the culture of the organization. While comparisons among groups are made, it is not the purpose of this report to make evaluative statements of which profile may be positive or negative. However, using the data presented in this report in conjunction with other evaluative activities, may provide useful insight into the organization. The OS administration at the Los Alamos Site was the ninth to occur at a Department of Energy (DOE) facility. All data from the OS is presented in group summaries, by organization, department or directorate within organization, supervisory level both overall and within organization, and staff classification within organization. Statistically significant differences between groups are identified and discussed. 9 refs., 94 figs., 11 tabs.

  20. The Los Alamos suite of relativistic atomic physics codes

    SciTech Connect

    Fontes, C. J.; Zhang, H. L.; Jr, J. Abdallah; Clark, R. E. H.; Kilcrease, D. P.; Colgan, J.; Cunningham, R. T.; Hakel, P.; Magee, N. H.; Sherrill, M. E.

    2015-05-28

    The Los Alamos SuitE of Relativistic (LASER) atomic physics codes is a robust, mature platform that has been used to model highly charged ions in a variety of ways. The suite includes capabilities for calculating data related to fundamental atomic structure, as well as the processes of photoexcitation, electron-impact excitation and ionization, photoionization and autoionization within a consistent framework. These data can be of a basic nature, such as cross sections and collision strengths, which are useful in making predictions that can be compared with experiments to test fundamental theories of highly charged ions, such as quantum electrodynamics. The suite can also be used to generate detailed models of energy levels and rate coefficients, and to apply them in the collisional-radiative modeling of plasmas over a wide range of conditions. Such modeling is useful, for example, in the interpretation of spectra generated by a variety of plasmas. In this work, we provide a brief overview of the capabilities within the Los Alamos relativistic suite along with some examples of its application to the modeling of highly charged ions.

  1. Fuels Inventories in the Los Alamos National Laboratory Region: 1997

    SciTech Connect

    Balice, R.G.; Oswald, B.P.; Martin, C.

    1999-03-01

    Fifty-four sites were surveyed for fuel levels, vegetational structures, and topographic characteristics. Most of the surveyed sites were on Los Alamos National Laboratory property, however, some surveys were also conducted on U.S. Forest Service property. The overall vegetation of these sites ranged from pinon-juniper woodlands to ponderosa pine forests to mixed conifer forests, and the topographic positions included canyons, mesas, and mountains. The results of these surveys indicate that the understory fuels are the greatest in mixed conifer forests and that overstory fuels are greatest in both mixed conifer forests and ponderosa pine forests on mesas. The geographic distribution of these fuels would suggest a most credible wildfire scenario for the Los Alamos region. Three major fires have occurred since 1954 and these fires behaved in a manner that is consistent with this scenario. The most credible wildfire scenario was also supported by the results of BEHAVE modeling that used the fuels inventory data as inputs. Output from the BEHAVE model suggested that catastrophic wildfires would continue to occur during any season with sufficiently dry, windy weather.

  2. Los Alamos energetic particle sensor systems at geostationary orbit

    SciTech Connect

    Baker, D.N.; Aiello, W.; Asbridge, J.R.; Belian, R.D.; Higbie, P.R.; Klebesadel, R.W.; Laros, J.G.; Tech, E.R.

    1985-01-01

    The Los Alamos National Laboratory has provided energetic particle sensors for a variety of spacecraft at the geostationary orbit (36,000 km altitude). The sensor system called the Charged Particle Analyzer (CPA) consists of four separate subsystems. The LoE and HiE subsystems measure electrons in the energy ranges 30 to 300 keV and 200 to 2000 keV, respectively. The LoP and HiP subsystems measure ions in the ranges 100 to 600 keV and 0.40 to 150 MeV, respectively. A separate sensor system called the spectrometer for energetic electrons (SEE) measures very high-energy electrons (2 to 15 MeV) using advanced scintillator design. In this paper we describe the relationship of operational anomalies and spacecraft upsets to the directly measured energetic particle environments at 6.6 R/sub E/. We also compare and contrast the CPA and SEE instrument design characteristics with the next generation of Los Alamos instruments to be flown at geostationary altitudes.

  3. The Los Alamos suite of relativistic atomic physics codes

    DOE PAGESBeta

    Fontes, C. J.; Zhang, H. L.; Jr, J. Abdallah; Clark, R. E. H.; Kilcrease, D. P.; Colgan, J.; Cunningham, R. T.; Hakel, P.; Magee, N. H.; Sherrill, M. E.

