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HIV bioinformatics

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https://www.readbyqxmd.com/read/29209209/nonribosomal-peptides-from-marine-microbes-and-their-antimicrobial-and-anticancer-potential
#1
REVIEW
Shivankar Agrawal, Debabrata Acharya, Alok Adholeya, Colin J Barrow, Sunil K Deshmukh
Marine environments are largely unexplored and can be a source of new molecules for the treatment of many diseases such as malaria, cancer, tuberculosis, HIV etc. The Marine environment is one of the untapped bioresource of getting pharmacologically active nonribosomal peptides (NRPs). Bioprospecting of marine microbes have achieved many remarkable milestones in pharmaceutics. Till date, more than 50% of drugs which are in clinical use belong to the nonribosomal peptide or mixed polyketide-nonribosomal peptide families of natural products isolated from marine bacteria, cyanobacteria and fungi...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/29168754/a-bioinformatic-pipeline-for-monitoring-of-the-mutational-stability-of-viral-drug-targets-with-deep-sequencing-technology
#2
Yuri Kravatsky, Vladimir Chechetkin, Daria Fedoseeva, Maria Gorbacheva, Galina Kravatskaya, Olga Kretova, Nickolai Tchurikov
The efficient development of antiviral drugs, including efficient antiviral small interfering RNAs (siRNAs), requires continuous monitoring of the strict correspondence between a drug and the related highly variable viral DNA/RNA target(s). Deep sequencing is able to provide an assessment of both the general target conservation and the frequency of particular mutations in the different target sites. The aim of this study was to develop a reliable bioinformatic pipeline for the analysis of millions of short, deep sequencing reads corresponding to selected highly variable viral sequences that are drug target(s)...
November 23, 2017: Viruses
https://www.readbyqxmd.com/read/29120899/association-of-a-3-untranslated-region-polymorphism-in-proprotein-convertase-subtilisin-kexin-type-9-with-hiv-viral-load-and-cd4-levels-in-hiv-hepatitis-c-virus-coinfected-women
#3
Mark H Kuniholm, Hua Liang, Kathryn Anastos, Deborah Gustafson, Seble Kassaye, Marek Nowicki, Beverly E Sha, Emilia J Pawlowski, Stephen J Gange, Bradley E Aouizerat, Tatiana Pushkarsky, Michael I Bukrinsky, Vinayaka R Prasad
OBJECTIVE: To assess variation in genes that regulate cholesterol metabolism in relation to the natural history of HIV infection. DESIGN: Cross-sectional and longitudinal analysis of the Women's Interagency HIV Study. METHODS: We examined 2050 single nucleotide polymorphisms (SNPs) in 19 genes known to regulate cholesterol metabolism in relation to HIV viral load and CD4 T-cell levels in a multiracial cohort of 1066 antiretroviral therapy-naive women...
November 28, 2017: AIDS
https://www.readbyqxmd.com/read/28968834/next-generation-human-immunodeficiency-virus-sequencing-for-patient-management-and-drug-resistance-surveillance
#4
Marc Noguera-Julian, Dianna Edgil, P Richard Harrigan, Paul Sandstrom, Catherine Godfrey, Roger Paredes
High-quality, simplified, and low-cost human immunodeficiency virus (HIV) drug resistance tests that are able to provide timely actionable HIV resistance data at individual, population, and programmatic levels are needed to confront the emerging drug-resistant HIV epidemic. Next-generation sequencing technologies embedded in automated cloud-computing analysis environments are ideally suited for such endeavor. Whereas NGS can reduce costs over Sanger sequencing, automated analysis pipelines make NGS accessible to molecular laboratories regardless of the available bioinformatic skills...
September 15, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28942522/hiv-1-genetic-diversity-geographical-linkages-and-antiretroviral-drug-resistance-among-individuals-from-pakistan
#5
Saeed Khan, Maria Zahid, Muhammad Asif Qureshi, Muhammad Nouman Mughal, Ikram Din Ujjan
Worldwide antiretroviral therapy (ART) has reduced the mortality and morbidity rates in individuals with HIV infection. However, the increasing occurrence of drug resistance is limiting treatment options. In recent years, Pakistan has witnessed a concentrated epidemic of HIV. It is very important to identify geographical linkages and mutations that generate selective pressure and drive resistance of HIV in our population. The aim of this work was to identify genetic diversity and drug resistance patterns of HIV in Pakistan, using available sequences and bioinformatics tools, which may help in selecting effective combination of available drugs...
