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HIV bioinformatics

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https://www.readbyqxmd.com/read/29669026/first-in-human-randomized-controlled-trial-of-mosaic-hiv-1-immunogens-delivered-via-a-modified-vaccinia-ankara-vector
#1
Lindsey R Baden, Stephen R Walsh, Michael S Seaman, Yehuda Z Cohen, Jennifer A Johnson, J Humberto Licona, Rachel D Filter, Jane A Kleinjan, Jon A Gothing, Julia Jennings, Lauren Peter, Joseph Nkolola, Peter Abbink, Erica N Borducchi, Marinela Kirilova, Kathryn E Stephenson, Poonam Pegu, Michael A Eller, Hung V Trinh, Mangala Rao, Julie A Ake, Michal Sarnecki, Steven Nijs, Katleen Callewaert, Hanneke Schuitemaker, Jenny Hendriks, Maria G Pau, Frank Tomaka, Bette T Korber, Galit Alter, Raphael Dolin, Patricia L Earl, Bernard Moss, Nelson L Michael, Merlin L Robb, Dan H Barouch
Background: Mosaic immunogens are bioinformatically engineered HIV-1 sequences designed to elicit clade independent coverage against globally circulating HIV-1 strains. Methods: This Phase 1 double-blind, randomized, placebo-controlled trial enrolled healthy HIV uninfected adults who received two doses of a modified vaccinia Ankara (MVA) vectored HIV-1 bivalent mosaic immunogen vaccine or placebo on days 0 and 84. Two groups were enrolled: those who were HIV-1 vaccine naïve (N=15) and those who had received an HIV-1 vaccine four to six years earlier (Ad26...
April 13, 2018: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/29620929/long-non-coding-rna-gas5-inhibits-hiv-1-replication-through-interaction-with-mir-873
#2
Liujun Chen, Lang Chen, Luoshiyuan Zuo, Ziang Gao, Yingying Shi, Peipei Yuan, Song Han, Jun Yin, Biwen Peng, Xiaohua He, Wanhong Liu
The human immunodeficiency virus (HIV) is the causative pathogen of acquired immunodeficiency syndrome (AIDS), which has generated worldwide concern. Long non-coding RNAs (lncRNAs) are a rising star in virus-host cross-talk pathways; they are differentially expressed during many viral infections and are involved in multiple biological processes. Currently, lncRNA growth arrest-specific transcript 5 (GAS5) is known to be down-regulated during HIV-1 infection. However, the functions and mechanisms of GAS5 in HIV-1 infection remain largely unknown...
March 12, 2018: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/29580818/tuberculosis-advances-and-challenges-in-development-of-new-diagnostics-and-biomarkers
#3
REVIEW
Gerhard Walzl, Ruth McNerney, Nelita du Plessis, Matthew Bates, Timothy D McHugh, Novel N Chegou, Alimuddin Zumla
Tuberculosis remains the leading cause of death from an infectious disease worldwide. Early and accurate diagnosis and detection of drug-sensitive and drug-resistant tuberculosis is essential for achieving global tuberculosis control. Despite the introduction of the Xpert MTB/RIF assay as the first-line rapid tuberculosis diagnostic test, the gap between global estimates of incidence and new case notifications is 4·1 million people. More accurate, rapid, and cost-effective screening tests are needed to improve case detection...
March 23, 2018: Lancet Infectious Diseases
https://www.readbyqxmd.com/read/29579063/in-silico-identification-of-micrornas-predicted-to-regulate-n-myristoyltransferase-and-methionine-aminopeptidase-2-functions-in-cancer-and-infectious-diseases
#4
Ranjit Chauhan, David Datzkiw, Shailly Varma Shrivastav, Anuraag Shrivastav
Protein myristoylation is a key protein modification carried out by N-Myristoyltransferase (NMT) after Methionine aminopeptidase 2 (MetAP2) removes methionine from the amino-terminus of the target protein. Protein myristoylation by NMT augments several signaling pathways involved in a myriad of cellular processes, including developmental pathways and pathways that when dysregulated lead to cancer or immune dysfunction. The emerging evidence pointing to NMT-mediated myristoylation as a major cellular regulator underscores the importance of understanding the framework of this type of signaling event...
