Cell Mass in Response to Increased Metabolic Demand Is Dependent on HNF-4␣
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Meta-Analysis of Nasopharyngeal Carcinoma
BMC Genomics BioMed Central Research article Open Access Meta-analysis of nasopharyngeal carcinoma microarray data explores mechanism of EBV-regulated neoplastic transformation Xia Chen†1,2, Shuang Liang†1, WenLing Zheng1,3, ZhiJun Liao1, Tao Shang1 and WenLi Ma*1 Address: 1Institute of Genetic Engineering, Southern Medical University, Guangzhou, PR China, 2Xiangya Pingkuang associated hospital, Pingxiang, Jiangxi, PR China and 3Southern Genomics Research Center, Guangzhou, Guangdong, PR China Email: Xia Chen - [email protected]; Shuang Liang - [email protected]; WenLing Zheng - [email protected]; ZhiJun Liao - [email protected]; Tao Shang - [email protected]; WenLi Ma* - [email protected] * Corresponding author †Equal contributors Published: 7 July 2008 Received: 16 February 2008 Accepted: 7 July 2008 BMC Genomics 2008, 9:322 doi:10.1186/1471-2164-9-322 This article is available from: http://www.biomedcentral.com/1471-2164/9/322 © 2008 Chen et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Epstein-Barr virus (EBV) presumably plays an important role in the pathogenesis of nasopharyngeal carcinoma (NPC), but the molecular mechanism of EBV-dependent neoplastic transformation is not well understood. The combination of bioinformatics with evidences from biological experiments paved a new way to gain more insights into the molecular mechanism of cancer. Results: We profiled gene expression using a meta-analysis approach. Two sets of meta-genes were obtained. Meta-A genes were identified by finding those commonly activated/deactivated upon EBV infection/reactivation. -
Concerted Genomic and Epigenomic Changes Accompany Stabilization of Arabidopsis Allopolyploids
ARTICLES https://doi.org/10.1038/s41559-021-01523-y Concerted genomic and epigenomic changes accompany stabilization of Arabidopsis allopolyploids Xinyu Jiang 1, Qingxin Song 1,2, Wenxue Ye 1 and Z. Jeffrey Chen 2 ✉ During evolution successful allopolyploids must overcome ‘genome shock’ between hybridizing species but the underlying pro- cess remains elusive. Here, we report concerted genomic and epigenomic changes in resynthesized and natural Arabidopsis suecica (TTAA) allotetraploids derived from Arabidopsis thaliana (TT) and Arabidopsis arenosa (AA). A. suecica shows con- served gene synteny and content with more gene family gain and loss in the A and T subgenomes than respective progenitors, although A. arenosa-derived subgenome has more structural variation and transposon distributions than A. thaliana-derived subgenome. These balanced genomic variations are accompanied by pervasive convergent and concerted changes in DNA methylation and gene expression among allotetraploids. The A subgenome is hypomethylated rapidly from F1 to resynthesized allotetraploids and convergently to the T-subgenome level in natural A. suecica, despite many other methylated loci being inher- ited from F1 to all allotetraploids. These changes in DNA methylation, including small RNAs, in allotetraploids may affect gene expression and phenotypic variation, including flowering, silencing of self-incompatibility and upregulation of meiosis- and mitosis-related genes. In conclusion, concerted genomic and epigenomic changes may improve stability and adaptation during polyploid evolution. olyploidy or whole-genome duplication (WGD) is a perva- species, including Aly24, Aha25 and Aka26, having been sequenced, sive feature of genome evolution in animals and flowering A. arenosa and A. suecica genomes are unavailable, except for a draft Pplants1–6. -
Drosophila and Human Transcriptomic Data Mining Provides Evidence for Therapeutic
