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Antonella Sferra, Fabiana Fattori, Teresa Rizza, Elsabetta Flex, Emanuele Bellacchio, Alessandro Bruselles, Stefania Petrini, Serena Cecchetti, Massimo Teson, Fabrizia Restaldi, Andrea Ciolfi, Filippo M Santorelli, Ginevra Zanni, Sabina Barresi, Claudia Castiglioni, Marco Tartaglia, Enrico Bertini
Microtubules participate in fundamental cellular processes, including chromosomal segregation and cell division, migration, and intracellular trafficking. Their proper function is required for correct central nervous system development and operative preservation, and mutations in genes coding tubulins, the constituting units of microtubules, underlie a family of neurodevelopmental and neurodegenerative diseases, collectively known as "tubulinopathies", characterized by a wide range of neuronal defects resulting from defective proliferation, migration, and function...
March 14, 2018: Human Molecular Genetics
Qiaozhen Meng, Zhenling Peng, Jianyi Yang
Motivation: Coenzyme A (CoA)-protein binding plays an important role in various cellular functions and metabolic pathways. However, no computational methods can be employed for CoA-binding residues prediction. Results: We developed three methods for the prediction of CoA- and CoA derivatives-binding residues, including an ab-initio method SVMpred, a template-based method TemPred, and a consensus-based method CoABind. In SVMpred, a comprehensive set of features are designed from two complementary sequence profiles and the predicted secondary structure and solvent accessibility...
March 14, 2018: Bioinformatics
Deepak Reddy Gade, Amareswararao Makkapati, Rajesh Babu Yarlagadda, Godefridus J Peters, B S Sastry, V V S Rajendra Prasad
Overexpression of P-glycoprotein (P-gp) leads to the emergence of multidrug resistance (MDR) in cancer treatment. Acridones have the potential to reverse MDR and sensitize cells. In the present study, we aimed to elucidate the chemosensitization potential of acridones by employing various molecular modelling techniques. Pharmacophore modeling was performed for the dataset of chemosensitizing acridones earlier proved for cytotoxic activity against MCF7 breast cancer cell line. Gaussian-based QSAR studies also performed to predict the favored and disfavored region of the acridone molecules...
February 24, 2018: Computational Biology and Chemistry
Judy F C Chow, William S B Yeung, Vivian C Y Lee, Estella Y L Lau, Ernest H Y Ng
OBJECTIVES: To evaluate the applicability of a commonly used next generation sequencing workflow in detecting unbalanced meiotic segregation products for reciprocal translocation and inversion carriers. STUDY DESIGN: All preimplantation genetic testing treatment cycles performed for reciprocal translocation or inversion carriers from 2012 to April 2017 were included. Three hundreds and forty-two archived whole genome amplified DNA, which had previously analyzed by array comparative genomic hybridization (aCGH), were retrospectively analyzed by next generation sequencing (NGS)...
March 9, 2018: European Journal of Obstetrics, Gynecology, and Reproductive Biology
Nicolas Hoertel, Hadi Faiz, Guillaume Airagnes, Carlos Blanco, Rachel Pascal De Raykeer, Silvia Franco, Géraldine Ducoutumany, Cédric Lemogne, Frédéric Limosin
BACKGROUND: Heavy drinkers are at high risk for suicide attempt and suicide. Multiple factors, when examined in isolation, have been implicated in the risk of suicide attempt in this population. In this report, we present a comprehensive model of the 3-year risk of suicide attempt in heavy drinkers using a longitudinal nationally representative study, the National Epidemiologic Survey on Alcohol and Related Conditions (NESARC; wave 1, 2001-2002; wave 2, 2004-2005). METHODS: We used structural equation modeling to simultaneously examine effects of four broad groups of clinical factors previously identified as potential predictors of attempted suicides: 1) alcohol use disorder severity, 2) severity of comorbidity, 3) sociodemographic characteristics and 4) help-seeking for alcohol problems...
March 7, 2018: Drug and Alcohol Dependence
Ognjen Perišić
Physical interactions between proteins are often difficult to decipher. The aim of this paper is to present an algorithm that is designed to recognize binding patches and supporting structural scaffolds of interacting heterodimer proteins using the Gaussian Network Model (GNM). The recognition is based on the (self) adjustable identification of kinetically hot residues and their connection to possible binding scaffolds. The kinetically hot residues are residues with the lowest entropy, i.e., the highest contribution to the weighted sum of the fastest modes per chain extracted via GNM...
