CRY1 and NPAS2 Are Associated with Unipolar Major Depression and CLOCK and VIP with Bipolar Disorder
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Gene Symbol Gene Description ACVR1B Activin a Receptor, Type IB
Table S1. Kinase clones included in human kinase cDNA library for yeast two-hybrid screening Gene Symbol Gene Description ACVR1B activin A receptor, type IB ADCK2 aarF domain containing kinase 2 ADCK4 aarF domain containing kinase 4 AGK multiple substrate lipid kinase;MULK AK1 adenylate kinase 1 AK3 adenylate kinase 3 like 1 AK3L1 adenylate kinase 3 ALDH18A1 aldehyde dehydrogenase 18 family, member A1;ALDH18A1 ALK anaplastic lymphoma kinase (Ki-1) ALPK1 alpha-kinase 1 ALPK2 alpha-kinase 2 AMHR2 anti-Mullerian hormone receptor, type II ARAF v-raf murine sarcoma 3611 viral oncogene homolog 1 ARSG arylsulfatase G;ARSG AURKB aurora kinase B AURKC aurora kinase C BCKDK branched chain alpha-ketoacid dehydrogenase kinase BMPR1A bone morphogenetic protein receptor, type IA BMPR2 bone morphogenetic protein receptor, type II (serine/threonine kinase) BRAF v-raf murine sarcoma viral oncogene homolog B1 BRD3 bromodomain containing 3 BRD4 bromodomain containing 4 BTK Bruton agammaglobulinemia tyrosine kinase BUB1 BUB1 budding uninhibited by benzimidazoles 1 homolog (yeast) BUB1B BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast) C9orf98 chromosome 9 open reading frame 98;C9orf98 CABC1 chaperone, ABC1 activity of bc1 complex like (S. pombe) CALM1 calmodulin 1 (phosphorylase kinase, delta) CALM2 calmodulin 2 (phosphorylase kinase, delta) CALM3 calmodulin 3 (phosphorylase kinase, delta) CAMK1 calcium/calmodulin-dependent protein kinase I CAMK2A calcium/calmodulin-dependent protein kinase (CaM kinase) II alpha CAMK2B calcium/calmodulin-dependent -
2017.08.28 Anne Barry-Reidy Thesis Final.Pdf
REGULATION OF BOVINE β-DEFENSIN EXPRESSION THIS THESIS IS SUBMITTED TO THE UNIVERSITY OF DUBLIN FOR THE DEGREE OF DOCTOR OF PHILOSOPHY 2017 ANNE BARRY-REIDY SCHOOL OF BIOCHEMISTRY & IMMUNOLOGY TRINITY COLLEGE DUBLIN SUPERVISORS: PROF. CLIONA O’FARRELLY & DR. KIERAN MEADE TABLE OF CONTENTS DECLARATION ................................................................................................................................. vii ACKNOWLEDGEMENTS ................................................................................................................... viii ABBREVIATIONS ................................................................................................................................ix LIST OF FIGURES............................................................................................................................. xiii LIST OF TABLES .............................................................................................................................. xvii ABSTRACT ........................................................................................................................................xix Chapter 1 Introduction ........................................................................................................ 1 1.1 Antimicrobial/Host-defence peptides ..................................................................... 1 1.2 Defensins................................................................................................................. 1 1.3 β-defensins ............................................................................................................. -
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. -
Supervised Group Lasso with Applications to Microarray Data Analysis
SUPERVISED GROUP LASSO WITH APPLICATIONS TO MICROARRAY DATA ANALYSIS Shuangge Ma1, Xiao Song2, and Jian Huang3 1Department of Epidemiology and Public Health, Yale University 2Department of Health Administration, Biostatistics and Epidemiology, University of Georgia 3Departments of Statistics and Actuarial Science, and Biostatistics, University of Iowa March 2007 The University of Iowa Department of Statistics and Actuarial Science Technical Report No. 375 1 Supervised group Lasso with applications to microarray data analysis Shuangge Ma¤1 Xiao Song 2and Jian Huang 3 1 Department of Epidemiology and Public Health, Yale University, New Haven, CT 06520, USA 2 Department of Health Administration, Biostatistics and Epidemiology, University of Georgia, Athens, GA 30602, USA 3 Department of Statistics and Actuarial Science, University of Iowa, Iowa City, IA 52242, USA Email: Shuangge Ma¤- [email protected]; Xiao Song - [email protected]; Jian Huang - [email protected]; ¤Corresponding author Abstract Background: A tremendous amount of e®orts have been devoted to identifying genes for diagnosis and prognosis of diseases using microarray gene expression data. It has been demonstrated that gene expression data have cluster structure, where the clusters consist of co-regulated genes which tend to have coordinated functions. However, most available statistical methods for gene selection do not take into consideration the cluster structure. Results: We propose a supervised group Lasso approach that takes into account the cluster structure in gene expression data for gene selection and predictive model building. For gene expression data without biological cluster information, we ¯rst divide genes into clusters using the K-means approach and determine the optimal number of clusters using the Gap method. -
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. -