September 23, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28933684/screening-of-primary-gp120-immunogens-to-formulate-the-next-generation-polyvalent-dna-prime-protein-boost-hiv-1-vaccines
#6
Shixia Wang, Te-Hui Chou, Anthony Hackett, Veronica Efros, Yan Wang, Dong Han, Aaron Wallace, Yuxin Chen, Guangnan Hu, Shuying Liu, Paul Clapham, James Arthos, David Montefiori, Shan Lu
Our previous preclinical studies and a Phase I clinical trial DP6-001 have indicated that a polyvalent Env formulation was able to elicit broadly reactive antibody responses including low titer neutralizing antibody responses against viral isolates of subtypes A, B, C and AE. In the current report, a panel of 62 gp120 immunogens were screened in a rabbit model to identify gp120 immunogens that can elicit improved binding and neutralizing antibody responses and some of them can be included in the next polyvalent formulation...
September 21, 2017: Human Vaccines & Immunotherapeutics
https://www.readbyqxmd.com/read/28926398/association-of-a-3-untranslated-region-polymorphism-in-pcsk9-with-hiv-viral-load-and-cd4-levels-in-hiv-hepatitis-c-virus-co-infected-women
#7
Mark H Kuniholm, Hua Liang, Kathryn Anastos, Deborah Gustafson, Seble Kassaye, Marek Nowicki, Beverly E Sha, Emilia J Pawlowski, Stephen J Gange, Bradley E Aouizerat, Tatiana Pushkarsky, Michael I Bukrinsky, Vinayaka R Prasad
OBJECTIVE: To assess variation in genes that regulate cholesterol metabolism in relation to the natural history of HIV infection. DESIGN: Cross-sectional and longitudinal analysis of the Women's Interagency HIV Study (WIHS). METHODS: We examined 2,050 single nucleotide polymorphisms (SNPs) in 19 genes known to regulate cholesterol metabolism in relation to HIV viral load and CD4 T cell levels in a multiracial cohort of 1,066 antiretroviral therapy (ART) naïve women...
September 18, 2017: AIDS
https://www.readbyqxmd.com/read/28881959/maboss-2-0-an-environment-for-stochastic-boolean-modeling
#8
Gautier Stoll, Barthélémy Caron, Eric Viara, Aurélien Dugourd, Andrei Zinovyev, Aurélien Naldi, Guido Kroemer, Emmanuel Barillot, Laurence Calzone
Motivation: Modeling of signaling pathways is an important step towards the understanding and the treatment of diseases such as cancers, HIV or auto-immune diseases. MaBoSS is a software that allows to simulate populations of cells and to model stochastically the intracellular mechanisms that are deregulated in diseases. MaBoSS provides an output of a Boolean model in the form of time-dependent probabilities, for all biological entities (genes, proteins, phenotypes, etc.) of the model...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28841646/prediction-of-coreceptor-usage-by-five-bioinformatics-tools-in-a-large-ethiopian-hiv-1-subtype-c-cohort
#9
Amare Worku Kalu, Nigus Fikrie Telele, Solomon Gebreselasie, Daniel Fekade, Samir Abdurahman, Gaetano Marrone, Anders Sönnerborg
BACKGROUND: Genotypic tropism testing (GTT) has been developed largely on HIV-1 subtype B. Although a few reports have analysed the utility of GTT in other subtypes, more studies using HIV-1 subtype C (HIV-1C) are needed, considering the huge contribution of HIV-1C to the global epidemic. METHODS: Plasma was obtained from 420 treatment-naïve HIV-1C infected Ethiopians recruited 2009-2011. The V3 region was sequenced and the coreceptor usage was predicted by five tools: Geno2Pheno clinical-and clonal-models, PhenoSeq-C, C-PSSM and Raymond's algorithm...
2017: PloS One
https://www.readbyqxmd.com/read/28822954/the-variability-of-hepatitis-b-envelope-is-associated-with-hbs-antigen-persistence-in-either-chronic-or-acute-hbv-genotype-a-infection
#10
Marine Eschlimann, Brice Malvé, Aurélie Velay, Honorine Fenaux, Sibel Berger, Jean-Pol Frippiat, Fabien Zoulim, Mouni Bensenane, Jean-Pierre Bronowicki, François Goehringer, Thierry May, Hélène Jeulin, Evelyne Schvoerer
BACKGROUND: More than 240 million people are chronically infected by hepatitis B virus (HBV) worldwide. Envelope proteins play a crucial role in viral cellular entry and immune recognition. The loss of HBs antigen (HBsAg) correlated with a good clinical prognosis is rarely achieved with or without treatment (3-16%). OBJECTIVES: HBV envelope variability was investigated according to HBsAg persistence. STUDY DESIGN: The cohort consisted of 15 HBV genotype A-infected patients divided into "resolvers", with HBsAg clearance, and "non-resolvers", with HBsAg persistence and in subgroups: acute (n=5, AHBV) or chronic infection (n=4, CHBV) and HBV/HIV coinfection (n=6, CHBV/HIV)...
