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https://www.readbyqxmd.com/read/28088762/the-super-n-motifs-model-a-novel-alignment-free-approach-for-representing-and-comparing-rna-secondary-structures
#1
Jean-Pierre Séhi Glouzon, Jean-Pierre Perreault, Shengrui Wang
MOTIVATION: Comparing ribonucleic acid (RNA) secondary structures of arbitrary size uncovers structural patterns that can provide a better understanding of RNA functions. However, performing fast and accurate secondary structure comparisons is challenging when we take into account the RNA configuration (i.e. linear or circular), the presence of pseudoknot and G-quadruplex (G4) motifs and the increasing number of secondary structures generated by high-throughput probing techniques. To address this challenge, we propose the super-n-motifs model based on a latent analysis of enhanced motifs comprising not only basic motifs but also adjacency relations...
January 14, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28088689/syntheses-structures-and-fluorescence-properties-of-three-rare-earth-containing-docosatungstates
#2
Hailou Li, Yajie Liu, Rui Zheng, Xing Ma, Lijuan Chen, Junwei Zhao
Three rare-earth containing docosatungstates Na3H2[RE(H2O)4][RE(H2O)5]2[W22O74H2]·36H2O [RE=Dy(III) (1), Ho(III) (2), Y(III) (3)] have been synthesized by reaction of Na2WO4·2H2O, dimethylamine hydrochloride (DMAHC) and RE(NO3)3·6H2O in the aqueous solution and characterized by elemental analyses, IR spectra, thermogravimetric (TG) analysis, powder X-ray diffraction (PXRD) and single-crystal X-ray diffraction. 1-3 are isomorphous and each molecular unit consists of a S-shaped docosatungstate [W22O74H2](14-) polyoxoanion with two supporting [RE(H2O)5](3+) cations and one disordered [RE(H2O)4](3+) cation...
January 9, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28088682/female-sexual-function-mediates-the-effects-of-medication-adherence-on-quality-of-life-in-people-with-epilepsy
#3
Chung-Ying Lin, Andrea Burri, Bengt Fridlund, Amir H Pakpour
PURPOSE: The purpose of this study was to understand the mediating effects of female sexual functioning in the association between medication adherence and quality of life (QoL) in Iranian women with epilepsy (WWE). METHODS: Women's sexual functioning was measured using Female Sexual Function Index; QoL using Quality of Life in Epilepsy; epilepsy severity using Liverpool Seizure Severity Scale; subjective medication adherence using Medication Adherence Report Scale; and objective medication adherence using serum level for antiepileptic drugs in 567 WWE...
January 12, 2017: Epilepsy & Behavior: E&B
https://www.readbyqxmd.com/read/28088669/micro-mechanical-properties-of-the-tendon-to-bone-attachment
#4
Alix C Deymier, Yiran An, John J Boyle, Andrea G Schwartz, Victor Birman, Guy M Genin, Stavros Thomopoulos, Asa H Barber
: The tendon-to-bone attachment (enthesis) is a complex hierarchical tissue that connects stiff bone to compliant tendon. The attachment site at the micrometer scale exhibits gradients in mineral content and collagen orientation, which likely act to minimize stress concentrations. The physiological micromechanics of the attachment thus define resultant performance, but difficulties in sample preparation and mechanical testing at this scale have restricted understanding of structure-mechanical function...
January 11, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/28088652/convergence-of-interoception-emotion-and-social-cognition-a-twofold-fmri-meta-analysis-and-lesion-approach
#5
Federico Adolfi, Blas Couto, Fabian Richter, Jean Decety, Jessica Lopez, Mariano Sigman, Facundo Manes, Agustín Ibáñez
Guided by indirect evidence, recent approaches propose a tripartite crosstalk among interoceptive signaling, emotional regulation, and low-level social cognition. Here we examined the neurocognitive convergence of such domains. First, we performed three meta-analyses of functional magnetic resonance imaging studies to identify which areas are consistently coactivated by these three systems. Multi-level Kernel Density Analysis (MKDA) revealed major overlaps in the right anterior insular and frontotemporal regions (viz...
