keyword
MENU ▼
Read by QxMD icon Read
search

HIV genomics

keyword
https://www.readbyqxmd.com/read/29468971/il-10-promoter-592-polymorphism-may-influence-resistance-to-hiv-infection-in-south-indian-population
#1
Murugesan Harishankar, Harini Ravikrishnan, Akshaya Ravishankar, Luke Hanna Elizabeth, Soumya Swaminathan, Paramasivam Selvaraj, Ramalingam Bethunaickan
BACKGROUND: Genetic factors play an important role in the development of disease susceptibility or protection. Cytokine gene polymorphisms are reported to be associated with altered levels of cytokine production that can impact disease progression in HIV and TB. OBJECTIVE: In this study, we studied IL-10 -592(C/A) and TGF-β -509 (C/T) promoter polymorphisms to understand their role in susceptibility or resistance to HIV and TB in a South Indian population. METHOD: Genomic DNA was isolated from healthy controls, pulmonary tuberculosis patients (n=122) and HIV positive individuals (n=100) and used for genotyping by polymerase chain reaction followed by restriction fragment length polymorphism (PCR-RFLP) method...
February 19, 2018: Current HIV Research
https://www.readbyqxmd.com/read/29463238/characterization-and-heterologous-expression-of-the-neoabyssomicin-abyssomicin-biosynthetic-gene-cluster-from-streptomyces-koyangensis-scsio-5802
#2
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/29461980/killer-cell-immunoglobulin-like-receptor-3dl1-variation-modifies-hla-b-57-protection-against-hiv-1
#3
Maureen P Martin, Vivek Naranbhai, Patrick R Shea, Ying Qi, Veron Ramsuran, Nicolas Vince, Xiaojiang Gao, Rasmi Thomas, Zabrina L Brumme, Jonathan M Carlson, Steven M Wolinsky, James J Goedert, Bruce D Walker, Florencia P Segal, Steven G Deeks, David W Haas, Stephen A Migueles, Mark Connors, Nelson Michael, Jacques Fellay, Emma Gostick, Sian Llewellyn-Lacey, David A Price, Bernard A Lafont, Phillip Pymm, Philippa M Saunders, Jacqueline Widjaja, Shu Cheng Wong, Julian P Vivian, Jamie Rossjohn, Andrew G Brooks, Mary Carrington
HLA-B*57 control of HIV involves enhanced CD8+ T cell responses against infected cells, but extensive heterogeneity exists in level of HIV control among B*57+ individuals. Using whole genome sequencing of untreated B*57+ HIV-1 infected controllers and non-controllers, we identified a single variant (rs643347A/G) encoding an isoleucine to valine substitution at position 47 (I47V) of the inhibitory killer cell immunoglobulin-like receptor, KIR3DL1, as the only significant modifier of B*57 protection. The association replicated in an independent cohort and across multiple outcomes...
February 20, 2018: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/29455571/genetic-variation-of-the-kinases-that-phosphorylate-tenofovir-and-emtricitabine-in-peripheral-blood-mononuclear-cells
#4
Dominique Figueroa, Erin Madeen, Joseph Tillotson, Paul Richardson, Leslie Cottle, Marybeth McCauley, Raphael Landovitz, Adriana Andrade, Craig W Hendrix, Kenneth H Mayer, T J Wilkin, Roy Gulick, Namandjé N Bumpus
Tenofovir (TFV) disoproxil fumarate and emtricitabine (FTC) are used in combination for HIV treatment and pre-exposure prophylaxis (PrEP). Tenofovir disoproxil fumarate is a prodrug that undergoes diester hydrolysis to TFV. FTC and TFV are nucleoside/nucleotide reverse transcriptase inhibitors that upon phosphorylation to nucleotide triphosphate analogs competitively inhibit HIV reverse transcriptase. We previously demonstrated that adenylate kinase 2, pyruvate kinase, muscle and pyruvate kinase, liver and red blood cell phosphorylate TFV in peripheral blood mononuclear cells (PBMC)...
February 17, 2018: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/29449904/expression-profiling-of-chromatin-modifying-enzymes-and-global-dna-methylation-in-cd4-t-cells-from-patients-with-chronic-hiv-infection-at-different-hiv-control-and-progression-states
#5
Roberta Nicoleta Bogoi, Alicia de Pablo, Eulalia Valencia, Luz Martín-Carbonero, Victoria Moreno, Helem Haydee Vilchez-Rueda, Victor Asensi, Rosa Rodriguez, Victor Toledano, Berta Rodés
Background: Integration of human immunodeficiency virus type 1 (HIV-1) into the host genome causes global disruption of the chromatin environment. The abundance level of various chromatin-modifying enzymes produces these alterations and affects both the provirus and cellular gene expression. Here, we investigated potential changes in enzyme expression and global DNA methylation in chronically infected individuals with HIV-1 and compared these changes with non-HIV infected individuals...
