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https://www.readbyqxmd.com/read/29786967/developmental-chromatin-restriction-of-pro-growth-gene-networks-acts-as-an-epigenetic-barrier-to-axon-regeneration-in-cortical-neurons
#1
Ishwariya Venkatesh, Vatsal Mehra, Zimei Wang, Ben Califf, Murray G Blackmore
Axon regeneration in the central nervous system is prevented in part by a developmental decline in the intrinsic regenerative ability of maturing neurons. This loss of axon growth ability likely reflects widespread changes in gene expression, but the mechanisms that drive this shift remain unclear. Chromatin accessibility has emerged as a key regulatory mechanism in other cellular contexts, raising the possibility that chromatin structure may contribute to the age-dependent loss of regenerative potential. Here we establish an integrated bioinformatic pipeline that combines analysis of developmentally dynamic gene networks with transcription factor regulation and genome-wide maps of chromatin accessibility...
May 22, 2018: Developmental Neurobiology
https://www.readbyqxmd.com/read/29786858/ecosystem-heterogeneity-and-diversity-mitigate-amazon-forest-resilience-to-frequent-extreme-droughts
#2
Marcos Longo, Ryan G Knox, Naomi M Levine, Luciana F Alves, Damien Bonal, Plinio B Camargo, David R Fitzjarrald, Matthew N Hayek, Natalia Restrepo-Coupe, Scott R Saleska, Rodrigo da Silva, Scott C Stark, Raphael P Tapajós, Kenia T Wiedemann, Ke Zhang, Steven C Wofsy, Paul R Moorcroft
The impact of increases in drought frequency on the Amazon forest's composition, structure and functioning remain uncertain. We used a process- and individual-based ecosystem model (ED2) to quantify the forest's vulnerability to increased drought recurrence. We generated meteorologically realistic, drier-than-observed rainfall scenarios for two Amazon forest sites, Paracou (wetter) and Tapajós (drier), to evaluate the impacts of more frequent droughts on forest biomass, structure and composition. The wet site was insensitive to the tested scenarios, whereas at the dry site biomass declined when average rainfall reduction exceeded 15%, due to high mortality of large-sized evergreen trees...
May 22, 2018: New Phytologist
https://www.readbyqxmd.com/read/29786503/relationships-between-theoretically-derived-short-term-outcomes-and-support-for-policy-among-the-public-and-decision-makers
#3
Carol L Schmitt, Laurel Curry, Vanessa Boudewyns, Pamela A Williams, LaShawn Glasgow, Deanna Van Hersh, Jeffrey Willett, Todd Rogers
PURPOSE AND OBJECTIVES: Policy change is a lengthy and complex process. Thus, it is important to articulate hypothesized causal pathways between advocacy activities and policy change outcomes and to identify and monitor early indicators of progress toward policy change. INTERVENTION APPROACH: The Kansas Health Foundation supports grantee efforts to address the public health effects of obesity through evidence-based policy, systems, and environmental change interventions...
May 17, 2018: Preventing Chronic Disease
https://www.readbyqxmd.com/read/29786430/galaxygpcrloop-template-based-and-ab-initio-structure-sampling-of-the-extracellular-loops-of-g-protein-coupled-receptors
#4
Jonghun Won, Gyu Rie Lee, Hahnbeom Park, Chaok Seok
The second extracellular loops (ECL2s) of G-protein-coupled receptors (GPCRs) are often involved in GPCR functions, and their structures have important implications in drug discovery. However, structure prediction of ECL2 is difficult because of its long length and the structural diversity among different GPCRs. In this study, a new ECL2 conformational sampling method involving both template-based and ab initio sampling was developed. Inspired by observation of similar ECL2 structures of closely related GPCRs, a template-based sampling method employing loop structure templates selected from the structure database was developed...
May 22, 2018: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29785882/the-relationship-between-repetitive-finger-movement-and-quality-of-life-in-parkinson-s-disease
#5
Elizabeth L Stegemöller, Jennifer Uzochukwu, Mack Shelley
BACKGROUND: Repetitive finger movement significantly impacts daily living activities, but there have been limited studies determining how repetitive finger movement impacts quality of life (QOL) in persons with Parkinson's disease (PD). The purpose of this study was to determine the relationship between impairment in repetitive finger movement and QOL in persons with PD. METHODS: Eighty-four participants with PD completed a repetitive movement task and the Parkinson's Disease Questionnaire (PDQ)...