    2015-05-28

    The Los Alamos SuitE of Relativistic (LASER) atomic physics codes is a robust, mature platform that has been used to model highly charged ions in a variety of ways. The suite includes capabilities for calculating data related to fundamental atomic structure, as well as the processes of photoexcitation, electron-impact excitation and ionization, photoionization and autoionization within a consistent framework. These data can be of a basic nature, such as cross sections and collision strengths, which are useful in making predictions that can be compared with experiments to test fundamental theories of highly charged ions, such as quantum electrodynamics. The suitemore » can also be used to generate detailed models of energy levels and rate coefficients, and to apply them in the collisional-radiative modeling of plasmas over a wide range of conditions. Such modeling is useful, for example, in the interpretation of spectra generated by a variety of plasmas. In this work, we provide a brief overview of the capabilities within the Los Alamos relativistic suite along with some examples of its application to the modeling of highly charged ions.« less

  4. Four Amino Acid Changes in HIV-2 Protease Confer Class-Wide Sensitivity to Protease Inhibitors

    PubMed Central

    Smith, Robert A.; Gottlieb, Geoffrey S.

    2015-01-01

    ABSTRACT Protease is essential for retroviral replication, and protease inhibitors (PI) are important for treating HIV infection. HIV-2 exhibits intrinsic resistance to most FDA-approved HIV-1 PI, retaining clinically useful susceptibility only to lopinavir, darunavir, and saquinavir. The mechanisms for this resistance are unclear; although HIV-1 and HIV-2 proteases share just 38 to 49% sequence identity, all critical structural features of proteases are conserved. Structural studies have implicated four amino acids in the ligand-binding pocket (positions 32, 47, 76, and 82). We constructed HIV-2ROD9 molecular clones encoding the corresponding wild-type HIV-1 amino acids (I32V, V47I, M76L, and I82V) either individually or together (clone PRΔ4) and compared the phenotypic sensitivities (50% effective concentration [EC50]) of mutant and wild-type viruses to nine FDA-approved PI. Single amino acid replacements I32V, V47I, and M76L increased the susceptibility of HIV-2 to multiple PI, but no single change conferred class-wide sensitivity. In contrast, clone PRΔ4 showed PI susceptibility equivalent to or greater than that of HIV-1 for all PI. We also compared crystallographic structures of wild-type HIV-1 and HIV-2 proteases complexed with amprenavir and darunavir to models of the PRΔ4 enzyme. These models suggest that the amprenavir sensitivity of PRΔ4 is attributable to stabilizing enzyme-inhibitor interactions in the P2 and P2′ pockets of the protease dimer. Together, our results show that the combination of four amino acid changes in HIV-2 protease confer a pattern of PI susceptibility comparable to that of HIV-1, providing a structural rationale for intrinsic HIV-2 PI resistance and resolving long-standing questions regarding the determinants of differential PI susceptibility in HIV-1 and HIV-2. IMPORTANCE Proteases are essential for retroviral replication, and HIV-1 and HIV-2 proteases share a great deal of structural similarity. However, only three of nine

  5. 1993 Annual PCB Document for Los Alamos National Laboratory EPA Region VI, January 1, 1993 through December 31, 1993

    SciTech Connect

    Wechsler, R.J.; Sandoval, T.M.; Bryant, D.E.; Hupke, L.; Esquibel, L.

    1995-12-31

    This document, the {open_quotes}1993 Annual PCB Document for Los Alamos National Laboratory{close_quotes} was prepared to fulffill the requirements of the federal PCB (Polychlorinated Biphenyl) regulation: 40 CFR 761 Subpart J General Records and Reports. The PCB Management Program at Los Alamos National Laboratory (LANL), Environmental Protection Group, compiled this 1993 Annual PCB Document. The overall format generally follows the sequence of the applicable regulations. Subsection 1.2 cross references those regulatory requirements with the applicable Document Section. The scope of this document also includes status summaries of various aspects of LANL`s PCB Management Program. The intent of this approach to the Annual Document is to provide an overview of LANL`s PCB Management Program and to increase the usefulness of this document as a management tool. Section 2.0, {open_quotes}Status of the PCB Management Program{close_quotes}, discusses the use, generation of waste, and storage of PCBs at LANL. Section 3.0 is the 1993 Annual Document Log required by 761.180(a). This Section also discusses the PCB Management Program`s policies for reporting under those regulatory requirements. Sections 4.0 and 5.0 contain the 1993 Annual Records for off-site and on-site disposal as required by 761.180(b). There is a tab for each manifest and its associated continuation sheets, receipt letters, and certificates of disposal.

