Circadian- and Sex-Dependent Increases in Intravenous Cocaine Self-Administration in Npas2 Mutant Mice
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Progesterone Receptor Coregulators As Factors Supporting the Function of the Corpus Luteum in Cows
G C A T T A C G G C A T genes Article Progesterone Receptor Coregulators as Factors Supporting the Function of the Corpus Luteum in Cows Robert Rekawiecki * , Karolina Dobrzyn, Jan Kotwica and Magdalena K. Kowalik Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Tuwima 10, 10–747 Olsztyn, Poland; [email protected] (K.D.); [email protected] (J.K.); [email protected] (M.K.K.) * Correspondence: [email protected]; Tel.: +48-89-539-31-17 Received: 5 July 2020; Accepted: 7 August 2020; Published: 12 August 2020 Abstract: Progesterone receptor (PGR) for its action required connection of the coregulatory proteins, including coactivators and corepressors. The former group exhibits a histone acetyltransferase (HAT) activity, while the latter cooperates with histone deacetylase (HDAC). Regulations of the coregulators mRNA and protein and HAT and HDAC activity can have an indirect effect on the PGR function and thus progesterone (P4) action on target cells. The highest mRNA expression levels for the coactivators—histone acetyltransferase p300 (P300), cAMP response element-binding protein (CREB), and steroid receptor coactivator-1 (SRC-1)—and nuclear receptor corepressor-2 (NCOR-2) were found in the corpus luteum (CL) on days 6 to 16 of the estrous cycle. The CREB protein level was higher on days 2–10, whereas SRC-1 and NCOR-2 were higher on days 2–5. The activity of HAT and HDAC was higher on days 6–10 of the estrous cycle. All of the coregulators were localized in the nuclei of small and large luteal cells. -
The Title of the Dissertation
UNIVERSITY OF CALIFORNIA SAN DIEGO Novel network-based integrated analyses of multi-omics data reveal new insights into CD8+ T cell differentiation and mouse embryogenesis A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Bioinformatics and Systems Biology by Kai Zhang Committee in charge: Professor Wei Wang, Chair Professor Pavel Arkadjevich Pevzner, Co-Chair Professor Vineet Bafna Professor Cornelis Murre Professor Bing Ren 2018 Copyright Kai Zhang, 2018 All rights reserved. The dissertation of Kai Zhang is approved, and it is accept- able in quality and form for publication on microfilm and electronically: Co-Chair Chair University of California San Diego 2018 iii EPIGRAPH The only true wisdom is in knowing you know nothing. —Socrates iv TABLE OF CONTENTS Signature Page ....................................... iii Epigraph ........................................... iv Table of Contents ...................................... v List of Figures ........................................ viii List of Tables ........................................ ix Acknowledgements ..................................... x Vita ............................................. xi Abstract of the Dissertation ................................. xii Chapter 1 General introduction ............................ 1 1.1 The applications of graph theory in bioinformatics ......... 1 1.2 Leveraging graphs to conduct integrated analyses .......... 4 1.3 References .............................. 6 Chapter 2 Systematic -
Substance Abuse and Dependence
9 Substance Abuse and Dependence CHAPTER CHAPTER OUTLINE CLASSIFICATION OF SUBSTANCE-RELATED THEORETICAL PERSPECTIVES 310–316 Residential Approaches DISORDERS 291–296 Biological Perspectives Psychodynamic Approaches Substance Abuse and Dependence Learning Perspectives Behavioral Approaches Addiction and Other Forms of Compulsive Cognitive Perspectives Relapse-Prevention Training Behavior Psychodynamic Perspectives SUMMING UP 325–326 Racial and Ethnic Differences in Substance Sociocultural Perspectives Use Disorders TREATMENT OF SUBSTANCE ABUSE Pathways to Drug Dependence AND DEPENDENCE 316–325 DRUGS OF ABUSE 296–310 Biological Approaches Depressants Culturally Sensitive Treatment Stimulants of Alcoholism Hallucinogens Nonprofessional Support Groups TRUTH or FICTION T❑ F❑ Heroin accounts for more deaths “Nothing and Nobody Comes Before than any other drug. (p. 291) T❑ F❑ You cannot be psychologically My