2018: Clinical Epigenetics
https://www.readbyqxmd.com/read/29439583/identification-of-a-novel-hiv-1-recombinant-form-b-c-in-men-who-have-sex-with-men-in-shaanxi-china
#6
Mengyan Zhang, Ruolei Xin, Wenhui Chang
Many new circulating recombinant forms (CRFs) and unique recombinant forms (URFs) of HIV-1 have been found in men who have sex with men (MSM) in recent years, in China. In this study, a unique HIV-1 recombinant genome (SN153) was characterized from an HIV-positive male infected through homosexual behavior in Shaanxi, China. The mosaic pattern had a complex intersubtype recombinant structure with six breakpoints, with three subtype C segments inserted into subtype B backbone. And three similar breakpoints with CRF07_BC were observed in the pol gene...
February 14, 2018: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/29438560/hiite-hiv-1-incidence-and-infection-time-estimator
#7
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/29438494/artificial-intelligence-in-drug-combination-therapy
#8
Igor F Tsigelny
Currently, the development of medicines for complex diseases requires the development of combination drug therapies. It is necessary because in many cases, one drug cannot target all necessary points of intervention. For example, in cancer therapy, a physician often meets a patient having a genomic profile including more than five molecular aberrations. Drug combination therapy has been an area of interest for a while, for example the classical work of Loewe devoted to the synergism of drugs was published in 1928-and it is still used in calculations for optimal drug combinations...
February 9, 2018: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29433524/measuring-replication-competent-hiv-1-advances-and-challenges-in-defining-the-latent-reservoir
#9
REVIEW
Zheng Wang, Francesco R Simonetti, Robert F Siliciano, Gregory M Laird
Antiretroviral therapy cannot cure HIV-1 infection due to the persistence of a small number of latently infected cells harboring replication-competent proviruses. Measuring persistent HIV-1 is challenging, as it consists of a mosaic population of defective and intact proviruses that can shift from a state of latency to active HIV-1 transcription. Due to this complexity, most of the current assays detect multiple categories of persistent HIV-1, leading to an overestimate of the true size of the latent reservoir...
February 13, 2018: Retrovirology
https://www.readbyqxmd.com/read/29419684/phylogenetic-and-temporal-dynamics-of-human-immunodeficiency-virus-type-1-crf01_ae-and-crf07_bc-among-recently-infected-antiretroviral-therapy-na%C3%A3-ve-men-who-have-sex-with-men-in-jiangsu-province-china-2012-to-2015-a-molecular-epidemiology-based-study
#10
Yue Yang, Xiu-Ping Zhao, Hua-Chun Zou, Min-Jie Chu, Ping Zhong, Xiao-Shan Li, Xiao-Yan Li, Yu-Hui Yu, Ke-Xin Zhu, Yu-Jia Chen, Fei Xia, Bo-Wen Zhu, Luan-Qi Ruan, Yi-Ning Bao, Xun Zhuang
The prevalence and incidence of human immunodeficiency virus type 1 (HIV-1) among men who have sex with men (MSM) are on the rise throughout China. With a large population of MSM, Jiangsu Province is facing an escalating HIV-1 epidemic.The aim of this study was to explore the phylogenetic and temporal dynamics of HIV-1 CRF01_AE and CRF07_BC among antiretroviral therapy (ART)-naïve MSM recently infected with HIV-1 in Jiangsu Province.We recruited MSM in Jiangsu Province (Suzhou, Wuxi, Nantong, Taizhou and Yancheng) 2012 to 2015...
February 2018: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29410097/hbv-bypasses-the-innate-immune-response-and-does-not-protect-hcv-from-antiviral-activity-of-interferon
#11
Pascal Mutz, Philippe Metz, Florian A Lempp, Silke Bender, Bingqian Qu, Katrin Schöneweis, Stefan Seitz, Thomas Tu, Agnese Restuccia, Jamie Frankish, Christopher Dächert, Benjamin Schusser, Ronald Koschny, Georgios Polychronidis, Peter Schemmer, Katrin Hoffmann, Thomas F Baumert, Marco Binder, Stephan Urban, Ralf Bartenschlager
BACKGROUND & AIMS: Hepatitis C virus (HCV) infection is sensitive to interferon (IFN)-based therapy whereas HBV infection is not. It is unclear whether HBV escapes detection by the IFN-mediated immune response or actively suppresses it. Moreover, little is known on how HBV and HCV influence each other in co-infected cells. We investigated interactions between HBV and the IFN-mediated immune response using HepaRG cells and primary human hepatocytes (PHHs). We analyzed the effects of HBV on HCV replication, and vice versa, at the single-cell level...