A Clinicopathological and Molecular Genetic Analysis of Low-Grade Glioma in Adults
A CLINICOPATHOLOGICAL AND MOLECULAR GENETIC ANALYSIS OF LOW-GRADE GLIOMA IN ADULTS Presented by ANUSHREE SINGH MSc A thesis submitted in partial fulfilment of the requirements of the University of Wolverhampton for the degree of Doctor of Philosophy Brain Tumour Research Centre Research Institute in Healthcare Sciences Faculty of Science and Engineering University of Wolverhampton November 2014 i DECLARATION This work or any part thereof has not previously been presented in any form to the University or to any other body whether for the purposes of assessment, publication or for any other purpose (unless otherwise indicated). Save for any express acknowledgments, references and/or bibliographies cited in the work, I confirm that the intellectual content of the work is the result of my own efforts and of no other person. The right of Anushree Singh to be identified as author of this work is asserted in accordance with ss.77 and 78 of the Copyright, Designs and Patents Act 1988. At this date copyright is owned by the author. Signature: Anushree Date: 30th November 2014 ii ABSTRACT The aim of the study was to identify molecular markers that can determine progression of low grade glioma. This was done using various approaches such as IDH1 and IDH2 mutation analysis, MGMT methylation analysis, copy number analysis using array comparative genomic hybridisation and identification of differentially expressed miRNAs using miRNA microarray analysis. IDH1 mutation was present at a frequency of 71% in low grade glioma and was identified as an independent marker for improved OS in a multivariate analysis, which confirms the previous findings in low grade glioma studies. -
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. -
Farnesol-Induced Apoptosis in Human Lung Carcinoma Cells Is Coupled to the Endoplasmic Reticulum Stress Response
Research Article Farnesol-Induced Apoptosis in Human Lung Carcinoma Cells Is Coupled to the Endoplasmic Reticulum Stress Response Joung Hyuck Joo,1 Grace Liao,1 Jennifer B. Collins,2 Sherry F. Grissom,2 and Anton M. Jetten1 1Cell Biology Section, LRB, and 2Microarray Group, Division of Intramural Research, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina Abstract range of fruits and vegetables (9, 10). Each isoprenoid has been Farnesol (FOH) and other isoprenoid alcohols induce apopto- shown to inhibit proliferation and induce apoptosis in a number of sis in various carcinoma cells and inhibit tumorigenesis in neoplastic cell lines from different origins (4, 11–14). In addition, in vivo these isoprenoids have been reported to be effective in chemo- several models. However, the mechanisms by which in vivo they mediate their effects are not yet fully understood. In this prevention and chemotherapy in various cancer models study, we show that FOH is an effective inducer of apoptosis in (10, 12, 15, 16). FOH has been reported to exhibit chemopreventive several lung carcinoma cells, including H460. This induction is effects in colon and pancreas carcinogenesis in rats (9, 17) whereas associated with activation of several caspases and cleavage of phase I and II clinical trials have indicated therapeutic potential poly(ADP-ribose) polymerase (PARP). To obtain insight into for POH (16, 18). The mechanisms by which these isoprenoids induce these effects are not yet fully understood. Isoprenoids have the mechanism involved in FOH-induced apoptosis, we compared the gene expression profiles of FOH-treated and been reported to inhibit posttranslational protein prenylation (19) control H460 cells by microarray analysis. -
Temporal Chip-On-Chip of RNA-Polymerase-II to Detect Novel Gene Activation Events During Photoreceptor Maturation
Molecular Vision 2010; 16:252-271 <http://www.molvis.org/molvis/v16/a32> © 2010 Molecular Vision Received 12 July 2009 | Accepted 10 February 2010 | Published 17 February 2010 Temporal ChIP-on-Chip of RNA-Polymerase-II to detect novel gene activation events during photoreceptor maturation Padmaja Tummala, Raghuveer S. Mali, Eduardo Guzman, Xiao Zhang, Kenneth P. Mitton (The first two authors contributed equally to this work.) Eye Research Institute, Oakland University, Rochester, MI Purpose: During retinal development, post-mitotic neural progenitor cells must activate thousands of genes to complete synaptogenesis and terminal maturation. While many of these genes are known, others remain beyond the sensitivity of expression microarray analysis. Some of these elusive gene activation events can be detected by mapping changes in RNA polymerase-II (Pol-II) association around transcription start sites. Methods: High-resolution (35 bp) chromatin immunoprecipitation (ChIP)-on-chip was used to map changes in Pol-II binding surrounding 26,000 gene transcription start sites during photoreceptor maturation of the mouse neural retina, comparing postnatal age 25 (P25) to P2. Coverage was 10–12 kb per transcription start site, including 2.5 kb downstream. Pol-II-active regions were mapped to the mouse genomic DNA sequence by using computational methods (Tiling Analysis Software-TAS program), and the ratio of maximum Pol-II binding (P25/P2) was calculated for each gene. A validation set of 36 genes (3%), representing a full range of Pol-II signal ratios (P25/P2), were examined with quantitative ChIP assays for transcriptionally active Pol-II. Gene expression assays were also performed for 19 genes of the validation set, again on independent samples. -
