A Case Study Involving Hexagenia Spp

Total Page:16

File Type:pdf, Size:1020Kb

A Case Study Involving Hexagenia Spp A Molecular Evolutionary Approach for Targeted-transcriptomics of PCB Exposure: A Case Study Involving Hexagenia spp. by Gina Louise Capretta A Thesis presented to The University of Guelph In partial fulfilment of requirements for the degree of Master of Science in Integrative Biology Guelph, Ontario, Canada © Gina Capretta, DecemBer, 2015 ABSTRACT A MOLECULAR EVOLUTIONARY APPROACH FOR TARGETED- TRANSCRIPTOMICS OF PCB EXPOSURE: A CASE STUDY INVOLVING Hexagenia spp. Gina Louise Capretta Advisor: University of Guelph, 2015 Dr. Mehrdad Hajibabaei This thesis developed a methodology to target candidate xenobiotic- interacting genes conserved across taxa, as well as tested the methodology as a tool to indicate chemical exposure and elucidate possible biological effects. Using PCBs as the chemical class, this thesis identified conserved candidate PCB-interacting genes and designed and tested degenerate primers to amplify those genes in divergent species. Using next-generation sequencing technology, this thesis also investigated the targeted-transcriptome response of H. rigida, a common ecotoxicological test species, following exposure of Hexagenia spp. to PCB-52 in a 96-hour water-only test, in which survivorship and bioaccumulation were also measured. Transcript sequences of target genes were generated for H. rigida and successfully annotated. Significant down-regulation of three genes (HSP90AB1, TUBA1C, and ALDH6A1) elucidated the biological processes that may be disrupted. This research shows the potential for linking molecular events to outcomes at higher levels of biological organization, an approach relevant to environmental risk assessment. Dedication To my family iii Acknowledgements There are many people to whom I owe a debt of gratitude; their contributions helped support and encourage me throughout this journey. Thank you, to my advisor, Dr. Mehrdad Hajibabaei, for challenging me to explore new technologies, new methodologies, and new ideas. Thank you for allowing me to travel to numerous conferences and encouraging me to present talks and posters. To all the members of the Hajibabaei lab (both past and present): Nicole, Mike, Steph, Rachel, Ian, and Katie, thanks for always being there to listen to my frustrations and for providing perspective when the going gets tough. To Shannon, lab manager and technician extraordinaire, thank you for helping me with RNA extractions and providing sound advice on lab protocols. A big thank you to Dr. Shadi Shokralla, for helping me through my entire thesis project, for providing both expertise and time, for guiding me through the sequencing and bioinformatics processes. Thank you to NSERC, OGS, the Ministry of Environment and Climate Change (MOECC), and the Department of Integrative Biology for providing funds for my degree. Thank you to my Advisory Committee. Thank you Dr. Glen Van Der Kraak for your advice and the Mus musculus and Danio rerio cDNA samples. Thank you Dr. Paul Sibley for your valuable comments and suggestions during the editing process. Your insight pushed me to do better. Thank you to Trudy Watson-Leung from MOECC, Aquatic Toxicology, Laboratory Services Branch. Thank you for collaborating on this project, for providing the Hexagenia organisms and set up for my PCB exposures, for providing me with tissue bioaccumulation data and water chemistry results, and thank you for your enthusiasm in integrating gene expression analysis in the work you do. Last, but not least, thank you to my family. To my daughters, Anabel and Elsa, who remind me everyday the importance for young girls to have strong and positive female role models in science. Thank you to my mom, dad, and sister for always encouraging my scientific pursuits. Thank you to Joel, my best friend, my colleague, and my partner in life – you encouraged me to start a Master’s, encouraged me to stick with it, and you are still encouraging me as I write this, providing me with your knowledge, expertise, guidance, support, time and above all else, love. iv Table of Contents Chapter 1. General Introduction ……...