keyword
MENU ▼
Read by QxMD icon Read
search

HIV molecular evolution

keyword
https://www.readbyqxmd.com/read/29442996/role-of-framework-mutations-and-antibody-flexibility-in-the-evolution-of-broadly-neutralizing-antibodies
#1
Victor Ovchinnikov, Joy E Louveau, John P Barton, Martin Karplus, Arup K Chakraborty
Eliciting antibodies that are cross reactive with surface proteins of diverse strains of highly mutable pathogens (e.g., HIV, influenza) could be key for developing effective universal vaccines. Mutations in the framework regions of such broadly neutralizing antibodies (bnAbs) have been reported to play a role in determining their properties. We used molecular dynamics simulations and models of affinity maturation to study specific bnAbs against HIV. Our results suggest specific classes of evolutionary lineages: if germline B cells that initiate affinity maturation have high affinity for the conserved residues of the targeted epitope, framework mutations increase antibody rigidity as affinity maturation progresses to evolve bnAbs...
February 14, 2018: ELife
https://www.readbyqxmd.com/read/29431588/aptamers-in-hiv-research-diagnosis-and-therapy
#2
Jyoti Bala, Srinivasan Chinnapaiyan, Rajib Kumar Dutta, Hoshang Unwalla
Aptamers are high affinity single-stranded nucleic acid or protein ligands which exhibit specificity and avidity comparable to, or exceeding that of antibodies and can be generated against most targets. The functionality of aptamers is based on their unique tertiary structure, complexity and their ability to attain unique binding pockets by folding. Aptamers are selected in vitro by a process called Systematic Evolution of Ligands by Exponential enrichment (SELEX). The Kd values for the selected aptamer are often in the picomolar to low nanomolar range...
February 12, 2018: RNA Biology
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
#3
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/29403002/effect-of-hiv-hcv-co-infection-on-the-protease-evolution-of-hiv-1b-a-pilot-study-in-a-pediatric-population
#4
Sara Domínguez-Rodríguez, Patricia Rojas, Carolina Fernández McPhee, Israel Pagán, María Luisa Navarro, José Tomás Ramos, África Holguín
This pilot study evaluates in pediatric patients the impact of HIV/HCV coinfection in the molecular evolution of the HIV-1 subtype B protease (HIV-1BPR). For this study, HIV-1B/HCV coinfected (15) and HIV-1B monoinfected (56) patients with available HIV-1B pol sequences were enrolled. Both groups of patients had comparable gender frequencies and average age, time of infection, antiretroviral treatment (ART) exposure and time under ART. Prevalence of drug resistance mutations (DRM), genetic diversity, number of synonymous (dS) and non-synonymous (dN) mutations per site and selection pressures (dN - dS) in the HIV-1BPR were estimated and compared between mono- and coinfected patients...
February 5, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29346413/genetic-diversity-and-potential-routes-of-transmission-of-mycobacterium-bovis-in-mozambique
#5
Adelina Machado, Teresa Rito, Solomon Ghebremichael, Nuelma Muhate, Gabriel Maxhuza, Custodia Macuamule, Ivania Moiane, Baltazar Macucule, Angelica Suzana Marranangumbe, Jorge Baptista, Joaquim Manguele, Tuija Koivula, Elizabeth Maria Streicher, Robin Mark Warren, Gunilla Kallenius, Paul van Helden, Margarida Correia-Neves
Bovine tuberculosis is a zoonotic disease with largely unknown impact in Africa, with risk factors such as HIV and direct contact with animals or consumption of Mycobacterium bovis infected animal products. In order to understand and quantify this risk and design intervention strategies, good epidemiological studies are needed. Such studies can include molecular typing of M. bovis isolates. The aim of this study was to apply these tools to provide novel information concerning the distribution of bovine tuberculosis in cattle in Mozambique and thereby provide relevant information to guide policy development and strategies to contain the disease in livestock, and reduce the risk associated with transmission to humans...
