Stress Susceptibility-Specific Phenotype Associated with Different
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Prioritization and Evaluation of Depression Candidate Genes by Combining Multidimensional Data Resources
Prioritization and Evaluation of Depression Candidate Genes by Combining Multidimensional Data Resources Chung-Feng Kao1, Yu-Sheng Fang2, Zhongming Zhao3, Po-Hsiu Kuo1,2,4* 1 Department of Public Health and Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan, 2 Institute of Clinical Medicine, School of Medicine, National Cheng-Kung University, Tainan, Taiwan, 3 Departments of Biomedical Informatics and Psychiatry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America, 4 Research Center for Genes, Environment and Human Health, National Taiwan University, Taipei, Taiwan Abstract Background: Large scale and individual genetic studies have suggested numerous susceptible genes for depression in the past decade without conclusive results. There is a strong need to review and integrate multi-dimensional data for follow up validation. The present study aimed to apply prioritization procedures to build-up an evidence-based candidate genes dataset for depression. Methods: Depression candidate genes were collected in human and animal studies across various data resources. Each gene was scored according to its magnitude of evidence related to depression and was multiplied by a source-specific weight to form a combined score measure. All genes were evaluated through a prioritization system to obtain an optimal weight matrix to rank their relative importance with depression using the combined scores. The resulting candidate gene list for depression (DEPgenes) was further evaluated by a genome-wide association (GWA) dataset and microarray gene expression in human tissues. Results: A total of 5,055 candidate genes (4,850 genes from human and 387 genes from animal studies with 182 being overlapped) were included from seven data sources. -
Whole-Genome Microarray Detects Deletions and Loss of Heterozygosity of Chromosome 3 Occurring Exclusively in Metastasizing Uveal Melanoma
Anatomy and Pathology Whole-Genome Microarray Detects Deletions and Loss of Heterozygosity of Chromosome 3 Occurring Exclusively in Metastasizing Uveal Melanoma Sarah L. Lake,1 Sarah E. Coupland,1 Azzam F. G. Taktak,2 and Bertil E. Damato3 PURPOSE. To detect deletions and loss of heterozygosity of disease is fatal in 92% of patients within 2 years of diagnosis. chromosome 3 in a rare subset of fatal, disomy 3 uveal mela- Clinical and histopathologic risk factors for UM metastasis noma (UM), undetectable by fluorescence in situ hybridization include large basal tumor diameter (LBD), ciliary body involve- (FISH). ment, epithelioid cytomorphology, extracellular matrix peri- ϩ ETHODS odic acid-Schiff-positive (PAS ) loops, and high mitotic M . Multiplex ligation-dependent probe amplification 3,4 5 (MLPA) with the P027 UM assay was performed on formalin- count. Prescher et al. showed that a nonrandom genetic fixed, paraffin-embedded (FFPE) whole tumor sections from 19 change, monosomy 3, correlates strongly with metastatic death, and the correlation has since been confirmed by several disomy 3 metastasizing UMs. Whole-genome microarray analy- 3,6–10 ses using a single-nucleotide polymorphism microarray (aSNP) groups. Consequently, fluorescence in situ hybridization were performed on frozen tissue samples from four fatal dis- (FISH) detection of chromosome 3 using a centromeric probe omy 3 metastasizing UMs and three disomy 3 tumors with Ͼ5 became routine practice for UM prognostication; however, 5% years’ metastasis-free survival. to 20% of disomy 3 UM patients unexpectedly develop metas- tases.11 Attempts have therefore been made to identify the RESULTS. Two metastasizing UMs that had been classified as minimal region(s) of deletion on chromosome 3.12–15 Despite disomy 3 by FISH analysis of a small tumor sample were found these studies, little progress has been made in defining the key on MLPA analysis to show monosomy 3. -
Analysis of Gene Expression Data for Gene Ontology
