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https://www.readbyqxmd.com/read/27914051/integration-of-molecular-dynamics-based-predictions-into-the-optimization-of-de-novo-protein-designs-limitations-and-benefits
#1
Henrique F Carvalho, Arménio J M Barbosa, Ana C A Roque, Olga Iranzo, Ricardo J F Branco
Recent advances in de novo protein design have gained considerable insight from the intrinsic dynamics of proteins, based on the integration of molecular dynamics simulations protocols on the state-of-the-art de novo protein design protocols used nowadays. With this protocol we illustrate how to set up and run a molecular dynamics simulation followed by a functional protein dynamics analysis. New users will be introduced to some useful open-source computational tools, including the GROMACS molecular dynamics simulation software package and ProDy for protein structural dynamics analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27913948/branched-chain-amino-acids-administration-suppresses-endurance-exercise-related-activation-of-ubiquitin-proteasome-signaling-in-trained-human-skeletal-muscle
#2
Evgeny A Lysenko, Tatiana F Vepkhvadze, Egor M Lednev, Olga L Vinogradova, Daniil V Popov
We tested whether post exercise ingestion of branched-chain amino acids (BCAA < 10 g) is sufficient to activate signaling associated with muscle protein synthesis and suppress exercise-induced activation of mechanisms associated with proteolysis in endurance-trained human skeletal muscle. Nine endurance-trained athletes performed a cycling bout with and without BCAA ingestion (0.1 g/kg). Post exercise ACC(Ser79/222) phosphorylation (endogenous marker of AMPK activity) was increased (~3-fold, P < 0...
December 3, 2016: Journal of Physiological Sciences: JPS
https://www.readbyqxmd.com/read/27913036/pattern-of-calcium-and-parathyroid-hormone-normalization-at-12-months-follow-up-after-parathyroid-operation
#3
Olga A Lavryk, Allan E Siperstein
BACKGROUND: At 12 months after a parathyroid operation, we expect cured patients to have biochemical profiles similar to those of healthy individuals. The aim of the current study was to compare the biochemical characteristics patients at 12 months after parathyroidectomy for primary sporadic hyperparathyroidism with those of healthy controls. METHODS: A total of 547 patients who underwent parathyroid neck operation for primary sporadic hyperparathyroidism from 2000-2014 were analyzed...
November 29, 2016: Surgery
https://www.readbyqxmd.com/read/27912963/overcoming-communication-challenges-in-integrative-supportive-cancer-care-the-integrative-physician-the-psycho-oncologist-and-the-patient
#4
Eran Ben-Arye, Efrat Shavit, Haya Wiental, Elad Schiff, Olga Agour, Noah Samuels
BACKGROUND: Complementary/integrative medicine (CIM) services are increasingly being integrated into conventional supportive cancer care, presenting a number of challenges to communication between healthcare professionals (HCPs). The purpose of the present study was to explore the impact of the communication between integrative physicians (IPs) trained in CIM and social workers (SWs) working as psycho-oncologists in the same oncology setting. We examine whether IP-SW communication correlates with the number of patient-SW sessions, as provided within the oncology department...
December 2016: Complementary Therapies in Medicine
https://www.readbyqxmd.com/read/27911474/is-chelation-therapy-efficient-for-the-treatment-of-intravenous-metallic-mercury-intoxication
#5
Daniela Pelclova, Stepanka Vlckova, Ondrej Bezdicek, Manuela Vaneckova, Pavel Urban, Petr Ridzon, Pavel Diblik, Tomas Navratil, Pavlina Klusackova, Kamil Vlcek, Olga Benesova, Pavel Trestik, Jiri Homolka, Sergey Zakharov
The efficacy of treatment for intravenous elemental mercury intoxication has not been fully studied with regard to clinical outcomes, and treatment recommendations vary. We treated a 41-year-old man with a history of drug abuse and depression who attempted suicide using 1 mL (13.53 g) metallic Hg i.v. He was admitted to the hospital two months later for dyspnoea and thoracic pain and was diagnosed with pneumonia. Hg deposits were seen in the lungs and extra-pulmonary organs. His blood level (372 μg/L) exceeded the population level of 5 μg/L by more than 70-fold...
December 2, 2016: Basic & Clinical Pharmacology & Toxicology
https://www.readbyqxmd.com/read/27911419/methods-of-soil-resampling-to-monitor-changes-in-the-chemical-concentrations-of-forest-soils
#6
Gregory B Lawrence, Ivan J Fernandez, Paul W Hazlett, Scott W Bailey, Donald S Ross, Thomas R Villars, Angelica Quintana, Rock Ouimet, Michael R McHale, Chris E Johnson, Russell D Briggs, Robert A Colter, Jason Siemion, Olivia L Bartlett, Olga Vargas, Michael R Antidormi, Mary M Koppers
Recent soils research has shown that important chemical soil characteristics can change in less than a decade, often the result of broad environmental changes. Repeated sampling to monitor these changes in forest soils is a relatively new practice that is not well documented in the literature and has only recently been broadly embraced by the scientific community. The objective of this protocol is therefore to synthesize the latest information on methods of soil resampling in a format that can be used to design and implement a soil monitoring program...