May 22, 2018: Neurological Research
https://www.readbyqxmd.com/read/29785835/predicting-the-ecological-impacts-of-large-dam-removals-on-a-river-network-based-on-habitat-network-structure-and-flow-regimes
#6
Nobuo Ishiyama, Masahiro Ryo, Taiga Kataoka, Shigeya Nagayama, Masanao Sueyoshi, Akira Terui, Terutaka Mori, Takumi Akasaka, Futoshi Nakamura
Large dams have provided vital protection and services to human life and the economy. However, an increasing number of large dams worldwide have aged considerably and have thus become hazardous due to impaired functions. The removal of large dams has excellent potential to restore habitat connectivity and flow regimes; therefore, projecting the related ecological consequences is a key emerging need for water resource and ecosystem management. However, no modeling methods are currently available for such projections at the basin scale...
May 22, 2018: Conservation Biology: the Journal of the Society for Conservation Biology
https://www.readbyqxmd.com/read/29785732/the-mental-representation-of-human-action
#7
Sydney Levine, Alan M Leslie, John Mikhail
Various theories of moral cognition posit that moral intuitions can be understood as the output of a computational process performed over structured mental representations of human action. We propose that action plan diagrams-"act trees"-can be a useful tool for theorists to succinctly and clearly present their hypotheses about the information contained in these representations. We then develop a methodology for using a series of linguistic probes to test the theories embodied in the act trees. In Study 1, we validate the method by testing a specific hypothesis (diagrammed by act trees) about how subjects are representing two classic moral dilemmas and finding that the data support the hypothesis...
May 21, 2018: Cognitive Science
https://www.readbyqxmd.com/read/29785722/electrostatic-recognition-in-substrate-binding-to-serine-proteases
#8
Birgit J Waldner, Johannes Kraml, Ursula Kahler, Alexander Spinn, Michael Schauperl, Maren Podewitz, Julian E Fuchs, Gabriele Cruciani, Klaus R Liedl
Serine proteases of the Chymotrypsin family are structurally very similar but have very different substrate preferences. This study investigates a set of 9 different proteases of this family comprising proteases that prefer substrates containing positively charged amino acids, negatively charged amino acids, and uncharged amino acids with varying degree of specificity. Here, we show that differences in electrostatic substrate preferences can be predicted reliably by electrostatic molecular interaction fields employing customized GRID probes...
May 22, 2018: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/29785641/in-silico-analysis-of-natural-resistance-associated-macrophage-protein-nramp-family-of-transporters-in-rice
#9
Anitha Mani, Kavitha Sankaranarayanan
In Oryza sativa (rice) there are seven members in the NRAMP (natural resistance- associated macrophage protein) family of transporter proteins. They have been identified as OsNRAMP1, OsNRAMP2, OsNRAMP3, OsNRAMP4, OsNRAMP5, OsNRAMP6 and OsNRAMP7. Several metal ions like Zn2+ , Mn2+ , Fe2+ , Cd2+ etc. have been studied to be transported via NRAMP transporter proteins in rice plant. In spite of this, very little information is available regarding these transporters. Hence it is important to computationally predict and characterize the OsNRAMP family of transporters for studying and understanding their molecular insights in future studies...
May 21, 2018: Protein Journal
https://www.readbyqxmd.com/read/29785561/reptb-a-gene-ontology-based-drug-repurposing-approach-for-tuberculosis
#10
Anurag Passi, Neeraj Kumar Rajput, David J Wild, Anshu Bhardwaj
Tuberculosis (TB) is the world's leading infectious killer with 1.8 million deaths in 2015 as reported by WHO. It is therefore imperative that alternate routes of identification of novel anti-TB compounds are explored given the time and costs involved in new drug discovery process. Towards this, we have developed RepTB. This is a unique drug repurposing approach for TB that uses molecular function correlations among known drug-target pairs to predict novel drug-target interactions. In this study, we have created a Gene Ontology based network containing 26,404 edges, 6630 drug and 4083 target nodes...
