DOCSLIB.ORG

UC San Francisco Electronic Theses and Dissertations

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

UCSF UC San Francisco Electronic Theses and Dissertations Title Uncovering virulence pathways facilitated by proteolysis in HIV and a HIV associated fungal pathogen, Cryptococcus neoformans Permalink https://escholarship.org/uc/item/7vv2p2fh Author Clarke, Starlynn Cascade Publication Date 2015 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California ii Acknowledgments I would first like to thank my thesis advisor, Dr. Charles Craik. Throughout my PhD Charly has been unfailingly optimistic and enthusiastic about my projects, but most importantly, he has always had confidence in my abilities. During the course of graduate school I have doubted myself and my capabilities almost daily, but Charly has always believed that I would be successful in my scientific endeavors and I cannot thank him enough for that. Charly is the most enthusiastic scientist that I have ever met and he has the capacity to find a silver lining to almost any event. He also understands the importance of presentation and has the resourcefulness to transform almost any situation into an opportunity. These are all traits that do not come naturally to me, but having Charly as a mentor has helped me to learn some of these important skills. I would also like to thank my thesis committee members, Dr. Raul Andino and Dr. John Gross who have both been incredibly supportive over the years. Despite the fact that my research ended up veering away from the original focus that was more in line with their expertise, they have continued to provide me with encouragement and thoughtful feedback during my thesis committee meetings as well as at other times that I sought their advice. Dr. Anthony O’Donoghue was my friend and mentor in the Craik lab for five years. His guidance and knowledge were instrumental in my research success. Besides that, Anthony is one of the most good-natured people that I have ever met and in spite of the long list of demands on his time, he always answered my questions and even went out of his way to check up on me and offer to discuss my project. When I was struggling with a project that was not working he helped me to find a new direction, something that I will always be grateful to him for. I would like to thank Dr. Hiten Madhani, Dr. Phillip Dumesic and Christina Homer, my collaborators on my research project studying peptidases secreted by Cryptococcus neoformans. I first proposed the project to Phillip and despite his extremely busy schedule with iii his numerous and successful projects, he made time to plan experiments with me and help me with reagents, experiments, and edits to our manuscript. Likewise, Christina has been a wealth of advice on the project as well as generously contributing her time to helping me with mouse experiments and editing our manuscript. Hiten has been supportive and helpful on the project as well. I am very fortunate to have had an expert in the field to help me construct the story and determine how best to present it for publication. My favorite aspect of the Craik lab is the wonderful people that have worked in the lab over the years. In addition to Anthony, Dr. Dan Hostetter, Dr. Jungmin Kim and Dr. Michael Winter were my mentors and friends in the Craik lab. All extremely knowledgeable, they have always been more than willing to answer any questions I have had, about science as well as career choices or life in general. However, there has always been a strong sense of camaraderie and support amongst all of the Craik lab members. At some point, I have sought help from almost everyone in the lab and been surprised and touched by how generously everyone has shared their time and expertise. In particular, I would like to thank Dr. Cheryl Tajon for helping me make and test nanosensors for HIV protease and the graduate students of my same year Dr. Jonathan Gable and Dr. Melody Lee for their support as we each achieved the mile stones of graduate school. I have met so many wonderful people at UCSF, first and foremost, my class mate, room mate and friend, Kelly Nissen. Kelly is the most supportive person that I have ever known and also a wonderful scientist. She has given me pep talks countless times throughout graduate school as well as thoughtful advice on my scientific writings and presentations. Dr. Manon Eckhardt is also a wonderful friend that I have made at UCSF. She is an excellent scientist and a fun and interesting person and has cheered me up many times. Nicole Olsen, a graduate student in the Craik lab has been a great friend to me and made lab a more enjoyable place. Finally, I would like to thank my mother Felice Clarke and my non-scientist friends for their support and love during this long process. They have always been there for me when things iv were not going well and when good