Biologists Name a Newly Discovered Threadworm After Physicist Max Planck 9 July 2013
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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. -
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. -
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 .............................................................................................................. -
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. -
Exosomes Secreted by Nematode Parasites Transfer Small Rnas to Mammalian Cells and Modulate Innate Immunity
s Buck, A. H. et al. (2014) Exosomes secreted by nematode parasites transfer small RNAs to mammalian cells and modulate innate immunity. Nature Communications, 5 (5488). ISSN 2041-1723 Copyright © 2014 Macmillan Publishers Limited http://eprints.gla.ac.uk/100121 Deposited on: 08 December 2014 Enlighten – Research publications by members of the University of Glasgow http://eprints.gla.ac.uk ARTICLE Received 8 Sep 2014 | Accepted 6 Oct 2014 | Published 25 Nov 2014 DOI: 10.1038/ncomms6488 OPEN Exosomes secreted by nematode parasites transfer small RNAs to mammalian cells and modulate innate immunity Amy H. Buck1,2, Gillian Coakley1,2,*, Fabio Simbari1,2,*, Henry J. McSorley1,2, Juan F. Quintana1,2, Thierry Le Bihan2,3, Sujai Kumar4, Cei Abreu-Goodger5, Marissa Lear1,2, Yvonne Harcus1,2, Alessandro Ceroni1,w, Simon A. Babayan2,w, Mark Blaxter2,3,6, Alasdair Ivens2 & Rick M. Maizels1,2 In mammalian systems RNA can move between cells via vesicles. Here we demonstrate that the gastrointestinal nematode Heligmosomoides polygyrus, which infects mice, secretes vesi- cles containing microRNAs (miRNAs) and Y RNAs as well as a nematode Argonaute protein. These vesicles are of intestinal origin and are enriched for homologues of mammalian exo- some proteins. Administration of the nematode exosomes to mice suppresses Type 2 innate responses and eosinophilia induced by the allergen Alternaria. Microarray analysis of mouse cells incubated with nematode exosomes in vitro identifies Il33r and Dusp1 as suppressed genes, and Dusp1 can be repressed by nematode miRNAs based on a reporter assay. We further identify miRNAs from the filarial nematode Litomosoides sigmodontis in the serum of infected mice, suggesting that miRNA secretion into host tissues is conserved among parasitic nematodes. -
Alteration of Microflora of the Facultative Parasitic Nematode Pristionchus Entomophagus and Its Potential Application As a Biological Control Agent
The University of Maine DigitalCommons@UMaine Honors College 5-2013 Alteration of Microflora of the Facultative Parasitic Nematode Pristionchus Entomophagus and its Potential Application as a Biological Control Agent Amy M. Michaud University of Maine - Main Follow this and additional works at: https://digitalcommons.library.umaine.edu/honors Part of the Biology Commons, Entomology Commons, and the Parasitology Commons Recommended Citation Michaud, Amy M., "Alteration of Microflora of the Facultative Parasitic Nematode Pristionchus Entomophagus and its Potential Application as a Biological Control Agent" (2013). Honors College. 134. https://digitalcommons.library.umaine.edu/honors/134 This Honors Thesis is brought to you for free and open access by DigitalCommons@UMaine. It has been accepted for inclusion in Honors College by an authorized administrator of DigitalCommons@UMaine. For more information, please contact [email protected]. ALTERATION OF MICROFLORA OF THE FACULTATIVE PARASITIC NEMATODE PRISTIONCHUS ENTOMOPHAGUS AND ITS POTENTIAL APPLICATION AS A BIOLOGICAL CONTROL AGENT by Amy M. Michaud A Thesis Submitted in Partial Fulfillment of the Requirements for a Degree with Honors (Biology) The Honors College University of Maine May 2013 Advisory Committee: Dr. Eleanor Groden, Professor of Entomology, Advisor Dr. Dave Lambert, Associate Professor of Plant Pathology Elissa Ballman, Research Associate in Invasive Species and Entomology Dr. Francois Amar, Associate Professor of Physical Chemistry Dr. John Singer, Professor of Microbiology Abstract: Pristionchus entomophagus is a microbivorous, facultative, parasitic nematode commonly found in soil and decaying organic matter in North America and Europe. This nematode can form an alternative juvenile life stage capable of infecting an insect host. The microflora of P. -
Rapid Diversification Associated with a Macroevolutionary Pulse Of
