Characterization and Functions of Beta Defensins in the Epididymis
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Bioinformatics Analysis and Identi Cation of Potential Biomarkers In
Bioinformatics Analysis and Identication of Potential Biomarkers in Gastric Cancer Jingdi Yang Nanchang University - Donghu Campus Bo Peng Nanchang University - Donghu Campus Xianzheng Qin Nanchang University Medical College: Medical College of Nanchang University Tian Zhou ( [email protected] ) Nanchang University Research Keywords: gastric cancer, differentially expressed genes, microarray, Kaplan-Meier analysis, COL1A1, BGN Posted Date: November 20th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-111288/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/24 Abstract Background: Although the morbidity and mortality of gastric cancer are declining, gastric cancer is still one of the most common causes of death. Early detection of gastric cancer is of great help to improve the survival rate, but the existing biomarkers are not sensitive to diagnose early gastric cancer. The aim of this study is to identify the novel biomarkers for gastric cancer. Methods: Three gene expression proles (GSE27342, GSE63089, GSE33335) were downloaded from Gene Expression Omnibus database to select differentially expressed genes. Then, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis were performed to explore the biological functions of differentially expressed genes. Cytoscape was utilized to construct protein-protein interaction network and hub genes were analyzed by plugin cytoHubba of Cytoscape. Furthermore, Gene Expression Proling Interactive Analysis and Kaplan-Meier plotter were used to verify the identied hub genes. Results: 35 overlapping differentially expressed genes were screened from gene expression datasets, which consisted of 11 up-regulated genes and 24 down-regulated genes. Gene Ontology functional enrichment analysis revealed that differentially expressed genes were signicantly enriched in digestion, regulation of biological quality, response to hormone and steroid hormone, and homeostatic process. -
S41467-020-16223-7.Pdf
ARTICLE https://doi.org/10.1038/s41467-020-16223-7 OPEN Trefoil factors share a lectin activity that defines their role in mucus Michael A. Järvå 1,2, James P. Lingford1,2, Alan John1,2, Niccolay Madiedo Soler1,2, Nichollas E. Scott 3 & ✉ Ethan D. Goddard-Borger 1,2 The mucosal epithelium secretes a host of protective disulfide-rich peptides, including the trefoil factors (TFFs). The TFFs increase the viscoelasticity of the mucosa and promote cell 1234567890():,; migration, though the molecular mechanisms underlying these functions have remained poorly defined. Here, we demonstrate that all TFFs are divalent lectins that recognise the GlcNAc-α-1,4-Gal disaccharide, which terminates some mucin-like O-glycans. Degradation of this disaccharide by a glycoside hydrolase abrogates TFF binding to mucins. Structural, mutagenic and biophysical data provide insights into how the TFFs recognise this dis- accharide and rationalise their ability to modulate the physical properties of mucus across different pH ranges. These data reveal that TFF activity is dependent on the glycosylation state of mucosal glycoproteins and alludes to a lectin function for trefoil domains in other human proteins. 1 The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia. 2 Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia. 3 Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, ✉ Parkville, VIC 3010, Australia. email: [email protected] NATURE COMMUNICATIONS | (2020) 11:2265 | https://doi.org/10.1038/s41467-020-16223-7 | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-020-16223-7 he three human TFFs (TFF1, TFF2, and TFF3)1 are ubi- considering the glycosylation state of mucosal proteins when Tquitous in mucosal environments. -
Role of Amylase in Ovarian Cancer Mai Mohamed University of South Florida, [email protected]
