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https://www.readbyqxmd.com/read/28088734/in-vivo-and-in-silico-sedative-hypnotic-like-activity-of-7-methyljuglone-isolated-from-diospyros-lotus-l
#1
Abdur Rauf, Sengul Uysal, Taibi Ben Hadda, Ghias Uddin, Muhammad Asif Nawaz, Haroon Khan, Bina S Siddiqui, Muslim Raza, Saud Bawazeer, Gokhan Zengin
Diospyros lotus L. possesses different therapeutic activities such as antioxidant, anti-proliferative, anti-microbial and sedative. However, no studies on the sedative-hypnotic activity of 7-methyljuglone are reported. In the present study, we have evaluated in vivo the anxiolytic-hypnotic like effects of 7-methyljuglone in mice with open field and phenobarbitone-induced sleeping time tests. We have also assessed in silico the involvement of GABAA, GABAB and 5HT1 neurotransmission in its mechanism of action...
January 12, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28088651/limitations-in-biexponential-fitting-of-nmr-inversion-recovery-curves
#2
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/28088521/signal-peptidase-i-processed-secretory-signal-sequences-selection-for-and-against-specific-amino-acids-at-the-second-position-of-mature-protein
#3
Yaramah M Zalucki, Michael P Jennings
Signal peptides direct proteins from the cytoplasm to the periplasm. These N-terminal peptides are cleaved upon entry to the periplasm by either signal peptidase I, or signal peptidase II for lipoproteins. Signal peptidase I is a serine protease that has either a serine-lysine or serine-histidine catalytic dyad present in the active site. The recognition site for signal peptide cleavage by signal peptidase I has been defined primarily by an Ala-X-Ala motif at the C-terminal end of the signal peptide, one amino acid away from the cleavage site...
January 11, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28088356/advancing-the-prediction-accuracy-of-protein-protein-interactions-by-utilizing-evolutionary-information-from-position-specific-scoring-matrix-and-ensemble-classifier
#4
Lei Wang, Zhu-Hong You, Shi-Xiong Xia, Feng Liu, Xing Chen, Xin Yan, Yong Zhou
Protein-Protein Interactions (PPIs) are essential to most biological processes and play a critical role in most cellular functions. With the development of high-throughput biological techniques and in silico methods, a large number of PPI data have been generated for various organisms, but many problems remain unsolved. These factors promoted the development of the in silico methods based on machine learning to predict PPIs. In this study, we propose a novel method by combining ensemble Rotation Forest (RF) classifier and Discrete Cosine Transform (DCT) algorithm to predict the interactions among proteins...
January 11, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28087426/next-generation-sequencing-of-a-large-gene-panel-in-patients-initially-diagnosed-with-idiopathic-ventricular-fibrillation
#5
Marloes Visser, Dennis Dooijes, Jasper J van der Smagt, Jeroen F van der Heijden, Pieter A Doevendans, Peter Loh, Folkert W Asselbergs, Rutger J Hassink
BACKGROUND: Idiopathic ventricular fibrillation (IVF) is a rare primary cardiac arrhythmia syndrome that is diagnosed in a resuscitated cardiac arrest victim, with documented ventricular fibrillation, in whom no underlying cause is identified after comprehensive clinical evaluation. In some patients causative genetic mutations are detected which facilitate patient treatment and follow-up. The feasibility of next generation sequencing (NGS) has increased with its greater availability and decreasing costs...
January 10, 2017: Heart Rhythm: the Official Journal of the Heart Rhythm Society
https://www.readbyqxmd.com/read/28087398/interaction-of-mal-de-r%C3%A3-o-cuarto-virus-fijivirus-genus-proteins-and-identification-of-putative-factors-determining-viroplasm-formation-and-decay
#6
Gabriela Llauger, Luis Alejandro de Haro, Victoria Alfonso, Mariana Del Vas
Mal de Río Cuarto virus (MRCV) is a member of the Fijivirus genus, within the Reoviridae family, that replicates and assembles in cytoplasmic inclusion bodies called viroplasms. In this study, we investigated interactions between ten MRCV proteins by yeast two-hybrid (Y2H) assays and identified interactions of non-structural proteins P6/P6, P9-2/P9-2 and P6/P9-1. P9-1 and P6 are the major and minor components of the viroplasms respectively, whereas P9-2 is an N-glycosylated membrane protein of unknown function...