ANALYSIS OF GENE EXPRESSION DATA FOR GENE ONTOLOGY BASED PROTEIN FUNCTION PREDICTION A Thesis Presented to The Graduate Faculty of The University of Akron In Partial Fulfillment of the Requirements for the Degree Master of Science Robert Daniel Macholan May 2011 ANALYSIS OF GENE EXPRESSION DATA FOR GENE ONTOLOGY BASED PROTEIN FUNCTION PREDICTION Robert Daniel Macholan Thesis Approved: Accepted: _______________________________ _______________________________ Advisor Department Chair Dr. Zhong-Hui Duan Dr. Chien-Chung Chan _______________________________ _______________________________ Committee Member Dean of the College Dr. Chien-Chung Chan Dr. Chand K. Midha _______________________________ _______________________________ Committee Member Dean of the Graduate School Dr. Yingcai Xiao Dr. George R. Newkome _______________________________ Date ii ABSTRACT A tremendous increase in genomic data has encouraged biologists to turn to bioinformatics in order to assist in its interpretation and processing. One of the present challenges that need to be overcome in order to understand this data more completely is the development of a reliable method to accurately predict the function of a protein from its genomic information. This study focuses on developing an effective algorithm for protein function prediction. The algorithm is based on proteins that have similar expression patterns. The similarity of the expression data is determined using a novel measure, the slope matrix. The slope matrix introduces a normalized method for the comparison of expression levels throughout a proteome. The algorithm is tested using real microarray gene expression data. Their functions are characterized using gene ontology annotations. The results of the case study indicate the protein function prediction algorithm developed is comparable to the prediction algorithms that are based on the annotations of homologous proteins. -
Transcriptional Regulation of RKIP in Prostate Cancer Progression
Health Science Campus FINAL APPROVAL OF DISSERTATION Doctor of Philosophy in Biomedical Sciences Transcriptional Regulation of RKIP in Prostate Cancer Progression Submitted by: Sandra Marie Beach In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biomedical Sciences Examination Committee Major Advisor: Kam Yeung, Ph.D. Academic William Maltese, Ph.D. Advisory Committee: Sonia Najjar, Ph.D. Han-Fei Ding, M.D., Ph.D. Manohar Ratnam, Ph.D. Senior Associate Dean College of Graduate Studies Michael S. Bisesi, Ph.D. Date of Defense: May 16, 2007 Transcriptional Regulation of RKIP in Prostate Cancer Progression Sandra Beach University of Toledo ACKNOWLDEGMENTS I thank my major advisor, Dr. Kam Yeung, for the opportunity to pursue my degree in his laboratory. I am also indebted to my advisory committee members past and present, Drs. Sonia Najjar, Han-Fei Ding, Manohar Ratnam, James Trempe, and Douglas Pittman for generously and judiciously guiding my studies and sharing reagents and equipment. I owe extended thanks to Dr. William Maltese as a committee member and chairman of my department for supporting my degree progress. The entire Department of Biochemistry and Cancer Biology has been most kind and helpful to me. Drs. Roy Collaco and Hong-Juan Cui have shared their excellent technical and practical advice with me throughout my studies. I thank members of the Yeung laboratory, Dr. Sungdae Park, Hui Hui Tang, Miranda Yeung for their support and collegiality. The data mining studies herein would not have been possible without the helpful advice of Dr. Robert Trumbly. I am also grateful for the exceptional assistance and shared microarray data of Dr. -
Activity of Selected Group of Monoterpenes in Alzheimer's
International Journal of Molecular Sciences Review Activity of Selected Group of Monoterpenes in Alzheimer’s Disease Symptoms in Experimental Model Studies—A Non-Systematic Review Karolina Wojtunik-Kulesza 1,*, Monika Rudkowska 2, Kamila Kasprzak-Drozd 1,* , Anna Oniszczuk 1 and Kinga Borowicz-Reutt 2 1 Department of Inorganic Chemistry, Medical University of Lublin, Chod´zki4a, 20-093 Lublin, Poland; [email protected] 2 Independent Experimental Neuropathophysiology Unit, Medical University of Lublin, Jaczewskiego 8b, 20-090 Lublin, Poland; [email protected] (M.R.); [email protected] (K.B.-R.) * Correspondence: [email protected] (K.W.-K.); [email protected] (K.K.-D.) Abstract: Alzheimer’s disease (AD) is the leading cause of dementia and cognitive function im- pairment. The multi-faced character of AD requires new drug solutions based on substances that incorporate a wide range of activities. Antioxidants, AChE/BChE inhibitors, BACE1, or anti-amyloid platelet aggregation substances are most desirable because they improve cognition with minimal side effects. Plant secondary metabolites, used in traditional medicine and pharmacy, are promising. Among these are the monoterpenes—low-molecular compounds with anti-inflammatory, antioxidant, Citation: Wojtunik-Kulesza, K.; enzyme inhibitory, analgesic, sedative, as well as other biological properties. The presented review Rudkowska, M.; Kasprzak-Drozd, K.; focuses on the pathophysiology of AD and a selected group of anti-neurodegenerative monoterpenes Oniszczuk, A.; Borowicz-Reutt, K. and monoterpenoids for which possible mechanisms of action have been explained. The main body Activity of Selected Group of of the article focuses on monoterpenes that have shown improved memory and learning, anxiolytic Monoterpenes in Alzheimer’s and sleep-regulating effects as determined by in vitro and in silico tests—followed by validation in Disease Symptoms in Experimental in vivo models. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