University of South Florida Scholar Commons Graduate Theses and Dissertations Graduate School July 2017 Role of Amylase in Ovarian Cancer Mai Mohamed University of South Florida, [email protected] Follow this and additional works at: http://scholarcommons.usf.edu/etd Part of the Pathology Commons Scholar Commons Citation Mohamed, Mai, "Role of Amylase in Ovarian Cancer" (2017). Graduate Theses and Dissertations. http://scholarcommons.usf.edu/etd/6907 This Dissertation is brought to you for free and open access by the Graduate School at Scholar Commons. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. Role of Amylase in Ovarian Cancer by Mai Mohamed A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Pathology and Cell Biology Morsani College of Medicine University of South Florida Major Professor: Patricia Kruk, Ph.D. Paula C. Bickford, Ph.D. Meera Nanjundan, Ph.D. Marzenna Wiranowska, Ph.D. Lauri Wright, Ph.D. Date of Approval: June 29, 2017 Keywords: ovarian cancer, amylase, computational analyses, glycocalyx, cellular invasion Copyright © 2017, Mai Mohamed Dedication This dissertation is dedicated to my parents, Ahmed and Fatma, who have always stressed the importance of education, and, throughout my education, have been my strongest source of encouragement and support. They always believed in me and I am eternally grateful to them. I would also like to thank my brothers, Mohamed and Hussien, and my sister, Mariam. I would also like to thank my husband, Ahmed. -
Analysis of Chromatin Structure Indicates a Role for Fluoxetine in Altering Nucleosome Distribution Ely Gracia
Florida State University Libraries Honors Theses The Division of Undergraduate Studies 2012 Analysis of Chromatin Structure Indicates a Role for Fluoxetine in Altering Nucleosome Distribution Ely Gracia Follow this and additional works at the FSU Digital Library. For more information, please contact [email protected] THE FLORIDA STATE UNIVERSITY COLLEGE OF ARTS & SCIENCES ANALYSIS OF CHROMATIN STRUCTURE INDICATES A ROLE FOR FLUOXETINE IN ALTERING NUCLEOSOME DISTRIBUTION By: ELY GRACIA A Thesis submitted to the Department of Biological Sciences in partial fulfillment of the requirements for graduation with Honors in the Major Degree Awarded: Spring, 2012 1 The members of the Defense Committee approve the thesis of Ely Gracia defended on April 17, 2012. __________________________ Dr. Jonathan H. Dennis Thesis Director __________________________ Dr. Debra A. Fadool Committee Member __________________________ Dr. Joab Corey Outside Committee Member 2 Dedication: To my mother and father for all their love and support. To Nicole Cordero for always believing in me and pushing me to meet and exceed my potential. To Dr. Jonathan Dennis for allowing me the opportunity to challenge myself. 3 Abstract An interesting stimulus for chromatin structural changes is the generic and popular anti-depressant drug Fluoxetine, commonly known as Prozac. Generally accepted as a Selective Serotonin Reuptake Inhibitors (SSRI’s), recent work has emerged suggesting that this antidepressant also functions as a Histone Deaceylase Inhibitors (HDIs). Studies have also come out indicating that Fluoxetine acts as an immunosuppressant drug. Treatment with Fluoxetine is believed to reduce the over- activation of the immune system associated with depression. We have used an innovative microarray technology to measure changes in nucleosomal positioning that stem from Fluoxetine treatment. -
Appendix 2. Significantly Differentially Regulated Genes in Term Compared with Second Trimester Amniotic Fluid Supernatant
Appendix 2. Significantly Differentially Regulated Genes in Term Compared With Second Trimester Amniotic Fluid Supernatant Fold Change in term vs second trimester Amniotic Affymetrix Duplicate Fluid Probe ID probes Symbol Entrez Gene Name 1019.9 217059_at D MUC7 mucin 7, secreted 424.5 211735_x_at D SFTPC surfactant protein C 416.2 206835_at STATH statherin 363.4 214387_x_at D SFTPC surfactant protein C 295.5 205982_x_at D SFTPC surfactant protein C 288.7 1553454_at RPTN repetin solute carrier family 34 (sodium 251.3 204124_at SLC34A2 phosphate), member 2 238.9 206786_at HTN3 histatin 3 161.5 220191_at GKN1 gastrokine 1 152.7 223678_s_at D SFTPA2 surfactant protein A2 130.9 207430_s_at D MSMB microseminoprotein, beta- 99.0 214199_at SFTPD surfactant protein D major histocompatibility complex, class II, 96.5 210982_s_at D HLA-DRA DR alpha 96.5 221133_s_at D CLDN18 claudin 18 94.4 238222_at GKN2 gastrokine 2 93.7 1557961_s_at D LOC100127983 uncharacterized LOC100127983 93.1 229584_at LRRK2 leucine-rich repeat kinase 2 HOXD cluster antisense RNA 1 (non- 88.6 242042_s_at D HOXD-AS1 protein coding) 86.0 205569_at LAMP3 lysosomal-associated membrane protein 3 85.4 232698_at BPIFB2 BPI fold containing family B, member 2 84.4 205979_at SCGB2A1 secretoglobin, family 2A, member 1 84.3 230469_at RTKN2 rhotekin 2 82.2 204130_at HSD11B2 hydroxysteroid (11-beta) dehydrogenase 2 81.9 222242_s_at KLK5 kallikrein-related peptidase 5 77.0 237281_at AKAP14 A kinase (PRKA) anchor protein 14 76.7 1553602_at MUCL1 mucin-like 1 76.3 216359_at D MUC7 mucin 7, -
