Comprehensive History of CSP Genes: Evolution, Phylogenetic Distribution and Functions
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AP Biology Planner
COURSE PLANNER Please note that not all activities for the course are listed, and many activities will be supplemented with additional activities such as diagram analysis, practice essays, etc. Intro to AP Biology/Scientific Method This course begins with introducing students to the seven science practices, in addition to the Big Ideas that unify the course. Students complete the lab exercises that emphasize the need for controls in experiments as well as to identify and explain potential sources of error as part of the normal scientific process. Reading in Campbell and Reece: Topics: • Intro to AP biology, the test and how to study. ♣ Activity: Theme-teams: Students research and present scientist who represent each Big Idea in AP Biology. ♣ Activity: Analyzing the AP multiple choice questions with diagrams. • Scientific Method: Steps and controlled experiments ♣ Activity: What is Science? Discussion/Poster Creation. ♣ Activity: Lab Safety activity: NIH’s Student Lab Safety Introduction Course. https://www.safetytraining.nih.gov/introcourse/labsafetyIntro.aspx ♣ Activity: Identify risks in procedures and materials (MSDS analysis) ♣ Activity: Guide to good graphing. ♣ Activity: Examining bias in science. ♣ Lab: Student Designed inquiry. The effect of environmental factors on the metabolic rate of yeast. In this student designed inquiry, students investigate environmental factors as they relate to CO2 production or O2 consumption in yeast. Students must select an independent variable and dependent variable, as well as design an experimental procedure based on an existing lab protocol. ECOLOGY The ecology unit introduces the ideas of energy processes and interactions, which are the focus of Big Idea 2 and 4. Ecology introduces students to creating, analyzing, and evaluating mathematical models in biology and prepares students to tackle evolution, the central unit in AP Biology. -
Identification of a Non-LTR Retrotransposon from the Gypsy Moth
Insect Molecular Biology (1999) 8(2), 231-242 Identification of a non-L TR retrotransposon from the gypsy moth K. J. Garner and J. M. Siavicek sposons (Boeke & Corces, 1989), or retroposons USDA Forest Service, Northeastern Research Station, (McClure, 1991). Many non-L TR retrotransposons Delaware, Ohio, U.S.A. have been described in insects, including the Doc (O'Hare et al., 1991), F (Di Nocera & Casari, 1987), I (Fawcett et al., 1986) and jockey (Priimiigi et al., 1988) Abstract elements of Drosophila melanogaster, the T1Ag A family of highly repetitive elements, named LDT1, (Besansky, 1990) and Q (Besansky et al., 1994) ele- has been identified in the gypsy moth, Lymantria ments of Anopheles gambiae, and the R1Bm (Xiong & dispar. The complete element is 5.4 kb in length and Eickbush, 1988a) and R2Bm (Burke et al., 1987) lacks long-terminal repeats, The element contains two families of ribosomal DNA insertions in Bombyx mori. open reading frames with a significant amino acid Gypsy moths (Lymantria dispar) are currently wide- sequence similarity to several non-L TR retrotrans- spread forest pests in the north-eastern United States posons. The first open reading frame contains a and the adjacent regions of Canada. Population region that potentially encodes a polypeptide similar markers have been sought to distinguish the North to DNA-binding GAG-like proteins. The second American gypsy moths introduced from Europe in 1869 encodes a polypeptide resembling both endonuclease from those recently introduced from Asia (Bogdano- and reverse transcriptase sequences. A" members of wicz et al., 1993; Pfeifer et al., 1995; Garner & Siavicek, the LDT1 element family sequenced thus far have poly- 1996; Schreiber et al., 1997). -
106Th Annual Meeting of the German Zoological Society Abstracts
