keyword
MENU ▼
Read by QxMD icon Read
search

HIV molecular evolution

keyword
https://www.readbyqxmd.com/read/28971485/evolution-of-the-serologic-and-virologic-course-of-occult-hbv-infection-in-therapy-experienced-hiv-co-infected-patients
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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...
August 23, 2017: Biochimie
https://www.readbyqxmd.com/read/28645318/detecting-consistent-patterns-of-directional-adaptation-using-differential-selection-codon-models
#8
Sahar Parto, Nicolas Lartillot
BACKGROUND: Phylogenetic codon models are often used to characterize the selective regimes acting on protein-coding sequences. Recent methodological developments have led to models explicitly accounting for the interplay between mutation and selection, by modeling the amino acid fitness landscape along the sequence. However, thus far, most of these models have assumed that the fitness landscape is constant over time. Fluctuations of the fitness landscape may often be random or depend on complex and unknown factors...
June 23, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28586237/a-unique-second-generation-recombinant-form-of-hiv-1-identified-among-men-who-have-sex-with-men-population-in-beijing-china
#9
Xue Li, Mingqiang Hao, Yinxiao Hao, Jingrong Ye, Ruolei Xin, Hongyan Lu
In China, CRF01_AE and CRF07_BC are the most circulating strains of HIV-1, more and more second-generation recombinant forms have been isolated around the two strains. The same situation happened in Beijing in recent years. In our study, we have isolated a new second-generation recombinant form of HIV-1 from a male patient who was infected by homosexual behavior. Polygenetic analysis revealed that the sequence includes five CRF01_AE fragments and four CRF07_BC fragments. CRF01_AE is the skeleton of the recombinant which was inserted with four CRF07_BC fragments...
October 2017: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/28542584/the-emergence-and-evolution-of-the-research-fronts-in-hiv-aids-research
#10
David Fajardo-Ortiz, Malaquias Lopez-Cervantes, Luis Duran, Michel Dumontier, Miguel Lara, Hector Ochoa, Victor M Castano
In this paper, we have identified and analyzed the emergence, structure and dynamics of the paradigmatic research fronts that established the fundamentals of the biomedical knowledge on HIV/AIDS. A search of papers with the identifiers "HIV/AIDS", "Human Immunodeficiency Virus", "HIV-1" and "Acquired Immunodeficiency Syndrome" in the Web of Science (Thomson Reuters), was carried out. A citation network of those papers was constructed. Then, a sub-network of the papers with the highest number of inter-citations (with a minimal in-degree of 28) was selected to perform a combination of network clustering and text mining to identify the paradigmatic research fronts and analyze their dynamics...
2017: PloS One
https://www.readbyqxmd.com/read/28497113/toward-a-cure-does-host-immunity-play-a-role
#11
Jielin Zhang, Clyde S Crumpacker
Three decades of research on human immunodeficiency virus (HIV) and AIDS reveal that the human body has developed through evolution a genome immune system embodying epigenetic regulation against pathogenic nucleic acid invasion. In HIV infection, this epigenetic regulation plays a cardinal role in HIV RNA production that silences HIV transcription at a molecular (RNA) level, controls viral load at a cellular (biological) level, and governs the viremic stage of AIDS at the clinical (patient) level. Even though the human genome is largely similar among humans and HIV is a single viral species, human hosts show significant differences in viral RNA levels, ranging from cell to organ to individual and expressed as elite controllers, posttreatment controllers, and patients with AIDS...
March 2017: MSphere
https://www.readbyqxmd.com/read/28484443/impact-of-genetic-variations-in-hiv-1-tat-on-ltr-mediated-transcription-via-tar-rna-interaction
#12
Larance Ronsard, Nilanjana Ganguli, Vivek K Singh, Kumaravel Mohankumar, Tripti Rai, Subhashree Sridharan, Sankar Pajaniradje, Binod Kumar, Devesh Rai, Suhnrita Chaudhuri, Mohane S Coumar, Vishnampettai G Ramachandran, Akhil C Banerjea
HIV-1 evades host defense through mutations and recombination events, generating numerous variants in an infected patient. These variants with an undiminished virulence can multiply rapidly in order to progress to AIDS. One of the targets to intervene in HIV-1 replication is the trans-activator of transcription (Tat), a major regulatory protein that transactivates the long terminal repeat promoter through its interaction with trans-activation response (TAR) RNA. In this study, HIV-1 infected patients (n = 120) from North India revealed Ser46Phe (20%) and Ser61Arg (2%) mutations in the Tat variants with a strong interaction toward TAR leading to enhanced transactivation activities...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28466391/mechanisms-of-hiv-1-control
#13
REVIEW
Mary Soliman, Geetha Srikrishna, Ashwin Balagopal
PURPOSE OF REVIEW: HIV-1 infection is of global importance, and still incurs substantial morbidity and mortality. Although major pharmacologic advances over the past two decades have resulted in remarkable HIV-1 control, a cure is still forthcoming. One approach to a cure is to exploit natural mechanisms by which the host restricts HIV-1. Herein, we review past and recent discoveries of HIV-1 restriction factors, a diverse set of host proteins that limit HIV-1 replication at multiple levels, including entry, reverse transcription, integration, translation of viral proteins, and packaging and release of virions...
