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https://www.readbyqxmd.com/read/28934476/crystal-structure-of-an-engineered-hiv-specific-recombinase-for-removal-of-integrated-proviral-dna
#1
Gretchen Meinke, Janet Karpinski, Frank Buchholz, Andrew Bohm
As part of the HIV infection cycle, viral DNA inserts into the genome of host cells such that the integrated DNA encoding the viral proteins is flanked by long terminal repeat (LTR) regions from the retrovirus. In an effort to develop novel genome editing techniques that safely excise HIV provirus from cells, Tre, an engineered version of Cre recombinase, was designed to target a 34-bp sequence within the HIV-1 LTR (loxLTR). The sequence targeted by Tre lacks the symmetry present in loxP, the natural DNA substrate for Cre...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28931690/conformational-changes-in-the-5-end-of-the-hiv-1-genome-dependent-on-the-debranching-enzyme-dbr1-during-early-stages-of-infection
#2
Alvaro E Galvis, Hugh E Fisher, Hung Fan, David Camerini
Previous studies in our laboratory showed that the RNA debranching enzyme (DBR1) is not required for early steps in HIV cDNA formation, but is necessary for synthesis of intermediate and late cDNA products. To further characterize this effect, we evaluated the topology of the 5' end of the HIV-1 RNA genome during early infection with and without inhibition of DBR1 synthesis. Cells were transfected with DBR1 shRNA followed 48 hours later by infection with an HIV-1 derived vector containing an RNase H deficient reverse transcriptase...
September 20, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28923862/antiviral-activity-of-bictegravir-and-cabotegravir-against-integrase-inhibitor-resistant-sivmac239-and-hiv-1
#3
Said A Hassounah, Ahmad Alikhani, Maureen Oliveira, Simrat Bharaj, Ruxandra-Ilinca Ibanescu, Nathan Osman, Hong-Tao Xu, Bluma G Brenner, Thibault Mesplède, Mark A Wainberg
Animal models are essential to study novel antiretroviral drugs, resistance-associated mutations (RAMs), and treatment strategies. Bictegravir (BIC) is a novel potent integrase (IN) strand transfer inhibitor (INSTI) that has shown promising results against HIV-1 infection in vitro and in vivo and against clinical isolates with resistance against INSTIs. BIC has a higher genetic barrier to the development of resistance than two clinically approved INSTIs termed raltegravir and elvitegravir. Another clinically approved INSTI, dolutegravir (DTG) also possesses a high genetic barrier to resistance while a fourth compound termed cabotegravir (CAB) is currently in late phases of clinical development...
September 18, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28920929/structural-investigation-of-nucleophosmin-interaction-with-the-tumor-suppressor-fbw7%C3%AE
#4
A Di Matteo, M Franceschini, A Paiardini, A Grottesi, S Chiarella, S Rocchio, C Di Natale, D Marasco, L Vitagliano, C Travaglini-Allocatelli, L Federici
Nucleophosmin (NPM1) is a multifunctional nucleolar protein implicated in ribogenesis, centrosome duplication, cell cycle control, regulation of DNA repair and apoptotic response to stress stimuli. The majority of these functions are played through the interactions with a variety of protein partners. NPM1 is frequently overexpressed in solid tumors of different histological origin. Furthermore NPM1 is the most frequently mutated protein in acute myeloid leukemia (AML) patients. Mutations map to the C-terminal domain and lead to the aberrant and stable localization of the protein in the cytoplasm of leukemic blasts...
September 18, 2017: Oncogenesis
https://www.readbyqxmd.com/read/28918073/a-directed-evolution-approach-to-select-for-novel-adeno-associated-virus-capsids-on-an-hiv-1-producer-t-cell-line
#5
Dawn P Wooley, Priyanka Sharma, John R Weinstein, Poornima Kotha Lakshmi Narayan, David V Schaffer, Katherine J D A Excoffon
A directed evolution approach was used to select for Adeno-associated virus (AAV) capsids that would exhibit more tropism toward an HIV-1 producer T cell line with the long-term goal of developing improved gene transfer vectors. A library of AAV variants was used to infect H9T cells previously infected or uninfected by HIV-1 followed by AAV amplification with wild-type adenovirus. Six rounds of biological selection were performed, including negative selection and diversification after round three. The H9T cells were successfully infected with all three wild-type viruses (AAV, adenovirus, and HIV-1)...
