DOCSLIB.ORG

PINTO-DISSERTATION-2014.Pdf

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
PINTO-DISSERTATION-2014.Pdf In vitro assays and zebrafish as an in vivo model to study nuclear receptor signaling _______________ A Dissertation Presented to The Faculty of the Department of Biology and Biochemistry University of Houston _______________ In Partial Fulfillment Of the Requirements for the Degree of Doctor of Philosophy _______________ By Caroline Lucia Pinto August, 2014 In vitro assays and zebrafish as an in vivo model to study nuclear receptor signaling _________________________ Caroline Lucia Pinto APPROVED: __________________________ Dr. Jan-Åke Gustafsson, Ph.D. Committee Chair ___________________________ Dr. Maria Bondesson Bolin, Ph.D. ___________________________ Dr. Robert Fox, Ph.D. ___________________________ Dr. Joseph Eichberg, Ph.D. ___________________________ Dr. Steven Bark, PhD. ___________________________ Dr. Paul Webb, PhD. _________________________ Dr. Dan Wells, Ph.D. Dean, College of Natural Sciences and Mathematics ii Acknowledgements This achievement would not have been possible without the help and encouragement from many people that I was blessed to meet during my Ph.D. I would like to start by thanking the Department of Biology and Biochemistry at University of Houston for allowing me to join the Ph.D. program, and be a part of this diverse academic community. I would like to thank Dr. Jan-Ake Gustafsson for the opportunity of joining the Center for Nuclear Receptors and Cell Signaling (CNRCS) and for his guidance and support throughout my Ph.D. I am grateful to Dr. Maria Bondesson for her support, kindness and encouragement with my projects, and for guiding me to become an autonomous scientist. I thank Dr. Anne Riu for her guidance, patience and always well-appreciated discussions and criticism, and for fostering critical thinking in me. I know the work is actually good when you say “it’s not so bad”. My gratitude also goes to other present and previous zebrafish lab group members. I appreciate Dr. Catherine McCollum and Sharanya Kalasekar for their help, support, ideas and friendship. I thank Dr. Ruixin Hao and Dr. Nicole Ducharme for their help and advice, and Triet Truong, Nestor Narvaez, Juan Narvaez and Muzamil Haq for the zebrafish care and maintenance. I also appreciate having been given the opportunity to work side by side with our collaborator Dr. Patrick Balaguer (INSERM, Montpellier, France) during the three iii months that he spent in the CNRCS, and for his always available and continuous scientific help. I also thank our collaborators Dr. Cecilia Williams (CNRCS) for her contribution, and Dr. Eric Swindell (University of Texas) for his expertise and scientific input in the zebrafish eye studies. I would like to thank my committee members Dr. Robert Fox, Dr. Joseph Eichberg, Dr. Paul Webb and Dr. Steven Bark for their time and advice throughout my graduate studies. I would also like to thank previous and current members of the CNRCS who have shared some of their knowledge and helped me throughout my PhD: Dr. Margaret Warner, Dr. Stefan Andersson (in memorian), Dr. Daniel Frigo, Dr. Anders Ström, Dr. Shaun Zhang, Dr. Philip Jonsson, Dr. Chiara Gabbi, Dr. Rodrigo Barros, Gayani Rajapaksa, Kim Anthony, Jeff Spencer, Dr. Armando Rivera, Dr. Yubing Dai, Dr. Laure Maneix, Dr. Anne Katchy, Dr. Wanfu Wu, Bilqees Bhatti, Kaberi Das, Christopher Brooks, Dr. Prasenjit Dey, Dr. Selvaraj Muthusamy, Fotis Nikolos and Igor Bado. I appreciate Odila Crandall, Roy Green, Sol Gomez and Heidi Vitrac for their friendship and support. Lastly, I would like to thank my mother Gladis, my sister Cristiane and brother Fabio for their unconditional support and for always letting me “fly” away. This dissertation is dedicated to my dear father, who would certainly be very proud to see me reach this milestone. iv In vitro assays and zebrafish as an in vivo model to study nuclear receptor signaling _______________ An Abstract of a Dissertation Presented to The Faculty of the Department of Biology and Biochemistry University of Houston _______________ In Partial Fulfillment Of the Requirements for the Degree of Doctor of Philosophy _______________ By Caroline Lucia Pinto August, 2014 v Abstract Humans are exposed daily to cocktails of chemicals from different sources. Some of these chemicals can interfere with hormonal signaling, and are referred to as endocrine disrupting chemicals (EDCs). A mechanism through which EDCs may act is by binding and modulating the activity of nuclear receptors (NRs), which could lead to adverse health outcomes, especially during critical developmental windows, such as fetal development and perinatal life. As we are exposed to chemical cocktails, there is an increased concern regarding adverse effects resulting from exposures to combinations of EDCs. Mixture effects of