Mechanisms of Sodium–Glucose Cotransporter 2 Inhibition
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Seq2pathway Vignette
seq2pathway Vignette Bin Wang, Xinan Holly Yang, Arjun Kinstlick May 19, 2021 Contents 1 Abstract 1 2 Package Installation 2 3 runseq2pathway 2 4 Two main functions 3 4.1 seq2gene . .3 4.1.1 seq2gene flowchart . .3 4.1.2 runseq2gene inputs/parameters . .5 4.1.3 runseq2gene outputs . .8 4.2 gene2pathway . 10 4.2.1 gene2pathway flowchart . 11 4.2.2 gene2pathway test inputs/parameters . 11 4.2.3 gene2pathway test outputs . 12 5 Examples 13 5.1 ChIP-seq data analysis . 13 5.1.1 Map ChIP-seq enriched peaks to genes using runseq2gene .................... 13 5.1.2 Discover enriched GO terms using gene2pathway_test with gene scores . 15 5.1.3 Discover enriched GO terms using Fisher's Exact test without gene scores . 17 5.1.4 Add description for genes . 20 5.2 RNA-seq data analysis . 20 6 R environment session 23 1 Abstract Seq2pathway is a novel computational tool to analyze functional gene-sets (including signaling pathways) using variable next-generation sequencing data[1]. Integral to this tool are the \seq2gene" and \gene2pathway" components in series that infer a quantitative pathway-level profile for each sample. The seq2gene function assigns phenotype-associated significance of genomic regions to gene-level scores, where the significance could be p-values of SNPs or point mutations, protein-binding affinity, or transcriptional expression level. The seq2gene function has the feasibility to assign non-exon regions to a range of neighboring genes besides the nearest one, thus facilitating the study of functional non-coding elements[2]. Then the gene2pathway summarizes gene-level measurements to pathway-level scores, comparing the quantity of significance for gene members within a pathway with those outside a pathway. -
Serum Concentrations of Afamin Are Elevated in Patients with Polycystic Ovary Syndrome
AKo¨ ninger et al. Afamin in patients with PCOS 1–7 3:120 Research Open Access Serum concentrations of afamin are elevated in patients with polycystic ovary syndrome Angela Ko¨ ninger, Philippos Edimiris, Laura Koch, Antje Enekwe, Claudia Lamina1, Sabine Kasimir-Bauer, Rainer Kimmig and Hans Dieplinger1,2 Correspondence Department of Gynecology and Obstetrics, University of Duisburg-Essen, D-45122 Essen, Germany should be addressed 1Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, to H Dieplinger Innsbruck Medical University, Scho¨ pfstrasse 41, A-6020 Innsbruck, Austria Email 2Vitateq Biotechnology GmbH, A-6020 Innsbruck, Austria [email protected] Abstract Oxidative stress seems to be present in patients with polycystic ovary syndrome (PCOS). Key Words The aim of this study was to evaluate the correlation between characteristics of PCOS and " vitamin E-binding protein serum concentrations of afamin, a novel binding protein for the antioxidant vitamin E. " afamin A total of 85 patients with PCOS and 76 control subjects were investigated in a pilot cross- " polycystic ovary syndrome sectional study design between 2009 and 2013 in the University Hospital of Essen, Germany. " oxidative stress Patients with PCOS were diagnosed according to the Rotterdam ESHRE/ASRM-sponsored " insulin resistance PCOS Consensus Workshop Group. Afamin and diagnostic parameters of PCOS were determined at early follicular phase. Afamin concentrations were significantly higher in Endocrine Connections patients with PCOS than in controls (odds ratio (OR) for a 10 mg/ml increase in afaminZ1.3, 95% CIZ1.08–1.58). This difference vanished in a model adjusting for age, BMI, free testosterone index (FTI), and sex hormone-binding globulin (SHBG) (ORZ1.05, 95% CIZ0.80–1.38). -
Transcriptomic Signature and Metabolic Programming of Bovine Classical and Nonclassical Monocytes Indicate Distinct Functional Specializations