January 2018: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29328787/immune-responses-to-retroviruses
#6
Asier Saez-Cirion, Nicolas Manel
Retroviruses are genome invaders that have shared a long history of coevolution with vertebrates and their immune system. Found endogenously in genomes as traces of past invasions, retroviruses are also considerable threats to human health when they exist as exogenous viruses such as HIV. The immune response to retroviruses is engaged by germline-encoded sensors of innate immunity that recognize viral components and damage induced by the infection. This response develops with the induction of antiviral effectors and launching of the clonal adaptive immune response, which can contribute to protective immunity...
January 12, 2018: Annual Review of Immunology
https://www.readbyqxmd.com/read/29244833/genomic-characterization-and-molecular-evolution-analysis-of-subtype-b-and-bf-recombinant-hiv-1-strains-among-argentinean-men-who-have-sex-with-men-reveal-a-complex-scenario
#7
Cintia G Cevallos, Leandro R Jones, Maria A Pando, Jean K Carr, Maria M Avila, Jorge Quarleri
Currently, data on HIV-1 circulating strains among men who have sex with men (MSM) in Argentina is scarce. In South America, the distribution and the prevalence of BF recombinants are dissimilar and exhibit an underappreciated heterogeneity of recombinant structures. Here, we studied for the first time the genetic diversity of HIV-1 BF recombinants and their evolution over time through in-depth phylogenetic analysis and multiple recombination detection methods involving 337 HIV-1 nucleotide sequences (25 near full-length (NFL) and 312 partial pol gene) obtained from Argentinean MSM...
2017: PloS One
https://www.readbyqxmd.com/read/29228218/nonhuman-primate-models-and-understanding-the-pathogenesis-of-hiv-infection-and-aids
#8
Ronald S Veazey, Andrew A Lackner
Research using nonhuman primates (NHPs) as models for human immunodeficiency virus (HIV) infection and acquired immunodeficiency syndrome (AIDS) has resulted in tremendous achievements not only in the prevention and treatment of HIV, but also in biomedical research more broadly. Once considered a death sentence, HIV infection is now fairly well controlled with combination antiretroviral treatments, almost all of which were first tested for efficacy and safety in nonhuman primates or other laboratory animals...
December 8, 2017: ILAR Journal
https://www.readbyqxmd.com/read/29202081/phylodynamic-applications-in-21st-century-global-infectious-disease-research
#9
Brittany D Rife, Carla Mavian, Xinguang Chen, Massimo Ciccozzi, Marco Salemi, Jae Min, Mattia Cf Prosperi
Background: Phylodynamics, the study of the interaction between epidemiological and pathogen evolutionary processes within and among populations, was originally defined in the context of rapidly evolving viruses and used to characterize transmission dynamics. The concept of phylodynamics has evolved since the early 21st century, extending its reach to slower-evolving pathogens, including bacteria and fungi, and to the identification of influential factors in disease spread and pathogen population dynamics...
2017: Global Health Research and Policy
https://www.readbyqxmd.com/read/29163435/evolutionary-analysis-of-hiv-1-pol-proteins-reveals-representative-residues-for-viral-subtype-differentiation
#10
Shohei Nagata, Junnosuke Imai, Gakuto Makino, Masaru Tomita, Akio Kanai
RNA viruses have been used as model systems to understand the patterns and processes of molecular evolution because they have high mutation rates and are genetically diverse. Human immunodeficiency virus 1 (HIV-1), the etiological agent of acquired immune deficiency syndrome, is highly genetically diverse, and is classified into several groups and subtypes. However, it has been difficult to use its diverse sequences to establish the overall phylogenetic relationships of different strains or the trends in sequence conservation with the construction of phylogenetic trees...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29142136/size-composition-and-evolution-of-hiv-dna-populations-during-early-antiretroviral-therapy-and-intensification-with-maraviroc
#11
Antoine Chaillon, Sara Gianella, Steven M Lada, Josué Perez-Santiago, Parris Jordan, Caroline Ignacio, Maile Karris, Douglas Richman, Sanjay R Mehta, Susan J Little, Joel O Wertheim, Davey M Smith
Residual viremia is common during antiretroviral therapy (ART), and could be caused by ongoing low-level virus replication or by release of viral particles from infected cells. ART Intensification should impact ongoing viral propagation but not virion release. Eighteen acutely infected men were enrolled in a randomized controlled trial, and followed for a median of 107 weeks. Participants started ART with (n=9) or without (n=9) intensification with maraviroc (MVC) within 90 days of infection. Levels of HIV DNA and cell-free RNA were quantified by droplet digital PCR...
