New Mesh Headings for 2017 Listed in Alphabetical Order with Heading, Scope Note, Annotation (AN), and Tree Locations
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The Switch from Fermentation to Respiration in Saccharomyces Cerevisiae Is Regulated by the Ert1 Transcriptional Activator/Repressor
INVESTIGATION The Switch from Fermentation to Respiration in Saccharomyces cerevisiae Is Regulated by the Ert1 Transcriptional Activator/Repressor Najla Gasmi,* Pierre-Etienne Jacques,† Natalia Klimova,† Xiao Guo,§ Alessandra Ricciardi,§ François Robert,†,** and Bernard Turcotte*,‡,§,1 ‡Department of Medicine, *Department of Biochemistry, and §Department of Microbiology and Immunology, McGill University Health Centre, McGill University, Montreal, QC, Canada H3A 1A1, †Institut de recherches cliniques de Montréal, Montréal, QC, Canada H2W 1R7, and **Département de Médecine, Faculté de Médecine, Université de Montréal, QC, Canada H3C 3J7 ABSTRACT In the yeast Saccharomyces cerevisiae, fermentation is the major pathway for energy production, even under aerobic conditions. However, when glucose becomes scarce, ethanol produced during fermentation is used as a carbon source, requiring a shift to respiration. This adaptation results in massive reprogramming of gene expression. Increased expression of genes for gluconeogenesis and the glyoxylate cycle is observed upon a shift to ethanol and, conversely, expression of some fermentation genes is reduced. The zinc cluster proteins Cat8, Sip4, and Rds2, as well as Adr1, have been shown to mediate this reprogramming of gene expression. In this study, we have characterized the gene YBR239C encoding a putative zinc cluster protein and it was named ERT1 (ethanol regulated transcription factor 1). ChIP-chip analysis showed that Ert1 binds to a limited number of targets in the presence of glucose. The strongest enrichment was observed at the promoter of PCK1 encoding an important gluconeogenic enzyme. With ethanol as the carbon source, enrichment was observed with many additional genes involved in gluconeogenesis and mitochondrial function. Use of lacZ reporters and quantitative RT-PCR analyses demonstrated that Ert1 regulates expression of its target genes in a manner that is highly redundant with other regulators of gluconeogenesis. -
When Stem Cells Grow Old: Phenotypes and Mechanisms of Stem Cell Aging Michael B
© 2016. Published by The Company of Biologists Ltd | Development (2016) 143, 3-14 doi:10.1242/dev.130633 REVIEW When stem cells grow old: phenotypes and mechanisms of stem cell aging Michael B. Schultz and David A. Sinclair* ABSTRACT Thus, a stark collapse of the hematological system does not occur All multicellular organisms undergo a decline in tissue and organ during normal aging. However, when murine HSCs with long-term + − function as they age. An attractive theory is that a loss in stem cell repopulating ability were isolated by selecting for c-Kit , lineage + number and/or activity over time causes this decline. In accordance (multiple markers), Sca-1 cells (KLS) (Ikuta and Weissman, 1992; with this theory, aging phenotypes have been described for stem cells Spangrude et al., 1988), the number of HSCs was found to steadily of multiple tissues, including those of the hematopoietic system, increase with age (de Haan et al., 1997; Morrison et al., 1996). Only intestine, muscle, brain, skin and germline. Here, we discuss recent when function was measured on a per-cell basis were old advances in our understanding of why adult stem cells age and how immunophenotypic HSCs shown to have a greatly reduced ability this aging impacts diseases and lifespan. With this increased to engraft and properly differentiate in new hosts (Dykstra et al., understanding, it is feasible to design and test interventions that 2011; Liang et al., 2005; Morrison et al., 1996). Furthermore, in delay stem cell aging and improve both health and lifespan. both mice and humans, the proportion of differentiated blood cells arising from just a few HSC clones increases, suggesting that the KEY WORDS: Age-related diseases, Hematopoietic stem cells, number of active, functional HSCs declines with age (Beerman Multicellular organisms et al., 2010; Genovese et al., 2014; Jaiswal et al., 2014). -
The Interactome of KRAB Zinc Finger Proteins Reveals the Evolutionary History of Their Functional Diversification