November 25, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27909547/gastrointestinal-tract-access-for-urological-natural-orifice-transluminal-endoscopic-surgery
#7
REVIEW
Olga Miakicheva, Zachary Hamilton, Alp T Beksac, Sean W Berquist, Abd-Elrahman Hassan, Marc Holden, Ithaar H Derweesh
We conducted a literature review of natural orifice transluminal endoscopic surgery (NOTES), focusing on urologic procedures with gastrointestinal tract access, to update on the development of this novel surgical approach. As part of the methods, a comprehensive electronic literature search for NOTES was conducted using PubMed and Cochrane Library from March 2002 to February 2016 for papers reporting urologic procedures performed utilizing gastrointestinal tract access. A total of 11 peer-reviewed studies examining utility of gastrointestinal access for NOTES urologic procedures were noted, with the first report in 2007...
November 16, 2016: World Journal of Gastrointestinal Endoscopy
https://www.readbyqxmd.com/read/27909059/the-role-of-the-histone-methyltransferase-enhancer-of-zeste-homolog-2-ezh2-in-the-pathobiological-mechanisms-underlying-inflammatory-bowel-disease-ibd
#8
Olga F Sarmento, Phyllis A Svingen, Yuning Xiong, Zhifu Sun, Adebowale O Bamidele, Angela J Mathison, Thomas C Smyrk, Asha A Nair, Michelle M Gonzalez, Mary R Sagstetter, Saurabh Baheti, Dermot P B McGovern, Jessica J Friton, Konstantinos A Papadakis, Goel Gautam, Ramnik J Xavier, Raul A Urrutia, William A Faubion
Regulatory T (Treg) cells expressing the transcription factor FOXP3 play a pivotal role in maintaining immunologic self-tolerance. We and others have previously shown that EZH2 is recruited to the FOXP3 promoter and its targets in Treg cells. To further address the role for EZH2 in Treg cellular function, we have now generated mice that lack EZH2 specifically in Treg cells (EZH2ΔFOXP3+). We find that EZH2 deficiency in FOXP3+ T cells results in lethal multi-organ autoimmunity. We further demonstrate that EZH2ΔFOXP3+ T cells lack a regulatory phenotype in vitro and secrete pro-inflammatory cytokines...
December 1, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27908161/technical-note-magnetic-field-effects-on-gafchromic-film-response-in-mr-igrt
#9
Francisco J Reynoso, Austen Curcuru, Olga Green, Sasa Mutic, Indra J Das, Lakshmi Santanam
PURPOSE: Magnetokinetic changes may affect crystal orientation and polymerization within the active layer of radiochromic film (RCF). This effect is investigated in a magnetic resonance image-guided radiotherapy unit within the context of film dosimetry. METHODS: Gafchromic EBT2 RCF was irradiated in a 30 × 30 × 30 cm(3) solid water phantom using a Co-60 MRI guided radiotherapy system (B = 0.35 T) under normal operating conditions, and under the exact conditions and setup without a magnetic field...
December 2016: Medical Physics
https://www.readbyqxmd.com/read/27908070/physical-constraints-of-cultural-evolution-of-dialects-in-killer-whales
#10
Olga A Filatova, Filipa I P Samarra, Lance G Barrett-Lennard, Patrick J O Miller, John K B Ford, Harald Yurk, Craig O Matkin, Erich Hoyt
Odontocete sounds are produced by two pairs of phonic lips situated in soft nares below the blowhole; the right pair is larger and is more likely to produce clicks, while the left pair is more likely to produce whistles. This has important implications for the cultural evolution of delphinid sounds: the greater the physical constraints, the greater the probability of random convergence. In this paper the authors examine the call structure of eight killer whale populations to identify structural constraints and to determine if they are consistent among all populations...
November 2016: Journal of the Acoustical Society of America
https://www.readbyqxmd.com/read/27907175/p53-specifically-binds-triplex-dna-in-vitro-and-in-cells
#11
Marie Brázdová, Vlastimil Tichý, Robert Helma, Pavla Bažantová, Alena Polášková, Aneta Krejčí, Marek Petr, Lucie Navrátilová, Olga Tichá, Karel Nejedlý, Martin L Bennink, Vinod Subramaniam, Zuzana Bábková, Tomáš Martínek, Matej Lexa, Matej Adámik
Triplex DNA is implicated in a wide range of biological activities, including regulation of gene expression and genomic instability leading to cancer. The tumor suppressor p53 is a central regulator of cell fate in response to different type of insults. Sequence and structure specific modes of DNA recognition are core attributes of the p53 protein. The focus of this work is the structure-specific binding of p53 to DNA containing triplex-forming sequences in vitro and in cells and the effect on p53-driven transcription...