November 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29137637/molecular-evolution-of-hiv-1-integrase-during-the-20%C3%A2-years-prior-to-the-first-approval-of-integrase-inhibitors
#12
Karolin Meixenberger, Kaveh Pouran Yousef, Maureen Rebecca Smith, Sybille Somogyi, Stefan Fiedler, Barbara Bartmeyer, Osamah Hamouda, Norbert Bannert, Max von Kleist, Claudia Kücherer
BACKGROUND: Detailed knowledge of the evolutionary potential of polymorphic sites in a viral protein is important for understanding the development of drug resistance in the presence of an inhibitor. We therefore set out to analyse the molecular evolution of the HIV-1 subtype B integrase at the inter-patient level in Germany during a 20-year period prior to the first introduction of integrase strand inhibitors (INSTIs). METHODS: We determined 337 HIV-1 integrase subtype B sequences (amino acids 1-278) from stored plasma samples of antiretroviral treatment-naïve individuals newly diagnosed with HIV-1 between 1986 and 2006...
November 14, 2017: Virology Journal
https://www.readbyqxmd.com/read/29054871/engineering-the-enantioselectivity-and-thermostability-of-a-%C3%AE-lactamase-from-microbacterium-hydrocarbonoxydans-for-the-kinetic-resolution-of-vince-lactam
#13
Shuaihua Gao, Shaozhou Zhu, Rong Huang, Hongxia Li, Hao Wang, Guojun Zheng
To produce promising biocatalysts, natural enzymes often need to be engineered to increase their catalytic performance. In this study, the enantioselectivity and thermostability of a (+)-γ-lactamase from Microbacterium hydrocarbonoxydans as the catalyst in the kinetic resolution of Vince lactam were improved. Enantiomerically pure (-)-Vince lactam is the key synthon in the synthesis of antiviral drugs such as carbovir and abacavir, which are used to fight against human HIV and hepatitis B viruses. The work was initialized by using the combinatorial active-site saturation test strategy to engineer the enantioselectivity of the enzyme...
October 20, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28971485/evolution-of-the-serologic-and-virologic-course-of-occult-hbv-infection-in-therapy-experienced-hiv-co-infected-patients
#14
Edina Amponsah-Dacosta, Selokela G Selabe, M Jeffrey Mphahlele
BACKGROUND: We investigated how the natural course of occult hepatitis B virus (HBV) infection (OBI) may evolve during HIV co-infection and long term HBV-active HAART. METHODS: From a cohort of 181 HIV infected patients who were consecutively recruited over a 5 year period, 28 HBV co-infected patients with sequential sera (n = 98) were identified. Iterative HBV serology and viral loads were determined before and during treatment. The viral HBsAg gene was then serially amplified, directly sequenced and molecularly characterized...
October 2, 2017: Journal of Medical Virology
https://www.readbyqxmd.com/read/28966263/creation-of-functional-molecules-based-on-biomolecular-interactions-development-toward-chemical-biology
#15
Wataru Nomura
Interactions between bio-macromolecules such as proteins, DNA, and polysaccharides play pivotal roles in maintaining homeostasis in living systems. For elucidating the function of biomolecules, peptides are powerful tools, compared to native proteins, because of their lower molecular weights, compatibility with chemical modification, and predictability of interaction with the target molecules. These advantages enabled us to develop peptide-based functional molecules. However, for the purposes of controlling or regulating biomolecule functions, designing artificial proteins is also an effective approach...
2017: Yakugaku Zasshi: Journal of the Pharmaceutical Society of Japan
https://www.readbyqxmd.com/read/28918303/decoding-noises-in-hiv-computational-genotyping
#16
MingRui Jia, Timothy Shaw, Xing Zhang, Dong Liu, Ye Shen, Amara E Ezeamama, Chunfu Yang, Ming Zhang
Lack of a consistent and reliable genotyping system can critically impede HIV genomic research on pathogenesis, fitness, virulence, drug resistance, and genomic-based healthcare and treatment. At present, mis-genotyping, i.e., background noises in molecular genotyping, and its impact on epidemic surveillance is unknown. For the first time, we present a comprehensive assessment of HIV genotyping quality. HIV sequence data were retrieved from worldwide published records, and subjected to a systematic genotyping assessment pipeline...