One-Month of High-Intensity Exercise Did Not Change the Food Intake And
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/ licenses/ by-nc-nd/3.0), which permits copy and redistribute the material in any medium or format, provided the original work is properly cited. 8 ENDOCRINE REGULATIONS, Vol. 53, No. 1, 8–13, 2019 doi:10.2478/enr-2019-0002 One-month of high-intensity exercise did not change the food intake and the hypothalamic arcuate nucleus proopiomelanocortin and neuropeptide Y expression levels in male Wistar rats Nazli Khajehnasiri1, Homayoun Khazali2, Farzam Sheikhzadeh3, Mahnaz Ghowsi4 1Department of Biological Sciences, Faculty of Basic Sciences, Higher Education Institute of Rab-Rashid, Tabriz, Iran; 2Department of Animal Sciences and Biotechnology, Faculty of Biological Sciences and Technology, Shahid Beheshti University, Tehran, Iran; 3Department of Animal Sciences, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran; 4Department of Biology, Faculty of Sciences, Razi University, Kermanshah, Iran E-mail: [email protected] Objective. The hypothalamic arcuate nucleus proopiomelanocortin (POMC) and neuropeptide Y (NPY) circuitries are involved in the inhibition and stimulation of the appetite, respectively. The aim of this study was to investigate the effects of one-month lasting high-intensity exercise on the POMC mRNA and NPY mRNA expression in the above-mentioned brain structure and appetite and food intake levels. Methods. Fourteen male Wistar rats (250±50 g) were used and kept in the well-controlled con- ditions (22±2 °C, 50±5% humidity, and 12 h dark/light cycle) with food and water ad libitum. The rats were divided into two groups (n=7): 1) control group (C, these rats served as controls) and 2) exercised group (RIE, these rats performed a high-intensity exercise for one month (5 days per week) 40 min daily with speed 35 m/min. -
List of Union Reference Dates A
Active substance name (INN) EU DLP BfArM / BAH DLP yearly PSUR 6-month-PSUR yearly PSUR bis DLP (List of Union PSUR Submission Reference Dates and Frequency (List of Union Frequency of Reference Dates and submission of Periodic Frequency of submission of Safety Update Reports, Periodic Safety Update 30 Nov. 2012) Reports, 30 Nov. -
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Supplementary Materials: High throughput virtual screening to discover inhibitors of the main protease of the coronavirus SARS-CoV-2 Olujide O. Olubiyi1,2*, Maryam Olagunju1, Monika Keutmann1, Jennifer Loschwitz1,3, and Birgit Strodel1,3* 1 Institute of Biological Information Processing: Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany 2 Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife, Nigeria 3 Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany * Corresponding authors: [email protected], [email protected] List of Figures S1 Chemical fragments majorly featured in the top performing 9,515 synthetic com- pounds obtained from screening against the crystal structure of the SARS-CoV-2 main protease 3CLpro. .................................. 2 S2 Chemical fragments majorly featured in the top 2,102 synthetic compounds obtained from ensemble docking and application of cutoff values of ∆G ≤ −7.0 kcal/mol and ddyad ≤ 3.5 Å. ............................ 2 S3 The poses and 3CLpro–compound interactions of phthalocyanine and hypericin. 3 S4 The poses and 3CLpro–compound interactions of the four best non-FDA-approved and investigational drugs. ............................... 4 S5 The poses and 3CLpro–compound interactions of zeylanone and glabrolide. 5 List of Tables S1 Names and properties of the compounds binding best to the active site of 3CLpro. 6 1 Supporting Material: High throughput virtual screening for 3CLpro inhibitors Figure S1: Chemical fragments majorly featured in the top performing 9,515 synthetic com- pounds obtained from screening against the crystal structure of the SARS-CoV-2 main pro- tease 3CLpro. The numbers represent the occurrence in absolute numbers. -
Dietary Fat Alters the Response of Hypothalamic Neuropeptide Y to Subsequent Energy Intake in Broiler Chickens Xiao J
