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Assessment of Pathogenic Bacteria Transfer from Pristionchus
Assessment of Pathogenic Bacteria Transfer From Pristionchus Entomophagus (Nematoda: Diplogasteridae) to the Invasive Ant Myrmica Rubra and Its Potential Role in Colony Mortality in Coastal Maine Suzanne Lynn Ishaq ( [email protected] ) School of Food and Agriculture, University of Maine, Orono, ME 04469 https://orcid.org/0000-0002- 2615-8055 Alice Hotopp University of Maine Samantha Silverbrand University of Maine Jonathan E. Dumont Husson University Amy Michaud University of California Davis Jean MacRae University of Maine S. Patricia Stock University of Arizona Eleanor Groden University of Maine Research Article Keywords: bacterial community, biological control, microbial transfer, nematodes, Illumina, Galleria mellonella larvae Posted Date: November 5th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-101817/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/38 Abstract Background: Necromenic nematode Pristionchus entomophagus has been frequently found in nests of the invasive European ant Myrmica rubra in coastal Maine, United States. The nematodes may contribute to ant mortality and collapse of colonies by transferring environmental bacteria. M. rubra ants naturally hosting nematodes were collected from collapsed wild nests in Maine and used for bacteria identication. Virulence assays were carried out to validate acquisition and vectoring of environmental bacteria to the ants. Results: Multiple bacteria species, including Paenibacillus spp., were found in the nematodes’ digestive tract. Serratia marcescens, Serratia nematodiphila, and Pseudomonas uorescens were collected from the hemolymph of nematode-infected Galleria mellonella larvae. Variability was observed in insect virulence in relation to the site origin of the nematodes. In vitro assays conrmed uptake of RFP-labeled Pseudomonas aeruginosa strain PA14 by nematodes. -
Repertoire and Evolution of Mirna Genes in Four Divergent Nematode Species
Downloaded from genome.cshlp.org on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press Resource Repertoire and evolution of miRNA genes in four divergent nematode species Elzo de Wit,1,3 Sam E.V. Linsen,1,3 Edwin Cuppen,1,2,4 and Eugene Berezikov1,2,4 1Hubrecht Institute-KNAW and University Medical Center Utrecht, Cancer Genomics Center, Utrecht 3584 CT, The Netherlands; 2InteRNA Genomics B.V., Bilthoven 3723 MB, The Netherlands miRNAs are ;22-nt RNA molecules that play important roles in post-transcriptional regulation. We have performed small RNA sequencing in the nematodes Caenorhabditis elegans, C. briggsae, C. remanei, and Pristionchus pacificus, which have diverged up to 400 million years ago, to establish the repertoire and evolutionary dynamics of miRNAs in these species. In addition to previously known miRNA genes from C. elegans and C. briggsae we demonstrate expression of many of their homologs in C. remanei and P. pacificus, and identified in total more than 100 novel expressed miRNA genes, the majority of which belong to P. pacificus. Interestingly, more than half of all identified miRNA genes are conserved at the seed level in all four nematode species, whereas only a few miRNAs appear to be species specific. In our compendium of miRNAs we observed evidence for known mechanisms of miRNA evolution including antisense transcription and arm switching, as well as miRNA family expansion through gene duplication. In addition, we identified a novel mode of miRNA evolution, termed ‘‘hairpin shifting,’’ in which an alternative hairpin is formed with up- or downstream sequences, leading to shifting of the hairpin and creation of novel miRNA* species. -
Parallel Adaptation to Higher Temperatures in Divergent Clades of the Nematode 2" Pristionchus Pacificus
