Toxicogenomics Applications of New Functional Genomics Technologies in Toxicology
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Whole Brain and Brain Regional Coexpression Network Interactions Associated with Predisposition to Alcohol Consumption Lauren A
Virginia Commonwealth University VCU Scholars Compass Study of Biological Complexity Publications Center for the Study of Biological Complexity 2013 Whole Brain and Brain Regional Coexpression Network Interactions Associated with Predisposition to Alcohol Consumption Lauren A. Vanderlinden University of Colorado at Aurora Laura M. Saba University of Colorado at Aurora Katerina Kechris University of Colorado at Aurora See next page for additional authors Follow this and additional works at: http://scholarscompass.vcu.edu/csbc_pubs Part of the Life Sciences Commons © 2013 Vanderlinden et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Downloaded from http://scholarscompass.vcu.edu/csbc_pubs/24 This Article is brought to you for free and open access by the Center for the Study of Biological Complexity at VCU Scholars Compass. It has been accepted for inclusion in Study of Biological Complexity Publications by an authorized administrator of VCU Scholars Compass. For more information, please contact [email protected]. Authors Lauren A. Vanderlinden, Laura M. Saba, Katerina Kechris, Michael F. Miles, Paula L. Hoffman, and Boris Tabakoff This article is available at VCU Scholars Compass: http://scholarscompass.vcu.edu/csbc_pubs/24 Whole Brain and Brain Regional Coexpression Network Interactions Associated with Predisposition to Alcohol Consumption Lauren -
Proteomic Analysis of the Venom of Jellyfishes Rhopilema Esculentum and Sanderia Malayensis
marine drugs Article Proteomic Analysis of the Venom of Jellyfishes Rhopilema esculentum and Sanderia malayensis 1, 2, 2 2, Thomas C. N. Leung y , Zhe Qu y , Wenyan Nong , Jerome H. L. Hui * and Sai Ming Ngai 1,* 1 State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China; [email protected] 2 Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China; [email protected] (Z.Q.); [email protected] (W.N.) * Correspondence: [email protected] (J.H.L.H.); [email protected] (S.M.N.) Contributed equally. y Received: 27 November 2020; Accepted: 17 December 2020; Published: 18 December 2020 Abstract: Venomics, the study of biological venoms, could potentially provide a new source of therapeutic compounds, yet information on the venoms from marine organisms, including cnidarians (sea anemones, corals, and jellyfish), is limited. This study identified the putative toxins of two species of jellyfish—edible jellyfish Rhopilema esculentum Kishinouye, 1891, also known as flame jellyfish, and Amuska jellyfish Sanderia malayensis Goette, 1886. Utilizing nano-flow liquid chromatography tandem mass spectrometry (nLC–MS/MS), 3000 proteins were identified from the nematocysts in each of the above two jellyfish species. Forty and fifty-one putative toxins were identified in R. esculentum and S. malayensis, respectively, which were further classified into eight toxin families according to their predicted functions. Amongst the identified putative toxins, hemostasis-impairing toxins and proteases were found to be the most dominant members (>60%). -
An Interactive Web Application to Explore Regeneration-Associated Gene Expression and Chromatin Accessibility
Supplementary Materials Regeneration Rosetta: An interactive web application to explore regeneration-associated gene expression and chromatin accessibility Andrea Rau, Sumona P. Dhara, Ava J. Udvadia, Paul L. Auer 1. Table S1. List of cholesterol metabolic genes from MGI database 2. Table S2. List of differentially expressed transcripts during optic nerve regeneration in zebrafish using the MGI cholesterol metabolic gene queries in the Regeneration Rosetta app 3. Table S3. List of transcription factor encoding genes from brain cell bodies following spinal cord injury in lamprey over a course of 12 weeKs 4. Table S4. List of transcription factor encoding genes from spinal cell bodies following spinal cord injury in lamprey over a course of 12 weeks Ensembl ID MGI Gene ID Symbol Name ENSMUSG00000015243 MGI:99607 Abca1 ATP-binding cassette, sub-family A (ABC1), member 1 ENSMUSG00000026944 MGI:99606 Abca2 ATP-binding cassette, sub-family A (ABC1), member 2 ENSMUSG00000024030 MGI:107704 Abcg1 ATP binding cassette subfamily G member 1 ENSMUSG00000026003 MGI:87866 Acadl acyl-Coenzyme A dehydrogenase, long-chain ENSMUSG00000018574 MGI:895149 Acadvl acyl-Coenzyme A dehydrogenase, very long chain ENSMUSG00000038641 MGI:2384785 Akr1d1 aldo-keto reductase family 1, member D1 ENSMUSG00000028553 MGI:1353627 Angptl3 angiopoietin-like 3 ENSMUSG00000031996 MGI:88047 Aplp2 amyloid beta (A4) precursor-like protein 2 ENSMUSG00000032083 MGI:88049 Apoa1 apolipoprotein A-I ENSMUSG00000005681 MGI:88050 Apoa2 apolipoprotein A-II ENSMUSG00000032080 MGI:88051 Apoa4 -
