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Φ-Features in Animal Cognition
φ-Features in Animal Cognition Chris Golston This paper argues that the core φ-features behind grammatical person, number, and gender are widely used in animal cognition and are in no way limited to humans or to communication. Based on this, it is hypothesized (i) that the semantics behind φ-features were fixed long before primates evolved, (ii) that most go back as far as far as vertebrates, and (iii) that some are shared with insects and plants. Keywords: animal cognition; gender; number; person 1. Introduction Bickerton claims that language is ill understood as a communication system: [F]or most of us, language seems primarily, or even exclusively, to be a means of communication. But it is not even primarily a means of communication. Rather, it is a system of representation, a means for sorting and manipulating the plethora of information that deluges us throughout our waking life. (Bickerton 1990: 5) As Berwick & Chomsky (2016: 102) put it recently “language is fundamentally a system of thought”. Since much of our system of representation seems to be shared with other animals, it has been argued that we should “search for the ancestry of language not in prior systems of animal communication, but in prior representational systems” (Bickerton 1990: 23). In support of this, I provide evidence that all the major φ-features are shared with primates, most with vertebrates, and some with plants; and that there are no φ-features whose semantics are unique to humans. Specifically human categories, including all things that vary across human cultures, seem to I’d like to thank Steve Adisasmito-Smith, Charles Ettner, Sean Fulop, Steven Moran, Nadine Müller, three anonymous reviewers for EvoLang, two anonymous reviewers for Biolinguistics and Kleanthes Grohmann for help in identifying weakness in earlier drafts, as well as audiences at California State University Fresno, Marburg Universität, and Universitetet i Tromsø for helpful discussion. -
Exploring the Non-Canonical Functions of Metabolic Enzymes Peiwei Huangyang1,2 and M
© 2018. Published by The Company of Biologists Ltd | Disease Models & Mechanisms (2018) 11, dmm033365. doi:10.1242/dmm.033365 REVIEW SPECIAL COLLECTION: CANCER METABOLISM Hidden features: exploring the non-canonical functions of metabolic enzymes Peiwei Huangyang1,2 and M. Celeste Simon1,3,* ABSTRACT A key finding from studies of metabolic enzymes is the existence The study of cellular metabolism has been rigorously revisited over the of mechanistic links between their nuclear localization and the past decade, especially in the field of cancer research, revealing new regulation of transcription. By modulating gene expression, insights that expand our understanding of malignancy. Among these metabolic enzymes themselves facilitate adaptation to rapidly insights isthe discovery that various metabolic enzymes have surprising changing environments. Furthermore, they can directly shape a ’ activities outside of their established metabolic roles, including in cell s epigenetic landscape (Kaelin and McKnight, 2013). the regulation of gene expression, DNA damage repair, cell cycle Strikingly, several metabolic enzymes exert completely distinct progression and apoptosis. Many of these newly identified functions are functions in different cellular compartments. Nuclear fructose activated in response to growth factor signaling, nutrient and oxygen bisphosphate aldolase, for example, directly interacts with RNA ́ availability, and external stress. As such, multifaceted enzymes directly polymerase III to control transcription (Ciesla et al., 2014), -
Ecotourism As a Means of Encouraging Ecological Recovery in the Flinders Ranges, South Australia