September 13, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28903577/a-2-4-amino-acid-deletion-in-the-v5-region-of-hiv-1-env-gp120-confers-viral-resistance-to-the-broadly-neutralizing-human-monoclonal-antibody-vrc01
#6
Shingo Tachibana, Maho Sasaki, Takako Tanaka, Mari Inoue, Youdiil Ophinni, Tomohiro Kotaki, Masanori Kameoka
The envelope glycoprotein (Env) gp120 of human immunodeficiency virus type 1 (HIV-1) plays a critical role in viral entry into host cells. The broadly neutralizing human monoclonal antibody VRC01, which recognizes the CD4 binding site on gp120, neutralizes more than 90% of HIV-1 isolates. However, some of the CRF01_AE viruses prevalent in Southeast Asia are resistant to VRC01-mediated neutralization. We previously reported that 3 amino acid residues at positions 185, 186, and 197 of gp120 played an important role in the VRC01 resistance of CRF01_AE Env (AE-Env) clones isolated from HIV-infected Thai individuals...
September 13, 2017: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/28900421/efficacy-analysis-of-combinatorial-sirnas-against-hiv-derived-from-one-double-hairpin-rna-precursor
#7
Chang Liu, Zhipin Liang, Xiaohong Kong
Combinatorial small interfering RNA duplexes (siRNAs) have the potential to be a gene therapy against HIV-1, and some studies have reported that transient combinatorial siRNA expression represses HIV replication, but the effects of long-term siRNA expression on HIV replication have not been studied in detail. In this study, HIV-1 replication under the influence of stable combinatorial siRNA expression from a single RNA transcript was analyzed. First, a series of cassettes encoding short hairpin RNA (shRNA)/long hairpin RNA (lhRNA)/double long hairpins (dlhRNA) was constructed and subjected to an analysis of inhibitory efficacy...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28899424/clade-homogeneity-and-low-rate-of-delta-virus-despite-hyperendemicity-of-hepatitis-b-virus-in-ethiopia
#8
Yeshambel Belyhun, Uwe Gerd Liebert, Melanie Maier
BACKGROUND: Although hepatitis B virus (HBV) is hyperendemic and heterogeneous in its genetic diversity in Ethiopia, little is known about hepatitis D virus (HDV) circulating genotypes and molecular diversity. METHODS: A total of 321 hepatitis B surface antigen (HBsAg) positives (125 HIV co-infected, 102 liver disease patients and 94 blood donors) were screened for anti-HDV antibody. The anti-HDV positive sera were subjected to Real time PCR for HDV-RNA confirmation...
September 12, 2017: Virology Journal
https://www.readbyqxmd.com/read/28879707/analysis-of-hepatitis-c-virus-ns5a-region-in-patients-with-cirrhosis-using-an-ultra-deep-pyrosequencing-method
#9
Fahriye Keskin, Sevgi Ciftci, Filiz Akyuz, Neslihan Abaci, Aris Cakiris, Umit Akyuz, Kadir Demir, Fatih Besisik, Duran Ustek, Sabahattin Kaymakoglu
BACKGROUND: HCV (Hepatitis C Virus) is genetically more diverse than HBV and HIV (Human Immunodeficiency Virus) and exists as quasispecies within infected individuals. This is due to the lack of efficient proofreading of the viral RNA-dependent RNA polymerase. Consequently, quasispecies emerge depending on the mutation rate of the viral polymerase, which may display a high level of genetic variability in a population. In infected individuals, HCV replicates and circulates as quasispecies composed of a complex mixture of different but closely related genomes that undergoes continuous change due to competitive selection and cooperation between arising mutants...
September 1, 2017: Clinical Laboratory
https://www.readbyqxmd.com/read/28878074/cooperation-of-the-ebola-proteins-vp40-and-gp1-2-with-bst2-to-activate-nf-%C3%AE%C2%BA%C3%AE-independently-of-virus-like-particle-trapping
#10
Maryan G Rizk, Christopher F Basler, John Guatelli
BST2 is a host protein with dual functions in response to viral infections: it traps newly assembled enveloped virions at the plasma membrane of infected cells, and it induces NF-κβ activity, especially in the context of retroviral assembly. In this study, we examined whether Ebola virus proteins affect BST2-mediated induction of NF-κβ. We found that the Ebola matrix protein, VP40, and envelope glycoprotein, GP, each cooperate with BST2 to induce NF-κβ activity, with maximal activity when all three proteins are expressed...
