Myosin Heavy Chain-Embryonic Regulates Skeletal Muscle
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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. -
Communication Pathways in Human Nonmuscle Myosin-2C 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Authors: 25 Krishna Chinthalapudia,B,C,1, Sarah M
1 Mechanistic Insights into the Active Site and Allosteric 2 Communication Pathways in Human Nonmuscle Myosin-2C 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Authors: 25 Krishna Chinthalapudia,b,c,1, Sarah M. Heisslera,d,1, Matthias Prellera,e, James R. Sellersd,2, and 26 Dietmar J. Mansteina,b,2 27 28 Author Affiliations 29 aInstitute for Biophysical Chemistry, OE4350 Hannover Medical School, 30625 Hannover, 30 Germany. 31 bDivision for Structural Biochemistry, OE8830, Hannover Medical School, 30625 Hannover, 32 Germany. 33 cCell Adhesion Laboratory, Department of Integrative Structural and Computational Biology, The 34 Scripps Research Institute, Jupiter, Florida 33458, USA. 35 dLaboratory of Molecular Physiology, NHLBI, National Institutes of Health, Bethesda, Maryland 36 20892, USA. 37 eCentre for Structural Systems Biology (CSSB), German Electron Synchrotron (DESY), 22607 38 Hamburg, Germany. 39 1K.C. and S.M.H. contributed equally to this work 40 2To whom correspondence may be addressed: E-mail: [email protected] or 41 [email protected] 42 43 1 44 Abstract 45 Despite a generic, highly conserved motor domain, ATP turnover kinetics and their activation by 46 F-actin vary greatly between myosin-2 isoforms. Here, we present a 2.25 Å crystal pre- 47 powerstroke state (ADPVO4) structure of the human nonmuscle myosin-2C motor domain, one 48 of the slowest myosins characterized. In combination with integrated mutagenesis, ensemble- 49 solution kinetics, and molecular dynamics simulation approaches, the structure reveals an 50 allosteric communication pathway that connects the distal end of the motor domain with the 51 active site. -
Insights from Conventional and Unconventional Myosins A
Structure-Function Analysis of Motor Proteins: Insights from Conventional and Unconventional Myosins A Thesis SUBMITTED TO THE FACULTY OF UNIVERSITY OF MINNESOTA BY Karl J. Petersen IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY Margaret A. Titus, Advisor David D. Thomas, Co-Advisor December 2016 © Karl J. Petersen 2016 Acknowledgements This thesis would not exist without the patient support of my advisors, Meg Titus and Dave Thomas. Any shortcomings are my own. Collaborators Holly Goodson, Anne Houdusse, and Gant Luxton also provided invaluable training and support. I am also grateful for essential services provided by departmental staff: Sarah Blakely Anderson, Octavian Cornea, Sarah Dittrich, Karen Hawkinson, Michelle Lewis, Mary Muwahid, Laurie O’Neill, Darlene Toedter, with apologies to others not listed. Thanks to friends and colleagues at the University of Minnesota: Ashley Arthur, Kelly Bower, Brett Colson, Sinziana Cornea, Chi Meng Fong, Greg Gillispie, Piyali Guhathakurta, Tejas Gupte, Tom Hays, Norma Jiménez Ramírez, Dawn Lowe, Allison MacLean, Santiago Martínez Cifuentes, Jared Matzke, Megan McCarthy, Joachim Mueller, Joe Muretta, Kurt Peterson, Mary Porter, Ewa Prochniewicz, Mike Ritt, Cosmo Saunders, Shiv Sivaramakrishnan, Ruth Sommese, Doug Tritschler, Brian Woolums. i Abstract Myosin motor proteins play fundamental roles in a multitude of cellular processes. Myosin generates force on cytoskeletal actin filaments to control cell shape, most dramatically during cytokinesis, and has a conserved role in defining cell polarity. Myosin contracts the actin cytoskeleton, ensuring prompt turnover of cellular adhesion sites, retracting the cell body during migration and development, and contracting muscle among diverse other functions. How myosins work, and why force generation is essential for their function, is in many cases an open question. -
Microrna Regulatory Pathways in the Control of the Actin–Myosin Cytoskeleton