bioRxiv preprint doi: https://doi.org/10.1101/096727; this version posted December 29, 2016. 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" Parallel adaptation to higher temperatures in divergent clades of the nematode 2" Pristionchus pacificus 3" 4" 5" Mark Leaver1, Merve Kayhan1,2, Angela McGaughran3,4, Christian Rodelsperger3, 6" Anthony A. Hyman1*, Ralf J. Sommer3* 7" 8" 9" 1 Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 10" 108, 01307, Dresden, Germany. 11" 2 Bilkent University, Department of Molecular Biology and Genetics, SB 12" Building, 06800 Ankara, Turkey. 13" 3 Max Planck Institute for Developmental Biology, Department of Evolutionary 14" Biology, Spemannstraße 37, 72076, Tübingen, Germany. 15" 4 Australian National University, Research School of Biology, Division of Evolution, 16" Ecology and Genetics, Canberra, ACT, 2601, Australia. 17" * Corresponding authors 18" Key words: Parallelism, reversion, adaptation, natural selection, temperature, 19" Pristionchus pacificus 1 bioRxiv preprint doi: https://doi.org/10.1101/096727; this version posted December 29, 2016. 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. 20" Abstract 21" Studying the effect of temperature on fertility is particularly important in the light of 22" ongoing climate change. We need to know if organisms can adapt to higher 23" temperatures and, if so, what are the evolutionary mechanisms behind such 24" adaptation. Such studies have been hampered by the lack different populations of 25" sufficient sizes with which to relate the phenotype of temperature tolerance to the 26" underlying genotypes. -
Zhylina, Shevchenko.Pdf
ЕКОЛОГІЯ H. B. Humenyuk, V. O. Khomenchuk, N. G. Zinkovska Ternopil Volodymyr Hnatiuk National Pedagogical University, Ukraine Taras Shevchenko Regional Humanitarian-Pedagogical Academy of Kremenets, Ukraine TYPES OF MODELLING THE ENVIRONMENT AND PECULIARITIES OF THEIR USE It is found that mathematical or imitating modeling is one of the most useful and effective forms of modeling, which represent the most significant features of real objects, processes, systems and phenomena studied by various sciences. The main purpose of factor analysis - reducing the dimension of the source data for the purpose of economical description by providing minimal loss of the initial information. The result of factor analysis is the transition from the set output variables to significantly fewer new variables - factors. Factor is interpreted as a common cause of the variability of the multiple output variables. The value of the revealed factors is 4,37 and 1.98 respectively. The selected factors include 79,5% of general dispersion (54,7 and 24,8 % respectively). Thus the accumulated percentage of both factors dispersion (79,5 %) defines how fully we can describe the set of date with the help of selected factors. The higher this index is the larger part of the data was factorized and the more credible the factorial model is. In widespread application of modeling in solving the problem of knowledge and environmental protection the combination of two tendencies which are characteristic of the modern science are singled out – cybernation and ecologization. The information systems are used to choose the optimal ways of different resources application in order to predict the consequences of environmental pollution. -
Molecular Markers, Indicator Taxa, and Community Indices: the Issue of Bioindication Accuracy
NEMATODES AS ENVIRONMENTAL INDICATORS This page intentionally left blank NEMATODES AS ENVIRONMENTAL INDICATORS Edited by Michael J. Wilson Institute of Biological and Environmental Sciences, The University of Aberdeen, Aberdeen, Scotland, UK Thomais Kakouli-Duarte EnviroCORE Department of Science and Health, Institute of Technology, Carlow, Ireland CABI is a trading name of CAB International CABI Head Office CABI North American Office Nosworthy Way 875 Massachusetts Avenue Wallingford 7th Floor Oxfordshire OX10 8DE Cambridge, MA 02139 UK USA Tel: +44 (0)1491 832111 Tel: +1 617 395 4056 Fax: +44 (0)1491 833508 Fax: +1 617 354 6875 E-mail: [email protected] E-mail: [email protected] Website: www.cabi.org © CAB International 2009. All rights reserved. No part of this publication may be reproduced in any form or by any means, electronically, mechanically, by photocopying, recording or otherwise, without the prior permission of the copyright owners. A catalogue record for this book is available from the British Library, London, UK. Library of Congress Cataloging-in-Publication Data Nematodes as environmental indicators / edited by Michael J. Wilson, Thomais Kakouli-Duarte. p. cm. Includes bibliographical references and index. ISBN 978-1-84593-385-2 (alk. paper) 1. Nematodes–Ecology. 2. Indicators (Biology) I. Wilson, Michael J. (Michael John), 1964- II. Kakouli-Duarte, Thomais. III. Title. QL391.N4N382 2009 592'.5717--dc22 2008049111 ISBN-13: 978 1 84593 385 2 Typeset by SPi, Pondicherry, India. Printed and bound in the UK by the MPG Books Group. The paper used for the text pages in this book is FSC certified. The FSC (Forest Stewardship Council) is an international network to promote responsible man- agement of the world’s forests. -
