Cells Epithelial Microbiota-Dependent DNA Methylation in Colonic Regulation of Gene Expression Through
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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. -
Enteric Alpha Defensins in Norm and Pathology Nikolai a Lisitsyn1*, Yulia a Bukurova1, Inna G Nikitina1, George S Krasnov1, Yuri Sykulev2 and Sergey F Beresten1
Lisitsyn et al. Annals of Clinical Microbiology and Antimicrobials 2012, 11:1 http://www.ann-clinmicrob.com/content/11/1/1 REVIEW Open Access Enteric alpha defensins in norm and pathology Nikolai A Lisitsyn1*, Yulia A Bukurova1, Inna G Nikitina1, George S Krasnov1, Yuri Sykulev2 and Sergey F Beresten1 Abstract Microbes living in the mammalian gut exist in constant contact with immunity system that prevents infection and maintains homeostasis. Enteric alpha defensins play an important role in regulation of bacterial colonization of the gut, as well as in activation of pro- and anti-inflammatory responses of the adaptive immune system cells in lamina propria. This review summarizes currently available data on functions of mammalian enteric alpha defensins in the immune defense and changes in their secretion in intestinal inflammatory diseases and cancer. Keywords: Enteric alpha defensins, Paneth cells, innate immunity, IBD, colon cancer Introduction hydrophobic structure with a positively charged hydro- Defensins are short, cysteine-rich, cationic peptides philic part) is essential for the insertion into the micro- found in vertebrates, invertebrates and plants, which bial membrane and the formation of a pore leading to play an important role in innate immunity against bac- membrane permeabilization and lysis of the microbe teria, fungi, protozoa, and viruses [1]. Mammalian [10]. Initial recognition of numerous microbial targets is defensins are predominantly expressed in epithelial cells a consequence of electrostatic interactions between the of skin, respiratory airways, gastrointestinal and geni- defensins arginine residues and the negatively charged tourinary tracts, which form physical barriers to external phospholipids of the microbial cytoplasmic membrane infectious agents [2,3], and also in leukocytes (mostly [2,5]. -
Identification of Potential Proteases for Abdominal Aortic Aneurysm by Weighted Gene Coexpression Network Analysis
Genome Identification of potential proteases for abdominal aortic aneurysm by weighted gene coexpression network analysis Journal: Genome Manuscript ID gen-2020-0041.R1 Manuscript Type: Article Date Submitted by the 28-Jun-2020 Author: Complete List of Authors: Zhang, Hui; Peking Union Medical College Hospital, Department of Vascular Surgery Yang, Dan; Chinese Academy of Medical Sciences and Peking Union Medical College, Department of Computational Biology and Bioinformatics,Draft Institute of Medicinal Plant Development Chen, Siliang; Peking Union Medical College Hospital, Department of Vascular Surgery Li, Fangda; Peking Union Medical College Hospital, Department of Vascular Surgery Cui, Liqiang; Peking Union Medical College Hospital, Department of Vascular Surgery Liu, Zhili; Peking Union Medical College Hospital, Department of Vascular Surgery Shao, Jiang; Peking Union Medical College Hospital, Department of Vascular Surgery Chen, Yuexin; Peking Union Medical College Hospital, Department of Vascular Surgery Liu, Bao; Peking Union Medical College Hospital, Department of Vascular Surgery Zheng, Yuehong; Peking Union Medical College Hospital, Department of Vascular Surgery Abdominal aortic aneurysm, next-generation sequencing, WGCNA, Keyword: proteases, matrix metalloproteinase Is the invited manuscript for consideration in a Special Not applicable (regular submission) Issue? : https://mc06.manuscriptcentral.com/genome-pubs Page 1 of 35 Genome 1 Identification of potential proteases for abdominal aortic aneurysm by weighted gene 2 coexpression network analysis 3 Short title: WGCNA identifies crucial proteases in AAA 4 5 Hui Zhang1, Dan Yang2, Siliang Chen1, Fangda Li1, Liqiang Cui1, Zhili Liu1, Jiang Shao1, Yuexin 6 Chen1, Bao Liu1, Yuehong Zheng1. 7 1Department of Vascular Surgery, Peking Union Medical College Hospital, Beijing 100730, PR 8 China; 2Department of Computational Biology and Bioinformatics, Institute of Medicinal Plant 9 Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 10 100730, PR China. -
