Reduced Insulin Secretion Correlates with Decreased Expression of Exocytotic Genes in Pancreatic Islets from Patients with Type 2 Diabetes
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In Vivo Analysis of Exosome Trafficking and Function in Drosophila Melanogaster
In vivo analysis of exosome trafficking and function in Drosophila melanogaster Senior thesis Presented to The Faculty of the School of Arts and Sciences Brandeis University Undergraduate Program in Biology Professor Avital A. Rodal, PhD, Advisor In partial fulfillment of the requirements for the degree of Bachelor of Science by Anna Yeh May 11, 2016 Copyright by Anna Yeh Committee members Name: _____________________________ Signature: _____________________________ Name: _____________________________ Signature: _____________________________ Name: _____________________________ Signature: _____________________________ 1 Table of Contents 1 Abstract 4 2 Introduction 5 2.1 Exosomes: function and therapeutic applications 6 2.2 Exosome cargo and targeting specificity 6 2.3 Exosomes and the endocytic process 7 2.3.1 Rab proteins play a role in exosome trafficking in the donor cell 7 2.3.2 SNARE machinery is necessary for exosomal trafficking from the donor cell 8 2.3.3 Exosome uptake by the recipient cell 9 2.4 Drosophila as an in vivo model organism to study exosome function and trafficking 10 2.4.1 Physiological function for neuronal exosomes in Drosophila 10 2.4.2 Organismal level of exosome trafficking 11 2.5 Current methods and techniques in exosome research 12 2.5.1 Biochemical approaches for exosome analysis 13 2.5.2 Genetic and molecular biology approaches for in vivo exosome research 14 Methods 16 3.1 Molecular cloning 16 3.1.1 Construction of pattB-13xLexAop2-Sun-5Myc-spGFP11 16 3.1.2 Construction of pUASt-attB-spGFP1-10-WPRE 16 3.1.3 -
Identification of Secretory Granule Phosphatidylinositol 4,5-Bisphosphate- Interacting Proteins Using an Affinity Pulldown Strategy*□S
Research Identification of Secretory Granule Phosphatidylinositol 4,5-Bisphosphate- interacting Proteins Using an Affinity Pulldown Strategy*□S Shona L. Osborne‡§, Tristan P. Wallis¶ʈ, Jose L. Jimenez**, Jeffrey J. Gorman¶ʈ, and Frederic A. Meunier‡§‡‡ Phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2) syn- required for secretion is synthesized on the plasma mem- thesis is required for calcium-dependent exocytosis in neu- brane (4), and the binding of vesicle-associated proteins to rosecretory cells. We developed a PtdIns(4,5)P2 bead pull- PtdIns(4,5)P2 in trans is thought to be important for bringing down strategy combined with subcellular fractionation to the vesicle and plasma membranes together prior to exocy- Downloaded from identify endogenous chromaffin granule proteins that inter- tosis to ensure rapid and efficient fusion upon calcium influx act with PtdIns(4,5)P . We identified two synaptotagmin iso- 2 (5). Putative PtdIns(4,5)P effectors include synaptotagmin 1 forms, synaptotagmins 1 and 7; spectrin; ␣-adaptin; and 2 (Syt1) (6, 7), calcium-activated protein for secretion (CAPS) (8, synaptotagmin-like protein 4 (granuphilin) by mass spec- 9), and rabphilin (10). trometry and Western blotting. The interaction between https://www.mcponline.org CAPS binds to PtdIns(4,5)P2 and is a potential PtdIns(4,5)P2 synaptotagmin 7 and PtdIns(4,5)P2 and its functional rele- vance was investigated. The 45-kDa isoform of synaptotag- effector for priming of secretory granule exocytosis (9). How- min 7 was found to be highly expressed in adrenal chromaf- ever, recent work on the CAPS1 knock-out mouse highlighted fin cells compared with PC12 cells and to mainly localize to an involvement of CAPS1 in the refilling or storage of cate- secretory granules by subcellular fractionation, immunoiso- cholamine in mature secretory granules therefore suggesting lation, and immunocytochemistry. -
Synaptotagmin 7 Switches Short-Term Synaptic Plasticity from Depression
www.nature.com/scientificreports OPEN Synaptotagmin 7 switches short‑term synaptic plasticity from depression to facilitation by suppressing synaptic transmission Takaaki Fujii1, Akira Sakurai1, J. Troy Littleton2 & Motojiro Yoshihara1* Short‑term synaptic plasticity is a fast and robust modifcation in neuronal presynaptic output that can enhance release strength to drive facilitation or diminish it to promote depression. The mechanisms that determine whether neurons display short‑term facilitation or depression are still unclear. Here we show that the Ca2+‑binding protein Synaptotagmin 7 (Syt7) determines the sign of short‑term synaptic plasticity by controlling the initial probability of synaptic vesicle (SV) fusion. Electrophysiological analysis of Syt7 null mutants at Drosophila embryonic neuromuscular junctions demonstrate loss of the protein converts the normally observed synaptic facilitation response during repetitive stimulation into synaptic depression. In contrast, overexpression of Syt7 dramatically enhanced