August 5, 2017: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
https://www.readbyqxmd.com/read/28791125/nkg2c-memory-like-nk-cells-contribute-to-the-control-of-hiv-viremia-during-primary-infection-optiprim-anrs-147
#11
Françoise Gondois-Rey, Antoine Chéret, Samuel Granjeaud, Françoise Mallet, Ghislain Bidaut, Camille Lécuroux, Mickaël Ploquin, Michaela Müller-Trutwin, Christine Rouzioux, Véronique Avettand-Fenoël, Alessandro Moretta, Gilles Pialoux, Cécile Goujard, Laurence Meyer, Daniel Olive
Natural-killer (NK) cells are important immune effectors during a viral infection. Latent CMV infection is widely spread and was demonstrated to shape the NK cell repertoire through the NKG2C receptor. An expansion of NKG2C(+) NK cells has been reported during primary HIV infection (PHI), but their role is not known. We previously found a correlation between the maturation state of the NK cell compartment and a lower viral load by studying patients from the ANRS 147 Optiprim trial. We investigated here extensively the NKG2C(+) NK cells at the time of PHI and its evolution after 3 months of early antiretroviral therapy (combination antiretroviral therapy (cART))...
July 2017: Clinical & Translational Immunology
https://www.readbyqxmd.com/read/28720122/enhance-the-performance-of-current-scoring-functions-with-the-aid-of-3d-protein-ligand-interaction-fingerprints
#12
Jie Liu, Minyi Su, Zhihai Liu, Jie Li, Yan Li, Renxiao Wang
BACKGROUND: In structure-based drug design, binding affinity prediction remains as a challenging goal for current scoring functions. Development of target-biased scoring functions provides a new possibility for tackling this problem, but this approach is also associated with certain technical difficulties. We previously reported the Knowledge-Guided Scoring (KGS) method as an alternative approach (BMC Bioinformatics, 2010, 11, 193-208). The key idea is to compute the binding affinity of a given protein-ligand complex based on the known binding data of an appropriate reference complex, so the error in binding affinity prediction can be reduced effectively...
July 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28695803/bioinformatic-analysis-of-differentially-expressed-genes-in-peripheral-blood-of-human-immunodeficiency-virus-tubercle-bacilli-co-infected-patients
#13
Rongqiang Zhang, Qiling Liu, Na Sun, Wulin Kang, Puwei Yuan
Objective To analyze the differentially expressed genes in peripheral blood of human immunodeficiency(HIV)/tubercle bacilli co-infected patients and explore the biological regulatory mechanism and network of key proteins,so as to provide new evidence for early diagnosis and clinical treatment of HIV/TB co-infected patients. Methods Microarray gene chip data of HIV/TB co-infected patients were downloaded from public databases GEO and imported into the analysis software GEO,STRING,PANTHER,and GenClip. The gene expression profiles,protein interaction networks,processes of molecular biology,and gene functions were analyzed...
June 20, 2017: Zhongguo Yi Xue Ke Xue Yuan Xue Bao. Acta Academiae Medicinae Sinicae
https://www.readbyqxmd.com/read/28692540/unique-microrna-expression-in-the-colonic-mucosa-during-chronic-hiv-1-infection
#14
Jennifer A Fulcher, Georgios Koukos, Marina Koutsioumpa, Julie Elliott, Alexandra Drakaki, Dimitrios Iliopoulos, Peter A Anton
OBJECTIVE: Chronic HIV-1 infection leads to widespread inflammation and immune dysregulation. The gastrointestinal mucosa, a primary site for HIV-1 replication, is thought to play a significant role in this response. MicroRNAs (miRs) are small noncoding RNAs that regulate gene expression, including immune activation and inflammation. Here we investigate miR expression and function in the colonic mucosa during HIV-1 infection. DESIGN AND METHODS: Using miR profiling, we examined miR expression in the colonic mucosa of HIV-infected patients...
September 10, 2017: AIDS
https://www.readbyqxmd.com/read/28624190/expression-of-herpes-simplex-virus-thymidine-kinase-ganciclovir-by-rna-trans-splicing-induces-selective-killing-of-hiv-producing-cells
#15
Carin K Ingemarsdotter, Sushmita Poddar, Sarah Mercier, Volker Patzel, Andrew M L Lever
Antiviral strategies targeting hijacked cellular processes are less easily evaded by the virus than viral targets. If selective for viral functions, they can have a high therapeutic index. We used RNA trans-splicing to deliver the herpes simplex virus thymidine kinase-ganciclovir (HSV-tk/GCV) cell suicide system into HIV-producing cells. Using an extensive in silico bioinformatics and RNA structural analysis approach, ten HIV RNA trans-splicing constructs were designed targeting eight different HIV splice donor or acceptor sites and were tested in cells expressing HIV...
