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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
#1
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/29244012/utilizing-knowledge-base-of-amino-acids-structural-neighborhoods-to-predict-protein-protein-interaction-sites
#2
Jan Jelínek, Petr Škoda, David Hoksza
BACKGROUND: Protein-protein interactions (PPI) play a key role in an investigation of various biochemical processes, and their identification is thus of great importance. Although computational prediction of which amino acids take part in a PPI has been an active field of research for some time, the quality of in-silico methods is still far from perfect. RESULTS: We have developed a novel prediction method called INSPiRE which benefits from a knowledge base built from data available in Protein Data Bank...
December 6, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29243852/functional-divergence-and-comparative-in-silico-study-of-cas4-proteins-of-duf83-class
#3
Vineeta Kaushik, Ved Vrat Verma, Manisha Goel
Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR associated (CRISPR-Cas) systems present in genomes of bacteria and archaea have been the focus of many research studies recently. The Cas4 proteins of these systems are thought to be responsible for the adaptation step in the CRISPR mechanism. Cas4 proteins exhibit low sequence similarity among themselves and are currently classified into 2 main classes: DUF83 and DUF911. The characteristic features of Cas4 proteins belonging to DUF83 class have been elucidated by determining the structures of Cas4 protein from Sulfolobus solfataricus and Pyrobaculum calidifontis...
December 15, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/29243584/prediction-and-analysis-of-three-dimensional-structure-of-the-p7-transactivated-protein1-of-hepatitis-c-virus
#4
Mahmoud M Elhefnawi, Mohamed E Hasan, Amal Mahmoud, Yehia A Khidr, El-Sayed A El-Absawy, Alaa A Hemeida
BACKGROUND: The p7-transactivated protein of Hepatitis C virus is a small integral membrane protein of 127 amino acids, which is crucial for assembly and release of infectious virions. Ab initio and comparative modelling, is an essential tool to solve the problem of protein structure prediction and to comprehend the physicochemical fundemental of how proteins fold in nature. RESULTS: Only one domain (1-127) of p7 had been predicted using the systematic in silico approach, ThreaDom...
December 15, 2017: Infectious Disorders Drug Targets
https://www.readbyqxmd.com/read/29243483/relative-binding-free-energy-calculations-in-drug-discovery-recent-advances-and-practical-considerations
#5
Zoe Cournia, Bryce Allen, Woody Sherman
Accurate in silico prediction of protein-ligand binding affinities has been a primary objective of structure-based drug design for decades due to the putative value it would bring to the drug discovery process. However, computational methods have historically failed to deliver value in real-world drug discovery applications due to a variety of scientific, technical, and practical challenges. Recently, a family of approaches commonly referred to as relative binding free energy (RBFE) calculations, which rely on physics-based molecular simulations and statistical mechanics, have shown promise in reliably generating accurate predictions in the context of drug discovery projects...
December 15, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29243271/dynamic-modelling-of-limitations-on-improving-leaf-co2-assimilation-under-fluctuating-irradiance
#6
Alejandro Morales, Elias Kaiser, Xinyou Yin, Jeremy Harbinson, Jaap Molenaar, Steven M Driever, Paul C Struik
A dynamic model of leaf CO2 assimilation was developed as an extension of the canonical steady-state model, by adding the effects of energy-dependent non-photochemical quenching (qE), chloroplast movement, photoinhibition, regulation of enzyme activity in the Calvin cycle, metabolite concentrations, and dynamic CO2 diffusion. The model was calibrated and tested successfully using published measurements of gas exchange and chlorophyll fluorescence on Arabidopsis thaliana ecotype Col-0 and several photosynthetic mutants and transformants affecting the regulation of Rubisco activity (rca-2 and rwt43), NPQ (npq4-1 and npq1-2) and sucrose synthesis (spsa1)...