Modeling the Ballistic-To-Diffusive Transition in Nematode Motility
Modeling the ballistic-to-diffusive transition in nematode motility reveals variation in exploratory behavior across species Stephen J. Helms∗1, W. Mathijs Rozemuller∗1, Antonio Carlos Costa∗2, Leon Avery3, Greg J. Stephens2,4, and Thomas S. Shimizu y1 1AMOLF Institute, Amsterdam, The Netherlands 2Dept. of Physics & Astronomy, Vrije Universiteit, Amsterdam, The Netherlands 3Dept. of Physiology and Biophysics, Virginia Commonwealth Univ., Richmond, VA, USA 4Okinawa Institute of Science and Technology, Onna-son, Okinawa, Japan Abstract A quantitative understanding of organism-level behavior requires pre- dictive models that can capture the richness of behavioral phenotypes, yet are simple enough to connect with underlying mechanistic processes. Here we investigate the motile behavior of nematodes at the level of their trans- lational motion on surfaces driven by undulatory propulsion. We broadly sample the nematode behavioral repertoire by measuring motile trajecto- ries of the canonical lab strain C. elegans N2 as well as wild strains and distant species. We focus on trajectory dynamics over timescales span- ning the transition from ballistic (straight) to diffusive (random) move- ment and find that salient features of the motility statistics are captured by a random walk model with independent dynamics in the speed, bear- arXiv:1501.00481v3 [q-bio.NC] 24 Mar 2019 ing and reversal events. We show that the model parameters vary among species in a correlated, low-dimensional manner suggestive of a common mode of behavioral control and a trade-off between exploration and ex- ploitation. The distribution of phenotypes along this primary mode of variation reveals that not only the mean but also the variance varies con- siderably across strains, suggesting that these nematode lineages employ contrasting \bet-hedging" strategies for foraging. -
Fisher Vs. the Worms: Extraordinary Sex Ratios in Nematodes and the Mechanisms That Produce Them
cells Review Fisher vs. the Worms: Extraordinary Sex Ratios in Nematodes and the Mechanisms that Produce Them Justin Van Goor 1,* , Diane C. Shakes 2 and Eric S. Haag 1 1 Department of Biology, University of Maryland, College Park, MD 20742, USA; [email protected] 2 Department of Biology, William and Mary, Williamsburg, VA 23187, USA; [email protected] * Correspondence: [email protected] Abstract: Parker, Baker, and Smith provided the first robust theory explaining why anisogamy evolves in parallel in multicellular organisms. Anisogamy sets the stage for the emergence of separate sexes, and for another phenomenon with which Parker is associated: sperm competition. In outcrossing taxa with separate sexes, Fisher proposed that the sex ratio will tend towards unity in large, randomly mating populations due to a fitness advantage that accrues in individuals of the rarer sex. This creates a vast excess of sperm over that required to fertilize all available eggs, and intense competition as a result. However, small, inbred populations can experience selection for skewed sex ratios. This is widely appreciated in haplodiploid organisms, in which females can control the sex ratio behaviorally. In this review, we discuss recent research in nematodes that has characterized the mechanisms underlying highly skewed sex ratios in fully diploid systems. These include self-fertile hermaphroditism and the adaptive elimination of sperm competition factors, facultative parthenogenesis, non-Mendelian meiotic oddities involving the sex chromosomes, and Citation: Van Goor, J.; Shakes, D.C.; Haag, E.S. Fisher vs. the Worms: environmental sex determination. By connecting sex ratio evolution and sperm biology in surprising Extraordinary Sex Ratios in ways, these phenomena link two “seminal” contributions of G. -
Pristionchus Pacificus* §