Coke” dependent on a drug without also being She had just caught me with cocaine again after I had managed to convince her that physically dependent on it. (p. 295) I hadn’t used in over a month. Of course I had been tooting (snorting) almost every T❑ F❑ More teenagers and young adults die day, but I had managed to cover my tracks a little better than usual. So she said to from alcohol-related motor vehicle accidents me that I was going to have to make a choice—either cocaine or her. Before she than from any other cause. (p. 297) finished the sentence, I knew what was coming, so I told her to think carefully about what she was going to say. It was clear to me that there wasn’t a choice. I love my T❑ F❑ It is safe to let someone who has wife, but I’m not going to choose anything over cocaine. -
UNIVERSITY of CALIFORNIA Los Angeles
UNIVERSITY OF CALIFORNIA Los Angeles Circadian Gene Networks In Bone Regeneration A thesis submitted in partial satisfaction of the requirements for the degree Master of Science in Oral Biology by Nathaniel Raphael Hassan 2012 ABSTRACT OF THESIS Circadian Gene Networks In Bone Regeneration By Nathaniel Raphael Hassan Master of Science in Oral Biology University of California, Los Angeles, 2012 Professor Ichiro Nishimura, Chair BACKGROUND: Previous studies suggested that vitamin D played a significant role in bone regeneration, facilitating the establishment of implant osseointegration. A whole genome microarray study further suggested that the vitamin D axis might involve circadian rhythm gene expression in the bone peripheral tissue. OBJECTIVES: To identify key gene networks involved with vitamin D receptor in the bone regeneration process and to explore any correlation with circadian rhythm gene expression in bone marrow mesenchymal stromal/stem cells (BMSC). METHODS: The available whole gene microarray data was analyzed using the weighted gene correlation network analysis (WGCNA) R package and Cytoscape software. Any gene expression correlation was examined for vitamin D receptor (VDR) as well as circadian rhythm ii genes. Separately, Per 1 luciferase transgenic Wistar rats were then applied for in vitro evaluation on BMSC circadian rhythm. Per1::luc BMSCs were seeded on 35mm dishes and forskolin-synchronized luminescence was recorded across different media conditions. The recording media included growth medium containing F12 (10% Fetal Bovine Serum, 1% Pen- Strep and antibiotic) supplemented with or without 1 nM 1,25D. Luminescence was also recorded in F12 growth medium containing bone differentiation factors (beta glycerophosphate, Ascorbic acid and Dexamethasone) supplemented with 0, 1 or 10 nM 1,25D. -
Engineering Zinc-Finger Protein and CRISPR/Cas9 Constructs to Model the Epigenetic and Transcriptional Phenomena That Underlie Cocaine-Related Behaviors
Engineering zinc-finger protein and CRISPR/Cas9 constructs to model the epigenetic and transcriptional phenomena that underlie cocaine-related behaviors Hamilton PJ, Heller EA, Ortiz Torres I, Burek DD, Lombroso SI, Pirpinias ST, Neve RL, Nestler EJ Multiple studies have implicated genome-wide epigenetic remodeling events in brain reward regions following drug exposure. However, only recently has it become possible to target a given type of epigenetic remodeling to a single gene of interest, in order to probe the causal relationship between such regulation and neuropsychiatric disease (Heller et al., Nat Neurosci, 2014). Our group has successfully utilized synthetic zinc- finger proteins (ZFPs), fused to either the transcriptional repressor, G9a, that promotes histone methylation or the transcriptional activator, p65, that promotes histone acetylation, to determine the behavioral effects of targeted in vivo epigenetic reprogramming in a locus-specific and cell-type specific manner. Given the success of our ZFP approaches, we have broadened our technical repertoire to include the more novel and flexible CRISPR/Cas9 technology. We designed guide RNAs to target nuclease-dead Cas9 (dCas9) fused to effector domains to the fosB gene locus, a locus heavily implicated in the pathogenesis of drug abuse. We observe that dCas9 fused to the transcriptional activator, VP64, or the transcriptional repressor, KRAB, and targeted to specific sites in the fosB promoter is sufficient to regulate FosB and ΔFosB mRNA levels, in both cultured cells and in the nucleus accumbens (NAc) of mice receiving viral delivery of CRISPR constructs. Next, we designed a fusion construct linking the dCas9 moiety to a pseudo-phosphorylated isoform of the transcription factor CREB (dCas9 CREB(S133D)). -
