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https://www.readbyqxmd.com/read/28917952/identification-of-potential-allosteric-communication-pathways-between-functional-sites-of-the-bacterial-ribosome-by-graph-and-elastic-network-models
#1
Pelin Guzel, Ozge Kurkcuoglu
BACKGROUND: Accumulated evidence indicates that bacterial ribosome employs allostery throughout its structure for protein synthesis. The nature of the allosteric communication between remote functional sites remains unclear, but the contact topology and dynamics of residues may play role in transmission of a perturbation to distant sites. METHODS/RESULTS: We employ two computationally efficient approaches - graph and elastic network modeling to gain insights about the allosteric communication in ribosome...
September 13, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28917570/detection-of-viable-but-nonculturable-legionella-in-hospital-water-network-following-monochloramine-disinfection
#2
Beatrice Casini, Angelo Baggiani, Michele Totaro, Antonella Mansi, Anna Laura Costa, Francesco Aquino, Mario Miccoli, Paola Valentini, Fabrizio Bruschi, Pier Luigi Lopalco, Gaetano Privitera
BACKGROUND: Prevention of legionellosis still remains a critical issue in healthcare settings where monochloramine (MC) disinfection was recently introduced as a good alternative to chlorine dioxide in controlling Legionella spp. contamination of the hospital water network. Continuous treatments with low MC doses in some instances have induced a viable but non-culturable state (VBNC) of Legionella spp. AIM: We investigated the occurrence of such dormant cells during a long period of continuous MC treatment...
September 13, 2017: Journal of Hospital Infection
https://www.readbyqxmd.com/read/28917254/stereotactic-radiotherapy-in-oligometastatic-cancer
#3
Thomas A C Kennedy, Mark T Corkum, Alexander V Louie
Oligometastatic cancer describes a disease state somewhere between localized and metastatic cancer. Proposed definitions of oligometastatic disease have typically used a cut-off of five or fewer sites of disease. Treatment of oligometastatic disease should have the goal of long-term local control, and in selected cases, disease remission. While several retrospective cohorts argue for surgical excision of limited metastases (metastasectomy) as the preferred treatment option for several clinical indications, limited randomized data exists for treating oligometastases...
September 2017: Chinese Clinical Oncology
https://www.readbyqxmd.com/read/28915819/bacteriophage-therapy-to-combat-bacterial-infections-in-poultry
#4
REVIEW
Andrzej Wernicki, Anna Nowaczek, Renata Urban-Chmiel
Infections in poultry are an economic and health problem in Europe and worldwide. The most common infections are associated with salmonellosis, colibacillosis, campylobacteriosis, and others. The prevalence of Campylobacter-positive poultry flocks in European countries varies from 18% to 90%. In the United States, the prevalence of infected flocks is nearly 90%. A similar percentage of infection has been noted for salmonellosis (about 75-90%) and E. coli (90-95%). The occurence of Clostridium perfringens is a major problem for the poultry industry, with some estimates suggesting colonization of as many as 95% of chickens, resulting in clinical or subclinical infections...
September 16, 2017: Virology Journal
https://www.readbyqxmd.com/read/28915705/promising-landscape-for-regulating-macrophage-polarization-epigenetic-viewpoint
#5
REVIEW
Dexi Zhou, Kui Yang, Lu Chen, Wen Zhang, Zhenyu Xu, Jian Zuo, Hui Jiang, Jiajie Luan
Macrophages are critical myeloid cells with the hallmark of phenotypic heterogeneity and functional plasticity. Macrophages phenotypes are commonly described as classically-activated M1 and alternatively-activated M2 macrophages which play an essential role in the tissues homeostasis and diseases pathogenesis. Alternations of macrophage polarization and function states require precise regulation of target-gene expression. Emerging data demonstrate that epigenetic mechanisms and transcriptional factors are becoming increasingly appreciated in the orchestration of macrophage polarization in response to local environmental signals...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28915352/all-atom-simulations-reveal-protein-charge-decoration-in-the-folded-and-unfolded-ensemble-is-key-in-thermophilic-adaptation
#6
Lucas Sawle, Jonathan Huihui, Kingshuk Ghosh
Thermophilic proteins denature at much higher temperature compared to their mesophilic homologues, in spite of high structural and sequential similarity. Computational approaches to understand this puzzle faces three major challenges: i) unfolded ensembles are usually neglected, ii) simulation studies of the folded states are often too short and iii) majority of investigations focus on a few protein pairs, obscuring the prevalence of different strategies across multiple protein systems. We address these concerns by carrying out all-atom simulations to characterize physicochemical properties of both the folded and disordered ensemble in multiple (12) thermophilic-mesophilic homologous protein pairs...