January 31, 2018: Gastroenterology
https://www.readbyqxmd.com/read/29408943/analysis-of-hbv-basal-core-promoter-precore-gene-variability-in-patients-with-hbv-drug-resistance-and-hiv-co-infection-in-northwest-ethiopia
#12
Yeshambel Belyhun, Uwe Gerd Liebert, Melanie Maier
BACKGROUND: We recently reported complex hepatitis B virus (HBV) drug resistant and concomitant vaccine escape hepatitis B surface antigen (HBsAg) variants during human immunodeficiency virus (HIV) co-infection and antiretroviral therapy (ART) exposure in Ethiopia. As a continuation of this report using the HBV positive sera from the same study participants, the current study further analyzed the HBV basal core promoter (BCP)/precore (PC) genes variability in patients with HBV drug resistance (at tyrosine-methionine-aspartate-aspartate (YMDD) reverse transcriptase (RT) motifs) and HIV co-infection in comparison with HBV mono-infected counterparts with no HBV drug resistant gene variants...
2018: PloS One
https://www.readbyqxmd.com/read/29406282/prevalence-of-cryptosporidium-species-isolated-from-hiv-aids-patients-in-southwest-of-iran
#13
Reza Ghafari, Abdollah Rafiei, Mehdi Tavalla, Parastoo Moradi Choghakabodi, Rohangez Nashibi, Reza Rafiei
This study aimed to determine the prevalence and species of Cryptosporidium among HIV/AIDS patients in southwest of Iran. Two hundred fifty faecal samples from HIV patients were examined for the presence of Cryptosporidium oocysts using a conventional coproscopic approach. Such oocysts were detected in 18 (7.2%) out of 250 faecal samples. Genomic DNAs from 250 samples were then subjected to a nested-PCR-RFLP technique targeting different loci of 18S rRNA gene for species identification. Out of 250 samples, 27 (10...
February 2018: Comparative Immunology, Microbiology and Infectious Diseases
https://www.readbyqxmd.com/read/29405478/extracting-functional-groups-of-allini-to-design-derivatives-of-fda-approved-drugs-inhibition-of-hiv-1-integrase
#14
Umesh Kalathiya, Monikaben Padariya, Maciej Baginski
HIV-1 integrase (IN) is crucial for integration of viral DNA into the host genome and a promising target in development of antiretroviral inhibitors. In this work, six new compounds were designed by linking the structures of two different class of HIV-1 IN inhibitors (active site binders and allosteric IN inhibitors (ALLINIs)). Among newly designed compounds, INRAT10b was found most potent HIV-1 IN inhibitor considering different docking results. To further validate protein-ligand interactions obtained from dockings, molecular dynamics simulations were performed for inhibitor raltegravir and INRAT10b placed either at active site or allosteric site of HIV-1 IN (monomer or dimer)...
February 6, 2018: Biotechnology and Applied Biochemistry
https://www.readbyqxmd.com/read/29402222/large-scale-genomic-analysis-shows-association-between-homoplastic-genetic-variation-in-mycobacterium-tuberculosis-genes-and-meningeal-or-pulmonary-tuberculosis
#15
Carolien Ruesen, Lidya Chaidir, Arjan van Laarhoven, Sofiati Dian, Ahmad Rizal Ganiem, Hanna Nebenzahl-Guimaraes, Martijn A Huynen, Bachti Alisjahbana, Bas E Dutilh, Reinout van Crevel
BACKGROUND: Meningitis is the most severe manifestation of tuberculosis. It is largely unknown why some people develop pulmonary TB (PTB) and others TB meningitis (TBM); we examined if the genetic background of infecting M. tuberculosis strains may be relevant. METHODS: We whole-genome sequenced M. tuberculosis strains isolated from 322 HIV-negative tuberculosis patients from Indonesia and compared isolates from patients with TBM (n = 106) and PTB (n = 216)...
February 5, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29395996/cerebral-tryptophan-metabolism-and-outcome-of-tuberculous-meningitis-an-observational-cohort-study
#16
Arjan van Laarhoven, Sofiati Dian, Raúl Aguirre-Gamboa, Julian Avila-Pacheco, Isis Ricaño-Ponce, Carolien Ruesen, Jessi Annisa, Valerie A C M Koeken, Lidya Chaidir, Yang Li, Tri Hanggono Achmad, Leo A B Joosten, Richard A Notebaart, Rovina Ruslami, Mihai G Netea, Marcel M Verbeek, Bachti Alisjahbana, Vinod Kumar, Clary B Clish, A Rizal Ganiem, Reinout van Crevel
BACKGROUND: Immunopathology contributes to the high mortality of tuberculous meningitis, but the biological pathways involved are mostly unknown. We aimed to compare cerebrospinal fluid (CSF) and serum metabolomes of patients with tuberculous meningitis with that of controls without tuberculous meningitis, and assess the link between metabolite concentrations and mortality. METHODS: In this observational cohort study at the Hasan Sadikin Hospital (Bandung, Indonesia) we measured 425 metabolites using liquid chromatography-mass spectrometry in CSF and serum from 33 HIV-negative Indonesian patients with confirmed or probable tuberculous meningitis and 22 control participants with complete clinical data between March 12, 2009, and Oct 27, 2013...