Caenorhabditis elegans Caenorhabditis elegans Pristionchus pacificus P. pacificus C. elegans C. elegans P Leptojacobus dorci P P P P P P P P P. pacificus • sensusensu sensu Mesorhabditis Mesorhabditis Caenorhabditis Rhabditis Rhabditoides inermis Poikilolaimus Dataset assembly. Inference methods. P. -
The Pristionchus Pacificus Genome Provides a Unique
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by UGD Academic Repository ARTICLES The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism Christoph Dieterich1, Sandra W Clifton2, Lisa N Schuster1, Asif Chinwalla2, Kimberly Delehaunty2, Iris Dinkelacker1, Lucinda Fulton2, Robert Fulton2, Jennifer Godfrey2, Pat Minx2, Makedonka Mitreva2, Waltraud Roeseler1, Huiyu Tian1, Hanh Witte1, Shiaw-Pyng Yang2, Richard K Wilson2 & Ralf J Sommer1 Here we present a draft genome sequence of the nematode Pristionchus pacificus, a species that is associated with beetles and is used as a model system in evolutionary biology. With 169 Mb and 23,500 predicted protein-coding genes, the P. pacificus genome is larger than those of Caenorhabditis elegans and the human parasite Brugia malayi. Compared to C. elegans,the P. pacificus genome has more genes encoding cytochrome P450 enzymes, glucosyltransferases, sulfotransferases and ABC transporters, many of which were experimentally validated. The P. pacificus genome contains genes encoding cellulase and diapausin, and cellulase activity is found in P. pacificus secretions, indicating that cellulases can be found in nematodes beyond plant parasites. The relatively higher number of detoxification and degradation enzymes in P. pacificus is consistent with its necromenic lifestyle and might represent a preadaptation for parasitism. Thus, comparative genomics analysis of three ecologically distinct nematodes offers a unique opportunity to investigate the association between genome structure and lifestyle. Nematodes occupy a wide range of ecological niches, from free-living larvae remain arrested in the dauer stage until the death of the insect microbivores or predators to parasites. -
Characterisation Of, and Entomopathogenic Studies On
Nematology 17 (2015) 567-580 brill.com/nemy Characterisation of, and entomopathogenic studies on, Pristionchus aerivorus (Cobb in Merrill & Ford, 1916) Chitwood, 1937 (Rhabditida: Diplogastridae) from North Carolina, USA ∗ Weimin YE 1, ,QingYU 2,NatsumiKANZAKI 3,PaulR.ADAMS 4 and Yasmin J. CARDOZA 4 1 Nematode Assay Section, Agronomic Division, North Carolina Department of Agriculture & Consumer Services, 4300 Reedy Creek Road, Raleigh, NC 27607, USA 2 Agriculture and Agri-Food Canada, Environmental Health Program/Invertebrate Biodiversity, Ottawa, ON, Canada K1A 0C6 3 Forest Pathology Laboratory, Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki 305-8687, Japan 4 Department of Entomology, North Carolina State University, Campus Box 7613, Raleigh, NC 27695-7613, USA Received: 23 December 2014; revised: 13 March 2015 Accepted for publication: 13 March 2015; available online: 25 April 2015 Summary – During a survey of entomopathogenic nematodes in North Carolina, USA, a Pristionchus species was recovered using the Galleria bait method. Morphological studies with light microscopy and scanning electron microscopy, mating tests with reference strains, as well as molecular analyses of the near-full-length small subunit rRNA gene (18S) and D2-D3 expansion segments of the large subunit rRNA gene (28S) identified this isolate as Pristionchus aerivorus. Exposed Galleria larvae were killed within 48 h and high numbers of nematodes were recovered from the cadavers about 5 days later. Preliminary tests revealed that this nematode is capable of infecting at least two other insect species (Helicoverpa zea and Tenebrio molitor) under laboratory conditions. The status of the genus Chroniodiplogaster is discussed and confirmed as a junior synonym of Pristionchus based on morphological observation and molecular phylogenetic analysis. -
Description of Three Pristionchus Species (Nematoda: Diplogastridae) from Japan That Form a Cryptic Species Complex with the Model Organism P