September 15, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28914607/cortex-wide-bold-fmri-activity-reflects-locally-recorded-slow-oscillation-associated-calcium-waves
#7
Miriam Schwalm, Florian Schmid, Lydia Wachsmuth, Hendrik Backhaus, Andrea Kronfeld, Felipe Aedo Jury, Pierre-Hugues Prouvot, Consuelo Fois, Franziska Albers, Timo van Alst, Cornelius Faber, Albrecht Stroh
Spontaneous slow oscillation-associated slow wave activity represents an internally generated state which is characterized by alternations of network quiescence and stereotypical episodes of neuronal activity - slow wave events. However, it remains unclear which macroscopic signal is related to these active periods of the slow wave rhythm. We used optic fiber-based calcium recordings of local neural populations in cortex and thalamus to detect neurophysiologically defined slow calcium waves in isoflurane anesthetized rats...
September 15, 2017: ELife
https://www.readbyqxmd.com/read/28914395/repetitive-on-demand-drug-release-from-polymeric-matrices-containing-a-macroscopic-spherical-iron-core
#8
Stefan A Rovers, Maartje F Kemmere, Jos T F Keurentjes, Richard Hoogenboom
A system for multiple on-demand drug release has been prepared that can be activated with an alternating magnetic field as external trigger. The core/shell samples have been developed based on a macroscopic spherical iron core coated with a thermoresponsive polymer, poly(styrene-stat-butyl methacrylate), containing ibuprofen as a model drug. During exposure of the samples to the magnetic field (ON state), the release rate of ibuprofen is significantly increased, up to 35 times the release rate without the magnetic field (OFF state)...
September 15, 2017: Journal of Materials Science. Materials in Medicine
https://www.readbyqxmd.com/read/28914302/li3co1-06-1-teo6-synthesis-single-crystal-structure-and-physical-properties-of-a-new-tellurate-compound-with-co-ii-co-iii-mixed-valence-and-orthogonally-oriented-li-ion-channels
#9
Gunter Heymann, Elisabeth Selb, Michaela Kogler, Thomas Götsch, Eva-Maria Köck, Simon Penner, Martina Tribus, Oliver Janka
A tellurate compound with Co(II)/Co(III) mixed valence states and lithium ions within orthogonally oriented channels was realized in Li3Co1.06(1)TeO6. The single-crystal structure determination revealed two independent and interpenetrating Li/O and (Co,Te)/O substructures with octahedral oxygen coordination of the metal atoms. In contrast to other mixed oxides, a honeycomb-like ordering of CoO6 and TeO6 octahedra was not observed. Li3Co1.06(1)TeO6 crystallizes orthorhombically with the following unit cell parameters and refinement results: Fddd, a = 588...
September 15, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28913590/challenges-of-anticoagulation-therapy-in-pregnancy
#10
REVIEW
Annemarie E Fogerty
Thrombotic complications in pregnancy represent a major cause of morbidity and mortality. Pregnancy is a primary hypercoagulable state due to enhanced production of clotting factors, a decrease in protein S activity, and inhibition of fibrinolysis. These physiologic changes will yield a collective rate of venous thromboembolism (VTE) of about 1-2 in 1000 pregnancies for the general obstetric population, which represents a five- to tenfold increased risk in pregnancy compared to age-matched non-pregnant peers...