ECOTOURISM AS A MEANS OF ENCOURAGING ECOLOGICAL RECOVERY IN THE FLINDERS RANGES, SOUTH AUSTRALIA By Emily Moskwa A thesis submitted in fulfilment of the degree of Doctor of Philosophy Discipline of Geographical and Environmental Studies School of Social Sciences Faculty of Humanities and Social Sciences The University of Adelaide May 2008 ii TABLE OF CONTENTS List of Figures………………………………………………………………………………….…….....v List of Tables…………………………………………………………………………………….….....vi Abstract………………………………………………………………………………………….……viii Acknowledgements…………………………………………………………………………….………ix Declaration……………………………………………………………………………………….……..x Section I: Preliminaries 1.0 INTRODUCTION .............................................................................. 2 1.1 Introduction ............................................................................................................... 2 1.2 Conceptual Basis for Thesis ...................................................................................... 2 1.3 Research Questions ................................................................................................... 3 1.4 Specific Objectives .................................................................................................... 5 1.5 Justifications for Research ........................................................................................ 6 1.6 Structure of the Thesis .............................................................................................. 8 1.7 Conclusion ................................................................................................................ -
Arthur Kornberg Discovered (The First) DNA Polymerase Four
Arthur Kornberg discovered (the first) DNA polymerase Using an “in vitro” system for DNA polymerase activity: 1. Grow E. coli 2. Break open cells 3. Prepare soluble extract 4. Fractionate extract to resolve different proteins from each other; repeat; repeat 5. Search for DNA polymerase activity using an biochemical assay: incorporate radioactive building blocks into DNA chains Four requirements of DNA-templated (DNA-dependent) DNA polymerases • single-stranded template • deoxyribonucleotides with 5’ triphosphate (dNTPs) • magnesium ions • annealed primer with 3’ OH Synthesis ONLY occurs in the 5’-3’ direction Fig 4-1 E. coli DNA polymerase I 5’-3’ polymerase activity Primer has a 3’-OH Incoming dNTP has a 5’ triphosphate Pyrophosphate (PP) is lost when dNMP adds to the chain E. coli DNA polymerase I: 3 separable enzyme activities in 3 protein domains 5’-3’ polymerase + 3’-5’ exonuclease = Klenow fragment N C 5’-3’ exonuclease Fig 4-3 E. coli DNA polymerase I 3’-5’ exonuclease Opposite polarity compared to polymerase: polymerase activity must stop to allow 3’-5’ exonuclease activity No dNTP can be re-made in reversed 3’-5’ direction: dNMP released by hydrolysis of phosphodiester backboneFig 4-4 Proof-reading (editing) of misincorporated 3’ dNMP by the 3’-5’ exonuclease Fidelity is accuracy of template-cognate dNTP selection. It depends on the polymerase active site structure and the balance of competing polymerase and exonuclease activities. A mismatch disfavors extension and favors the exonuclease.Fig 4-5 Superimposed structure of the Klenow fragment of DNA pol I with two different DNAs “Fingers” “Thumb” “Palm” red/orange helix: 3’ in red is elongating blue/cyan helix: 3’ in blue is getting edited Fig 4-6 E. -
Downloaded by [New York University] at 06:54 14 August 2016 Classic Case Studies in Psychology
Downloaded by [New York University] at 06:54 14 August 2016 Classic Case Studies in Psychology The human mind is both extraordinary and compelling. But this is more than a collection of case studies; it is a selection of stories that illustrate some of the most extreme forms of human behaviour. From the leader who convinced his followers to kill themselves to the man who lost his memory; from the boy who was brought up as a girl to the woman with several personalities, Geoff Rolls illustrates some of the most fundamental tenets of psychology. Each case study has provided invaluable insights for scholars and researchers, and amazed the public at large. Several have been the inspiration for works of fiction, for example the story of Kim Peek, the real Rain Man. This new edition features three new case studies, including the story of Charles Decker who was tried for the attempted murder of two people but acquitted on the basis of a neurological condition, and Dorothy Martin, whose persisting belief in an impending alien invasion is an illuminating example of cognitive dissonance. In addition, each case study is contextualized with more typical behaviour, while the latest thinking in each sub-field is also discussed. Classic Case Studies in Psychology is accessibly written and requires no prior knowledge of psychology, but simply an interest in the human condition. It is a book that will amaze, sometimes disturb, but above all enlighten its readers. Downloaded by [New York University] at 06:54 14 August 2016 Geoff Rolls is Head of Psychology at Peter Symonds College in Winchester and formerly a Research Fellow at Southampton University, UK. -