bisphenol A and phytoestrogens, well-known xenoestrogens, were assessed in transactivation assays mediated by the estrogen receptors (ERs) and in MCF-7 cell proliferation assays. We observed additive effects with a combination of nanomolar concentrations of these chemicals, levels that are relevant to human exposure. Another major concern is the need to refine, reduce and replace animal models, and zebrafish have been used as an alternative in vivo model. However, to support zebrafish for risk assessment of EDCs, it is crucial to evaluate the transcriptional activity/selectivity of mammalian NR ligands towards their zebrafish homologues. By using stable reporter cell lines expressing human or zebrafish NRs, we observed clear differences in the selectivity/activity of ER and peroxisome-proliferator activated receptor gamma (PPAR) ligands between human and their zebrafish counterparts, demonstrating the importance of assessing the transcriptional profile of EDCs prior to using them in vivo. vi Liver X receptors (LXRs), also NRs, are key regulators of lipid and cholesterol metabolism in mammals. Transcriptomic analysis of zebrafish larvae treated with the mammalian LXR agonists T0901317 and GW3965, also activators of zebrafish LXR, revealed a primary role of LXR in regulating lipid metabolism and transport during zebrafish development. Tissue enrichment analysis predicted the liver, the yolk syncytial layer and the eye to be affected by LXR activation in zebrafish, which correlated with increased lipid uptake from the yolk, and with morphological abnormalities in the retina and lens of developing zebrafish. The expression of important genes for eye development and maintenance of photoreceptors, was modulated in zebrafish exposed to the ligands as well as in LXR knockout mice, revealing, for the first time, a new potential physiological role of LXRs in regulating expression of gene networks important for visual function in vertebrates. vii Table of Contents Chapter 1. Introduction .................................................................................................. 1 1.1 Nuclear Hormone Receptor Superfamily ................................................................ 2 1.1.1 Estrogen Receptors .......................................................................................... 6 1.1.2 Peroxisome Proliferator-activated Receptor (PPAR).................................. 8 1.1.3 Liver X Receptors (LXRs) .............................................................................. 9 1.2 Endocrine disruptors ............................................................................................. 13 1.2.1 EDCs targeting estrogen receptors (ERs) ...................................................... 15 1.2.2 EDCs targeting peroxisome proliferator activated-receptor (PPAR)........ 18 1.2.3 EDCs targeting Liver X Receptors (LXRs) .................................................. 19 1.3 In vitro and in vivo models to assess the effects of EDCs targeting NRs ............. 21 1.3.1 In vitro assays for EDC screening ................................................................. 22 1.3.2 In vivo assays for EDC screening .................................................................. 25 1.3.3 Toxicogenomics ............................................................................................ 27 1.4 Zebrafish as an alternative model organism ......................................................... 28 1.4.1 Zebrafish as a model for developmental studies ........................................... 29 1.4.2 Zebrafish as a model for toxicological studies and chemical screens targeting NRs ......................................................................................................................... 30 1.5 Project aims and objectives ................................................................................... 33 Chapter 2. Materials and Methods .............................................................................. 35 2.1 Chemicals and materials ....................................................................................... 36 2.2 Cell lines ............................................................................................................... 37 2.2.1 HELN reporter cells stably expressing hERs and zfERs .............................. 37 2.2.2 HG5LN reporter cells expressing GAL4-hPPAR/zfPPAR/zfLXR chimeras ................................................................................................................................ 38 2.2.3 Human breast cancer MCF-7 cells ................................................................ 41 2.3 Luciferase reporter assays ..................................................................................... 41 2.4 MCF-7 Cell
Load more

Recommended publications
  • 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.