CRISPR Activation Screening of Circulating Tumor Cells Identifies Enhancers of Blood-Based Metastasis
CRISPR Activation Screening of Circulating Tumor Cells Identifies Enhancers of Blood-Based Metastasis The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Ebright, Richard Yon. 2020. CRISPR Activation Screening of Circulating Tumor Cells Identifies Enhancers of Blood-Based Metastasis. Doctoral dissertation, Harvard University, Graduate School of Arts & Sciences. Citable link https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37365157 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA CRISPR activation screening of circulating tumor cells identifies enhancers of blood-based metastasis A dissertation presented by Richard Yon Ebright to The Division of Medical Sciences in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the subject of Biological and Biomedical Sciences Harvard University Cambridge, Massachusetts September 2019 © 2019 Richard Yon Ebright All rights reserved. Dissertation Advisors: Daniel A. Haber & Shyamala Maheswaran Richard Yon Ebright CRISPR activation screening of circulating tumor cells identifies enhancers of blood-based metastasis Abstract Over ninety percent of cancer mortality is attributable to metastasis, most commonly due to the blood-borne dissemination of cancer cells from a primary tumor to secondary tissues. However, the vast majority of these cancer cells in the circulation, known as circulating tumor cells (CTCs), never go on to form clinically relevant metastases, instead dying or senescing in the circulation or at distant sites. -
Expression Signatures of the Lipid-Based Akt Inhibitors Phosphatidylinositol Ether Lipid Analogues in NSCLC Cells
Published OnlineFirst May 6, 2011; DOI: 10.1158/1535-7163.MCT-10-1028 Molecular Cancer Therapeutic Discovery Therapeutics Expression Signatures of the Lipid-Based Akt Inhibitors Phosphatidylinositol Ether Lipid Analogues in NSCLC Cells Chunyu Zhang1, Abdel G. Elkahloun2, Hongling Liao3, Shannon Delaney1, Barbara Saber1, Betsy Morrow1, George C. Prendergast4, M. Christine Hollander1, Joell J. Gills1, and Phillip A. Dennis1 Abstract Activation of the serine/threonine kinase Akt contributes to the formation, maintenance, and therapeutic resistance of cancer, which is driving development of compounds that inhibit Akt. Phosphatidylinositol ether lipid analogues (PIA) are analogues of the products of phosphoinositide-3-kinase (PI3K) that inhibit Akt activation, translocation, and the proliferation of a broad spectrum of cancer cell types. To gain insight into the mechanism of PIAs, time-dependent transcriptional profiling of five active PIAs and the PI3K inhibitor LY294002 (LY) was conducted in non–small cell lung carcinoma cells using high-density oligonucleotide arrays. Gene ontology analysis revealed that genes involved in apoptosis, wounding response, and angiogen- esis were upregulated by PIAs, whereas genes involved in DNA replication, repair, and mitosis were suppressed. Genes that exhibited early differential expression were partitioned into three groups; those induced by PIAs only (DUSP1, KLF6, CENTD2, BHLHB2, and PREX1), those commonly induced by PIAs and LY (TRIB1, KLF2, RHOB, and CDKN1A), and those commonly suppressed by PIAs and LY (IGFBP3, PCNA, PRIM1, MCM3, and HSPA1B). Increased expression of the tumor suppressors RHOB (RhoB), KLF6 (COPEB), and CDKN1A (p21Cip1/Waf1) was validated as an Akt-independent effect that contributed to PIA-induced cytotoxicity. Despite some overlap with LY, active PIAs have a distinct expression signature that contributes to their enhanced cytotoxicity. -
Per2 Antibody
Product Datasheet Per2 Antibody Catalog No: #SAB436 Orders: [email protected] Description Support: [email protected] Product Name Per2 Antibody Host Species Rabbit Clonality Polyclonal Purification Antibodies were produced by immunizing rabbits with synthetic peptide and KLH conjugates. Antibodies were purified by affinity-chromatography using epitope-specific peptide. Applications Custom antibody Species Reactivity Ms Immunogen Type Peptide-KLH Target Name Per2 Other Names Period circadian protein homolog 2 Accession No. uniprot:O54943 Calculated MW 136kDa Formulation Supplied at 1.0mg/mL in phosphate buffered saline (without Mg2+ and Ca2+), pH 7.4, 150mM NaCl, 0.02% sodium azide and 85% glycerol. Storage Store at -20°C for long term preservation (recommended). Store at 4°C for short term use. Application Details Western blotting: 1:500~1:1000 Background Transcriptional repressor which forms a core component of the circadian clock. The circadian clock, an internal time-keeping system, regulates various physiological processes through the generation of approximately 24 hour circadian rhythms in gene expression, which are translated into rhythms in metabolism and behavior. It is derived from the Latin roots 'circa' (about) and 'diem' (day) and acts as an important regulator of a wide array of physiological functions including metabolism, sleep, body temperature, blood pressure, endocrine, immune, cardiovascular, and renal function. Consists of two major components: the central clock, residing in the suprachiasmatic nucleus (SCN) of the brain, and the peripheral clocks that are present in nearly every tissue and organ system. Both the central and peripheral clocks can be reset by environmental cues, also known as Zeitgebers (German for 'timegivers').