September 6, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28878072/high-throughput-protein-engineering-improves-the-antigenicity-and-stability-of-soluble-hiv-1-envelope-glycoprotein-sosip-trimers
#11
Jonathan T Sullivan, Chidananda Sulli, Alberto Nilo, Anila Yasmeen, Gabriel Ozorowski, Rogier W Sanders, Andrew B Ward, P J Klasse, John P Moore, Benjamin J Doranz
Soluble envelope glycoprotein (Env) trimers (SOSIP.664 gp140) are attractive HIV-1 vaccine candidates, with structures that mimic the native membrane-bound Env spike (gp160). Since engineering trimers can be limited by the difficulty of rationally predicting beneficial mutations, here we used a more comprehensive mutagenesis approach with the goal of identifying trimer variants with improved antigenic and stability properties. We created 341 cysteine pairs at predicted points of stabilization throughout gp140, 149 proline residue substitutions at every residue of the gp41 ectodomain, and 362 space-filling residue substitutions at every hydrophobic and aromatic residue in gp140...
September 6, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28877726/the-effect-of-bovine-bst2a1-on-the-release-and-cell-to-cell-transmission-of-retroviruses
#12
Zhibin Liang, Yang Zhang, Jie Song, Hui Zhang, Suzhen Zhang, Yue Li, Juan Tan, Wentao Qiao
BACKGROUND: Human BST2 (hBST2, also called Tetherin) is a host restriction factor that blocks the release of various enveloped viruses. BST2s from different mammals also possess antiviral activity. Bovine BST2s (bBST2s), bBST2A1 and bBST2A2, reduce production of cell-free bovine leukemia virus (BLV) and vesicular stomatitis virus (VSV). However, the effect of bBST2 on other retroviruses remains unstudied. RESULTS: Here, we studied the antiviral activity of wildtype and mutant bBST2A1 proteins on retroviruses including human immunodeficiency virus type 1 (HIV-1), prototypic foamy virus (PFV), bovine foamy virus (BFV) and bovine immunodeficiency virus (BIV)...
September 6, 2017: Virology Journal
https://www.readbyqxmd.com/read/28871089/cd81-association-with-samhd1-enhances-hiv-1-reverse-transcription-by-increasing-dntp-levels
#13
Vera Rocha-Perugini, Henar Suárez, Susana Álvarez, Soraya López-Martín, Gina M Lenzi, Felipe Vences-Catalán, Shoshana Levy, Baek Kim, María A Muñoz-Fernández, Francisco Sánchez-Madrid, Maria Yáñez-Mó
In this study, we report that the tetraspanin CD81 enhances human immunodeficiency virus (HIV)-1 reverse transcription in HIV-1-infected cells. This is enabled by the direct interaction of CD81 with the deoxynucleoside triphosphate phosphohydrolase SAMHD1. This interaction prevents endosomal accumulation and favours the proteasome-dependent degradation of SAMHD1. Consequently, CD81 depletion results in SAMHD1 increased expression, decreasing the availability of deoxynucleoside triphosphates (dNTP) and thus HIV-1 reverse transcription...
September 4, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28870251/hiv-1-tolerates-changes-in-a-count-in-a-small-segment-of-the-pol-gene
#14
Bep Klaver, Yme van der Velden, Formijn van Hemert, Antoinette C van der Kuyl, Ben Berkhout
BACKGROUND: The HIV-1 RNA genome has a biased nucleotide composition with a surplus of As. Several hypotheses have been put forward to explain this striking phenomenon, but the A-count of the HIV-1 genome has thus far not been systematically manipulated. The reason for this reservation is the likelihood that known and unknown sequence motifs will be affected by such a massive mutational approach, thus resulting in replication-impaired virus mutants. We present the first attempt to increase and decrease the A-count in a relatively small polymerase (pol) gene segment of HIV-1 RNA...
September 5, 2017: Retrovirology
https://www.readbyqxmd.com/read/28855504/biosynthesis-of-ilamycins-featuring-unusual-building-blocks-and-engineered-production-of-enhanced-anti-tuberculosis-agents
#15
Junying Ma, Hongbo Huang, Yunchang Xie, Zhiyong Liu, Jin Zhao, Chunyan Zhang, Yanxi Jia, Yun Zhang, Hua Zhang, Tianyu Zhang, Jianhua Ju
Tuberculosis remains one of the world's deadliest communicable diseases, novel anti-tuberculosis agents are urgently needed due to severe drug resistance and the co-epidemic of tuberculosis/human immunodeficiency virus. Here, we show the isolation of six anti-mycobacterial ilamycin congeners (1-6) bearing rare L-3-nitro-tyrosine and L-2-amino-4-hexenoic acid structural units from the deep sea-derived Streptomyces atratus SCSIO ZH16. The biosynthesis of the rare L-3-nitrotyrosine and L-2-amino-4-hexenoic acid units as well as three pre-tailoring and two post-tailoring steps are probed in the ilamycin biosynthetic machinery through a series of gene inactivation, precursor chemical complementation, isotope-labeled precursor feeding experiments, as well as structural elucidation of three intermediates (6-8) from the respective mutants...