December 15, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/29243125/minichromosome-maintenance-complex-component-6-mcm6-expression-correlates-with-histological-grade-and-survival-in-endometrioid-endometrial-adenocarcinoma
#7
Judicaël Hotton, Mikaël Agopiantz, Agnès Leroux, Claire Charra-Brunaud, Béatrice Marie, Hélène Busby-Venner, Olivier Morel, Jean-Louis Guéant, Jean-Michel Vignaud, Shyue-Fang Battaglia-Hsu, Guillaume Gauchotte
Minichromosome maintenance complex component 6 (MCM6) is involved in initiating DNA replication and is upregulated during licensed G0 phase of the cell cycle. This early expression permits its labeling of more proliferating cells than those by Ki-67. Here using a cohort of 89 endometrioid adenocarcinoma, we report findings made on the prognostic value of MCM6 based on immunohistochemical labeling index (LI) of the protein in comparison with that of Ki67 as no such information is currently available. Additionally, we examined the prognostic values of these markers based on their mRNA expression using a cohort of uterine corpus endometrial carcinoma (UCEC, n = 307) taken from The Cancer Genome Atlas (TCGA) database...
December 14, 2017: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/29242834/novel-its1-fungal-primers-for-characterization-of-the-mycobiome
#8
Mykhaylo Usyk, Christine P Zolnik, Hitesh Patel, Michael H Levi, Robert D Burk
Studies of the human microbiome frequently omit characterization of fungal communities (the mycobiome), which limits our ability to investigate how fungal communities influence human health. The internal transcribed spacer 1 (ITS1) region of the eukaryotic ribosomal cluster has features allowing for wide taxonomic coverage and has been recognized as a suitable barcode region for species-level identification of fungal organisms. We developed custom ITS1 primer sets using iterative alignment refinement. Primer performance was evaluated using in silico testing and experimental testing of fungal cultures and human samples...
November 2017: MSphere
https://www.readbyqxmd.com/read/29242385/differential-regulation-of-zfp30-expression-in-murine-airway-epithelia-through-altered-binding-of-zfp148-to-rs51434084
#9
Lucas T Laudermilk, Joseph M Thomas, Samir N Kelada
Neutrophil chemotaxis to the airways is a key aspect of host response to microbes and a feature of multiple pulmonary diseases including asthma. Tight regulation of this recruitment is critical to prevent unwanted host tissue damage and inflammation. Using a mouse (Mus musculus) model of asthma applied to the Collaborative Cross (CC), we previously identified a lung gene expression quantitative trait locus (eQTL) for Zinc finger protein 30 (Zfp30) that was also a QTL for neutrophil recruitment and the hallmark neutrophil chemokine CXCL1...
December 14, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29241563/two-metallocarboxypeptidase-inhibitors-are-implicated-in-tomato-fruit-development-and-regulated-by-the-inner-no-outer-transcription-factor
#10
B Molesini, G L Rotino, V Dusi, R Chignola, T Sala, G Mennella, G Francese, T Pandolfini
The TCMP-1 and TCMP-2 genes of tomato code for metallocarboxypeptidase inhibitors and show sequential, tightly regulated expression patterns during flower and fruit development. In particular, TCMP-1 is highly expressed in flower buds before anthesis, while TCMP-2 in ripe fruits. Their expression pattern suggests that they might play a role in fruit development. Here, to investigate their function, we altered their endogenous levels by generating transgenic plants harbouring a chimeric gene expressing the TCMP-1 coding sequence under the control of the TCMP-2 promoter...
January 2018: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/29241414/molecular-mechanisms-of-allosteric-probe-dependence-in-%C3%AE-opioid-receptor
#11
Damian Bartuzi, Agnieszka A Kaczor, Dariusz Matosiuk
Allostery is one of the most important features of proteins. It greatly contributes to the complexity of life, since it enables possibility of precise tuning of protein function, as well as performing more than one function per protein. Probe dependence is one of unique features of allostery. It allows a protein to respond differently to the same allosteric modulator when different drugs or transmitters are bound. Unfortunately, allosteric mechanisms are difficult to investigate experimentally. Instead, they can be reproduced artificially in simulations...