June 2017: Current HIV/AIDS Reports
https://www.readbyqxmd.com/read/28454556/molecular-and-epidemiological-characterization-of-hiv-1-subtypes-among-libyan-patients
#14
Mohamed A Daw, Abdallah El-Bouzedi, Mohamed O Ahmed, Aghnyia A Dau
BACKGROUND: The epidemiological and clinical aspects of human immunodeficiency virus subtypes are of great interest worldwide. These subtypes are rarely studied in North African countries. Libya is a large country with the longest coast on the Mediterranean Sea, facing the Southern European countries. Studies on the characterization of HIV-1 subtypes are limited in Libya. This study aimed to determine the magnitude of the HIV problem among the Libyan population and to better understand the genetic diversity and the epidemiologic dynamics of HIV 1, as well as to correlate that with the risk factors involved...
April 28, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28401776/molecular-characteristics-of-the-envelope-of-vertically-transmitted-hiv-1-strains-from-infants-with-hiv-infection
#15
Manickam Ashokkumar, Manohar Nesakumar, Narayaniah Cheedarla, K K Vidyavijayan, Hemalatha Babu, Srikanth P Tripathy, Luke Elizabeth Hanna
Mother-to-child transmission (MTCT) of HIV offers a good opportunity to study the dynamics of early viral evolution in the host environment to which the virus has partially adapted. Such studies would throw light on the unique features of the infecting viruses, which will subsequently help to design preventive or therapeutic measures against the newly infecting and evolving strains of HIV. Therefore, we undertook a study to determine the genetic divergence of proviral envelope sequences from the HIV-infected infants (<2 years)...
August 2017: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/28373274/the-variable-internal-structure-of-the-mycoplasma-penetrans-attachment-organelle-revealed-by-biochemical-and-microscopic-analyses-implications-for-attachment-organelle-mechanism-and-evolution
#16
Steven L Distelhorst, Dominika A Jurkovic, Jian Shi, Grant J Jensen, Mitchell F Balish
Although mycoplasmas have small genomes, many of them, including the HIV-associated opportunist Mycoplasma penetrans, construct a polar attachment organelle (AO) that is used for both adherence to host cells and gliding motility. However, the irregular phylogenetic distribution of similar structures within the mycoplasmas, as well as compositional and ultrastructural differences among these AOs, suggests that AOs have arisen several times through convergent evolution. We investigated the ultrastructure and protein composition of the cytoskeleton-like material of the M...
June 15, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28348854/bayesian-codon-substitution-modelling-to-identify-sources-of-pathogen-evolutionary-rate-variation
#17
Guy Baele, Marc A Suchard, Filip Bielejec, Philippe Lemey
Phylodynamic reconstructions rely on a measurable molecular footprint of epidemic processes in pathogen genomes. Identifying the factors that govern the tempo and mode by which these processes leave a footprint in pathogen genomes represents an important goal towards understanding infectious disease evolution. Discriminating between synonymous and non-synonymous substitution rates is crucial for testing hypotheses about the sources of evolutionary rate variation. Here, we implement a codon substitution model in a Bayesian statistical framework to estimate absolute rates of synonymous and non-synonymous substitution in unknown evolutionary histories...
June 2016: Microbial Genomics
https://www.readbyqxmd.com/read/28332348/molecular-epidemiology-of-human-immunodeficiency-virus
#18
REVIEW
Bum Sik Chin
During the evolution of human immunodeficiency virus (HIV), transmissions between humans and primates resulted in multiple HIV lineages in humans. This evolution has been rapid, giving rise to a complex classification and allowing for worldwide spread and intermixing of subtypes, which has consequently led to dozens of circulating recombinant forms. In the Republic of Korea, 12,522 cases of HIV infection have been reported between 1985, when AIDS was first identified, and 2015. This review focuses on the evolution of HIV infection worldwide and the molecular epidemiologic characteristics of HIV in Korea...
March 2017: Infection & Chemotherapy
https://www.readbyqxmd.com/read/28187688/identification-of-a-novel-hiv-type-1-recombinant-form-crf01_ae-crf07_bc-in-men-who-have-sex-with-men-in-zhejiang-china
#19
Yufan Xu, Xiaorong Peng, Tiansheng Xie, Xiangyun Lu, Nanping Wu
The prevalence of HIV-1 is increasing rapidly among the population of men who have sex with men (MSM) in China. Here, we report a novel HIV type 1 recombinant form consisting of CRF01_AE and CRF07_BC detected in a male patient through homosexual behavior. A phylogenic analysis revealed that this unique recombinant form (URF) exhibits a complex genomic structure with three CRF07_BC regions inserted into the CRF01_AE backbone. Recently, several second-generation recombinant forms (e.g., CRF01_AE/CRF07_BC) have been identified among MSM in China...
April 12, 2017: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/28086923/multiple-hiv-1-m%C3%A2-%C3%A2-hiv-1-o-dual-infections-and-new-hiv-1-mo-inter-group-recombinant-forms-detected-in-cameroon
#20
Fabienne De Oliveira, Thomas Mourez, Aurélia Vessiere, Paul-Alain Ngoupo, Elodie Alessandri-Gradt, François Simon, Dominique Rousset, Jean-Christophe Plantier
BACKGROUND: Due to the prevalence of HIV-1 group M and the endemicity of HIV-1 group O infections in Cameroon, patients may be infected with both viruses and/or with HIV-1/MO recombinant forms. Such atypical infections may be deleterious in terms of diagnosis and therapeutic management due to the high divergence of HIV-1/O. The aim of this study was to identify prospectively such atypical infections in Cameroon. RESULTS: Based on serological screening by env-V3 serotyping and a molecular strategy using group-specific (RT)-PCRs, we identified 10 Cameroonian patients harboring three different profiles of infection: (1) 4 HIV-1/M + O dual infections without evidence of recombinant; (2) 5 recombinants associated with one or both parental strains; and (3) 1 new recombinant form without parental strains...
January 13, 2017: Retrovirology
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"