things happen they are ready to celebrate with me. I have had the opportunity to work on several great projects at UCSF and publish with some amazing scientists. I am sixth author on Dr. Stefanie Jager’s paper “Global landscape of HIV-human protein complexes” Pubmed ID: PMC3310911 where I contributed studies of the interactions between HIV protease and the eukaryotic translation initiation complex 3 (eIF3). I am fourth author on Christina Homer’s paper “Convergent evolution of a peptide-based cell-cell signaling system required for the virulence of a eukaryotic pathogen” (submitted to Cell). For this project I helped to determine that the peptidase secretion of C. neoformans is affected by a quorum sensing pathway discovered by Christina. I am second author on Dr. Steven Jones’s paper “Evolutionary selection on barrier activity: The aspartyl protease Bar1 is an enzyme with novel substrate specificity” (submitted to mBio) where I contributed to identifying the unique specificity of a peptidase secreted by Candida albicans called Bar1. Finally, my findings on the secreted peptidases of C. neoformans will be published in collaboration with Dr. Phillip Dumesic, Dr. Christina Homer, Dr. Anthony O’Donoghue, Lenka, Pallova, Dr. Pavel Maher, Dr. Hiten Madhani and Dr. Charles Craik, “Integrated activity and genetic profiling of secreted peptidases in Cryptococcus neoformans reveals an asparty peptidase required for low pH survival and virulence” (submitted to PLOS Pathogens). v Uncovering virulence pathways facilitated by proteolysis in HIV and a HIV associated fungal pathogen, Cryptococcus neoformans By Starlynn Clarke Abstract Peptidases are enzymes that cleave proteins or peptides, irreversibly modifying their substrates. Proteolytic activity is essential for many biological processes, however these enzymes are also associated with many pathological states. In particular, peptidases are frequently used by pathogenic organisms for purposes such as host invasion, immune system evasion and nutrient acquisition. Both HIV and the HIV/AIDS associated fungal pathogen, Cryptococcus neoformans, are known to employ peptidases to promote virulence. HIV expresses a protease that has a well characterized role in maturation of infectious viral particles by cleaving viral polyproteins into their individual constituents. However, in this work we present evidence that this enzyme has a dual purpose. Our results indicate that in addition to processing viral proteins, HIV protease cleaves numerous host-proteins to optimize the host environment for viral replication. We conducted a study of HIV protease host-protein interactions using an affinity purification-mass spectrometry based approach with tagged, inactive HIV protease. Over 50 candidate substrate proteins were identified through this technique. We then individually studied over 40 of these proteins, revealing that eight are cleaved by HIV protease in vitro. Through experiments assaying viral replication in combination with siRNA knock-down of host proteins, we discovered one vi of these host-proteins, the eukaryotic translation initiation factor 3d (eIF3d) restricts viral reverse transcription. Therefore, we hypothesize that cleavage of this protein by HIV protease may promote reverse transcription during viral infection. In this work we also investigate the secreted peptidases of C. neoformans, an opportunistic fungal pathogen responsible for over 600,000 deaths every year. This organism is known to secrete peptidases but the functions, regulation and characteristics of these enzymes have remained mysterious. We used an unbiased activity based approach to detail the specificity and regulation of extracellular peptidase activity produced by this pathogen grown under two different culture conditions. We pinpoint a principle enzyme responsible for secreted peptidase activity and find that this enzyme is important for tolerance to low pH environments as well as virulence in a mouse model of cryptococcus infection. Using knowledge of the substrate specificity of this enzyme, we screen a focused library of small molecule inhibitors, identifying four potent compounds. Our study of the functions and characteristics of peptidases from viral and fungal pathogens reveals important information regarding the host-pathogen biology of these organisms. Our results may be informative for the development of alternative therapeutic strategies for combating these intractable pathogens. Furthermore, the approaches and techniques we describe are useful for the investigation of proteolytic activity secreted by other disease-causing organisms. vii TABLE OF CONTENTS CHAPTER 1: INTRODUCTION 1 1.1 Peptidases: an overview 1 1.2 Investigating substrate specificity
Recommended publications
  • Integrative Genomic and Epigenomic Analyses Identified IRAK1 As a Novel Target for Chronic Inflammation-Driven Prostate Tumorigenesis