Reproductive Biology and Endocrinology Biomed Central
Reproductive Biology and Endocrinology BioMed Central Research Open Access Identification, cloning and functional characterization of novel beta-defensins in the rat (Rattus norvegicus) Suresh Yenugu1,3, Vishnu Chintalgattu2, Christopher J Wingard2, Yashwanth Radhakrishnan1, Frank S French1 and Susan H Hall*1 Address: 1Laboratories for Reproductive Biology, Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina 27599, USA, 2Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, North Carolina 27834, USA and 3Department of Biochemistry and Molecular Biology, Pondicherry University, Pondicherry, 605014, India Email: Suresh Yenugu - [email protected]; Vishnu Chintalgattu - [email protected]; Christopher J Wingard - [email protected]; Yashwanth Radhakrishnan - [email protected]; Frank S French - [email protected]; Susan H Hall* - [email protected] * Corresponding author Published: 04 February 2006 Received: 23 November 2005 Accepted: 04 February 2006 Reproductive Biology and Endocrinology2006, 4:7 doi:10.1186/1477-7827-4-7 This article is available from: http://www.rbej.com/content/4/1/7 © 2006Yenugu 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: beta-defensins are small cationic peptides that exhibit broad spectrum antimicrobial properties. The majority of beta-defensins identified in humans are predominantly expressed in the male reproductive tract and have roles in non-immunological processes such as sperm maturation and capacitation. Characterization of novel defensins in the male reproductive tract can lead to increased understanding of their dual roles in immunity and sperm maturation. -
Looking for Missing Proteins in the Proteome Of
Looking for Missing Proteins in the Proteome of Human Spermatozoa: An Update Yves Vandenbrouck, Lydie Lane, Christine Carapito, Paula Duek, Karine Rondel, Christophe Bruley, Charlotte Macron, Anne Gonzalez de Peredo, Yohann Coute, Karima Chaoui, et al. To cite this version: Yves Vandenbrouck, Lydie Lane, Christine Carapito, Paula Duek, Karine Rondel, et al.. Looking for Missing Proteins in the Proteome of Human Spermatozoa: An Update. Journal of Proteome Research, American Chemical Society, 2016, 15 (11), pp.3998-4019. 10.1021/acs.jproteome.6b00400. hal-02191502 HAL Id: hal-02191502 https://hal.archives-ouvertes.fr/hal-02191502 Submitted on 19 Mar 2021 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. Journal of Proteome Research 1 2 3 Looking for missing proteins in the proteome of human spermatozoa: an 4 update 5 6 Yves Vandenbrouck1,2,3,#,§, Lydie Lane4,5,#, Christine Carapito6, Paula Duek5, Karine Rondel7, 7 Christophe Bruley1,2,3, Charlotte Macron6, Anne Gonzalez de Peredo8, Yohann Couté1,2,3, 8 Karima Chaoui8, Emmanuelle Com7, Alain Gateau5, AnneMarie Hesse1,2,3, Marlene 9 Marcellin8, Loren Méar7, Emmanuelle MoutonBarbosa8, Thibault Robin9, Odile Burlet- 10 Schiltz8, Sarah Cianferani6, Myriam Ferro1,2,3, Thomas Fréour10,11, Cecilia Lindskog12,Jérôme 11 1,2,3 7,§ 12 Garin , Charles Pineau . -
Chromosome 21 Leading Edge Gene Set
Chromosome 21 Leading Edge Gene Set Genes from chr21q22 that are part of the GSEA leading edge set identifying differences between trisomic and euploid samples. Multiple probe set IDs corresponding to a single gene symbol are combined as part of the GSEA analysis. Gene Symbol Probe Set IDs Gene Title 203865_s_at, 207999_s_at, 209979_at, adenosine deaminase, RNA-specific, B1 ADARB1 234539_at, 234799_at (RED1 homolog rat) UDP-Gal:betaGlcNAc beta 1,3- B3GALT5 206947_at galactosyltransferase, polypeptide 5 BACE2 217867_x_at, 222446_s_at beta-site APP-cleaving enzyme 2 1553227_s_at, 214820_at, 219280_at, 225446_at, 231860_at, 231960_at, bromodomain and WD repeat domain BRWD1 244622_at containing 1 C21orf121 240809_at