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https://www.readbyqxmd.com/read/28214450/in-silico-structural-and-functional-analysis-of-mesorhizobium-acc-deaminase
#1
Krishnendu Pramanik, Tithi Soren, Soumik Mitra, Tushar Kanti Maiti
Nodulation is one of the very important processes of legume plants as it is the initiating event of fixing nitrogen. Although ethylene has essential role in normal plant metabolism but it has also negative impact on plants particularly in nodule formation in legume plants. It is also produced due to a variety of biotic or abiotic stresses. 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase is a rhizobial enzyme which cleaves ACC (immediate precursor of ethylene) into α-ketobutyrate and ammonia. As a result, the level of ethylene from the plant cells is decreased and the negative impact of ethylene on nodule formation is reduced...
February 11, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28214359/gene-expression-plasticity-in-response-to-salinity-acclimation-in-threespine-stickleback-ecotypes-from-different-salinity-habitats
#2
Taylor C Gibbons, David C H Metzger, Timothy M Healy, Patricia M Schulte
Phenotypic plasticity is thought to facilitate the colonization of novel environments and shape the direction of evolution in colonizing populations. However, the relative prevalence of various predicted patterns of changes in phenotypic plasticity following colonization remain unclear. Here we use a whole-transcriptome approach to characterize patterns of gene expression plasticity in the gills of a freshwater-adapted and a saltwater-adapted ecotype of threespine stickleback (Gasterosteus aculeatus) exposed to a range of salinities...
February 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28213894/controllable-rotating-behavior-of-individual-dielectric-micro-rod-in-a-rotating-electric-field
#3
Weiyu Liu, Yukun Ren, Ye Tao, Yanbo Li, Xiaoming Chen
We report herein controllable rotating behavior of an individual dielectric micro-rod driven by a background rotating electric field. By disposing or removing structured floating microelectrode, the rigid rod suspended in electrolyte solution accordingly exhibits co-field or anti-field rotating motion. In the absence of the ideally polarizable metal surface, the dielectric rod rotates opposite to propagation of electric field, with the measured rotating rate much larger than predicted by Maxwell-Wager interfacial polarization theory incorporating surface conduction of fixed bond charge...
February 18, 2017: Electrophoresis
https://www.readbyqxmd.com/read/28213527/advancing-viral-rna-structure-prediction-measuring-the-thermodynamics-of-pyrimidine-rich-internal-loops
#4
Andy Phan, Katherine Mailey, Jessica Sakai, Xiaobo Gu, Susan J Schroeder
Accurate thermodynamic parameters improve RNA structure predictions and thus accelerate understanding of RNA function and the identification of RNA drug binding sites. Many viral RNA structures, such as internal ribosome entry sites, have internal loops and bulges that are potential drug target sites. Current models used to predict internal loops are biased towards small, symmetric purine loops, and thus poorly predict asymmetric, pyrimidine-rich loops with more than 6 nucleotides that occur frequently in viral RNA...
February 17, 2017: RNA
https://www.readbyqxmd.com/read/28213340/demographic-and-indication-specific-characteristics-have-limited-association-with-social-network-engagement-evidence-from-24-954-members-of-four-health-care-support-groups
#5
Trevor van Mierlo, Xinlong Li, Douglas Hyatt, Andrew T Ching
BACKGROUND: Digital health social networks (DHSNs) are widespread, and the consensus is that they contribute to wellness by offering social support and knowledge sharing. The success of a DHSN is based on the number of participants and their consistent creation of externalities through the generation of new content. To promote network growth, it would be helpful to identify characteristics of superusers or actors who create value by generating positive network externalities. OBJECTIVE: The aim of the study was to investigate the feasibility of developing predictive models that identify potential superusers in real time...