…………………………….. 1 Chapter 2. In silico identification of candidate PCB-interacting genes conserved in animals Introduction ………………………………………6 Materials and Methods ………………………………………9 Identification of candidate PCB-interacting genes with known invertebrate homologues ………………………………………9 Sequence alignment and analysis …………………………………….10 Functional characterization …………………………………….10 Results …………………………………….11 Discussion and Conclusion …………………………………….12 Tables and Figures …………………………………….16 Chapter 3. Design and validation of degenerate primers for candidate PCB-interacting genes conserved in animals Introduction …………………………………….22 Materials and Methods …………………………………….24 CODEHOP degenerate primers design …………………………………….24 Validation of degenerate CODEHOP primers …………………………………….25 RNA isolation and cDNA synthesis …………………………………….26 PCR amplification …………………………………….27 Visual confirmation …………………………………….28 Bioinformatics confirmation …………………………………….28 Sanger sequencing and analysis …………………………………….28 Results …………………………………….29 Discussion and Conclusion …………………………………….31 Tables and Figures …………………………………….34 Chapter 4. Assesssing the targeted-transcriptome response of Hexagenia rigida to PCB-52 using PCB-interacting genes conserved across taxa Introduction …………………………………….42 Materials and Methods …………………………………….45 Exposures …………………………………….45 Tissue bioaccumulation of PCB-52 …………………………………….46 Selection of candidate genes …………………………………….46 DNA barcoding for species verification …………………………………….47 Total RNA-extraction for targeted- transcriptomics …………………………………….47 RT-PCR for cDNA synthesis …………………………………….48 v Library preparation for Illumina MiSeq sequencing …………………………………….48 Sequencing on Illumina MiSeq …………………………………….49 Data pre-processing …………………………………….49 Annotation and alignment …………………………………….49 Statistical analysis on technical replicates …………………………………….50 Differential gene expression analysis …………………………………….51 Results …………………………………….52 Discussion and Conclusion …………………………………….53 Tables and Figures …………………………………….62 Chapter 5. General Conclusion …………………………………….66 References …………………………………….68 Appendix …………………………………….81 vi List of Tables Table 2.1 Number and sources of mRNA sequences used. 6.23 ± 0.75 = average (± SD) number of sequences per gene alignment 109 = total number of homologous PCB-interacting genes, at least 1 invertebrate sequence/gene; 279.86 ± 116.88 base pairs = average (± SD) length of domain per gene. Table 2.2 Domain conservation of candidate PCB-interacting genes in each KEGG pathway. Table 2.3 Functional characterization of candidate PCB-interacting conserved across taxa (N=109). * = multi-functional ; Lower conservation: < 49.5% conservation/domain; Higher conservation: ≥ 49.5% conservation/domain. Table 3.1 Candidate PCB-interacting genes conserved in animals used for degenerate primer design (N=71 ≥ 49.5% nucleotide conservation for domain selected). Table 3.2 Annealing temperature for each gene’s primer pair. *=housekeeping gene. Primers in bold were tested on Sample 2 of H. limbata. Table 3.3 Number of primer sets considered successful at each confirmation level for each species. Table 4.1 Degenerate primers used in targeted RNA-seq analysis. * housekeeping gene; TA = annealing temperature; Uppercase letters = non degenerate core; Lower letters = degenerate clamp. Insect homologue gene name and symbol is represented by D. melanogaster. Table 4.2 Water chemistry, survivorship, and tissue bioaccumulation results from 96 hour PCB-52 exposure. Table 4.3 Number of each species of Hexagenia per treatment. Table 4.4 Sequencing and annotation results from initial bioinformatics processing. Table 4.5 Log2 fold change values of all genes for the acetone (carrier solution) control and 0.033 µg/L PCB-52. Asterisks denote log2 