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https://www.readbyqxmd.com/read/27923202/structure-based-optimization-of-salt-bridge-network-across-the-complex-interface-of-ptpn4-pdz-domain-with-its-peptide-ligands-in-neuroglioma
#1
Xian Xiao, Qiang-Hua He, Li-Yan Yu, Song-Qing Wang, Yang Li, Hua Yang, Ai-Hua Zhang, Xiao-Hong Ma, Yu-Jie Peng, Bing Chen
The PTP non-receptor type 4 (PTPN4) is an important regulator protein in learning, spatial memory and cerebellar synaptic plasticity; targeting the PDZ domain of PTPN4 has become as attractive therapeutic strategy for human neuroglioma. Here, we systematically examined the complex crystal structures of PTPN4 PDZ domain with its known peptide ligands; a number of charged amino acid residues were identified in these ligands and in the peptide-binding pocket of PDZ domain, which can constitute a complicated salt-bridge network across the complex interface...
November 30, 2016: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/27923179/structural-dynamics-of-casein-kinase-i-cki-from-malarial-parasite-plasmodium-falciparum-isolate-3d7-insights-from-theoretical-modelling-and-molecular-simulations
#2
Budheswar Dehury, Santosh Kumar Behera, Namita Mahapatra
The protein kinases (PKs), belonging to serine/threonine kinase (STKs), are important drug targets for a wide spectrum of diseases in human. Among protein kinases, the Casein Kinases (CKs) are vastly expanded in various organisms, where, the malarial parasite Plasmodium falciparum possesses a single member i.e., PfCKI, which can phosphorylate various proteins in parasite extracts in vitro condition. But, the structure-function relationship of PfCKI and dynamics of ATP binding is yet to be understood. Henceforth, an attempt was made to study the dynamics, stability, and ATP binding mechanisms of PfCKI through computational modelling, docking, molecular dynamics (MD) simulations, and MM/PBSA binding free energy estimation...
November 21, 2016: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/27923068/gene-expression-correlates-with-the-number-of-herpes-viral-genomes-initiating-infection-in-single-cells
#3
Efrat M Cohen, Oren Kobiler
Viral gene expression varies significantly among genetically identical cells. The sources of these variations are not well understood and have been suggested to involve both deterministic host differences and stochastic viral host interactions. For herpesviruses, only a limited number of incoming viral genomes initiate expression and replication in each infected cell. To elucidate the effect of this limited number of productively infecting genomes on viral gene expression in single cells, we constructed a set of fluorescence-expressing genetically tagged herpes recombinants...
December 6, 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/27923063/control-of-gene-expression-by-rna-binding-protein-action-on-alternative-translation-initiation-sites
#4
Angela Re, Levi Waldron, Alessandro Quattrone
Transcript levels do not faithfully predict protein levels, due to post-transcriptional regulation of gene expression mediated by RNA binding proteins (RBPs) and non-coding RNAs. We developed a multivariate linear regression model integrating RBP levels and predicted RBP-mRNA regulatory interactions from matched transcript and protein datasets. RBPs significantly improved the accuracy in predicting protein abundance of a portion of the total modeled mRNAs in three panels of tissues and cells and for different methods employed in the detection of mRNA and protein...
December 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27922941/exercise-training-ameliorates-glucosamine-induced-insulin-resistance-in-ovariectomized-rats
#5
Chung-Hwan Chen, Tsang-Hai Huang, Tsung-Lin Cheng, Chi-Fen Chang, Chau-Zen Wang, Meng-Hsing Wu, Lin Kang
OBJECTIVE: Glucosamine (GlcN), which has been reported to induce insulin resistance (IR), is a popular nutritional supplement used to treat osteoarthritis in menopausal women. We previously demonstrated that GlcN treatment caused IR in ovariectomized rats by reducing the expression of glucose transport protein subtype 4 (GLUT-4) in skeletal muscle. In the present study, we hypothesized that endurance exercise training can reverse GlcN-induced IR. METHODS: Fifty female rats were randomly divided into five groups with 10 rats in each group: (1) sham-operated group; (2) sham-operated group with GlcN treatment for 14 days; (3) ovariectomy (OVX) group; (4) OVX with GlcN treatment; and (5) OVX with GlcN treatment followed by exercise training (running program) for 8 weeks...