    Integrative Genomic and Epigenomic Analyses Identified IRAK1 As a Novel Target for Chronic Inflammation-Driven Prostate Tumorigenesis

    bioRxiv preprint doi: https://doi.org/10.1101/2021.06.16.447920; this version posted June 16, 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. Integrative genomic and epigenomic analyses identified IRAK1 as a novel target for chronic inflammation-driven prostate tumorigenesis Saheed Oluwasina Oseni1,*, Olayinka Adebayo2, Adeyinka Adebayo3, Alexander Kwakye4, Mirjana Pavlovic5, Waseem Asghar5, James Hartmann1, Gregg B. Fields6, and James Kumi-Diaka1 Affiliations 1 Department of Biological Sciences, Florida Atlantic University, Florida, USA 2 Morehouse School of Medicine, Atlanta, Georgia, USA 3 Georgia Institute of Technology, Atlanta, Georgia, USA 4 College of Medicine, Florida Atlantic University, Florida, USA 5 Department of Computer and Electrical Engineering, Florida Atlantic University, Florida, USA 6 Department of Chemistry & Biochemistry and I-HEALTH, Florida Atlantic University, Florida, USA Corresponding Author: [email protected] (S.O.O) Running Title: Chronic inflammation signaling in prostate tumorigenesis bioRxiv preprint doi: https://doi.org/10.1101/2021.06.16.447920; this version posted June 16, 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 The impacts of many inflammatory genes in prostate tumorigenesis remain understudied despite the increasing evidence that associates chronic inflammation with prostate cancer (PCa) initiation, progression, and therapy resistance.
  • Database of Cattle Candidate Genes and Genetic Markers for Milk Production and Mastitis

    Database of Cattle Candidate Genes and Genetic Markers for Milk Production and Mastitis

    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central doi:10.1111/j.1365-2052.2009.01921.x Database of cattle candidate genes and genetic markers for milk production and mastitis J. Ogorevc*, T. Kunej*, A. Razpet and P. Dovc Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia Summary A cattle database of candidate genes and genetic markers for milk production and mastitis has been developed to provide an integrated research tool incorporating different types of information supporting a genomic approach to study lactation, udder development and health. The database contains 943 genes and genetic markers involved in mammary gland development and function, representing candidates for further functional studies. The candidate loci were drawn on a genetic map to reveal positional overlaps. For identification of candidate loci, data from seven different research approaches were exploited: (i) gene knockouts or transgenes in mice that result in specific phenotypes associated with mam- mary gland (143 loci); (ii) cattle QTL for milk production (344) and mastitis related traits (71); (iii) loci with sequence variations that show specific allele-phenotype interactions associated with milk production (24) or mastitis (10) in cattle; (iv) genes with expression profiles associated with milk production (207) or mastitis (107) in cattle or mouse; (v) cattle milk protein genes that exist in different genetic variants (9); (vi) miRNAs expressed in bovine mammary gland (32) and (vii) epigenetically regulated cattle genes associated with mammary gland function (1). Fourty-four genes found by multiple independent analyses were suggested as the most promising candidates and were further in silico analysed for expression levels in lactating mammary gland, genetic variability and top biological func- tions in functional networks.
  • Mir-379 Deletion Ameliorates Features of Diabetic Kidney Disease By

    Mir-379 Deletion Ameliorates Features of Diabetic Kidney Disease By

    ARTICLE https://doi.org/10.1038/s42003-020-01516-w OPEN miR-379 deletion ameliorates features of diabetic kidney disease by enhancing adaptive mitophagy via FIS1 ✉ Mitsuo Kato 1,8 , Maryam Abdollahi 1,8, Ragadeepthi Tunduguru1, Walter Tsark2, Zhuo Chen 1, 1234567890():,; Xiwei Wu3, Jinhui Wang3, Zhen Bouman Chen 1,4, Feng-Mao Lin1, Linda Lanting1, Mei Wang1, Janice Huss5, ✉ Patrick T Fueger 5,6, David Chan7 & Rama Natarajan 1,4 Diabetic kidney disease (DKD) is a major complication of diabetes. Expression of members of the microRNA (miRNA) miR-379 cluster is increased in DKD. miR-379, the most upstream 5′-miRNA in the cluster, functions in endoplasmic reticulum (ER) stress by targeting EDEM3. However, the in vivo functions of miR-379 remain unclear. We created miR-379 knockout (KO) mice using CRISPR-Cas9 nickase and dual guide RNA technique and characterized their phenotype in diabetes. We screened for miR-379 targets in renal mesangial cells from WT vs. miR-379KO mice using AGO2-immunopreciptation and CLASH (cross-linking, ligation, sequencing hybrids) and identified the redox protein thioredoxin and mitochondrial fission-1 protein. miR-379KO mice were protected from features of DKD as well as body weight loss associated with mitochondrial dysfunction, ER- and oxidative stress. These results reveal a role for miR-379 in DKD and metabolic processes via reducing adaptive mitophagy. Strate- gies targeting miR-379 could offer therapeutic options for DKD. 1 Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA.
  • Bioinformatic Analysis of Structure and Function of LIM Domains of Human Zyxin Family Proteins