December 29, 2016: Cortex; a Journal Devoted to the Study of the Nervous System and Behavior
https://www.readbyqxmd.com/read/28088651/limitations-in-biexponential-fitting-of-nmr-inversion-recovery-curves
#6
Mohammed Salman Shazeeb, Christopher H Sotak
NMR relaxation agents have long been employed as contrast agents in MRI. In many cases, the contrast agent is confined to either (i) the vascular and/or extracellular compartment (EC), as is the case with gadolinium(III)-based agents, or (ii) the intracellular compartment (IC), as is the case with manganese(II) ions. The compartmentalization of contrast agents often results in tissue-water (1)H relaxation profiles that are well modeled as biexponential. It has long been recognized that water exchange between compartments modifies the biexponential relaxation parameters (amplitudes and rate constants) from those that would be found in the absence of exchange...
January 6, 2017: Journal of Magnetic Resonance
https://www.readbyqxmd.com/read/28088650/assessing-the-identity-and-expression-level-of-the-cytochrome-p450-20a1-cyp20a1-gene-in-the-bpa-bde-47-and-waf-exposed-copepods-tigriopus-japonicus-and-paracyclopina-nana
#7
Jeonghoon Han, Duck-Hyun Kim, Jung Soo Seo, Il-Chan Kim, David R Nelson, Jayesh Puthumana, Jae-Seong Lee
CYP20A1 is a member of the cytochrome P450 (CYP) superfamily, identified as an orphan P450 without any assigned biological function; hence, its continued status as an "orphan" gene. In order to address this shortcoming in our understanding of this superfamily, we sought to characterize the CYP20A1 gene in the copepods Tigriopus japonicus (Tj-CYP20A1) and Paracyclopina nana (Pn-CYP20A1) at their mRNA transcriptional level. We assessed the response of this gene's expression in various developmental stages and in response to treatment with bisphenol A (BPA), 2, 2', 4, 4'-tetrabromodiphenyl ether (BDE-47), and water accommodated fractions (WAFs) of crude oil...
January 11, 2017: Comparative Biochemistry and Physiology. Toxicology & Pharmacology: CBP
https://www.readbyqxmd.com/read/28088647/the-developmental-relationship-between-specific-cognitive-domains-and-grey-matter-in-the-cerebellum
#8
Dorothea M Moore, Anila M D'Mello, Lauren M McGrath, Catherine J Stoodley
There is growing evidence that the cerebellum is involved in cognition and cognitive development, yet little is known about the developmental relationship between cerebellar structure and cognitive subdomains in children. We used voxel-based morphometry to assess the relationship between cerebellar grey matter (GM) and language, reading, working memory, executive function, and processing speed in 110 individuals aged 8-17 years from the Pediatric Imaging, Neurocognition, and Genetics (PING) Study. Further, we examined the effect of age on the relationships between cerebellar GM and cognition...
December 21, 2016: Developmental Cognitive Neuroscience
https://www.readbyqxmd.com/read/28088624/oxidative-phospholipidomics-in-health-and-disease-achievements-challenges-and-hopes
#9
REVIEW
Ana Reis
Phospholipid peroxidation products are recognized as important bioactive lipid mediators playing an active role as modulators in signalling events in inflammation, immunity and infection. The biochemical responses are determined by the oxidation structural features present in oxPL modulating biophysical and biological properties in model membranes and lipoproteins. In spite of the extensive work conducted with model systems over the last 20 years, the study of oxPL in biological systems has virtually stagnated...
January 11, 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/28088615/cloning-heterologous-expression-and-biochemical-characterization-of-a-non-specific-endoglucanase-family-12-from-aspergillus-terreus-nih2624
#10
Fernando Segato, Bruno Dias, Gabriela L Berto, Dyoni M de Oliveira, Flávio H M De Souza, Matheus Augusto R N da Silva, Ana Paula Citadini, Mario T Murakami, André R L Damásio, Fábio Márcio Squina, Igor Polikarpov
The cellulases from Glycoside Hydrolyses family 12 (GH12) play an important role in cellulose degradation and plant cell wall deconstruction being widely used in a number of bioindustrial processes. Aiming to contribute toward better comprehension of these class of the enzymes, here we describe a high-yield secretion of a endoglucanase GH12 from Aspegillus terreus (AtGH12), which was cloned and expressed in Aspergillus nidulans strain A773. The purified protein was used for complete biochemical and functional characterization...