December 14, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29241333/online-hplc-esi-hrms-method-for-the-analysis-and-comparison-of-different-dissolved-organic-matter-samples
#12
Claudia Patriarca, Jonas Bergquist, Per J R Sjöberg, Lars Tranvik, Jeffrey Alistair Hawkes
Natural dissolved organic matter (DOM) is an ultra-complex mixture that is essential to global carbon cycling, but is poorly understood because of its complexity. The most powerful tool for the DOM characterization is high-resolution mass spectrometry (HRMS) generally combined to direct infusion (DI) as sample introduction. Liquid chromatography (LC) represents a compelling alternative to DI; however state-of-the-art techniques involve only offline LC-HRMS approaches, which have important logistical drawbacks that make DOM analysis more challenging...
December 15, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/29240767/mitf-a-controls-branching-morphogenesis-and-nephron-endowment
#13
Aurélie Phelep, Denise Laouari, Kapil Bharti, Martine Burtin, Salvina Tammaccaro, Serge Garbay, Clément Nguyen, Florence Vasseur, Thomas Blanc, Sophie Berissi, Francina Langa-Vives, Evelyne Fischer, Anne Druilhe, Heinz Arnheiter, Gerard Friedlander, Marco Pontoglio, Fabiola Terzi
Congenital nephron number varies widely in the human population and individuals with low nephron number are at risk of developing hypertension and chronic kidney disease. The development of the kidney occurs via an orchestrated morphogenetic process where metanephric mesenchyme and ureteric bud reciprocally interact to induce nephron formation. The genetic networks that modulate the extent of this process and set the final nephron number are mostly unknown. Here, we identified a specific isoform of MITF (MITF-A), a bHLH-Zip transcription factor, as a novel regulator of the final nephron number...
December 14, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/29239234/adoption-of-in-vitro-systems-and-zebrafish-embryos-as-alternative-models-for-reducing-rodent-use-in-assessments-of-immunological-and-oxidative-stress-responses-to-nanomaterials
#14
Helinor J Johnston, Rachel Verdon, Suzanne Gillies, David M Brown, Teresa F Fernandes, Theodore B Henry, Adriano G Rossi, Lang Tran, Carl Tucker, Charles R Tyler, Vicki Stone
Assessing the safety of engineered nanomaterials (NMs) is paramount to the responsible and sustainable development of nanotechnology, which provides huge societal benefits. Currently, there is no evidence that engineered NMs cause detrimental health effects in humans. However, investigation of NM toxicity using in vivo, in vitro, in chemico, and in silico models has demonstrated that some NMs stimulate oxidative stress and inflammation, which may lead to adverse health effects. Accordingly, investigation of these responses currently dominates NM safety assessments...
December 14, 2017: Critical Reviews in Toxicology
https://www.readbyqxmd.com/read/29239233/in-vitro-metabolism-study-of-a-novel-p38-kinase-inhibitor-in-silico-predictions-structure-elucidation-using-ms-ms-i
#15
Hanaa Ma Hashem, Marianne A Mahrouse
AIM: Metabolism study of PH-797804, a promising newly developed drug for treatment of chronic inflammation which inhibits P38 mitogen-activated protein kinase. MATERIALS & METHODS: Susceptibility of PH-797804 to metabolism was first investigated using SMARTCyp and Xenosite web servers. Molecular docking of the drug into CYP3A4 crystal structures evaluated binding interactions with active site. The predicted results were confirmed by in vitro incubation with rat S9 fraction...
December 14, 2017: Future Medicinal Chemistry
https://www.readbyqxmd.com/read/29238904/anti-inflammatory-activity-of-anti-hyperlipidemic-drug-fenofibrate-and-its-phase-i-metabolite-fenofibric-acid-in-silico-in-vitro-and-in-vivo-studies
#16
G Shyam Prasad, P Govardhan, G Deepika, V Vakdevi, R B Sashidhar
Fenofibrate, an anti-hyperlipidemic drug and its phase-I biotransformed metabolite fenofibric acid, was studied for COX-1 (PDB ID: 3N8Y) and COX-2 (PDB ID: 1PXX) inhibition potentials in silico and in vitro for their effects on human recombinant COX-2 enzyme isolated from a Baculovirus expression system in sf21 cells (EC 1.14.99.1) using a conventional spectrophotometric assay. Furthermore, the compounds were also screened for their anti-inflammatory potentials in vivo using carrageenan-induced paw oedema method in Wistar rats...