fold changes ≥ |1| that are statistically significant (p < 0.05). vii Table 4.6 Induction of HSP90 by several environmental stressors in various invertebrate species. Appendix Table A1. Candidate PCB-interacting genes conserved in animals (N=109). Table A2. Summary statistics for domain nucleotide conservation of candidate PCB-interacting genes per KEGG pathway. Table A3. Summary statistics for domain amino acid conservation of candidate PCB-interacting genes per KEGG pathway. Table A4. CODEHOP primers and primer properties (N=68). Upper case letters = non-degenerate core; Lower case letter = degenerate clamp; D=degeneracy; Tm=melting temperature; *=housekeeping gene. Table A5. BLAST output for all genes tested using CODEHOP primers for all species. Q=query; SL=sequence length. List of Figures Figure 1.1 Generic structure of PCBs. Numbering is on the left ring and positioing on the right ring (From Richardson and Schlenk 2011). Figure 1.2 Thesis conceptual framework, divided by objective. A candidate PCB-interacting gene is a gene with a documented effect on gene expression associated with any polychlorinated biphenyl in any organism across any level of biological organization. Figure 2.1 Workflow to identify candidate PCB-interacting genes conserved across taxa using available online databases and bioinformatics tools used in molecular evolution. * nucleotide conservation is represented by the number of identical bases over the total numbers of bases for the region selected. Figure 2.2 Relative frequency of candidate PCB-interacting genes conserved in animals per KEGG Pathway. Figure 3.1 CODEHOP design strategy of degenerate primers for PCB-interacting genes conserved in animals * organisms
Recommended publications
  • Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle
    Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle Slim Ben-Jemaa, Gabriele Senczuk, Elena Ciani, Roberta Ciampolini, Gennaro Catillo, Mekki Boussaha, Fabio Pilla, Baldassare Portolano, Salvatore Mastrangelo To cite this version: Slim Ben-Jemaa, Gabriele Senczuk, Elena Ciani, Roberta Ciampolini, Gennaro Catillo, et al.. Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle. Frontiers in Genetics, Frontiers, 2021, 10.3389/fgene.2021.675569. hal-03210766 HAL Id: hal-03210766 https://hal.inrae.fr/hal-03210766 Submitted on 28 Apr 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License ORIGINAL RESEARCH published: 28 April 2021 doi: 10.3389/fgene.2021.675569 Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle Slim Ben-Jemaa 1, Gabriele Senczuk 2, Elena Ciani 3, Roberta
    [Show full text]
  • 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.
    [Show full text]
  • Extensive Characterization of IFN-Induced Gtpases Mgbp1 to Mgbp10 Involved in Host Defense
    Extensive Characterization of IFN-Induced GTPases mGBP1 to mGBP10 Involved in Host Defense This information is current as Daniel Degrandi, Carolin Konermann, Cornelia of October 1, 2021. Beuter-Gunia, Alexandra Kresse, Jan Würthner, Stefanie Kurig, Sandra Beer and Klaus Pfeffer J Immunol 2007; 179:7729-7740; ; doi: 10.4049/jimmunol.179.11.7729 http://www.jimmunol.org/content/179/11/7729 Downloaded from Supplementary http://www.jimmunol.org/content/suppl/2008/03/10/179.11.7729.DC1 Material http://www.jimmunol.org/ References This article cites 56 articles, 23 of which you can access for free at: http://www.jimmunol.org/content/179/11/7729.full#ref-list-1 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists by guest on October 1, 2021 • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2007 by The American Association of Immunologists All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Extensive Characterization of IFN-Induced GTPases mGBP1 to mGBP10 Involved in Host Defense1 Daniel Degrandi,2 Carolin Konermann,2 Cornelia Beuter-Gunia,2 Alexandra Kresse, Jan Wu¨rthner, Stefanie Kurig, Sandra Beer,3 and Klaus Pfeffer3 IFN-␥ orchestrates a potent antimicrobial host response.