bioRxiv preprint doi: https://doi.org/10.1101/2020.10.30.362731; this version posted November 1, 2020. 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. Transcriptomic signature and metabolic programming of bovine classical and nonclassical monocytes indicate distinct functional specializations Stephanie C. Talker1,2, G. Tuba Barut1,2, Reto Rufener3, Lilly von Münchow4, Artur Summerfield1,2 1Institute of Virology and Immunology, Bern and Mittelhäusern, Switzerland 2Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland 3Institute of Parasitology, Vetsuisse Faculty, University of Bern, Bern, Switzerland 4 Bucher Biotec AG, Basel, Switzerland *Correspondence: Corresponding Author [email protected] Keywords: monocyte subsets, transcriptome, metabolism, cattle Abstract Similar to human monocytes, bovine monocytes can be split into CD14+CD16- classical and CD14-CD16+ nonclassical monocytes (cM and ncM, respectively). Here, we present an in-depth analysis of their steady-state transcriptomes, highlighting pronounced functional specializations. Gene transcription indicates that pro-inflammatory and antibacterial processes are associated with cM, while ncM appear to be specialized in regulatory/anti-inflammatory functions and tissue repair, as well as antiviral responses and T-cell immunomodulation. In support of these functional differences, we found that oxidative phosphorylation prevails in ncM, whereas cM are clearly biased towards aerobic glycolysis. Furthermore, bovine monocyte subsets differed in their responsiveness to TLR ligands, supporting an antiviral role of ncM. Taken together, these data clearly indicate a variety of subset-specific functions in cM and ncM that are likely to be transferable to monocyte subsets of other species, including humans. -
Antisense Afp Transcripts in Mouse Liver and Their Potential Role in Afp Gene Regulation
University of Kentucky UKnowledge Theses and Dissertations--Microbiology, Microbiology, Immunology, and Molecular Immunology, and Molecular Genetics Genetics 2017 ANTISENSE AFP TRANSCRIPTS IN MOUSE LIVER AND THEIR POTENTIAL ROLE IN AFP GENE REGULATION Maria S. Dixon University of Kentucky, [email protected] Digital Object Identifier: https://doi.org/10.13023/ETD.2017.356 Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Dixon, Maria S., "ANTISENSE AFP TRANSCRIPTS IN MOUSE LIVER AND THEIR POTENTIAL ROLE IN AFP GENE REGULATION" (2017). Theses and Dissertations--Microbiology, Immunology, and Molecular Genetics. 14. https://uknowledge.uky.edu/microbio_etds/14 This Doctoral Dissertation is brought to you for free and open access by the Microbiology, Immunology, and Molecular Genetics at UKnowledge. It has been accepted for inclusion in Theses and Dissertations--Microbiology, Immunology, and Molecular Genetics by an authorized administrator of UKnowledge. For more information, please contact [email protected]. STUDENT AGREEMENT: I represent that my thesis or dissertation and abstract are my original work. Proper attribution has been given to all outside sources. I understand that I am solely responsible for obtaining any needed copyright permissions. I have obtained needed written permission statement(s) from the owner(s) of each third-party copyrighted matter to be included in my work, allowing electronic distribution (if such use is not permitted by the fair use doctrine) which will be submitted to UKnowledge as Additional File. I hereby grant to The University of Kentucky and its agents the irrevocable, non-exclusive, and royalty-free license to archive and make accessible my work in whole or in part in all forms of media, now or hereafter known. -
In Silico Prediction and in Vitro Characterization of Multifunctional Human Rnase3
Hindawi Publishing Corporation BioMed Research International Volume 2013, Article ID 170398, 12 pages http://dx.doi.org/10.1155/2013/170398 Research Article In Silico Prediction and In Vitro Characterization of Multifunctional Human RNase3 Pei-Chun Lien,1 Ping-Hsueh Kuo,1 Chien-Jung Chen,1 Hsiu-Hui Chang,1 Shun-lung Fang,1 Wei-Shuo Wu,2 Yiu-Kay Lai,2 Tun-Wen Pai,3 and Margaret Dah-Tsyr Chang1, 4 1 InstituteofMolecularandCellularBiology,NationalTsingHuaUniversity,No.101,Section2,KuangFuRoad, Hsinchu 30013, Taiwan 2 Institute of Biotechnology, National Tsing Hua University, No. 101, Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan 3 Department of Computer Science and Engineering, National Taiwan Ocean University, 2 Pei Ning Road, Keelung 20224, Taiwan 4 Department of Medical Science, National Tsing Hua University, No. 101, Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan Correspondence should be addressed to Margaret Dah-Tsyr Chang; [email protected] Received 31 October 2012; Accepted 2 December 