March 16, 2018: Pharmaceuticals
Shuai Yang, Yu Wang, Wengang Ao, Yun Bai, Chuan Li
Based on the consumption of fossil energy, the CO₂ emissions of Chongqing are calculated and analyzed from 1997 to 2015 in this paper. Based on the calculation results, the consumption of fossil fuels and the corresponding CO₂ emissions of Chongqing in 2020 are predicted, and the supporting data and corresponding policies are provided for the government of Chongqing to reach its goal as the economic unit of low-carbon emission in the '13th Five-Year Plan'. The results of the analysis show that there is a rapid decreasing trend of CO₂ emissions in Chongqing during the '12th Five-Year Plan', which are caused by the adjustment policy of the energy structure in Chongqing...
March 16, 2018: International Journal of Environmental Research and Public Health
Brin Freund, James J Gugger, Alexandra Reynolds, William O Tatum, Jan Claassen, Peter W Kaplan
PURPOSE: Periodic discharges (PDs) are EEG patterns denoting brain dysfunction and ictal tendency. Their exact meaning regarding etiology and outcomes is not well known. In particular, bilateral independent PDs (BIPDs) are poorly described. METHODS: We performed a retrospective, multicenter study evaluating neuroimaging, epileptic, clinical, and EEG correlates of BIPDs. RESULTS: Twenty-five patients studied with a mean Glasgow Coma Scale 6...
March 15, 2018: Journal of Clinical Neurophysiology: Official Publication of the American Electroencephalographic Society
Jiaye Su, Yunzhen Zhao, Chang Fang
Graphene is a versatile 2D material and attracts increasing attentions from a broad scientific community, including novel nanofluidic devices. In this work, we use molecular dynamics simulations to study the pressure driven water transport through graphene layers, focusing on the pore size homogeneity, realized by the arrangement of two pore sizes. For a given layer number, we find the water flux exhibits an excellent linear behavior with the pressure, in agreement with the prediction of Hagen-Poiseuille equation...
March 16, 2018: Nanotechnology
Caleb J Bashor, James J Collins
Engineering synthetic gene regulatory circuits proceeds through iterative cycles of design, building, and testing. Initial circuit designs must rely on often-incomplete models of regulation established by fields of reductive inquiry-biochemistry and molecular and systems biology. As differences in designed and experimentally observed circuit behavior are inevitably encountered, investigated, and resolved, each turn of the engineering cycle can force a resynthesis in understanding of natural network function...
March 16, 2018: Annual Review of Biophysics
Diego Jaramillo-Cano, Maud Formanek, Christos N Likos, Manuel Camargo
Star block-copolymers (SBCs) have been demonstrated to constitute self-assembling building blocks with specific softness, functionalization, shape and flexibility. In this work we study the behaviour of an isolated SBC under shear flow by means of particle-based multi-scale simulations. We systematically analyse the conformational properties of low-functionality stars as well as the formation of attractive patches on their corona as a function of the shear rate. We cover a wide range of system parameters, including functionality, amphiphilicity and solvent quality...
March 16, 2018: Journal of Physical Chemistry. B
Sen Xu, Xiaofeng Fan, Jialin Liu, David J Singh, Qing Jiang, Weitao Zheng
We report an investigation of the interactions of Li with silicene. We find silicene to be a promising anode material for high energy density lithium-ion batteries. Based on first-principles calculations, we study the interaction between Li and silicene and explore the microscopic mechanism of Li storage on silicene. We find that Li ion is adsorbed on hollow sites at a very low concentration of less than 1.56%. At a high concentration of Li, the Li chains with up-down pairs on top sites become popular. With the formation of the Li chains, the local structure of silicene is modulated...
March 16, 2018: Physical Chemistry Chemical Physics: PCCP
Sunandan Mukherjee, Chandran Nithin, Yasaswi Divakaruni, Ranjit Prasad Bahadur
We dissect the protein-protein interfaces into water preservation (WP), water hydration (WH) and water dehydration (WD) sites by comparing the water mediated hydrogen bonds (H-bond) in the bound and unbound states of the interacting subunits. Upon subunit complexation, if a H-bond between an interface water and a protein polar group is retained, we assign it as WP site; if it is lost, we assign it as WD site and if a new H-bond is created, we assign it as WH site. We find that the density of WD sites is highest followed by WH and WP sites except in antigen and (or) antibody complexes, where the density of WH sites is highest followed by WD and WP sites...