    [Show full text]
  • Product Datasheet Qprest
    Product Datasheet QPrEST PRODUCT SPECIFICATION Product Name QPrEST TMM98 Mass Spectrometry Protein Standard Product Number QPrEST39234 Protein Name Transmembrane protein 98 Uniprot ID Q9Y2Y6 Gene TMEM98 Product Description Stable isotope-labeled standard for absolute protein quantification of Transmembrane protein 98. Lys (13C and 15N) and Arg (13C and 15N) metabolically labeled recombinant human protein fragment. Application Absolute protein quantification using mass spectrometry Sequence (excluding CRQRYCRPRDLLQRYDSKPIVDLIGAMETQSEPSELELDDVVITNPHIEA fusion tag) ILENEDWIEDASGLMSHCIAILKICHTLTEKLVAMTMGSGAKMKTSASVS Theoretical MW 28997 Da including N-terminal His6ABP fusion tag Fusion Tag A purification and quantification tag (QTag) consisting of a hexahistidine sequence followed by an Albumin Binding Protein (ABP) domain derived from Streptococcal Protein G. Expression Host Escherichia coli LysA ArgA BL21(DE3) Purification IMAC purification Purity >90% as determined by Bioanalyzer Protein 230 Purity Assay Isotopic Incorporation >99% Concentration >5 μM after reconstitution in 100 μl H20 Concentration Concentration determined by LC-MS/MS using a highly pure amino acid analyzed internal Determination reference (QTag), CV ≤10%. Amount >0.5 nmol per vial, two vials supplied. Formulation Lyophilized in 100 mM Tris-HCl 5% Trehalose, pH 8.0 Instructions for Spin vial before opening. Add 100 μL ultrapure H2O to the vial. Vortex thoroughly and spin Reconstitution down. For further dilution, see Application Protocol. Shipping Shipped at ambient temperature Storage Lyophilized product shall be stored at -20°C. See COA for expiry date. Reconstituted product can be stored at -20°C for up to 4 weeks. Avoid repeated freeze-thaw cycles. Notes For research use only Product of Sweden. For research use only. Not intended for pharmaceutical development, diagnostic, therapeutic or any in vivo use.
    [Show full text]
  • Viewer 4.0 Software [73]
    BMC Genomics BioMed Central Research Open Access Bioinformatic search of plant microtubule-and cell cycle related serine-threonine protein kinases Pavel A Karpov1, Elena S Nadezhdina2,3,AllaIYemets1, Vadym G Matusov1, Alexey Yu Nyporko1,NadezhdaYuShashina3 and Yaroslav B Blume*1 Addresses: 1Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 04123 Kyiv, Ukraine, 2Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russian Federation and 3AN Belozersky Institute of Physical- Chemical Biology, Moscow State University, Leninsky Gory, 119992 Moscow, Russian Federation E-mail: Pavel A Karpov - [email protected]; Elena S Nadezhdina - [email protected]; Alla I Yemets - [email protected]; Vadym G Matusov - [email protected]; Alexey Yu Nyporko - [email protected]; Nadezhda Yu Shashina - [email protected]; Yaroslav B Blume* - [email protected] *Corresponding author from International Workshop on Computational Systems Biology Approaches to Analysis of Genome Complexity and Regulatory Gene Networks Singapore 20-25 November 2008 Published: 10 February 2010 BMC Genomics 2010, 11(Suppl 1):S14 doi: 10.1186/1471-2164-11-S1-S14 This article is available from: http://www.biomedcentral.com/1471-2164/11/S1/S14 Publication of this supplement was made possible with help from the Bioinformatics Agency for Science, Technology and Research of Singapore and the Institute for Mathematical Sciences at the National University of Singapore. © 2010 Karpov et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
    [Show full text]
  • WO 2019/079361 Al 25 April 2019 (25.04.2019) W 1P O PCT
    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization I International Bureau (10) International Publication Number (43) International Publication Date WO 2019/079361 Al 25 April 2019 (25.04.2019) W 1P O PCT (51) International Patent Classification: CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, C12Q 1/68 (2018.01) A61P 31/18 (2006.01) DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, C12Q 1/70 (2006.01) HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, (21) International Application Number: MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, PCT/US2018/056167 OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, (22) International Filing Date: SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, 16 October 2018 (16. 10.2018) TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (25) Filing Language: English (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, (26) Publication Language: English GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, (30) Priority Data: UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, 62/573,025 16 October 2017 (16. 10.2017) US TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, ΓΕ , IS, IT, LT, LU, LV, (71) Applicant: MASSACHUSETTS INSTITUTE OF MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, TECHNOLOGY [US/US]; 77 Massachusetts Avenue, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, Cambridge, Massachusetts 02139 (US).