chromosome 21 open reading frame 121 C21orf130 240068_at chromosome 21 open reading frame 130 C21orf22 1560881_a_at chromosome 21 open reading frame 22 C21orf29 1552570_at, 1555048_at_at, 1555049_at chromosome 21 open reading frame 29 C21orf33 202217_at, 210667_s_at chromosome 21 open reading frame 33 C21orf45 219004_s_at, 228597_at, 229671_s_at chromosome 21 open reading frame 45 C21orf51 1554430_at, 1554432_x_at, 228239_at chromosome 21 open reading frame 51 C21orf56 223360_at chromosome 21 open reading frame 56 C21orf59 218123_at, 244369_at chromosome 21 open reading frame 59 C21orf66 1555125_at, 218515_at, 221158_at chromosome 21 open reading frame 66 C21orf7 221211_s_at chromosome 21 open reading frame 7 C21orf77 220826_at chromosome 21 open reading frame 77 C21orf84 239968_at, 240589_at chromosome 21 open reading frame 84 -
Understanding the Role of Transforming Growth Factor Beta Signalling and Epigenomics in Osteoarthritis
Understanding the role of Transforming Growth Factor Beta signalling and Epigenomics in Osteoarthritis by ©Erfan Aref-Eshghi A thesis submitted to the School of Graduate Studies In partial fulfilment of the requirements for the degree of Doctor of Philosophy in Medicine - Human Genetics Discipline of Genetics, Faculty of Medicine Memorial University of Newfoundland St. John’s, Newfoundland and Labrador, Canada May 2016 i Abstract Osteoarthritis (OA) is the most common form of arthritis with a high socioeconomic burden, with an incompletely understood etiology. Evidence suggests a role for the transforming growth factor beta (TGF-ß) signalling pathway and epigenomics in OA. The aim of this thesis was to understand the involvement of the TGF-ß pathway in OA and to determine the DNA methylation patterns of OA-affected cartilage as compared to the OA-free cartilage. First, I found that a common SNP in the BMP2 gene, a ligand in the Bone morphogenetic protein (BMP) subunit of TGF-ß pathway, was associated with OA in the Newfoundland population. I also showed a genetic association between SMAD3 - a signal transducer in the TGF-ß subunit of the TGF-ß signalling pathway - and the total radiographic burden of OA. I further demonstrated that SMAD3 is over-expressed in OA cartilage, suggesting an over activation of the TGF-ß signalling in OA. Next, I examined the connection of these genes in the regulation of matrix metallopeptidase 13 (MMP13) - an enzyme known to destroy extracellular matrix in OA cartilage - in the context of the TGF-ß signalling. The analyses showed that TGF-ß, MMP13, and SMAD3 were overexpressed in OA cartilage, whereas the expression of BMP2 was significantly reduced. -
Trefoil Factor Family (TFF) Peptides and Their Diverse Molecular Functions in Mucus Barrier Protection and More: Changing the Paradigm
International Journal of Molecular Sciences Review Trefoil Factor Family (TFF) Peptides and Their Diverse Molecular Functions in Mucus Barrier Protection and More: Changing the Paradigm Werner Hoffmann Institute ofReview Molecular Biology and Medicinal Chemistry, Otto-von-Guericke University Magdeburg, LeipzigerT Str.refoil 44, 39120 Factor Magdeburg, Family Germany; (TFF werner.ho) Peptidesff[email protected] and Their Received:Diverse 19 May 2020; Molecular Accepted: 19 June Functions 2020; Published: in 25 JuneMucus 2020 Barrier Abstract:ProtectionTrefoil factor family and peptidesMore: (TFF1,Chang TFF2,ing TFF3) the are Paradigm typically co-secreted together with mucins. Tff1 represents a gastric tumor suppressor gene in mice. TFFs are also synthesized in minute Werner Hoffmann amounts in the immune and central nervous systems. In mucous epithelia, they support rapid repair byInstitute enhancing of Molecul cellar migrationBiology and Medicinal (“restitution”) Chemistry, Otto via-von their-Guericke weak University chemotactic Magdeburg and, anti-apoptotic Leipziger Str. 44, 39120 Magdeburg, Germany; [email protected] effects. For a long time, as a paradigm, this was considered as their major biological function. Within Received: 19 May 2020; Accepted: 19 June; Published: 25 June 2020 recent years, the formation of disulfide-linked heterodimers was documented for TFF1 and TFF3, e.g., withAbstract: gastrokine-2 Trefoil andfactor IgGfamily Fc peptides binding (TFF1, protein TFF2, TFF3) (FCGBP). are typically Furthermore, co-secreted lectintogether activities with were recognizedmucins as enabling. Tff1 represents binding a gastric to atumor lipopolysaccharide suppressor gene in mice of .Helicobacter TFFs are also synthesized pylori (TFF1, in minute TFF3) or to a amounts in the immune and central nervous systems. -