Drosophila and human transcriptomic data mining provides evidence for therapeutic mechanism of pentylenetetrazole in Down syndrome Author Abhay Sharma Institute of Genomics and Integrative Biology Council of Scientific and Industrial Research Delhi University Campus, Mall Road Delhi 110007, India Tel: +91-11-27666156, Fax: +91-11-27662407 Email: [email protected] Nature Precedings : hdl:10101/npre.2010.4330.1 Posted 5 Apr 2010 Running head: Pentylenetetrazole mechanism in Down syndrome 1 Abstract Pentylenetetrazole (PTZ) has recently been found to ameliorate cognitive impairment in rodent models of Down syndrome (DS). The mechanism underlying PTZ’s therapeutic effect is however not clear. Microarray profiling has previously reported differential expression of genes in DS. No mammalian transcriptomic data on PTZ treatment however exists. Nevertheless, a Drosophila model inspired by rodent models of PTZ induced kindling plasticity has recently been described. Microarray profiling has shown PTZ’s downregulatory effect on gene expression in fly heads. In a comparative transcriptomics approach, I have analyzed the available microarray data in order to identify potential mechanism of PTZ action in DS. I find that transcriptomic correlates of chronic PTZ in Drosophila and DS counteract each other. A significant enrichment is observed between PTZ downregulated and DS upregulated genes, and a significant depletion between PTZ downregulated and DS dowwnregulated genes. Further, the common genes in PTZ Nature Precedings : hdl:10101/npre.2010.4330.1 Posted 5 Apr 2010 downregulated and DS upregulated sets show enrichment for MAP kinase pathway. My analysis suggests that downregulation of MAP kinase pathway may mediate therapeutic effect of PTZ in DS. Existing evidence implicating MAP kinase pathway in DS supports this observation. -
Endosomal PI(3)P Regulation by the COMMD/CCDC22/CCDC93
ARTICLE https://doi.org/10.1038/s41467-019-12221-6 OPEN Endosomal PI(3)P regulation by the COMMD/ CCDC22/CCDC93 (CCC) complex controls membrane protein recycling Amika Singla 1,5, Alina Fedoseienko2,5, Sai S.P. Giridharan3, Brittany L. Overlee2, Adam Lopez1, Da Jia 4, Jie Song1, Kayci Huff-Hardy1, Lois Weisman3, Ezra Burstein 1,6 & Daniel D. Billadeau2,6 1234567890():,; Protein recycling through the endolysosomal system relies on molecular assemblies that interact with cargo proteins, membranes, and effector molecules. Among them, the COMMD/CCDC22/CCDC93 (CCC) complex plays a critical role in recycling events. While CCC is closely associated with retriever, a cargo recognition complex, its mechanism of action remains unexplained. Herein we show that CCC and retriever are closely linked through sharing a common subunit (VPS35L), yet the integrity of CCC, but not retriever, is required to maintain normal endosomal levels of phosphatidylinositol-3-phosphate (PI(3)P). CCC complex depletion leads to elevated PI(3)P levels, enhanced recruitment and activation of WASH (an actin nucleation promoting factor), excess endosomal F-actin and trapping of internalized receptors. Mechanistically, we find that CCC regulates the phosphorylation and endosomal recruitment of the PI(3)P phosphatase MTMR2. Taken together, we show that the regulation of PI(3)P levels by the CCC complex is critical to protein recycling in the endosomal compartment. 1 Department of Internal Medicine, and Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. 2 Division of Oncology Research and Department of Biochemistry and Molecular Biology, College of Medicine, Mayo Clinic, Rochester, MN 55905, USA. -
An Atlas of Cell Types in the Mouse Epididymis and Vas Deferens
TOOLS AND RESOURCES An atlas of cell types in the mouse epididymis and vas deferens Vera D Rinaldi1†, Elisa Donnard2†, Kyle Gellatly2, Morten Rasmussen1‡, Alper Kucukural2, Onur Yukselen2, Manuel Garber2,3, Upasna Sharma4, Oliver J Rando1* 1Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States; 2Department of Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, United States; 3Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States; 4Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, United States Abstract Following testicular spermatogenesis, mammalian sperm continue to mature in a long epithelial tube known as the epididymis, which plays key roles in remodeling sperm protein, lipid, and RNA composition. To understand the roles for the epididymis in reproductive biology, we generated a single-cell atlas of the murine epididymis and vas deferens. We recovered key epithelial cell types including principal cells, clear cells, and basal cells, along with associated *For correspondence: support cells that include fibroblasts, smooth muscle, macrophages and other immune cells. [email protected] Moreover, our data illuminate extensive regional specialization of principal cell populations across †These authors contributed the length of the epididymis. In addition to region-specific specialization of principal cells, we find equally to this work evidence for functionally specialized subpopulations of stromal cells, and, most notably, two ‡ distinct populations of clear cells. Our dataset extends on existing knowledge of epididymal Present address: Department of Virus and Microbiological biology, and provides a wealth of information on potential regulatory and signaling factors that Special Diagnostics, Statens bear future investigation. -