    [Show full text]
  • Recurrence of Hexagenia Mayflies Demonstrates Improved Water Quality in Pool 2 and Lake Pepin, Upper Mississippi River
    OpenRiver Cal Fremling Papers Cal Fremling Archive 1990 Recurrence of hexagenia mayflies demonstrates improved water quality in Pool 2 and Lake Pepin, Upper Mississippi River Cal R. Fremling Winona State University Follow this and additional works at: https://openriver.winona.edu/calfremlingpapers Recommended Citation Fremling, Cal R., "Recurrence of hexagenia mayflies demonstrates improved water quality in Pool 2 and Lake Pepin, Upper Mississippi River" (1990). Cal Fremling Papers. 35. https://openriver.winona.edu/calfremlingpapers/35 This Book is brought to you for free and open access by the Cal Fremling Archive at OpenRiver. It has been accepted for inclusion in Cal Fremling Papers by an authorized administrator of OpenRiver. For more information, please contact [email protected]. i\ ooj>. at RECURRENCE OF HEXAGENIA MAYFLIES DEMONSTRATES IMPROVED WATER QUALITY IN POOL 2 AND LAKE PEPIN, UPPER MISSISSIPPI RIVER Calvin R. Fremling1 and D. Kent Johnson2 1 Biology Department, Winona State University, Winona, Minnesota, 55987, USA 2Metropolitan Waste Control Commission, St. Paul, Minnesota, 55101, USA ABSTRACT Hexagenia mayflies are good indicators of general water quality because they have long life cycles and because their burrowing nymphs, which are unable to tolerate anaerobic conditions or swim long distances, live in sediments where toxins tend to accumulate. While chemical tests only describe water quality in terms of specific parameters and times, Hexagenia distribution indicates synergistic effects of many toxins, anoxia and other stresses throughout the year. Over 1,400 collections of imagoes and subimagoes along the Upper Mississippi River in 1957-1968,1976 showed that most of the 29 navigation pools supported large populations, as did impoundments upstream of Minneapolis-St.Paul.
    [Show full text]
  • Supplemental Figure and Table Legends
    Supplemental figure and table legends Supplementary Figure 1: KIAA1841 is well conserved among vertebrates. NCBI HomoloGene pairwise alignment scores of human KIAA1841 sequence compared to other vertebrate orthologs. Supplementary Figure 2: µ-germline transcripts (GLT) and AID mRNA expression are not affected by overexpression of KIAA1841. Splenic B cells were isolated from wild-type mice, and transduced with retroviral vector control (pMIG) or a vector expressing KIAA1841. Levels of µ-GLT and AID mRNA were determined at 72h post-infection by RT-qPCR, and normalized to -actin mRNA and the pMIG control. The mean of three independent experiments +/- SD is shown. NS, p = not significant, p 0.05, two-tailed paired student’s t-test. Supplementary Figure 3: Overexpression of untagged and Xpress-tagged KIAA1841 does not affect cell proliferation. Splenic B cells were isolated from wild-type mice, stimulated with LPS+IL4, and transduced with retroviral vector control (pMIG) or a vector expressing KIAA1841 or Xpress (Xp)-tagged KIAA1841. Cells are labeled with seminaphthorhodafluor (SNARF) cell tracking dye and SNARF intensity was measured at 0h, 24h, and 48h after retroviral infection. Histograms of transduced cells (GFP+) for pMIG control, KIAA1841 and Xp-KIAA1841 were superimposed at each time point. Three independent retroviral infection experiments are shown. Supplementary Figure 4: Sequence alignment of the putative SANT domain of KIAA1841 with the SANT domain of SWI3. Alignment was performed using ClustalOmega; *, conserved residue, :, strongly similar residues, ., weakly similar residues. Numbers indicate amino acid residues in each sequence. Helix 3, which has been reported to be important for the chromatin remodeling function of SWI3 (Boyer et.
