Comparative Transcriptomics Reveals Similarities and Differences
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FK506-Binding Protein 12.6/1B, a Negative Regulator of [Ca2+], Rescues Memory and Restores Genomic Regulation in the Hippocampus of Aging Rats
This Accepted Manuscript has not been copyedited and formatted. The final version may differ from this version. A link to any extended data will be provided when the final version is posted online. Research Articles: Neurobiology of Disease FK506-Binding Protein 12.6/1b, a negative regulator of [Ca2+], rescues memory and restores genomic regulation in the hippocampus of aging rats John C. Gant1, Eric M. Blalock1, Kuey-Chu Chen1, Inga Kadish2, Olivier Thibault1, Nada M. Porter1 and Philip W. Landfield1 1Department of Pharmacology & Nutritional Sciences, University of Kentucky, Lexington, KY 40536 2Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294 DOI: 10.1523/JNEUROSCI.2234-17.2017 Received: 7 August 2017 Revised: 10 October 2017 Accepted: 24 November 2017 Published: 18 December 2017 Author contributions: J.C.G. and P.W.L. designed research; J.C.G., E.M.B., K.-c.C., and I.K. performed research; J.C.G., E.M.B., K.-c.C., I.K., and P.W.L. analyzed data; J.C.G., E.M.B., O.T., N.M.P., and P.W.L. wrote the paper. Conflict of Interest: The authors declare no competing financial interests. NIH grants AG004542, AG033649, AG052050, AG037868 and McAlpine Foundation for Neuroscience Research Corresponding author: Philip W. Landfield, [email protected], Department of Pharmacology & Nutritional Sciences, University of Kentucky, 800 Rose Street, UKMC MS 307, Lexington, KY 40536 Cite as: J. Neurosci ; 10.1523/JNEUROSCI.2234-17.2017 Alerts: Sign up at www.jneurosci.org/cgi/alerts to receive customized email alerts when the fully formatted version of this article is published. -
The Function of the Zinc Finger Transcription Factor Insm1 in Neuronal Progenitors Madeleine Julie Larrosa
The function of the zinc finger transcription factor Insm1 in neuronal progenitors Inaugural-Dissertation To obtain the academic degree Doctor rerum naturalium (Dr. rer. nat.) Submitted to the Department of Biology, Chemistry and Pharmacy of Freie Universität Berlin By Madeleine Julie Larrosa From Paris 2019 This work was carried out at the Max Delbrück Centrum for Molecular Medicine in Berlin from November 2015 to October 2019 under the supervision of Prof. Dr. Carmen Birchmeier and Prof. Dr. Holger Gerhardt. 1st Reviewer: Prof. Dr. Holger Gerhardt 2nd Reviewer: Prof. Dr. Stephan Sigrist Date of PhD Defense: This doctoral thesis is dedicated to my mother Juliette Ban, who offered unconditional love and endless devotion, and taught me to work hard for the things I aspire to achieve. I also dedicate this work to Mohammed Marine, who has been a constant source of support and encouragement, and without whom I would not have completed this doctoral thesis. In loving memory of my friend Lorelei Arbeille, who taught me to never give up through her incredible strength and perseverance. Statement of contribution I confirm that the work presented in this doctoral thesis is my own and that all information derived from other sources is indicated. Madlen Sohn, technician in the group of Prof. Dr. Wei Chen at the MDC, performed the sequencing of the immunoprecipitated chromatin and the transcriptome for the ChIP-seq and RNA-seq experiments, respectively. Dr. Mahmoud Ibrahim and Dr. Scott Lacadie, bioinformaticians in the group of Prof. Dr. Uwe Ohler at the MDC, analyzed the ChIP-seq data and Dr. -
Updates on the Role of Molecular Alterations and NOTCH Signalling in the Development of Neuroendocrine Neoplasms
Journal of Clinical Medicine Review Updates on the Role of Molecular Alterations and NOTCH Signalling in the Development of Neuroendocrine Neoplasms 1,2, 1, 3, 4 Claudia von Arx y , Monica Capozzi y, Elena López-Jiménez y, Alessandro Ottaiano , Fabiana Tatangelo 5 , Annabella Di Mauro 5, Guglielmo Nasti 4, Maria Lina Tornesello 6,* and Salvatore Tafuto 1,* On behalf of ENETs (European NeuroEndocrine Tumor Society) Center of Excellence of Naples, Italy 1 Department of Abdominal Oncology, Istituto Nazionale Tumori, IRCCS Fondazione “G. Pascale”, 80131 Naples, Italy 2 Department of Surgery and Cancer, Imperial College London, London W12 0HS, UK 3 Cancer Cell Metabolism Group. Centre for Haematology, Immunology and Inflammation Department, Imperial College London, London W12 0HS, UK 