    [Show full text]
  • Ingenuity Pathway Analysis of Differentially Expressed Genes Involved in Signaling Pathways and Molecular Networks in Rhoe Gene‑Edited Cardiomyocytes
    INTERNATIONAL JOURNAL OF MOleCular meDICine 46: 1225-1238, 2020 Ingenuity pathway analysis of differentially expressed genes involved in signaling pathways and molecular networks in RhoE gene‑edited cardiomyocytes ZHONGMING SHAO1*, KEKE WANG1*, SHUYA ZHANG2, JIANLING YUAN1, XIAOMING LIAO1, CAIXIA WU1, YUAN ZOU1, YANPING HA1, ZHIHUA SHEN1, JUNLI GUO2 and WEI JIE1,2 1Department of Pathology, School of Basic Medicine Sciences, Guangdong Medical University, Zhanjiang, Guangdong 524023; 2Hainan Provincial Key Laboratory for Tropical Cardiovascular Diseases Research and Key Laboratory of Emergency and Trauma of Ministry of Education, Institute of Cardiovascular Research of The First Affiliated Hospital, Hainan Medical University, Haikou, Hainan 571199, P.R. China Received January 7, 2020; Accepted May 20, 2020 DOI: 10.3892/ijmm.2020.4661 Abstract. RhoE/Rnd3 is an atypical member of the Rho super- injury and abnormalities, cell‑to‑cell signaling and interaction, family of proteins, However, the global biological function and molecular transport. In addition, 885 upstream regulators profile of this protein remains unsolved. In the present study, a were enriched, including 59 molecules that were predicated RhoE‑knockout H9C2 cardiomyocyte cell line was established to be strongly activated (Z‑score >2) and 60 molecules that using CRISPR/Cas9 technology, following which differentially were predicated to be significantly inhibited (Z‑scores <‑2). In expressed genes (DEGs) between the knockout and wild‑type particular, 33 regulatory effects and 25 networks were revealed cell lines were screened using whole genome expression gene to be associated with the DEGs. Among them, the most signifi- chips. A total of 829 DEGs, including 417 upregulated and cant regulatory effects were ‘adhesion of endothelial cells’ and 412 downregulated, were identified using the threshold of ‘recruitment of myeloid cells’ and the top network was ‘neuro- fold changes ≥1.2 and P<0.05.
    [Show full text]
  • Enzyme DHRS7
    Toward the identification of a function of the “orphan” enzyme DHRS7 Inauguraldissertation zur Erlangung der Würde eines Doktors der Philosophie vorgelegt der Philosophisch-Naturwissenschaftlichen Fakultät der Universität Basel von Selene Araya, aus Lugano, Tessin Basel, 2018 Originaldokument gespeichert auf dem Dokumentenserver der Universität Basel edoc.unibas.ch Genehmigt von der Philosophisch-Naturwissenschaftlichen Fakultät auf Antrag von Prof. Dr. Alex Odermatt (Fakultätsverantwortlicher) und Prof. Dr. Michael Arand (Korreferent) Basel, den 26.6.2018 ________________________ Dekan Prof. Dr. Martin Spiess I. List of Abbreviations 3α/βAdiol 3α/β-Androstanediol (5α-Androstane-3α/β,17β-diol) 3α/βHSD 3α/β-hydroxysteroid dehydrogenase 17β-HSD 17β-Hydroxysteroid Dehydrogenase 17αOHProg 17α-Hydroxyprogesterone 20α/βOHProg 20α/β-Hydroxyprogesterone 17α,20α/βdiOHProg 20α/βdihydroxyprogesterone ADT Androgen deprivation therapy ANOVA Analysis of variance AR Androgen Receptor AKR Aldo-Keto Reductase ATCC American Type Culture Collection CAM Cell Adhesion Molecule CYP Cytochrome P450 CBR1 Carbonyl reductase 1 CRPC Castration resistant prostate cancer Ct-value Cycle threshold-value DHRS7 (B/C) Dehydrogenase/Reductase Short Chain Dehydrogenase Family Member 7 (B/C) DHEA Dehydroepiandrosterone DHP Dehydroprogesterone DHT 5α-Dihydrotestosterone DMEM Dulbecco's Modified Eagle's Medium DMSO Dimethyl Sulfoxide DTT Dithiothreitol E1 Estrone E2 Estradiol ECM Extracellular Membrane EDTA Ethylenediaminetetraacetic acid EMT Epithelial-mesenchymal transition ER Endoplasmic Reticulum ERα/β Estrogen Receptor α/β FBS Fetal Bovine Serum 3 FDR False discovery rate FGF Fibroblast growth factor HEPES 4-(2-Hydroxyethyl)-1-Piperazineethanesulfonic Acid HMDB Human Metabolome Database HPLC High Performance Liquid Chromatography HSD Hydroxysteroid Dehydrogenase IC50 Half-Maximal Inhibitory Concentration LNCaP Lymph node carcinoma of the prostate mRNA Messenger Ribonucleic Acid n.d.