    [Show full text]
  • Functions of Drosophila Pak (P21-Activated Kinase) in Morphogenesis: a Mechanistic Model Based on Cellular, Molecular, and Genetic Studies
    Functions of Drosophila Pak (p21-activated kinase) in Morphogenesis: A Mechanistic Model based on Cellular, Molecular, and Genetic Studies Item Type text; Electronic Dissertation Authors Lewis, Sara Ann Publisher The University of Arizona. Rights Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author. Download date 07/10/2021 10:07:41 Link to Item http://hdl.handle.net/10150/594389 FUNCTIONS OF DROSOPHILA PAK (P21-ACTIVATED KINASE) IN MORPHOGENESIS: A MECHANISTIC MODEL BASED ON CELLULAR, MOLECULAR, AND GENETIC STUDIES by Sara Lewis A Dissertation Submitted to the Faculty of the GRADUATE INTERDISCIPLINARY PROGRAM in Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY IN NEUROSCIENCE In the Graduate College THE UNIVERSITY OF ARIZONA 2015 THE UNIVERSITY OF ARIZONA GRADUATE COLLEGE As members of the Dissertation Committee, we certify that we have read the dissertation prepared by Sara Lewis, titled “Functions of Drosophila Pak (p21-activated kinase) in morphogenesis: a mechanistic model based on cellular, molecular and genetic studies” and recommend that it be accepted as fulfilling the dissertation requirement for the Degree of Doctor of Philosophy. _______________________________________________________________________ Date: November 18, 2015 Dr. Linda Restifo _______________________________________________________________________ Date: November 18, 2015 Dr. Jean Wilson _______________________________________________________________________ Date: November 18, 2015 Dr. Konrad Zinsmaier _______________________________________________________________________ Date: November 18, 2015 Dr. Lynne Oland Final approval and acceptance of this dissertation is contingent upon the candidate’s submission of the final copies of the dissertation to the Graduate College.
    [Show full text]
  • United States Patent (10) Patent No.: US 9,562,241 B2 Burk Et Al
    USOO9562241 B2 (12) United States Patent (10) Patent No.: US 9,562,241 B2 Burk et al. (45) Date of Patent: Feb. 7, 2017 (54) SEMI-SYNTHETIC TEREPHTHALIC ACID 5,487.987 A * 1/1996 Frost .................... C12N 9,0069 VLAMCROORGANISMIS THAT PRODUCE 5,504.004 A 4/1996 Guettler et all 435,142 MUCONCACID 5,521,075- W I A 5/1996 Guettler et al.a (71) Applicant: GENOMATICA, INC., San Diego, CA 3. A '95 seal. (US) 5,686,276 A 11/1997 Lafend et al. 5,700.934 A 12/1997 Wolters et al. (72) Inventors: Mark J. Burk, San Diego, CA (US); (Continued) Robin E. Osterhout, San Diego, CA (US); Jun Sun, San Diego, CA (US) FOREIGN PATENT DOCUMENTS (73) Assignee: Genomatica, Inc., San Diego, CA (US) CN 1 358 841 T 2002 EP O 494 O78 7, 1992 (*) Notice: Subject to any disclaimer, the term of this (Continued) patent is extended or adjusted under 35 U.S.C. 154(b) by 0 days. OTHER PUBLICATIONS (21) Appl. No.: 14/308,292 Abadjieva et al., “The Yeast ARG7 Gene Product is Autoproteolyzed to Two Subunit Peptides, Yielding Active (22) Filed: Jun. 18, 2014 Ornithine Acetyltransferase,” J. Biol. Chem. 275(15): 11361-11367 2000). (65) Prior Publication Data . al., “Discovery of amide (peptide) bond synthetic activity in US 2014/0302573 A1 Oct. 9, 2014 Acyl-CoA synthetase,” J. Biol. Chem. 28.3(17): 11312-11321 (2008). Aberhart and Hsu, "Stereospecific hydrogen loss in the conversion Related U.S. Application Data of H, isobutyrate to f—hydroxyisobutyrate in Pseudomonas (63) Continuation of application No.
