TMX1 Determines Cancer Cell Metabolism As a Thiol- Based Modulator of ER–Mitochondria Ca2+ Flux
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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. -
Preclinical Evaluation of Protein Disulfide Isomerase Inhibitors for the Treatment of Glioblastoma by Andrea Shergalis
Preclinical Evaluation of Protein Disulfide Isomerase Inhibitors for the Treatment of Glioblastoma By Andrea Shergalis A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Medicinal Chemistry) in the University of Michigan 2020 Doctoral Committee: Professor Nouri Neamati, Chair Professor George A. Garcia Professor Peter J. H. Scott Professor Shaomeng Wang Andrea G. Shergalis [email protected] ORCID 0000-0002-1155-1583 © Andrea Shergalis 2020 All Rights Reserved ACKNOWLEDGEMENTS So many people have been involved in bringing this project to life and making this dissertation possible. First, I want to thank my advisor, Prof. Nouri Neamati, for his guidance, encouragement, and patience. Prof. Neamati instilled an enthusiasm in me for science and drug discovery, while allowing me the space to independently explore complex biochemical problems, and I am grateful for his kind and patient mentorship. I also thank my committee members, Profs. George Garcia, Peter Scott, and Shaomeng Wang, for their patience, guidance, and support throughout my graduate career. I am thankful to them for taking time to meet with me and have thoughtful conversations about medicinal chemistry and science in general. From the Neamati lab, I would like to thank so many. First and foremost, I have to thank Shuzo Tamara for being an incredible, kind, and patient teacher and mentor. Shuzo is one of the hardest workers I know. In addition to a strong work ethic, he taught me pretty much everything I know and laid the foundation for the article published as Chapter 3 of this dissertation. The work published in this dissertation really began with the initial identification of PDI as a target by Shili Xu, and I am grateful for his advice and guidance (from afar!). -
Modulating Hallmarks of Cholangiocarcinoma
University of Nebraska Medical Center DigitalCommons@UNMC Theses & Dissertations Graduate Studies Fall 12-14-2018 Modulating Hallmarks of Cholangiocarcinoma Cody Wehrkamp University of Nebraska Medical Center Follow this and additional works at: https://digitalcommons.unmc.edu/etd Part of the Molecular Biology Commons Recommended Citation Wehrkamp, Cody, "Modulating Hallmarks of Cholangiocarcinoma" (2018). Theses & Dissertations. 337. https://digitalcommons.unmc.edu/etd/337 This Dissertation is brought to you for free and open access by the Graduate Studies at DigitalCommons@UNMC. It has been accepted for inclusion in Theses & Dissertations by an authorized administrator of DigitalCommons@UNMC. For more information, please contact [email protected]. MODULATING HALLMARKS OF CHOLANGIOCARCINOMA by Cody J. Wehrkamp A DISSERTATION Presented to the Faculty of the University of Nebraska Graduate College in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Biochemistry and Molecular Biology Graduate Program Under the Supervision of Professor Justin L. Mott University of Nebraska Medical Center Omaha, Nebraska November 2018 Supervisory Committee: Kaustubh Datta, Ph.D. Melissa Teoh‐Fitzgerald, Ph.D. Richard G. MacDonald, Ph.D. Acknowledgements This endeavor has led to scientific as well as personal growth for me. I am indebted to many for their knowledge, influence, and support along the way. To my mentor, Dr. Justin L. Mott, you have been an incomparable teacher and invaluable guide. You upheld for me the concept that science is intrepid, even when the experience is trying. Through my training, and now here at the end, I can say that it has been an honor to be your protégé. When you have shaped your future graduates to be and do great, I will be privileged to say that I was your first one. -
Anti-Inflammatory Role of Curcumin in LPS Treated A549 Cells at Global Proteome Level and on Mycobacterial Infection