    [Show full text]
  • Identification and Characterization of Genes That Control Fat
    Claire D’Andre et al. Journal of Animal Science and Biotechnology 2013, 4:43 http://www.jasbsci.com/content/4/1/43 JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY RESEARCH Open Access Identification and characterization of genes that control fat deposition in chickens Hirwa Claire D’Andre1,3*, Wallace Paul2, Xu Shen3, Xinzheng Jia3, Rong Zhang3, Liang Sun3 and Xiquan Zhang3 Abstract Background: Fat deposits in chickens contribute significantly to meat quality attributes such as juiciness, flavor, taste and other organoleptic properties. The quantity of fat deposited increases faster and earlier in the fast- growing chickens than in slow-growing chickens. In this study, Affymetrix Genechip® Chicken Genome Arrays 32773 transcripts were used to compare gene expression profiles in liver and hypothalamus tissues of fast-growing and slow-growing chicken at 8 wk of age. Real-time RT-PCR was used to validate the differential expression of genes selected from the microarray analysis. The mRNA expression of the genes was further examined in fat tissues. The association of single nucleotide polymorphisms of four lipid-related genes with fat traits was examined in a F2 resource population. Results: Four hundred genes in the liver tissues and 220 genes hypothalamus tissues, respectively, were identified to be differentially expressed in fast-growing chickens and slow-growing chickens. Expression levels of genes for lipid metabolism (SULT1B1, ACSBG2, PNPLA3, LPL, AOAH) carbohydrate metabolism (MGAT4B, XYLB, GBE1, PGM1, HKDC1)cholesttrol biosynthesis (FDPS, LSS, HMGCR, NSDHL, DHCR24, IDI1, ME1) HSD17B7 and other reaction or pro- cesses (CYP1A4, CYP1A1, AKR1B1, CYP4V2, DDO) were higher in the fast-growing White Recessive Rock chickens than in the slow-growing Xinghua chickens.
    [Show full text]
  • Identification and Characterization of Genes That Control Fat Deposition In
    Claire D’Andre et al. Journal of Animal Science and Biotechnology 2013, 4:43 http://www.jasbsci.com/content/4/1/43 JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY RESEARCH Open Access Identification and characterization of genes that control fat deposition in chickens Hirwa Claire D’Andre1,3*, Wallace Paul2, Xu Shen3, Xinzheng Jia3, Rong Zhang3, Liang Sun3 and Xiquan Zhang3 Abstract Background: Fat deposits in chickens contribute significantly to meat quality attributes such as juiciness, flavor, taste and other organoleptic properties. The quantity of fat deposited increases faster and earlier in the fast- growing chickens than in slow-growing chickens. In this study, Affymetrix Genechip® Chicken Genome Arrays 32773 transcripts were used to compare gene expression profiles in liver and hypothalamus tissues of fast-growing and slow-growing chicken at 8 wk of age. Real-time RT-PCR was used to validate the differential expression of genes selected from the microarray analysis. The mRNA expression of the genes was further examined in fat tissues. The association of single nucleotide polymorphisms of four lipid-related genes with fat traits was examined in a F2 resource population. Results: Four hundred genes in the liver tissues and 220 genes hypothalamus tissues, respectively, were identified to be differentially expressed in fast-growing chickens and slow-growing chickens. Expression levels of genes for lipid metabolism (SULT1B1, ACSBG2, PNPLA3, LPL, AOAH) carbohydrate metabolism (MGAT4B, XYLB, GBE1, PGM1, HKDC1)cholesttrol biosynthesis (FDPS, LSS, HMGCR, NSDHL, DHCR24, IDI1, ME1) HSD17B7 and other reaction or pro- cesses (CYP1A4, CYP1A1, AKR1B1, CYP4V2, DDO) were higher in the fast-growing White Recessive Rock chickens than in the slow-growing Xinghua chickens.