  6. HIV disclosure among adults living with HIV.

    PubMed

    Mayfield Arnold, E; Rice, E; Flannery, D; Rotheram-Borus, M J

    2008-01-01

    Research on disclosure among heterosexual adult person(s) living with HIV (PLH) was reviewed, omitting disclosure of parental HIV to children. Disclosure has been studied within five additional relational contexts: with partners, family members, friends, healthcare professionals and in work settings. Disclosure is higher among women than men, among Latino and white compared to African-American families, and among younger compared to older HIV-positive adults. Most PLH disclose to their sexual partners and family members, yet there is a significant minority who do not disclose. Similarly, rates of disclosure to employers range from 27-68%, suggesting broad variability in perceived consequences of employment disclosures. Of concern, 40% of PLH do not consistently disclose to their healthcare professionals. Rather than examine HIV disclosures in the context of relationships, it is possible to understand disclosures around personal identity. Disclosure decisions are often made to tell everyone (making HIV status a central attribute of one's identity), no one (requiring strategies for securing social support while remaining anonymous) or some people (requiring strategic decisions based on context). Given that disclosure decisions are central to personal identity, future data on disclosure and interventions designed to increase disclosure or comfort with disclosure must focus on communication strategies adopted by PLH to present a coherent identity. PMID:18278618

  7. The Genetic Diversity and Evolution of HIV-1 Subtype B Epidemic in Puerto Rico

    PubMed Central

    López, Pablo; Rivera-Amill, Vanessa; Rodríguez, Nayra; Vargas, Freddie; Yamamura, Yasuhiro

    2015-01-01

    HIV-1 epidemics in Caribbean countries, including Puerto Rico, have been reported to be almost exclusively associated with the subtype B virus (HIV-1B). However, while HIV infections associated with other clades have been only sporadically reported, no organized data exist to accurately assess the prevalence of non-subtype B HIV-1 infection. We analyzed the nucleotide sequence data of the HIV pol gene associated with HIV isolates from Puerto Rican patients. The sequences (n = 945) were obtained from our “HIV Genotyping” test file, which has been generated over a period of 14 years (2001–2014). REGA subtyping tool found the following subtypes: B (90%), B-like (3%), B/D recombinant (6%), and D/B recombinant (0.6%). Though there were fewer cases, the following subtypes were also found (in the given proportions): A1B (0.3%), BF1 (0.2%), subtype A (01-AE) (0.1%), subtype A (A2) (0.1%), subtype F (12BF) (0.1%), CRF-39 BF-like (0.1%), and others (0.1%). Some of the recombinants were identified as early as 2001. Although the HIV epidemic in Puerto Rico is primarily associated with HIV-1B virus, our analysis uncovered the presence of other subtypes. There was no indication of subtype C, which has been predominantly associated with heterosexual transmission in other parts of the world. PMID:26703695

  8. HIV-Associated Tuberculosis.

    PubMed

    Naidoo, Kogieleum; Naidoo, Kasavan; Padayatchi, Nesri; Abdool Karim, Quarraisha

    2011-01-01

    The intersecting HIV and Tuberculosis epidemics in countries with a high disease burden of both infections pose many challenges and opportunities. For patients infected with HIV in high TB burden countries, the diagnosis of TB, ARV drug choices in treating HIV-TB coinfected patients, when to initiate ARV treatment in relation to TB treatment, managing immune reconstitution, minimising risk of getting infected with TB and/or managing recurrent TB, minimizing airborne transmission, and infection control are key issues. In addition, given the disproportionate burden of HIV in women in these settings, sexual reproductive health issues and particular high mortality rates associated with TB during pregnancy are important. The scaleup and resource allocation to access antiretroviral treatment in these high HIV and TB settings provide a unique opportunity to strengthen both services and impact positively in meeting Millennium Development Goal 6. PMID:20871843