December 13, 2017: Inflammopharmacology
https://www.readbyqxmd.com/read/29238888/synthesis-and-evaluation-of-bile-acid-amides-of-formula-see-text-cyanostilbenes-as-anticancer-agents
#17
Devesh S Agarwal, Rajnish Prakash Singh, K Lohitesh, Prabhat N Jha, Rajdeep Chowdhury, Rajeev Sakhuja
A series of amino-substituted [Formula: see text]-cyanostilbene derivatives and their bile acid (cholic and deoxycholic acid) amides were designed and synthesized. A comparative study on the anticancer and antibacterial activity evaluation on the synthesized analogs was carried against the human osteosarcoma (HOS) cancer cell line, and two gram -ve (E. coli and S. typhi) and two gram [Formula: see text]ve (B. subtilis and S. aureus) bacterial strains. All the cholic acid [Formula: see text]-cyanostilbene amides showed an [Formula: see text] in the range 2-13 [Formula: see text] against human osteosarcoma cells (HOS) with the most active analog (6g) possessing an [Formula: see text] of [Formula: see text]...
December 13, 2017: Molecular Diversity
https://www.readbyqxmd.com/read/29238706/angular-phenozaxine-ethers-as-potent-multi-microbial-targets-inhibitors-design-synthesis-and-molecular-docking-studies
#18
Mercy A Ezeokonkwo, Onyinyechi N Ogbonna, Sunday N Okafor, Evelyn U Godwin-Nwakwasi, Fidelia N Ibeanu, Uchechukwu C Okoro
The reaction of diaza-5H-benzo[a]phenoxazin-5-one and 5H-benzo[a]phenoxazin-5-one with various phenols catalyzed by Pd/t-BuXPhos/K3PO4 system gave previously unknown ether derivatives (7a-f and 8a-f) in good yields. UV-visible, FTIR, and 1H NMR data were used to confirm structures of the synthesized compounds. The parent compounds and the derivatives were screened in-silico for their drug-likeness and binding affinities to the microbial targets through molecular docking. Molinspiration software and AutoDock were used for the drug-likeness and docking studies, respectively...
2017: Frontiers in Chemistry
https://www.readbyqxmd.com/read/29238565/new-specific-primers-for-amplification-of-the-internal-transcribed-spacer-region-in-clitellata-annelida
#19
Yingkui Liu, Christer Erséus
Nuclear molecular evidence, for example, the rapidly evolving Internal Transcribed Spacer region (ITS), integrated with maternally inherited (mitochondrial) COI barcodes, has provided new insights into the diversity of clitellate annelids. PCR amplification and sequencing of ITS, however, are often hampered by poor specificity of primers used. Therefore, new clitellate-specific primers for amplifying the whole ITS region (ITS: 29F/1084R) and a part of it (ITS2: 606F/1082R) were developed on the basis of a collection of previously published ITS sequences with flanking rDNA coding regions...
December 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/29238347/langerhans-cells-programmed-by-the-epidermis
#20
REVIEW
Kalum Clayton, Andres F Vallejo, James Davies, Sofia Sirvent, Marta E Polak
Langerhans cells (LCs) reside in the epidermis as a dense network of immune system sentinels. These cells determine the appropriate adaptive immune response (inflammation or tolerance) by interpreting the microenvironmental context in which they encounter foreign substances. In a normal physiological, "non-dangerous" situation, LCs coordinate a continuous state of immune tolerance, preventing unnecessary and harmful immune activation. Conversely, when they sense a danger signal, for example during infection or when the physical integrity of skin has been compromised as a result of a trauma, they instruct T lymphocytes of the adaptive immune system to mount efficient effector responses...
2017: Frontiers in Immunology
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