the magnitude of short‑term facilitation. These changes in short‑term plasticity were mirrored by corresponding alterations in the initial evoked response, with SV release probability enhanced in Syt7 mutants and suppressed following Syt7 overexpression. Indeed, Syt7 mutants were able to display facilitation in lower [Ca2+] where release was reduced. These data suggest Syt7 does not act by directly sensing residual Ca2+ and argues for the existence of a distinct Ca2+ sensor beyond Syt7 that mediates facilitation. Instead, Syt7 normally suppresses synaptic transmission to maintain an output range where facilitation is available to the neuron. Synaptotagmins (Syts) are a large family of Ca2+ binding proteins, with the Syt1 isoform functioning as the major Ca2+ sensor for synchronous synaptic vesicle (SV) fusion1. Ca2+ also controls presynaptic forms of short-term plasticity, with other Syt isoforms representing promising candidates to mediate these processes. -
Communication Between the Endoplasmic Reticulum and Peroxisomes in Mammalian Cells
Communication between the Endoplasmic Reticulum and Peroxisomes in Mammalian Cells by Rong Hua A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Department of Biochemistry University of Toronto © Copyright by Rong Hua (2017) ii Communication between the Endoplasmic Reticulum and Peroxisomes in Mammalian Cells Rong Hua Doctor of Philosophy Department of Biochemistry University of Toronto 2017 Abstract Peroxisomes are important metabolic organelles found in virtually all eukaryotic cells. Since their discovery, peroxisomes have long been seen in close proximity to the endoplasmic reticulum (ER). The interplay between the two organelles is suggested to be important for peroxisome biogenesis as the ER may serve as a source for both lipids and peroxisomal membrane proteins (PMPs) for peroxisome growth and maintenance. On the other hand, various lipid molecules are exchanged between them for the biosynthesis of specialized lipids such as bile acids, plasmalogens and cholesterol. However, how proteins and lipids are transported between the two organelles is not yet fully understood. Previously, the peroxisomal biogenesis factor PEX16 was shown to serve as a receptor for PMPs in the ER and also as a mediator of the subsequent transport of these ER-targeted PMPs to peroxisomes. Here, I extended these results by carrying out a comprehensive mutational analysis of PEX16 aimed at gaining insights into the molecular targeting signals responsible for its ER-to-peroxisome trafficking and the domain(s) involved in its PMP recruitment function at the ER. I also showed that the recruitment function of PEX16 is conserved in plants. To gain further mechanistic insight into PEX16 function, the proteins proximal to iii PEX16 were identified using the proximity-dependent BioID analysis. -
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. -
The Role of Molecular Scaffolds at the Active Zone in Synaptic Vesicle Distribution and Release Probability
The Role of Molecular Scaffolds at the Active Zone in Synaptic Vesicle Distribution and Release Probability DISSERTATION To obtain the academic degree Doctor rerum naturalium (Dr. rer. nat.) submitted to the Department of Biology, Chemistry and Pharmacy Freie Universität Berlin Berlin, 2016 by Christina Beis (née Hollmann) This thesis was completed under the supervision of Prof. Dr. Stephan Sigrist from February 2011 to June 2016 at the Institute for Biology/ Genetics of Freie Universität Berlin, Germany. 1st reviewer: Prof. Dr. Stephan Sigrist 2nd reviewer: Prof. Dr. Hans-Joachim Pflüger Date of Defense: 21.11.2016 Statement of Authorship I hereby declare that the work presented in this thesis has been written independently and without inappropriate support. All sources of information are referenced. I hereby declare that this thesis has not been submitted, either in the same or in a different form, to this or any other university for a degree. ____________________________ Christina Beis Contents 1. Summary / Zusammenfassung .................................................................................................. 1 Summary....................................................................................................................................... 1 Zusammenfassung ........................................................................................................................ 3 2. Introduction .................................................................................................................................... -
Effects of Neonatal Stress and Morphine on Murine Hippocampal Gene Expression