cells Review MicroRNA Regulatory Pathways in the Control of the Actin–Myosin Cytoskeleton , , Karen Uray * y , Evelin Major and Beata Lontay * y Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; [email protected] * Correspondence: [email protected] (K.U.); [email protected] (B.L.); Tel.: +36-52-412345 (K.U. & B.L.) The authors contributed equally to the manuscript. y Received: 11 June 2020; Accepted: 7 July 2020; Published: 9 July 2020 Abstract: MicroRNAs (miRNAs) are key modulators of post-transcriptional gene regulation in a plethora of processes, including actin–myosin cytoskeleton dynamics. Recent evidence points to the widespread effects of miRNAs on actin–myosin cytoskeleton dynamics, either directly on the expression of actin and myosin genes or indirectly on the diverse signaling cascades modulating cytoskeletal arrangement. Furthermore, studies from various human models indicate that miRNAs contribute to the development of various human disorders. The potentially huge impact of miRNA-based mechanisms on cytoskeletal elements is just starting to be recognized. In this review, we summarize recent knowledge about the importance of microRNA modulation of the actin–myosin cytoskeleton affecting physiological processes, including cardiovascular function, hematopoiesis, podocyte physiology, and osteogenesis. Keywords: miRNA; actin; myosin; actin–myosin complex; Rho kinase; cancer; smooth muscle; hematopoiesis; stress fiber; gene expression; cardiovascular system; striated muscle; muscle cell differentiation; therapy 1. Introduction Actin–myosin interactions are the primary source of force generation in mammalian cells. Actin forms a cytoskeletal network and the myosin motor proteins pull actin filaments to produce contractile force. All eukaryotic cells contain an actin–myosin network inferring contractile properties to these cells. -
A Curated Gene List for Reporting Results of Newborn Genomic Sequencing
© American College of Medical Genetics and Genomics ORIGINAL RESEARCH ARTICLE A curated gene list for reporting results of newborn genomic sequencing Ozge Ceyhan-Birsoy, PhD1,2,3, Kalotina Machini, PhD1,2,3, Matthew S. Lebo, PhD1,2,3, Tim W. Yu, MD3,4,5, Pankaj B. Agrawal, MD, MMSC3,4,6, Richard B. Parad, MD, MPH3,7, Ingrid A. Holm, MD, MPH3,4, Amy McGuire, PhD8, Robert C. Green, MD, MPH3,9,10, Alan H. Beggs, PhD3,4, Heidi L. Rehm, PhD1,2,3,10; for the BabySeq Project Purpose: Genomic sequencing (GS) for newborns may enable detec- of newborn GS (nGS), and used our curated list for the first 15 new- tion of conditions for which early knowledge can improve health out- borns sequenced in this project. comes. One of the major challenges hindering its broader application Results: Here, we present our curated list for 1,514 gene–disease is the time it takes to assess the clinical relevance of detected variants associations. Overall, 954 genes met our criteria for return in nGS. and the genes they impact so that disease risk is reported appropri- This reference list eliminated manual assessment for 41% of rare vari- ately. ants identified in 15 newborns. Methods: To facilitate rapid interpretation of GS results in new- Conclusion: Our list provides a resource that can assist in guiding borns, we curated a catalog of genes with putative pediatric relevance the interpretive scope of clinical GS for newborns and potentially for their validity based on the ClinGen clinical validity classification other populations. framework criteria, age of onset, penetrance, and mode of inheri- tance through systematic evaluation of published evidence. -
Rashid Thesis 2015