Anti-inflammatory Role of Curcumin in LPS Treated A549 cells at Global Proteome level and on Mycobacterial infection. Suchita Singh1,+, Rakesh Arya2,3,+, Rhishikesh R Bargaje1, Mrinal Kumar Das2,4, Subia Akram2, Hossain Md. Faruquee2,5, Rajendra Kumar Behera3, Ranjan Kumar Nanda2,*, Anurag Agrawal1 1Center of Excellence for Translational Research in Asthma and Lung Disease, CSIR- Institute of Genomics and Integrative Biology, New Delhi, 110025, India. 2Translational Health Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India. 3School of Life Sciences, Sambalpur University, Jyoti Vihar, Sambalpur, Orissa, 768019, India. 4Department of Respiratory Sciences, #211, Maurice Shock Building, University of Leicester, LE1 9HN 5Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia- 7003, Bangladesh. +Contributed equally for this work. S-1 70 G1 S 60 G2/M 50 40 30 % of cells 20 10 0 CURI LPSI LPSCUR Figure S1: Effect of curcumin and/or LPS treatment on A549 cell viability A549 cells were treated with curcumin (10 µM) and/or LPS or 1 µg/ml for the indicated times and after fixation were stained with propidium iodide and Annexin V-FITC. The DNA contents were determined by flow cytometry to calculate percentage of cells present in each phase of the cell cycle (G1, S and G2/M) using Flowing analysis software. S-2 Figure S2: Total proteins identified in all the three experiments and their distribution betwee curcumin and/or LPS treated conditions. The proteins showing differential expressions (log2 fold change≥2) in these experiments were presented in the venn diagram and certain number of proteins are common in all three experiments. -
Core Circadian Clock Transcription Factor BMAL1 Regulates Mammary Epithelial Cell
bioRxiv preprint doi: https://doi.org/10.1101/2021.02.23.432439; this version posted February 23, 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 4.0 International license. 1 Title: Core circadian clock transcription factor BMAL1 regulates mammary epithelial cell 2 growth, differentiation, and milk component synthesis. 3 Authors: Theresa Casey1ǂ, Aridany Suarez-Trujillo1, Shelby Cummings1, Katelyn Huff1, 4 Jennifer Crodian1, Ketaki Bhide2, Clare Aduwari1, Kelsey Teeple1, Avi Shamay3, Sameer J. 5 Mabjeesh4, Phillip San Miguel5, Jyothi Thimmapuram2, and Karen Plaut1 6 Affiliations: 1. Department of Animal Science, Purdue University, West Lafayette, IN, USA; 2. 7 Bioinformatics Core, Purdue University; 3. Animal Science Institute, Agriculture Research 8 Origination, The Volcani Center, Rishon Letsiyon, Israel. 4. Department of Animal Sciences, 9 The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of 10 Jerusalem, Rehovot, Israel. 5. Genomics Core, Purdue University 11 Grant support: Binational Agricultural Research Development (BARD) Research Project US- 12 4715-14; Photoperiod effects on milk production in goats: Are they mediated by the molecular 13 clock in the mammary gland? 14 ǂAddress for correspondence. 15 Theresa M. Casey 16 BCHM Room 326 17 175 South University St. 18 West Lafayette, IN 47907 19 Email: [email protected] 20 Phone: 802-373-1319 21 22 bioRxiv preprint doi: https://doi.org/10.1101/2021.02.23.432439; this version posted February 23, 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. -
The Physiological Functions of Mammalian Endoplasmic Oxidoreductin 1: on Disulfides and More
ANTIOXIDANTS & REDOX SIGNALING Volume 16, Number 10, 2012 FORUM REVIEW ARTICLE ª Mary Ann Liebert, Inc. DOI: 10.1089/ars.2011.4475 The Physiological Functions of Mammalian Endoplasmic Oxidoreductin 1: On Disulfides and More Thomas Ramming and Christian Appenzeller-Herzog Abstract Significance: The oxidative process of disulfide-bond formation is essential for the folding of most secretory and membrane proteins in the endoplasmic reticulum (ER). It is driven by electron relay pathways that transfer two electrons derived from the fusion of two adjacent cysteinyl side chains onto various types of chemical oxidants. The conserved, ER-resident endoplasmic oxidoreductin 1 (Ero1) sulfhydryl oxidases that reduce molecular oxygen to generate an active-site disulfide represent one of these pathways. In mammals, two family members exist, Ero1a and Ero1b. Recent Advances: The two mammalian Ero1 enzymes differ in transcriptional and post- translational regulation, tissue distribution, and catalytic turnover. A specific protein–protein interaction be- tween either isoform and protein disulfide isomerase (PDI) facilitates the propagation of disulfides from Ero1 via PDI to nascent polypeptides, and inbuilt oxidative shutdown mechanisms in Ero1a and Ero1b prevent excessive oxidation of PDI. Critical Issues: Besides disulfide-bond generation, Ero1a also regulates calcium release from the ER and the secretion of disulfide-linked oligomers through its reversible association with the chaperone ERp44. This review explores the functional repertoire and possible redundancy of mammalian Ero1 enzymes. Future Directions: Systematic analyses of different knockout mouse models will be the most promising strategy to shed new light on unique and tissue-specific roles of Ero1a and Ero1b. Moreover, in-depth characterization of the known physical interactions of Ero1 with peroxidases and PDI family members will help broaden our functional and mechanistic understanding of Ero1 enzymes. -