September 13–16, 2013 106th Annual Meeting of the German Zoological Society Ludwig-Maximilians-Universität München Geschwister-Scholl-Platz 1, 80539 Munich, Germany Abstracts ISBN 978-3-00-043583-6 1 munich Information Content Local Organizers: Abstracts Prof. Dr. Benedikt Grothe, LMU Munich Satellite Symposium I – Neuroethology .......................................... 4 Prof. Dr. Oliver Behrend, MCN-LMU Munich Satellite Symposium II – Perspectives in Animal Physiology .... 33 Satellite Symposium III – 3D EM .......................................................... 59 Conference Office Behavioral Biology ................................................................................... 83 event lab. GmbH Dufourstraße 15 Developmental Biology ......................................................................... 135 D-04107 Leipzig Ecology ......................................................................................................... 148 Germany Evolutionary Biology ............................................................................... 174 www.eventlab.org Morphology................................................................................................ 223 Neurobiology ............................................................................................. 272 Physiology ................................................................................................... 376 ISBN 978-3-00-043583-6 Zoological Systematics ........................................................................... 416 -
The Significance of the Evolutionary Relationship of Prion Proteins and ZIP Transporters in Health and Disease
The Significance of the Evolutionary Relationship of Prion Proteins and ZIP Transporters in Health and Disease by Sepehr Ehsani A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Department of Laboratory Medicine and Pathobiology University of Toronto © Copyright by Sepehr Ehsani 2012 The Significance of the Evolutionary Relationship of Prion Proteins and ZIP Transporters in Health and Disease Sepehr Ehsani Doctor of Philosophy Department of Laboratory Medicine and Pathobiology University of Toronto 2012 Abstract The cellular prion protein (PrPC) is unique amongst mammalian proteins in that it not only has the capacity to aggregate (in the form of scrapie PrP; PrPSc) and cause neuronal degeneration, but can also act as an independent vector for the transmission of disease from one individual to another of the same or, in some instances, other species. Since the discovery of PrPC nearly thirty years ago, two salient questions have remained largely unanswered, namely, (i) what is the normal function of the cellular protein in the central nervous system, and (ii) what is/are the factor(s) involved in the misfolding of PrPC into PrPSc? To shed light on aspects of these questions, we undertook a discovery-based interactome investigation of PrPC in mouse neuroblastoma cells (Chapter 2), and among the candidate interactors, identified two members of the ZIP family of zinc transporters (ZIP6 and ZIP10) as possessing a PrP-like domain. Detailed analyses revealed that the LIV-1 subfamily of ZIP transporters (to which ZIPs 6 and 10 belong) are in fact the evolutionary ancestors of prions (Chapter 3). -
Using Rnai to Elucidate Mechanisms of Human Disease
Cell Death and Differentiation (2008) 15, 809–819 & 2008 Nature Publishing Group All rights reserved 1350-9047/08 $30.00 www.nature.com/cdd Review From sequence to function: using RNAi to elucidate mechanisms of human disease NM Wolters1 and JP MacKeigan*,1 RNA interference (RNAi) has emerged as one of the most powerful tools for functionally characterizing large sets of genomic data. Capabilities of RNAi place it at the forefront of high-throughput screens, which are able to span the human genome in search of novel targets. Although RNAi screens have been used to elucidate pathway components and discover potential drug targets in lower organisms, including Caenorhabditis elegans and Drosophila, only recently has the technology been advanced to a state in which large-scale screens can be performed in mammalian cells. In this review, we will evaluate the major advancements in the field of mammalian RNAi, specifically in terms of high-throughput assays. Crucial points of experimental design will be highlighted, as well as suggestions as to how to interpret and follow-up on potential cell death targets. Finally, we assess the prospective applications of high-throughput screens, the data they are capable of generating, and the potential for this technique to further our understanding of human disease. Cell Death and Differentiation (2008) 15, 809–819; doi:10.1038/sj.cdd.4402311; published online 18 January 2008 The sequencing of the human genome ushered a new era into maintaining the balance between cell survival, cell death, the field of modern biology; it is now possible to elucidate and autophagy represents a crucial regulatory point in human molecular pathways relevant to development and disease health and that when this balance is tipped, a variety of with a breadth never before seen. -