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. -
Supplementary Information Integrative Analyses of Splicing in the Aging Brain: Role in Susceptibility to Alzheimer’S Disease
Supplementary Information Integrative analyses of splicing in the aging brain: role in susceptibility to Alzheimer’s Disease Contents 1. Supplementary Notes 1.1. Religious Orders Study and Memory and Aging Project 1.2. Mount Sinai Brain Bank Alzheimer’s Disease 1.3. CommonMind Consortium 1.4. Data Availability 2. Supplementary Tables 3. Supplementary Figures Note: Supplementary Tables are provided as separate Excel files. 1. Supplementary Notes 1.1. Religious Orders Study and Memory and Aging Project Gene expression data1. Gene expression data were generated using RNA- sequencing from Dorsolateral Prefrontal Cortex (DLPFC) of 540 individuals, at an average sequence depth of 90M reads. Detailed description of data generation and processing was previously described2 (Mostafavi, Gaiteri et al., under review). Samples were submitted to the Broad Institute’s Genomics Platform for transcriptome analysis following the dUTP protocol with Poly(A) selection developed by Levin and colleagues3. All samples were chosen to pass two initial quality filters: RNA integrity (RIN) score >5 and quantity threshold of 5 ug (and were selected from a larger set of 724 samples). Sequencing was performed on the Illumina HiSeq with 101bp paired-end reads and achieved coverage of 150M reads of the first 12 samples. These 12 samples will serve as a deep coverage reference and included 2 males and 2 females of nonimpaired, mild cognitive impaired, and Alzheimer's cases. The remaining samples were sequenced with target coverage of 50M reads; the mean coverage for the samples passing QC is 95 million reads (median 90 million reads). The libraries were constructed and pooled according to the RIN scores such that similar RIN scores would be pooled together. -
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. -
Noelia Díaz Blanco
Effects of environmental factors on the gonadal transcriptome of European sea bass (Dicentrarchus labrax), juvenile growth and sex ratios Noelia Díaz Blanco Ph.D. thesis 2014 Submitted in partial fulfillment of the requirements for the Ph.D. degree from the Universitat Pompeu Fabra (UPF). This work has been carried out at the Group of Biology of Reproduction (GBR), at the Department of Renewable Marine Resources of the Institute of Marine Sciences (ICM-CSIC). Thesis supervisor: Dr. Francesc Piferrer Professor d’Investigació Institut de Ciències del Mar (ICM-CSIC) i ii A mis padres A Xavi iii iv Acknowledgements This thesis has been made possible by the support of many people who in one way or another, many times unknowingly, gave me the strength to overcome this "long and winding road". First of all, I would like to thank my supervisor, Dr. Francesc Piferrer, for his patience, guidance and wise advice throughout all this Ph.D. experience. But above all, for the trust he placed on me almost seven years ago when he offered me the opportunity to be part of his team. Thanks also for teaching me how to question always everything, for sharing with me your enthusiasm for science and for giving me the opportunity of learning from you by participating in many projects, collaborations and scientific meetings. I am also thankful to my colleagues (former and present Group of Biology of Reproduction members) for your support and encouragement throughout this journey. To the “exGBRs”, thanks for helping me with my first steps into this world. Working as an undergrad with you Dr. -
Role of Amylase in Ovarian Cancer Mai Mohamed University of South Florida, [email protected]