Resource The interactome of KRAB zinc finger proteins reveals the evolutionary history of their functional diversification Pierre-Yves Helleboid1,†, Moritz Heusel2,†, Julien Duc1, Cécile Piot1, Christian W Thorball1, Andrea Coluccio1, Julien Pontis1, Michaël Imbeault1, Priscilla Turelli1, Ruedi Aebersold2,3,* & Didier Trono1,** Abstract years ago (MYA) (Imbeault et al, 2017). Their products harbor an N-terminal KRAB (Kru¨ppel-associated box) domain related to that of Krüppel-associated box (KRAB)-containing zinc finger proteins Meisetz (a.k.a. PRDM9), a protein that originated prior to the diver- (KZFPs) are encoded in the hundreds by the genomes of higher gence of chordates and echinoderms, and a C-terminal array of zinc vertebrates, and many act with the heterochromatin-inducing fingers (ZNF) with sequence-specific DNA-binding potential (Urru- KAP1 as repressors of transposable elements (TEs) during early tia, 2003; Birtle & Ponting, 2006; Imbeault et al, 2017). KZFP genes embryogenesis. Yet, their widespread expression in adult tissues multiplied by gene and segment duplication to count today more and enrichment at other genetic loci indicate additional roles. than 350 and 700 representatives in the human and mouse Here, we characterized the protein interactome of 101 of the ~350 genomes, respectively (Urrutia, 2003; Kauzlaric et al, 2017). A human KZFPs. Consistent with their targeting of TEs, most KZFPs majority of human KZFPs including all primate-restricted family conserved up to placental mammals essentially recruit KAP1 and members target sequences derived from TEs, that is, DNA trans- associated effectors. In contrast, a subset of more ancient KZFPs posons, ERVs (endogenous retroviruses), LINEs, SINEs (long and rather interacts with factors related to functions such as genome short interspersed nuclear elements, respectively), or SVAs (SINE- architecture or RNA processing. -
This Thesis Has Been Submitted in Fulfilment of the Requirements for a Postgraduate Degree (E.G
This thesis has been submitted in fulfilment of the requirements for a postgraduate degree (e.g. PhD, MPhil, DClinPsychol) at the University of Edinburgh. Please note the following terms and conditions of use: This work is protected by copyright and other intellectual property rights, which are retained by the thesis author, unless otherwise stated. A copy can be downloaded for personal non-commercial research or study, without prior permission or charge. This thesis cannot be reproduced or quoted extensively from without first obtaining permission in writing from the author. The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the author. When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given. Isolation, Characterisation and In Vitro Potential of Oogonial Stem Cells Cheryl Elizabeth Dunlop BSc Med Sci (Hons), University of Edinburgh MBChB (Hons), University of Edinburgh Doctor of Philosophy (PhD) – The University of Edinburgh – 2016 Declaration This thesis has been composed by myself and the research described herein is my own, except where work by others has been duly acknowledged. The work described in this thesis has not been submitted for any other degree or professional qualification. Cheryl Dunlop 2016 i Abstract The longstanding belief that women are born with a finite ovarian reserve has been debated for over a decade, ever since the discovery, and subsequent isolation, of purported oogonial stem cells (OSCs) from adult mammalian ovaries. This rare cell population has now been reported in the mouse, rat, pig, rhesus macaque monkey and humans and, although a physiological role for the cells has not been proven, they do appear to generate oocytes when cultured in specific environments, resulting in live offspring in rodents. -
WO 2013/002880 Al O O© O