2018: PloS One
https://www.readbyqxmd.com/read/29554213/scotch-subtype-a-coreceptor-tropism-classification-in-hiv-1
#5
Hannah F Löchel, Mona Riemenschneider, Dmitrij Frishman, Dominik Heider
Motivation: The V3 loop of the gp120 glycoprotein of the Human Immunodeficiency Virus 1 (HIV-1) is considered to be responsible for viral coreceptor tropism. gp120 interacts with the CD4 receptor of the host cell and subsequently V3 binds either CCR5 or CXCR4. Due to the fact that the CCR5 coreceptor is targeted by entry inhibitors, a reliable prediction of the coreceptor usage of HIV-1 is of great interest for antiretroviral therapy. Although several methods for the prediction of coreceptor tropism are available, almost all of them have been developed based on only subtype B sequences, and it has been shown in several studies that the prediction of non-B sequences, in particular subtype A sequences, are less reliable...
March 15, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29520099/comparative-proteomic-profiling-and-biomarker-identification-of-traditional-chinese-medicine-based-hiv-aids-syndromes
#6
Li Wen, Ye-Fang Liu, Cen Jiang, Shao-Qian Zeng, Yue Su, Wen-Jun Wu, Xi-Yang Liu, Jian Wang, Ying Liu, Chen Su, Bai-Xue Li, Quan-Sheng Feng
Given the challenges in exploring lifelong therapy with little side effect for human immunodeficiency virus infection and acquired immune deficiency syndrome (HIV/AIDS) cases, there is increasing interest in developing traditional Chinese medicine (TCM) treatments based on specific TCM syndrome. However, there are few objective and biological evidences for classification and diagnosis of HIV/AIDS TCM syndromes to date. In this study, iTRAQ-2DLC-MS/MS coupled with bioinformatics were firstly employed for comparative proteomic profiling of top popular TCM syndromes of HIV/AIDS: accumulation of heat-toxicity (AHT) and Yang deficiency of spleen and kidney (YDSK)...
March 8, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29514950/mir-130a-and-mir-212-disrupt-the-intestinal-epithelial-barrier-through-modulation-of-ppar%C3%AE-and-occludin-expression-in-chronic-simian-immunodeficiency-virus-infected-rhesus-macaques
#7
Vinay Kumar, Joshua Mansfield, Rong Fan, Andrew MacLean, Jian Li, Mahesh Mohan
Intestinal epithelial barrier dysfunction is a well-known sequela of HIV/SIV infection that persists despite antiretroviral therapy. Although inflammation is a triggering factor, the underlying molecular mechanisms remain unknown. Emerging evidence suggests that epithelial barrier function is epigenetically regulated by inflammation-induced microRNAs (miRNAs). Accordingly, we profiled and characterized miRNA/mRNA expression exclusively in colonic epithelium and identified 46 differentially expressed miRNAs (20 upregulated and 26 downregulated) in chronically SIV-infected rhesus macaques ( Macaca mulatta )...
March 7, 2018: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/29508932/genome-wide-expression-profiling-analysis-to-identify-key-genes-in-the-anti-hiv-mechanism-of-cd4-and-cd8-t-cells
#8
Lijie Gao, Yunqi Wang, Yi Li, Ya Dong, Aimin Yang, Jie Zhang, Fengying Li, Rongqiang Zhang
Objectives Comprehensive bioinformatics analyses were performed to explore the key biomarkers in response to HIV infection of CD4+ and CD8+ T cells. Methods The numbers of CD4+ and CD8+ T cells of HIV infected individuals were analyzed and the GEO database (GSE6740) was screened for deferentially expressed genes (DEGs) in HIV infected CD4+ and CD8+ T cells. Gene Ontology enrichment, KEGG pathway analyses and protein-protein interaction (PPI) network were performed to identify the key pathway and core proteins in anti-HIV virus process of CD4+ and CD8+ T cells...