March 16, 2018: Journal of Biomolecular Structure & Dynamics
Noorakmar Jusoh, Hasanuddin Zainal, Azzmer Azzar Abdul Hamid, Noraslinda M Bunnori, Khairul Bariyyah Abd Halim, Shafida Abd Hamid
Recent outbreaks of highly pathogenic influenza strains have highlighted the need to develop new anti-influenza drugs. Here, we report an in silico study of carvone derivatives to analyze their binding modes with neuraminidase (NA) active sites. Two proposed carvone analogues, CV(A) and CV(B), with 36 designed ligands were predicted to inhibit NA (PDB ID: 3TI6) using molecular docking. The design is based on structural resemblance with the commercial inhibitor, oseltamivir (OTV), ligand polarity, and amino acid residues in the NA active sites...
March 15, 2018: Journal of Molecular Modeling
Zoë W Hawks, Natasha Marrus, Anne L Glowinski, John N Constantino
Previous research has suggested that behavioral comorbidity is the rule rather than the exception in autism. The present study aimed to trace the respective origins of autistic and general psychopathologic traits-and their association-to infancy. Measurements of autistic traits and early liability for general psychopathology were assessed in 314 twins at 18 months, ascertained from the general population using birth records. 222 twins were re-evaluated at 36 months. Standardized ratings of variation in social communication at 18 months were highly heritable and strongly predicted autistic trait scores at 36 months...
March 16, 2018: Journal of Abnormal Child Psychology
Fırat Kurt, Ertugrul Filiz
Iron (Fe) is an essential element for plant life. Its deficiency impedes growth and development and excessive iron can cause the toxic effect via the Fenton reaction. Thus, plants have developed various mechanisms to acquire, distribute and utilize Fe for the maintenance of their iron homeostasis at cellular and systemic levels. A basic helix-loop-helix (bHLH) transcription factor family plays essential roles in many regulatory and development processes in plants. In this study, we aimed to understand the roles of bHLH38, bHLH39, bHLH100 and bHLH101 genes for Fe homeostasis in Arabidopsis, tomato, rice, soybean and maize species by using bioinformatics approaches...
March 15, 2018: Biometals: An International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine
Lokesh K Narnoliya, Rajender S Sangwan, Sudhir P Singh
Rose-scented geranium (Pelargonium sp.) is widely known as aromatic and medicinal herb, accumulating specialized metabolites of high economic importance, such as essential oils, ascorbic acid, and tartaric acid. Ascorbic acid and tartaric acid are multifunctional metabolites of human value to be used as vital antioxidants and flavor enhancing agents in food products. No information is available related to the structural and functional properties of the enzymes involved in ascorbic acid and tartaric acid biosynthesis in rose-scented geranium...
March 15, 2018: Molecular Biology Reports
Kara Pham, Emma Turian, Kai Liu, Shuwang Li, John Lowengrub
We consider the nonlinear dynamics of an avascular tumor at the tissue scale using a two-fluid flow Stokes model, where the viscosity of the tumor and host microenvironment may be different. The viscosities reflect the combined properties of cell and extracellular matrix mixtures. We perform a linear morphological stability analysis of the tumors, and we investigate the role of nonlinearity using boundary-integral simulations in two dimensions. The tumor is non-necrotic, although cell death may occur through apoptosis...
March 15, 2018: Journal of Mathematical Biology
Jennifer Morozink Boylan, Jenny M Cundiff, Karen P Jakubowski, Dustin A Pardini, Karen A Matthews
Background: Exposure to low socioeconomic status (SES) in childhood predicts increased morbidity and mortality. However, little prospective evidence is available to test pathways linking low childhood SES to adult health. Purpose: In the current study, indirect effects through positive parenting in adolescence and adult SES were tested in the association between childhood SES and adult health behaviors and psychological resources. Methods: Men (n = 305; 53% Black) were followed longitudinally from ages 7 to 32...
March 13, 2018: Annals of Behavioral Medicine: a Publication of the Society of Behavioral Medicine
Anthony W Gannon, Jill E Langer, Richard Bellah, Sarah Ratcliffe, Jennifer Pizza, Sogol Mostoufi-Moab, Anne R Cappola, Andrew J Bauer
Context: Thyroid nodules are increasingly recognized in children and are associated with a greater risk for thyroid cancer compared to adults. Thyroid ultrasound is the favored tool for evaluation of thyroid nodules; however, there are limited data regarding the accuracy of thyroid ultrasound to confirm features associated with a low risk of thyroid cancer in children. Objectives: We examined whether thyroid ultrasound is capable of accurately identifying thyroid nodules at a low risk of malignancy in children...
March 12, 2018: Journal of Clinical Endocrinology and Metabolism
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