    [Show full text]
  • Gene Networks Activated by Specific Patterns of Action Potentials in Dorsal Root Ganglia Neurons Received: 10 August 2016 Philip R
    www.nature.com/scientificreports OPEN Gene networks activated by specific patterns of action potentials in dorsal root ganglia neurons Received: 10 August 2016 Philip R. Lee1,*, Jonathan E. Cohen1,*, Dumitru A. Iacobas2,3, Sanda Iacobas2 & Accepted: 23 January 2017 R. Douglas Fields1 Published: 03 March 2017 Gene regulatory networks underlie the long-term changes in cell specification, growth of synaptic connections, and adaptation that occur throughout neonatal and postnatal life. Here we show that the transcriptional response in neurons is exquisitely sensitive to the temporal nature of action potential firing patterns. Neurons were electrically stimulated with the same number of action potentials, but with different inter-burst intervals. We found that these subtle alterations in the timing of action potential firing differentially regulates hundreds of genes, across many functional categories, through the activation or repression of distinct transcriptional networks. Our results demonstrate that the transcriptional response in neurons to environmental stimuli, coded in the pattern of action potential firing, can be very sensitive to the temporal nature of action potential delivery rather than the intensity of stimulation or the total number of action potentials delivered. These data identify temporal kinetics of action potential firing as critical components regulating intracellular signalling pathways and gene expression in neurons to extracellular cues during early development and throughout life. Adaptation in the nervous system in response to external stimuli requires synthesis of new gene products in order to elicit long lasting changes in processes such as development, response to injury, learning, and memory1. Information in the environment is coded in the pattern of action-potential firing, therefore gene transcription must be regulated by the pattern of neuronal firing.
    [Show full text]
  • ORM-Like Protein (ORMDL) – Annäherung an Die Funktion Über Die Interaktion
    ORM-like protein (ORMDL) - Annäherung an die Funktion über die Interaktion Julian Klingbeil München 2019 Aus der Kinderklinik und Kinderpoliklinik im Dr. von Haunerschen Kinderspital der Ludwig–Maximilians–Universität München Direktor: Prof. Dr. med. Dr. sci. nat. C. Klein ORM-like protein (ORMDL) – Annäherung an die Funktion über die Interaktion Dissertation zum Erwerb des Doktorgrades der Medizin an der Medizinischen Fakultät der Ludwig–Maximilians–Universität zu München vorgelegt von Julian Malte Klingbeil aus Berlin 2019 Mit Genehmigung der Medizinischen Fakultät der Universität München Berichterstatterin: Prof. Dr. Ania Muntau Mitberichterstatter: Prof. Dr. Katja Radon PD Dr. Anne Hilgendorff Prof. Dr. Jürgen Behr Prof. Dr. Ortrud Steinlein Mitbetreuung durch den promovierten Mitarbeiter: Prof. Dr. Søren Gersting Dekan: Prof. Dr. med. dent. Reinhard Hickel Tag der mündlichen Prüfung: 10.10.2019 Inhaltsverzeichnis Zusammenfassung xiii 1 Einleitung 1 1.1 Asthma bronchiale . .1 1.1.1 Epidemiologie, Pathogenese und Klassifikation . .2 1.1.2 Therapie . .4 1.1.3 Gen-Umwelt-Interaktionen und Genomweite Assoziationsstudien5 1.2 Das neue Asthma-Risikogen ORMDL . .8 1.3 Der β2-Adrenorezeptor . 11 1.4 Protein-Protein-Interaktionen . 13 1.4.1 Biolumineszenz-Resonanz-Energie-Transfer . 15 1.5 Zielsetzung der Arbeit . 18 2 Material und Methoden 19 2.1 Material . 19 2.1.1 Laborgeräte . 19 2.1.2 Allgemeine Verbrauchsmaterialien, Chemikalien und Reagenzien . 21 2.1.3 Lösungen, Reagenzien-Kits und Puffer . 26 2.1.4 Medium . 28 2.1.5 Zelllinien und Bakterienstämme . 28 2.1.6 Antikörper . 29 2.1.7 β-Sympathomimetika . 29 2.1.8 Restriktionsenzyme . 30 2.1.9 Vektoren und DNA .