NPAS2 As a Transcriptional Regulator of Non-Rapid Eye Movement Sleep: Genotype and Sex Interactions
NPAS2 as a transcriptional regulator of non-rapid eye movement sleep: Genotype and sex interactions Paul Franken*†‡, Carol A. Dudley§, Sandi Jo Estill§, Monique Barakat*, Ryan Thomason¶, Bruce F. O’Hara¶, and Steven L. McKnight‡§ §Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390; *Department of Biological Sciences, Stanford University, Stanford, CA 94305; ¶Department of Biology, University of Kentucky, Lexington, KY 40506; and †Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne-Dorigny, Switzerland Contributed by Steven L. McKnight, March 13, 2006 Because the transcription factor neuronal Per-Arnt-Sim-type sig- delta frequency range is a sensitive marker of time spent awake (4, nal-sensor protein-domain protein 2 (NPAS2) acts both as a sensor 7) and local cortical activation (8) and is therefore widely used as and an effector of intracellular energy balance, and because sleep an index of NREMS need and intensity. is thought to correct an energy imbalance incurred during waking, The PAS-domain proteins, CLOCK, BMAL1, PERIOD-1 we examined NPAS2’s role in sleep homeostasis using npas2 (PER1), and PER2, play crucial roles in circadian rhythm gener- knockout (npas2؊/؊) mice. We found that, under conditions of ation (9). The NPAS2 paralog CLOCK, like NPAS2, can induce the increased sleep need, i.e., at the end of the active period or after transcription of per1, per2, cryptochrome-1 (cry1), and cry2. PER and sleep deprivation (SD), NPAS2 allows for sleep to occur at times CRY proteins, in turn, inhibit CLOCK- and NPAS2-induced when mice are normally awake. Lack of npas2 affected electroen- transcription, thereby closing a negative-feedback loop that is cephalogram activity of thalamocortical origin; during non-rapid thought to underlie circadian rhythm generation. -
Estrogen Receptor-Α Interaction with the CREB Binding Protein
307 Estrogen receptor- interaction with the CREB binding protein coactivator is regulated by the cellular environment B M Jaber, R Mukopadhyay and C L Smith Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA (Requests for offprints should be addressed to C L Smith; Email: [email protected]) Abstract The p160 coactivators, steroid receptor coactivator-1 (SRC-1), transcriptional intermediary factor-2 (TIF2) and receptor-associated coactivator-3 (RAC3), as well as the coactivator/integrator CBP, mediate estrogen receptor- (ER)-dependent gene expression. Although these coactivators are widely expressed, ER transcriptional activity is cell-type dependent. In this study, we investigated ER interaction with p160 coactivators and CBP in HeLa and HepG2 cell lines. Basal and estradiol (E2)-dependent interactions between the ER ligand-binding domain (LBD) and SRC-1, TIF2 or RAC3 were observed in HeLa and HepG2 cells. The extents of hormone-dependent interactions were similar and interactions between each of the p160 coactivators and the ER LBD were not enhanced by 4-hydroxytamoxifen in either cell type. In contrast to the situation for p160 coactivators, E2-dependent interaction of the ER LBD with CBP or p300 was detected in HeLa but not HepG2 cells by mammalian two-hybrid and coimmunoprecipitation assays, indicating that the cellular environment modulates ER-CBP/p300 interaction. Furthermore, interactions between CBP and p160 coactivators are much more robust in HeLa than HepG2 cells suggesting that poor CBP-p160 interactions are insufficient to support ER–CBP–p160 ternary complexes important for nuclear receptor–CBP interactions. Alterations in p160 coactivators or CBP expression between these two cell types did not account for differences in ER–p160–CBP interactions. -
Evidence-Based Guidelines for the Pharmacological Management of Substance Abuse, Harmful Use, Addictio