December 5, 2016: Menopause: the Journal of the North American Menopause Society
https://www.readbyqxmd.com/read/27922839/safety-of-perioperative-glucocorticoids-in-elective-noncardiac-surgery-a-systematic-review-and-meta-analysis
#6
Andrew J Toner, Vyhunthan Ganeshanathan, Matthew T Chan, Kwok M Ho, Tomas B Corcoran
BACKGROUND: Glucocorticoids are increasingly used perioperatively, principally to prevent nausea and vomiting. Safety concerns focus on the potential for hyperglycemia and increased infection. The authors hypothesized that glucocorticoids predispose to such adverse outcomes in a dose-dependent fashion after elective noncardiac surgery. METHODS: The authors conducted a systematic literature search of the major medical databases from their inception to April 2016...
December 6, 2016: Anesthesiology
https://www.readbyqxmd.com/read/27922825/model-of-turnover-kinetics-in-the-lamellipodium-implications-of-slow-and-fast-diffusing-capping-protein-and-arp2-3-complex
#7
Laura M McMillen, Dimitrios Vavylonis
Cell protrusion through polymerization of actin filaments at the leading edge of motile cells may be influenced by spatial gradients of diffuse actin and regulators. Here we study the distribution of two of the most important regulators, capping protein and Arp2/3 complex, which regulate actin polymerization in the lamellipodium through capping and nucleation of free barbed ends. We modeled their kinetics using data from prior single molecule microscopy experiments on XTC cells. These experiments have provided evidence for a broad distribution of diffusion coefficients of both capping protein and Arp2/3 complex...
December 6, 2016: Physical Biology
https://www.readbyqxmd.com/read/27922762/nonchemotherapy-drug-induced-agranulocytosis-in-children-detected-by-a-prospective-pharmacovigilance-program
#8
Nicolás Medrano-Casique, Hoi Y Tong, Alberto M Borobia, Antonio J Carcas, Jesús Frías, Elena Ramírez
OBJECTIVES: A prospective evaluation of nonchemotherapy drug-induced agranulocytosis (DIA) cases, which are infrequent in the pediatric population. We characterize agranulocytosis cases and assess lab test differences between drug- and nondrug-induced agranulocytosis. METHODS: Through our Prospective Pharmacovigilance Program from Laboratory Signals at Hospital we detected pediatric agranulocytosis cases from July 2007 to December 2010. This program estimates the incidence, drug causality, clinical features, outcomes of DIA pediatric cases, and assesses laboratory differences with respect to non-DIA...
December 6, 2016: Pediatric Hematology and Oncology
https://www.readbyqxmd.com/read/27922744/lung-pathologies-in-a-chronic-inflammation-mouse-model-are-independent-of-eosinophil-degranulation
#9
Elizabeth A Jacobsen, Sergei I Ochkur, Alfred D Doyle, William E LeSuer, Wen Li, Cheryl A Protheroe, Dana Colbert, Katie R Zellner, HuaHao H Shen, Charles G Irvin, James J Lee, Nancy A Lee
RATIONALE: The release of eosinophil granule proteins in the lungs of asthma patients has been dogmatically linked with lung remodeling and airway hyperresponsiveness (AHR). However, the demonstrated inability of established mouse models to display the eosinophil degranulation occurring in human subjects has prevented a definitive in vivo test of this hypothesis. OBJECTIVES: To demonstrate in vivo causative links between induced pulmonary histopathologies/lung dysfunction and eosinophil degranulation...
December 6, 2016: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/27922694/cpkc%C3%AE-membrane-translocation-is-involved-in-herkinorin%C3%A2-induced-neuroprotection-against-cerebral-ischemia-reperfusion-injury-in-mice
#10
Xiaochen Gui, Xu Cui, Haiping Wei, Guang Feng, Xuezheng Zhang, Yongjin He, Junfa Li, Tianzuo Li
Herkinorin is an opiate analgesic with limited adverse effects, functioning as a primary selective atypical opioid µ agonist. The present study aimed to identify whether herkinorin has a positive effect on ischemic/reperfusion (I/R) injury. Adult male C57BL/6 mice were randomly divided into five groups: i) Naïve, ii) sham, iii) I/R, iv) I/R with dimethyl sulfoxide (I/R+D) and v) I/R with herkinorin (I/R+H). The I/R injury model was induced by occluding the middle cerebral artery for 1 h followed by 24 h or 7 days of reperfusion...