Protein Profile and Directed Gene Expression of Developing C2C12 cells By Susan Rashid Submitted in Partial Fulfillment of the Requirements For the Degree of Master of Science In the Biological Sciences Program YOUNGSTOWN STATE UNIVERSITY August 3, 2015 Protein Profile and Directed Gene Expression of Developing C2C12 cells Susan Rashid I hereby release this thesis to the public. I understand that this will be made available from the OhioLINK ETD Center and the Maag Library Circulation Desk for public access. I also authorize the University or other individuals to make copies of this thesis as needed for scholarly research. Signature: ___________________________________________________ Susan Rashid, Student Date Approvals: ___________________________________________________ Dr. Gary Walker, Thesis Advisor 'ate ___________________________________________________ Dr. Jonathan Caguiat, Committee Member Date ___________________________________________________ Dr. David Asch, Committee Member Date ___________________________________________________ Dr. Sal Sanders, Associate Dean, Graduate Studies Date ABSTRACT Myogenesis is a tightly regulated process resulting in unique structures called myotubes or myofibers, which compose skeletal muscle. Myotubes are multi-nucleated fibers containing a functional unit composed of cytoskeletal proteins called the sarcomere. The specific arrangement of these proteins in the sarcomere works to contract and relax muscles. During embryonic and post-embryonic development, fluctuations in expression of growth factors throughout the program account for the dramatic structural changes from cell to mature muscle fiber. In vivo, these growth factors are strictly spatiotemporally regulated according to a ‘myogenic program.’ In order to assess the dynamics of protein expression throughout this program, we conducted a time course study using the mouse myoblast cell line C2C12, in which cells were allowed to differentiate and insoluble protein fractions were collected at seven time points. -
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Expanding genotype/phenotype of neuromuscular diseases by comprehensive target capture/NGS Xia Tian, PhD* ABSTRACT * Wen-Chen Liang, MD Objective: To establish and evaluate the effectiveness of a comprehensive next-generation * Yanming Feng, PhD sequencing (NGS) approach to simultaneously analyze all genes known to be responsible for Jing Wang, MD the most clinically and genetically heterogeneous neuromuscular diseases (NMDs) involving spi- Victor Wei Zhang, PhD nal motoneurons, neuromuscular junctions, nerves, and muscles. Chih-Hung Chou, MS Methods: All coding exons and at least 20 bp of flanking intronic sequences of 236 genes causing Hsien-Da Huang, PhD NMDs were enriched by using SeqCap EZ solution-based capture and enrichment method fol- Ching Wan Lam, PhD lowed by massively parallel sequencing on Illumina HiSeq2000. Ya-Yun Hsu, PhD ; 3 Thy-Sheng Lin, MD Results: The target gene capture/deep sequencing provides an average coverage of 1,000 per Wan-Tzu Chen, MS nucleotide. Thirty-five unrelated NMD families (38 patients) with clinical and/or muscle pathologic Lee-Jun Wong, PhD diagnoses but without identified causative genetic defects were analyzed. Deleterious mutations Yuh-Jyh Jong, MD were found in 29 families (83%). Definitive causative mutations were identified in 21 families (60%) and likely diagnoses were established in 8 families (23%). Six families were left without diagnosis due to uncertainty in phenotype/genotype correlation and/or unidentified causative Correspondence to genes. Using this comprehensive panel, we not only identified mutations in expected genes but Dr. Wong: also expanded phenotype/genotype among different subcategories of NMDs. [email protected] or Dr. Jong: Conclusions: Target gene capture/deep sequencing approach can greatly improve the genetic [email protected] diagnosis of NMDs. -
Premyogenic Progenitors Derived from Human Pluripotent Stem Cells
www.nature.com/scientificreports OPEN Premyogenic progenitors derived from human pluripotent stem cells expand in foating culture and Received: 23 January 2018 Accepted: 12 April 2018 diferentiate into transplantable Published: xx xx xxxx myogenic progenitors Fusako Sakai-Takemura, Asako Narita, Satoru Masuda, Toshifumi Wakamatsu, Nobuharu Watanabe, Takashi Nishiyama, Ken’ichiro Nogami, Matthias Blanc, Shin’ichi Takeda & Yuko Miyagoe-Suzuki Human induced pluripotent stem cells (hiPSCs) are a potential source for cell therapy of Duchenne muscular dystrophy. To reliably obtain skeletal muscle progenitors from hiPSCs, we treated hiPS cells with a Wnt activator, CHIR-99021 and a BMP receptor