May 21, 2018: Journal of Cheminformatics
https://www.readbyqxmd.com/read/29785435/assessing-the-performance-of-mm-pbsa-and-mm-gbsa-methods-7-entropy-effects-on-the-performance-of-end-point-binding-free-energy-calculation-approaches
#11
Huiyong Sun, Lili Duan, Fu Chen, Hui Liu, Zhe Wang, Peichen Pan, Feng Zhu, John Z H Zhang, Tingjun Hou
Entropy effects play an important role in drug-target interactions, but the entropic contribution to ligand-binding affinity is often neglected by end-point binding free energy calculation methods, such as MM/GBSA and MM/PBSA, due to the expensive computational cost of normal mode analysis (NMA). Here, we systematically investigated entropy effects on the prediction power of MM/GBSA and MM/PBSA using >1500 protein-ligand systems and six representative AMBER force fields. Two computationally efficient methods, including NMA based on truncated structures and the interaction entropy approach, were used to estimate the entropic contributions to ligand-target binding free energies...
May 22, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29785278/reserve-building-activities-attenuate-treatment-burden-in-chronic-illness-the-mediating-role-of-appraisal-and-social-support
#12
Carolyn E Schwartz, Jie Zhang, Wesley Michael, David T Eton, Bruce D Rapkin
This study examines the importance of four psychosocial factors-personality, cognitive appraisal of quality of life, social support, and current reserve-building-in predicting treatment burden in chronically ill patients. Chronically ill patients ( n  = 446) completed web-based measures. Structural equation modeling was used to investigate psychosocial factors predicting treatment burden. Reserve-building activities indirectly reduced treatment burden by: (1) reducing health worries appraisals, (2) reducing financial difficulties, (3) increasing calm and peaceful appraisals, and (4) increasing perceived social support...
January 2018: Health Psychology Open
https://www.readbyqxmd.com/read/29785124/upregulation-of-circ_0066444-promotes-the-proliferation-invasion-and-migration-of-gastric-cancer-cells
#13
Dawei Rong, Chaoxi Dong, Kai Fu, Hanjin Wang, Weiwei Tang, Hongyong Cao
Background: Circular RNAs (circRNAs), which have closed-loop structure, are involved in the pathogenesis of human diseases including various types of carcinomas. The present study aimed to investigate the relationship between a new circular RNA named circ_0066444 and gastric cancer (GC) carcinogenesis. Materials and methods: The circ_0066444 levels in 106 paired gastric carcinoma tissues and related adjacent normal tissues were detected by real-time quantitative reverse-transcription polymerase chain reaction...
2018: OncoTargets and Therapy
https://www.readbyqxmd.com/read/29785055/mindfulness-training-induces-structural-connectome-changes-in-insula-networks
#14
Paul B Sharp, Bradley P Sutton, Erick J Paul, Nikolai Sherepa, Charles H Hillman, Neal J Cohen, Arthur F Kramer, Ruchika Shaurya Prakash, Wendy Heller, Eva H Telzer, Aron K Barbey
Although mindfulness meditation is known to provide a wealth of psychological benefits, the neural mechanisms involved in these effects remain to be well characterized. A central question is whether the observed benefits of mindfulness training derive from specific changes in the structural brain connectome that do not result from alternative forms of experimental intervention. Measures of whole-brain and node-level structural connectome changes induced by mindfulness training were compared with those induced by cognitive and physical fitness training within a large, multi-group intervention protocol (n = 86)...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29785034/trophic-overlap-between-expanding-and-contracting-fish-predators-in-a-range-margin-undergoing-change
#15
Mats Westerbom, Antti Lappalainen, Olli Mustonen, Alf Norkko
Climate change is predicted to cause a freshening of the Baltic Sea, facilitating range expansions of freshwater species and contractions of marine. Resident marine flounders (Platichthys flesus) and expansive freshwater roach (Rutilus rutilus) are dominant consumers in the Baltic Sea sublittoral where they occur in partial sympatry. By comparing patterns of resource use by flounders and roach along a declining resource gradient of blue mussels (Mytilus trossulus) our aim was to explore predator functional responses and the degree of trophic overlap...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29785007/characterization-and-prevalence-of-two-novel-chek2-large-deletions-in-greek-breast-cancer-patients
#16
Paraskevi Apostolou, Florentia Fostira, Vasiliki Mollaki, Angeliki Delimitsou, Metaxia Vlassi, George Pentheroudakis, Eleni Faliakou, Panagoula Kollia, George Fountzilas, Drakoulis Yannoukakos, Irene Konstantopoulou
Germline CHEK2 mutations confer increased cancer risk, for breast and other types, which is variable depending on the specific mutation. Of these, Large Genomic Rearrangements (LGRs) have been rarely reported; to date only eight LGRs have been published with just the Czech founder mutation, the deletion of exons 9 and 10, being molecularly characterized and studied extensively. The present study aimed to molecularly define and determine the contribution of two rare, apparently novel CHEK2 LGRs, among Greek breast cancer patients...
May 22, 2018: Journal of Human Genetics
https://www.readbyqxmd.com/read/29784983/thermodynamic-and-crystallographic-model-for-anion-uptake-by-hydrated-calcium-aluminate-afm-an-example-of-molybdenum
#17
Nicolas C M Marty, Sylvain Grangeon, Erik Elkaïm, Christophe Tournassat, Clémence Fauchet, Francis Claret
Amongst all cement phases, hydrated calcium aluminate (AFm) plays a major role in the retention of anionic species. Molybdenum (Mo), whose 93 Mo isotope is considered a major steel activation product, will be released mainly under the form of MoO4 2- in a radioactive waste repository. Understanding its fate is of primary importance in a safety analysis of such disposal. This necessitates models that can both predict quantitatively the sorption of Mo by AFm and determine the nature of the sorption process (i...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29784955/integration-of-large-scale-data-for-extraction-of-integrated-arabidopsis-root-cell-type-specific-models
#18
Michael Scheunemann, Siobhan M Brady, Zoran Nikoloski
Plant organs consist of multiple cell types that do not operate in isolation, but communicate with each other to maintain proper functions. Here, we extract models specific to three developmental stages of eight root cell types or tissue layers in Arabidopsis thaliana based on a state-of-the-art constraint-based modeling approach with all publicly available transcriptomics and metabolomics data from this system to date. We integrate these models into a multi-cell root model which we investigate with respect to network structure, distribution of fluxes, and concordance to transcriptomics and proteomics data...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29784884/the-effector-gene-xopae-of-xanthomonas-euvesicatoria-85-10-is-part-of-an-operon-and-encodes-an-e3-ubiquitin-ligase
#19
Georgy Popov, Bharat Bhusan Majhi, Guido Sessa
The type III effector XopAE from the Xanthomonas euvesicatoria strain 85-10 ( Xe 85-10) was previously shown to inhibit plant immunity and enhance pathogen-induced disease symptoms. Evolutionary analysis of 60 xopAE alleles ( AEal ) revealed that the xopAE locus is conserved in multiple Xanthomonas species. The majority of xopAE alleles (55 out of 60) encodes a single ORF ( xopAE ), while in 5 alleles, including AEal 37 of the Xe 85-10 strain, a frame-shift splits the locus into two ORFs ( hpaF and a truncated xopAE )...
May 21, 2018: Journal of Bacteriology
https://www.readbyqxmd.com/read/29784778/extant-fold-switching-proteins-are-widespread
#20
Lauren L Porter, Loren L Looger
A central tenet of biology is that globular proteins have a unique 3D structure under physiological conditions. Recent work has challenged this notion by demonstrating that some proteins switch folds, a process that involves remodeling of secondary structure in response to a few mutations (evolved fold switchers) or cellular stimuli (extant fold switchers). To date, extant fold switchers have been viewed as rare byproducts of evolution, but their frequency has been neither quantified nor estimated. By systematically and exhaustively searching the Protein Data Bank (PDB), we found ∼100 extant fold-switching proteins...
May 21, 2018: Proceedings of the National Academy of Sciences of the United States of America
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