Description of Three Pristionchus Species (Nematoda: Diplogastridae) from Japan that Form a Cryptic Species Complex with the Model Organism P. pacificus Author(s): Natsumi Kanzaki, Erik J. Ragsdale, Matthias Herrmann, Werner E. Mayer and Ralf J. Sommer Source: Zoological Science, 29(6):403-417. 2012. Published By: Zoological Society of Japan DOI: http://dx.doi.org/10.2108/zsj.29.403 URL: http://www.bioone.org/doi/full/10.2108/zsj.29.403 BioOne (www.bioone.org) is a nonprofit, online aggregation of core research in the biological, ecological, and environmental sciences. BioOne provides a sustainable online platform for over 170 journals and books published by nonprofit societies, associations, museums, institutions, and presses. Your use of this PDF, the BioOne Web site, and all posted and associated content indicates your acceptance of BioOne’s Terms of Use, available at www.bioone.org/page/terms_of_use. Usage of BioOne content is strictly limited to personal, educational, and non-commercial use. Commercial inquiries or rights and permissions requests should be directed to the individual publisher as copyright holder. BioOne sees sustainable scholarly publishing as an inherently collaborative enterprise connecting authors, nonprofit publishers, academic institutions, research libraries, and research funders in the common goal of maximizing access to critical research. ZOOLOGICAL SCIENCE 29: 403–417 (2012) ¤ 2012 Zoological Society of Japan Description of Three Pristionchus Species (Nematoda: Diplogastridae) from Japan that Form a Cryptic Species Complex with the Model Organism P. pacificus Natsumi Kanzaki1‡, Erik J. Ragsdale2‡, Matthias Herrmann2‡, Werner E. Mayer2†‡, and Ralf J. Sommer2* 1Forest Pathology Laboratory, Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki 305-8687, Japan 2Max Planck Institute for Developmental Biology, Department of Evolutionary Biology, Spemannstraße 37, 72076 Tübingen, Germany Three new species of Pristionchus (P. -
Mechanism of Murderous Mushrooms Paves Path for Parasitic Helminth Halt
COMMENTARY Mechanism of murderous mushrooms paves path for parasitic helminth halt COMMENTARY Tess Renahana and Ralf J. Sommera,1 “In the animal kingdom, the rule is, eat or be eaten” Intact Cilia of Head Sensory Neurons Needed (ref. 1, p. 20). We will expand academic Thomas for Instantaneous Paralysis Szasz’s statement to include the fungi, because in Using carnivorous Pleurotus ostreatus and free-living the multifaceted interactions of fungi and nematodes, Caenorhabditis elegans, Lee et al. (7) uncover a strik- this is often a steadfast rule. Indeed, soil systems that ing mechanism of a predation tactic that differs from appear inert or lifeless to the naked human eye in re- other well-described nematophageous fungi and ality teem with microscopic life dominated by interac- successfully acts against a diversity of nematodes. tions between nematodes and fungi. Numerous free- Fungi relying on trapping mechanisms have co-opted living Bursaphelenchus nematodes are mycophagous the use of nematode ascaroside pheromones to lure (2), and beetle-associated Pristionchus pacificus has ex- them into their snares. Among the worms, ascarosides panded its dietary range to include consumption of are used for various behaviors and communication, fungi in addition to bacteria and other nematodes including mating and sensing population size (3). Parasitic Deladenus nematodes are even commer- (10). While these wedged worms wiggle for hours, cially used for their mycophagous phase to keep fun- P. ostreatus immobilizes C. elegans almost immediately gus Amylostereum in check; however, the fungus has upon contact with fungal hyphae, as Lee et al. observe responded with hyphal invasion through the worms’ in their study in PNAS. -
Bacterial Derived Vitamin B12 Enhances Predatory Behaviors In
bioRxiv preprint doi: https://doi.org/10.1101/797803; this version posted October 8, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Bacterial derived vitamin B12 enhances predatory behaviors 2 in nematodes 3 Nermin Akduman1, James W. Lightfoot1, Waltraud Röseler1, Hanh Witte1, Wen- 4 Sui Lo1, Christian Rödelsperger1, Ralf J. Sommer1* 5 *corresponding author: [email protected] 6 Affiliations: 1Department for Evolutionary Biology, Max Planck Institute for 7 Developmental Biology, Max Planck Ring 9, 72076 Tübingen Germany 8 KEYWORDS 9 Microbiome, microbiota, diet, surplus killing, metabolism, development, Pristionchus 10 pacificus, Caenorhabditis elegans 1 bioRxiv preprint doi: https://doi.org/10.1101/797803; this version posted October 8, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 11 The microbiome is known to affect host development, metabolism and 12 immunity, however, its impact on behaviors is only beginning to be 13 understood. Here, we investigate how bacteria modulate complex behaviors in 14 the nematode model organism Pristionchus pacificus. P. pacificus is a 15 predator feeding on the larvae of other nematodes including Caenorhabditis 16 elegans. Growing P. pacificus on different bacteria and testing their ability to 17 kill C.