    [Show full text]
  • Declines in an Abundant Aquatic Insect, the Burrowing Mayfly, Across
    Declines in an abundant aquatic insect, the burrowing mayfly, across major North American waterways Phillip M. Stepaniana,b,c,1 , Sally A. Entrekind, Charlotte E. Wainwrightc , Djordje Mirkovice , Jennifer L. Tankf , and Jeffrey F. Kellya,b aDepartment of Biology, University of Oklahoma, Norman, OK 73019; bCorix Plains Institute, University of Oklahoma, Norman, OK 73019; cDepartment of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN 46556; dDepartment of Entomology, Virginia Tech, Blacksburg, VA 24060; eCooperative Institute for Mesoscale Meteorological Studies, University of Oklahoma, Norman, OK 73072; and fDepartment of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556 Edited by David W. Schindler, University of Alberta, Edmonton, Canada, and approved December 12, 2019 (received for review August 6, 2019) Seasonal animal movement among disparate habitats is a fun- while also serving as a perennial annoyance for waterside resi- damental mechanism by which energy, nutrients, and biomass dents; most of all, these mayfly emergences were a conspicuous are transported across ecotones. A dramatic example of such sign of a productive, functional aquatic ecosystem (14–17). How- exchange is the annual emergence of mayfly swarms from fresh- ever, by 1970, these mass emergences had largely disappeared. water benthic habitats, but their characterization at macroscales The combination of increasing eutrophication from agricultural has remained impossible. We analyzed radar observations of runoff, chronic hypoxia, hydrologic engineering, and environ- mayfly emergence flights to quantify long-term changes in annual mental toxicity resulted in the disappearance of Hexagenia from biomass transport along the Upper Mississippi River and West- many prominent midwestern waterways, with complete extir- ern Lake Erie Basin.
    [Show full text]
  • Some Ecological Relationships of Mayflies, Caddisflies, and Fish in the Mississippi River Near Keokuk, Iowa " (1965)
    Iowa State University Capstones, Theses and Retrospective Theses and Dissertations Dissertations 1965 Some ecological relationships of mayflies, caddisflies, nda fish in the Mississippi River near Keokuk, Iowa Thomas Lee Wenke Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/rtd Part of the Zoology Commons Recommended Citation Wenke, Thomas Lee, "Some ecological relationships of mayflies, caddisflies, and fish in the Mississippi River near Keokuk, Iowa " (1965). Retrospective Theses and Dissertations. 2845. https://lib.dr.iastate.edu/rtd/2845 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Retrospective Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. This dissertation has been micioiihned exactly as received 66-3909 WENKEi Thomas Lee, 1935- SOME ECOLOGICAL RELATIONSHIPS OF MAYFLIES, CADDISFLIES, AND FISH IN THE MISSISSIPPI RIVER NEAR KEOKUK, IOWA. Iowa State University of Science and Technology Ph.D., 1965 Zoology University Microfilms, Inc., Ann Arbor, Michigan SOME ECOLOGICAL RELATIONSHIPS OF MAYFLIES, CADDISFLIES, AND FISH IN THE MISSISSIPPI RIVER NEAR KEOKUK, IOWA by Thomas Lee Wenke A Dissertation Submitted to the Graduate Faculty in Partial Fulfillment of The Requirements for the Degree of DOCTOR OF PHILOSOPHY Major Subject: Zoology Approved: Signature was redacted for privacy. Signature was redacted for privacy. Head of Major Department Signature was redacted for privacy. ramlate College Iowa State University Of Science and Technology Ames, Iowa 1965 PLEASE NOTE: Figure pages are not original copy.
    [Show full text]