March 6, 2018: Journal of Medical Virology
https://www.readbyqxmd.com/read/29463238/characterization-and-heterologous-expression-of-the-neoabyssomicin-abyssomicin-biosynthetic-gene-cluster-from-streptomyces-koyangensis-scsio-5802
#9
Jiajia Tu, Siting Li, Jiang Chen, Yongxiang Song, Shaobin Fu, Jianhua Ju, Qinglian Li
BACKGROUND: The deep-sea-derived microbe Streptomyces koyangensis SCSIO 5802 produces neoabyssomicins A-B (1-2) and abyssomicins 2 (3) and 4 (4). Neoabyssomicin A (1) augments human immunodeficiency virus-1 (HIV-1) replication whereas abyssomicin 2 (3) selectively reactivates latent HIV and is also active against Gram-positive pathogens including methicillin-resistant Staphylococcus aureus (MRSA). Structurally, neoabyssomicins A-B constitute a new subtype within the abyssomicin family and feature unique structural traits characteristic of extremely interesting biosynthetic transformations...
February 20, 2018: Microbial Cell Factories
https://www.readbyqxmd.com/read/29452580/measuring-integrated-hiv-dna-ex-vivo-and-in-vitro-provides-insights-about-how-reservoirs-are-formed-and-maintained
#10
REVIEW
Marilia Rita Pinzone, Una O'Doherty
The identification of the most appropriate marker to measure reservoir size has been a great challenge for the HIV field. Quantitative viral outgrowth assay (QVOA), the reference standard to quantify the amount of replication-competent virus, has several limitations, as it is laborious, expensive, and unable to robustly reactivate every single integrated provirus. PCR-based assays have been developed as an easier, cheaper and less error-prone alternative to QVOA, but also have limitations. Historically, measuring integrated HIV DNA has provided insights about how reservoirs are formed and maintained...
February 17, 2018: Retrovirology
https://www.readbyqxmd.com/read/29444253/hiv-1-genotypic-resistance-testing-using-the-vela-automated-next-generation-sequencing-platform
#11
Stéphanie Raymond, Florence Nicot, Romain Carcenac, Caroline Lefebvre, Nicolas Jeanne, Karine Saune, Pierre Delobel, Jacques Izopet
Objectives: To evaluate the diagnostic performance of the Vela next-generation sequencing (NGS) system in conjunction with the Sentosa SQ HIV Genotyping Assay for genotyping HIV-1. Methods: Plasma RNA was extracted and templates prepared with the Sentosa SX instrument before sequencing the HIV-1 polymerase on the Sentosa SQ301 Sequencer (PGM IonTorrent). The Vela NGS System was compared with direct sequencing and the 454 GS-FLX (Roche) and MiSeq (Illumina) systems for genotypic resistance testing on clinical samples...
February 12, 2018: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29438560/hiite-hiv-1-incidence-and-infection-time-estimator
#12
Sung Yong Park, Tanzy M T Love, Shivankur Kapoor, Ha Youn Lee, John Hancock
Motivation: Around 2.1 million new HIV-1 infections were reported in 2015, alerting that the HIV-1 epidemic remains a significant global health challenge. Precise incidence assessment strengthens epidemic monitoring efforts and guides strategy optimization for prevention programs. Estimating the onset time of HIV-1 infection can facilitate optimal clinical management and identify key populations largely responsible for epidemic spread and thereby infer HIV-1 transmission chains. Our goal is to develop a genomic assay estimating the incidence and infection time in a single cross-sectional survey setting...