inhibitor, LDN-193189, and then induced skeletal muscle cells using a previously reported sphere-based culture. This protocol greatly improved sphere formation efciency and stably induced the diferentiation of myogenic cells from hiPS cells generated from both healthy donors and a patient with congenital myasthenic syndrome. hiPSC-derived myogenic progenitors were enriched in the CD57(−) CD108(−) CD271(+) ERBB3(+) cell fraction, and their diferentiation was greatly promoted by TGF-β inhibitors. TGF-β inhibitors down-regulated the NFIX transcription factor, and NFIX short hairpin RNA (shRNA) improved the diferentiation of iPS cell- derived myogenic progenitors. These results suggest that NFIX inhibited diferentiation of myogenic progenitors. hiPSC-derived myogenic cells diferentiated into myofbers in muscles of NSG-mdx4Cv mice after direct transplantation. Our results indicate that our new muscle induction protocol is useful for cell therapy of muscular dystrophies. Currently, there is no satisfactory therapy for Duchenne muscular dystrophy (DMD). Myoblast transplantation is one of the promising therapeutic strategies because wild-type mouse myoblasts have been shown to fuse with host dystrophic myofbers and express dystrophin at the sarcolemma in a DMD model, the mdx mouse1. -
Chemical Agent and Antibodies B-Raf Inhibitor RAF265
Supplemental Materials and Methods: Chemical agent and antibodies B-Raf inhibitor RAF265 [5-(2-(5-(trifluromethyl)-1H-imidazol-2-yl)pyridin-4-yloxy)-N-(4-trifluoromethyl)phenyl-1-methyl-1H-benzp{D, }imidazol-2- amine] was kindly provided by Novartis Pharma AG and dissolved in solvent ethanol:propylene glycol:2.5% tween-80 (percentage 6:23:71) for oral delivery to mice by gavage. Antibodies to phospho-ERK1/2 Thr202/Tyr204(4370), phosphoMEK1/2(2338 and 9121)), phospho-cyclin D1(3300), cyclin D1 (2978), PLK1 (4513) BIM (2933), BAX (2772), BCL2 (2876) were from Cell Signaling Technology. Additional antibodies for phospho-ERK1,2 detection for western blot were from Promega (V803A), and Santa Cruz (E-Y, SC7383). Total ERK antibody for western blot analysis was K-23 from Santa Cruz (SC-94). Ki67 antibody (ab833) was from ABCAM, Mcl1 antibody (559027) was from BD Biosciences, Factor VIII antibody was from Dako (A082), CD31 antibody was from Dianova, (DIA310), and Cot antibody was from Santa Cruz Biotechnology (sc-373677). For the cyclin D1 second antibody staining was with an Alexa Fluor 568 donkey anti-rabbit IgG (Invitrogen, A10042) (1:200 dilution). The pMEK1 fluorescence was developed using the Alexa Fluor 488 chicken anti-rabbit IgG second antibody (1:200 dilution).TUNEL staining kits were from Promega (G2350). Mouse Implant Studies: Biopsy tissues were delivered to research laboratory in ice-cold Dulbecco's Modified Eagle Medium (DMEM) buffer solution. As the tissue mass available from each biopsy was limited, we first passaged the biopsy tissue in Balb/c nu/Foxn1 athymic nude mice (6-8 weeks of age and weighing 22-25g, purchased from Harlan Sprague Dawley, USA) to increase the volume of tumor for further implantation. -
Human Induced Pluripotent Stem Cell–Derived Podocytes Mature Into Vascularized Glomeruli Upon Experimental Transplantation
BASIC RESEARCH www.jasn.org Human Induced Pluripotent Stem Cell–Derived Podocytes Mature into Vascularized Glomeruli upon Experimental Transplantation † Sazia Sharmin,* Atsuhiro Taguchi,* Yusuke Kaku,* Yasuhiro Yoshimura,* Tomoko Ohmori,* ‡ † ‡ Tetsushi Sakuma, Masashi Mukoyama, Takashi Yamamoto, Hidetake Kurihara,§ and | Ryuichi Nishinakamura* *Department of Kidney Development, Institute of Molecular Embryology and Genetics, and †Department of Nephrology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan; ‡Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan; §Division of Anatomy, Juntendo University School of Medicine, Tokyo, Japan; and |Japan Science and Technology Agency, CREST, Kumamoto, Japan ABSTRACT Glomerular podocytes express proteins, such as nephrin, that constitute the slit diaphragm, thereby contributing to the filtration process in the kidney. Glomerular development has been analyzed mainly in mice, whereas analysis of human kidney development has been minimal because of limited access to embryonic kidneys. We previously reported the induction of three-dimensional primordial glomeruli from human induced pluripotent stem (iPS) cells. Here, using transcription activator–like effector nuclease-mediated homologous recombination, we generated human iPS cell lines that express green fluorescent protein (GFP) in the NPHS1 locus, which encodes nephrin, and we show that GFP expression facilitated accurate visualization of nephrin-positive podocyte formation in -