Pristionchus pacificus* § Ralf J. Sommer , Max-Planck Institut für Entwicklungsbiologie, Abteilung Evolutionsbiologie, D-72076 Tübingen, Germany Table of Contents 1. Biology ..................................................................................................................................1 2. Developmental biology ............................................................................................................. 3 3. Phylogeny ..............................................................................................................................3 4. Ecology .................................................................................................................................3 5. Genetics .................................................................................................................................4 5.1. Formal genetics and sex determination .............................................................................. 4 5.2. Nomenclature ............................................................................................................... 5 6. Genomics ...............................................................................................................................5 6.1. Macrosynteny: chromosome homology and genome size ...................................................... 5 6.2. Microsynteny ............................................................................................................... 6 6.3. Trans-splicing .............................................................................................................. -
Field Studies Reveal a Close Relative of C. Elegans Thrives in the Fresh Figs
Woodruf and Phillips BMC Ecol (2018) 18:26 https://doi.org/10.1186/s12898-018-0182-z BMC Ecology RESEARCH ARTICLE Open Access Field studies reveal a close relative of C. elegans thrives in the fresh fgs of Ficus septica and disperses on its Ceratosolen pollinating wasps Gavin C. Woodruf1,2* and Patrick C. Phillips2 Abstract Background: Biotic interactions are ubiquitous and require information from ecology, evolutionary biology, and functional genetics in order to be understood. However, study systems that are amenable to investigations across such disparate felds are rare. Figs and fg wasps are a classic system for ecology and evolutionary biology with poor functional genetics; Caenorhabditis elegans is a classic system for functional genetics with poor ecology. In order to help bridge these disciplines, here we describe the natural history of a close relative of C. elegans, Caenorhabditis inopi- nata, that is associated with the fg Ficus septica and its pollinating Ceratosolen wasps. Results: To understand the natural context of fg-associated Caenorhabditis, fresh F. septica fgs from four Okinawan islands were sampled, dissected, and observed under microscopy. C. inopinata was found in all islands where F. septica fgs were found. C.i nopinata was routinely found in the fg interior and almost never observed on the outside surface. C. inopinata was only found in pollinated fgs, and C. inopinata was more likely to be observed in fgs with more foun- dress pollinating wasps. Actively reproducing C. inopinata dominated early phase fgs, whereas late phase fgs with emerging wasp progeny harbored C. inopinata dauer larvae. Additionally, C. inopinata was observed dismounting from Ceratosolen pollinating wasps that were placed on agar plates. -
"Structure, Function and Evolution of the Nematode Genome"
Structure, Function and Advanced article Evolution of The Article Contents . Introduction Nematode Genome . Main Text Online posting date: 15th February 2013 Christian Ro¨delsperger, Max Planck Institute for Developmental Biology, Tuebingen, Germany Adrian Streit, Max Planck Institute for Developmental Biology, Tuebingen, Germany Ralf J Sommer, Max Planck Institute for Developmental Biology, Tuebingen, Germany In the past few years, an increasing number of draft gen- numerous variations. In some instances, multiple alter- ome sequences of multiple free-living and parasitic native forms for particular developmental stages exist, nematodes have been published. Although nematode most notably dauer juveniles, an alternative third juvenile genomes vary in size within an order of magnitude, com- stage capable of surviving long periods of starvation and other adverse conditions. Some or all stages can be para- pared with mammalian genomes, they are all very small. sitic (Anderson, 2000; Community; Eckert et al., 2005; Nevertheless, nematodes possess only marginally fewer Riddle et al., 1997). The minimal generation times and the genes than mammals do. Nematode genomes are very life expectancies vary greatly among nematodes and range compact and therefore form a highly attractive system for from a few days to several years. comparative studies of genome structure and evolution. Among the nematodes, numerous parasites of plants and Strikingly, approximately one-third of the genes in every animals, including man are of great medical and economic sequenced nematode genome has no recognisable importance (Lee, 2002). From phylogenetic analyses, it can homologues outside their genus. One observes high rates be concluded that parasitic life styles evolved at least seven of gene losses and gains, among them numerous examples times independently within the nematodes (four times with of gene acquisition by horizontal gene transfer. -