On the Role of Chromosomal Rearrangements in Evolution
On the role of chromosomal rearrangements in evolution: Reconstruction of genome reshuffling in rodents and analysis of Robertsonian fusions in a house mouse chromosomal polymorphism zone by Laia Capilla Pérez A thesis submitted for the degree of Doctor of Philosophy in Animal Biology Supervisors: Dra. Aurora Ruiz-Herrera Moreno and Dr. Jacint Ventura Queija Institut de Biotecnologia i Biomedicina (IBB) Departament de Biologia Cel·lular, Fisiologia i Immunologia Departament de Biologia Animal, Biologia Vegetal i Ecologia Universitat Autònoma de Barcelona Supervisor Supervisor PhD candidate Aurora Ruiz-Herrera Moreno Jacint Ventura Queija Laia Capilla Pérez Bellaterra, 2015 A la mare Al pare Al mano “Visto a la luz de la evolución, la biología es, quizás, la ciencia más satisfactoria e inspiradora. Sin esa luz, se convierte en un montón de hechos varios, algunos de ellos interesantes o curiosos, pero sin formar ninguna visión conjunta.” Theodosius Dobzhansky “La evolución es tan creativa. Por eso tenemos jirafas.” Kurt Vonnegut This thesis was supported by grants from: • Ministerio de Economía y Competitividad (CGL2010-15243 and CGL2010- 20170). • Generalitat de Catalunya, GRQ 1057. • Ministerio de Economía y Competitividad. Beca de Formación de Personal Investigador (FPI) (BES-2011-047722). • Ministerio de Economía y Competitividad. Beca para la realización de estancias breves (EEBB-2011-07350). Covers designed by cintamontserrat.blogspot.com INDEX Abstract 15-17 Acronyms 19-20 1. GENERAL INTRODUCTION 21-60 1.1 Chromosomal rearrangements -
A High Throughput, Functional Screen of Human Body Mass Index GWAS Loci Using Tissue-Specific Rnai Drosophila Melanogaster Crosses Thomas J
Washington University School of Medicine Digital Commons@Becker Open Access Publications 2018 A high throughput, functional screen of human Body Mass Index GWAS loci using tissue-specific RNAi Drosophila melanogaster crosses Thomas J. Baranski Washington University School of Medicine in St. Louis Aldi T. Kraja Washington University School of Medicine in St. Louis Jill L. Fink Washington University School of Medicine in St. Louis Mary Feitosa Washington University School of Medicine in St. Louis Petra A. Lenzini Washington University School of Medicine in St. Louis See next page for additional authors Follow this and additional works at: https://digitalcommons.wustl.edu/open_access_pubs Recommended Citation Baranski, Thomas J.; Kraja, Aldi T.; Fink, Jill L.; Feitosa, Mary; Lenzini, Petra A.; Borecki, Ingrid B.; Liu, Ching-Ti; Cupples, L. Adrienne; North, Kari E.; and Province, Michael A., ,"A high throughput, functional screen of human Body Mass Index GWAS loci using tissue-specific RNAi Drosophila melanogaster crosses." PLoS Genetics.14,4. e1007222. (2018). https://digitalcommons.wustl.edu/open_access_pubs/6820 This Open Access Publication is brought to you for free and open access by Digital Commons@Becker. It has been accepted for inclusion in Open Access Publications by an authorized administrator of Digital Commons@Becker. For more information, please contact [email protected]. Authors Thomas J. Baranski, Aldi T. Kraja, Jill L. Fink, Mary Feitosa, Petra A. Lenzini, Ingrid B. Borecki, Ching-Ti Liu, L. Adrienne Cupples, Kari E. North, and Michael A. Province This open access publication is available at Digital Commons@Becker: https://digitalcommons.wustl.edu/open_access_pubs/6820 RESEARCH ARTICLE A high throughput, functional screen of human Body Mass Index GWAS loci using tissue-specific RNAi Drosophila melanogaster crosses Thomas J. -