Downloaded from the Protein Data Bank (PDB
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.07.451411; this version posted July 7, 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-ND 4.0 International license. CAT, AGTR2, L-SIGN and DC-SIGN are potential receptors for the entry of SARS-CoV-2 into human cells Dongjie Guo 1, 2, #, Ruifang Guo1, 2, #, Zhaoyang Li 1, 2, Yuyang Zhang 1, 2, Wei Zheng 3, Xiaoqiang Huang 3, Tursunjan Aziz 1, 2, Yang Zhang 3, 4, Lijun Liu 1, 2, * 1 College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning, China 2 Key Laboratory of Data Analytics and Optimization for Smart Industry (Ministry of Education), Northeastern University, Shenyang, Liaoning, China 3 Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA 4 Department of Biological Chemistry, University of Michigan, Ann Arbor, USA * Corresponding author. College of Life and Health Sciences, Northeastern University, Shenyang, 110169, China. E-mail address: [email protected] (L. Liu) # These authors contributed equally to this work. 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.07.07.451411; this version posted July 7, 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-ND 4.0 International license. Abstract Since December 2019, the COVID-19 caused by SARS-CoV-2 has been widely spread all over the world. -
A New Vision of Iga Nephropathy: the Missing Link
International Journal of Molecular Sciences Review A New Vision of IgA Nephropathy: The Missing Link Fabio Sallustio 1,2,* , Claudia Curci 2,3,* , Vincenzo Di Leo 3 , Anna Gallone 2, Francesco Pesce 3 and Loreto Gesualdo 3 1 Interdisciplinary Department of Medicine (DIM), University of Bari “Aldo Moro”, 70124 Bari, Italy 2 Department of Basic Medical Sciences, Neuroscience and Sense Organs, University of Bari “Aldo Moro”, 70124 Bari, Italy; [email protected] 3 Nephrology, Dialysis and Transplantation Unit, DETO, University “Aldo Moro”, 70124 Bari, Italy; [email protected] (V.D.L.); [email protected] (F.P.); [email protected] (L.G.) * Correspondence: [email protected] (F.S.); [email protected] (C.C.) Received: 7 December 2019; Accepted: 24 December 2019; Published: 26 December 2019 Abstract: IgA Nephropathy (IgAN) is a primary glomerulonephritis problem worldwide that develops mainly in the 2nd and 3rd decade of life and reaches end-stage kidney disease after 20 years from the biopsy-proven diagnosis, implying a great socio-economic burden. IgAN may occur in a sporadic or familial form. Studies on familial IgAN have shown that 66% of asymptomatic relatives carry immunological defects such as high IgA serum levels, abnormal spontaneous in vitro production of IgA from peripheral blood mononuclear cells (PBMCs), high serum levels of aberrantly glycosylated IgA1, and an altered PBMC cytokine production profile. Recent findings led us to focus our attention on a new perspective to study the pathogenesis of this disease, and new studies showed the involvement of factors driven by environment, lifestyle or diet that could affect the disease. -
Ontogeny of the Intestinal Circadian Clock and Its Role in the Response to Clostridium Difficile Toxin B
Ontogeny of the intestinal circadian clock and its role in the response to Clostridium difficile toxin B A dissertation submitted to the Graduate School of the University of Cincinnati in partial fulfilment of the requirements for the degree of Doctor of Philosophy In the Department of Pharmacology & Systems Physiology of the College of Medicine by Andrew Rosselot B.S. Biology, Wittenberg University October 2019 Committee Chair: Christian I. Hong Ph.D. Abstract: The endogenous clock of the intestine regulates physiological processes ranging from nutrient absorption to the pathogenic response. The developmental timepoint when