January 10, 2017: Virus Research
https://www.readbyqxmd.com/read/28087198/cloning-characterization-and-transmission-blocking-potential-of-midgut-carboxypeptidase-a-in-anopheles-stephensi
#7
V VenkatRao, Surendra K Kumar, P Sridevi, Vijaykumar Muley, R K Chaitanya
Transmission-blocking vaccines (TBV) interrupt malaria parasite transmission and hence form an important component for malaria eradication. Mosquito midgut exopeptidases such as aminopeptidase N & carboxypeptidase B have demonstrated TBV potential. In the present study, we cloned and characterized carboxypeptidase A (CPA) from the midgut of an important malarial vector, Anopheles stephensi. ClustalW amino acid alignment and in silico 3-dimensional structure analysis of CPA predicted the presence of active sites involved in zinc and substrate binding that are conserved among all the known mosquito species...
January 10, 2017: Acta Tropica
https://www.readbyqxmd.com/read/28086783/de-novo-transcriptome-analysis-of-rose-scented-geranium-provides-insights-into-the-metabolic-specificity-of-terpene-and-tartaric-acid-biosynthesis
#8
Lokesh K Narnoliya, Girija Kaushal, Sudhir P Singh, Rajender S Sangwan
BACKGROUND: Rose-scented geranium (Pelargonium sp.) is a perennial herb that produces a high value essential oil of fragrant significance due to the characteristic compositional blend of rose-oxide and acyclic monoterpenoids in foliage. Recently, the plant has also been shown to produce tartaric acid in leaf tissues. Rose-scented geranium represents top-tier cash crop in terms of economic returns and significance of the plant and plant products. However, there has hardly been any study on its metabolism and functional genomics, nor any genomic expression dataset resource is available in public domain...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28081509/in-silico-prediction-of-toxicity-of-phenols-to-tetrahymena-pyriformis-by-using-genetic-algorithm-and-decision-tree-based-modeling-approach
#9
Fatemeh Abbasitabar, Vahid Zare-Shahabadi
Risk assessment of chemicals is an important issue in environmental protection; however, there is a huge lack of experimental data for a large number of end-points. The experimental determination of toxicity of chemicals involves high costs and time-consuming process. In silico tools such as quantitative structure-toxicity relationship (QSTR) models, which are constructed on the basis of computational molecular descriptors, can predict missing data for toxic end-points for existing or even not yet synthesized chemicals...
January 2, 2017: Chemosphere
https://www.readbyqxmd.com/read/28081503/in-silico-identification-of-alternative-oxidase-2-aox2-in-monocots-a-new-evolutionary-scenario
#10
José Hélio Costa, Clesivan Pereira Dos Santos, Beatriz de Sousa E Lima, Anthônio Nunes Moreira Netto, Kátia Daniella da Cruz Saraiva, Birgit Arnholdt-Schmitt
We identified AOX2 genes in monocot species from Lemnoideae (Spirodela polyrhiza, Lemna gibba and Landoltia punctata), Pothoideae (Anthurium andraeanum and Anthurium amnicola) and Monsteroideae (Epipremnum aureum) subfamilies within the Araceae, an early-diverging monocot family. These findings highlight the presence of AOX2 in the most ancient monocot ancestor and also that at least partial loss of this gene occurred during speciation events within several monocot orders. The presence of AOX2 in monocot species challenges (1) new understanding of the evolutionary history of the AOX gene family in angiosperms and (2) drives experimental and bioinformatics efforts to explore functional relevance of the two AOX gene family members for plant growth and development...