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2013/002880 Al 3 January 2013 (03.01.2013) P O P C T (51) International Patent Classification: (74) Agents: LAURO, Peter C. et al; Edwards Wildman C12N 5/00 (2006.01) C12N 5/075 (2010.01) Palmer LLP, P.O. Box 55874, Boston, MA 02205 (US). (21) International Application Number: (81) Designated States (unless otherwise indicated, for every PCT/US2012/033672 kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, (22) Date: International Filing CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, 13 April 2012 (13.04.2012) DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, (25) Filing Language: English HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, ME, (26) Publication Language: English MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, (30) Priority Data: OM, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SC, SD, 61/502,840 29 June 201 1 (29.06.201 1) US SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, 61/600,529 17 February 2012 (17.02.2012) US TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (71) Applicants (for all designated States except US): THE (84) Designated States (unless otherwise indicated, for every GENERAL HOSPITAL CORPORATION [US/US]; 55 kind of regional protection available): ARIPO (BW, GH, Fruit Street, Boston, MA 021 14 (US). -
A Negative Feedback Loop of the TOR Signaling Moderates Growth And
bioRxiv preprint doi: https://doi.org/10.1101/2020.09.06.284745; this version posted September 7, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 A negative feedback loop of the TOR signaling moderates 2 growth and enables rapid sensing of stress signals in plants 3 Muhammed Jamsheer K1#*<, Sunita Jindal1#>, Mohan Sharma1, Manvi Sharma1, Sreejath Sivaj2, 4 Chanchal Thomas Mannully1^, Ashverya Laxmi1* 5 1National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India 6 2Department of Mechanical Engineering, Indian Institute of Technology Delhi, New Delhi, 110016, 7 India 8 9 <Current affiliation: Amity Food & Agriculture Foundation, Amity University Uttar Pradesh, Sector 10 125, Noida 201313, India 11 ^Current affiliation: Cell Metabolism Laboratory, School of Pharmacy, The Hebrew University of 12 Jerusalem, Jerusalem, 9112102, Israel 13 >Current affiliation: Department of Molecular Biology and Radiology, Mendel University in Brno, 14 Brno, 613 00, Czech Republic 15 16 #Equal first authors 17 18 *Corresponding authors 19 Ashverya Laxmi 20 Muhammed Jamsheer K 21 Email: AL: [email protected] (Lead Contact); MJK: [email protected] 22 ORCID: Ashverya Laxmi (0000-0002-3430-4200); Muhammed Jamsheer K (0000-0002-2135- 23 8760) 24 25 26 27 28 29 30 31 32 33 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.09.06.284745; this version posted September 7, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. -
Supplemental Table 3 Site ID Intron Poly(A) Site Type NM/KG Inum
Supplemental Table 3 Site ID Intron Poly(A) site Type NM/KG Inum Region Gene ID Gene Symbol Gene Annotation Hs.120277.1.10 chr3:170997234:170996860 170996950 b NM_153353 7 CDS 151827 LRRC34 leucine rich repeat containing 34 Hs.134470.1.27 chr17:53059664:53084458 53065543 b NM_138962 10 CDS 124540 MSI2 musashi homolog 2 (Drosophila) Hs.162889.1.18 chr14:80367239:80329208 80366262 b NM_152446 12 CDS 145508 C14orf145 chromosome 14 open reading frame 145 Hs.187898.1.27 chr22:28403623:28415294 28404458 b NM_181832 16 3UTR 4771 NF2 neurofibromin 2 (bilateral acoustic neuroma) Hs.228320.1.6 chr10:115527009:115530350 115527470 b BC036365 5 CDS 79949 C10orf81 chromosome 10 open reading frame 81 Hs.266308.1.2 chr11:117279579:117278191 117278967 b NM_032046 12 CDS 84000 TMPRSS13 transmembrane protease, serine 13 Hs.266308.1.4 chr11:117284536:117281662 117283722 b NM_032046 9 CDS 84000 TMPRSS13 transmembrane protease, serine 13 Hs.2689.1.4 chr10:53492398:53563605 53492622 b NM_006258 7 CDS 5592 PRKG1 protein kinase, cGMP-dependent, type I Hs.280781.1.6 chr18:64715646:64829150 64715837 b NM_024781 4 CDS 79839 C18orf14 chromosome 18 open reading frame 14 Hs.305985.2.25 chr12:8983686:8984438 8983942 b BX640639 17 3UTR NA NA NA Hs.312098.1.36 chr1:151843991:151844258 151844232 b NM_003815 15 CDS 8751 ADAM15 a disintegrin and metalloproteinase domain 15 (metargidin) Hs.314338.1.11 chr21:39490293:39481214 39487623 b NM_018963 41 CDS 54014 BRWD1 bromodomain and WD repeat domain containing 1 Hs.33368.1.3 chr15:92685158:92689361 92688314 b NM_018349 6 CDS 55784 MCTP2 multiple C2-domains with two transmembrane regions 2 Hs.346736.1.21 chr2:99270738:99281614 99272414 b AK126402 10 3UTR 51263 MRPL30 mitochondrial ribosomal protein L30 Hs.445061.1.19 chr16:69322898:69290216 69322712 b NM_018052 14 CDS 55697 VAC14 Vac14 homolog (S. -
Stem Cells/ Cloning Michael K