the human intestinal clock becomes active is unknown. We investigated intestinal circadian clock ontogeny using in vitro samples that are representative of distinct developmental timepoints. Induced pluripotent stem cells (iPSCs) were differentiated into 3D human intestinal organoids (HIOs) to mimic intestinal embryonic development in vitro. HIOs were then matured beyond their early fetal state via kidney capsule transplantation. Differentiation of iPSCs into HIOs did not activate robust circadian clock activity. Enteroids isolated from kidney capsule matured HIOs possessed a functional circadian clock, similar to adult biopsy derived human intestinal enteroids (bHIEs). Samples were challenged with toxin B (TcdB) from Clostridium difficile to provide functional insights on intestinal clock activity. The necrotic cell death response to TcdB was clock phase- dependent in samples that possessed an active clock and anti-phasic between mouse enteroids and bHIEs. RNA-seq analysis of mouse enteroids and bHIEs showed both possess robust rhythmic gene expression with up to 20% and 8% of their transcriptome oscillating, respectively. The phase and identity of rhythmic genes was however species-dependent. -
Gen-2020-0136.Pdf
Genome Gut microbiome mediated epigenetic regulation of brain disorder and application of machine learning for multi- omics data analysis Journal: Genome Manuscript ID gen-2020-0136.R1 Manuscript Type: Mini Review Date Submitted by the 25-Sep-2020 Author: Complete List of Authors: Kaur, Harpreet; University of North Dakota School of Medicine and Health Sciences, Department of Biomedical Science Singh, Yuvraj; University of Calgary Faculty of Science, Department of Biological SciencesDraft Singh, Surjeet; University of Lethbridge, Department of Neuroscience, Canadian Centre for Behavioural Neuroscience (CCBN) Singh, Raja; University of Alberta, Faculty of Medicine and Dentistry; University of Calgary Cumming School of Medicine Gut-brain axis, epigenetics, neurodegenerative diseases, Machine Keyword: learning, Microbiota Is the invited manuscript for consideration in a Special Genome Biology Issue? : © The Author(s) or their Institution(s) Page 1 of 46 Genome 1 Gut microbiome mediated epigenetic regulation of brain disorder and application of 2 machine learning for multi-omics data analysis 3 4 Harpreet Kaur1*#, Yuvraj Singh2#, Surjeet Singh3, Raja B Singh4,5 5 1Department of Biomedical Sciences, School of Medicine and Health Sciences, University of 6 North Dakota, Grand Forks, ND, USA 7 2Department of Biological Sciences, Faculty of Science, University of Calgary, Alberta, Canada 8 3Department of Neuroscience, Canadian Centre for Behavioural Neuroscience (CCBN), 9 University of Lethbridge, Lethbridge, AB, Canada 10 4Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada 11 5Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada 12 13 # equal contribution 14 15 Draft 16 17 18 19 20 21 *Corresponding author: 22 Harpreet Kaur, PhD 23 Department of Biomedical Sciences 24 School of Medicine and Health Sciences 25 University of North Dakota 26 Grand Forks, ND, 58202, USA. -
Maintenance of Mammary Epithelial Phenotype by Transcription Factor Runx1 Through Mitotic Gene Bookmarking Joshua Rose University of Vermont
University of Vermont ScholarWorks @ UVM Graduate College Dissertations and Theses Dissertations and Theses 2019 Maintenance Of Mammary Epithelial Phenotype By Transcription Factor Runx1 Through Mitotic Gene Bookmarking Joshua Rose University of Vermont Follow this and additional works at: https://scholarworks.uvm.edu/graddis Part of the Biochemistry Commons, and the Genetics and Genomics Commons Recommended Citation Rose, Joshua, "Maintenance Of Mammary Epithelial Phenotype By Transcription Factor Runx1 Through Mitotic Gene Bookmarking" (2019). Graduate College Dissertations and Theses. 