January 23, 2018: Lancet Infectious Diseases
https://www.readbyqxmd.com/read/29389981/a-high-hiv-1-strain-variability-in-london-uk-revealed-by-full-genome-analysis-results-from-the-iconic-project
#17
Gonzalo Yebra, Dan Frampton, Tiziano Gallo Cassarino, Jade Raffle, Jonathan Hubb, R Bridget Ferns, Laura Waters, C Y William Tong, Zisis Kozlakidis, Andrew Hayward, Paul Kellam, Deenan Pillay, Duncan Clark, Eleni Nastouli, Andrew J Leigh Brown
BACKGROUND & METHODS: The ICONIC project has developed an automated high-throughput pipeline to generate HIV nearly full-length genomes (NFLG, i.e. from gag to nef) from next-generation sequencing (NGS) data. The pipeline was applied to 420 HIV samples collected at University College London Hospitals NHS Trust and Barts Health NHS Trust (London) and sequenced using an Illumina MiSeq at the Wellcome Trust Sanger Institute (Cambridge). Consensus genomes were generated and subtyped using COMET, and unique recombinants were studied with jpHMM and SimPlot...
2018: PloS One
https://www.readbyqxmd.com/read/29384862/plasma-soluble-factor-following-two-decades-prolonged-suppressive-antiretroviral-therapy-in-hiv-1-positive-males-a-cross-sectional-study
#18
Maike Sperk, Wang Zhang, Piotr Nowak, Ujjwal Neogi
Acute human immunodeficiency virus (HIV) infection is associated with a marked induction of several pathways that are linked to inflammation and CD4 T-cell depletion. Many of these processes do not fully resolve on short-term combination antiretroviral therapy (cART) (<5 years), despite complete and durable suppression of viremia. The effects of long-term (>15 years) successful antiretroviral therapy (ART) and the linkage between levels of biomarkers remain unclear. Therefore, the present study aims to assess the host plasma proteome in a well-defined clinical material from HIV-1-positive male patients on successful long-term ART (>15 years) and compared them with age-matched healthy controls and treatment-naïve male patients with viremia in a cross-sectional manner...
February 2018: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29378643/a-reproducibility-based-computational-framework-identifies-an-inducible-enhanced-antiviral-state-in-dendritic-cells-from-hiv-1-elite-controllers
#19
Enrique Martin-Gayo, Michael B Cole, Kellie E Kolb, Zhengyu Ouyang, Jacqueline Cronin, Samuel W Kazer, Jose Ordovas-Montanes, Mathias Lichterfeld, Bruce D Walker, Nir Yosef, Alex K Shalek, Xu G Yu
BACKGROUND: Human immunity relies on the coordinated responses of many cellular subsets and functional states. Inter-individual variations in cellular composition and communication could thus potentially alter host protection. Here, we explore this hypothesis by applying single-cell RNA-sequencing to examine viral responses among the dendritic cells (DCs) of three elite controllers (ECs) of HIV-1 infection. RESULTS: To overcome the potentially confounding effects of donor-to-donor variability, we present a generally applicable computational framework for identifying reproducible patterns in gene expression across donors who share a unifying classification...
January 29, 2018: Genome Biology
https://www.readbyqxmd.com/read/29377940/global-synonymous-mutagenesis-identifies-cis-acting-rna-elements-that-regulate-hiv-1-splicing-and-replication
#20
Matthew Takata, Steven J Soll, Ann Emery, Daniel Blanco-Melo, Ronald Swanstrom, Paul D Bieniasz
The ~9.5 kilobase HIV-1 genome contains RNA sequences and structures that control many aspects of viral replication, including transcription, splicing, nuclear export, translation, packaging and reverse transcription. Nonetheless, chemical probing and other approaches suggest that the HIV-1 genome may contain many more RNA secondary structures of unknown importance and function. To determine whether there are additional, undiscovered cis-acting RNA elements in the HIV-1 genome that are important for viral replication, we undertook a global silent mutagenesis experiment...
January 29, 2018: PLoS Pathogens
keyword
keyword
97764
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"