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Maryam Rajaee, David W Ow
We have previously described a recombinase-mediated gene stacking system in which the Cre recombinase is used to remove lox-site flanked DNA no longer needed after each round of Bxb1 integrase-mediated site-specific integration. The Cre recombinase can be conveniently introduced by hybridization with a cre-expressing plant. However, maintaining an efficient cre-expressing line over many generations can be a problem, as high production of this DNA binding protein might interfere with normal chromosome activities...
March 19, 2017: Plant Biotechnology Journal
Ping Xue, Huan-Huan Lu, Yuan-Yuan Zhu, Xiu-Lian Ju, Christophe Pannecouque, Xiao-Jiao Zheng, Gen-Yan Liu, Xiu-Lan Zhang, Shuang-Xi Gu
Based on the strategy of molecular hybridization, diketo acid fragment as a classical phamacophore of integrase inhibitors was introduced to reverse transcriptase inhibitors diarylpyrimidines to design a series of diarylpyrimidine-diketo acid hybrids (DAPY-DKAs). The target molecules 10b and 11b showed inhibitory activities against WT HIV-1 with EC50 values of 0.18μM and 0.14μM, respectively. And the results of molecular docking demonstrated the potential binding mode and revealed that the DKA moiety and its ester could both be tolerated in the nonnucleoside binding site (NNBS) of HIV-1 RT...
March 7, 2017: Bioorganic & Medicinal Chemistry Letters
Francesco Saladini, Alessia Giannini, Adele Boccuto, Ilaria Vicenti, Maurizio Zazzi
BACKGROUND: Although clinical management of drug resistance is routinely based on genotypic methods, phenotypic assays remain necessary for the characterization of novel HIV-1 inhibitors, particularly against common drug-resistant variants. We describe the development and assessment of the performance of a recombinant virus assay for measuring HIV-1 susceptibility to protease (PR), reverse transcriptase (RT), and integrase (IN) inhibitors. METHODS: The system is based on the creation of replication-competent chimeric viruses through homologous recombination between patient or laboratory virus-derived PCR fragments and the corresponding NL4-3 vector where the whole Gag-PR, RT-RNaseH or IN coding regions has been deleted through inverse PCR...
March 17, 2017: Journal of Clinical Laboratory Analysis
Franco Maggiolo, Roberto Gulminetti, Layla Pagnucco, Margherita Digaetano, Simone Benatti, Daniela Valenti, Annapaola Callegaro, Diego Ripamonti, Cristina Mussini
BACKGROUND: Little is known about the applicability of dual treatments based on integrase inhibitors. We explored the combination of lamivudine + dolutegravir as an option when switching from standard cART in virologically suppressed patients. METHODS: In this prospective cohort we enrolled patients previously switched to 3TC + DTG who were 18 years or older, with no previous resistance mutations to the used drugs, having a HIV-RNA <50 copies/ml for 6 months or longer, negative for HBsAg and on a stable (>6 months) cART...
March 16, 2017: BMC Infectious Diseases
Utsab Debnath, Prachi Kumar, Aakanksha Agarwal, Ajay Kesharwani, Satish K Gupta, Seturam B Katti
An in silico method has been used to discover N-hydroxy substituted 2-aryl acetamide analogues as a new class of HIV-1 integrase inhibitors. Based on the molecular requirements of the binding pocket of catalytic active site, two molecules (compounds 2 and 4b) were designed as fragments. These were further synthesized and biologically evaluated. In vitro potency along with docking studies highlighted compound 4b as an active fragment which was further used to synthesize new leads as HIV-1 integrase inhibitors...
March 13, 2017: Chemical Biology & Drug Design
Julia Grawenhoff, Alan N Engelman
Retroviral replication proceeds through the integration of a DNA copy of the viral RNA genome into the host cellular genome, a process that is mediated by the viral integrase (IN) protein. IN catalyzes two distinct chemical reactions: 3'-processing, whereby the viral DNA is recessed by a di- or trinucleotide at its 3'-ends, and strand transfer, in which the processed viral DNA ends are inserted into host chromosomal DNA. Although IN has been studied as a recombinant protein since the 1980s, detailed structural understanding of its catalytic functions awaited high resolution structures of functional IN-DNA complexes or intasomes, initially obtained in 2010 for the spumavirus prototype foamy virus (PFV)...
February 26, 2017: World Journal of Biological Chemistry
Sridhar Mandali, Kushol Gupta, Anthony R Dawson, Gregory D Van Duyne, Reid C Johnson
The serine integrase of phage A118 catalyzes integrative recombination between attP on the phage and a specific attB locus on the chromosome of Listeriamonocytogenes but is unable to promote excisive recombination between the hybrid attL and attR sites found on the integrated prophage without assistance from a Recombination Directionality Factor (RDF). We have identified and characterized the phage-encoded RDF, Gp44, which activates the A118 integrase for excision and inhibits integration. Gp44 binds to the C-terminal DNA binding domain of integrase, and we have localized the primary binding site to be within the mobile coiled-coil (CC) motif but distinct from the distal tip of the CC that is required for recombination...