June 16, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28591401/an-overview-of-the-molecular-and-epidemiological-features-of-hiv-1-infection-in-two-major-cities-of-bahia-state-brazil
#16
Amanda Gm Amaral, Isabele B Oliveira, Diego C Carneiro, Luiz Cj Alcantara, Joana P Monteiro-Cunha
BACKGROUND: The high mutation rate of the human immunodeficiency virus (HIV) has created a public health challenge because the use of antiretroviral drugs can generate selective pressure that drives resistance in these viruses. OBJECTIVE: The aim of this work was to characterise the molecular and epidemiological profile of HIV in Bahia, Brazil. METHODS: DNA sequences from regions of HIV gag, pol, and env genes were obtained from previous studies performed in this area between 2002 and 2012...
June 2017: Memórias do Instituto Oswaldo Cruz
https://www.readbyqxmd.com/read/28582463/drug-resistance-testing-through-remote-genotyping-and-predicted-treatment-options-in-human-immunodeficiency-virus-type-1-infected-tanzanian-subjects-failing-first-or-second-line-antiretroviral-therapy
#17
Jenny Svärd, Sabina Mugusi, Doreen Mloka, Ujjwal Neogi, Genny Meini, Ferdinand Mugusi, Francesca Incardona, Maurizio Zazzi, Anders Sönnerborg
INTRODUCTION: Antiretroviral therapy (ART) has been successfully introduced in low-middle income countries. However an increasing rate of ART failure with resistant virus is reported. We therefore described the pattern of drug resistance mutations at antiretroviral treatment (ART) failure in a real-life Tanzanian setting using the remote genotyping procedure and thereafter predicted future treatment options using rule-based algorithm and the EuResist bioinformatics predictive engine. According to national guidelines, the default first-line regimen is tenofovir + lamivudine + efavirenz, but variations including nevirapine, stavudine or emtricitabine can be considered...
2017: PloS One
https://www.readbyqxmd.com/read/28534892/minimizing-next-generation-sequencing-errors-for-hiv-drug-resistance-testing
#18
José A Fernández-Caballero, Natalia Chueca, Eva Poveda, Federico García
Next-generation sequencing prototypes for the routine diagnosis of resistance to antiretrovirals approved for the treatment of HIV infection are now being used in many clinical diagnostic laboratories. As some of the next-generation sequencing platforms may be a source of errors, it is necessary to improve the currently available protocols and implement bioinformatic tools that may help to correctly identify the presence of resistance mutations with clinical impact. Several studies have addressed these issues in recent years...
May 23, 2017: AIDS Reviews
https://www.readbyqxmd.com/read/28446664/analysis-of-competing-hiv-1-splice-donor-sites-uncovers-a-tight-cluster-of-splicing-regulatory-elements-within-exon-2-2b
#19
Anna-Lena Brillen, Lara Walotka, Frank Hillebrand, Lisa Müller, Marek Widera, Stephan Theiss, Heiner Schaal
The HIV-1 accessory protein Vif is essential for viral replication by counteracting the host restriction factor APOBEC3G (A3G), and balanced levels of both proteins are required for efficient viral replication. Noncoding exons 2/2b contain the Vif start codon between their alternatively used splice donors 2 and 2b (D2 and D2b). For vif mRNA, intron 1 must be removed while intron 2 must be retained. Thus, splice acceptor 1 (A1) must be activated by U1 snRNP binding to either D2 or D2b, while splicing at D2 or D2b must be prevented...
July 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28377903/the-bioinformatics-analysis-of-comparative-genomics-of-mycobacterium-tuberculosis-complex-mtbc-provides-insight-into-dissimilarities-between-intraspecific-groups-differing-in-host-association-virulence-and-epitope-diversity
#20
COMPARATIVE STUDY
Xinmiao Jia, Li Yang, Mengxing Dong, Suting Chen, Lingna Lv, Dandan Cao, Jing Fu, Tingting Yang, Ju Zhang, Xiangli Zhang, Yuanyuan Shang, Guirong Wang, Yongjie Sheng, Hairong Huang, Fei Chen
Tuberculosis now exceeds HIV as the top infectious disease cause of mortality, and is caused by the Mycobacterium tuberculosis complex (MTBC). MTBC strains have highly conserved genome sequences (similarity >99%) but dramatically different phenotypes. To analyze the relationship between genotype and phenotype, we conducted the comparative genomic analysis on 12 MTBC strains representing different lineages (i.e., Mycobacterium bovis; M. bovis BCG; M. microti; M. africanum; M. tuberculosis H37Rv; M. tuberculosis H37Ra, and six M...
2017: Frontiers in Cellular and Infection Microbiology
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