    Bioinformatic Analysis of Structure and Function of LIM Domains of Human Zyxin Family Proteins

    International Journal of Molecular Sciences Article Bioinformatic Analysis of Structure and Function of LIM Domains of Human Zyxin Family Proteins M. Quadir Siddiqui 1,† , Maulik D. Badmalia 1,† and Trushar R. Patel 1,2,3,* 1 Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada; [email protected] (M.Q.S.); [email protected] (M.D.B.) 2 Department of Microbiology, Immunology and Infectious Disease, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive, Calgary, AB T2N 4N1, Canada 3 Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB T6G 2E1, Canada * Correspondence: [email protected] † These authors contributed equally to the work. Abstract: Members of the human Zyxin family are LIM domain-containing proteins that perform critical cellular functions and are indispensable for cellular integrity. Despite their importance, not much is known about their structure, functions, interactions and dynamics. To provide insights into these, we used a set of in-silico tools and databases and analyzed their amino acid sequence, phylogeny, post-translational modifications, structure-dynamics, molecular interactions, and func- tions. Our analysis revealed that zyxin members are ohnologs. Presence of a conserved nuclear export signal composed of LxxLxL/LxxxLxL consensus sequence, as well as a possible nuclear localization signal, suggesting that Zyxin family members may have nuclear and cytoplasmic roles. The molecular modeling and structural analysis indicated that Zyxin family LIM domains share Citation: Siddiqui, M.Q.; Badmalia, similarities with transcriptional regulators and have positively charged electrostatic patches, which M.D.; Patel, T.R.
  • UBQLN2 Polyclonal Antibody C-Terminal Ubiquitin-Associated Domain

    UBQLN2 Polyclonal Antibody C-Terminal Ubiquitin-Associated Domain

    UBQLN2 polyclonal antibody C-terminal ubiquitin-associated domain. They physically associate with both proteasomes and ubiquitin ligases, Catalog Number: PAB1699 and thus thought to functionally link the ubiquitination machinery to the proteasome to affect in vivo protein Regulatory Status: For research use only (RUO) degradation. This ubiquilin has also been shown to bind the ATPase domain of the Hsp70-like Stch protein. Product Description: Rabbit polyclonal antibody raised [provided by RefSeq] against synthetic peptide of UBQLN2. References: Immunogen: A synthetic peptide (conjugated with KLH) 1. Structural studies of the interaction between ubiquitin corresponding to C-terminus of human UBQLN2. family proteins and proteasome subunit S5a. Walters KJ, Kleijnen MF, Goh AM, Wagner G, Howley PM. Host: Rabbit Biochemistry. 2002 Feb 12;41(6):1767-77. 2. The hPLIC proteins may provide a link between the Reactivity: Human ubiquitination machinery and the proteasome. Kleijnen Applications: WB-Ce MF, Shih AH, Zhou P, Kumar S, Soccio RE, Kedersha (See our web site product page for detailed applications NL, Gill G, Howley PM. Mol Cell. 2000 Aug;6(2):409-19. information) 3. Selection system for genes encoding nuclear-targeted proteins. Ueki N, Oda T, Kondo M, Yano K, Noguchi T, Protocols: See our web site at Muramatsu M. Nat Biotechnol. 1998 http://www.abnova.com/support/protocols.asp or product Dec;16(13):1338-42. page for detailed protocols Form: Liquid Purification: Protein G purification Recommend Usage: Western Blot (1:1000) The optimal working dilution should be determined by the end user. Storage Buffer: In PBS (0.09% sodium azide) Storage Instruction: Store at 4°C.
  • (12) Patent Application Publication (10) Pub. No.: US 2005/0010974A1 Milligan Et Al

