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https://www.readbyqxmd.com/read/28724269/association-of-human-methionine-synthase-a2756g-transition-with-prostate-cancer-a-case-control-study-and-in-silico-analysis
#1
Arezou Ebrahimi, Abasalt Hosseinzadeh Colagar, Mohammad Karimian
Methionine synthase (MTR) is one of the key enzymes of folate pathway, which play a key role in the construction, repair, and methylation of DNA. In this study, an association of MTR A2756G gene transition with prostate cancer in men populations of Kashan-Iran was investigated by a case-control study and an in silico analysis. The 200 samples including 100 patients with prostate cancer, as case group and 100 healthy men, as control group included in this study. MTR-A2756G genotyping was performed by PCR-RFLP technique...
May 2017: Acta Medica Iranica
https://www.readbyqxmd.com/read/28724227/carbon-and-nitrogen-allocation-strategy-in-posidonia-oceanica-is-altered-by-seawater-acidification
#2
Andrea Scartazza, Stefano Moscatello, Olga Gavrichkova, Maria Cristina Buia, Marco Lauteri, Alberto Battistelli, Maurizio Lorenti, Samantha Laird Garrard, Carlo Calfapietra, Enrico Brugnoli
Rising atmospheric CO2 causes ocean acidification that represents one of the major ecological threats for marine biota. We tested the hypothesis that long-term exposure to increased CO2 level and acidification in a natural CO2 vent system alters carbon (C) and nitrogen (N) metabolism in Posidonia oceanica L. (Delile), affecting its resilience, or capability to restore the physiological homeostasis, and the nutritional quality of organic matter available for grazers. Seawater acidification decreased the C to N ratio in P...
July 14, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28723971/termination-factor-rho-from-the-control-of-pervasive-transcription-to-cell-fate-determination-in-bacillus-subtilis
#3
Vladimir Bidnenko, Pierre Nicolas, Aleksandra Grylak-Mielnicka, Olivier Delumeau, Sandrine Auger, Anne Aucouturier, Cyprien Guerin, Repoila Francis, Jacek Bardowski, Stéphane Aymerich, Elena Bidnenko
In eukaryotes, RNA species originating from pervasive transcription are regulators of various cellular processes, from the expression of individual genes to the control of cellular development and oncogenesis. In prokaryotes, the function of pervasive transcription and its output on cell physiology is still unknown. Most bacteria possess termination factor Rho, which represses pervasive, mostly antisense, transcription. Here, we investigate the biological significance of Rho-controlled transcription in the Gram-positive model bacterium Bacillus subtilis...
July 19, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28723955/crystal-structure-and-functional-characterization-of-an-isoaspartyl-dipeptidase-cpsiada-from-colwellia-psychrerythraea-strain-34h
#4
Sun-Ha Park, Chang Woo Lee, Sung Gu Lee, Seung Chul Shin, Hak Jun Kim, Hyun Park, Jun Hyuck Lee
Isoaspartyl dipeptidase (IadA) is an enzyme that catalyzes the hydrolysis of an isoaspartyl dipeptide-like moiety, which can be inappropriately formed in proteins, between the β-carboxyl group side chain of Asp and the amino group of the following amino acid. Here, we have determined the structures of an isoaspartyl dipeptidase (CpsIadA) from Colwellia psychrerythraea, both ligand-free and that complexed with β-isoaspartyl lysine, at 1.85-Å and 2.33-Å resolution, respectively. In both structures, CpsIadA formed an octamer with two Zn ions in the active site...
2017: PloS One
https://www.readbyqxmd.com/read/28723946/the-mitochondrial-genome-of-the-terrestrial-carnivorous-plant-utricularia-reniformis-lentibulariaceae-structure-comparative-analysis-and-evolutionary-landmarks
#5
Saura R Silva, Danillo O Alvarenga, Yani Aranguren, Helen A Penha, Camila C Fernandes, Daniel G Pinheiro, Marcos T Oliveira, Todd P Michael, Vitor F O Miranda, Alessandro M Varani
The carnivorous plants of the family Lentibulariaceae have attained recent attention not only because of their interesting lifestyle, but also because of their dynamic nuclear genome size. Lentibulariaceae genomes span an order of magnitude and include species with the smallest genomes in angiosperms, making them a powerful system to study the mechanisms of genome expansion and contraction. However, little is known about mitochondrial DNA (mtDNA) sequences of this family, and the evolutionary forces that shape this organellar genome...