Supplementary Material Contents
Supplementary Material Contents Immune modulating proteins identified from exosomal samples.....................................................................2 Figure S1: Overlap between exosomal and soluble proteomes.................................................................................... 4 Bacterial strains:..............................................................................................................................................4 Figure S2: Variability between subjects of effects of exosomes on BL21-lux growth.................................................... 5 Figure S3: Early effects of exosomes on growth of BL21 E. coli .................................................................................... 5 Figure S4: Exosomal Lysis............................................................................................................................................ 6 Figure S5: Effect of pH on exosomal action.................................................................................................................. 7 Figure S6: Effect of exosomes on growth of UPEC (pH = 6.5) suspended in exosome-depleted urine supernatant ....... 8 Effective exosomal concentration....................................................................................................................8 Figure S7: Sample constitution for luminometry experiments..................................................................................... 8 Figure S8: Determining effective concentration ......................................................................................................... -
1 Mucosal Effects of Tenofovir 1% Gel 1 Florian Hladik1,2,5*, Adam
1 Mucosal effects of tenofovir 1% gel 2 Florian Hladik1,2,5*, Adam Burgener8,9, Lamar Ballweber5, Raphael Gottardo4,5,6, Lucia Vojtech1, 3 Slim Fourati7, James Y. Dai4,6, Mark J. Cameron7, Johanna Strobl5, Sean M. Hughes1, Craig 4 Hoesley10, Philip Andrew12, Sherri Johnson12, Jeanna Piper13, David R. Friend14, T. Blake Ball8,9, 5 Ross D. Cranston11,16, Kenneth H. Mayer15, M. Juliana McElrath2,3,5 & Ian McGowan11,16 6 Departments of 1Obstetrics and Gynecology, 2Medicine, 3Global Health, 4Biostatistics, University 7 of Washington, Seattle, USA; 5Vaccine and Infectious Disease Division, 6Public Health Sciences 8 Division, Fred Hutchinson Cancer Research Center, Seattle, USA; 7Vaccine and Gene Therapy 9 Institute-Florida, Port St. Lucie, USA; 8Department of Medical Microbiology, University of 10 Manitoba, Winnipeg, Canada; 9National HIV and Retrovirology Laboratories, Public Health 11 Agency of Canada; 10University of Alabama, Birmingham, USA; 11University of Pittsburgh 12 School of Medicine, Pittsburgh, USA; 12FHI 360, Durham, USA; 13Division of AIDS, NIAID, NIH, 13 Bethesda, USA; 14CONRAD, Eastern Virginia Medical School, Arlington, USA; 15Fenway Health, 14 Beth Israel Deaconess Hospital and Harvard Medical School, Boston, USA; 16Microbicide Trials 15 Network, Magee-Women’s Research Institute, Pittsburgh, USA. 16 Adam Burgener and Lamar Ballweber contributed equally to this work. 17 *Corresponding author E-mail: [email protected] 18 Address reprint requests to Florian Hladik at [email protected] or Ian McGowan at 19 [email protected]. 20 Abstract: 150 words. Main text (without Methods): 2,603 words. Methods: 3,953 words 1 21 ABSTRACT 22 Tenofovir gel is being evaluated for vaginal and rectal pre-exposure prophylaxis against HIV 23 transmission.