March 13, 2017: Journal of Bacteriology
Muthukumar Balasubramaniam, Benem Davids, Amma B Addai, Jui Pandhare, Chandravanu Dash
HIV-1 envelope proteins engage cognate receptors on the target cell surface, which leads to viral-cell membrane fusion followed by the release of the viral capsid (CA) core into the cytoplasm. Subsequently, the viral Reverse Transcriptase (RT), as part of a namesake nucleoprotein complex termed the Reverse Transcription Complex (RTC), converts the viral single-stranded RNA genome into a double-stranded DNA copy (vDNA). This leads to the biogenesis of another nucleoprotein complex, termed the pre-integration complex (PIC), composed of the vDNA and associated virus proteins and host factors...
February 22, 2017: Journal of Visualized Experiments: JoVE
Kosuke Tomimatsu, Kenji Kokura, Tadashi Nishida, Yuki Yoshimura, Yasuhiro Kazuki, Masashi Narita, Mitsuo Oshimura, Tetsuya Ohbayashi
The site-specific excision of a target DNA sequence for genetic knockout or lineage tracing is a powerful tool for investigating biological systems. Currently, site-specific recombinases (SSRs), such as Cre or Flp recombination target cassettes, have been successfully excised or inverted by a single SSR to regulate transgene expression. However, the use of a single SSR might restrict the complex control of gene expression. This study investigated the potential for expanding the multiple regulation of transgenes using three different integrase systems (TP901-1, R4, and Bxb1)...
March 2017: FEBS Open Bio
John D Schreier, Mark W Embrey, Izzat T Raheem, Guillaume Barbe, Louis-Charles Campeau, David Dubost, Jamie McCabe Dunn, Jay Grobler, Timothy J Hartingh, Daria J Hazuda, Daniel Klein, Michael D Miller, Keith P Moore, Natalie Nguyen, Natasa Pajkovic, David A Powell, Vanessa Rada, John M Sanders, John Sisko, Thomas G Steele, John Wai, Abbas Walji, Min Xu, Paul J Coleman
HIV integrase strand transfer inhibitors (InSTIs) represent an important class of antiviral therapeutics with proven efficacy and excellent tolerability for the treatment of HIV infections. In 2007, Raltegravir became the first marketed strand transfer inhibitor pioneering the way to a first-line therapy for treatment-naïve patients. Challenges with this class of therapeutics remain, including frequency of the dosing regimen and the genetic barrier to resistance. To address these issues, research towards next-generation integrase inhibitors has focused on imparting potency against RAL-resistent mutants and improving pharmacokinetic profiles...
February 20, 2017: Bioorganic & Medicinal Chemistry Letters
Carl-Fredrik Flach, Chandan Pal, Carl Johan Svensson, Erik Kristiansson, Marcus Östman, Johan Bengtsson-Palme, Mats Tysklind, D G Joakim Larsson
There is concern that heavy metals and biocides contribute to the development of antibiotic resistance via co-selection. Most antifouling paints contain high amounts of such substances, which risks turning painted ship hulls into highly mobile refuges and breeding grounds for antibiotic-resistant bacteria. The objectives of this study were to start investigate if heavy-metal based antifouling paints can pose a risk for co-selection of antibiotic-resistant bacteria and, if so, identify the underlying genetic basis...
March 8, 2017: Science of the Total Environment
Esti Michael, Margarita Gomila, Jorge Lalucat, Yeshayahu Nitzan, Izabella Pechatnikov, Rivka Cahan
The organization and expression of Pseudomonas stutzeri ST-9 genes related to toluene catabolism and porin synthesis was investigated. Toluene-degrading genes were found to be localized in the chromosome close to a phage-type integrase. A regulatory gene and 21 genes related to an aromatics degradation pathway are organized as a putative operon. These proteins are upregulated in the presence of toluene. Fourteen outer membrane proteins were identified as porins in the ST-9 genome. The identified porins showed that the main detected porins are related to the OmpA and OprD superfamilies...
March 9, 2017: Journal of Proteome Research
W Snippenburg, Fjb Nellen, C Smit, Amj Wensing, M H Godfried, T Mudrikova
OBJECTIVE: To identify factors associated with the time to viral suppression in women starting antiretroviral treatment (ART) during pregnancy. Knowledge on duration of viral load (VL) decline could help deciding the timing of treatment initiation. METHODS: Highly active antiretroviral treatment (HAART)-naive pregnant women over 18 years of age who started treatment during pregnancy were included. The time to viral suppression was calculated and compared between subgroups...