Identification of Novel Mouse Delta1 Target Genes: Combination of Transcriptomics and Proteomics
Institut für Experimentelle Genetik GSF – Forschungszentrum für Umwelt und Gesundheit Identification of novel mouse Delta1 target genes: Combination of transcriptomics and proteomics Christine Hutterer Vollständiger Abdruck der von der Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt der Technischen Universität München zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften genehmigten Dissertation. Vorsitzender: Univ.-Prof. Dr. A. Gierl Prüfer der Dissertation: 1. apl. Prof. Dr. J. Adamski 2. Univ.-Prof. Dr. W. Wurst Die Dissertation wurde am 31.01.2005 bei der Technischen Universität München eingereicht und durch die Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt am 13.05.2005 angenommen. DANKSAGUNG Besonderer Dank gebührt Prof. Dr. Martin Hrabé de Angelis, Leiter des Instituts für experimentelle Genetik. Unter anderem durch seine Leidenschaft für die Wissenschaft wollte ich am IEG arbeiten. Ich möchte mich jedoch nicht nur für die wissenschaftlichen Ratschläge und Diskussionen bedanken, sondern auch für viele interessante nicht-wissenschaftliche Gespräche. Ebenfalls besonders bedanke ich mich bei meinem Doktorvater Dr. Jurek Adamski, dessen fachliche Meinung und positive Einstellung mich sehr motivierte. Großen Dank möchte ich der gesamten „Beckers-Arbeitsgruppe“ aussprechen. Allen voran Dr. Johannes Beckers, Leiter der Genregulation und Expression Profiling Arbeitsgruppe, für die Überlassung des Themas und die Betreuung meiner Doktorarbeit, die mir viel Entscheidungsfreiraum ließ, sowie für zahlreiche gute Ideen und lehrreiche Gespräche. Bei Tomek Mijalski möchte ich mich für seine stetige Hilfsbereitschaft und die entstandene Freundschaft besonders bedanken. Weiterhin bedanke ich mich ganz herzlich bei Dr. Sonja Becker für wertvolle Labortricks und Kniffe, die Durchsicht des Manuskripts und ihre herzliche Art. Vielen Dank an dieser Stelle auch an Kathrin Seidel für die gute technische Unterstützung im Labor und mit der Mausarbeit. -
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 -
Anti-ERO1L Antibody (ARG42132)
Product datasheet [email protected] ARG42132 Package: 50 μg anti-ERO1L antibody Store at: -20°C Summary Product Description Goat Polyclonal antibody recognizes ERO1L Tested Reactivity Hu Predict Reactivity Ms, Rat, Cow, Dog, Pig Tested Application IHC-P, WB Host Goat Clonality Polyclonal Isotype IgG Target Name ERO1L Antigen Species Human Immunogen Synthetic peptide around the internal region of Human ERO1L. (C-QSDEVPDGIKSASY) (NP_055399.1) Conjugation Un-conjugated Alternate Names ERO1-like protein alpha; ERO1L; Endoplasmic oxidoreductin-1-like protein; ERO1-alpha; ERO1-L-alpha; Ero1alpha; Oxidoreductin-1-L-alpha; EC 1.8.4.-; ERO1LA; ERO1-L Application Instructions Application table Application Dilution IHC-P 5 µg/ml WB 0.1 - 0.3 µg/ml Application Note WB: Recommend incubate at RT for 1h. IHC-P: Antigen Retrieval: Steam tissue section in Citrate buffer (pH 6.0). * The dilutions indicate recommended starting dilutions and the optimal dilutions or concentrations should be determined by the scientist. Positive Control A431 Calculated Mw 54 kDa Observed Size ~ 70 kDa Properties Form Liquid Purification Ammonium sulphate precipitation followed by affinity purification with immunogen. Buffer Tris saline (pH 7.3), 0.02% Sodium azide and 0.5% BSA. Preservative 0.02% Sodium azide Stabilizer 0.5% BSA www.arigobio.com 1/2 Concentration 0.5 mg/ml 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 or below. Storage in frost free freezers is not recommended. Avoid repeated freeze/thaw cycles. Suggest spin the vial prior to opening. -
Gene Expression Profiles Reveal Alternative Targets of Therapeutic Intervention for the Treatment of Drug-Resistant Non-Small Cell Lung Cancers