September 14, 2017: Current Treatment Options in Cardiovascular Medicine
https://www.readbyqxmd.com/read/28912340/donor-recipient-identification-in-para-and-poly-phyletic-trees-under-alternative-hiv-1-transmission-hypotheses-using-approximate-bayesian-computation
#11
Ethan O Romero-Severson, Ingo Bulla, Nick Hengartner, Inês Bártolo, Ana Abecasis, José M Azevedo-Pereira, Nuno Taveira, Thomas Leitner
Diversity of the founding population of Human Immunodeficiency Virus Type 1 (HIV-1) transmissions raises many important biological, clinical, and epidemiological issues. In up to 40% of sexual infections there is clear evidence for multiple founding variants, which can influence the efficacy of putative prevention methods and the reconstruction of epidemiologic histories. To infer who-infected-whom and to compute the probability of alternative transmission scenarios, while explicitly taking phylogenetic uncertainty into account, we created an Approximate Bayesian Computation (ABC) method based on a set of statistics measuring phylogenetic topology, branch lengths, and genetic diversity...
September 14, 2017: Genetics
https://www.readbyqxmd.com/read/28912168/alternative-polyadenylation-of-prelid1-regulates-mitochondrial-ros-signaling-and-cancer-outcomes
#12
Austin E Gillen, Heather M Brechbuhl, Tomomi M Yamamoto, Enos C Kline, Manoj Pillai, Jay Hesselberth, Peter Kabos
Disruption of post-transcriptional gene regulation is a critical step in oncogenesis that can be difficult to observe using traditional molecular techniques. To overcome this limitation, a modified polyadenylation site sequencing (PAS-seq) protocol was used to generate a genome-wide map of alternative polyadenylation (APA) events in human primary breast tumor specimens and matched normal tissue. This approach identified an APA event in the PRELID1 mRNA that enhances its steady state level and translational efficiency, and is a strong breast cancer subtype-dependent predictor of patient clinical outcomes...
September 14, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28912037/the-role-of-mental-imagery-in-mood-amplification-an-investigation-across-subclinical-features-of-bipolar-disorders
#13
Caitlin O'Donnell, Martina Di Simplicio, Randi Brown, Emily A Holmes, Stephanie Burnett Heyes
Vivid emotional mental imagery has been identified across a range of mental disorders. In bipolar spectrum disorders - psychopathologies characterized by mood swings that alternate between depression and mania, and include irritability and mixed affect states - mental imagery has been proposed to drive instability in both 'positive' and 'negative' mood. That is, mental imagery can act as an "emotional amplifier". The current experimental study tested this hypothesis and investigated imagery characteristics associated with mood amplification using a spectrum approach to psychopathology...
August 18, 2017: Cortex; a Journal Devoted to the Study of the Nervous System and Behavior
https://www.readbyqxmd.com/read/28911963/evolution-of-computed-tomography-imaging-the-first-year-after-endovascular-sealing-of-infrarenal-aortic-aneurysms-using-the-nellix-device
#14
Leo H van den Ham, Thijs G Ter Mors, Johannes T Boersen, Jean Paul P M de Vries, Patrick W Vriens, Jan M Heyligers, Michel M P J Reijnen
INTRODUCTION: The Nellix Endovascular Aneurysm Sealing (EVAS) System is an alternative endovascular treatment option for infrarenal aortic aneurysms (AAA) with a unique appearance on Computed Tomography Angiography (CTA). Normal evolution of post-EVAS CTA appearance follow-up is still largely unknown and important in order to timely detect eventual complications. OBJECTIVE: To assess the normal appearance of CTA images 30 days and 1 year after EVAS in 50 consecutive patients...
September 11, 2017: Annals of Vascular Surgery
https://www.readbyqxmd.com/read/28911330/extensive-transcriptomic-and-epigenomic-remodelling-occurs-during-arabidopsis-thaliana-germination
#15
Reena Narsai, Quentin Gouil, David Secco, Akanksha Srivastava, Yuliya V Karpievitch, Lim Chee Liew, Ryan Lister, Mathew G Lewsey, James Whelan
BACKGROUND: Seed germination involves progression from complete metabolic dormancy to a highly active, growing seedling. Many factors regulate germination and these interact extensively, forming a complex network of inputs that control the seed-to-seedling transition. Our understanding of the direct regulation of gene expression and the dynamic changes in the epigenome and small RNAs during germination is limited. The interactions between genome, transcriptome and epigenome must be revealed in order to identify the regulatory mechanisms that control seed germination...