998. https://scholarworks.uvm.edu/graddis/998 This Thesis is brought to you for free and open access by the Dissertations and Theses at ScholarWorks @ UVM. It has been accepted for inclusion in Graduate College Dissertations and Theses by an authorized administrator of ScholarWorks @ UVM. For more information, please contact [email protected]. MAINTENANCE OF MAMMARY EPITHELIAL PHENOTYPE BY TRANSCRIPTION FACTOR RUNX1 THROUGH MITOTIC GENE BOOKMARKING A Thesis Presented by Joshua Rose to The Faculty of the Graduate College of The University of Vermont In Partial Fulfillment of the Requirements for the Degree of Master of Science Specializing in Cellular, Molecular, and Biomedical Sciences January, 2019 Defense Date: November 12, 2018 Thesis Examination Committee: Sayyed Kaleem Zaidi, Ph.D., Advisor Gary Stein, Ph.D., Advisor Seth Frietze, Ph.D., Chairperson Janet Stein, Ph.D. Jonathan Gordon, Ph.D. Cynthia J. Forehand, Ph.D. Dean of the Graduate College ABSTRACT Breast cancer arises from a series of acquired mutations that disrupt normal mammary epithelial homeostasis and create multi-potent cancer stem cells that can differentiate into clinically distinct breast cancer subtypes. Despite improved therapies and advances in early detection, breast cancer remains the leading diagnosed cancer in women. -
Severity of Experimental Autoimmune Uveitis Is Reduced by Pretreatment with Live Probiotic Escherichia Coli Nissle 1917
cells Article Severity of Experimental Autoimmune Uveitis Is Reduced by Pretreatment with Live Probiotic Escherichia coli Nissle 1917 Otakar Dusek 1, Alena Fajstova 2, Aneta Klimova 1, Petra Svozilkova 1 , Tomas Hrncir 3 , Miloslav Kverka 2,* , Stepan Coufal 2 , Johan Slemin 2, Helena Tlaskalova-Hogenova 2, John V. Forrester 4,5,6 and Jarmila Heissigerova 1 1 Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 08 Prague, Czech Republic; [email protected] (O.D.); [email protected] (A.K.); [email protected] (P.S.); [email protected] (J.H.) 2 Institute of Microbiology of the Czech Academy of Sciences, v.v.i., 142 20 Prague, Czech Republic; [email protected] (A.F.); [email protected] (S.C.); [email protected] (J.S.); [email protected] (H.T.-H.) 3 Institute of Microbiology of the Czech Academy of Sciences, v.v.i., 549 22 Novy Hradek, Czech Republic; [email protected] 4 Section of Immunology and Infection, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB24 3FX, UK; [email protected] 5 Immunology and Virology Program, Centre for Ophthalmology and Visual Science, The University of Western Australia, Crawley, Western Australia 6009, Australia 6 Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia 6009, Australia * Correspondence: [email protected]; Tel.: +420-24106-2452 Abstract: Non-infectious uveitis is considered an autoimmune disease responsible for a significant burden of blindness in developed countries and recent studies have linked its pathogenesis to dys- regulation of the gut microbiota. -
Targeting Mlst8 in Mtorc2-Dependent Cancers by Laura Chonghae Kim Dissertation Submitted to the Faculty of the Graduate School
Targeting mLST8 in mTORC2-dependent cancers By Laura Chonghae Kim Dissertation Submitted to the Faculty of the Graduate School of Vanderbilt University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in Cancer Biology June 30th, 2020 Nashville, Tennessee Approved: Albert B. Reynolds, Ph.D. (chair) Mark R. Boothby, M.D., Ph.D. Christine M. Lovly, M.D. Ph.D. William P. Tansey, Ph.D. Jin Chen, M.D., Ph.D. (adviser) DEDICATION This dissertation is dedicated to all cancer patients and their loved ones for their strength and courage in the fight against this disease. This is also dedicated to my family (Kalhee and Jenny Kim, Stephanie Kim) for their unwavering love and support. ii ACKNOWLEDGEMENTS Completion of this work would have been impossible without the support of many, and I would like to express my sincere gratitude here. First and foremost, I must thank my mentor, Jin Chen. Her support, mentorship, and high-fives have been invaluable in my development as a scientist, and I plan to continue seeking her guidance even when I am many years beyond graduate school. I would also like to acknowledge my committee members Al Reynolds, Bill Tansey, Mark Boothby, Rebecca Cook, and Christine Lovly, who continuously challenged me and provided scientific guidance. Much of this work stems from their insightful questions, and I am extremely appreciative of the time they put into thinking about my projects. I would also like to thank the past and present members of the Chen Lab: Shan Wang, Deanna Edwards, Wenqiang Song, Dana Brantley-Sieders, Katherine Hastings, Victoria Youngblood, Tammy Sobolik, Yoonha Hwang, Eileen Shiuan, Kalin Wilson, Verra Ngwa, Ashwin Inala, and Chris Rhee. -