A New Entrez Database Transitioning from Locuslink to Entrez
NCBI News National Center for Biotechnology Information National Library of Medicine National Institutes of Health Spring 2004 Department of Health and Human Services Transitioning from LocusLink to Entrez Gene Cancer Chromosomes: a New Entrez Database A gene-based view of annotated The Entrez Gene help document genomes is essential to capitalize on provides tips to ease the transition Three databases, the NCI/NCBI the increase in the sequencing and for LocusLink users to the current SKY (Spectral Karyotyping)/M- analysis of model genomes. The Entrez Gene database. FISH (Multiplex-FISH) and CGH Entrez Gene database has been (Comparative Genomic The default display format for developed to supply key connections Hybridization) Database, the NCI Entrez Gene is the graphics display between maps, sequences, expression Mitelman Database of Chromosome shown in Figure 1 for BMP7, which profiles, structure, function, homolo- Aberrations in Cancer, and the NCI resembles the traditional view of a gy data, and the scientific literature. Recurrent Chromosome Aberrations LocusLink record. The array of col- Unique identifiers are assigned to in Cancer databases are now integrat- ored boxes at the head of LocusLink genes with defining sequence, genes ed into NCBI’s Entrez system as the reports that provide links to gene- with known map positions, and “Cancer Chromosomes” database. related resources is replaced by the genes inferred from phenotypic Cancer Chromosomes supports “Links” menu in Gene, which information. These gene identifiers searches for cytogenetic, clinical, or includes additional links, such as are tracked, and functional informa- reference information using the flexi- those to Books, GEO, UniSTS, and tion is added when available. -
Complete, Duplication-Aware Phylogenetic Trees in Vertebrates
Downloaded from genome.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Resource EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates Albert J. Vilella,1 Jessica Severin,1,3 Abel Ureta-Vidal,1,4 Li Heng,2 Richard Durbin,2 and Ewan Birney1,5 1EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom; 2Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, United Kingdom We have developed a comprehensive gene orientated phylogenetic resource, EnsemblCompara GeneTrees, based on a computational pipeline to handle clustering, multiple alignment, and tree generation, including the handling of large gene families. We developed two novel non-sequence-based metrics of gene tree correctness and benchmarked a number of tree methods. The TreeBeST method from TreeFam shows the best performance in our hands. We also compared this phylogenetic approach to clustering approaches for ortholog prediction, showing a large increase in coverage using the phylogenetic approach. All data are made available in a number of formats and will be kept up to date with the Ensembl project. [Supplemental material is available online at www.genome.org.] The use of phylogenetic trees to describe the evolution of bi- provide links to these model organisms. In this paper we provide ological processes was established in the 1950s (Hennig 1952) and the motivation, implementation, and benchmarking of this method remains a fundamental approach to understanding the evolution and document the display and access methods for these trees. of individual genes through to complete genomes; for example, in There have been a number of methods proposed for routine the mouse (Mouse Genome Sequencing Consortium 2002), rat generation of genomewide orthology descriptions, including (Gibbs et al. -
The Ribosomal Protein Genes and Minute Loci of Drosophila