    (12) Patent Application Publication (10) Pub. No.: US 2005/0010974A1 Milligan Et Al

    US 20050010974A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2005/0010974A1 Milligan et al. (43) Pub. Date: Jan. 13, 2005 (54) PROMOTERS FOR REGULATION OF GENE Publication Classification EXPRESSION IN PLANT ROOTS (51) Int. Cl." ............................ C12N 15/82; C12O 1/68; (76) Inventors: Stephen B Milligan, Kirkland, WA C12N 15/87; C12N 15/63; (US); Dale Skalla, Research Triangle C12N 15/85; C12N 5/10; Park, NC (US); Kay Lawton, Research C12N 15/09; CO7H 21/04 Triangle Park, NC (US) (52) U.S. Cl. ..................... 800/287; 536/23.6; 435/320.1; 435/455; 435/419; 435/468; Correspondence Address: 800/278; 435/6; 536/24.33 Randee S Schwatz Syngenta Biotechnology 3054 Cornwallis Road (57) ABSTRACT Research Triangle Park, NC 27709 (US) The present invention is directed to promoters isolated from (21) Appl. No.: 10/490,147 maize and functional equivalents thereto. The promoters of the present invention have particular utility in driving root (22) PCT Filed: Nov. 4, 2002 Specific expression of heterologous genes that impart (86) PCT No.: PCT/US02/35374 increased agronomic, horticultural and/or pesticidal charac teristics to a given promoters of the invention and trans (30) Foreign Application Priority Data formed plant tissues containing DNA molecules comprising a promoter of the invention operably linked to a heterolo Nov. 7, 2001 (US)........................................... 60337026 gous gene or genes, and Seeds thereof. US 2005/0010974 A1 Jan. 13, 2005 PROMOTERS FOR REGULATION OF GENE latory Sequences may be short regions of DNA sequence EXPRESSION IN PLANT ROOTS 6-100 base pairs that define the binding sites for trans-acting factors, Such as transcription factors.
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus

    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.
  • Downloaded and Searched Against the Dbest Database to Identify Ests

    Downloaded and Searched Against the Dbest Database to Identify Ests

    BMC Genomics BioMed Central Research article Open Access A transcription map of the 6p22.3 reading disability locus identifying candidate genes Eric R Londin1, Haiying Meng2 and Jeffrey R Gruen*2 Address: 1Graduate Program in Genetics, State University of New York at Stony Brook, NY, USA and 2Yale Child Health Research Center, Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA Email: Eric R Londin - [email protected]; Haiying Meng - [email protected]; Jeffrey R Gruen* - [email protected] * Corresponding author Published: 30 June 2003 Received: 22 April 2003 Accepted: 30 June 2003 BMC Genomics 2003, 4:25 This article is available from: http://www.biomedcentral.com/1471-2164/4/25 © 2003 Londin et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL. reading disabilitydyslexia6p22.3In silicoESTs Abstract Background: Reading disability (RD) is a common syndrome with a large genetic component. Chromosome 6 has been identified in several linkage studies as playing a significant role. A more recent study identified a peak of transmission disequilibrium to marker JA04 (G72384) on chromosome 6p22.3, suggesting that a gene is located near this marker. Results: In silico cloning was used to identify possible candidate genes located near the JA04 marker. The 2 million base pairs of sequence surrounding JA04 was downloaded and searched against the dbEST database to identify ESTs. In total, 623 ESTs from 80 different tissues were identified and assembled into 153 putative coding regions from 19 genes and 2 pseudogenes encoded near JA04.
  • Noninvasive Sleep Monitoring in Large-Scale Screening of Knock-Out Mice