Managing DNA Polymerases: Coordinating DNA Replication, DNA Repair, and DNA Recombination
Colloquium Managing DNA polymerases: Coordinating DNA replication, DNA repair, and DNA recombination Mark D. Sutton and Graham C. Walker* Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 Two important and timely questions with respect to DNA replica- A Superfamily of DNA Polymerases Involved in Replication of Imper- tion, DNA recombination, and DNA repair are: (i) what controls fect DNA Templates. Recently, the field of translesion DNA which DNA polymerase gains access to a particular primer-termi- synthesis and induced mutagenesis has generated a great deal of nus, and (ii) what determines whether a DNA polymerase hands off excitement because of the discovery that key gene products its DNA substrate to either a different DNA polymerase or to a required for these processes, in both prokaryotes (9, 10) and in different protein(s) for the completion of the specific biological eukaryotes (11, 12), possess an intrinsic DNA polymerase ac- process? These questions have taken on added importance in light tivity (refs. 6, 7, and 13–20 and reviewed in refs. 21–24). A of the fact that the number of known template-dependent DNA common, defining feature of these DNA polymerases is a polymerases in both eukaryotes and in prokaryotes has grown remarkable ability to replicate imperfect DNA templates. De- tremendously in the past two years. Most notably, the current list pending on the DNA polymerase, these include templates such now includes a completely new family of enzymes that are capable as those containing a misaligned primer–template junction (13), of replicating imperfect DNA templates. This UmuC-DinB-Rad30- an abasic site (6, 7), a cyclobutane dimer (15, 16, 25), or a pyrimidine–pyrimidone (6–4) photoproduct (25). -
Key for Exam 3 • Biology II • Winter 2013 Multiple Choice Questions
Key for Exam 3 • Biology II • Winter 2013 Multiple Choice Questions. Circle the one best answer for each question. (1 point each) 1. Which of the following is not part of the cell theory: A. All cells come from other cells. B. Only eukaryotic cells have membrane-bounded organelles. C. The cell is the smallest living unit of a living thing. D. All living things are made up of cells. 2. A protein that belongs in the plasma membrane of a eukaryotic cell might be found (at some point) in which organelle: A. Golgi apparatus B. ribosome C. cytoplasmic reticulum D. nucleus E. mitochondrion 3. A phospholipid is composed of: A. three fatty acids and a molecule of glycerol B. chains of hydrophobic amino acids C. two fatty acids, a molecule of glycerol and a highly hydrophilic group D. amphipathic fatty acids E. a phosphate, a ribose or deoxyribose sugar, and a fatty acid 4. A membrane would be more permeable if: A. …its phospholipids had longer tails. B. …its phospholipids had shorter tails. C. …it contained more cholesterol. D. …its phospholipids had more saturated tails. E. …its proteins were more hydrophobic. 5. An enzyme is working at its Vmax: A. …at the high point of the product vs. time curve. B. …when its active site is continuously full of substrate. C. …when the concentration of substrate is equal to its km. D. …when it is assayed at its optimum temperature and pH. E. …at the early time points when its slope is the steepest. 6. In an enzyme-catalyzed reaction, the role of the enzyme is to: A. -
DNA Polymerases at the Eukaryotic Replication Fork Thirty Years After: Connection to Cancer