4 SSD Innovative Therapies for Abdominal Metastases—Department of Abdominal Oncology, Istituto Nazionale Tumori, IRCCS—Fondazione “G. Pascale”, 80131 Naples, Italy 5 Department of Pathology, Istituto Nazionale Tumori, IRCCS—Fondazione “G. Pascale”, 80131 Naples, Italy 6 Unit of Molecular Biology and Viral Oncology, Department of Research, Istituto Nazionale Tumori IRCCS Fondazione Pascale, 80131 Naples, Italy * Correspondence: [email protected] (M.L.T.); [email protected] (S.T.) These authors contributed to this paper equally. y Received: 10 July 2019; Accepted: 20 August 2019; Published: 22 August 2019 Abstract: Neuroendocrine neoplasms (NENs) comprise a heterogeneous group of rare malignancies, mainly originating from hormone-secreting cells, which are widespread in human tissues. The identification of mutations in ATRX/DAXX genes in sporadic NENs, as well as the high burden of mutations scattered throughout the multiple endocrine neoplasia type 1 (MEN-1) gene in both sporadic and inherited syndromes, provided new insights into the molecular biology of tumour development. -
Michael Antoni
Stress Management Effects on Biological and Molecular Pathways in Women Treated for Breast Cancer APS/NCI Conference on “Toward Precision Cancer Care: Biobehavioral Contributions to the Exposome” Chicago IL Michael H. Antoni, Ph.D. Department of Psychology Div of Health Psychology Director, Center for Psycho- Oncology Director, Cancer Prevention and Control Research, Sylvester Cancer Center University of Miami E.g., Stress Management for Women with Breast Cancer • Rationale – Breast Cancer (BCa) is a stressor – Challenges of surgery and adjuvant tx – Patient assets can facilitate adjustment – Cognitive Behavioral Stress Management (CBSM) can fortify these assets in women with BCa – Improving Psychosocial Adaptation may Affect Physiological Adaptation Theoretical Model for CBSM during CA Tx Negative Adapt Positive Adapt Physical Funct Awareness C ∆ Cog Appraisals B Physical Emot Processing + Health Beh. S Health M Relaxation QOL Social Support Normalize endocrine and immune regulation Antoni (2003). Stress Management for Women with Breast Cancer. American Psychological Association. Assessment Time Points T1 T2 T3 T4 B SMART-10 wks. 2-8 wks post 3 months post 6 months post surgery One year post surgery Topics of CBSM Week Relaxation Stress Management 1 PMR 7 Stress & Awareness 2 PMR 4/D.B. Stress & Awareness/Stress Appraisals 3 D.B./PMR Disease-Specific, Automatic Thoughts 4 Autogenics Auto. Thghts, Distortions, Thght Rep. 5 D.B./Visualiz. Cognitive Restructuring 6 Sunlight Med. Effective Coping I 7 Color Meditation Effective Coping -
Genomic Correlates of Relationship QTL Involved in Fore- Versus Hind Limb Divergence in Mice
Loyola University Chicago Loyola eCommons Biology: Faculty Publications and Other Works Faculty Publications 2013 Genomic Correlates of Relationship QTL Involved in Fore- Versus Hind Limb Divergence in Mice Mihaela Palicev Gunter P. Wagner James P. Noonan Benedikt Hallgrimsson James M. Cheverud Loyola University Chicago, [email protected] Follow this and additional works at: https://ecommons.luc.edu/biology_facpubs Part of the Biology Commons Recommended Citation Palicev, M, GP Wagner, JP Noonan, B Hallgrimsson, and JM Cheverud. "Genomic Correlates of Relationship QTL Involved in Fore- Versus Hind Limb Divergence in Mice." Genome Biology and Evolution 5(10), 2013. This Article is brought to you for free and open access by the Faculty Publications at Loyola eCommons. It has been accepted for inclusion in Biology: Faculty Publications and Other Works by an authorized administrator of Loyola eCommons. For more information, please contact [email protected]. This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 License. © Palicev et al., 2013. GBE Genomic Correlates of Relationship QTL Involved in Fore- versus Hind Limb Divergence in Mice Mihaela Pavlicev1,2,*, Gu¨ nter P. Wagner3, James P. Noonan4, Benedikt Hallgrı´msson5,and James M. Cheverud6 1Konrad Lorenz Institute for Evolution and Cognition Research, Altenberg, Austria 2Department of Pediatrics, Cincinnati Children‘s Hospital Medical Center, Cincinnati, Ohio 3Yale Systems Biology Institute and Department of Ecology and Evolutionary Biology, Yale University 4Department of Genetics, Yale University School of Medicine 5Department of Cell Biology and Anatomy, The McCaig Institute for Bone and Joint Health and the Alberta Children’s Hospital Research Institute for Child and Maternal Health, University of Calgary, Calgary, Canada 6Department of Anatomy and Neurobiology, Washington University *Corresponding author: E-mail: [email protected]. -