2012 Academic Editor: Hao-Teng Chang Copyright © 2013 Pei-Chun Lien et al. is 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. Human ribonucleases A (hRNaseA) superfamily consists of thirteen members with high-structure similarities but exhibits divergent physiological functions other than RNase activity. Evolution of hRNaseA superfamily has gained novel functions which may be preserved in a unique region or domain to account for additional molecular interactions. hRNase3 has multiple functions including ribonucleolytic, heparan sulfate (HS) binding, cellular binding, endocytic, lipid destabilization, cytotoxic, and antimicrobial activities. -
Anti-CST2 / Cystatin SA Antibody (ARG59583)
Product datasheet [email protected] ARG59583 Package: 100 μl anti-CST2 / Cystatin SA antibody Store at: -20°C Summary Product Description Rabbit Polyclonal antibody recognizes CST2 / Cystatin SA Tested Reactivity Ms Tested Application WB Host Rabbit Clonality Polyclonal Isotype IgG Target Name CST2 / Cystatin SA Antigen Species Human Immunogen Recombinant fusion protein corresponding to aa. 20-141 of Human CST2 (NP_001313.1). Conjugation Un-conjugated Alternate Names Cystatin-2; Cystatin-SA; Cystatin-S5 Application Instructions Application table Application Dilution WB 1:500 - 1:2000 Application Note * The dilutions indicate recommended starting dilutions and the optimal dilutions or concentrations should be determined by the scientist. Positive Control Mouse heart Calculated Mw 16 kDa Observed Size 16 kDa Properties Form Liquid Purification Affinity purified. Buffer PBS (pH 7.3), 0.02% Sodium azide and 50% Glycerol. Preservative 0.02% Sodium azide Stabilizer 50% Glycerol Storage instruction For continuous use, store undiluted antibody at 2-8°C for up to a week. For long-term storage, aliquot and store at -20°C. Storage in frost free freezers is not recommended. Avoid repeated freeze/thaw cycles. Suggest spin the vial prior to opening. The antibody solution should be gently mixed before use. Note For laboratory research only, not for drug, diagnostic or other use. www.arigobio.com 1/2 Bioinformation Gene Symbol CST2 Gene Full Name cystatin SA Background The cystatin superfamily encompasses proteins that contain multiple cystatin-like sequences. Some of the members are active cysteine protease inhibitors, while others have lost or perhaps never acquired this inhibitory activity. There are three inhibitory families in the superfamily, including the type 1 cystatins (stefins), type 2 cystatins and the kininogens. -
Entrez Exercises
1 NCBI Exercises 1/12/2007 Entrez Exercises Global Query: Controlled Vocabularies and Limits Type the word “cancer” in the search box on the NCBI homepage and run the search. This query returns results in all of the Entrez databases. However the query is interpreted differently in different databases. PubMed Retrieve the result for the PubMed database. Click the “Details” tab to see how the query was interpreted in this database. Notice that the term cancer was translated to the Medical Subject Heading (MeSH) term “neoplasms” ("neoplasms"[MeSH Terms]). 2 NCBI Exercises 1/12/2007 MeSH is a controlled vocabulary that is used to index all articles in PubMed. In the details box, edit the query to remove the portion that searched for cancer as a text word and run the search. Notice that the number of articles retrieved has changed. These will be a more relevant set of results. You can force the PubMed engine to only search the MeSH vocabulary or specify any other indexed field through the “Limits” tab. Use the Web browser’s back button to return to the Global query page and retrieve the PubMed results again. Now click on the “Limits” tab. Select “MeSH terms” from the first drop-down menu, the one headed by “All Fields”. Now run the search with the limit in place and check the “Details” tab to verify that only the MeSH term translation was used. Nucleotide Use the Web browser’s back button to return to the Global query page. Retrieve the results for the nucleotide database. 3 NCBI Exercises 1/12/2007 The Nucleotide database in the Global query is now three separate databases. -
Collapse of the Hepatic Gene Regulatory Network in the Absence of Foxa Factors
