Identification of Differentially Expressed Genes Using Microarray Analysis and COL6A1 Induction of Bone Metastasis in Non‑Small Cell Lung Cancer
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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. -
Noelia Díaz Blanco
Effects of environmental factors on the gonadal transcriptome of European sea bass (Dicentrarchus labrax), juvenile growth and sex ratios Noelia Díaz Blanco Ph.D. thesis 2014 Submitted in partial fulfillment of the requirements for the Ph.D. degree from the Universitat Pompeu Fabra (UPF). This work has been carried out at the Group of Biology of Reproduction (GBR), at the Department of Renewable Marine Resources of the Institute of Marine Sciences (ICM-CSIC). Thesis supervisor: Dr. Francesc Piferrer Professor d’Investigació Institut de Ciències del Mar (ICM-CSIC) i ii A mis padres A Xavi iii iv Acknowledgements This thesis has been made possible by the support of many people who in one way or another, many times unknowingly, gave me the strength to overcome this "long and winding road". First of all, I would like to thank my supervisor, Dr. Francesc Piferrer, for his patience, guidance and wise advice throughout all this Ph.D. experience. But above all, for the trust he placed on me almost seven years ago when he offered me the opportunity to be part of his team. Thanks also for teaching me how to question always everything, for sharing with me your enthusiasm for science and for giving me the opportunity of learning from you by participating in many projects, collaborations and scientific meetings. I am also thankful to my colleagues (former and present Group of Biology of Reproduction members) for your support and encouragement throughout this journey. To the “exGBRs”, thanks for helping me with my first steps into this world. Working as an undergrad with you Dr. -
Distinct Regions of RPB11 Are Required for Heterodimerization with RPB3 in Human and Yeast RNA Polymerase II Wagane J
Distinct regions of RPB11 are required for heterodimerization with RPB3 in human and yeast RNA polymerase II Wagane J. Benga, Sylvie Grandemange, George V. Shpakovski, Elena K. Shematorova, Claude Kedinger, Marc Vigneron To cite this version: Wagane J. Benga, Sylvie Grandemange, George V. Shpakovski, Elena K. Shematorova, Claude Kedinger, et al.. Distinct regions of RPB11 are required for heterodimerization with RPB3 in hu- man and yeast RNA polymerase II. Nucleic Acids Research, Oxford University Press, 2005, 33 (11), pp.3582-3590. 10.1093/nar/gki672. hal-02981340 HAL Id: hal-02981340 https://hal.archives-ouvertes.fr/hal-02981340 Submitted on 27 Oct 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. 3582–3590 Nucleic Acids Research, 2005, Vol. 33, No. 11 doi:10.1093/nar/gki672 Distinct regions of RPB11 are required for heterodimerization with RPB3 in human and yeast RNA polymerase II Wagane J. Benga, Sylvie Grandemange1, George V. Shpakovski2, Elena K. Shematorova2, Claude Kedinger and Marc Vigneron* Unite´ Mixte de Recherche 7100 CNRS–Universite´ Louis Pasteur, Ecole Supe´rieure de Biotechnologie de Strasbourg, Boulevard Se´bastien Brandt, BP 10413, 67412 Illkirch Cedex, France, 1Ge´ne´tique des Maladies Inflammatoires, Institut de Ge´ne´tique Humaine UPR 1142, CNRS. -
The Human Isoform of RNA Polymerase II Subunit Hrpb11bα Specifically Interacts with Transcription Factor ATF4