2016: PloS One
https://www.readbyqxmd.com/read/27903933/translocator-positron-emission-tomography-and-magnetic-resonance-spectroscopic-imaging-of-brain-glial-cell-activation-in-multiple-sclerosis
#12
Gourab Datta, Ines R Violante, Gregory Scott, Karl Zimmerman, Andre Santos-Ribeiro, Eugenii A Rabiner, Roger N Gunn, Omar Malik, Olga Ciccarelli, Richard Nicholas, Paul M Matthews
BACKGROUND: Multiple sclerosis (MS) is characterised by a diffuse inflammatory response mediated by microglia and astrocytes. Brain translocator protein (TSPO) positron-emission tomography (PET) and [myo-inositol] magnetic resonance spectroscopy (MRS) were used together to assess this. OBJECTIVE: To explore the in vivo relationships between MRS and PET [(11)C]PBR28 in MS over a range of brain inflammatory burden. METHODS: A total of 23 patients were studied...
November 30, 2016: Multiple Sclerosis: Clinical and Laboratory Research
https://www.readbyqxmd.com/read/27903904/yeast-dna-polymerase-%C3%AE-maintains-consistent-activity-and-mutagenicity-across-a-wide-range-of-physiological-dntp-concentrations
#13
Olga V Kochenova, Rachel Bezalel-Buch, Phong Tran, Alena V Makarova, Andrei Chabes, Peter M J Burgers, Polina V Shcherbakova
In yeast, dNTP pools expand drastically during DNA damage response. We show that similar dNTP elevation occurs in strains, in which intrinsic replisome defects promote the participation of error-prone DNA polymerase ζ (Polζ) in replication of undamaged DNA. To understand the significance of dNTP pools increase for Polζ function, we studied the activity and fidelity of four-subunit Polζ (Polζ4) and Polζ4-Rev1 (Polζ5) complexes in vitro at 'normal S-phase' and 'damage-response' dNTP concentrations. The presence of Rev1 inhibited the activity of Polζ and greatly increased the rate of all three 'X-dCTP' mispairs, which Polζ4 alone made extremely inefficiently...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27902484/depletion-of-mitochondrial-reactive-oxygen-species-downregulates-epithelial-to-mesenchymal-transition-in-cervical-cancer-cells
#14
Galina Shagieva, Lidiya Domnina, Olga Makarevich, Boris Chernyak, Vladimir Skulachev, Vera Dugina
In the course of cancer progression, epithelial cells often acquire morphological and functional characteristics of mesenchymal cells, a process known as epithelial-to-mesenchymal transition (EMT). EMT provides epithelial cells with migratory, invasive, and stem cell capabilities. Reactive oxygen species produced by mitochondria (mtROS) could be of special importance for pro-tumorigenic signaling and EMT.In our study, we used mitochondria-targeted antioxidant SkQ1 to lower the mtROS level and analyze their role in the regulation of the actin cytoskeleton, adhesion junctions, and signaling pathways critical for tumorigenesis of cervical carcinomas...
November 25, 2016: Oncotarget
https://www.readbyqxmd.com/read/27902217/microvirga-ossetica-sp-nov-a-new-species-of-rhizobia-isolated-from-root-nodules-of-the-legume-species-vicia-alpestris-steven-originated-from-north-ossetia-region-in-the-caucasus
#15
Vera Safronova, Irina Kuznetsova, Anna Sazanova, Andrey Belimov, Evgeny Andronov, Elizaveta Chirak, Yuri Osledkin, Olga Onishchuk, Oksana Kurchak, Alexander Shaposhnikov, Anne Willems, Igor Tikhonovich
Gram-negative, rod-shaped strains V5/3MT, V5/5K, V5/5M and V5/13 with a medium growth rate were isolated from root nodules of Vicia alpestris plants growing in the North Ossetia region (Caucasus). The sequencing of the partial 16S rDNA gene (rrs) and four housekeeping genes (dnaK, gyrB, recA and rpoB ) showed that the isolates from V. alpestris were most closely related to the species Microvirga zambiemsis (order Rhizobiales, family Methylobacteriaceae) which was described for the single isolate from root nodule of Listia angolensis growing in Zambia...