  9. Ethical issues in HIV.

    PubMed

    Dhai, Amaboo; Noble, Ray

    2005-04-01

    The number of people with HIV/AIDS continues to increase globally. Women, who represent the subgroup with the fastest rate of increase, are usually informed of their serostatus by the obstetrician/gynaecologist. As treatment of infected women raises a number of ethical issues, an understanding of the theoretical background for ethical decision making is requisite to ensure these problems are resolved within a morally appropriate framework. Vigorous debate has arisen from the tensions between the competing goals of HIV testing, third party disclosure, management of the critically ill HIV-infected woman, infertility management in the background of HIV/AIDS, and gender-based violence as cause or result of acquiring HIV infection. Women may be differently empowered economically, socially and culturally. What may be a satisfactory solution in the context of the USA and Europe may be far from ideal in that of the developing world. PMID:15778114

  10. HIV and neurocognitive dysfunction.

    PubMed

    Spudich, Serena

    2013-09-01

    The spectrum of HIV-associated neurocognitive disorder (HAND) has been dramatically altered in the setting of widely available effective antiretroviral therapy (ART). Once culminating in dementia in many individuals infected with HIV, HAND now typically manifests as more subtle, though still morbid, forms of cognitive impairment in persons surviving long-term with treated HIV infection. Despite the substantial improvement in severity of this disorder, the fact that neurologic injury persists despite ART remains a challenge to the community of patients, providers and investigators aiming to optimize quality of life for those living with HIV. Cognitive dysfunction in treated HIV may reflect early irreversible CNS injury accrued before ART is typically initiated, ongoing low-level CNS infection and progressive injury in the setting of ART, or comborbidities including effects of treatment which may confound the beneficial reduction in viral replication and immune activation effected by ART. PMID:23860944

  11. Use of screening action levels in risk management at Los Alamos National Laboratory

    SciTech Connect

    Beck, J.R.; Hueske, K.L.; Dorries, A.M.

    1994-04-01

    The screening assessment approach used at Los Alamos National Laboratory has proved to be a valuable risk management tool in making decisions that are cost-effective, efficient, and defensible. Los Alamos has successfully used screening action levels to prioritize RFI activities, streamline data evaluation, and insure analytical methods are adequately sensitive to be protective of human health.

  12. Recollections of a very junior physicist at Los Alamos, 1944-1946

    NASA Astrophysics Data System (ADS)

    French, Anthony P.

    2008-04-01

    The author came to Los Alamos as a member of the British Mission after two years of making fission cross section measurements at the Cavendish Laboratory. He worked in a group headed by Egon Bretscher in Enrico Fermi's F Division. The talk presents his personal memories and experiences at Los Alamos as compared to his life and work in wartime Britain.

  13. School Finance in a Federal City: Los Alamos as a Case Study.

    ERIC Educational Resources Information Center

    Smith, Duane W.

    The Los Alamos schools obtain support from a combination of local, state, and Department of Energy funds mandated by the Atomic Energy Commission Community Act. Each year the Los Alamos schools prepare three budgets, and during any week the schools may work directly with all three levels of government concerning funding. In 1974 the state of New…

  14. The Pajarito Site operating procedures for the Los Alamos Critical Experiments Facility

    SciTech Connect

    Malenfant, R.E.

    1991-12-01

    Operating procedures consistent with DOE Order 5480.6, and the American National Standard Safety Guide for the Performance of Critical Experiments are defined for the Los Alamos Critical Experiments Facility (LACEF) of the Los Alamos National Laboratory. These operating procedures supersede and update those previously published in 1983 and apply to any criticality experiment performed at the facility. 11 refs.

  15. Recombinant Viruses and Early Global HIV-1 Epidemic

    PubMed Central

    Robbins, Kenneth E.; Pieniazek, Danuta; Schaefer, Amanda; Nzilambi, Nzila; Quinn, Thomas C.; St. Louis, Michael E.; Youngpairoj, Ae S.; Phillips, Jonathan; Jaffe, Harold W.; Folks, Thomas M.

    2004-01-01

    Central Africa was the epicenter of the HIV type 1 (HIV-1) pandemic. Understanding the early epidemic in the Democratic Republic of the Congo, formerly Zaire, could provide insight into how HIV evolved and assist vaccine design and intervention efforts. Using enzyme immunosorbent assays, we tested 3,988 serum samples collected in Kinshasa in the mid-1980s and confirmed seroreactivity by Western blot. Polymerase chain reaction of gag p17, env C2V3C3, and/or gp41; DNA sequencing; and genetic analyses were performed. Gene regions representing all the HIV-1 group M clades and unclassifiable sequences were found. From two or three short gene regions, 37% of the strains represented recombinant viruses, multiple infections, or both, which suggests that if whole genome sequences were available, most of these strains would have mosaic genomes. We propose that the HIV epidemic was well established in central Africa by the early 1980s and that some recombinant viruses most likely seeded the early global epidemic. PMID:15324542

  16. [Epidemiology of HIV].