© 2017. Published by The Company of Biologists Ltd | Journal of Experimental Biology (2017) 220, 607-614 doi:10.1242/jeb.143792 RESEARCH ARTICLE Dietary fat alters the response of hypothalamic neuropeptide Y to subsequent energy intake in broiler chickens Xiao J. Wang, Shao H. Xu, Lei Liu, Zhi G. Song, Hong C. Jiao and Hai Lin* ABSTRACT Several studies have shown that these hypothalamic neuropeptides Dietary fat affects appetite and appetite-related peptides in birds and are sensitive to body energy status and critical to whole-body mammals; however, the effect of dietary fat on appetite is still unclear metabolic adjustment. NPY reduces energy expenditure by in chickens faced with different energy statuses. Two experiments decreasing adipose tissue thermogenesis (Egawa et al., 1991; Patel were conducted to investigate the effects of dietary fat on food intake et al., 2006; Chao et al., 2011; Zhang et al., 2014). The obesity of and hypothalamic neuropeptides in chickens subjected to two ob/ob mice is attenuated when NPY is knocked out (Erickson et al., fi feeding states or two diets. In Experiment 1, chickens were fed a 1996; Segal-Lieberman et al., 2003). NPY de ciency attenuates high-fat (HF) or low-fat (LF) diet for 35 days, and then subjected to fed responses to a palatable high fat diet in mice (Hollopeter et al., 1998; (HF-fed, LF-fed) or fasted (HF-fasted, LF-fasted) conditions for 24 h. Patel et al., 2006). Animals in which POMC neurons have been In Experiment 2, chickens that were fed a HF or LF diet for 35 days knocked out are obese and hyperphagic (Butler and Cone, 2002; were fasted for 24 h and then re-fed with HF (HF-RHF, LF-RHF) or LF Mencarelli et al., 2012; Diané et al., 2014; Raffan et al., 2016). -
Global Proteomic Analysis Deciphers the Mechanism of Action of Plant
www.nature.com/scientificreports OPEN Global proteomic analysis deciphers the mechanism of action of plant derived oleic acid against Candida albicans virulence and bioflm formation Subramanian Muthamil1,2, Krishnan Ganesh Prasath1,2, Arumugam Priya1, Pitchai Precilla1 & Shunmugiah Karutha Pandian1* Candida albicans is a commensal fungus in humans, mostly found on the mucosal surfaces of the mouth, gut, vagina and skin. Incidence of ever increasing invasive candidiasis in immunocompromised patients, alarming occurrence of antifungal resistance and insufcient diagnostic methods demand more focused research into C. albicans pathogenicity. Consequently, in the present study, oleic acid from Murraya koenigii was shown to have the efcacy to inhibit bioflm formation and virulence of Candida spp. Results of in vitro virulence assays and gene expression analysis, impelled to study the protein targets which are involved in the molecular pathways of C. albicans pathogenicity. Proteomic studies of diferentially expressed proteins reveals that oleic acid induces oxidative stress responses and mainly targets the proteins involved in glucose metabolism, ergosterol biosynthesis, lipase production, iron homeostasis and amino acid biosynthesis. The current study emphasizes anti-virulent potential of oleic acid which can be used as a therapeutic agent to treat Candida infections. Candida is a genus of yeast with remarkable phenotypic characteristics and found as a commensal fungus in humans. Candida species are most commonly present in the genital tracts and other membrane tracts such as mucosal oral cavity, respiratory tract, gastrointestinal tract etc1. Although over hundred Candida species belong to this genus, C. albicans is responsible for the majority of Candida infection. Other medically important Candida species are Candida glabrata, Candida tropicalis, Candida dubliniensis, and Candida parapsilosis2. -
Identification of Potential Key Genes and Pathway Linked with Sporadic Creutzfeldt-Jakob Disease Based on Integrated Bioinformatics Analyses
medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Identification of potential key genes and pathway linked with sporadic Creutzfeldt-Jakob disease based on integrated bioinformatics analyses Basavaraj Vastrad1, Chanabasayya Vastrad*2 , Iranna Kotturshetti 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. 3. Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, Karnataka 562209, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Abstract Sporadic Creutzfeldt-Jakob disease (sCJD) is neurodegenerative disease also called prion disease linked with poor prognosis. The aim of the current study was to illuminate the underlying molecular mechanisms of sCJD. The mRNA microarray dataset GSE124571 was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened.