Metastatic Colorectal Cancer and Severe Hypocalcemia Following
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
DNA Methylation Patterns from Peripheral Blood Separate Coronary Artery Disease Patients with and Without Heart Failure
ESC HEART FAILURE ORIGINAL RESEARCH ARTICLE ESC Heart Failure 2020; 7: 2468–2478 Published online 2 July 2020 in Wiley Online Library (wileyonlinelibrary.com) DOI: 10.1002/ehf2.12810 DNA methylation patterns from peripheral blood separate coronary artery disease patients with and without heart failure Chris R. Bain1,2,3*†† , Mark Ziemann1,3,4,5††, Antony Kaspi1,3,4, Abdul Waheed Khan1, Rachael Taylor1, Hugh Trahair1, Ishant Khurana1,3,4, Harikrishnan Kaipananickal1,3,4,6, Sophie Wallace2,3, Assam El-Osta1,3,4,7,8, Paul S. Myles2,3 and Kiymet Bozaoglu1,9 1Baker IDI Heart and Diabetes Institute, Melbourne, VIC, Australia; 2Department of Anaesthesiology and Perioperative Medicine, The Alfred Hospital and Monash University, The Alfred Centre, Level 6, 99 Commercial Road, Melbourne, VIC 3004, Australia; 3Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia; 4Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia; 5School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Melbourne, VIC, Australia; 6Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia; 7Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Shatin, Hong Kong SAR; 8Faculty of Health, Department of Technology, Biomedical Laboratory Science, University College Copenhagen, Copenhagen, Denmark; 9Murdoch Children’s Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia Abstract Aims Natriuretic peptides are useful for diagnosis and prognostication of heart failure of any cause. Now, research aims to discover novel biomarkers that will more specifically define the heart failure phenotype. -
Molecular Effects of Isoflavone Supplementation Human Intervention Studies and Quantitative Models for Risk Assessment
Molecular effects of isoflavone supplementation Human intervention studies and quantitative models for risk assessment Vera van der Velpen Thesis committee Promotors Prof. Dr Pieter van ‘t Veer Professor of Nutritional Epidemiology Wageningen University Prof. Dr Evert G. Schouten Emeritus Professor of Epidemiology and Prevention Wageningen University Co-promotors Dr Anouk Geelen Assistant professor, Division of Human Nutrition Wageningen University Dr Lydia A. Afman Assistant professor, Division of Human Nutrition Wageningen University Other members Prof. Dr Jaap Keijer, Wageningen University Dr Hubert P.J.M. Noteborn, Netherlands Food en Consumer Product Safety Authority Prof. Dr Yvonne T. van der Schouw, UMC Utrecht Dr Wendy L. Hall, King’s College London This research was conducted under the auspices of the Graduate School VLAG (Advanced studies in Food Technology, Agrobiotechnology, Nutrition and Health Sciences). Molecular effects of isoflavone supplementation Human intervention studies and quantitative models for risk assessment Vera van der Velpen Thesis submitted in fulfilment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus Prof. Dr M.J. Kropff, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Friday 20 June 2014 at 13.30 p.m. in the Aula. Vera van der Velpen Molecular effects of isoflavone supplementation: Human intervention studies and quantitative models for risk assessment 154 pages PhD thesis, Wageningen University, Wageningen, NL (2014) With references, with summaries in Dutch and English ISBN: 978-94-6173-952-0 ABSTRact Background: Risk assessment can potentially be improved by closely linked experiments in the disciplines of epidemiology and toxicology. -
Bioinformatics Tools for the Analysis of Gene-Phenotype Relationships Coupled with a Next Generation Chip-Sequencing Data Processing Pipeline
Bioinformatics Tools for the Analysis of Gene-Phenotype Relationships Coupled with a Next Generation ChIP-Sequencing Data Processing Pipeline Erinija Pranckeviciene Thesis submitted to the Faculty of Graduate and Postdoctoral Studies in partial fulfillment of the requirements for the Doctorate in Philosophy degree in Cellular and Molecular Medicine Department of Cellular and Molecular Medicine Faculty of Medicine University of Ottawa c Erinija Pranckeviciene, Ottawa, Canada, 2015 Abstract The rapidly advancing high-throughput and next generation sequencing technologies facilitate deeper insights into the molecular mechanisms underlying the expression of phenotypes in living organisms. Experimental data and scientific publications following this technological advance- ment have rapidly accumulated in public databases. Meaningful analysis of currently avail- able data in genomic databases requires sophisticated computational tools and algorithms, and presents considerable challenges to molecular biologists without specialized training in bioinfor- matics. To study their phenotype of interest molecular biologists must prioritize large lists of poorly characterized genes generated in high-throughput experiments. To date, prioritization tools have primarily been designed to work with phenotypes of human diseases as defined by the genes known to be associated with those diseases. There is therefore a need for more prioritiza- tion tools for phenotypes which are not related with diseases generally or diseases with which no genes have yet been associated in particular. Chromatin immunoprecipitation followed by next generation sequencing (ChIP-Seq) is a method of choice to study the gene regulation processes responsible for the expression of cellular phenotypes. Among publicly available computational pipelines for the processing of ChIP-Seq data, there is a lack of tools for the downstream analysis of composite motifs and preferred binding distances of the DNA binding proteins. -
RHNO1 Bidirectional Genes in Cancer
RESEARCH ARTICLE Co-regulation and function of FOXM1/ RHNO1 bidirectional genes in cancer Carter J Barger1, Linda Chee1, Mustafa Albahrani1, Catalina Munoz-Trujillo1, Lidia Boghean1, Connor Branick1, Kunle Odunsi2, Ronny Drapkin3, Lee Zou4, Adam R Karpf1* 1Eppley Institute for Cancer Research and Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, United States; 2Departments of Gynecologic Oncology, Immunology, and Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, United States; 3Penn Ovarian Cancer Research Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States; 4Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, United States Abstract The FOXM1 transcription factor is an oncoprotein and a top biomarker of poor prognosis in human cancer. Overexpression and activation of FOXM1 is frequent in high-grade serous carcinoma (HGSC), the most common and lethal form of human ovarian cancer, and is linked to copy number gains at chromosome 12p13.33. We show that FOXM1 is co-amplified and co- expressed with RHNO1, a gene involved in the ATR-Chk1 signaling pathway that functions in the DNA replication stress response. We demonstrate that FOXM1 and RHNO1 are head-to-head (i.e., bidirectional) genes (BDG) regulated by a bidirectional promoter (BDP) (named F/R-BDP). FOXM1 and RHNO1 each promote oncogenic phenotypes in HGSC cells, including clonogenic growth, DNA homologous recombination repair, and poly-ADP ribosylase inhibitor resistance. FOXM1 and RHNO1 are one of the first examples of oncogenic BDG, and therapeutic targeting of FOXM1/ RHNO1 BDG is a potential therapeutic approach for ovarian and other cancers. *For correspondence: [email protected] Introduction Competing interests: The The forkhead/winged helix domain transcription factor FOXM1 promotes cancer by transactivating authors declare that no genes with oncogenic potential (Halasi and Gartel, 2013a; Kalathil et al., 2020). -
Entrez ID Gene Name Fold Change Q-Value Description
Entrez ID gene name fold change q-value description 4283 CXCL9 -7.25 5.28E-05 chemokine (C-X-C motif) ligand 9 3627 CXCL10 -6.88 6.58E-05 chemokine (C-X-C motif) ligand 10 6373 CXCL11 -5.65 3.69E-04 chemokine (C-X-C motif) ligand 11 405753 DUOXA2 -3.97 3.05E-06 dual oxidase maturation factor 2 4843 NOS2 -3.62 5.43E-03 nitric oxide synthase 2, inducible 50506 DUOX2 -3.24 5.01E-06 dual oxidase 2 6355 CCL8 -3.07 3.67E-03 chemokine (C-C motif) ligand 8 10964 IFI44L -3.06 4.43E-04 interferon-induced protein 44-like 115362 GBP5 -2.94 6.83E-04 guanylate binding protein 5 3620 IDO1 -2.91 5.65E-06 indoleamine 2,3-dioxygenase 1 8519 IFITM1 -2.67 5.65E-06 interferon induced transmembrane protein 1 3433 IFIT2 -2.61 2.28E-03 interferon-induced protein with tetratricopeptide repeats 2 54898 ELOVL2 -2.61 4.38E-07 ELOVL fatty acid elongase 2 2892 GRIA3 -2.60 3.06E-05 glutamate receptor, ionotropic, AMPA 3 6376 CX3CL1 -2.57 4.43E-04 chemokine (C-X3-C motif) ligand 1 7098 TLR3 -2.55 5.76E-06 toll-like receptor 3 79689 STEAP4 -2.50 8.35E-05 STEAP family member 4 3434 IFIT1 -2.48 2.64E-03 interferon-induced protein with tetratricopeptide repeats 1 4321 MMP12 -2.45 2.30E-04 matrix metallopeptidase 12 (macrophage elastase) 10826 FAXDC2 -2.42 5.01E-06 fatty acid hydroxylase domain containing 2 8626 TP63 -2.41 2.02E-05 tumor protein p63 64577 ALDH8A1 -2.41 6.05E-06 aldehyde dehydrogenase 8 family, member A1 8740 TNFSF14 -2.40 6.35E-05 tumor necrosis factor (ligand) superfamily, member 14 10417 SPON2 -2.39 2.46E-06 spondin 2, extracellular matrix protein 3437 -
Content Based Search in Gene Expression Databases and a Meta-Analysis of Host Responses to Infection
Content Based Search in Gene Expression Databases and a Meta-analysis of Host Responses to Infection A Thesis Submitted to the Faculty of Drexel University by Francis X. Bell in partial fulfillment of the requirements for the degree of Doctor of Philosophy November 2015 c Copyright 2015 Francis X. Bell. All Rights Reserved. ii Acknowledgments I would like to acknowledge and thank my advisor, Dr. Ahmet Sacan. Without his advice, support, and patience I would not have been able to accomplish all that I have. I would also like to thank my committee members and the Biomed Faculty that have guided me. I would like to give a special thanks for the members of the bioinformatics lab, in particular the members of the Sacan lab: Rehman Qureshi, Daisy Heng Yang, April Chunyu Zhao, and Yiqian Zhou. Thank you for creating a pleasant and friendly environment in the lab. I give the members of my family my sincerest gratitude for all that they have done for me. I cannot begin to repay my parents for their sacrifices. I am eternally grateful for everything they have done. The support of my sisters and their encouragement gave me the strength to persevere to the end. iii Table of Contents LIST OF TABLES.......................................................................... vii LIST OF FIGURES ........................................................................ xiv ABSTRACT ................................................................................ xvii 1. A BRIEF INTRODUCTION TO GENE EXPRESSION............................. 1 1.1 Central Dogma of Molecular Biology........................................... 1 1.1.1 Basic Transfers .......................................................... 1 1.1.2 Uncommon Transfers ................................................... 3 1.2 Gene Expression ................................................................. 4 1.2.1 Estimating Gene Expression ............................................ 4 1.2.2 DNA Microarrays ...................................................... -
Original Article Dysregulated Expression of Micrornas and Mrnas in Myocardial Infarction
Am J Transl Res 2015;7(11):2291-2304 www.ajtr.org /ISSN:1943-8141/AJTR0012948 Original Article Dysregulated expression of microRNAs and mRNAs in myocardial infarction Yaping Wang1,2, Xiaohong Pan1, Youqi Fan1, Xinyang Hu1,2, Xianbao Liu1,2, Meixiang Xiang1,2, Jian’an Wang1,2 1Department of Cardiology, Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310009, PR China; 2Key Lab of Cardiovascular Disease, Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310009, PR China Received July 15, 2015; Accepted October 31, 2015; Epub November 15, 2015; Published November 30, 2015 Abstract: Acute myocardial infarction (AMI) is a major cause of mortality in the general population. However, the molecular phenotypes and therapeutic targets of AMI patients remain unclear. By profiling genome-wide transcripts and microRNAs (miRNAs) in a cohort of 23 AMI patients and 23 non-AMI patients, we found 218 dysregulated genes identified in the infarcted heart tissues from AMI patients relative to non-AMI controls. Pathway enrichment analy- sis of the dysregulated genes pointed to cell signaling/communication, cell/organism defense and cell structure/ motility. We next compared the expression profiles of potential regulating miRNAs, suggesting that dysregulation of a number of AMI-associated genes (e.g., IL12A, KIF1A, HIF1α and CDK13) may be attributed to the dysregulation of their respective regulating miRNAs. One potentially pathogenic miRNA-mRNA pair, miR-210-HIF1α, was confirmed in a mouse model of myocardial infarction (MI). Inhibition of miR-210 expression improved the survival and cardiac function of MI mice. In conclusion, we presented the pathologic relationships between miRNAs and their gene targets in AMI. -
Microarray Bioinformatics and Its Applications to Clinical Research
Microarray Bioinformatics and Its Applications to Clinical Research A dissertation presented to the School of Electrical and Information Engineering of the University of Sydney in fulfillment of the requirements for the degree of Doctor of Philosophy i JLI ··_L - -> ...·. ...,. by Ilene Y. Chen Acknowledgment This thesis owes its existence to the mercy, support and inspiration of many people. In the first place, having suffering from adult-onset asthma, interstitial cystitis and cold agglutinin disease, I would like to express my deepest sense of appreciation and gratitude to Professors Hong Yan and David Levy for harbouring me these last three years and providing me a place at the University of Sydney to pursue a very meaningful course of research. I am also indebted to Dr. Craig Jin, who has been a source of enthusiasm and encouragement on my research over many years. In the second place, for contexts concerning biological and medical aspects covered in this thesis, I am very indebted to Dr. Ling-Hong Tseng, Dr. Shian-Sehn Shie, Dr. Wen-Hung Chung and Professor Chyi-Long Lee at Change Gung Memorial Hospital and University of Chang Gung School of Medicine (Taoyuan, Taiwan) as well as Professor Keith Lloyd at University of Alabama School of Medicine (AL, USA). All of them have contributed substantially to this work. In the third place, I would like to thank Mrs. Inge Rogers and Mr. William Ballinger for their helpful comments and suggestions for the writing of my papers and thesis. In the fourth place, I would like to thank my swim coach, Hirota Homma. -
Mouse Models of Inherited Retinal Degeneration with Photoreceptor Cell Loss
cells Review Mouse Models of Inherited Retinal Degeneration with Photoreceptor Cell Loss 1, 1, 1 1,2,3 1 Gayle B. Collin y, Navdeep Gogna y, Bo Chang , Nattaya Damkham , Jai Pinkney , Lillian F. Hyde 1, Lisa Stone 1 , Jürgen K. Naggert 1 , Patsy M. Nishina 1,* and Mark P. Krebs 1,* 1 The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA; [email protected] (G.B.C.); [email protected] (N.G.); [email protected] (B.C.); [email protected] (N.D.); [email protected] (J.P.); [email protected] (L.F.H.); [email protected] (L.S.); [email protected] (J.K.N.) 2 Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand 3 Siriraj Center of Excellence for Stem Cell Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand * Correspondence: [email protected] (P.M.N.); [email protected] (M.P.K.); Tel.: +1-207-2886-383 (P.M.N.); +1-207-2886-000 (M.P.K.) These authors contributed equally to this work. y Received: 29 February 2020; Accepted: 7 April 2020; Published: 10 April 2020 Abstract: Inherited retinal degeneration (RD) leads to the impairment or loss of vision in millions of individuals worldwide, most frequently due to the loss of photoreceptor (PR) cells. Animal models, particularly the laboratory mouse, have been used to understand the pathogenic mechanisms that underlie PR cell loss and to explore therapies that may prevent, delay, or reverse RD. Here, we reviewed entries in the Mouse Genome Informatics and PubMed databases to compile a comprehensive list of monogenic mouse models in which PR cell loss is demonstrated. -
NIH Public Access Author Manuscript Biochim Biophys Acta
NIH Public Access Author Manuscript Biochim Biophys Acta. Author manuscript; available in PMC 2013 October 01. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: Biochim Biophys Acta. 2012 October ; 1817(10): 1796–1802. doi:10.1016/j.bbabio.2012.04.004. Mitochondrial and Ion Channel Gene Alterations in Autism Moyra Smith1, Pamela L. Flodman1, John J. Gargus1, Mariella T Simon1, Kimberley Verrell1, Richard Haas2, Gail E. Reiner2, Robert Naviaux2, Katherine Osann1, M. Anne Spence1, and Douglas C. Wallace3 Moyra Smith: [email protected]; Pamela L. Flodman: [email protected]; John J. Gargus: [email protected]; Mariella T Simon: [email protected]; Kimberley Verrell: [email protected]; Richard Haas: [email protected]; Gail E. Reiner: [email protected]; Robert Naviaux: [email protected]; Katherine Osann: [email protected]; M. Anne Spence: [email protected]; Douglas C. Wallace: [email protected] 1Dept. of Pediatrics University of California, Irvine 2Mitochondrial Genetics, University of California, San Diego 3Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital Philadelphia and Department of Pathology and Laboratory Medicine, University of Pennsylvania Abstract To evaluate the potential importance in autistic subjects of copy number variants (CNVs) that alter genes of relevance to bioenergetics, ionic metabolism, and synaptic function, we conducted a detailed microarray analysis of 69 autism probands and 35 parents, compared to 89 CEU HapMap controls. This revealed that the frequency CNVs of ≥ 100 kb and CNVs of ≥ 10 Kb were markedly increased in probands over parents and in probands and parents over controls. Evaluation of CNVs ≥ 1 Mb by chromosomal FISH confirmed the molecular identity of a subset of the CNVs, some of which were associated with chromosomal rearrangements. -
Genome-Wide Association Study Identifies Candidate Genes
animals Article Genome-Wide Association Study Identifies Candidate Genes Associated with Feet and Leg Conformation Traits in Chinese Holstein Cattle Ismail Mohamed Abdalla 1, Xubin Lu 1 , Mudasir Nazar 1, Abdelaziz Adam Idriss Arbab 1,2, Tianle Xu 3 , Mohammed Husien Yousif 4, Yongjiang Mao 1 and Zhangping Yang 1,* 1 College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; [email protected] (I.M.A.); [email protected] (X.L.); [email protected] (M.N.); [email protected] (A.A.I.A.); [email protected] (Y.M.) 2 Biomedical Research Institute, Darfur College, Nyala 63313, Sudan 3 Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225009, China; [email protected] 4 Faculty of Animal Production, West Kordufan University, Alnuhud City 12942, Sudan; [email protected] * Correspondence: [email protected]; Tel.: +86-0514-87979269 Simple Summary: Feet and leg problems are among the major reasons for dairy cows leaving the herd, as well as having direct association with production and reproduction efficiency, health (e.g., claw disorders and lameness) and welfare. Hence, understanding the genetic architecture underlying feet and conformation traits in dairy cattle offers new opportunities toward the genetic improvement and long-term selection. Through a genome-wide association study on Chinese Holstein cattle, we identified several candidate genes associated with feet and leg conformation traits. These results could provide useful information about the molecular breeding basis of feet and leg traits, thus Citation: Abdalla, I.M.; Lu, X.; Nazar, improving the longevity and productivity of dairy cattle. -
FLAME: a Web Tool for Functional and Literature Enrichment Analysis of Multiple Gene Lists
bioRxiv preprint doi: https://doi.org/10.1101/2021.06.02.446692; this version posted June 2, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. FLAME: a web tool for functional and literature enrichment analysis of multiple gene lists Foteini Thanati1,†, Evangelos Karatzas1,†, Fotis A. Baltoumas1, Dimitrios J. Stravopodis2, Aristides G. Eliopoulos3,4,5, Georgios A. Pavlopoulos1,4,* 1 Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Athens, Greece 2 Department of Biology, National and Kapodistrian University of Athens, Athens, Greece 3 Department of Biology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece 4 Center for New Biotechnologies and Precision Medicine, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece 5 Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece †Equally contributing authors *To whom correspondence should be addressed. Tel: +30-210-9656310; Fax: +30-210-9653934; Email: [email protected] Present Address: Georgios A. Pavlopoulos, Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", 34 Fleming Street, Vari, 16672, Greece ABSTRACT Functional enrichment is a widely used method for interpreting experimental results by identifying classes of proteins/genes associated with certain biological functions, pathways, diseases or phenotypes. Despite the variety of existing tools, most of them can process a single list per time, thus making a more combinatorial analysis more complicated and prone to errors. In this article, we present FLAME, a web tool for combining multiple lists prior to enrichment analysis.