The Zinc-Finger Protein CNBP Is Required for Forebrain Formation In
Development 130, 1367-1379 1367 © 2003 The Company of Biologists Ltd doi:10.1242/dev.00349 The zinc-finger protein CNBP is required for forebrain formation in the mouse Wei Chen1,2, Yuqiong Liang1, Wenjie Deng1, Ken Shimizu1, Amir M. Ashique1,2, En Li3 and Yi-Ping Li1,2,* 1Department of Cytokine Biology, The Forsyth Institute, Boston, MA 02115, USA 2Harvard-Forsyth Department of Oral Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA 3Cardiovascular Research Center, Massachusetts General Hospital, Department of Medicine, Harvard Medical School, Charlestown, MA 02129, USA *Author for correspondence (e-mail: [email protected]) Accepted 19 December 2002 SUMMARY Mouse mutants have allowed us to gain significant insight (AME), headfolds and forebrain. In Cnbp–/– embryos, the into axis development. However, much remains to be visceral endoderm remains in the distal tip of the conceptus learned about the cellular and molecular basis of early and the ADE fails to form, whereas the node and notochord forebrain patterning. We describe a lethal mutation mouse form normally. A substantial reduction in cell proliferation strain generated using promoter-trap mutagenesis. The was observed in the anterior regions of Cnbp–/– embryos at mutants exhibit severe forebrain truncation in homozygous gastrulation and neural-fold stages. In these regions, Myc mouse embryos and various craniofacial defects in expression was absent, indicating CNBP targets Myc in heterozygotes. We show that the defects are caused by rostral head formation. Our findings demonstrate that disruption of the gene encoding cellular nucleic acid Cnbp is essential for the forebrain induction and binding protein (CNBP); Cnbp transgenic mice were able specification. -
Transcriptional Events Co-Regulated by Hypoxia and Cold Stresses In
Long et al. BMC Genomics (2015) 16:385 DOI 10.1186/s12864-015-1560-y RESEARCH ARTICLE Open Access Transcriptional events co-regulated by hypoxia and cold stresses in Zebrafish larvae Yong Long1, Junjun Yan1,2, Guili Song1, Xiaohui Li1,2, Xixi Li1,2, Qing Li1* and Zongbin Cui1* Abstract Background: Hypoxia and temperature stress are two major adverse environmental conditions often encountered by fishes. The interaction between hypoxia and temperature stresses has been well documented and oxygen is considered to be the limiting factor for the thermal tolerance of fish. Although both high and low temperature stresses can impair the cardiovascular function and the cross-resistance between hypoxia and heat stress has been found, it is not clear whether hypoxia acclimation can protect fish from cold injury. Results: Pre-acclimation of 96-hpf zebrafish larvae to mild hypoxia (5% O2) significantly improved their resistance to lethal hypoxia (2.5% O2) and increased the survival rate of zebrafish larvae after lethal cold (10°C) exposure. However, pre-acclimation of 96-hpf larvae to cold (18°C) decreased their tolerance to lethal hypoxia although their ability to endure lethal cold increased. RNA-seq analysis identified 132 up-regulated and 41 down-regulated genes upon mild hypoxia exposure. Gene ontology enrichment analyses revealed that genes up-regulated by hypoxia are primarily involved in oxygen transport, oxidation-reduction process, hemoglobin biosynthetic process, erythrocyte development and cellular iron ion homeostasis. Hypoxia-inhibited genes are enriched in inorganic anion transport, sodium ion transport, very long-chain fatty acid biosynthetic process and cytidine deamination. A comparison with the dataset of cold-regulated gene expression identified 23 genes co-induced by hypoxia and cold and these genes are mainly associated with oxidation-reduction process, oxygen transport, hemopoiesis, hemoglobin biosynthetic process and cellular iron ion homeostasis. -
Delta-Like Protein 3 Prevalence in Small Cell Lung Cancer and DLL3 (SP347) Assay Characteristics