January 1, 2017: Journal of Virus Eradication
Sybille Schwendener, Kerstin Cotting, Vincent Perreten
Methicillin-resistant Macrococcus caseolyticus strains from bovine and canine origins were found to carry a novel mecD gene conferring resistance to all classes of β-lactams including anti-MRSA cephalosporins. Association of β-lactam resistance with mecD was demonstrated by gene expression in S. aureus and deletion of the mecD-containing island in M. caseolyticus. The mecD gene was located either on an 18,134-bp M. caseolyticus resistance island (McRImecD-1) or a 16,188-bp McRImecD-2. Both islands were integrated at the 3' end of the rpsI gene, carried the mecD operon (mecD-mecR1m-mecIm), and genes for an integrase of the tyrosine recombinase family and a putative virulence-associated protein (virE)...
March 8, 2017: Scientific Reports
Shah M Rashed, Nur A Hasan, Munirul Alam, Abdus Sadique, Marzia Sultana, Md Mozammel Hoq, R Bradley Sack, Rita R Colwell, Anwar Huq
Cholera outbreaks occur each year in the remote coastal areas of Bangladesh and epidemiological surveillance and routine monitoring of cholera in these areas is challenging. In this study, a total of 97 Vibrio cholerae O1 isolates from Mathbaria, Bangladesh, collected during 2010 and 2014 were analyzed for phenotypic and genotypic traits, including antimicrobial susceptibility. Of the 97 isolates, 95 possessed CTX-phage mediated genes, ctxA, ace, and zot, and two lacked the cholera toxin gene, ctxA. Also both CTX(+) and CTX(-)V...
2017: Frontiers in Microbiology
Megan R Carpenter, Sai S Kalburge, Joseph D Borowski, Molly C Peters, Rita R Colwell, E Fidelma Boyd
Pathogenicity islands (PAIs) are mobile integrated genetic elements that contain a diverse range of virulence factors. PAIs integrate into the host chromosome at a tRNA locus that contains their specific bacterial attachment site, attB, via integrase mediated site-specific recombination generating attL and attR sites. We identified conserved recombination modules (integrases and att sites) previously described in choleragenic V. cholerae PAIs but with novel cargo genes. Clustered regularly interspaced short palindromic repeat (CRISPR)-associated proteins (Cas proteins) and a type VI secretion system (T6SS) gene cluster were identified at the Vibrio Pathogenicity Island-1 (VPI-1) insertion site in nineteen V...
March 6, 2017: Journal of Bacteriology
Alessandro Carnelli, Federica Mauri, Antonella Demarta
Aeromonas spp. and fecal coliforms, two abundant and cultivable bacterial populations that can be found in water ecosystems, might substantially contribute to the spread of antibiotic resistance. We investigated the presence and spread of transposons (elements that can move from one location to another in the genome), integrons (structures able to capture and incorporate gene cassettes) and resistance plasmids in strains isolated from polluted and unpolluted water. We recovered 231 Aeromonas and 250 fecal coliforms from water samplings with different degrees of pollution (hospital sewage, activated sludge of a wastewater treatment plant, river water before and after treatment and water from an alpine lake)...
March 2, 2017: Research in Microbiology
Yi Shang, Fei Yang, Alan H Schulman, Jinghuan Zhu, Yong Jia, Junmei Wang, Xiao-Qi Zhang, Qiaojun Jia, Wei Hua, Jianming Yang, Chengdao Li
A poly-row branched spike (prbs) barley mutant was obtained from soaking a two-rowed barley inflorescence in a solution of maize genomic DNA. Positional cloning and sequencing demonstrated that the prbs mutant resulted from a 28 kb deletion including the inflorescence architecture gene HvRA2. Sequence annotation revealed that the HvRA2 gene is flanked by two LTR (long terminal repeat) retrotransposons (BARE) sharing 89% sequence identity. A recombination between the integrase (IN) gene regions of the two BARE copies resulted in the formation of an intact BARE and loss of HvRA2...
March 2, 2017: Scientific Reports
Philip L Tzou, Xiaoqiu Huang, Robert W Shafer
BACKGROUND: Current nucleotide-to-amino acid alignment software programs were developed primarily for detecting gene exons within eukaryotic genomes and were therefore optimized for speed across long genetic sequences. We developed a nucleotide-to-amino acid alignment program NucAmino optimized for virus sequencing. RESULTS: NucAmino is an open source program written in the high-level language Go. NucAmino is more likely to align codons flush with a reference sequence's amino acids and can be modified to facilitate the placement of insertions and deletions at specific positions...
March 1, 2017: BMC Bioinformatics
Yang Li, Yanbin Wu, Aixia Yan
HIV-1 integrase (IN) is a promising target for anti-AIDS therapy, and LEDGF/p75 is proved to enhance the HIV-1 integrase strand transfer activity in vitro. Blocking the interaction between IN and LEDGF/p75 is an effective way to inhibit HIV replication infection. In this work, 274 LEDGF/p75-IN inhibitors were collected as the dataset. Support Vector Machine (SVM), Decision Tree (DT), Function Tree (FT) and Random Forest (RF) were applied to build several computational models for predicting whether a compound is an active or weakly active LEDGF/p75-IN inhibitor...
February 28, 2017: Molecular Informatics
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