International Journal of Molecular Sciences Article The Human Isoform of RNA Polymerase II Subunit hRPB11bα Specifically Interacts with Transcription Factor ATF4 Sergey A. Proshkin 1,2, Elena K. Shematorova 1 and George V. Shpakovski 1,* 1 Laboratory of Mechanisms of Gene Expression, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; [email protected] (S.A.P.); [email protected] (E.K.S.) 2 Engelhardt Institute of Molecular Biology, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, 119991 Moscow, Russia * Correspondence: [email protected]; Tel.: +7-495-3306583; Fax: +7-495-3357103 Received: 25 November 2019; Accepted: 22 December 2019; Published: 24 December 2019 Abstract: Rpb11 subunit of RNA polymerase II of Eukaryotes is related to N-terminal domain of eubacterial α subunit and forms a complex with Rpb3 subunit analogous to prokaryotic α2 homodimer, which is involved in RNA polymerase assembly and promoter recognition. In humans, a POLR2J gene family has been identified that potentially encodes several hRPB11 proteins differing mainly in their short C-terminal regions. The functions of the different human specific isoforms are still mainly unknown. To further characterize the minor human specific isoform of RNA polymerase II subunit hRPB11bα, the only one from hRPB11 (POLR2J) homologues that can replace its yeast counterpart in vivo, we used it as bait in a yeast two-hybrid screening of a human fetal brain cDNA library. By this analysis and subsequent co-purification assay in vitro, we identified transcription factor ATF4 as a prominent partner of the minor RNA polymerase II (RNAP II) subunit hRPB11bα. -
Bovine NK-Lysin: Copy Number Variation and PNAS PLUS Functional Diversification
Bovine NK-lysin: Copy number variation and PNAS PLUS functional diversification Junfeng Chena, John Huddlestonb,c, Reuben M. Buckleyd, Maika Maligb, Sara D. Lawhona, Loren C. Skowe, Mi Ok Leea, Evan E. Eichlerb,c, Leif Anderssone,f,g, and James E. Womacka,1 aDepartment of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843; bDepartment of Genome Sciences, University of Washington, Seattle, WA 98195; cHoward Hughes Medical Institute, University of Washington, Seattle, WA 98195; dSchool of Biological Sciences, University of Adelaide, Adelaide 5005, Australia; eDepartment of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843; fDepartment of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, SE 75123, Sweden; and gDepartment of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, SE 75007, Sweden Contributed by James E. Womack, November 20, 2015 (sent for review November 5, 2015; reviewed by Denis M. Larkin and Harris A. Lewin) NK-lysin is an antimicrobial peptide and effector protein in the host compared with humans and mice. These include genes coding innate immune system. It is coded by a single gene in humans and AMPs such as the cathelicidins and β-defensins, members of most other mammalian species. In this study, we provide evidence the IFN gene family, C-type lysozyme, and lipopolysaccharide- for the existence of four NK-lysin genes in a repetitive region on binding protein (ULBP) (23–28). Expansion of these gene fam- cattle chromosome 11. The NK2A, NK2B,andNK2C genes are tan- ilies potentially can give rise to new functional paralogs with demly arrayed as three copies in ∼30–35-kb segments, located implications in the unique gastric physiology of ruminants or in 41.8 kb upstream of NK1. -
Molecular Signatures Differentiate Immune States in Type 1 Diabetes Families
Page 1 of 65 Diabetes Molecular signatures differentiate immune states in Type 1 diabetes families Yi-Guang Chen1, Susanne M. Cabrera1, Shuang Jia1, Mary L. Kaldunski1, Joanna Kramer1, Sami Cheong2, Rhonda Geoffrey1, Mark F. Roethle1, Jeffrey E. Woodliff3, Carla J. Greenbaum4, Xujing Wang5, and Martin J. Hessner1 1The Max McGee National Research Center for Juvenile Diabetes, Children's Research Institute of Children's Hospital of Wisconsin, and Department of Pediatrics at the Medical College of Wisconsin Milwaukee, WI 53226, USA. 2The Department of Mathematical Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA. 3Flow Cytometry & Cell Separation Facility, Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA. 4Diabetes Research Program, Benaroya Research Institute, Seattle, WA, 98101, USA. 5Systems Biology Center, the National Heart, Lung, and Blood Institute, the National Institutes of Health, Bethesda, MD 20824, USA. Corresponding author: Martin J. Hessner, Ph.D., The Department of Pediatrics, The Medical College of Wisconsin, Milwaukee, WI 53226, USA Tel: 011-1-414-955-4496; Fax: 011-1-414-955-6663; E-mail: [email protected]. Running title: Innate Inflammation in T1D Families Word count: 3999 Number of Tables: 1 Number of Figures: 7 1 For Peer Review Only Diabetes Publish Ahead of Print, published online April 23, 2014 Diabetes Page 2 of 65 ABSTRACT Mechanisms associated with Type 1 diabetes (T1D) development remain incompletely defined. Employing a sensitive array-based bioassay where patient plasma is used to induce transcriptional responses in healthy leukocytes, we previously reported disease-specific, partially IL-1 dependent, signatures associated with pre and recent onset (RO) T1D relative to unrelated healthy controls (uHC). -
Array-Based Comparative Genomic Hybridization for Genome-Wide Screening of DNA Copy Number in Bladder Tumors1
[CANCER RESEARCH 63, 2872–2880, June 1, 2003] Array-based Comparative Genomic Hybridization for Genome-Wide Screening of DNA Copy Number in Bladder Tumors1 Joris A. Veltman, Jane Fridlyand, Sunanda Pejavar, Adam B. Olshen, James E. Korkola, Sandy DeVries, Peter Carroll, Wen-Lin Kuo, Daniel Pinkel, Donna Albertson, Carlos Cordon-Cardo, Ajay N. Jain, and Frederic M. Waldman2 Cancer Center [J. F., S. P., A. B. O., J. E. K., S. D., W-L. K.]; and Departments of Laboratory Medicine [D. P., D. A., A. N. J., F. M. W.] and Urology [P. C.], University of California-San Francisco, San Francisco, California 94143-0808; Department of Human Genetics, University Medical Center Nijmegen, Nijmegen, the Netherlands [J. A. V.]; and Department of Epidemiology and Biostatistics [A. B. O.] and Department of Pathology [C. C-C.], Memorial Sloan-Kettering Cancer Center, New York, New York ABSTRACT analysis of copy number changes at high resolution throughout the genome (1, 2). This quantitative measurement of DNA copy number Genome-wide copy number profiles were characterized in 41 primary across the genome may facilitate oncogene identification (3) and can bladder tumors using array-based comparative genomic hybridization also be used for tumor classification (4). (array CGH). In addition to previously identified alterations in large chromosomal regions, alterations were identified in many small genomic In this study, we have used array-based CGH for high resolution regions, some with high-level amplifications or homozygous deletions. mapping of copy number changes in different stages of bladder High-level amplifications were detected for 192 genomic clones, most carcinogenesis in 41 primary human tumors. -
POLR2K (NM 005034) Human Untagged Clone – SC116985
OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for SC116985 POLR2K (NM_005034) Human Untagged Clone Product data: Product Type: Expression Plasmids Product Name: POLR2K (NM_005034) Human Untagged Clone Tag: Tag Free Symbol: POLR2K Synonyms: ABC10-alpha; hRPB7.0; hsRPB10a; RPABC4; RPB7.0; RPB10alpha; RPB12 Vector: pCMV6-XL5 E. coli Selection: Ampicillin (100 ug/mL) Cell Selection: None Fully Sequenced ORF: >OriGene ORF sequence for NM_005034 edited ATGGACACCCAGAAGGACGTTCAACCTCCAAAGCAGCAACCAATGATATATATCTGTGGA GAGTGTCACACAGAAAATGAAATAAAATCTAGGGATCCAATCAKATGCAGAGAATGTGGA TACAGAATAATGTACAAGAAAAGGACTAAAAGATTGGTCGTTTTTGATGCTCGATGA 5' Read Nucleotide >OriGene 5' read for NM_005034 unedited Sequence: AATACGACTCACTATAGGGCGGCCGCGAATTCGGCACGAGGCCGGGTTGTATTTGGAAAC GCGGAGTGAGTTTTTCCGTGCTGTGTAGGGGCTAACAATGGACACCCAGAAGGACGTTCA ACCTCCAAAGCAGCAACCAATGATATATATCTGTGGAGAGTGTCACACAGAAAATGAAAT AAAATCTAGGGATCCAATCAGATGCAGAGAATGTGGATACAGAATAATGTACAAGAAAAG GACTAAAAGATTGGTCGTTTTTGATGCTCGATGAATGCTGGGAATTCAGAGGAATGTCTT CACTTATACTTGGATTTGCTCTCTTCCCATTTCTGATTGTTGTATAGCTTTCGATTTTGC TTACAGTAGTTCCCCCTTATCTTCGGGAGATACATTCCAAGGCCCCCAGTGAACTCCTGA AACCTCAAACAGTACCAAACCTTTATACACTGTTTTTTCCATATATATATACCTATGATA AAGTATAATGTATAAATTAAGCATAGCAAGAGATTAATAATAATGTAATAGAACAATGAT AACATACTATAATAAAAGTTATGTGAATGTGGTTGGTCTCTCTTGCTNTCAAAATATCTT CTTGTACAGTACTCACCTATTTTAGAATGTGGTTGACTACAGGTAACCAAAACCACAGAA AGGGAAACTTTGGATGAGGNGGGCACTACTGTACTTANGAATACANCTATATACATATGA -
Download Special Issue
BioMed Research International Novel Bioinformatics Approaches for Analysis of High-Throughput Biological Data Guest Editors: Julia Tzu-Ya Weng, Li-Ching Wu, Wen-Chi Chang, Tzu-Hao Chang, Tatsuya Akutsu, and Tzong-Yi Lee Novel Bioinformatics Approaches for Analysis of High-Throughput Biological Data BioMed Research International Novel Bioinformatics Approaches for Analysis of High-Throughput Biological Data Guest Editors: Julia Tzu-Ya Weng, Li-Ching Wu, Wen-Chi Chang, Tzu-Hao Chang, Tatsuya Akutsu, and Tzong-Yi Lee Copyright © 2014 Hindawi Publishing Corporation. All rights reserved. This is a special issue published in “BioMed Research International.” All articles are open access articles distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Contents Novel Bioinformatics Approaches for Analysis of High-Throughput Biological Data,JuliaTzu-YaWeng, Li-Ching Wu, Wen-Chi Chang, Tzu-Hao Chang, Tatsuya Akutsu, and Tzong-Yi Lee Volume2014,ArticleID814092,3pages Evolution of Network Biomarkers from Early to Late Stage Bladder Cancer Samples,Yung-HaoWong, Cheng-Wei Li, and Bor-Sen Chen Volume 2014, Article ID 159078, 23 pages MicroRNA Expression Profiling Altered by Variant Dosage of Radiation Exposure,Kuei-FangLee, Yi-Cheng Chen, Paul Wei-Che Hsu, Ingrid Y. Liu, and Lawrence Shih-Hsin Wu Volume2014,ArticleID456323,10pages EXIA2: Web Server of Accurate and Rapid Protein Catalytic Residue Prediction, Chih-Hao Lu, Chin-Sheng -
Genetic Tools to Improve Reproduction Traits in Dairy Cattle
Genetic tools to improve reproduction traits in dairy cattle Aurelien Capitan, Pauline Michot, Aurélia Baur, Romain Saintilan, Chris Hoze, Damien Valour, François Guillaume, D Boichon, Anne Barbat, Didier Boichard, et al. To cite this version: Aurelien Capitan, Pauline Michot, Aurélia Baur, Romain Saintilan, Chris Hoze, et al.. Genetic tools to improve reproduction traits in dairy cattle. Reproduction, Fertility and Development, CSIRO Publishing, 2015, 27 (1), pp.14-21. 10.1071/RD14379. hal-01194016 HAL Id: hal-01194016 https://hal.archives-ouvertes.fr/hal-01194016 Submitted on 28 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. CSIRO PUBLISHING Reproduction, Fertility and Development, 2015, 27, 14–21 http://dx.doi.org/10.1071/RD14379 Genetic tools to improve reproduction traits in dairy cattle A. CapitanA,B,F, P. MichotA,B, A. BaurA,B, R. SaintilanA,B, C. Hoze´ A,B, D. ValourA,D, F. GuillaumeC, D. BoichonE, A. BarbatB, D. BoichardB, L. SchiblerA and S. FritzA,B AUNCEIA (Union Nationale des Coope´ratives d’Elevage et d’Inse´mination Animale), 149 rue de Bercy, 75012 Paris, France. BINRA (Institut National de la Recherche Agronomique), UMR1313 Ge´ne´tique Animale et Biologie Inte´grative, Domaine de Vilvert, 78352 Jouy-en-Josas, France. -
Histone Chaperone Nucleophosmin Regulates Transcription of Key Genes Involved in Oral