Species-Specific Recognition of Beetle Cues by the Nematode Pristionchus Maupasi
EVOLUTION & DEVELOPMENT 10:3, 273–279 (2008) Species-specific recognition of beetle cues by the nematode Pristionchus maupasi RayL.Hong,a Alesˇ Svatosˇ,b Matthias Herrmann,a and Ralf J. Sommera,Ã aDepartment for Evolutionary Biology, Max-Planck Institute for Developmental Biology, Tuebingen, Germany bMax-Planck Institute for Chemical Ecology, Mass Spectrometry Research Group, Jena, Germany ÃAuthor for correspondence (email: [email protected]) SUMMARY The environment has a strong effect on studies originally established in Caenorhabditis elegans.We development as is best seen in the various examples of observed that P. maupasi is exclusively attracted to phenol, phenotypic plasticity. Besides abiotic factors, the interactions one of the sex attractants of Melolontha beetles, and that between organisms are part of the adaptive forces shaping the attraction was also observed when washes of adult beetles evolution of species. To study how ecology influences were used instead of pure compounds. Furthermore, development, model organisms have to be investigated in P. maupasi chemoattraction to phenol synergizes with plant their environmental context. We have recently shown that the volatiles such as the green leaf alcohol and linalool, nematode Pristionchus pacificus and its relatives are closely demonstrating that nematodes can integrate distinct associated with scarab beetles with a high degree of species chemical senses from multiple trophic levels. In contrast, specificity. For example, P. pacificus is associated with the another cockchafer-associated nematode, Diplogasteriodes oriental beetle Exomala orientalis in Japan and the magnus, was not strongly attracted to phenol. We conclude northeastern United States, whereas Pristionchus maupasi that interception of the insect communication system might be is primarily isolated from cockchafers of the genus Melolontha a recurring strategy of Pristionchus nematodes but that in Europe. -
An Introduction to the UCSC Genome Browser* Raymond Lee§ Division of Biology, California Institute of Technology, Pasadena CA 91125, USA
An introduction to the UCSC Genome Browser* Raymond Lee§ Division of Biology, California Institute of Technology, Pasadena CA 91125, USA The Genome Browser at the University of California Santa Cruz provides a uniform graphical interface to sequences, features, and annotations of genomes across a wide spectrum of organisms, from yeast to humans. In particular, it covers seven nematode genomes: Caenorhabditis elegans, C. sp. 11, C. brenneri, C. briggsae, C. remanei, C. japonica, and Pristionchus pacificus and thus is particularly useful for multiple-genome comparative analysis. One can use the provided tools and visual aides to facilitate sequence feature detection and examination. This article provides a brief introduction for using the Genome Browser from the perspective of a C. elegans researcher. Interested users should read the official user guide and explore the site more deeply as there are many more features not mentioned here. To begin, one should choose the nematode clade, then the organism C. elegans, a version of genome sequence assembly (e.g., WS220), and a region of the genome (Figure 1). Browser behavior is context sensitive, depending on the choices made in order from left to right. There are three basic ways to specify a region to browse: by a range of chromosomal numerical positions, by a gene name and by an accession number. More flexibly, instead of exact positions, one can also search for a descriptive term (such as “kinase inhibitor”) that is present in gene records. Some restrictions are worth noting. Chromosome positions must start with “chr”. Gene names recognized by the browser are limited to those in RefSeq and Ensembl entries.