August 30, 2017: Nature Communications
https://www.readbyqxmd.com/read/28843613/evolution-of-inhibitor-resistant-natural-mutant-forms-of-hiv-1-protease-probed-by-pre-steady-state-kinetic-analysis
#16
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/28834754/samhd1-promotes-dna-end-resection-to-facilitate-dna-repair-by-homologous-recombination
#17
Waaqo Daddacha, Allyson E Koyen, Amanda J Bastien, PamelaSara E Head, Vishal R Dhere, Geraldine N Nabeta, Erin C Connolly, Erica Werner, Matthew Z Madden, Michele B Daly, Elizabeth V Minten, Donna R Whelan, Ashley J Schlafstein, Hui Zhang, Roopesh Anand, Christine Doronio, Allison E Withers, Caitlin Shepard, Ranjini K Sundaram, Xingming Deng, William S Dynan, Ya Wang, Ranjit S Bindra, Petr Cejka, Eli Rothenberg, Paul W Doetsch, Baek Kim, David S Yu
DNA double-strand break (DSB) repair by homologous recombination (HR) is initiated by CtIP/MRN-mediated DNA end resection to maintain genome integrity. SAMHD1 is a dNTP triphosphohydrolase, which restricts HIV-1 infection, and mutations are associated with Aicardi-Goutières syndrome and cancer. We show that SAMHD1 has a dNTPase-independent function in promoting DNA end resection to facilitate DSB repair by HR. SAMHD1 deficiency or Vpx-mediated degradation causes hypersensitivity to DSB-inducing agents, and SAMHD1 is recruited to DSBs...
August 22, 2017: Cell Reports
https://www.readbyqxmd.com/read/28827354/covalent-inhibitors-for-eradication-of-drug-resistant-hiv-1-reverse-transcriptase-from-design-to-protein-crystallography
#18
Albert H Chan, Won-Gil Lee, Krasimir A Spasov, José A Cisneros, Shalley N Kudalkar, Zaritza O Petrova, Amanda B Buckingham, Karen S Anderson, William L Jorgensen
Development of resistance remains a major challenge for drugs to treat HIV-1 infections, including those targeting the essential viral polymerase, HIV-1 reverse transcriptase (RT). Resistance associated with the Tyr181Cys mutation in HIV-1 RT has been a key roadblock in the discovery of nonnucleoside RT inhibitors (NNRTIs). It is the principal point mutation that arises from treatment of HIV-infected patients with nevirapine, the first-in-class drug still widely used, especially in developing countries. We report covalent inhibitors of Tyr181Cys RT (CRTIs) that can completely knock out activity of the resistant mutant and of the particularly challenging Lys103Asn/Tyr181Cys variant...
August 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28825755/influence-of-the-dna-sequence-length-and-ph-on-deaminase-activity-as-well-as-the-roles-of-the-amino-acid-residues-around-the-catalytic-center-of-apobec3f
#19
Li Wan, Takashi Nagata, Masato Katahira
APOBEC3F (A3F), an apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) family protein, catalyzes cytosine-to-uracil conversion in single-stranded (ss) DNA. A3F acts as an inhibitor of retrovirus replication and exhibits antiviral activity against viral infectivity factor (Vif)-deficient human immunodeficiency virus 1 (HIV-1). Previous studies have mostly been focused on the interaction between A3F and Vif, and the studies on A3F's deamination properties are limited. Here, we report comprehensive characterization of the deaminase activity and ssDNA binding of the C-terminal domain (CTD) of A3F...
August 21, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28820066/mutational-impact-on-the-interaction-between-human-il27-and-gp130-in-silico-approach-for-defending-hiv-infection
#20
Arundhati Banerjee, Rakhi Dasgupta, Sujay Ray
INTRODUCTION: With advances in proteomics, it is essential to investigate the molecular-level participation of IL27 and gp130 to hinder HIV infection. Their interaction causes cell-cycle arrest in HIV+ cells by activating the receptor-associated JAK signaling and causing apoptosis of cancerous cells. METHODOLOGY: The best human wild-type WT_IL27 model was prepared after varied molecular modeling techniques. The vital tyrosine residues in WT_IL27 were identified, mutated and IL27 was re-modeled...
August 17, 2017: Current HIV Research
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