University of South Florida Scholar Commons Graduate Theses and Dissertations Graduate School July 2017 Role of Amylase in Ovarian Cancer Mai Mohamed University of South Florida, [email protected] Follow this and additional works at: http://scholarcommons.usf.edu/etd Part of the Pathology Commons Scholar Commons Citation Mohamed, Mai, "Role of Amylase in Ovarian Cancer" (2017). Graduate Theses and Dissertations. http://scholarcommons.usf.edu/etd/6907 This Dissertation is brought to you for free and open access by the Graduate School at Scholar Commons. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. Role of Amylase in Ovarian Cancer by Mai Mohamed A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Pathology and Cell Biology Morsani College of Medicine University of South Florida Major Professor: Patricia Kruk, Ph.D. Paula C. Bickford, Ph.D. Meera Nanjundan, Ph.D. Marzenna Wiranowska, Ph.D. Lauri Wright, Ph.D. Date of Approval: June 29, 2017 Keywords: ovarian cancer, amylase, computational analyses, glycocalyx, cellular invasion Copyright © 2017, Mai Mohamed Dedication This dissertation is dedicated to my parents, Ahmed and Fatma, who have always stressed the importance of education, and, throughout my education, have been my strongest source of encouragement and support. They always believed in me and I am eternally grateful to them. I would also like to thank my brothers, Mohamed and Hussien, and my sister, Mariam. I would also like to thank my husband, Ahmed. -
Genomic Dose Response
Genomic Dose Response: The Picture NTP Genomic Dose Response Modeling Expert Panel Meeting October 23, 2017 Russell Thomas Director National Center for Computational Toxicology The views expressed in this presentation are those of the author and do not necessarily reflect the views or policies of the U.S. EPA Scott May Want To Rethink Asking Me To Be The “Big Picture Guy”… National Center for Computational Toxicology It is a Well Known Fact that Toxicology Continues to Have a Data Problem US National Research Council, 1984 Size of Estimate Mean Percent Category Category In the Select Universe Pesticides and Inert Ingredients of Pesticides 3,350 Formulations 10 24 2 26 38 Cosmetic Ingredients 3,410 2 14 10 18 56 Drugs and Excipients Used in Drug Formulations 1,815 18 18 3 36 25 Food Additives 8,627 • Major challenge is too many 5 14 1 34 46 Chemicals in Commerce: chemicals and not enough At Least 1 Million 12,860 Pounds/Year data 11 11 78 Chemicals in Commerce: • Total # chemicals = 65,725 Less than 1 Million 13,911 Pounds/Year • Chemicals with no toxicity 12 12 76 data of any kind = ~46,000 Chemicals in Commerce: Production Unknown or 21,752 Inaccessible 10 8 82 Complete Partial Minimal Some No Toxicity Health Health Toxicity Toxicity Information Hazard Hazard Information Information Available Assessment Assessment Available Available 2 Possible Possible (But Below Minimal) National Center for Computational Toxicology It is a Well Known Fact that Toxicology Continues to Have a Data Problem 70 60 50 40 30 20 Percent of Chemicals <1% 10 0 Acute Cancer Gentox Dev Tox Repro Tox EDSP Tier 1 Modified from Judson et al., EHP 2009 3 National Center for Computational Toxicology For Those With Data, Have We Been Truly Predictive or Just Protective? …data compiled from 150 compounds with 221 human toxicity events reported. -
Whole Exome Sequencing in Families at High Risk for Hodgkin Lymphoma: Identification of a Predisposing Mutation in the KDR Gene
Hodgkin Lymphoma SUPPLEMENTARY APPENDIX Whole exome sequencing in families at high risk for Hodgkin lymphoma: identification of a predisposing mutation in the KDR gene Melissa Rotunno, 1 Mary L. McMaster, 1 Joseph Boland, 2 Sara Bass, 2 Xijun Zhang, 2 Laurie Burdett, 2 Belynda Hicks, 2 Sarangan Ravichandran, 3 Brian T. Luke, 3 Meredith Yeager, 2 Laura Fontaine, 4 Paula L. Hyland, 1 Alisa M. Goldstein, 1 NCI DCEG Cancer Sequencing Working Group, NCI DCEG Cancer Genomics Research Laboratory, Stephen J. Chanock, 5 Neil E. Caporaso, 1 Margaret A. Tucker, 6 and Lynn R. Goldin 1 1Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; 2Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; 3Ad - vanced Biomedical Computing Center, Leidos Biomedical Research Inc.; Frederick National Laboratory for Cancer Research, Frederick, MD; 4Westat, Inc., Rockville MD; 5Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; and 6Human Genetics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA ©2016 Ferrata Storti Foundation. This is an open-access paper. doi:10.3324/haematol.2015.135475 Received: August 19, 2015. Accepted: January 7, 2016. Pre-published: June 13, 2016. Correspondence: [email protected] Supplemental Author Information: NCI DCEG Cancer Sequencing Working Group: Mark H. Greene, Allan Hildesheim, Nan Hu, Maria Theresa Landi, Jennifer Loud, Phuong Mai, Lisa Mirabello, Lindsay Morton, Dilys Parry, Anand Pathak, Douglas R. Stewart, Philip R. Taylor, Geoffrey S. Tobias, Xiaohong R. Yang, Guoqin Yu NCI DCEG Cancer Genomics Research Laboratory: Salma Chowdhury, Michael Cullen, Casey Dagnall, Herbert Higson, Amy A. -