February 17, 2017: Journal of Medical Internet Research
https://www.readbyqxmd.com/read/28213213/titanium-iv-ion-modified-covalent-organic-frameworks-for-specific-enrichment-of-phosphopeptides
#6
Heping Wang, Fenglong Jiao, Fangyuan Gao, Yayao Lv, Qiong Wu, Yan Zhao, Yehua Shen, Yangjun Zhang, Xiaohong Qian
To date, plenty of new alternative materials for phosphopeptides enrichment prior to mass spectrometry (MS) analysis appear, especially immobilized metal ion affinity chromatography (IMAC) materials. The variable combinations with different metal ions, chelating ligands and solid supports offer full of optionality for IMAC. However, further improvement was predicted by the tedious and complex synthetic process. In this work, a novel covalent organic framework (COF)-based IMAC material (denoted TpPa-2-Ti(4+)) was prepared simply by direct immobilizing Ti (IV) into TpPa-2 COFs without any extra chelating ligands...
May 1, 2017: Talanta
https://www.readbyqxmd.com/read/28213207/epimetabolites-discovering-metabolism-beyond-building-and-burning
#7
REVIEW
Megan R Showalter, Tomas Cajka, Oliver Fiehn
Enzymatic transformations of primary, canonical metabolites generate active biomolecules that regulate important cellular and physiological processes. Roles include regulation of histone demethylation in epigenetics, inflammation in tissue injury, insulin sensitivity, cancer cell invasion, stem cell pluripotency status, inhibition of nitric oxide signaling and others. Such modified compounds, defined as epimetabolites, have functions distinct from classic hormones as well as removed from generic anabolism and catabolism...
February 14, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28213174/evidence-of-the-presence-of-a-calmodulin-sensitive-plasma-membrane-ca-2-atpase-in-trypanosoma-equiperdum
#8
María Carolina Pérez-Gordones, José Rubén Ramírez-Iglesias, Vincenza Cervino, Graciela L Uzcanga, Gustavo Benaim, Marta Mendoza
Trypanosoma equiperdum belongs to the subgenus Trypanozoon, which has a significant socio-economic impact by limiting animal protein productivity worldwide. Proteins involved in the intracellular Ca(2+) regulation are prospective chemotherapeutic targets since several drugs used in experimental treatment against trypanosomatids exert their action through the disruption of the parasite intracellular Ca(2+) homeostasis. Therefore, the plasma membrane Ca(2+)-ATPase (PMCA) is considered as a potential drug target...
February 14, 2017: Molecular and Biochemical Parasitology
https://www.readbyqxmd.com/read/28212856/probis-tools-algorithm-database-and-web-servers-for-predicting-and-modeling-of-biologically-interesting-proteins
#9
REVIEW
Janez Konc, Dušanka Janežič
ProBiS (Protein Binding Sites) Tools consist of algorithm, database, and web servers for prediction of binding sites and protein ligands based on the detection of structurally similar binding sites in the Protein Data Bank. In this article, we review the operations that ProBiS Tools perform, provide comments on the evolution of the tools, and give some implementation details. We review some of its applications to biologically interesting proteins. ProBiS Tools are freely available at http://probis.cmm.ki.si and http://probis...
February 14, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28212855/depth-dependent-amino-acid-substitution-matrices-and-its-use-in-predicting-deleterious-mutations
#10
REVIEW
Nida Farheen, Neeladri Sen, Sanjana Nair, Kuan Pern Tan, M S Madhusudhan
The 20 naturally occurring amino acids have different environmental preferences of where they are likely to occur in protein structures. Environments in a protein can be classified by their proximity to solvent by the residue depth measure. Since the frequencies of amino acids are different at various depth levels, the substitution frequencies should vary according to depth. To quantify these substitution frequencies, we built depth dependent substitution matrices. The dataset used for creation of the matrices consisted of 3696 high quality, non redundant pairwise protein structural alignments...
February 14, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28212667/assessing-the-interruption-of-the-transmission-of-human-helminths-with-mass-drug-administration-alone-optimizing-the-design-of-cluster-randomized-trials
#11
Roy Anderson, Sam Farrell, Hugo Turner, Judd Walson, Christl A Donnelly, James Truscott
BACKGROUND: A method is outlined for the use of an individual-based stochastic model of parasite transmission dynamics to assess different designs for a cluster randomized trial in which mass drug administration (MDA) is employed in attempts to eliminate the transmission of soil-transmitted helminths (STH) in defined geographic locations. The hypothesis to be tested is: Can MDA alone interrupt the transmission of STH species in defined settings? Clustering is at a village level and the choice of clusters of villages is stratified by transmission intensity (low, medium and high) and parasite species mix (either Ascaris, Trichuris or hookworm dominant)...
February 17, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28212534/association-between-echocardiographic-structural-parameters-and-body-weight-in-wistar-rats
#12
Silvio A Oliveira-Junior, Paula F Martinez, William Y C Fan, Bruno T Nakatani, Luana U Pagan, Carlos R Padovani, Antonio C Cicogna, Marina P Okoshi, Katashi Okoshi
BACKGROUND: The association between echocardiographic structural parameters and body weight (BW) during rat development has been poorly addressed. We evaluated echocardiographic variables: left ventricular (LV) end-diastolic (LVDD) and end-systolic (LVSD) diameters, LV diastolic posterior wall thickness (PWT), left atrial diameter (LA), and aortic diameter (AO) in function of BW during development.Results/Materials and Methods: Male Wistar rats (n = 328, BW: 302-702 g) were retrospectively used to construct regression models and 95% confidence intervals relating to cardiac structural parameters and BW...
February 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/28212499/validation-of-the-french-version-of-the-dsm-5-yale-food-addiction-scale-in-a-nonclinical-sample
#13
Paul Brunault, Robert Courtois, Ashley N Gearhardt, Philippe Gaillard, Kevin Journiac, Sarah Cathelain, Christian Réveillère, Nicolas Ballon
OBJECTIVE: The Yale Food Addiction Scale (YFAS) is the only questionnaire that assesses food addiction (FA) based on substance dependence criteria in the Diagnostic and Statistical Manual of Mental Disorders (DSM), Fourth Edition, Text Revision. Following recent updating of addiction criteria, a new DSM-5 version (YFAS 2.0) has been developed. Our study tested the psychometric properties of the French YFAS 2.0 in a nonclinical population. METHOD: We assessed 330 nonclinical participants for FA (French YFAS 2...
March 2017: Canadian Journal of Psychiatry. Revue Canadienne de Psychiatrie
https://www.readbyqxmd.com/read/28212420/transcriptome-using-illumina-sequencing-reveals-the-traits-of-spermatogenesis-and-developing-testes-in-eriocheir-sinensis
#14
Gen-Liang Li, Hui Qian
Chinese mitten crab (Eriocheir sinensis) has the spermatozoa with typical aflagellate, decondensed chromatin, cup-shaped nuclei, and radial arms. However, the mechanism of spermatogenesis during which the specific spermatozoa are generated in this species is yet unclear. Here, the transcriptome of developing testis in E. sinensis was analyzed using the ways of RNA-seq and bioinformatics analysis to identify candidate genes potentially involved in development of testis and spermatogenesis. The Illumina HiSeq2500 sequencing of three replicons of samples produced a total of 145...
2017: PloS One
https://www.readbyqxmd.com/read/28212084/objective-quality-assessment-of-screen-content-images-by-uncertainty-weighting
#15
Yuming Fang, Jiebin Yan, Jiaying Liu, Shiqi Wang, Qiaohong Li, Zongming Guo
In this paper, we propose a novel full-reference objective quality assessment metric for screen content images (SCIs) by structure features and uncertainty weighting (SFUW). The input SCI is first divided into textual and pictorial regions. The visual quality of textual regions is estimated based on perceptual structural similarity, where the gradient information is adopted as the structural feature. To predict the visual quality of pictorial regions in SCIs, we extract the structural features and luminance features for similarity computation between the reference and distorted pictorial patches...