University of Kentucky UKnowledge Theses and Dissertations--Pharmacy College of Pharmacy 2017 GENE EXPRESSION PROFILES REVEAL ALTERNATIVE TARGETS OF THERAPEUTIC INTERVENTION FOR THE TREATMENT OF DRUG-RESISTANT NON-SMALL CELL LUNG CANCERS Madeline J. Krentz Gober University of Kentucky, [email protected] Author ORCID Identifier: https://orcid.org/0000-0001-7761-6741 Digital Object Identifier: https://doi.org/10.13023/ETD.2017.309 Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Krentz Gober, Madeline J., "GENE EXPRESSION PROFILES REVEAL ALTERNATIVE TARGETS OF THERAPEUTIC INTERVENTION FOR THE TREATMENT OF DRUG-RESISTANT NON-SMALL CELL LUNG CANCERS" (2017). Theses and Dissertations--Pharmacy. 78. https://uknowledge.uky.edu/pharmacy_etds/78 This Doctoral Dissertation is brought to you for free and open access by the College of Pharmacy at UKnowledge. It has been accepted for inclusion in Theses and Dissertations--Pharmacy 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. -
TMX2) Regulates the Ran Protein Gradient and Importin-Β-Dependent Nuclear Cargo Transport Ami Oguro1,2 & Susumu Imaoka1
www.nature.com/scientificreports OPEN Thioredoxin-related transmembrane protein 2 (TMX2) regulates the Ran protein gradient and importin-β-dependent nuclear cargo transport Ami Oguro1,2 & Susumu Imaoka1 TMX2 is a thioredoxin family protein, but its functions have not been clarifed. To elucidate the function of TMX2, we explored TMX2-interacting proteins by LC-MS. As a result, importin-β, Ran GTPase (Ran), RanGAP, and RanBP2 were identifed. Importin-β is an adaptor protein which imports cargoes from cytosol to the nucleus, and is exported into the cytosol by interaction with RanGTP. At the cytoplasmic nuclear pore, RanGAP and RanBP2 facilitate hydrolysis of RanGTP to RanGDP and the disassembly of the Ran-importin-β complex, which allows the recycling of importin-β and reentry of Ran into the nucleus. Despite its interaction of TMX2 with importin-β, we showed that TMX2 is not a transport cargo. We found that TMX2 localizes in the outer nuclear membrane with its N-terminus and C-terminus facing the cytoplasm, where it co-localizes with importin-β and Ran. Ran is predominantly distributed in the nucleus, but TMX2 knockdown disrupted the nucleocytoplasmic Ran gradient, and the cysteine 112 residue of Ran was important in its regulation by TMX2. In addition, knockdown of TMX2 suppressed importin-β-mediated transport of protein. These results suggest that TMX2 works as a regulator of protein nuclear transport, and that TMX2 facilitates the nucleocytoplasmic Ran cycle by interaction with nuclear pore proteins. Tioredoxin-related transmembrane proteins (TMXs) are protein disulfde isomerase (PDI) family members and possess a transmembrane region. -
Human Social Genomics in the Multi-Ethnic Study of Atherosclerosis
Getting “Under the Skin”: Human Social Genomics in the Multi-Ethnic Study of Atherosclerosis by Kristen Monét Brown A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Epidemiological Science) in the University of Michigan 2017 Doctoral Committee: Professor Ana V. Diez-Roux, Co-Chair, Drexel University Professor Sharon R. Kardia, Co-Chair Professor Bhramar Mukherjee Assistant Professor Belinda Needham Assistant Professor Jennifer A. Smith © Kristen Monét Brown, 2017 [email protected] ORCID iD: 0000-0002-9955-0568 Dedication I dedicate this dissertation to my grandmother, Gertrude Delores Hampton. Nanny, no one wanted to see me become “Dr. Brown” more than you. I know that you are standing over the bannister of heaven smiling and beaming with pride. I love you more than my words could ever fully express. ii Acknowledgements First, I give honor to God, who is the head of my life. Truly, without Him, none of this would be possible. Countless times throughout this doctoral journey I have relied my favorite scripture, “And we know that all things work together for good, to them that love God, to them who are called according to His purpose (Romans 8:28).” Secondly, I acknowledge my parents, James and Marilyn Brown. From an early age, you two instilled in me the value of education and have been my biggest cheerleaders throughout my entire life. I thank you for your unconditional love, encouragement, sacrifices, and support. I would not be here today without you. I truly thank God that out of the all of the people in the world that He could have chosen to be my parents, that He chose the two of you.