    Noninvasive Sleep Monitoring in Large-Scale Screening of Knock-Out Mice

    bioRxiv preprint doi: https://doi.org/10.1101/517680; this version posted January 11, 2019. 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-ND 4.0 International license. Noninvasive sleep monitoring in large-scale screening of knock-out mice reveals novel sleep-related genes Shreyas S. Joshi1*, Mansi Sethi1*, Martin Striz1, Neil Cole2, James M. Denegre2, Jennifer Ryan2, Michael E. Lhamon3, Anuj Agarwal3, Steve Murray2, Robert E. Braun2, David W. Fardo4, Vivek Kumar2, Kevin D. Donohue3,5, Sridhar Sunderam6, Elissa J. Chesler2, Karen L. Svenson2, Bruce F. O'Hara1,3 1Dept. of Biology, University of Kentucky, Lexington, KY 40506, USA, 2The Jackson Laboratory, Bar Harbor, ME 04609, USA, 3Signal solutions, LLC, Lexington, KY 40503, USA, 4Dept. of Biostatistics, University of Kentucky, Lexington, KY 40536, USA, 5Dept. of Electrical and Computer Engineering, University of Kentucky, Lexington, KY 40506, USA. 6Dept. of Biomedical Engineering, University of Kentucky, Lexington, KY 40506, USA. *These authors contributed equally Address for correspondence and proofs: Shreyas S. Joshi, Ph.D. Dept. of Biology University of Kentucky 675 Rose Street 101 Morgan Building Lexington, KY 40506 U.S.A. Phone: (859) 257-2805 FAX: (859) 257-1717 Email: [email protected] Running title: Sleep changes in knockout mice bioRxiv preprint doi: https://doi.org/10.1101/517680; this version posted January 11, 2019. 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.
  • 1 Supporting Information for a Microrna Network Regulates

    1 Supporting Information for a Microrna Network Regulates

    Supporting Information for A microRNA Network Regulates Expression and Biosynthesis of CFTR and CFTR-ΔF508 Shyam Ramachandrana,b, Philip H. Karpc, Peng Jiangc, Lynda S. Ostedgaardc, Amy E. Walza, John T. Fishere, Shaf Keshavjeeh, Kim A. Lennoxi, Ashley M. Jacobii, Scott D. Rosei, Mark A. Behlkei, Michael J. Welshb,c,d,g, Yi Xingb,c,f, Paul B. McCray Jr.a,b,c Author Affiliations: Department of Pediatricsa, Interdisciplinary Program in Geneticsb, Departments of Internal Medicinec, Molecular Physiology and Biophysicsd, Anatomy and Cell Biologye, Biomedical Engineeringf, Howard Hughes Medical Instituteg, Carver College of Medicine, University of Iowa, Iowa City, IA-52242 Division of Thoracic Surgeryh, Toronto General Hospital, University Health Network, University of Toronto, Toronto, Canada-M5G 2C4 Integrated DNA Technologiesi, Coralville, IA-52241 To whom correspondence should be addressed: Email: [email protected] (M.J.W.); yi- [email protected] (Y.X.); Email: [email protected] (P.B.M.) This PDF file includes: Materials and Methods References Fig. S1. miR-138 regulates SIN3A in a dose-dependent and site-specific manner. Fig. S2. miR-138 regulates endogenous SIN3A protein expression. Fig. S3. miR-138 regulates endogenous CFTR protein expression in Calu-3 cells. Fig. S4. miR-138 regulates endogenous CFTR protein expression in primary human airway epithelia. Fig. S5. miR-138 regulates CFTR expression in HeLa cells. Fig. S6. miR-138 regulates CFTR expression in HEK293T cells. Fig. S7. HeLa cells exhibit CFTR channel activity. Fig. S8. miR-138 improves CFTR processing. Fig. S9. miR-138 improves CFTR-ΔF508 processing. Fig. S10. SIN3A inhibition yields partial rescue of Cl- transport in CF epithelia.
  • Anti-P4HA2 (Aa 289-338) Polyclonal Antibody (DPABH-10980) This Product Is for Research Use Only and Is Not Intended for Diagnostic Use