February 15, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28211907/identification-of-extracellular-segments-by-mass-spectrometry-improves-topology-prediction-of-transmembrane-proteins
#16
Tamás Langó, Gergely Róna, Éva Hunyadi-Gulyás, Lilla Turiák, Julia Varga, László Dobson, György Várady, László Drahos, Beáta G Vértessy, Katalin F Medzihradszky, Gergely Szakács, Gábor E Tusnády
Transmembrane proteins play crucial role in signaling, ion transport, nutrient uptake, as well as in maintaining the dynamic equilibrium between the internal and external environment of cells. Despite their important biological functions and abundance, less than 2% of all determined structures are transmembrane proteins. Given the persisting technical difficulties associated with high resolution structure determination of transmembrane proteins, additional methods, including computational and experimental techniques remain vital in promoting our understanding of their topologies, 3D structures, functions and interactions...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28211741/enhanced-crystal-growth-in-binary-lennard-jones-mixtures
#17
M Radu, K Kremer
We study the crystal growth in binary Lennard-Jones mixtures by molecular dynamics simulations. Growth dynamics, the structure of the liquid-solid interfaces as well as droplet incorporation into the crystal vary with solution properties. For demixed systems we observe a strongly enhanced crystal growth at the cost of enclosed impurities. Furthermore, we find different interface morphologies depending on solubility. We relate our observations to growth mechanisms based on the Gibbs-Thomson effect as well as to predictions of the Kardar-Parisi-Zhang theory in 2+1 dimensions...
February 3, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28211708/direct-observation-of-spatiotemporal-dynamics-of-short-electron-bunches-in-storage-rings
#18
C Evain, E Roussel, M Le Parquier, C Szwaj, M-A Tordeux, J-B Brubach, L Manceron, P Roy, S Bielawski
In recent synchrotron radiation facilities, the use of short (picosecond) electron bunches is a powerful method for producing giant pulses of terahertz coherent synchrotron radiation. Here we report on the first direct observation of these pulse shapes with a few picoseconds resolution, and of their dynamics over a long time. We thus confirm in a very direct way the theories predicting an interplay between two physical processes. Below a critical bunch charge, we observe a train of identical THz pulses (a broadband Terahertz comb) stemming from the shortness of the electron bunches...
February 3, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28211705/small-x-asymptotics-of-the-quark-helicity-distribution
#19
Yuri V Kovchegov, Daniel Pitonyak, Matthew D Sievert
We construct a numerical solution of the small-x evolution equations derived in our recent work [J. High Energy Phys. 01 (2016) 072.JHEPFG1029-847910.1007/JHEP01(2016)072] for the (anti)quark transverse momentum dependent helicity TMDs and parton distribution functions (PDFs) as well as the g_{1} structure function. We focus on the case of large N_{c}, where one finds a closed set of equations. Employing the extracted intercept, we are able to predict directly from theory the behavior of the quark helicity PDFs at small x, which should have important phenomenological consequences...
February 3, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28211620/benchmark-ditopic-binding-of-cl-and-cs-by-the-macrocycle-hexacyclen
#20
Juan Ramon Aviles-Moreno, Giel Berden, Jos Oomens, Bruno Martinez-Haya
The ditopic binding of organic and inorganic anions and cations constitutes a distinct feature of polyazamacrocycles that underlies their action as intermediate docking and exchange ionophoric sites for tailored supramolecular synthesis and sensors. This work investigates the Cl- and Cs+ complexes formed by hexacyclen (1,4,7,10,13,16-hexaazacyclooctadecane, ha18c6), a benchmark building block of ion-pair polyamine receptors. Infrared action spectroscopy is employed to characterize the anionic and cationic complexes under controlled environmental conditions in an ion trap...
February 17, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
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