December 27, 2016: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28081487/comparative-genome-wide-phylogenetic-and-expression-analysis-of-sbp-genes-from-potato-solanum-tuberosum
#11
Musa Kavas, Aslıhan Kurt Kızıldoğan, Büşra Abanoz
Flowering time is a very important phase in transition to reproductive stage of life in higher plants. SQUAMOSA promoter-binding protein (SBP) gene family encodes plant-specific transcription factors that are involved in regulation of several developmental processes, especially flowering. Although SBP-box genes have been identified in different plants, there have been no study indicating the regulatory effect of SBP box in potato flowering. Here, we report for the first time the identification and characterization of SBP-box transcription factors as well as determination of expression level of SBP-box genes in Solanum tuberosum L...
January 4, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28081267/single-nucleotide-variants-of-candidate-genes-in-aggrecan-metabolic-pathway-are-associated-with-lumbar-disc-degeneration-and-modic-changes
#12
Romain Shanil Perera, Poruwalage Harsha Dissanayake, Upul Senarath, Lalith Sirimevan Wijayaratne, Aranjan Lional Karunanayake, Vajira Harshadeva Weerabaddana Dissanayake
INTRODUCTION: Lumbar disc degeneration (LDD) is genetically determined and severity of LDD is associated with Modic changes. Aggrecan is a major proteoglycan in the intervertebral disc and end plate. Progressive reduction of aggrecan is a main feature of LDD and Modic changes. OBJECTIVES: The study investigated the associations of single nucleotide variants (SNVs) of candidate genes in the aggrecan metabolic pathway with the severity of LDD and Modic changes. In-silico functional analysis of significant SNVs was also assessed...
2017: PloS One
https://www.readbyqxmd.com/read/28079226/in-silico-kinetics-of-alkaline-hydrolysis-of-1-3-5-trinitro-1-3-5-triazinane-rdx-m06-2x-investigation
#13
L K Sviatenko, L Gorb, D Leszczynska, S I Okovytyy, M K Shukla, J Leszczynski
Alkaline hydrolysis of RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine), as one of the most promising methods for nitrocompound remediation, was investigated computationally at the PCM(Pauling)/M06-2X/6-311++G(d,p) level of theory. Computational simulation shows that RDX hydrolysis is a highly exothermic multistep process involving initial deprotonation and nitrite elimination, cycle cleavage, further transformation of cycle-opened intermediates to end products caused by a series of C-N bond ruptures, hydroxide attachments, and proton transfers...
January 12, 2017: Environmental Science. Processes & Impacts
https://www.readbyqxmd.com/read/28079168/molecular-dynamics-studies-unravel-role-of-conserved-residues-responsible-for-movement-of-ions-into-active-site-of-dhbps
#14
Ranajit Nivrutti Shinde, Subramanian Karthikeyan, Balvinder Singh
3,4-dihydroxy-2-butanone-4-phosphate synthase (DHBPS) catalyzes the conversion of D-ribulose 5-phosphate (Ru5P) to L-3,4-dihydroxy-2-butanone-4-phosphate in the presence of Mg(2+). Although crystal structures of DHBPS in complex with Ru5P and non-catalytic metal ions have been reported, structure with Ru5P along with Mg(2+) is still elusive. Therefore, mechanistic role played by Mg(2+) in the structure of DHBPS is poorly understood. In this study, molecular dynamics simulations of DHBPS-Ru5P complex along with Mg(2+) have shown entry of Mg(2+) from bulk solvent into active site...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28078985/designing-isoform-selective-inhibitors-against-classical-hdacs-for-effective-anticancer-therapy-insight-and-perspectives-from-in-silico
#15
Shabir Ahmad Ganai
Histone deacetylase inhibitors, the small molecules modulating the biological activity of histone deacetylases are emerging as potent chemotherapeutic agents. Despite their considerable therapeutic benefits in disease models, the lack of isoform specificity culminates in debilitating off target effects, raising serious concerns regarding their applicability. This emphasizes the pressing and unmet medical need of designing isoform selective inhibitors for safe and effective anticancer therapy. Keeping these grim facts in view, the current article sheds light on structural basis of off-targeting...