2017: PloS One
https://www.readbyqxmd.com/read/28723918/heterogeneity-of-p53-dependent-genomic-responses-following-ethanol-exposure-in-a-developmental-mouse-model-of-fetal-alcohol-spectrum-disorder
#6
Maria Camargo Moreno, Sandra M Mooney, Frank A Middleton
Prenatal ethanol exposure can produce structural and functional deficits in the brain and result in Fetal Alcohol Spectrum Disorder (FASD). In rodent models acute exposure to a high concentration of alcohol causes increased apoptosis in the developing brain. A single causal molecular switch that signals for this increase in apoptosis has yet to be identified. The protein p53 has been suggested to play a pivotal role in enabling cells to engage in pro-apoptotic processes, and thus figures prominently as a hub molecule in the intracellular cascade of responses elicited by alcohol exposure...
2017: PloS One
https://www.readbyqxmd.com/read/28723680/meiotic-recombination-in-the-giraffe-g-reticulata
#7
Miluse Vozdova, Jan Fröhlich, Svatava Kubickova, Hana Sebestova, Jiri Rubes
Recently, the reticulated giraffe (G. reticulata) was identified as a distinct species, which emphasized the need for intensive research in this interesting animal. To shed light on the meiotic process as a source of biodiversity, we analysed the frequency and distribution of meiotic recombination in 2 reticulated giraffe males. We used immunofluorescence detection of synaptonemal complex protein (SYCP3), meiotic double strand breaks (DSB, marked as RAD51 foci) in leptonema, and crossovers (COs, as MLH1 foci) in pachynema...
July 20, 2017: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/28723607/production-of-recombinant-porin-from-y-pseudotuberculosis-in-a-water-soluble-form-for-pseudotuberculosis-diagnostics
#8
Vasily A Golotin, Olga Y Portnyagina, Natalia S Chopenko, Natalia Y Kim, Valery A Rasskazov, Olga D Novikova
OmpF porin from the outer membrane of Yersinia pseudotuberculosis was cloned into pET-40b(+) plasmid. Using E. coli Rosetta (DE3) strain, MX-medium, IPTG concentration of 0.2 mM and post-induction cultivation at 14 °C overnight allowed us to obtain a water-soluble form of the recombinant protein (rs-OmpF). Rs-OmpF was shown to have the ordered spatial structure at the levels of secondary and tertiary structure. Rs-OmpF was found to be effective as diagnostic antigen in ELISA for pseudotuberculosis diagnostics...
July 26, 2017: Biological Chemistry
https://www.readbyqxmd.com/read/28723582/overexpression-and-purification-of-dicer-and-accessory-proteins-for-biochemical-and-structural-studies
#9
Niladri K Sinha, Brenda L Bass
The Dicer family of ribonucleases plays a key role in small RNA-based regulatory pathways by generating short dsRNA fragments that modulate expression of endogenous genes, or protect the host from invasive nucleic acids. Beginning with its initial discovery, biochemical characterization of Dicer has provided insight about its catalytic properties. However, a comprehensive understanding of how Dicer's domains contribute to substrate-specific recognition and catalysis is lacking. One reason for this void is the lack of high-resolution structural information for a metazoan Dicer in the apo- or substrate-bound state...
July 16, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28723557/crystal-structure-of-the-human-ribosome-in-complex-with-denr-mct-1
#10
Ivan B Lomakin, Elena A Stolboushkina, Anand T Vaidya, Chenguang Zhao, Maria B Garber, Sergey E Dmitriev, Thomas A Steitz
The repertoire of the density-regulated protein (DENR) and the malignant T cell-amplified sequence 1 (MCT-1/MCTS1) oncoprotein was recently expanded to include translational control of a specific set of cancer-related mRNAs. DENR and MCT-1 form the heterodimer, which binds to the ribosome and operates at both translation initiation and reinitiation steps, though by a mechanism that is yet unclear. Here, we determined the crystal structure of the human small ribosomal subunit in complex with DENR-MCT-1. The structure reveals the location of the DENR-MCT-1 dimer bound to the small ribosomal subunit...