November 2017: Virology
https://www.readbyqxmd.com/read/28912478/the-molecular-epidemiology-of-hiv-1-in-the-comunidad-valenciana-spain-analysis-of-transmission-clusters
#17
Juan Ángel Patiño-Galindo, Manoli Torres-Puente, María Alma Bracho, Ignacio Alastrué, Amparo Juan, David Navarro, María José Galindo, Dolores Ocete, Enrique Ortega, Concepción Gimeno, Josefina Belda, Victoria Domínguez, Rosario Moreno, Fernando González-Candelas
HIV infections are still a very serious concern for public heath worldwide. We have applied molecular evolution methods to study the HIV-1 epidemics in the Comunidad Valenciana (CV, Spain) from a public health surveillance perspective. For this, we analysed 1804 HIV-1 sequences comprising protease and reverse transcriptase (PR/RT) coding regions, sampled between 2004 and 2014. These sequences were subtyped and subjected to phylogenetic analyses in order to detect transmission clusters. In addition, univariate and multinomial comparisons were performed to detect epidemiological differences between HIV-1 subtypes, and risk groups...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28852479/collapsing-glomerulopathy-a-30-year-perspective-and-single-large-center-experience
#18
L Nicholas Cossey, Christopher P Larsen, Helen Liapis
Collapsing glomerulopathy (CGP) is a pattern of kidney injury seen on renal biopsy with multiple associations and etiologies. It is most commonly described in African-Americans and others with recent African ancestry. The disease is rapidly progressive and often presents with abrupt onset of renal failure and nephrotic-range proteinuria. Since its description 30 years ago, this entity has transformed from a morphologic diagnosis typically seen in the setting of HIV infection to a complicated diagnosis with numerous etiologies, many of which are associated with underlying apolipoprotein L1 (APOL1)-risk variants or other genetic disorders...
August 2017: Clinical Kidney Journal
https://www.readbyqxmd.com/read/28844146/a-novel-recombinant-form-of-hiv-1-crf01_ae-crf07_bc-identified-by-near-full-length-genome-in-shaanxi-china
#19
Mengyan Zhang, Ruolei Xin, Wenhui Chang
Recently multiple kinds of unique recombinant forms (URFs) of HIV-1 CRF01_AE/CRF07_BC were identified in China. In this study, we report another near full-length genome of a novel recombinant form (SN121) between CRF01_AE and CRF07_BC from an HIV-1 infected male through heterosexual behavior in Shaanxi province, China. The analysis of SN121 showed that the genome composed of 7 interlaced segments, including 3 CRF07_BC and 4 CRF01_AE segments with CRF01_AE as the backbone. Six breakpoints were observed in the pol and env gene regions, which are different from the previously identified CRF01_AE/07_BC recombinant forms in China...
August 26, 2017: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/28843613/evolution-of-inhibitor-resistant-natural-mutant-forms-of-hiv-1-protease-probed-by-pre-steady-state-kinetic-analysis
#20
Maria Yu Zakharova, Alexandra A Kuznetsova, Elena N Kaliberda, Maria A Dronina, Alexander V Kolesnikov, Arina V Kozyr, Ivan V Smirnov, Lev D Rumsh, Olga S Fedorova, Dmitry G Knorre, Alexander G Gabibov, Nikita A Kuznetsov
Pre-steady state kinetic analysis of mechanistic features of substrate binding and processing is crucial for insight into the evolution of inhibitor-resistant forms of HIV-1 protease. These data may provide a correct vector for rational drug design assuming possible intrinsic dynamic effects. These data should also give some clues to the molecular mechanism of protease action and resistance to inhibitors. Here we report pre-steady state kinetics of the interaction of wild type or mutant forms of HIV-1 protease with a FRET-labeled peptide...
November 2017: Biochimie
keyword
keyword
98354
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"