cancers Review DNA Polymerases at the Eukaryotic Replication Fork Thirty Years after: Connection to Cancer Youri I. Pavlov 1,2,* , Anna S. Zhuk 3 and Elena I. Stepchenkova 2,4 1 Eppley Institute for Research in Cancer and Allied Diseases and Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA 2 Department of Genetics and Biotechnology, Saint-Petersburg State University, 199034 Saint Petersburg, Russia; [email protected] 3 International Laboratory of Computer Technologies, ITMO University, 197101 Saint Petersburg, Russia; [email protected] 4 Laboratory of Mutagenesis and Genetic Toxicology, Vavilov Institute of General Genetics, Saint-Petersburg Branch, Russian Academy of Sciences, 199034 Saint Petersburg, Russia * Correspondence: [email protected] Received: 30 September 2020; Accepted: 13 November 2020; Published: 24 November 2020 Simple Summary: The etiology of cancer is linked to the occurrence of mutations during the reduplication of genetic material. Mutations leading to low replication fidelity are the culprits of many hereditary and sporadic cancers. The archetype of the current model of replication fork was proposed 30 years ago. In the sequel to our 2010 review with the words “years after” in the title inspired by A. Dumas’s novels, we go over new developments in the DNA replication field and analyze how they help elucidate the effects of the genetic variants of DNA polymerases on cancer. Abstract: Recent studies on tumor genomes revealed that mutations in genes of replicative DNA polymerases cause a predisposition for cancer by increasing genome instability. The past 10 years have uncovered exciting details about the structure and function of replicative DNA polymerases and the replication fork organization. -
Transcriptional Studies of the Muscle-Specific Expression of the Rabbit Muscle Phosphofructokinase Gene
Louisiana State University LSU Digital Commons LSU Historical Dissertations and Theses Graduate School 1995 Transcriptional Studies of the Muscle-Specific Expression of the Rabbit Muscle Phosphofructokinase Gene. Haiqing Fu Schiltz Louisiana State University and Agricultural & Mechanical College Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_disstheses Recommended Citation Schiltz, Haiqing Fu, "Transcriptional Studies of the Muscle-Specific Expression of the Rabbit Muscle Phosphofructokinase Gene." (1995). LSU Historical Dissertations and Theses. 6075. https://digitalcommons.lsu.edu/gradschool_disstheses/6075 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Historical Dissertations and Theses by an authorized administrator of LSU Digital Commons. For more information, please contact [email protected]. INFORMATION TO USERS This manuscript has been reproduced from the microfilm master. UMI films the text directly from the original or copy submitted. Thus, some thesis and dissertation copies are in typewriter face, while others may be from any type of computer printer. Hie quality of this reproduction Is dependent upon the quality of the copy snbmitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleedthrough, substandardm a rg in * , and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send UMI a complete manuscript and there are mi«ing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. Oversize materials (e.g^ maps, drawings, charts) are reproduced by sectioning the original, beginning at the upper left-hand comer and confirming from left to right in equal sections with small overlaps. -
The Genetic Program of Pancreatic Beta-Cell Replication in Vivo
Page 1 of 65 Diabetes The genetic program of pancreatic beta-cell replication in vivo Agnes Klochendler1, Inbal Caspi2, Noa Corem1, Maya Moran3, Oriel Friedlich1, Sharona Elgavish4, Yuval Nevo4, Aharon Helman1, Benjamin Glaser5, Amir Eden3, Shalev Itzkovitz2, Yuval Dor1,* 1Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel 2Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel. 3Department of Cell and Developmental Biology, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel 4Info-CORE, Bioinformatics Unit of the I-CORE Computation Center, The Hebrew University and Hadassah, The Institute for Medical Research Israel- Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel 5Endocrinology and Metabolism Service, Department of Internal Medicine, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel *Correspondence: [email protected] Running title: The genetic program of pancreatic β-cell replication 1 Diabetes Publish Ahead of Print, published online March 18, 2016 Diabetes Page 2 of 65 Abstract The molecular program underlying infrequent replication of pancreatic beta- cells remains largely inaccessible. Using transgenic mice expressing GFP in cycling cells we sorted live, replicating beta-cells and determined their transcriptome. Replicating beta-cells upregulate hundreds of proliferation- related genes, along with many novel putative cell cycle components. Strikingly, genes involved in beta-cell functions, namely glucose sensing and insulin secretion were repressed. Further studies using single molecule RNA in situ hybridization revealed that in fact, replicating beta-cells double the amount of RNA for most genes, but this upregulation excludes genes involved in beta-cell function. -