February 9, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29369160/hla-associated-polymorphisms-in-the-hiv-2-capsid-highlight-key-differences-between-hiv-1-and-hiv-2-immune-adaptation
#13
Thushan I de Silva, Aleksandra Leligdowicz, Jonathan Carlson, Miguel Garcia-Knight, Clayton Onyango, Nicholas Miller, Louis-Marie Yindom, Stephane Hué, Assan Jaye, Tao Dong, Matthew Cotten, Sarah L Rowland-Jones
OBJECTIVE: HIV-1 frequently adapts in response to immune pressure from cytotoxic T-lymphocytes (CTL). Many HIV-2 infected individuals have robust capsid-specific CTL responses associated with viral control. Despite this CTL pressure, adaptive changes in this key immunogenic HIV-2 protein have not previously been described. We sought to compare selective pressure on HIV-1 and HIV-2 capsids and identify HLA-associated viral polymorphisms in HIV-2. DESIGN AND METHODS: Bioinformatic algorithms to identify sites under positive and negative selective pressure and a statistical model of evolution to identify HLA-associated polymorphisms in HIV-2 was applied to sequences from a community cohort in Guinea-Bissau...
January 23, 2018: AIDS
https://www.readbyqxmd.com/read/29322922/analysis-of-viral-diversity-for-vaccine-target-discovery
#14
Asif M Khan, Yongli Hu, Olivo Miotto, Natascha M Thevasagayam, Rashmi Sukumaran, Hadia Syahirah Abd Raman, Vladimir Brusic, Tin Wee Tan, J Thomas August
BACKGROUND: Viral vaccine target discovery requires understanding the diversity of both the virus and the human immune system. The readily available and rapidly growing pool of viral sequence data in the public domain enable the identification and characterization of immune targets relevant to adaptive immunity. A systematic bioinformatics approach is necessary to facilitate the analysis of such large datasets for selection of potential candidate vaccine targets. RESULTS: This work describes a computational methodology to achieve this analysis, with data of dengue, West Nile, hepatitis A, HIV-1, and influenza A viruses as examples...
December 21, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29291225/application-of-viromics-a-new-approach-to-the-understanding-of-viral-infections-in-humans
#15
REVIEW
Mageshbabu Ramamurthy, Sathish Sankar, Rajesh Kannangai, Balaji Nandagopal, Gopalan Sridharan
This review is focused at exploring the strengths of modern technology driven data compiled in the areas of virus gene sequencing, virus protein structures and their implication to viral diagnosis and therapy. The information for virome analysis (viromics) is generated by the study of viral genomes (entire nucleotide sequence) and viral genes (coding for protein). Presently, the study of viral infectious diseases in terms of etiopathogenesis and development of newer therapeutics is undergoing rapid changes...
December 2017: Virusdisease
https://www.readbyqxmd.com/read/29243131/analysis-of-variability-of-urinary-excreted-jc-virus-strains-in-patients-infected-with-hiv-and-healthy-donors
#16
Danijela Karalic, Ivana Lazarevic, Ana Banko, Maja Cupic, Djordje Jevtovic, Tanja Jovanovic
In immunocompromised individuals, especially in patients with T cell immunodeficiency, reactivation of JCPyV can cause serious life-threatening diseases. Nowadays, HIV infection is one of the most important factor for reactivation of JCPyV and the development of of the progressive multifocal leukoencephalopathy (PML). Mutations in the outer loops of the VP1 region can lead to the selection of the viral variants with changed tropism and increased pathological potential. The aims of this study were to determine sequence variation and amino acid changes within VP1 loops and the structure of non-coding control region (NCCR) of urinary excreted JCPyV isolates among HIV-infected patients and healthy donors...
December 14, 2017: Journal of Neurovirology
https://www.readbyqxmd.com/read/29209209/nonribosomal-peptides-from-marine-microbes-and-their-antimicrobial-and-anticancer-potential
#17
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
#18
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
#19
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
#20
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...
December 1, 2017: Journal of Infectious Diseases
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