444324 JOP0010.1177/0269881112444324Lingford-Hughes et al.Journal of Psychopharmacology 2012 BAP Guidelines BAP updated guidelines: evidence-based guidelines for the pharmacological management of substance abuse, Journal of Psychopharmacology 0(0) 1 –54 harmful use, addiction and comorbidity: © The Author(s) 2012 Reprints and permission: sagepub.co.uk/journalsPermissions.nav recommendations from BAP DOI: 10.1177/0269881112444324 jop.sagepub.com AR Lingford-Hughes1, S Welch2, L Peters3 and DJ Nutt 1 With expert reviewers (in alphabetical order): Ball D, Buntwal N, Chick J, Crome I, Daly C, Dar K, Day E, Duka T, Finch E, Law F, Marshall EJ, Munafo M, Myles J, Porter S, Raistrick D, Reed LJ, Reid A, Sell L, Sinclair J, Tyrer P, West R, Williams T, Winstock A Abstract The British Association for Psychopharmacology guidelines for the treatment of substance abuse, harmful use, addiction and comorbidity with psychiatric disorders primarily focus on their pharmacological management. They are based explicitly on the available evidence and presented as recommendations to aid clinical decision making for practitioners alongside a detailed review of the evidence. A consensus meeting, involving experts in the treatment of these disorders, reviewed key areas and considered the strength of the evidence and clinical implications. The guidelines were drawn up after feedback from participants. The guidelines primarily cover the pharmacological management of withdrawal, short- and long-term substitution, maintenance of abstinence and prevention of complications, where appropriate, for substance abuse or harmful use or addiction as well management in pregnancy, comorbidity with psychiatric disorders and in younger and older people. Keywords Substance misuse, addiction, guidelines, pharmacotherapy, comorbidity Introduction guidelines (e.g. -
Neurobiological Functions of the Period Circadian Clock 2 Gene, Per2
Review Biomol Ther 26(4), 358-367 (2018) Neurobiological Functions of the Period Circadian Clock 2 Gene, Per2 Mikyung Kim, June Bryan de la Peña, Jae Hoon Cheong and Hee Jin Kim* Department of Pharmacy, Uimyung Research Institute for Neuroscience, Sahmyook University, Seoul 01795, Republic of Korea Abstract Most organisms have adapted to a circadian rhythm that follows a roughly 24-hour cycle, which is modulated by both internal (clock-related genes) and external (environment) factors. In such organisms, the central nervous system (CNS) is influenced by the circadian rhythm of individual cells. Furthermore, the period circadian clock 2 (Per2) gene is an important component of the circadian clock, which modulates the circadian rhythm. Per2 is mainly expressed in the suprachiasmatic nucleus (SCN) of the hypothalamus as well as other brain areas, including the midbrain and forebrain. This indicates that Per2 may affect various neurobiological activities such as sleeping, depression, and addiction. In this review, we focus on the neurobiological functions of Per2, which could help to better understand its roles in the CNS. Key Words: Circadian rhythm, Per2 gene, Sleep, Depression, Addiction, Neurotransmitter INTRODUCTION and lives in organisms because it can impart effects from the level of cells to organs including the brain. Thus, it is neces- A circadian rhythm is any physiological process that displays sary to understand clock-related genes that are controlling the a roughly 24 hour cycle in living beings, such as mammals, circadian rhythm endogenously. plants, fungi and cyanobacteria (Albrecht, 2012). In organ- The Period2 (Per2) gene is a member of the Period family isms, most biological functions such as sleeping and feeding of genes consisting of Per1, Per2, and Per3, and is mainly patterns are adapted to the circadian rhythm. -
Treatment of Patients with Substance Use Disorders Second Edition