January 11, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28088564/doping-and-vacancy-effects-of-graphyne-on-so2-adsorption
#11
Sunkyung Kim, Jin Yong Lee
The adsorption of sulfur dioxide (SO2) on pristine and modified graphyne (including boron- or nitrogen- doping and introducing a single carbon atom defect) was investigated by density functional theory calculations. The structural, electronic, and magnetic properties of graphyne were changed according to the dopant atom site of doping and vacancy. SO2 adsorption was obviously affected by modification of graphyne. SO2 weakly interacted with pristine and nitrogen-doped graphynes. Boron doping at the sp-hybridized carbon site and introducing a single carbon atom vacancy in graphyne brought about a dramatic enhancement in SO2 adsorption...
January 6, 2017: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/28088516/structural-study-of-the-effects-of-mutations-in-proteins-to-identify-the-molecular-basis-of-the-loss-of-local-structural-fluidity-leading-to-the-onset-of-autoimmune-diseases
#12
Ananya Ali, Semanti Ghosh, Angshuman Bagchi
Protein-Protein Interactions (PPIs) are crucial in most of the biological processes and PPI dysfunctions are known to be associated with the onsets of various diseases. One of such diseases is the auto-immune disease. Auto-immune diseases are one among the less studied group of diseases with very high mortality rates. Thus, we tried to correlate the appearances of mutations with their probable biochemical basis of the molecular mechanisms leading to the onset of the disease phenotypes. We compared the effects of the Single Amino Acid Variants (SAVs) in the wild type and mutated proteins to identify any structural deformities that might lead to altered PPIs leading ultimately to disease onset...
January 11, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28088508/relationship-between-central-retinal-vessel-trunk-location-and-visual-field-loss-in-glaucoma
#13
Mengyu Wang, Hui Wang, Louis R Pasquale, Neda Baniasadi, Lucy Q Shen, Peter J Bex, Tobias Elze
PURPOSE: To study the relationship between horizontal central retinal vessel trunk location (CRVTL) on glaucomatous optic discs and sector-specific visual field (VF) loss. DESIGN: Retrospective, cross-sectional study. METHODS: CRVTL of 421 eyes from 421 patients was manually tracked on the horizontal optic disc axis on fundus images. Focal circumpapillary retinal nerve fiber layer thickness (cpRNFLT) measurements were extracted from optical coherence tomography (OCT)...
January 11, 2017: American Journal of Ophthalmology
https://www.readbyqxmd.com/read/28088504/novel-insights-into-the-transport-mechanism-of-the-human-amino-acid-transporter-lat1-slc7a5-probing-critical-residues-for-substrate-translocation
#14
Lara Napolitano, Michele Galluccio, Mariafrancesca Scalise, Chiara Parravicini, Luca Palazzolo, Ivano Eberini, Cesare Indiveri
BACKGROUND: LAT1 (SLC7A5) is the transport competent unit of the heterodimer formed with the glycoprotein CD98 (SLC3A2). It catalyzes antiport of His and some neutral amino acids such as Ile, Leu, Val, Cys, Met, Gln and Phe thus being involved in amino acid metabolism. Interestingly, LAT1 is over-expressed in many human cancers that are characterized by increased demand of amino acids. Therefore LAT1 was recently acknowledged as a novel target for cancer therapy. However, knowledge on molecular mechanism of LAT1 transport is still scarce...
January 11, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28088481/saxs-structural-studies-of-dps-from-deinococcus-radiodurans-highlights-the-conformation-of-the-mobile-n-terminal-extensions
#15
Sandra P Santos, Maxime G Cuypers, Adam Round, Stephanie Finet, Theyencheri Narayanan, Edward P Mitchell, Célia V Romão
The radiation resistant bacterium Deinococcus radiodurans contains two DNA binding proteins from starved cells (Dps): Dps1 (DR2263) and Dps2 (DRB0092). These are suggested to play a role in DNA interaction, manganese and iron storage. The proteins assemble as a conserved dodecameric structure with structurally uncharacterized N-terminal extensions. In the case of DrDps1 these extensions have been proposed to be involved in DNA interactions, while in DrDps2 their function has yet to be established. The reported data reveals the relative position of the N-terminal extensions to the dodecameric sphere in solution for both Dps...