    [Show full text]
  • Identification of Expression Qtls Targeting Candidate Genes For
    ISSN: 2378-3648 Salleh et al. J Genet Genome Res 2018, 5:035 DOI: 10.23937/2378-3648/1410035 Volume 5 | Issue 1 Journal of Open Access Genetics and Genome Research RESEARCH ARTICLE Identification of Expression QTLs Targeting Candidate Genes for Residual Feed Intake in Dairy Cattle Using Systems Genomics Salleh MS1,2, Mazzoni G2, Nielsen MO1, Løvendahl P3 and Kadarmideen HN2,4* 1Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark Check for 2Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark updates 3Department of Molecular Biology and Genetics-Center for Quantitative Genetics and Genomics, Aarhus University, AU Foulum, Tjele, Denmark 4Department of Applied Mathematics and Computer Science, Technical University of Denmark, Lyngby, Denmark *Corresponding author: Kadarmideen HN, Department of Applied Mathematics and Computer Science, Technical University of Denmark, DK-2800, Kgs. Lyngby, Denmark, E-mail: [email protected] Abstract body weight gain and net merit). The eQTLs and biological pathways identified in this study improve our understanding Background: Residual feed intake (RFI) is the difference of the complex biological and genetic mechanisms that de- between actual and predicted feed intake and an important termine FE traits in dairy cattle. The identified eQTLs/genet- factor determining feed efficiency (FE). Recently, 170 can- ic variants can potentially be used in new genomic selection didate genes were associated with RFI, but no expression methods that include biological/functional information on quantitative trait loci (eQTL) mapping has hitherto been per- SNPs. formed on FE related genes in dairy cows. In this study, an integrative systems genetics approach was applied to map Keywords eQTLs in Holstein and Jersey cows fed two different diets to eQTL, RNA-seq, Genotype, Data integration, Systems improve identification of candidate genes for FE.
    [Show full text]
  • Inhibitory G-Protein Modulation of CNS Excitability by Jason Howard
    Inhibitory G-protein Modulation of CNS Excitability by Jason Howard Kehrl A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Pharmacology) in the University of Michigan 2014 Doctoral Committee: Professor Richard R. Neubig, Michigan State University, Co-Chair Professor Lori L. Isom, Co-Chair Professor Helen A. Baghdoyan Assistant Professor Asim A. Beg Research Associate Professor Geoffrey G. Murphy © Jason Howard Kehrl 2014 DEDICATION For Bud, Gagi, and Judy ii ACKNOWLEDGEMENTS This work would not have been possible without tremendous help from so many people. Scientifically my mentor, Rick, as he prefers to be called, was always available for collaborative discussions. He also provided me a great level of scientific freedom in pursuing what I found interesting, affording me the opportunity to learn more than I would have in most any other environment. Beyond what I’ve learned about the subject of pharmacology, what he has instilled in me is a sharp eye in the analysis of data-driven arguments, a great problem-solving toolset, and the ability to lead a team. This is what I will always value, no matter where I go in life. To my undergrads I am also exceedingly grateful. There are so many of you that I dare not name you individually for risk of putting some rank-order to the amount of fun and joy you each brought to my thesis work. I hope you each grew and learned from the experience as much as I learned from my attempts at mentoring each of you. This thesis is in no small part due to all the contributions you made.
    [Show full text]
  • Cystatin-B Negatively Regulates the Malignant Characteristics of Oral Squamous Cell Carcinoma Possibly Via the Epithelium Proliferation/ Differentiation Program
    ORIGINAL RESEARCH published: 24 August 2021 doi: 10.3389/fonc.2021.707066 Cystatin-B Negatively Regulates the Malignant Characteristics of Oral Squamous Cell Carcinoma Possibly Via the Epithelium Proliferation/ Differentiation Program Tian-Tian Xu 1, Xiao-Wen Zeng 1, Xin-Hong Wang 2, Lu-Xi Yang 1, Gang Luo 1* and Ting Yu 1* 1 Department of Periodontics, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China, 2 Department of Oral Pathology and Medicine, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China Disturbance in the proteolytic process is one of the malignant signs of tumors. Proteolysis Edited by: Eva Csosz, is highly orchestrated by cysteine cathepsin and its inhibitors. Cystatin-B (CSTB) is a University of Debrecen, Hungary general cysteine cathepsin inhibitor that prevents cysteine cathepsin from leaking from Reviewed by: lysosomes and causing inappropriate proteolysis. Our study found that CSTB was Csongor Kiss, downregulated in both oral squamous cell carcinoma (OSCC) tissues and cells University of Debrecen, Hungary Gergely Nagy, compared with normal controls. Immunohistochemical analysis showed that CSTB was University of Debrecen, Hungary mainly distributed in the epithelial structure of OSCC tissues, and its expression intensity *Correspondence: was related to the grade classification. A correlation analysis between CSTB and clinical Gang Luo [email protected] prognosis was performed using gene expression data and clinical information acquired Ting Yu from The Cancer Genome Atlas (TCGA) database. Patients with lower expression levels of [email protected] CSTB had shorter disease-free survival times and poorer clinicopathological features Specialty section: (e.g., lymph node metastases, perineural invasion, low degree of differentiation, and This article was submitted to advanced tumor stage).