EARLY ONLINE RELEASE Note: This article was posted on the Archives Web site as an Early Online Release. Early Online Release articles have been peer reviewed, copyedited, and reviewed by the authors. Additional changes or corrections may appear in these articles when they appear in a future print issue of the Archives. Early Online Release articles are citable by using the Digital Object Identifier (DOI), a unique number given to every article. The DOI will typically appear at the end of the abstract. The DOI for this manuscript is doi: 10.5858/arpa.2018-0497-OA The final published version of this manuscript will replace the Early Online Release version at the above DOI once it is available. © 2019 College of American Pathologists Original Article Delta-like Protein 3 Prevalence in Small Cell Lung Cancer and DLL3 (SP347) Assay Characteristics Richard S. P. Huang, MD; Burton F. Holmes, PhD; Courtney Powell; Raji V. Marati, PhD; Dusty Tyree, MS; Brittany Admire, PhD; Ashley Streator; Amy E. Hanlon Newell, PhD; Javier Perez, PhD; Deepa Dalvi; Ehab A. ElGabry, MD Context.—Delta-like protein 3 (DLL3) is a protein that is Results.—Cytoplasmic and/or membranous staining was implicated in the Notch pathway. observed in 1040 of 1362 specimens of small cell lung Objective.—To present data on DLL3 prevalence in cancer (76.4%). Homogenous and/or heterogeneous and small cell lung cancer and staining characteristics of the partial and/or circumferential granular staining with varied VENTANA DLL3 (SP347) Assay. In addition, the assay’s immunoreactivity with other neoplastic and nonneoplastic intensities was noted. -
Mig-6 Controls EGFR Trafficking and Suppresses Gliomagenesis
Mig-6 controls EGFR trafficking and suppresses gliomagenesis Haoqiang Yinga,1, Hongwu Zhenga,1, Kenneth Scotta, Ruprecht Wiedemeyera, Haiyan Yana, Carol Lima, Joseph Huanga, Sabin Dhakala, Elena Ivanovab, Yonghong Xiaob,HaileiZhangb,JianHua, Jayne M. Stommela, Michelle A. Leea, An-Jou Chena, Ji-Hye Paika,OresteSegattoc, Cameron Brennand,e, Lisa A. Elferinkf,Y.AlanWanga,b, Lynda China,b,g, and Ronald A. DePinhoa,b,h,2 aDepartment of Medical Oncology, bBelfer Institute for Applied Cancer Science, Belfer Foundation Institute for Innovative Cancer Science, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115; cLaboratory of Immunology, Istituto Regina Elena, Rome 00158, Italy; dHuman Oncology and Pathogenesis Program and eDepartment of Neurosurgery, Memorial Sloan-Kettering Cancer Center, New York, NY 10065; fDepartment of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX 77555; gDepartment of Dermatology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115; and hDepartment of Medicine and Genetics, Harvard Medical School, Boston, MA 02115 Edited* by Webster K. Cavenee, Ludwig Institute, University of California, La Jolla, CA, and approved March 8, 2010 (received for review December 23, 2009) Glioblastoma multiforme (GBM) is the most common and lethal structural aberrations that serve as a key pathological driving primary brain cancer that is driven by aberrant signaling of growth force for tumor progression and many of them remain to be factor receptors, particularly the epidermal growth factor receptor characterized (6, 7). GBM possesses a highly rearranged genome (EGFR). EGFR signaling is tightly regulated by receptor endocytosis and high-resolution genome analysis has uncovered myriad and lysosome-mediated degradation, although the molecular somatic alterations on the genomic and epigenetic levels (2, 3). -
Interactions Between the Parasite Philasterides Dicentrarchi and the Immune System of the Turbot Scophthalmus Maximus.A Transcriptomic Analysis
biology Article Interactions between the Parasite Philasterides dicentrarchi and the Immune System of the Turbot Scophthalmus maximus.A Transcriptomic Analysis Alejandra Valle 1 , José Manuel Leiro 2 , Patricia Pereiro 3 , Antonio Figueras 3 , Beatriz Novoa 3, Ron P. H. Dirks 4 and Jesús Lamas 1,* 1 Department of Fundamental Biology, Institute of Aquaculture, Campus Vida, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain; [email protected] 2 Department of Microbiology and Parasitology, Laboratory of Parasitology, Institute of Research on Chemical and Biological Analysis, Campus Vida, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain; [email protected] 3 Institute of Marine Research, Consejo Superior de Investigaciones Científicas-CSIC, 36208 Vigo, Spain; [email protected] (P.P.); antoniofi[email protected] (A.F.); [email protected] (B.N.) 4 Future Genomics Technologies, Leiden BioScience Park, 2333 BE Leiden, The Netherlands; [email protected] * Correspondence: [email protected]; Tel.: +34-88-181-6951; Fax: +34-88-159-6904 Received: 4 September 