July 18, 2017: Cell Reports
https://www.readbyqxmd.com/read/28723472/human-prostate-tissue-derived-extracellular-matrix-as-a-model-of-prostate-microenvironment
#11
Walter Cazzaniga, Manuela Nebuloni, Erika Longhi, Irene Locatelli, Raffaele Allevi, Roberta Lucianò, Gelsomina Senatore, Eugenio Ventimiglia, Vito Cucchiara, Luca Genovese, Francesco Montorsi, Massimo Alfano, Andrea Salonia, Ilaria Cavarretta
BACKGROUND: Clinical experience highlights the wide heterogeneity of primary prostate cancer (PPCa), even when potentially related to the same grade and stage. Currently available prediction tools and biomarkers do not always allow for early recognition of PPCa aggressive phenotype, sometimes making it impossible to distinguish among men harbouring indolent tumours or life-threatening disease. OBJECTIVE: To establish a novel ex vivo/in vitro model suitable to estimate the invasive phenotype of PPCa cells (PPCaC)...
October 2016: European Urology Focus
https://www.readbyqxmd.com/read/28723250/application-of-molecular-dynamic-simulation-to-study-food-proteins-a-review
#12
Ashutosh Singh, Sai Kranthi Vanga, Valerie Orsat, Vijaya Raghavan
This review presents an overview of the application of molecular dynamic simulation to study food proteins. Processing of food using thermal, chemical, radiation, electromagnetic and mechanical techniques subject its macromolecular bio-components such as carbohydrates and proteins to extreme heat, ionic strength, pH and mechanical deformation. These processing factors affect protein's functional properties such as emulsification, dough formation, gelation, etc. which are associated with changes in their structure...
July 19, 2017: Critical Reviews in Food Science and Nutrition
https://www.readbyqxmd.com/read/28723241/the-effects-of-stretch-activation-on-ionic-selectivity-of-the-trek-2-k2p-k-channel
#13
Ehsan Nematian-Ardestani, Viwan Jarerattanachat, Prafulla Aryal, Mark S P Sansom, Stephen J Tucker
The TREK-2 (KCNK10) K2P potassium channel can be regulated by variety of polymodal stimuli including pressure. In a recent study, we demonstrated that this mechanosensitive K(+) channel responds to changes in membrane tension by undergoing a major structural change from its 'down' state to the more expanded 'up' state conformation. These changes are mostly restricted to the lower part of the protein within the bilayer, but are allosterically coupled to the primary gating mechanism located within the selectivity filter...
July 19, 2017: Channels
https://www.readbyqxmd.com/read/28723239/disruption-of-cdk-resistant-chromatin-association-by-prb-causes-dna-damage-mitotic-errors-and-reduces-condensin-ii-recruitment
#14
Charles A Ishak, Courtney H Coschi, Michael V Roes, Frederick A Dick
Organization of chromatin structure is indispensible to the maintenance of genome integrity. The retinoblastoma tumor suppressor protein (pRB) mediates both transcriptional repression and chromatin organization, but the independent contributions of these functions have been difficult to study. Here, we utilize a synthetic Rb1 mutant allele (F832A) that maintains pRB association at cell cycle gene promoters, but disrupts a cyclin-dependent kinase (CDK)-resistant interaction with E2F1 to reduce occupancy of pRB on intergenic chromatin...
July 19, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28723234/flexible-small-molecular-anti-estrogens-with-n-n-dialkylated-2-5-diethoxy-4-morpholinoaniline-scaffold-targets-multiple-estrogen-receptor-conformations
#15
Bethany K Asare, Emmanuel Yawson, Rajendram V Rajnarayanan
Estrogen mediates various cellular processes including cell proliferation, differentiation, growth and mammary gland function. Estrogen Receptors (ERs) are expressed in 70% of breast cancers. Consequently, estrogen mediated ER signaling plays a critical role in breast cancer diagnosis, prognosis, and treatment. Estrogen Receptors are ligand-triggered transcription factors. However, in the absence of a cognate estrogenic ligand, ERs can be activated by a variety of other extracellular signals. Tamoxifen, an anti-estrogen that selectively targets ER, induces substantial regression of breast tumors and an increase in disease-free survival...