TFF2, a MUC6-Binding Lectin Stabilizing the Gastric Mucus Barrier and More (Review)
806 INTERNATIONAL JOURNAL OF ONCOLOGY 47: 806-816, 2015 TFF2, a MUC6-binding lectin stabilizing the gastric mucus barrier and more (Review) WERNER HOFFMANN Institute of Molecular Biology and Medicinal Chemistry, Otto-von-Guericke-University Magdeburg, D-39120 Magdeburg, Germany Received June 16, 2015; Accepted July 7, 2015 DOI: 10.3892/ijo.2015.3090 Abstract. The peptide TFF2 (formerly ‘spasmolytic polypep- Contents tide’), a member of the trefoil factor family (TFF) containing two TFF domains, is mainly expressed together with the mucin 1. Introduction MUC6 in the gastric epithelium and duodenal Brunner's glands. 2. TFF2 and its function in the gastric mucus barrier Pathologically, TFF2 expression is observed ectopically during 3. Conclusions and future perspectives stone diseases, chronic inflammatory conditions and in several metaplastic and neoplastic epithelia; most prominent being the ‘spasmolytic polypeptide-expressing metaplasia’ (SPEM), 1. Introduction which is an established gastric precancerous lesion. TFF2 plays a critical role in maintaining gastric mucosal integrity Mucous epithelia cover the inner surfaces of our body and are and appears to restrain tumorigenesis in the stomach. Recently, essential for interaction with the outside world (e.g., respira- porcine TFF2 has been shown to interact with the gastric tion, uptake and digestion of food, excretion, reproduction, mucin MUC6 and thus stabilize the gastric mucus barrier. visual and auditory systems). These delicate epithelia are On the one hand, TFF2 binds to MUC6 via non-covalent exposed to a myriad of noxious agents and thus rely on multiple lectin interactions with the glycotope GlcNAcα1→4Galβ1→R. mucosal protection and defense mechanisms (1), including On the other hand, TFF2 is probably also covalently bound the: i) mucosal barrier (i.e., the extracellular mucous gel, the to MUC6 via disulfide bridges. -
Single-Cell Transcriptomes Reveal a Complex Cellular Landscape in the Middle Ear and Differential Capacities for Acute Response to Infection
fgene-11-00358 April 9, 2020 Time: 15:55 # 1 ORIGINAL RESEARCH published: 15 April 2020 doi: 10.3389/fgene.2020.00358 Single-Cell Transcriptomes Reveal a Complex Cellular Landscape in the Middle Ear and Differential Capacities for Acute Response to Infection Allen F. Ryan1*, Chanond A. Nasamran2, Kwang Pak1, Clara Draf1, Kathleen M. Fisch2, Nicholas Webster3 and Arwa Kurabi1 1 Departments of Surgery/Otolaryngology, UC San Diego School of Medicine, VA Medical Center, La Jolla, CA, United States, 2 Medicine/Center for Computational Biology & Bioinformatics, UC San Diego School of Medicine, VA Medical Center, La Jolla, CA, United States, 3 Medicine/Endocrinology, UC San Diego School of Medicine, VA Medical Center, La Jolla, CA, United States Single-cell transcriptomics was used to profile cells of the normal murine middle ear. Clustering analysis of 6770 transcriptomes identified 17 cell clusters corresponding to distinct cell types: five epithelial, three stromal, three lymphocyte, two monocyte, Edited by: two endothelial, one pericyte and one melanocyte cluster. Within some clusters, Amélie Bonnefond, Institut National de la Santé et de la cell subtypes were identified. While many corresponded to those cell types known Recherche Médicale (INSERM), from prior studies, several novel types or subtypes were noted. The results indicate France unexpected cellular diversity within the resting middle ear mucosa. The resolution of Reviewed by: Fabien Delahaye, uncomplicated, acute, otitis media is too rapid for cognate immunity to play a major Institut Pasteur de Lille, France role. Thus innate immunity is likely responsible for normal recovery from middle ear Nelson L. S. Tang, infection. The need for rapid response to pathogens suggests that innate immune The Chinese University of Hong Kong, China genes may be constitutively expressed by middle ear cells.