bioRxiv preprint doi: https://doi.org/10.1101/852095; this version posted November 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Histone chaperone Nucleophosmin regulates transcription of key genes involved in oral tumorigenesis Parijat Senapati1, Suchismita Dey1, Deepthi Sudarshan1, Aditya Bhattacharya1, Shyla G2, Sadhan Das1, Surabhi Sudevan1, Tessy Thomas Maliekal2, Tapas K. Kundu1* 1Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore – 560064, Karnataka, India. 2Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram – 695014, Kerala, India. *Corresponding Author: Tapas K. Kundu, Ph.D. Professor Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore: 560064, India. Phone: +91-80-22082840 Fax: +91-80-22082766 E-mail: [email protected] Running title: Role of NPM1 in transcription regulation. Keywords: histone chaperone, NPM1, acetylated NPM1, transcription, ChIP-seq, RNA-seq, protein microarray, oral cancer bioRxiv preprint doi: https://doi.org/10.1101/852095; this version posted November 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. ABSTRACT Nucleophosmin (NPM1) is a multifunctional histone chaperone that can activate RNA Polymerase II-driven chromatin transcription. Acetylation of NPM1 by acetyltransferase p300 has been shown to further enhance its transcription activation potential. Moreover, its total and acetylated pools are increased in oral squamous cell carcinoma. However, the role of NPM1 or its acetylated form (AcNPM1) in transcriptional regulation in cells is not fully elucidated. -
Comparative Analysis of the Ubiquitin-Proteasome System in Homo Sapiens and Saccharomyces Cerevisiae
Comparative Analysis of the Ubiquitin-proteasome system in Homo sapiens and Saccharomyces cerevisiae Inaugural-Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakultät der Universität zu Köln vorgelegt von Hartmut Scheel aus Rheinbach Köln, 2005 Berichterstatter: Prof. Dr. R. Jürgen Dohmen Prof. Dr. Thomas Langer Dr. Kay Hofmann Tag der mündlichen Prüfung: 18.07.2005 Zusammenfassung I Zusammenfassung Das Ubiquitin-Proteasom System (UPS) stellt den wichtigsten Abbauweg für intrazelluläre Proteine in eukaryotischen Zellen dar. Das abzubauende Protein wird zunächst über eine Enzym-Kaskade mit einer kovalent gebundenen Ubiquitinkette markiert. Anschließend wird das konjugierte Substrat vom Proteasom erkannt und proteolytisch gespalten. Ubiquitin besitzt eine Reihe von Homologen, die ebenfalls posttranslational an Proteine gekoppelt werden können, wie z.B. SUMO und NEDD8. Die hierbei verwendeten Aktivierungs- und Konjugations-Kaskaden sind vollständig analog zu der des Ubiquitin- Systems. Es ist charakteristisch für das UPS, daß sich die Vielzahl der daran beteiligten Proteine aus nur wenigen Proteinfamilien rekrutiert, die durch gemeinsame, funktionale Homologiedomänen gekennzeichnet sind. Einige dieser funktionalen Domänen sind auch in den Modifikations-Systemen der Ubiquitin-Homologen zu finden, jedoch verfügen diese Systeme zusätzlich über spezifische Domänentypen. Homologiedomänen lassen sich als mathematische Modelle in Form von Domänen- deskriptoren (Profile) beschreiben. Diese Deskriptoren können wiederum dazu verwendet werden, mit Hilfe geeigneter Verfahren eine gegebene Proteinsequenz auf das Vorliegen von entsprechenden Homologiedomänen zu untersuchen. Da die im UPS involvierten Homologie- domänen fast ausschließlich auf dieses System und seine Analoga beschränkt sind, können domänen-spezifische Profile zur Katalogisierung der UPS-relevanten Proteine einer Spezies verwendet werden. Auf dieser Basis können dann die entsprechenden UPS-Repertoires verschiedener Spezies miteinander verglichen werden.