The Beaver's Phylogenetic Lineage Illuminated by Retroposon Reads
www.nature.com/scientificreports OPEN The Beaver’s Phylogenetic Lineage Illuminated by Retroposon Reads Liliya Doronina1,*, Andreas Matzke1,*, Gennady Churakov1,2, Monika Stoll3, Andreas Huge3 & Jürgen Schmitz1 Received: 13 October 2016 Solving problematic phylogenetic relationships often requires high quality genome data. However, Accepted: 25 January 2017 for many organisms such data are still not available. Among rodents, the phylogenetic position of the Published: 03 March 2017 beaver has always attracted special interest. The arrangement of the beaver’s masseter (jaw-closer) muscle once suggested a strong affinity to some sciurid rodents (e.g., squirrels), placing them in the Sciuromorpha suborder. Modern molecular data, however, suggested a closer relationship of beaver to the representatives of the mouse-related clade, but significant data from virtually homoplasy- free markers (for example retroposon insertions) for the exact position of the beaver have not been available. We derived a gross genome assembly from deposited genomic Illumina paired-end reads and extracted thousands of potential phylogenetically informative retroposon markers using the new bioinformatics coordinate extractor fastCOEX, enabling us to evaluate different hypotheses for the phylogenetic position of the beaver. Comparative results provided significant support for a clear relationship between beavers (Castoridae) and kangaroo rat-related species (Geomyoidea) (p < 0.0015, six markers, no conflicting data) within a significantly supported mouse-related clade (including Myodonta, Anomaluromorpha, and Castorimorpha) (p < 0.0015, six markers, no conflicting data). Most of an organism’s phylogenetic history is fossilized in their heritable genomic material. Using data from genome sequencing projects, particularly informative regions of this material can be extracted in sufficient num- bers to resolve the deepest history of speciation. -
Gene Families in the Desert Locust Schistocerca Gregaria
Molecular Elements Involved in Locust Olfaction: Gene Families in the Desert Locust Schistocerca gregaria Dissertation for Obtaining the Doctoral Degree of Natural Sciences (Dr. rer. nat.) Faculty of Natural Sciences University of Hohenheim From the Institute of Physiology Prof. Dr. H. Breer Submitted by Xingcong Jiang Heze (Provinz Shandong), V.R. China 2018 Dean: Prof. Dr. Uwe Beifuß 1st reviewer: Prof. Dr. Heinz Breer 2nd reviewer: Prof. Dr. Jürgen Krieger Submitted on: Oral examination on: 10.08.2018 This work was accepted by the Faculty of Natural Sciences at the University of Hohenheim as “Dissertation for Obtaining the Doctoral Degree of Natural Sciences”. Annex 2 to the University of Hohenheim doctoral degree regulations for Dr. rer. nat. Affidavit according to Sec. 7(7) of the University of Hohenheim doctoral degree regulations for Dr. rer. nat. 1. For the dissertation submitted on the topic Molecular Elements Involved in Locust Olfaction: Gene Families in the Desert Locust Schistocerca gregaria I hereby declare that I independently completed the work. 2. I only used the sources and aids documented and only made use of permissible assistance by third parties. In particular, I properly documented any contents which I used - either by directly quoting or paraphrasing - from other works. 3. I did not accept any assistance from a commercial doctoral agency or consulting firm. 4. I am aware of the meaning of this affidavit and the criminal penalties of an incorrect or incomplete affidavit. I hereby confirm the correctness of the above declaration: I hereby affirm in lieu of oath that I have, to the best of my knowledge, declared nothing but the truth and have not omitted any information. -
A Field Guide to Eukaryotic Transposable Elements