September 15, 2017: Genome Biology
https://www.readbyqxmd.com/read/28910762/deep-edge-guided-recurrent-residual-learning-for-image-super-resolution
#16
Wenhan Yang, Jiashi Feng, Jianchao Yang, Fang Zhao, Jiaying Liu, Zongming Guo, Shuicheng Yan
In this work, we consider the image super-resolution (SR) problem. The main challenge of image SR is to recover high-frequency details of a low-resolution (LR) image that are important for human perception. To address this essentially illposed problem, we introduce a Deep Edge Guided REcurrent rEsidual (DEGREE) network to progressively recover the highfrequency details. Different from most of existing methods that aim at predicting high-resolution (HR) images directly, DEGREE investigates an alternative route to recover the difference between a pair of LR and HR images by recurrent residual learning...
September 8, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28910620/ctag-paperclip-reveals-alternative-polyadenylation-promotes-cell-type-specific-protein-diversity-and-shifts-araf-isoforms-with-microglia-activation
#17
Hun-Way Hwang, Yuhki Saito, Christopher Y Park, Nathalie E Blachère, Yoko Tajima, John J Fak, Ilana Zucker-Scharff, Robert B Darnell
Alternative polyadenylation (APA) is increasingly recognized to regulate gene expression across different cell types, but obtaining APA maps from individual cell types typically requires prior purification, a stressful procedure that can itself alter cellular states. Here, we describe a new platform, cTag-PAPERCLIP, that generates APA profiles from single cell populations in intact tissues; cTag-PAPERCLIP requires no tissue dissociation and preserves transcripts in native states. Applying cTag-PAPERCLIP to profile four major cell types in the mouse brain revealed common APA preferences between excitatory and inhibitory neurons distinct from astrocytes and microglia, regulated in part by neuron-specific RNA-binding proteins NOVA2 and PTBP2...
September 13, 2017: Neuron
https://www.readbyqxmd.com/read/28910569/hierarchical-recruitment-of-polycomb-complexes-revisited
#18
Eshagh Dorafshan, Tatyana G Kahn, Yuri B Schwartz
Polycomb Group (PcG) proteins epigenetically repress key developmental genes and thereby control alternative cell fates. PcG proteins act as complexes that can modify histones and these histone modifications play a role in transmitting the "memory" of the repressed state as cells divide. Here we consider mainstream models that link histone modifications to hierarchical recruitment of PcG complexes and compare them to results of a direct test of interdependence between PcG complexes for recruitment to Drosophila genes...
September 14, 2017: Nucleus
https://www.readbyqxmd.com/read/28910388/structure-of-the-human-transcobalamin-beta-domain-in-four-distinct-states
#19
Joël S Bloch, Markus Ruetz, Bernhard Kräutler, Kaspar P Locher
Vitamin B12 (cyanocobalamin, CNCbl) is an essential cofactor-precursor for two biochemical reactions in humans. When ingested, cobalamins (Cbl) are transported via a multistep transport system into the bloodstream, where the soluble protein transcobalamin (TC) binds Cbl and the complex is taken up into the cells via receptor mediated endocytosis. Crystal structures of TC in complex with CNCbl have been solved previously. However, the initial steps of holo-TC assembly have remained elusive. Here, we present four crystal structures of the beta domain of human TC (TC-beta) in different substrate-bound states...
2017: PloS One
https://www.readbyqxmd.com/read/28910213/the-challenge-of-transforming-the-diagnostic-system-of-personality-disorders
#20
Sabine C Herpertz, Steven K Huprich, Martin Bohus, Andrew Chanen, Marianne Goodman, Lars Mehlum, Paul Moran, Giles Newton-Howes, Lori Scott, Carla Sharp
While the DSM-5 alternative model of personality disorder (PD) diagnosis allows the field to systematically compare categorical and dimensional classifications, the ICD-11 proposal suggests a radical change by restricting the classification of PDs to one category, deleting all specific types, basing clinical service provision exclusively upon a severity dimension, and restricting trait domains to secondary qualifiers without defining cutoff points. This article reflects broad international agreement about the state of PD diagnosis...
September 14, 2017: Journal of Personality Disorders
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