    PubMed

    Ledergerber, Bruno; Battegay, Manuel

    2014-08-01

    Globally, an estimated 35 million people were living with HIV in 2012; of these, 69 % in sub-Saharan Africa. There were 2.3 million new HIV infections globally and 1.6 million AIDS deaths in 2012. As a result of large roll-out programs with integrated voluntary counselling and testing and prevention programs in resource limited settings, sexual transmission of HIV decreased substantially over the last years. However, the world is not on track to reduced HIV transmission among people who inject drugs. Especially in Eastern Europe and Asia prevention coverage for people who inject drugs remains low. In addition, effective prevention among these people is undermined by stigmatisation, discrimination, punitive policy frameworks and law enforcement practices, which discourage people from seeking the health and social services they need. Antiretroviral coverage among pregnant women living with HIV reached 62 % in 2012 resulting in a reduction of newly infected children by 35 % from 2009. In 2012, 9.7 million people in low and middle-income countries received antiretroviral therapy, representing 61 % of all who were eligible under the 2010 WHO HIV treatment guidelines. Under the 2013 guidelines, this represents only 34 % of the 28.3 million people eligible in 2013. A new concept to curb the HIV epidemic is "Test and Treat" which involves population-wide HIV tests with immediate initiation of antiretroviral therapy among all HIV infected individuals. However, there are concerns regarding the sustainability of such treatment programs for decades due to lost to follow up and insufficient adherence and the danger of a large increase of resistant HIV which jeopardize the effectiveness of affordable treatments. PMID:25093307

  17. Multiple Origins of Virus Persistence during Natural Control of HIV Infection.

    PubMed

    Boritz, Eli A; Darko, Samuel; Swaszek, Luke; Wolf, Gideon; Wells, David; Wu, Xiaolin; Henry, Amy R; Laboune, Farida; Hu, Jianfei; Ambrozak, David; Hughes, Marybeth S; Hoh, Rebecca; Casazza, Joseph P; Vostal, Alexander; Bunis, Daniel; Nganou-Makamdop, Krystelle; Lee, James S; Migueles, Stephen A; Koup, Richard A; Connors, Mark; Moir, Susan; Schacker, Timothy; Maldarelli, Frank; Hughes, Stephen H; Deeks, Steven G; Douek, Daniel C

    2016-08-11

    Targeted HIV cure strategies require definition of the mechanisms that maintain the virus. Here, we tracked HIV replication and the persistence of infected CD4 T cells in individuals with natural virologic control by sequencing viruses, T cell receptor genes, HIV integration sites, and cellular transcriptomes. Our results revealed three mechanisms of HIV persistence operating within distinct anatomic and functional compartments. In lymph node, we detected viruses with genetic and transcriptional attributes of active replication in both T follicular helper (TFH) cells and non-TFH memory cells. In blood, we detected inducible proviruses of archival origin among highly differentiated, clonally expanded cells. Linking the lymph node and blood was a small population of circulating cells harboring inducible proviruses of recent origin. Thus, HIV replication in lymphoid tissue, clonal expansion of infected cells, and recirculation of recently infected cells act together to maintain the virus in HIV controllers despite effective antiviral immunity. PMID:27453467

  18. Developing High-Throughput HIV Incidence Assay with Pyrosequencing Platform

    PubMed Central

    Park, Sung Yong; Goeken, Nolan; Lee, Hyo Jin; Bolan, Robert; Dubé, Michael P.