Spring 2018 – Systems Biology of Reproduction Lecture Outline – Gametogenesis/ Stem Cells/ Cloning Michael K. Skinner – Biol 475/575 CUE 418, 10:35-11:50 am, Tuesday & Thursday March 20, 2018 Week 11 Gametogenesis/ Stem Cells/ Cloning - Gametogenesis - Spermatogenesis - Cell Development Stages - Meiosis - Male Germline Stem Cell and Niche - Cell Biology - Niche - Regulatory Factors - Germ Cell Transplantation - Oogenesis - Cell Development - Meiosis - Female Germline Stem Cells - Embryonic Stem Cells - Cloning REFERENCES Ahn J, Park YJ, Chen P, et al. (2017) Comparative expression profiling of testis-enriched genes regulated during the development of spermatogonial cells. PLoS One. 12(4):e0175787. Vicens A, Borziak K, Karr TL, Roldan ERS, Dorus S. (2017) Comparative Sperm Proteomics in Mouse Species with Divergent Mating Systems. Mol Biol Evol. 34(6):1403-1416. Goldmann JM, Wong WS, Pinelli M, et al (2016) Parent-of-origin-specific signatures of de novo mutations. Nat Genet. 48(8):935-9 Virant-Klun I, Leicht S, Hughes C, Krijgsveld J. (2016) Identification of Maturation- Specific Proteins by Single-Cell Proteomics of Human Oocytes. Mol Cell Proteomics. 15(8):2616-27. Ball RL, Fujiwara Y, Sun F, Hu J, Hibbs MA, Handel MA, Carter GW. (2016) Regulatory complexity revealed by integrated cytological and RNA-seq analyses of meiotic substages in mouse spermatocytes. BMC Genomics. 17(1):628. Totonchi M, Hassani SN, Sharifi-Zarchi A, et al. (2017) Blockage of the Epithelial-to- Mesenchymal Transition Is Required for Embryonic Stem Cell Derivation. Stem Cell Reports. 9(4):1275-1290. Pal D, Rao MRS. (2017) Long Noncoding RNAs in Pluripotency of Stem Cells and Cell Fate Specification. -
Supplementary Table 1
Supplementary Table 1. 492 genes are unique to 0 h post-heat timepoint. The name, p-value, fold change, location and family of each gene are indicated. Genes were filtered for an absolute value log2 ration 1.5 and a significance value of p ≤ 0.05. Symbol p-value Log Gene Name Location Family Ratio ABCA13 1.87E-02 3.292 ATP-binding cassette, sub-family unknown transporter A (ABC1), member 13 ABCB1 1.93E-02 −1.819 ATP-binding cassette, sub-family Plasma transporter B (MDR/TAP), member 1 Membrane ABCC3 2.83E-02 2.016 ATP-binding cassette, sub-family Plasma transporter C (CFTR/MRP), member 3 Membrane ABHD6 7.79E-03 −2.717 abhydrolase domain containing 6 Cytoplasm enzyme ACAT1 4.10E-02 3.009 acetyl-CoA acetyltransferase 1 Cytoplasm enzyme ACBD4 2.66E-03 1.722 acyl-CoA binding domain unknown other containing 4 ACSL5 1.86E-02 −2.876 acyl-CoA synthetase long-chain Cytoplasm enzyme family member 5 ADAM23 3.33E-02 −3.008 ADAM metallopeptidase domain Plasma peptidase 23 Membrane ADAM29 5.58E-03 3.463 ADAM metallopeptidase domain Plasma peptidase 29 Membrane ADAMTS17 2.67E-04 3.051 ADAM metallopeptidase with Extracellular other thrombospondin type 1 motif, 17 Space ADCYAP1R1 1.20E-02 1.848 adenylate cyclase activating Plasma G-protein polypeptide 1 (pituitary) receptor Membrane coupled type I receptor ADH6 (includes 4.02E-02 −1.845 alcohol dehydrogenase 6 (class Cytoplasm enzyme EG:130) V) AHSA2 1.54E-04 −1.6 AHA1, activator of heat shock unknown other 90kDa protein ATPase homolog 2 (yeast) AK5 3.32E-02 1.658 adenylate kinase 5 Cytoplasm kinase AK7 -
Open Hester Dissertation W Appendix.Pdf
The Pennsylvania State University The Graduate School Intercollege Graduate Degree Program in Physiology THE IMPACT OF ZINC DEFICIENCY DURING OOGENESIS, FOLLICLE ASSEMBLY, AND GROWTH A Dissertation in Integrative and Biomedical Physiology by James M. Hester 2018 James Hester Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy December 2018 ii The dissertation of James Hester was reviewed and approved* by the following: Francisco J. Diaz Associate Professor of Reproductive Biology Dissertation Advisor Chair of Committee Wendy Hanna-Rose Associate Professor and Department Head Biochemistry and Molecular Biology Alan L. Johnson Walther H. Ott Professor in Avian Biology Claire M. Thomas Associate Professor of Biology and Biochemistry and Molecular Biology Donna H. Korzick Professor of Physiology and Kinesiology Chair, Intercollege Graduate Degree Program in Physiology *Signatures are on file in the Graduate School iii ABSTRACT The ovarian follicle is the fundamental unit of the ovary and of female reproduction in mammals. Each follicle contains one oocyte enclosed in somatic cells and follicle number is determined during fetal development in humans. Growth and development of ovarian follicles (folliculogenesis) is necessary to produce viable gametes as well as ovarian hormones including estrogen and progesterone. Folliculogenesis begins in the fetal ovary and may span several decades of life. Environmental and nutritional factors that affect folliculogenesis have the potential to impact health and fertility, and may be a source of new biotechnological innovation. One such factor, zinc, has previously been found to impact the final stages of follicle development including meiotic division, ovulation, epigenetic modification, fertilization, and embryo development. However, the role of zinc during the early stages of folliculogenesis have not been evaluated. -
FACS-Sorted Putative Oogonial Stem Cells from the Ovary Are Neither
www.nature.com/scientificreports OPEN FACS-sorted putative oogonial stem cells from the ovary are neither DDX4-positive nor germ Received: 30 March 2016 Accepted: 26 May 2016 cells Published: 15 June 2016 Larissa Zarate-Garcia, Simon I. R. Lane, Julie A. Merriman & Keith T. Jones Whether the adult mammalian ovary contains oogonial stem cells (OSCs) is controversial. They have been isolated by a live-cell sorting method using the germ cell marker DDX4, which has previously been assumed to be cytoplasmic, not surface-bound. Furthermore their stem cell and germ cell characteristics remain disputed. Here we show that although OSC-like cells can be isolated from the ovary using an antibody to DDX4, there is no good in silico modelling to support the existence of a surface-bound DDX4. Furthermore these cells when isolated were not expressing DDX4, and did not initially possess germline identity. Despite these unremarkable beginnings, they acquired some pre- meiotic markers in culture, including DDX4, but critically never expressed oocyte-specific markers, and furthermore were not immortal but died after a few months. Our results suggest that freshly isolated OSCs are not germ stem cells, and are not being isolated by their DDX4 expression. However it may be that culture induces some pre-meiotic markers. In summary the present study offers weight to the dogma that the adult ovary is populated by a fixed number of oocytes and that adultde novo production is a rare or insignificant event. The prevailing dogma in the field of reproductive biology for over 60 years has been that the adult mammalian ovary lacks germ stem cells1. -
Transcriptomic Regulation of Alternative Phenotypic Trajectories in Embryos of the Annual Killifish Austrofundulus Limnaeus
Portland State University PDXScholar Dissertations and Theses Dissertations and Theses Fall 11-30-2017 Transcriptomic Regulation of Alternative Phenotypic Trajectories in Embryos of the Annual Killifish Austrofundulus limnaeus Amie L. Romney Portland State University Follow this and additional works at: https://pdxscholar.library.pdx.edu/open_access_etds Part of the Biology Commons, and the Genetics and Genomics Commons Let us know how access to this document benefits ou.y Recommended Citation Romney, Amie L., "Transcriptomic Regulation of Alternative Phenotypic Trajectories in Embryos of the Annual Killifish Austrofundulus limnaeus" (2017). Dissertations and Theses. Paper 4033. https://doi.org/10.15760/etd.5917 This Dissertation is brought to you for free and open access. It has been accepted for inclusion in Dissertations and Theses by an authorized administrator of PDXScholar. Please contact us if we can make this document more accessible: [email protected]. Transcriptomic Regulation of Alternative Phenotypic Trajectories in embryos of the Annual Killifish Austrofundulus limnaeus by Amie Lynn Thomas Romney A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biology Dissertation Committee Jason Podrabsky, Chair Suzanne Estes Bradley Buckley Todd Rosenstiel Dirk Iwata-Reuyl Portland State University 2017 © 2017 Amie Lynn Thomas Romney ABSTRACT The Annual Killifish, Austrofundulus limnaeus, survives the seasonal drying of their pond habitat in the form of embryos entering diapause midway through development. The diapause trajectory is one of two developmental phenotypes. Alternatively, individuals can “escape” entry into diapause and develop continuously until hatching. The alternative phenotypes of A. limnaeus are a form of developmental plasticity that provides this species with a physiological adaption for surviving stressful environments.