GE54CH23_Feschotte ARjats.cls September 12, 2020 7:34 Annual Review of Genetics A Field Guide to Eukaryotic Transposable Elements Jonathan N. Wells and Cédric Feschotte Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850; email: [email protected], [email protected] Annu. Rev. Genet. 2020. 54:23.1–23.23 Keywords The Annual Review of Genetics is online at transposons, retrotransposons, transposition mechanisms, transposable genet.annualreviews.org element origins, genome evolution https://doi.org/10.1146/annurev-genet-040620- 022145 Abstract Annu. Rev. Genet. 2020.54. Downloaded from www.annualreviews.org Access provided by Cornell University on 09/26/20. For personal use only. Copyright © 2020 by Annual Reviews. Transposable elements (TEs) are mobile DNA sequences that propagate All rights reserved within genomes. Through diverse invasion strategies, TEs have come to oc- cupy a substantial fraction of nearly all eukaryotic genomes, and they rep- resent a major source of genetic variation and novelty. Here we review the defining features of each major group of eukaryotic TEs and explore their evolutionary origins and relationships. We discuss how the unique biology of different TEs influences their propagation and distribution within and across genomes. Environmental and genetic factors acting at the level of the host species further modulate the activity, diversification, and fate of TEs, producing the dramatic variation in TE content observed across eukaryotes. We argue that cataloging TE diversity and dissecting the idiosyncratic be- havior of individual elements are crucial to expanding our comprehension of their impact on the biology of genomes and the evolution of species. 23.1 Review in Advance first posted on , September 21, 2020. -
Mg-SINE: a Short Interspersed Nuclear Element from the Rice Blast Fungus, Magnaporthe Grisea (Transposon/Repeated DNA) PRADEEP KACHROO*, SALLY A
Proc. Natl. Acad. Sci. USA Vol. 92, pp. 11125-11129, November 1995 Genetics Mg-SINE: A short interspersed nuclear element from the rice blast fungus, Magnaporthe grisea (transposon/repeated DNA) PRADEEP KACHROO*, SALLY A. LEONGt, AND BHARAT B. CHATTOO*t *Department of Microbiology and Biotechnology Center, Faculty of Science, M. S. University of Baroda, Baroda 390 002, India; and tU.S. Department of Agriculture-Agricultural Research Service Plant Disease Research Unit, 1630 Linden Drive, University of Wisconsin, Madison, WI 53706 Communicated by M. S. Swaminathan, M. S. Swaminathan Research Foundation, Madras, India, June 28, 1995 ABSTRACT A short interspersed nuclear element, Mg- Magnaporthe grisea, an ascomycetous fungus responsible for SINE, was isolated and characterized from the genome of the the blast disease of rice (Oryza sativa), is known to generate rice blast fungus, Magnaporthe grisea. Mg-SINE was isolated new pathogenic variants at a high frequency (15). Various as an insertion element within Pot2, an inverted-repeat trans- mechanisms have been postulated to explain pathogenic vari- poson from M. grisea and shows typical features of a mam- ability in this fungus (15-17), although its molecular basis malian SINE. Mg-SINE is present as a 0.47-kb interspersed remains elusive. We initiated an analysis of repeated DNA sequence at "100 copies per haploid genome in both rice and sequences of M. grisea in order to delineate their role in non-rice isolates of M. grisea, indicating a common evolution- genome organization and generation of variability. We report ary origin. Secondary structure analysis ofMg-SINE revealed here the presence of a SINE sequence in the genome of M. -
Identification of Candidate Chemosensory Genes in Mythimna Separata by Transcriptomic Analysis
Du et al. BMC Genomics (2018) 19:518 https://doi.org/10.1186/s12864-018-4898-0 RESEARCH ARTICLE Open Access Identification of candidate chemosensory genes in Mythimna separata by transcriptomic analysis Lixiao Du1†, Xincheng Zhao2†, Xiangzhi Liang1, Xiwu Gao3, Yang Liu1* and Guirong Wang1* Abstract Background: The oriental armyworm, Mythimna separata, is an economically important and common Lepidopteran pest of cereal crops. Chemoreception plays a key role in insect life, such as foraging, oviposition site selection, and mating partners. To better understand the chemosensory mechanisms in M. separata, transcriptomic analysis of antennae, labial palps, and proboscises were conducted using next-generation sequencing technology to identify members of the major chemosensory related genes. Results: In this study, 62 putative odorant receptors (OR), 20 ionotropic receptors (IR), 16 gustatory receptors (GR), 38 odorant binding proteins (OBP), 26 chemosensory proteins (CSP), and 2 sensory neuron membrane proteins (SNMP) were identified in M. separata by bioinformatics analysis. Phylogenetic analysis of these candidate proteins was performed. Differentially expressed genes (DEGs) analysis was used to determine the expressions of all candidate chemosensory genes and then the expression profiles of the three families of receptor genes were confirmed by real-time quantitative RT-PCR (qPCR). Conclusions: The important genes for chemoreception have now been identified in M. separata. This study will provide valuable information for further functional studies of chemoreception mechanisms in this important agricultural pest. Keywords: Mythimna separata, Transcriptome, Chemosensory gene, Expression analysis Background receptor neurons (GRNs) are distributed on different Insects live in environments where they are constantly taste organs over the entire body surface of insects in- surrounded by various chemical signals, including olfac- cluding the proboscis, legs, wings, and even the female tory and taste. -