October 16, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27902209/fimbriiglobus-ruber-gen-nov-sp-nov-a-gemmata-like-planctomycete-from-sphagnum-peat-bog-and-the-proposal-of-gemmataceae-fam-nov
#16
Irina S Kulichevskaya, Anastasia A Ivanova, Olga I Baulina, W Irene C Rijpstra, Jaap S Sinninghe Damsté, Svetlana N Dedysh
An aerobic, budding, dark pink to red-pigmented bacterium was isolated from an acidic boreal Sphagnum peat bog and designated strain SP5T. Cells of this strain were non-motile spheres that were uniformly covered with crateriform pits and fimbria, and tended to form aggregates during growth in liquid media. Strain SP5T was capable of growth at pH values between 4.0 and 6.8 (optimum at pH 5.5-6.0) and at temperatures between 10 and 30oC (optimum 20-25oC). The preferred growth substrates were sugars and some heteropolysaccharides...
October 24, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27901542/redox-trends-in-cyclometalated-palladium-ii-complexes
#17
Yulia B Dudkina, Kirill V Kholin, Tatyana V Gryaznova, Daut R Islamov, Olga N Kataeva, Ildar Kh Rizvanov, Alina I Levitskaya, Olga D Fominykh, Marina Yu Balakina, Oleg G Sinyashin, Yulia H Budnikova
A series of diverse binuclear and mononuclear cyclometalated palladium(ii) complexes of different structure was investigated by electrochemical techniques combined with density functional theory (DFT) calculations. The studies including cyclic and differential pulse voltammetry, X-ray structure analysis and quantum chemical calculations revealed a regularity of the complexes oxidation potential on the metal-metal distance in the complexes: the larger Pd-Pd distance, the higher oxidation potentials. The reduction potentials feature unusually high negative values while no correlation depending on the structure could be observed...
November 30, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/27901294/performance-of-functional-fibrinogen-thromboelastography-in-children-undergoing-congenital-heart-surgery
#18
Nischal K Gautam, Chunyan Cai, Olga Pawelek, Muhammad B Rafique, Davide Cattano, Evan G Pivalizza
BACKGROUND: Functional Fibrinogen assay of the Thromboelastography (FFTEG), a whole blood viscoelastic hemostatic assay, has been used to estimate fibrinogen levels in adult patients undergoing major surgery but its performance in pediatric patients undergoing cardiac surgery requires evaluation. In this study, we evaluate the correlation between FFTEG parameters and standard laboratory tests for fibrinogen and platelet counts before and after cardiopulmonary bypass in children undergoing repair for congenital heart disease...
November 30, 2016: Paediatric Anaesthesia
https://www.readbyqxmd.com/read/27900825/fungal-infection-dynamics-in-response-to-temperature-in-the-lepidopteran-insect-galleria-mellonella
#19
Vadim Y Kryukov, Olga N Yaroslavtseva, Miranda M A Whitten, Maksim V Tyurin, Katherine J Ficken, Carolyn Greig, Nadja R Melo, Viktor V Glupov, Ivan M Dubovskiy, Tariq M Butt
This study examines how the dynamics of fungus - insect interactions can be modulated by temperature. The wax moth, Galleria mellonella, is a well-studied and important model insect whose larvae in the wild develop optimally at around 34°C in beehives. However, surprisingly little research on wax moths has been conducted at relevant temperatures. In this study, the entomopathogenic fungus Metarhizium robertsii inflicted rapid and substantial mortality on wax moth larvae maintained at a constant temperature of 24°C, but at 34°C a ten-fold higher dose was required to achieve an equivalent mortality...
November 29, 2016: Insect Science
https://www.readbyqxmd.com/read/27900258/adipocyte-specific-hypoxia-inducible-gene-2-promotes-fat-deposition-and-diet-induced-insulin-resistance
#20
Marina T DiStefano, Rachel J Roth Flach, Ozlem Senol-Cosar, Laura V Danai, Joseph V Virbasius, Sarah M Nicoloro, Juerg Straubhaar, Sezin Dagdeviren, Martin Wabitsch, Olga T Gupta, Jason K Kim, Michael P Czech
OBJECTIVE: Adipose tissue relies on lipid droplet (LD) proteins in its role as a lipid-storing endocrine organ that controls whole body metabolism. Hypoxia-inducible Gene 2 (Hig2) is a recently identified LD-associated protein in hepatocytes that promotes hepatic lipid storage, but its role in the adipocyte had not been investigated. Here we tested the hypothesis that Hig2 localization to LDs in adipocytes promotes adipose tissue lipid deposition and systemic glucose homeostasis. METHOD: White and brown adipocyte-deficient (Hig2(fl/fl) × Adiponection cre+) and selective brown/beige adipocyte-deficient (Hig2(fl/fl) × Ucp1 cre+) mice were generated to investigate the role of Hig2 in adipose depots...
December 2016: Molecular Metabolism
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