2020; Accepted: 14 October 2020; Published: 15 October 2020 Simple Summary: Philasterides dicentrarchi is a free-living ciliate that causes high mortality in marine cultured fish, particularly flatfish, and in fish kept in aquaria. At present, there is still no clear picture of what makes this ciliate a fish pathogen and what makes fish resistant to this ciliate. In the present study, we used transcriptomic techniques to evaluate the interactions between P. dicentrarchi and turbot leucocytes during the early stages of infection. The findings enabled us to identify some parasite genes/proteins that may be involved in virulence and host resistance, some of which may be good candidates for inclusion in fish vaccines. -
Integrating Single-Step GWAS and Bipartite Networks Reconstruction Provides Novel Insights Into Yearling Weight and Carcass Traits in Hanwoo Beef Cattle
animals Article Integrating Single-Step GWAS and Bipartite Networks Reconstruction Provides Novel Insights into Yearling Weight and Carcass Traits in Hanwoo Beef Cattle Masoumeh Naserkheil 1 , Abolfazl Bahrami 1 , Deukhwan Lee 2,* and Hossein Mehrban 3 1 Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj 77871-31587, Iran; [email protected] (M.N.); [email protected] (A.B.) 2 Department of Animal Life and Environment Sciences, Hankyong National University, Jungang-ro 327, Anseong-si, Gyeonggi-do 17579, Korea 3 Department of Animal Science, Shahrekord University, Shahrekord 88186-34141, Iran; [email protected] * Correspondence: [email protected]; Tel.: +82-31-670-5091 Received: 25 August 2020; Accepted: 6 October 2020; Published: 9 October 2020 Simple Summary: Hanwoo is an indigenous cattle breed in Korea and popular for meat production owing to its rapid growth and high-quality meat. Its yearling weight and carcass traits (backfat thickness, carcass weight, eye muscle area, and marbling score) are economically important for the selection of young and proven bulls. In recent decades, the advent of high throughput genotyping technologies has made it possible to perform genome-wide association studies (GWAS) for the detection of genomic regions associated with traits of economic interest in different species. In this study, we conducted a weighted single-step genome-wide association study which combines all genotypes, phenotypes and pedigree data in one step (ssGBLUP). It allows for the use of all SNPs simultaneously along with all phenotypes from genotyped and ungenotyped animals. Our results revealed 33 relevant genomic regions related to the traits of interest. -
Discovering Novel Hearing Loss Genes: Roles for Esrp1 and Gas2 in Inner Ear Development and Auditory Function
University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2018 Discovering Novel Hearing Loss Genes: Roles For Esrp1 And Gas2 In Inner Ear Development And Auditory Function Alex Martin Rohacek University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Cell Biology Commons, Developmental Biology Commons, and the Molecular Biology Commons Recommended Citation Rohacek, Alex Martin, "Discovering Novel Hearing Loss Genes: Roles For Esrp1 And Gas2 In Inner Ear Development And Auditory Function" (2018). Publicly Accessible Penn Dissertations. 2843. https://repository.upenn.edu/edissertations/2843 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/2843 For more information, please contact [email protected]. Discovering Novel Hearing Loss Genes: Roles For Esrp1 And Gas2 In Inner Ear Development And Auditory Function Abstract Hearing loss is the most common form of congenital birth defect, affecting an estimated 35 million children worldwide. To date, nearly 100 genes have been identified which contribute to a deafness phenotype in humans, however, many cases remain in which a causative mutation has yet to be found. In addition, the exact mechanism by which hearing loss occurs in the presence of many of these mutations is still not understood. This is due, in part, to the complex nature of the development and function of the cochlear duct, the organ of hearing. The cochlea undergoes an intricate morphogenetic development and requires the proper specification and maintenance of dozens of different cell types in order to function correctly. In the mature duct, an interplay between mechanotransducing sensory hair cells, supporting pillar and Dieters' cells, and generation of electrochemical potential by the stria vascularis are necessary to respond to sound stimuli.