December 6, 2016: Molecular Medicine Reports
https://www.readbyqxmd.com/read/27922670/downregulation-of-laptm5-suppresses-cell-proliferation-and-viability-inducing-cell-cycle-arrest-at-g0-g1-phase-of-bladder-cancer-cells
#11
Liang Chen, Gang Wang, Yi Luo, Yongzhi Wang, Conghua Xie, Wei Jiang, Yu Xiao, Guofeng Qian, Xinghuan Wang
Our transcriptome analysis revealed in bladder cancer (BCa) tissues a significant induction of lysosomal-associated multispanning membrane protein 5 (LAPTM5), a lysosomal membrane protein preferentially expressing in immune cells and hematopoietic cells. Transportation of LAPTM5 from Golgi to lysosome could be inhibited by deficiency of Nedd4, a key member of E3 ubiquitin ligase family overexpressing in invasive BCa and promoting its progression. Therefore, we hypothesize that LAPTM5 may be closely correlated with BCa tumorigenesis...
December 5, 2016: International Journal of Oncology
https://www.readbyqxmd.com/read/27922641/ip3-accumulation-and-or-inositol-depletion-two-downstream-lithium-s-effects-that-may-mediate-its-behavioral-and-cellular-changes
#12
Y Sade, L Toker, N Z Kara, H Einat, S Rapoport, D Moechars, G T Berry, Y Bersudsky, G Agam
Lithium is the prototype mood stabilizer but its mechanism is still unresolved. Two hypotheses dominate-the consequences of lithium's inhibition of inositol monophosphatase at therapeutically relevant concentrations (the 'inositol depletion' hypothesis), and of glycogen-synthase kinase-3. To further elaborate the inositol depletion hypothesis that did not decisively determine whether inositol depletion per se, or phosphoinositols accumulation induces the beneficial effects, we utilized knockout mice of either of two inositol metabolism-related genes-IMPA1 or SMIT1, both mimic several lithium's behavioral and biochemical effects...
December 6, 2016: Translational Psychiatry
https://www.readbyqxmd.com/read/27922631/dataset-of-eye-disease-related-proteins-analyzed-using-the-unfolding-mutation-screen
#13
Caitlyn L McCafferty, Yuri V Sergeev
A number of genetic diseases are a result of missense mutations in protein structure. These mutations can lead to severe protein destabilization and misfolding. The unfolding mutation screen (UMS) is a computational method that calculates unfolding propensities for every possible missense mutation in a protein structure. The UMS validation demonstrated a good agreement with experimental and phenotypical data. 15 protein structures (a combination of homology models and crystal structures) were analyzed using UMS...
December 6, 2016: Scientific Data
https://www.readbyqxmd.com/read/27922594/cacna1c-in-the-prefrontal-cortex-regulates-depression-related-behaviors-via-redd1
#14
Zeeba D Kabir, Anni S Lee, Caitlin E Burgdorf, Delaney Fischer, Aditi M Rajadhyaksha, Ethan Mok, Bryant Rizzo, Richard C Rice, Kamalpreet Singh, Kristie T Ota, Danielle M Gerhard, Kathryn C Schierberl, Michael Glass, Ronald S Duman, Anjali M Rajadhyaksha
The CACNA1C gene that encodes the L-type Ca(2+) channel (LTCC) Cav1.2 subunit has emerged as a candidate risk gene for multiple neuropsychiatric disorders including bipolar disorder, major depressive disorder and schizophrenia, all marked with depression-related symptoms. Although cacna1c heterozygous (HET) mice have been previously reported to exhibit an antidepressant-like phenotype, the molecular and circuit-level dysfunction remains unknown. Here we report that viral vector-mediated deletion of cacna1c in the adult prefrontal cortex (PFC) of mice recapitulates the antidepressant-like effect observed in cacna1c HET mice using the sucrose preference test (SPT), the forced swim test (FST), and the tail suspension test (TST)...
December 6, 2016: Neuropsychopharmacology: Official Publication of the American College of Neuropsychopharmacology
https://www.readbyqxmd.com/read/27922179/a-carbon-dioxide-stripping-model-for-mammalian-cell-culture-in-manufacturing-scale-bioreactors
#15
Zizhuo Xing, Amanda M Lewis, Michael C Borys, Zheng Jian Li
Control of carbon dioxide within the optimum range is important in mammalian bioprocesses at the manufacturing scale in order to ensure robust cell growth, high protein yields, and consistent quality attributes. The majority of bioprocess development work is done in laboratory bioreactors, in which carbon dioxide levels are more easily controlled. Some challenges in carbon dioxide control can present themselves when cell culture processes are scaled up, because carbon dioxide accumulation is a common feature due to longer gas-residence time of mammalian cell culture in large scale bioreactors...