Next-Generation Sequencing Data for Use in Risk Assessment Bruce Alexander Merrick
Available online at www.sciencedirect.com Current Opinion in ScienceDirect Toxicology Next-generation sequencing data for use in risk assessment Bruce Alexander Merrick Abstract fluorescently labeled nucleotides and capillary electro- Next-generation sequencing (NGS) represents several phoresis that gave rise to automated sequencing in- powerful platforms that have revolutionized RNA and DNA struments such as the Applied Biosystems, Inc. model analysis. The parallel sequencing of millions of DNA molecules 370A sequencers and others, on the basis of Sanger can provide mechanistic insights into toxicology and provide chemistries [2]. Read length per each sample was at 500e new avenues for biomarker discovery with growing relevance 800 nucleotides, and sample throughput was limited. for risk assessment. The evolution of NGS technologies has improved over the last decade with increased sensitivity and Sanger-based DNA sequencing instruments are accuracy to foster new biomarker assays from tissue, blood, considered first-generation platforms. Instruments that and other biofluids. NGS technologies can identify transcrip- perform multiple sequencing reactions simultaneously tional changes and genomic targets with base pair precision in in a ‘massively parallel’ fashion have been dubbed, response to chemical exposure. Furthermore, there are ‘NextGeneration’ or NextGen Sequencing [3]. How several exciting movements within the toxicology community NGS came about compared with other genomic plat- that incorporate NGS platforms into new strategies for more forms is interlinked with microarray technology rapid toxicological characterizations. These include the Tox21 (Figure 1). Both platforms can provide whole genomic in vitro high-throughput transcriptomic screening program, approaches to research problems. Microarrays are a development of organotypic spheroids, alternative animal fluorescent probe hybridization-based technology with models, mining archival tissues, liquid biopsy, and epige- origins in the mid-1990s that are now a mature genomic nomics. -
Baboon JMP CES Paper
Baboon carboxylesterases 1 and 2: sequences, structures and phylogenetic relationships with human and other primate carboxylesterases Author Holmes, Roger S, Glenn, Jeremy P, VandeBerg, John L, Cox, Laura A Published 2009 Journal Title Journal of Medical Primatology DOI https://doi.org/10.1111/j.1600-0684.2008.00315.x Copyright Statement © 2009 John Wiley & Sons A/S. This is the author-manuscript version of the paper. Reproduced in accordance with the copyright policy of the publisher.The definitive version is available at www.interscience.wiley.com Downloaded from http://hdl.handle.net/10072/29362 Griffith Research Online https://research-repository.griffith.edu.au Baboon Carboxylesterases 1 and 2: Sequences, Structures and Phylogenetic Relationships with Human and other Primate Carboxylesterases Roger S. Holmes 1,2,3 , Jeremy P. Glenn 1, John L. VandeBerg 1,2 , Laura A. Cox 1,2,4 1. Department of Genetics and 2. Southwest National Primate Research Center, Southwest Foundation for Biomedical Research, San Antonio, TX, USA, and 3. School of Biomolecular and Physical Sciences, Griffith University, Nathan. Queensland, Australia 4. Corresponding Author: Laura A. Cox, Ph.D. Department of Genetics Southwest National Primate Research Center Southwest Foundation for Biomedical Research San Antonio, TX, USA 78227 Email: [email protected] Phone: 210-258-9687 Fax: 210-258-9600 Keywords: cDNA sequence; amino acid sequence; 3-D structure Running Head: Carboxylesterases: sequences and phylogeny Published in Journal of Medical Primatology (2009) 38: 27-38. Abstract Background Carboxylesterase (CES) is predominantly responsible for the detoxification of a wide range of drugs and narcotics, and catalyze several reactions in cholesterol and fatty acid metabolism.