PRACTICE GUIDELINE FOR THE Treatment of Patients With Substance Use Disorders Second Edition WORK GROUP ON SUBSTANCE USE DISORDERS Herbert D. Kleber, M.D., Chair Roger D. Weiss, M.D., Vice-Chair Raymond F. Anton Jr., M.D. To n y P. G e o r ge , M .D . Shelly F. Greenfield, M.D., M.P.H. Thomas R. Kosten, M.D. Charles P. O’Brien, M.D., Ph.D. Bruce J. Rounsaville, M.D. Eric C. Strain, M.D. Douglas M. Ziedonis, M.D. Grace Hennessy, M.D. (Consultant) Hilary Smith Connery, M.D., Ph.D. (Consultant) This practice guideline was approved in December 2005 and published in August 2006. A guideline watch, summarizing significant developments in the scientific literature since publication of this guideline, may be available in the Psychiatric Practice section of the APA web site at www.psych.org. 1 Copyright 2010, American Psychiatric Association. APA makes this practice guideline freely available to promote its dissemination and use; however, copyright protections are enforced in full. No part of this guideline may be reproduced except as permitted under Sections 107 and 108 of U.S. Copyright Act. For permission for reuse, visit APPI Permissions & Licensing Center at http://www.appi.org/CustomerService/Pages/Permissions.aspx. AMERICAN PSYCHIATRIC ASSOCIATION STEERING COMMITTEE ON PRACTICE GUIDELINES John S. McIntyre, M.D., Chair Sara C. Charles, M.D., Vice-Chair Daniel J. Anzia, M.D. Ian A. Cook, M.D. Molly T. Finnerty, M.D. Bradley R. Johnson, M.D. James E. Nininger, M.D. Paul Summergrad, M.D. Sherwyn M. -
Correlation Between Circadian Gene Variants and Serum Levels of Sex Steroids and Insulin-Like Growth Factor-I
3268 Correlation between Circadian Gene Variants and Serum Levels of Sex Steroids and Insulin-like Growth Factor-I Lisa W. Chu,1,2 Yong Zhu,3 Kai Yu,1 Tongzhang Zheng,3 Anand P. Chokkalingam,4 Frank Z. Stanczyk,5 Yu-Tang Gao,6 and Ann W. Hsing1 1Division of Cancer Epidemiology and Genetics and 2Cancer Prevention Fellowship Program, Office of Preventive Oncology, National Cancer Institute, NIH, Bethesda, Maryland; 3Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, Connecticut; 4Division of Epidemiology, School of Public Health, University of California at Berkeley, Berkeley, California; 5Department of Obstetrics and Gynecology, Keck School of Medicine, University of Southern California, Los Angeles, California; and 6Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China Abstract A variety of biological processes, including steroid the GG genotype. In addition, the PER1 variant was hormone secretion, have circadian rhythms, which are associated with higher serum levels of sex hormone- P influenced by nine known circadian genes. Previously, binding globulin levels ( trend = 0.03), decreasing we reported that certain variants in circadian genes 5A-androstane-3A,17B-diol glucuronide levels P P were associated with risk for prostate cancer. To pro- ( trend = 0.02), and decreasing IGFBP3 levels ( trend = vide some biological insight into these findings, we 0.05). Furthermore, the CSNK1E variant C allele was examined the relationship of five variants of circadian associated with higher -
The Role of Gata2 in Hematopoietic and Vascular Development By
The Role of Gata2 in Hematopoietic and Vascular Development by William D Brandt A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Cellular and Molecular Biology) in The University of Michigan 2009 Doctoral Committee: Professor James Douglas Engel, Chair Professor Eric R Fearon Professor Deborah L Gumucio Associate Professor Thomas M Glaser William D Brandt 2009 Dedication To my family, without whom this PhD would never have been possible. ii Acknowledgements The Engel lab and the University of Michigan will always have my deepest gratitude, particularly the lab’s proprietor and my thesis advisor Doug Engel, whose love of science and good nature has always been a source of inspiration. Doug has been instrumental in my growth as a nascent scientist and I will forever be indebted to him. My gratitude also goes to Kim-Chew Lim and Tomo Hosoya, whose wealth of knowledge and support were relied upon regularly. To Deb Gumucio, Tom Glaser, and Eric Fearon, whose advice and support facilitated my maturation from a naïve student to a proficient scientist – thank you. And to Lori Longeway and Kristin Hug, whose capabilities as department representatives I repeatedly put to the test; you came through for me every time. Thank you. Finally, no amount of words can express how truly grateful and indebted I am to my parents and sister – Cary, Kim, and Jenelle. I would not be in this position today without their unerring love and support. iii Table of Contents Dedication ii Acknowledgements iii List of Figures v List of Tables vi Abstract vii Chapter 1.