0031-3998/11/6904-0285 Vol. 69, No. 4, 2011 PEDIATRIC RESEARCH Printed in U.S.A. Copyright © 2011 International Pediatric Research Foundation, Inc. Effects of Neonatal Stress and Morphine on Murine Hippocampal Gene Expression SANDRA E. JUUL, RICHARD P. BEYER, THEO K. BAMMLER, FEDERICO M. FARIN, AND CHRISTINE A. GLEASON Department of Pediatrics [S.E.J., C.A.G.], Department of Environmental and Occupational Health Sciences [R.P.B., T.K.B., F.M.F.], University of Washington, Seattle, Washington 98195 ABSTRACT: Critically ill preterm infants experience multiple to severe impairment occurring in close to 50% of ex- stressors while hospitalized. Morphine is commonly prescribed to tremely LBW infants (4). Autism, attention deficit disorder, ameliorate their pain and stress. We hypothesized that neonatal and school failure also occur more frequently in NICU stress will have a dose-dependent effect on hippocampal gene survivors (5). Although some degree of impairment might expression, and these effects will be altered by morphine treat- ment. Male C57BL/6 mice were exposed to five treatment condi- be inevitable, it is likely that the stress and treatments these tions between postnatal d 5 and 9: 1) control, 2) mild stress ϩ infants undergo impact neurologic outcome. Improved un- saline, 3) mild stress ϩ morphine, 4) severe stress ϩ saline, and derstanding of these factors will provide the basis of better 5) severe stress ϩ morphine. Hippocampal RNA was extracted treatments and subsequent improvement in outcomes. and analyzed using Affymetrix Mouse Gene 1.0 ST Arrays. Single Many preterm infants receive opiates for sedation or gene analysis and gene set analysis were used to compare groups analgesia during their NICU stay. -
Synaptotagmin13 Is a Neuroendocrine Marker in Brain, Intestine and Pancreas
Synaptotagmin13 Is A Neuroendocrine Marker In Brain, Intestine And Pancreas Marta Tarquis-Medina Helmholtz Zentrum München Katharina Scheibner Helmholtz Zentrum München Ismael Gonzalez Garcia Helmholtz Zentrum München Aimée Bastidas-Ponce Helmholtz Zentrum München Michael Sterr Helmholtz Zentrum München Jessica Jaki Helmholtz Zentrum München Silvia Schirge Helmholtz Zentrum München Cristina García-Cáceres Helmholtz Zentrum München Heiko Lickert Helmholtz Zentrum München Mostafa Bakhti ( [email protected] ) Helmholtz Zentrum München Research Article Keywords: Synaptotagmin 13, Syt13, uorescent reporter, endocrine lineage, brain, intestine, pancreas Posted Date: June 22nd, 2021 DOI: https://doi.org/10.21203/rs.3.rs-622505/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/18 Abstract Synaptotagmin13 (Syt13) is an atypical member of the vesicle tracking Synaptotagmin protein family. The expression pattern and the biological function of this Ca2+-independent protein are not well resolved. Here, we have generated a novel Syt13-Venus fusion (Syt13-VF) uorescence reporter allele to track and isolate tissues and cells expressing Syt13 protein. The reporter allele is regulated by endogenous cis- regulatory elements of Syt13 and the fusion protein follows an identical expression pattern of the endogenous Syt13 protein. The homozygous reporter mice are viable and fertile. We identify the expression of the Syt13-VF reporter in different regions of the brain with high expression in tyrosine hydroxylase (TH)-expressing and oxytocin-producing neuroendocrine cells. Moreover, Syt13-VF is highly restricted to all enteroendocrine cells in the adult intestine that can be traced in live imaging. Finally, Syt13-VF protein is expressed in the pancreatic endocrine lineage allowing their specic isolation by ow sorting. -
Pharmacological Mechanisms Underlying the Hepatoprotective Effects of Ecliptae Herba on Hepatocellular Carcinoma
Hindawi Evidence-Based Complementary and Alternative Medicine Volume 2021, Article ID 5591402, 17 pages https://doi.org/10.1155/2021/5591402 Research Article Pharmacological Mechanisms Underlying the Hepatoprotective Effects of Ecliptae herba on Hepatocellular Carcinoma Botao Pan ,1 Wenxiu Pan ,2 Zheng Lu ,3 and Chenglai Xia 1,4 1Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan 528000, China 2Department of Laboratory, Fifth People’s Hospital of Foshan, Foshan 528000, China 3Wuzhou Maternal and Child Health-Care Hospital, Wuzhou 543000, China 4School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China Correspondence should be addressed to Zheng Lu; [email protected] and Chenglai Xia; [email protected] Received 30 January 2021; Revised 31 May 2021; Accepted 3 July 2021; Published 16 July 2021 Academic Editor: Hongcai Shang Copyright © 2021 Botao Pan 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. Background. -e number of hepatocellular carcinoma (HCC) cases worldwide has increased significantly. As a traditional Chinese medicine (TCM) with a long history, Ecliptae herba (EH) has been widely used in HCC patients in China, but its hepatoprotective mechanism is still unclear. Methods. In this study, we applied a network pharmacology-based strategy and experimental ver- ification to systematically unravel the underlying mechanisms of EH against HCC. First, six active ingredients of EH were screened from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) by the ADME method. Subsequently, 52 potential targets of 6 active ingredients acting on HCC were screened from various databases, including TCMSP, DGIdb, SwissTargetPrediction, CTD, and GeneCards. -