    Anti-P4HA2 (Aa 289-338) Polyclonal Antibody (DPABH-10980) This Product Is for Research Use Only and Is Not Intended for Diagnostic Use

    Anti-P4HA2 (aa 289-338) polyclonal antibody (DPABH-10980) This product is for research use only and is not intended for diagnostic use. PRODUCT INFORMATION Antigen Description Catalyzes the post-translational formation of 4-hydroxyproline in -Xaa-Pro-Gly- sequences in collagens and other proteins. Immunogen Synthetic peptide corresponding to a region within C terminal amino acids 289-338 (VYESLCRGEG VKLTPRRQKR LFCRYHHGNR APQLLIAPFK EEDEWDSPHI) of Human P4HA2, isoform 2 (NP_001017973). Isotype IgG Source/Host Rabbit Species Reactivity Human Purification Immunogen affinity purified Conjugate Unconjugated Applications IHC - Wholemount, WB Format Liquid Size 50 μg Buffer Constituents: 97% PBS, 2% Sucrose Preservative None Storage Shipped at 4°C. Upon delivery aliquot and store at -20°C. Avoid repeated freeze / thaw cycles. GENE INFORMATION Gene Name P4HA2 prolyl 4-hydroxylase, alpha polypeptide II [ Homo sapiens ] Official Symbol P4HA2 Synonyms P4HA2; prolyl 4-hydroxylase, alpha polypeptide II; procollagen proline, 2 oxoglutarate 4 dioxygenase (proline 4 hydroxylase), alpha polypeptide II; prolyl 4-hydroxylase subunit alpha-2; 4 PH alpha 2; C P4Halpha(II); collagen prolyl 4 hydroxylase alpha(II); 4-PH alpha 2; 4-PH alpha-2; 45-1 Ramsey Road, Shirley, NY 11967, USA Email: [email protected] Tel: 1-631-624-4882 Fax: 1-631-938-8221 1 © Creative Diagnostics All Rights Reserved C-P4Halpha(II); collagen prolyl 4-hydroxylase alpha(II); procollagen-proline,2-oxoglutarate-4- dioxygenase subunit alpha-2; procollagen-proline, 2-oxoglutarate
  • Effects of B-K-Casein (CSN2-CSN3) Haplotypes and B-Lactoglobulin

    Effects of B-K-Casein (CSN2-CSN3) Haplotypes and B-Lactoglobulin

    J. Dairy Sci. 93 :3797–3808 doi: 10.3168/jds.2009-2778 © American Dairy Science Association®, 2010 . Effects of β-κ-casein (CSN2-CSN3) haplotypes and β-lactoglobulin (BLG) genotypes on milk production traits and detailed protein composition of individual milk of Simmental cows 1 V. Bonfatti ,* G. Di Martino ,* A. Cecchinato ,* D. Vicario ,† and P. Carnier * * Department of Animal Science, University of Padova, viale dell’Università 16, 35020, Legnaro, Padova, Italy † Italian Simmental Cattle Breeders Association, via Nievo 19, 33100, Udine, Italy ABSTRACT and αS1-CN. Estimated additive genetic variance for investigated traits ranged from 14 to 39% of total vari- The aim of this study was to investigate the effects ance. Increasing the frequency of specific genotypes or of CSN2-CSN3 (β-κ-casein) haplotypes and BLG haplotypes by selective breeding might be an effective (β-lactoglobulin) genotypes on milk production traits, way to change milk protein composition. content of protein fractions, and detailed protein compo- Key words: casein haplotypes , BLG genotype , milk sition of individual milk of Simmental cows. Content of protein composition , Simmental the major protein fractions was measured by reversed- phase HPLC in individual milk samples of 2,167 cows. INTRODUCTION Protein composition was measured as percentage of each casein (CN) fraction to total CN and as percent- Most research concerning milk protein polymor- age of β-lactoglobulin (β-LG) to total whey protein. phisms has focused on the associations of CSN3 (κ-CN) Genotypes at CSN2, CSN3, and BLG were ascertained and BLG (β-LG) polymorphisms with milk production by reversed-phase HPLC, and CSN2-CSN3 haplotype traits, coagulation time, curd firmness, and cheese yield.