bioRxiv preprint doi: https://doi.org/10.1101/2020.03.31.016006; this version posted April 1, 2020. 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. Collapse of the hepatic gene regulatory network in the absence of FoxA factors Yitzhak Reizel1, Ashleigh Morgan1, Long Gao1, Yemin Lan2, Elisabetta Manduchi3, Eric L. Waite1, Amber W. Wang1, Andrew Wells4, and Klaus H. Kaestner1* 1Department of Genetics, University of Pennsylvania, Philadelphia, PA 2Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 3Department of Biostatistics, Epidemiology & Informatics, University of Pennsylvania, Philadelphia, PA 4Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA *Correspondence to: Klaus H Kaestner at [email protected] Phone: 215-898-8759 Fax: 215-573-5892 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.03.31.016006; this version posted April 1, 2020. 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 The FoxA transcription factors are critical for liver development through their pioneering activity, which initiates a highly complex regulatory network thought to become progressively resistant to the loss of any individual hepatic transcription factor via mutual redundancy. To investigate the dispensability of FoxA factors for maintaining this regulatory network, we ablated all FoxA genes in the adult mouse liver. Remarkably, loss of FoxA caused rapid hepatocyte dedifferentiation manifested by a massive reduction in the expression of key liver genes. Interestingly, expression of these genes was reduced back to the low levels of the fetal prehepatic endoderm stage, leading to necrosis and lethality within days. -
Page 1 of 76 Diabetes Diabetes Publish Ahead of Print, Published Online September 14, 2020
Page 1 of 76 Diabetes Peters, Annette; Helmholtz Center Munich German Research Center for Environmental Health, Epidemiology Institute Waldenberger, Melanie; Helmholtz Center Munich German Research Center for Environmental Health, Molecular Epidemiology Diabetes Publish Ahead of Print, published online September 14, 2020 Diabetes Page 2 of 76 Deciphering the Plasma Proteome of Type 2 Diabetes Mohamed A. Elhadad1,2,3 MSc., Christian Jonasson4,5 PhD, Cornelia Huth2,6 PhD, Rory Wilson1,2 MSc, Christian Gieger1,2,6 PhD, Pamela Matias1,2,3 MSc, Harald Grallert1,2,6 PhD, Johannes Graumann7,8 PhD, Valerie Gailus-Durner9 PhD, Wolfgang Rathmann6,10 MD, Christine von Toerne11 PhD, Stefanie M. Hauck11 PhD, Wolfgang Koenig3,12,13 MD, FRCP, FESC, FACC, FAHA, Moritz F. Sinner3,14 MD, MPH, Tudor I Oprea15,16,17 MD, PhD, Karsten Suhre18 PhD, Barbara Thorand2,6 PhD, Kristian Hveem4,5 PhD, Annette Peters2,3,6,19 PhD, Melanie Waldenberger1,2,3 PhD 1. Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany. 2. Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany 3. German Research Center for Cardiovascular Disease (DZHK), Partner site Munich Heart Alliance, Germany 4. K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health, NTNU - Norwegian University of Science and Technology, Trondheim, Norway 5. HUNT Research Center, Department of Public Health, NTNU - Norwegian University of Science and Technology, Levanger, Norway 6. German Center for Diabetes Research (DZD), München-Neuherberg, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany 7. Biomolecular Mass Spectrometry, Max Planck Institute for Heart and Lung Research, Ludwigstrasse 43, Bad Nauheim 61231, Germany 8. -
Role and Regulation of the P53-Homolog P73 in the Transformation of Normal Human Fibroblasts
Role and regulation of the p53-homolog p73 in the transformation of normal human fibroblasts Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades der Bayerischen Julius-Maximilians-Universität Würzburg vorgelegt von Lars Hofmann aus Aschaffenburg Würzburg 2007 Eingereicht am Mitglieder der Promotionskommission: Vorsitzender: Prof. Dr. Dr. Martin J. Müller Gutachter: Prof. Dr. Michael P. Schön Gutachter : Prof. Dr. Georg Krohne Tag des Promotionskolloquiums: Doktorurkunde ausgehändigt am Erklärung Hiermit erkläre ich, dass ich die vorliegende Arbeit selbständig angefertigt und keine anderen als die angegebenen Hilfsmittel und Quellen verwendet habe. Diese Arbeit wurde weder in gleicher noch in ähnlicher Form in einem anderen Prüfungsverfahren vorgelegt. Ich habe früher, außer den mit dem Zulassungsgesuch urkundlichen Graden, keine weiteren akademischen Grade erworben und zu erwerben gesucht. Würzburg, Lars Hofmann Content SUMMARY ................................................................................................................ IV ZUSAMMENFASSUNG ............................................................................................. V 1. INTRODUCTION ................................................................................................. 