    [Show full text]
  • Development of a Genomic Reference Population for Bovine Respiratory Disease in Pre-Weaning Dairy Calves Using Thoracic Ultrasonography
    Development of a genomic reference population for bovine respiratory disease in pre-weaning dairy calves using thoracic ultrasonography Allison E. Quick, T.L. Ollivett, M.R. Skiba, A.M. Nuttleman, D.S. Weigel, R.L. Wallace, K.A. Weigel 2 Objectives Establish a protocol for objective and efficient assessment of bovine respiratory disease (BRD) phenotypes in dairy calves to build a large reference population and enable genomic selection for reduced incidence and severity Specific Aim 1: Identify markers associated with BRD in a genome wide association study using the established reference population Specific Aim 2: Estimate genomic breeding values of reference population animals and relatives to facilitate whole genome selection against BRD 3 Establishing a Reference Population . 1107 Holstein calves . 6 dairy farms in southern Wisconsin . 4 trained evaluators . Data collection from May to August 2017 . Each calf measured at 3-weeks and 6-weeks of age . Clinical Disease Scoring . UW-Madison Vet Med Calf Health Scorer iPad tool . Subclinical Disease Scoring . Thoracic Ultrasound (TUS) Evaluation 4 Clinical Scoring . Sensitivity = 62% . Specificity = 74% . Compared with gold standard post-mortem evaluation (Buczinski et al., 2015) https://www.vetmed.wisc.edu/dms/fapm/fapmtools/calves.htm 5 Subclinical Scoring: TUS . Sensitivity = 94% . Specificity = 100% . Compared with gold standard post-mortem evaluation (Ollivett et al, 2015) . 0 to 5 Scale (4 and 5 are multiple consolidated lobes) Score 0: Normal lung Score 2: Lesion > 1cm Score 3: Consolidated lobe 6 Overall BRD Scores Example: Calf 19893 Clinical Scores: Cough = 2 Temperature = 3 Subclinical Score: Ultrasound = 5 Overall BRD Score: 6 Clinical Lobar Pneumonia 7 Frequency using Overall BRD Scores 3-Week 6-Week Incidence Rate Incidence Rate (%) (%) Healthy (1) 81.1 77.1 Upper Respiratory Tract Infection (2) 2.9 2.7 Subclinical Lobular Pneumonia (3) 11.9 12.5 Subclinical Lobar Pneumonia (4) 2.6 5.3 Clinical Lobular Pneumonia (5) 0.8 1.4 Clinical Lobar Pneumonia (6) 0.7 1.0 8 Preliminary Genetic Analysis .
    [Show full text]
  • Genome-Wide Mapping in a House Mouse Hybrid Zone Reveals Hybrid Sterility Loci and Dobzhansky-Muller Interactions Leslie M Turner1,2, Bettina Harr1*
    RESEARCH ARTICLE elifesciences.org Genome-wide mapping in a house mouse hybrid zone reveals hybrid sterility loci and Dobzhansky-Muller interactions Leslie M Turner1,2, Bettina Harr1* 1Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany; 2Laboratory of Genetics, University of Wisconsin, Madison, United States Abstract Mapping hybrid defects in contact zones between incipient species can identify genomic regions contributing to reproductive isolation and reveal genetic mechanisms of speciation. The house mouse features a rare combination of sophisticated genetic tools and natural hybrid zones between subspecies. Male hybrids often show reduced fertility, a common reproductive barrier between incipient species. Laboratory crosses have identified sterility loci, but each encompasses hundreds of genes. We map genetic determinants of testis weight and testis gene expression using offspring of mice captured in a hybrid zone between M. musculus musculus and M. m. domesticus. Many generations of admixture enables high-resolution mapping of loci contributing to these sterility-related phenotypes. We identify complex interactions among sterility loci, suggesting multiple, non-independent genetic incompatibilities contribute to barriers to gene flow in the hybrid zone. DOI: 10.7554/eLife.02504.001 Introduction *For correspondence: harr@ New species arise when reproductive barriers form, preventing gene flow between populations evolbio.mpg.de (Coyne and Orr, 2004). Recently, two approaches have substantially
    [Show full text]