5' Exonuclease ERL1 in Chloroplast Ribosomal RNA
Dissertation zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) im Fachbereich 18 - Naturwissenschaften der Universität Kassel vorgelegt von: Heiko Tobias Schumacher Kassel im Mai 2009 Datum der Disputation: 16. Juli 2009 Die Natur ist aller Meister Meister, sie zeigt uns erst den Geist der Geister Johann Wolfgang v. Goethe Erklärung Hiermit versichere ich, dass ich die vorliegende Dissertation selbständig und ohne unerlaubte Hilfe angefertigt und andere als die in der Dissertation angegebenen Hilfsmittel nicht benutzt habe. Alle Stellen, die wörtlich oder sinngemäß aus veröffentlichten oder unveröffentlichten Schriften entnommen sind, habe ich als solche kenntlich gemacht. Kein Teil dieser Arbeit ist in einem anderen Promotions- oder Habilitationsverfahren verwendet worden. Kassel, den 03. Mai 2009 __________________________________ Heiko Tobias Schumacher Zusätzliche Erklärung über kooperative Arbeiten und Publikation Teile der in dieser Dissertation präsentierten Resultate sind das Ergebnis kooperativer Arbeiten von Heiko Tobias Schumacher (Universität Kassel) und Jutta Maria Helm (Universität für Bodenkultur Wien) am Institut für Molekularbiologie und Biotech- nologie in Heraklion, Griechenland. Die folgenden Arbeiten wurden von Jutta Maria Helm durchgeführt: • Herstellung transgener Nicotiana benthamiana-Pflanzen zur Überexpression bzw. Suppression von ERL1 (vergl. Abschnitt 2.2.6.). • Herstellung doppelt-homozygoter Kreuzungen zwischen der GFP-exprimieren- den Nicotiana benthamiana-Linie GFP 6.4 mit ERL1-überexprimierenden Pflan- zen (vergl. Abschnitt 3.3.2.). • Chlorophyll a Fluoreszenz-Messungen zur Charakterisierung grundlegender bioenergetischer Parameter in ERL1-überexprimierenden Pflanzen (vergl. Ab- schnitt 3.4.3.). • Klonierung kleiner ribosomaler RNAs zur Analyse der 3’-Enden pflanzlicher 5.8S, 5S und 4.5S rRNAs (vergl. Abschnitte 2.2.11. und 3.6.1.). Der Elektronenmikroskop-Service wurde von Eva Papadogiorgaki geleitet. -
Bioinformatics-Based Identification of Chemosensory Proteins in African Malaria Mosquito, Anopheles Gambiae
Article Bioinformatics-Based Identi¯cation of Chemosensory Proteins in African Malaria Mosquito, Anopheles gambiae Zhengxi Li1*, Zuorui Shen1, Jingjiang Zhou2, and Lin Field2 1 Department of Entomology, China Agricultural University, Beijing 100094, China; 2 Biological Chemistry Division, Rothamsted Research, Harpenden, Herts. AL5 2JQ, UK. Chemosensory proteins (CSPs) are identi¯able by four spatially conserved Cys- teine residues in their primary structure or by two disul¯de bridges in their ter- tiary structure according to the previously identi¯ed olfactory speci¯c-D related proteins. A genomics- and bioinformatics-based approach is taken in the present study to identify the putative CSPs in the malaria-carrying mosquito, Anopheles gambiae. The results show that ¯ve out of the nine annotated candidates are the most possible Anopheles CSPs of A. gambiae. This study lays the foundation for further functional identi¯cation of Anopheles CSPs, though all of these candidates need additional experimental veri¯cation. Key words: chemosensory protein, proteomics, bioinformatics, olfaction, African malaria mosqui- to, Anopheles gambiae Introduction Anopheles gambiae (A. gambiae) is the principal vec- (OBPs) and olfactory speci¯c-D (OS-D) related pro- tor of malaria that a²icts more than 500 million peo- teins (3 ; 4 ). OS-D related proteins (average 13 kDa) ple and causes more than 1 million deaths each year. were ¯rst identi¯ed by subtractive hybridisation ex- Analysis of the whole genome of A. gambiae revealed periments using antennae of Drosophila melanogaster strong evidence for about 14,000 protein-coding tran- (5 ; 6 ). Many OS-D homologues were subsequently scripts, which need further annotation and experi- identi¯ed based on sequence similarity in di®erent in- mental veri¯cation (1 ).