December 6, 2016: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/27922175/a-framework-to-quantify-karyotype-variation-associated-with-cho-production-instability
#16
Jong Youn Baik, Kelvin H Lee
Chinese hamster ovary (CHO) cells, major mammalian host cells for biomanufacturing of therapeutic proteins, have been extensively investigated to enhance productivity and product quality. However, cell line instability resulting in unexpected changes in productivity or product quality is challenging for biomanufacturing. Based on previous reports about causes and characteristics of production instability, we hypothesized that chromosomal rearrangements due to genomic instability are associated with production instability...
December 6, 2016: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/27922102/slc2a8-glut8-is-a-mammalian-trehalose-transporter-required-for-trehalose-induced-autophagy
#17
Allyson L Mayer, Cassandra B Higgins, Monique R Heitmeier, Thomas E Kraft, Xia Qian, Jan R Crowley, Krzysztof L Hyrc, Wandy L Beatty, Kevin E Yarasheski, Paul W Hruz, Brian J DeBosch
Trehalose is a disaccharide demonstrated to mitigate disease burden in multiple murine neurodegenerative models. We recently revealed that trehalose rapidly induces hepatic autophagy and abrogates hepatic steatosis by inhibiting hexose transport via the SLC2A family of facilitative transporters. Prior studies, however, postulate that intracellular trehalose is sufficient to induce cellular autophagy. The objective of the current study was to identify the means by which trehalose accesses the hepatocyte cytoplasm, and define the distal signaling mechanisms by which trehalose induces autophagy...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27922098/comparison-of-432-pseudomonas-strains-through-integration-of-genomic-functional-metabolic-and-expression-data
#18
Jasper J Koehorst, Jesse C J van Dam, Ruben G A van Heck, Edoardo Saccenti, Vitor A P Martins Dos Santos, Maria Suarez-Diez, Peter J Schaap
Pseudomonas is a highly versatile genus containing species that can be harmful to humans and plants while others are widely used for bioengineering and bioremediation. We analysed 432 sequenced Pseudomonas strains by integrating results from a large scale functional comparison using protein domains with data from six metabolic models, nearly a thousand transcriptome measurements and four large scale transposon mutagenesis experiments. Through heterogeneous data integration we linked gene essentiality, persistence and expression variability...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27922049/identification-of-kiaa1199-as-a-biomarker-for-pancreatic-intraepithelial-neoplasia
#19
Han Na Suh, Sohee Jun, Ah-Young Oh, Mrinal Srivastava, Sunhye Lee, Cullen M Taniguchi, Songlin Zhang, Won Sup Lee, Junjie Chen, Bum-Joon Park, Jae-Il Park
Pancreatic cancer is one of the most aggressive cancers and has an extremely poor prognosis. Despite recent progress in both basic and clinical research, most pancreatic cancers are detected at an incurable stage owing to the absence of disease-specific symptoms. Thus, developing novel approaches for detecting pancreatic cancer at an early stage is imperative. Our in silico and immunohistochemical analyses showed that KIAA1199 is specifically expressed in human pancreatic cancer cells and pancreatic intraepithelial neoplasia, the early lesion of pancreatic cancer, in a genetically engineered mouse model and in human patient samples...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27922015/cryoem-structure-of-the-methanospirillum-hungatei-archaellum-reveals-structural-features-distinct-from-the-bacterial-flagellum-and-type-iv-pili
#20
Nicole Poweleit, Peng Ge, Hong H Nguyen, Rachel R Ogorzalek Loo, Robert P Gunsalus, Z Hong Zhou
Archaea use flagella known as archaella-distinct both in protein composition and structure from bacterial flagella-to drive cell motility, but the structural basis of this function is unknown. Here, we report an atomic model of the archaella, based on the cryo electron microscopy (cryoEM) structure of the Methanospirillum hungatei archaellum at 3.4 Å resolution. Each archaellum contains ∼61,500 archaellin subunits organized into a curved helix with a diameter of 10 nm and average length of 10,000 nm...
December 5, 2016: Nature Microbiology
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