Identification of Key Genes and Pathways Involved in Response To
Deng et al. Biol Res (2018) 51:25 https://doi.org/10.1186/s40659-018-0174-7 Biological Research RESEARCH ARTICLE Open Access Identifcation of key genes and pathways involved in response to pain in goat and sheep by transcriptome sequencing Xiuling Deng1,2†, Dong Wang3†, Shenyuan Wang1, Haisheng Wang2 and Huanmin Zhou1* Abstract Purpose: This aim of this study was to investigate the key genes and pathways involved in the response to pain in goat and sheep by transcriptome sequencing. Methods: Chronic pain was induced with the injection of the complete Freund’s adjuvant (CFA) in sheep and goats. The animals were divided into four groups: CFA-treated sheep, control sheep, CFA-treated goat, and control goat groups (n 3 in each group). The dorsal root ganglions of these animals were isolated and used for the construction of a cDNA= library and transcriptome sequencing. Diferentially expressed genes (DEGs) were identifed in CFA-induced sheep and goats and gene ontology (GO) enrichment analysis was performed. Results: In total, 1748 and 2441 DEGs were identifed in CFA-treated goat and sheep, respectively. The DEGs identi- fed in CFA-treated goats, such as C-C motif chemokine ligand 27 (CCL27), glutamate receptor 2 (GRIA2), and sodium voltage-gated channel alpha subunit 3 (SCN3A), were mainly enriched in GO functions associated with N-methyl- D-aspartate (NMDA) receptor, infammatory response, and immune response. The DEGs identifed in CFA-treated sheep, such as gamma-aminobutyric acid (GABA)-related DEGs (gamma-aminobutyric acid type A receptor gamma 3 subunit [GABRG3], GABRB2, and GABRB1), SCN9A, and transient receptor potential cation channel subfamily V member 1 (TRPV1), were mainly enriched in GO functions related to neuroactive ligand-receptor interaction, NMDA receptor, and defense response. -
Lipid Droplets Protect Human Β Cells from Lipotoxic-Induced Stress and Cell
bioRxiv preprint doi: https://doi.org/10.1101/2021.06.19.449124; this version posted June 20, 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. Lipid droplets protect human β cells from lipotoxic-induced stress and cell identity changes Xin Tong1 and Roland Stein1,2 1Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 2Corresponding author: [email protected]; Tel: 615-322-7026 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.06.19.449124; this version posted June 20, 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 (200 words) Free fatty acids (FFAs) are often stored in lipid droplet (LD) depots for eventual metabolic and/or synthetic use in many cell types, such a muscle, liver, and fat. In pancreatic islets, overt LD accumulation was detected in humans but not mice. LD buildup in islets was principally observed after roughly 11 years of age, increasing throughout adulthood under physiologic conditions, and also enriched in type 2 diabetes. To obtain insight into the role of LDs in human islet β cell function, the levels of a key LD structural protein, perilipin2 (PLIN2), were manipulated by lentiviral-mediated knock-down (KD) or over-expression (OE) in EndoCβH2-Cre cells, a human cell line with adult islet β-like properties. -
Figure S1. SYT1 and SYT3 Are Induced Under Abiotic Stress (Related to Figure 1)
Figure S1. SYT1 and SYT3 are induced under abiotic stress (related to Figure 1). (A) Phylogenetic clustering of the Arabidopsis protein coding sequence of SYT1, SYT2, SYT3, SYT4, SYT5 and the Homo sapiens E-Syt1. Phylogenetic tree was inferred using the Neighbor-Joining method. The optimal tree with the sum of branch length = 3.26 is shown. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the p-distance method and are in the units of the number of amino acid differences per site. This analysis involved 11 amino acid sequences. All ambiguous positions were removed for each sequence pair (pairwise deletion option). There were a total of 1752 positions in the final dataset. Evolutionary analyses were conducted using MEGA X (Kumar et al., 2018). (B) Gene expression profiles based on RNA-seq analysis of SYT1, SYT2, SYT3, SYT4, and SYT5 in vegetative tissues at different developmental stages from TRAVA database http://travadb.org/). Each dot represent a RNAseq value and the bar represent the median. (C) Gene expression profiles based on RNA-seq analysis of SYT1, SYT3, and SYT5 in eFP-seq Browser after various abiotic stresses (https://bar.utoronto.ca/eFP-Seq_Browser/).https://bar.utoronto.ca/eFP- Seq_Browser/). (D) Heatmap representing the expression responses to abiotic stress of SYT1, SYT3 and SYT5. Expression levels genes are represented as the fold-change relative to the control. Red represents a gene that is induced, and blue represents a gene that is repressed in response to the indicated abiotic stress.