    2014-01-01

    ABSTRACT Human immunodeficiency virus (HIV) incidence is an important measure for monitoring the epidemic and evaluating the efficacy of intervention and prevention trials. This study developed a high-throughput, single-measure incidence assay by implementing a pyrosequencing platform. We devised a signal-masking bioinformatics pipeline, which yielded a process error rate of 5.8 × 10−4 per base. The pipeline was then applied to analyze 18,434 envelope gene segments (HXB2 7212 to 7601) obtained from 12 incident and 24 chronic patients who had documented HIV-negative and/or -positive tests. The pyrosequencing data were cross-checked by using the single-genome-amplification (SGA) method to independently obtain 302 sequences from 13 patients. Using two genomic biomarkers that probe for the presence of similar sequences, the pyrosequencing platform correctly classified all 12 incident subjects (100% sensitivity) and 23 of 24 chronic subjects (96% specificity). One misclassified subject's chronic infection was correctly classified by conducting the same analysis with SGA data. The biomarkers were statistically associated across the two platforms, suggesting the assay's reproducibility and robustness. Sampling simulations showed that the biomarkers were tolerant of sequencing errors and template resampling, two factors most likely to affect the accuracy of pyrosequencing results. We observed comparable biomarker scores between AIDS and non-AIDS chronic patients (multivariate analysis of variance [MANOVA], P = 0.12), indicating that the stage of HIV disease itself does not affect the classification scheme. The high-throughput genomic HIV incidence marks a significant step toward determining incidence from a single measure in cross-sectional surveys. IMPORTANCE Annual HIV incidence, the number of newly infected individuals within a year, is the key measure of monitoring the epidemic's rise and decline. Developing reliable assays differentiating recent from chronic

  19. Anti-HIV screening for cell-penetrating peptides using chloroquine and identification of anti-HIV peptides derived from matrix proteins.

    PubMed

    Mizuguchi, Takaaki; Ohashi, Nami; Nomura, Wataru; Komoriya, Mao; Hashimoto, Chie; Yamamoto, Naoki; Murakami, Tsutomu; Tamamura, Hirokazu

    2015-08-01

    Previously, compounds which inhibit the HIV-1 replication cycle were found in overlapping peptide libraries covering the whole sequence of an HIV-1 matrix (MA) protein constructed with the addition of an octa-arginyl group. The two top lead compounds are sequential fragments MA-8L and MA-9L. In the present study, the addition of chloroquine in cell-based anti-HIV assays was proven to be an efficient method with which to find anti-HIV compounds among several peptides conjugated by cell-penetrating signals such as an octa-arginyl group: the conjugation of an octa-arginyl group to individual peptides contained in whole proteins in combination with the addition of chloroquine in cells is a useful assay method to search active peptides. To find more potent fragment peptides, individual peptides between MA-8L and MA-9L, having the same peptide chain length but with sequences shifted by one amino acid residue, were synthesized in this paper and their anti-HIV activity was evaluated with an anti-HIV assay using chloroquine. As a result, the peptides in the C-terminal side of the series, which are relatively close to MA-9L, showed more potent inhibitory activity against both X4-HIV-1 and R5-HIV-1 than the peptides in the N-terminal side. PMID:26094944

  20. An AP-1 binding site in the enhancer/core element of the HIV-1 promoter controls the ability of HIV-1 to establish latent infection.

    PubMed

    Duverger, Alexandra; Wolschendorf, Frank; Zhang, Mingce; Wagner, Fredric; Hatcher, Brandon; Jones, Jennifer; Cron, Randall Q; van der Sluis, Renee M; Jeeninga, Rienk E; Berkhout, Ben; Kutsch, Olaf

    2013-02-01

    Following integration, HIV-1 in most cases produces active infection events; however, in some rare instances, latent infection events are established. The latter have major clinical implications, as latent infection allows the virus to persist despite antiretroviral therapy. Both the cellular factors and the viral elements that potentially determine whether HIV-1 establishes active or latent infection events remain largely elusive. We detail here the contribution of different long terminal repeat (LTR) sequences for the establishment of latent HIV-1 infection. Using a panel of full-length replication-competent virus constructs that reflect naturally occurring differences of HIV-1 subtype-specific LTRs and targeted LTR mutants, we found the primary ability of HIV-1 to establish latent infection in this system to be controlled by a four-nucleotide (nt) AP-1 element just upstream of the NF-κB element in the viral promoter. Deletion of this AP-1 site mostly deprived HIV-1 of the ability to establish latent HIV-1 infection. Extension of this site to a 7-nt AP-1 sequence massively promoted latency establishment, suggesting that this promoter region represents a latency establishment element (LEE). Given that these minimal changes in a transcription factor binding site affect latency establishment to such large extent, our data support the notion that HIV-1 latency is a transcription factor restriction phenomenon. PMID:23236059