July 19, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28723226/improving-the-quality-and-safety-of-frozen-muscle-foods-by-emerging-freezing-technologies-a-review
#16
Ximing Zhan, Da-Wen Sun, Zhiwei Zhu, Qi-Jin Wang
Freezing is one of the most widespread used preservation methods for meats including fish meat. Traditional freezing methods such as air blast freezing and cryogenic freezing could induce some quality deterioration such as damage to cell structure, increased drip loss and poor sensory value. Therefore, novel freezing methods have been developed to minimize the disadvantages of traditional freezing methods. This review describes the enhancement of quality attributes of muscle tissues frozen by novel freezing technologies, including high pressure freezing, electrically and magnetically assisted freezing, ultrasound assisted freezing and antifreeze protein...
July 19, 2017: Critical Reviews in Food Science and Nutrition
https://www.readbyqxmd.com/read/28723224/high-throughput-automated-preparation-and-simulation-of-membrane-proteins-with-htmd
#17
Stefan Doerr, Toni Giorgino, Gerard Martinez-Rosell, João M Damas, Gianni De Fabritiis
HTMD is a programmable scientific platform intended to facilitate simulation-based research in molecular systems. This paper presents the functionalities of HTMD for the preparation of a molecular dynamics simulation starting from PDB structures, building the system using well-known forcefields and applying standardized protocols for running the simulations. We demonstrate the framework's flexibility for high-throughput molecular simulations by applying a preparation, building and simulation protocol with multiple force-fields on all of the seven hundred eukaryotic membrane proteins resolved to-date from the orientation of proteins in membranes (OPM) database...
July 19, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28723223/free-energy-of-binding-and-mechanism-of-interaction-for-the-meevd-tpr2a-peptide-protein-complex
#18
Mauro Lapelosa
The association between the MEEVD C-terminal peptide from the heat shock protein 90 (Hsp90) and tetratricopeptide repeat A (TPR2A) domain of the heat shock organizing protein (Hop) is a useful prototype to study the fundamental molecular details about the Hop-Hsp90 interaction. We study here the mechanism of binding/unbinding, and compute the standard binding free energy and potential of mean force for the association of the MEEVD peptide to the TPR2A domain using the Adaptive Biasing Force (ABF) methodology...
July 19, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28723202/structure-guided-design-of-protein-biosensors-for-phenolic-pollutants
#19
Shamayeeta Ray, Santosh Panjikar, Ruchi Anand
Phenolic aromatic compounds are a major source of environmental pollution. Currently there are no in situ methods for specifically and selectively detecting these pollutants. Here, we exploit the nature's biosensory machinery by employing Acinetobacter calcoaceticus NCIB8250 protein, MopR, as a model system to develop biosensors for selective detection of a spectrum of these pollutants. The X-ray structure of the sensor domain of MopR was used as a scaffold for logic-based tunable biosensor design. By employing a combination of in silico structure guided approaches, mutagenesis and isothermal calorimetric studies, we were able to generate biosensor templates, that can selectively and specifically sense harmful compounds like chlorophenols, cresols, catechol, and xylenols...
March 24, 2017: ACS Sensors
https://www.readbyqxmd.com/read/28723100/to-be-or-not-to-be-five-guidelines-to-avoid-misassignments-in-cross-linking-mass-spectrometry
#20
Claudio Iacobucci, Andrea Sinz
The number of publications in the field of chemical cross-linking/mass spectrometry (MS) for deriving protein 3D structures and for probing protein/protein interactions has largely increased during the last years. MS analysis of the large cross-linking datasets requires an automated data analysis by dedicated software tools, but applying scoring procedures with statistical methods does not eliminate the fun-damental problems of a misassignment of cross-linked products. In fact, we have observed a significant rate of misassigned cross-links in a number of publications, mainly due to the presence of isobaric cross-linked species, an incomplete fragmentation of cross-linked products, and low-mass accuracy fragment ion data...
July 19, 2017: Analytical Chemistry
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