12, 2017: Current Drug Targets
https://www.readbyqxmd.com/read/28078782/pacmans-a-bioinformatically-informed-algorithm-to-predict-design-and-disrupt-protease-on-protease-hydrolysis
#16
Meghan C Ferrall-Fairbanks, Zachary T Barry, Maurizio Affer, Marc A Shuler, Ellen W Moomaw, Manu O Platt
Multiple proteases in a system hydrolyze target substrates, but recent evidence indicates that some proteases will degrade other proteases as well. Cathepsin S hydrolysis of cathepsin K is one such example. These interactions may be uni- or bi-directional and change the expected kinetics. To explore potential protease-on-protease interactions in silico, a program was developed for users to input two proteases: 1) the protease-ase that hydrolyzes 2) the substrate, protease. This program identifies putative sites on the substrate protease highly susceptible to cleavage by the protease-ase, using a sliding window approach that scores amino acid sequences by their preference in the protease-ase active site, culled from MEROPS database...
January 12, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28078591/sketching-of-cd95-oligomers-by-in-silico-investigations
#17
Nicolas Levoin
This work aimed at building a 3D model of trimeric apo CD95. By combining different molecular modeling approaches and experimental information, we have been able to obtain a consensual organization of the complex. Our strategy permitted the construction of a plausible trimer, and to sketch the interface between protomers. The final model will guide further experimental investigations and understanding of CD95 structure and functions.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28078411/in-vitro-and-in-silico-assessment-of-the-structure-dependent-binding-of-bisphenol-analogues-to-glucocorticoid-receptor
#18
Jie Zhang, Tiehua Zhang, Tianzhu Guan, Hansong Yu, Tiezhu Li
Widespread use of bisphenol A (BPA) and other bisphenol analogues has attracted increasing attention for their potential adverse effects. As environmental endocrine-disrupting compounds (EDCs), bisphenols (BPs) may activate a variety of nuclear receptors, including glucocorticoid receptor (GR). In this work, the binding of 11 BPs to GR was investigated by fluorescence polarization (FP) assay in combination with molecular dynamics simulations. The human glucocorticoid receptor was prepared as a soluble recombinant protein...
January 11, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28078104/discovery-of-flavivirus-derived-endogenous-viral-elements-in-anopheles-mosquito-genomes-supports-the-existence-of-anopheles-associated-insect-specific-flaviviruses
#19
Sebastian Lequime, Louis Lambrechts
The Flavivirus genus encompasses several arboviruses of public health significance such as dengue, yellow fever, and Zika viruses. It also includes insect-specific flaviviruses (ISFs) that are only capable of infecting insect hosts. The vast majority of mosquito-infecting flaviviruses have been associated with mosquito species of the Aedes and Culex genera in the Culicinae subfamily, which also includes most arbovirus vectors. Mosquitoes of the Anophelinae subfamily are not considered significant arbovirus vectors; however, flaviviruses have occasionally been detected in field-caught Anopheles specimens...
January 2017: Virus Evolution
https://www.readbyqxmd.com/read/28077797/repression-of-fyn-related-kinase-in-breast-cancer-cells-is-associated-with-promoter-site-specific-cpg-methylation
#20
Edward T Bagu, Sayem Miah, Chenlu Dai, Travis Spriggs, Yetunde Ogunbolude, Erika Beaton, Michelle Sanders, Raghuveera K Goel, Keith Bonham, Kiven E Lukong
The triple-negative breast cancer subtype is highly aggressive and has no defined therapeutic target. Fyn-related kinase (FRK) is a non-receptor tyrosine kinase, reported to be downregulated in breast cancer and gliomas, where it is suggested to have tumor suppressor activity. We examined the expression profile of FRK in a panel of 40 breast cancer cells representing all the major subtypes, as well as in 4 non-malignant mammary epithelial cell lines. We found that FRK expression was significantly repressed in a proportion of basal B breast cancer cell lines...
January 6, 2017: Oncotarget
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