January 11, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28088480/sensing-membrane-curvature-in-macroautophagy
#16
REVIEW
Nathan Nguyen, Vladimir Shteyn, Thomas J Melia
In response to intracellular stress events ranging from starvation to pathogen invasion, the cell activates one or more forms of macroautophagy. The key event in these related pathways is the de novo formation of a new organelle called the autophagosome, which surrounds and sequesters either random portions of the cytoplasm or selectively targets individual intracellular challenges. Thus the autophagosome is a flexible membrane platform with dimensions that ultimately depend upon the target cargo. The intermediate membrane, termed the phagophore or isolation membrane, is a cup-like structure with a clear concave face and a highly curved rim...
January 11, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28088479/three-dimensional-structure-of-full-length-ntrx-an-unusual-member-of-the-ntrc-family-of-response-regulators
#17
Ignacio Fernández, Irina Cornaciu, Mariela Del Carmen Carrica, Emiko Uchikawa, Guillaume Hoffmann, Rodrigo Sieira, José Antonio Márquez, Fernando A Goldbaum
Bacteria sense and adapt to environmental changes using two-component systems (TCS). These signaling pathways are formed by a histidine kinase (HK) that phosphorylates a response regulator (RR), which finally modulates the transcription of target genes. The bacterium Brucella abortus codes for a TCS formed by the HK NtrY and the RR NtrX that participates in sensing low oxygen tension and in generating an adaptive response. NtrX is a modular protein with REC, AAA+ and DNA binding domains, an architecture that classifies it among the NtrC subfamily of RRs...
January 11, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28088391/changes-in-the-cerebellar-and-cerebro-cerebellar-circuit-in-type-2-diabetes
#18
Peng Fang, Jie An, Xin Tan, Ling-Li Zeng, Hui Shen, Shijun Qiu, Dewen Hu
Currently, 422 million adults suffer from diabetes worldwide, leading to tremendous disabilities and a great burden to families and society. Functional and structural MRIs have demonstrated that patients with type 2 diabetes mellitus (T2DM) exhibit abnormalities in brain regions in the cerebral cortex. However, the changes of cerebellar anatomical connections in diabetic patients remains unclear. In the current study, diffusion tensor imaging deterministic tractography and statistical analysis were employed to investigate abnormal cerebellar anatomical connections in diabetic patients...
January 11, 2017: Brain Research Bulletin
https://www.readbyqxmd.com/read/28088364/antibodies-from-novel-repertoires-to-defining-and-refining-the-structure-of-biologically-important-targets
#19
REVIEW
Paul J Conroy, Ruby H P Law, Tom Caradoc-Davies, James C Whisstock
Antibodies represent a highly successful class of molecules that bind a wide-range of targets in therapeutic-, diagnostic- and research-based applications. The antibody repertoire is composed of the building blocks required to develop an effective adaptive immune response against foreign insults. A number of species have developed novel genetic and structural mechanisms from which they derive these antibody repertoires, however, traditionally antibodies are derived from human, and rodent sources. Due to their high-value therapeutic, diagnostic, biotechnological and research applications, much innovation has resulted in techniques and approaches to isolate novel antibodies...
January 11, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28088340/the-role-of-magnetic-resonance-imaging-techniques-in-evaluation-and-management-of-the-idiopathic-inflammatory-myopathies
#20
REVIEW
Jessica Day, Sandy Patel, Vidya Limaye
Magnetic resonance imaging (MRI) is an important tool in the evaluation of neuromuscular disorders. MRI accurately demonstrates muscle oedema, atrophy, subcutaneous pathology and fatty infiltration and also highlights the distribution of muscle involvement. This review examines the role of MRI in evaluation of the idiopathic inflammatory myopathies (IIMs), a heterogeneous group of autoimmune conditions characterised by muscle inflammation and a variety of extra-muscular manifestations. MRI has a clear role in aiding diagnosis of these conditions, guiding muscle biopsy, differentiating subtypes of IIM using a pattern-based approach, and monitoring disease activity in a longitudinal fashion...
November 5, 2016: Seminars in Arthritis and Rheumatism
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