1 1.1. Molecular basics of cancer .......................................................................................... 1 1.2. Early research on tumorigenesis ................................................................................. 3 1.3. Developing -
Functional Specialization of Human Salivary Glands and Origins of Proteins Intrinsic to Human Saliva
UCSF UC San Francisco Previously Published Works Title Functional Specialization of Human Salivary Glands and Origins of Proteins Intrinsic to Human Saliva. Permalink https://escholarship.org/uc/item/95h5g8mq Journal Cell reports, 33(7) ISSN 2211-1247 Authors Saitou, Marie Gaylord, Eliza A Xu, Erica et al. Publication Date 2020-11-01 DOI 10.1016/j.celrep.2020.108402 Peer reviewed eScholarship.org Powered by the California Digital Library University of California HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Cell Rep Manuscript Author . Author manuscript; Manuscript Author available in PMC 2020 November 30. Published in final edited form as: Cell Rep. 2020 November 17; 33(7): 108402. doi:10.1016/j.celrep.2020.108402. Functional Specialization of Human Salivary Glands and Origins of Proteins Intrinsic to Human Saliva Marie Saitou1,2,3, Eliza A. Gaylord4, Erica Xu1,7, Alison J. May4, Lubov Neznanova5, Sara Nathan4, Anissa Grawe4, Jolie Chang6, William Ryan6, Stefan Ruhl5,*, Sarah M. Knox4,*, Omer Gokcumen1,8,* 1Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY, U.S.A 2Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, U.S.A 3Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Viken, Norway 4Program in Craniofacial Biology, Department of Cell and Tissue Biology, School of Dentistry, University of California, San Francisco, CA, U.S.A 5Department of Oral Biology, School of Dental Medicine, University at Buffalo, The State University of New York, Buffalo, NY, U.S.A 6Department of Otolaryngology, School of Medicine, University of California, San Francisco, CA, U.S.A 7Present address: Weill-Cornell Medical College, Physiology and Biophysics Department 8Lead Contact SUMMARY Salivary proteins are essential for maintaining health in the oral cavity and proximal digestive tract, and they serve as potential diagnostic markers for monitoring human health and disease. -
Unveiling the Multifaceted Antimicrobial Mechanism of Action of Human Host Defence Rnases
ADVERTIMENT. Lʼaccés als continguts dʼaquesta tesi queda condicionat a lʼacceptació de les condicions dʼús establertes per la següent llicència Creative Commons: http://cat.creativecommons.org/?page_id=184 ADVERTENCIA. El acceso a los contenidos de esta tesis queda condicionado a la aceptación de las condiciones de uso establecidas por la siguiente licencia Creative Commons: http://es.creativecommons.org/blog/licencias/ WARNING. The access to the contents of this doctoral thesis it is limited to the acceptance of the use conditions set by the following Creative Commons license: https://creativecommons.org/licenses/?lang=en Departament de Bioquímica, Biología Molecular i Biomedicina Unveiling the multifaceted antimicrobial mechanism of action of human host defence RNases Tesis presentada por Javier Arranz Trullén para optar al grado de Doctor en Bioquímica, Biología Molecular y Biomedicina bajo la dirección de la Dra. Ester Boix Borràs y el Dr. David Pulido Gómez Unitat de Biociències del Departament de Bioquímica i Biología Molecular. Universitat Autònoma de Barcelona Dra. Ester Boix Borràs Dr. David Pulido Gómez Javier Arranz Trullén Campus de Bellaterra, Septiembre 2016 1 2 Biochemistry, Molecular Biology and Biomedicine Department Unveiling the multifaceted antimicrobial mechanism of action of human host defence RNases Thesis presented by Javier Arranz Trullén to obtain the PhD in Biochemistry, Molecular Biology and Biomedicine directed by Dr. Ester Boix Borràs and Dr. David Pulido Gómez Biosciences Unit of the Biochemistry and Molecular