Identification of Macrophage Polarization-Related Genes As Biomarkers of Chronic Obstructive Pulmonary Disease Based on Bioinformatics Analyses
Hindawi BioMed Research International Volume 2021, Article ID 9921012, 17 pages https://doi.org/10.1155/2021/9921012 Research Article Identification of Macrophage Polarization-Related Genes as Biomarkers of Chronic Obstructive Pulmonary Disease Based on Bioinformatics Analyses Yalin Zhao , Meihua Li, Yanxia Yang, Tao Wu, Qingyuan Huang, Qinghua Wu, and Chaofeng Ren Respiratory and Critical Care Medicine, Kunming First People’s Hospital, Kunming, Yunnan Province, China Correspondence should be addressed to Yalin Zhao; [email protected] and Chaofeng Ren; [email protected] Received 31 March 2021; Accepted 4 June 2021; Published 21 June 2021 Academic Editor: Nagarajan Raju Copyright © 2021 Yalin Zhao et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Objectives. Chronic obstructive pulmonary disease (COPD) is characterized by lung inflammation and remodeling. Macrophage polarization is associated with inflammation and tissue remodeling, as well as immunity. Therefore, this study attempts to investigate the diagnostic value and regulatory mechanism of macrophage polarization-related genes for COPD by bioinformatics analysis and to provide a new theoretical basis for experimental research. Methods. The raw gene expression profile dataset (GSE124180) was collected from the Gene Expression Omnibus (GEO) database. Next, a weighted gene coexpression network analysis (WGCNA) was conducted to screen macrophage polarization-related genes. The differentially expressed genes (DEGs) between the COPD and normal samples were generated using DESeq2 v3.11 and overlapped with the macrophage polarization-related genes. Moreover, functional annotations of overlapped genes were conducted by Database for Annotation, Visualization and Integrated Discovery (DAVID) Bioinformatics Resource. -
Inflammatory Bowel Disease
INFLAMMATORY BOWEL DISEASE Edited by Imre Szabo INFLAMMATORY BOWEL DISEASE Edited by Imre Szabo Inflammatory Bowel Disease http://dx.doi.org/10.5772/46222 Edited by Imre Szabo Contributors Hyunjo Kim, Rahul Anil Sheth, Michael Gee, Valeriu Surlin, Adrian Saftoiu, Catalin Copaescu, Diehl, Yves-Jacques Schneider, Alina Martirosyan, Madeleine Polet, Alexandra Bazes, Thérèse Sergent, Ladislava Bartosova, Michal Kolorz, Milan Bartos, Katerina Wroblova, Michael Wannemuehler, Albert E. Jergens, Amanda E. Ramer-Tait, Anne-Marie C. Overstreet, Brankica Mijandrusic Sincic, Ana Brajdić Published by InTech Janeza Trdine 9, 51000 Rijeka, Croatia Copyright © 2012 InTech All chapters are Open Access distributed under the Creative Commons Attribution 3.0 license, which allows users to download, copy and build upon published articles even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. After this work has been published by InTech, authors have the right to republish it, in whole or part, in any publication of which they are the author, and to make other personal use of the work. Any republication, referencing or personal use of the work must explicitly identify the original source. Notice Statements and opinions expressed in the chapters are these of the individual contributors and not necessarily those of the editors or publisher. No responsibility is accepted for the accuracy of information contained in the published chapters. The publisher assumes no responsibility for any damage or injury to persons or property arising out of the use of any materials, instructions, methods or ideas contained in the book.