Open Access Research2007MarygoldetVolume al. 8, Issue 10, Article R216 The ribosomal protein genes and Minute loci of Drosophila melanogaster Steven J Marygold*, John Roote†, Gunter Reuter‡, Andrew Lambertsson§, Michael Ashburner†, Gillian H Millburn†, Paul M Harrison¶, Zhan Yu¶, Naoya Kenmochi¥, Thomas C Kaufman#, Sally J Leevers* and Kevin R Cook# Addresses: *Growth Regulation Laboratory, Cancer Research UK London Research Institute, Lincoln's Inn Fields, London WC2A 3PX, UK. †Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK. ‡Institute of Genetics, Biologicum, Martin Luther University Halle-Wittenberg, Weinbergweg, Halle D-06108, Germany. §Institute of Molecular Biosciences, University of Oslo, Blindern, Olso N-0316, Norway. ¶Department of Biology, McGill University, Dr Penfield Ave, Montreal, Quebec H3A 1B1, Canada. ¥Frontier Science Research Center, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan. #Department of Biology, Indiana University, E. Third Street, Bloomington, IN 47405-7005, USA. Correspondence: Steven J Marygold. Email: [email protected]. Kevin R Cook. Email: [email protected] Published: 10 October 2007 Received: 17 June 2007 Revised: 10 October 2007 Genome Biology 2007, 8:R216 (doi:10.1186/gb-2007-8-10-r216) Accepted: 10 October 2007 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2007/8/10/R216 © 2007 Marygold et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. -
A Systematic Genome-Wide Association Analysis for Inflammatory Bowel Diseases (IBD)
A systematic genome-wide association analysis for inflammatory bowel diseases (IBD) Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakultät der Christian-Albrechts-Universität zu Kiel vorgelegt von Dipl.-Biol. ANDRE FRANKE Kiel, im September 2006 Referent: Prof. Dr. Dr. h.c. Thomas C.G. Bosch Koreferent: Prof. Dr. Stefan Schreiber Tag der mündlichen Prüfung: Zum Druck genehmigt: der Dekan “After great pain a formal feeling comes.” (Emily Dickinson) To my wife and family ii Table of contents Abbreviations, units, symbols, and acronyms . vi List of figures . xiii List of tables . .xv 1 Introduction . .1 1.1 Inflammatory bowel diseases, a complex disorder . 1 1.1.1 Pathogenesis and pathophysiology. .2 1.2 Genetics basis of inflammatory bowel diseases . 6 1.2.1 Genetic evidence from family and twin studies . .6 1.2.2 Single nucleotide polymorphisms (SNPs) . .7 1.2.3 Linkage studies . .8 1.2.4 Association studies . 10 1.2.5 Known susceptibility genes . 12 1.2.5.1 CARD15. .12 1.2.5.2 CARD4. .15 1.2.5.3 TNF-α . .15 1.2.5.4 5q31 haplotype . .16 1.2.5.5 DLG5 . .17 1.2.5.6 TNFSF15 . .18 1.2.5.7 HLA/MHC on chromosome 6 . .19 1.2.5.8 Other proposed IBD susceptibility genes . .20 1.2.6 Animal models. 21 1.3 Aims of this study . 23 2 Methods . .24 2.1 Laboratory information management system (LIMS) . 24 2.2 Recruitment. 25 2.3 Sample preparation. 27 2.3.1 DNA extraction from blood. 27 2.3.2 Plate design . -
ST5 Positively Regulates Osteoclastogenesis Via Src/Syk/Calcium Signaling Pathways
Molecules and Cells ST5 Positively Regulates Osteoclastogenesis via Src/Syk/Calcium Signaling Pathways Min Kyung Kim, Bongjun Kim, Jun-Oh Kwon, Min-Kyoung Song, Suhan Jung, Zang Hee Lee, and Hong- Hee Kim* Department of Cell and Developmental Biology, BK21 Program and Dental Research Institute (DRI), School of Dentistry, Seoul National University, Seoul 03080, Korea *Correspondence: [email protected] https://doi.org/10.14348/molcells.2019.0189 www.molcells.org For physiological or pathological understanding of bone INTRODUCTION disease caused by abnormal behavior of osteoclasts (OCs), functional studies of molecules that regulate the generation Bone is a dynamic organ that is constantly being disrupted and action of OCs are required. In a microarray approach, and restructured for maintenance of homeostasis (Zaidi, we found the suppression of tumorigenicity 5 (ST5) gene 2007). The process of bone resorption is controlled by ac- is upregulated by receptor activator of nuclear factor-κB tion of osteoclasts (OCs), which are multinucleated cells ligand (RANKL), the OC differentiation factor. Although the (MNCs) generated from a monocyte/macrophage lineage of roles of ST5 in cancer and β-cells have been reported, the hemopoietic cells (Boyle et al., 2003; Rho et al., 2004). The function of ST5 in bone cells has not yet been investigated. action of excessive OCs induces an imbalance in homeostasis, Knockdown of ST5 by siRNA reduced OC differentiation triggering pathological bone diseases, such as osteoporosis from primary precursors. Moreover, ST5 downregulation (Zaidi, 2007). decreased expression of NFATc1, a key transcription factor Osteoclastogenesis is a multi-step process including com- for osteoclastogenesis. In contrast, overexpression of ST5 mitment of OC precursor cells to mononucleated preosteo- resulted in the opposite phenotype of ST5 knockdown.