An Open Introduction to Logic
For All X The Lorain County Remix P.D. Magnus University at Albany, State University of New York and Cathal Woods Virginia Wesleyan University and J. Robert Loftis Lorain County Community College Licensed under a Creative Commons license. (Attribution-NonComercial-ShareAlike 4.0 International ) https://creativecommons.org/licenses/by-nc-sa/4.0/ This is version 0.1 of An Open Introduction to Logic. It is current as of December 22, 2017. © 2005{2017 by Cathal Woods, P.D. Magnus, and J. Robert Loftis. Some rights reserved. Licensed under a Creative Commons license. (Attribution-NonComercial-ShareAlike 4.0 International ) https://creativecommons.org/licenses/by-nc-sa/4.0/ This book incorporates material from An Introduction to Reasoning by Cathal Woods, available at sites.google.com/site/anintroductiontoreasoning/ and For All X by P.D. Magnus (version 1.27 [090604]), available at www.fecundity.com/logic. Introduction to Reasoning © 2007{2014 by Cathal Woods. Some rights reserved. Licensed under a Creative Commons license: Attribution-NonCommercial-ShareAlike 3.0 Unported. http://creativecommons.org/licenses/by-nc-sa/3.0/ For All X © 2005{2010 by P.D. Magnus. Some rights reserved. Licensed under a Creative Commons license: Attribution ShareAlike http://creativecommons.org/licenses/by-sa/3.0/ J. Robert Loftis compiled this edition and wrote original material for it. He takes full responsibility for any mistakes remaining in this version of the text. Typesetting was carried out entirely in LATEX2". The style for typesetting proofs is based on fitch.sty (v0.4) by Peter Selinger, University of Ottawa. \When you come to any passage you don't understand, read it again: if you still don't understand it, read it again: if you fail, even after three readings, very likely your brain is getting a little tired. -
A Novel DNA Primase-Helicase Pair Encoded by Sccmec Elements Aleksandra Bebel†, Melissa a Walsh, Ignacio Mir-Sanchis‡, Phoebe a Rice*
RESEARCH ARTICLE A novel DNA primase-helicase pair encoded by SCCmec elements Aleksandra Bebel†, Melissa A Walsh, Ignacio Mir-Sanchis‡, Phoebe A Rice* Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States Abstract Mobile genetic elements (MGEs) are a rich source of new enzymes, and conversely, understanding the activities of MGE-encoded proteins can elucidate MGE function. Here, we biochemically characterize three proteins encoded by a conserved operon carried by the Staphylococcal Cassette Chromosome (SCCmec), an MGE that confers methicillin resistance to Staphylococcus aureus, creating MRSA strains. The first of these proteins, CCPol, is an active A-family DNA polymerase. The middle protein, MP, binds tightly to CCPol and confers upon it the ability to synthesize DNA primers de novo. The CCPol-MP complex is therefore a unique primase- polymerase enzyme unrelated to either known primase family. The third protein, Cch2, is a 3’-to-5’ helicase. Cch2 additionally binds specifically to a dsDNA sequence downstream of its gene that is also a preferred initiation site for priming by CCPol-MP. Taken together, our results suggest that this is a functional replication module for SCCmec. *For correspondence: Introduction [email protected] Staphylococcus aureus is a dangerous human pathogen, due in part to the emergence of multi- drug-resistant strains such as MRSA (methicillin-resistant S. aureus). MRSA strains have acquired † Present address: Phage resistance to b-lactam antibiotics (including methicillin) mainly through horizontal gene transfer of a Consultants, Gdynia, Poland; mobile genomic island called staphylococcal cassette chromosome (SCC) (Moellering, 2012). ‡Umea˚ University, Umea˚ , SCCmec is a variant of SCC that carries a methicillin resistance gene, mecA.