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Wang Y, Song H, Wang S, Cai Q, Chen J. Design, Synthesis, Nematicidal Activity, and Mechanism of Novel Amide Derivatives Containing an 1,2,4-Oxadiazole Moiety. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:128-139. [PMID: 38154095 DOI: 10.1021/acs.jafc.3c04945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2023]
Abstract
To discover new nematicides, a series of novel amide derivatives containing 1,2,4-oxadiazole were designed and synthesized. Several compounds showed excellent nematicidal activity. The LC50 values of compounds A7, A18, and A20-A22 against pine wood nematode (Bursaphelenchus xylophilus), rice stem nematode (Aphelenchoides besseyi), and sweet potato stem nematode (Ditylenchus destructor) were 1.39-3.09 mg/L, which were significantly better than the control nematicide tioxazafen (106, 49.0, and 75.0 mg/L, respectively). Compound A7 had an outstanding inhibitory effect on nematode feeding, reproductive ability, and egg hatching. Compound A7 effectively promoted the oxidative stress of nematodes and caused intestinal damage to nematodes. Compound A7 significantly inhibited the activity of succinate dehydrogenase (SDH) in nematodes, leading to blockage of electron transfer in the respiratory chain and thereby hindering the synthesis of adenosine triphosphate (ATP), which consequently affects the entire oxidative phosphorylation process to finally cause nematode death. Therefore, compound A7 can be used as a potential SDH inhibitor in nematicide applications.
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Affiliation(s)
- Yu Wang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Hongyi Song
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Sheng Wang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Qingfeng Cai
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Jixiang Chen
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
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2
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Fallon AM. Wolbachia: Advancing into a Second Century. Methods Mol Biol 2024; 2739:1-13. [PMID: 38006542 DOI: 10.1007/978-1-0716-3553-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2023]
Abstract
Wolbachia pipientis had its scientific debut nearly a century ago and has recently emerged as a target for therapeutic treatment of filarial infections and an attractive tool for control of arthropod pests. Wolbachia was known as a biological entity before DNA was recognized as the molecule that carries the genetic information on which life depends, and before arthropods and nematodes were grouped in the Ecdysozoa. Today, some investigators consider Wolbachia the most abundant endosymbiont on earth, given the numbers of its hosts and its diverse mutualistic, commensal, and parasitic roles in their life histories. Recent advances in molecular technologies have revolutionized our understanding of Wolbachia and its associated reproductive phenotypes. New models have emerged for its investigation, and substantial progress has been made towards Wolbachia-based interventions in medicine and agriculture. Here I introduce Wolbachia, with a focus on aspects of its biology that are covered in greater detail in subsequent chapters.
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Affiliation(s)
- Ann M Fallon
- Department of Entomology, University of Minnesota, Saint Paul, MN, USA.
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3
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Villegas LI, Ferretti L, Wiehe T, Waldvogel A, Schiffer PH. Parthenogenomics: Insights on mutation rates and nucleotide diversity in parthenogenetic Panagrolaimus nematodes. Ecol Evol 2024; 14:e10831. [PMID: 38192904 PMCID: PMC10771965 DOI: 10.1002/ece3.10831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 01/10/2024] Open
Abstract
Asexual reproduction is assumed to lead to the accumulation of deleterious mutations, and reduced heterozygosity due to the absence of recombination. Panagrolaimid nematode species display different modes of reproduction. Sexual reproduction with distinct males and females, asexual reproduction through parthenogenesis in the genus Panagrolaimus, and hermaphroditism in Propanagrolaimus. Here, we compared genomic features of free-living nematodes in populations and species isolated from geographically distant regions to study diversity, and genome-wide differentiation under different modes of reproduction. We firstly estimated genome-wide spontaneous mutation rates in a triploid parthenogenetic Panagrolaimus, and a diploid hermaphroditic Propanagrolaimus via long-term mutation accumulation lines. Secondly, we calculated population genetic parameters including nucleotide diversity, and fixation index (F ST) between populations of asexually and sexually reproducing nematodes. Thirdly, we used phylogenetic network methods on sexually and asexually reproducing Panagrolaimus populations to understand evolutionary relationships between them. The estimated mutation rate was slightly lower for the asexual population, as expected for taxa with this reproductive mode. Natural polyploid asexual populations revealed higher nucleotide diversity. Despite their common ancestor, a gene network revealed a high level of genetic differentiation among asexual populations. The elevated heterozygosity found in the triploid parthenogens could be explained by the third genome copy. Given their tendentially lower mutation rates it can be hypothesized that this is part of the mechanism to evade Muller's ratchet. Our findings in parthenogenetic triploid nematode populations seem to challenge common expectations of evolution under asexuality.
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Affiliation(s)
| | | | - Thomas Wiehe
- Institute for GeneticsUniversity of CologneKölnGermany
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4
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Ishita Y, Onodera A, Ekino T, Chihara T, Okumura M. Co-option of an Astacin Metalloprotease Is Associated with an Evolutionarily Novel Feeding Morphology in a Predatory Nematode. Mol Biol Evol 2023; 40:msad266. [PMID: 38105444 PMCID: PMC10753534 DOI: 10.1093/molbev/msad266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 10/14/2023] [Accepted: 11/16/2023] [Indexed: 12/19/2023] Open
Abstract
Animals consume a wide variety of food sources to adapt to different environments. However, the genetic mechanisms underlying the acquisition of evolutionarily novel feeding morphology remain largely unknown. While the nematode Caenorhabditis elegans feeds on bacteria, the satellite species Pristionchus pacificus exhibits predatory feeding behavior toward other nematodes, which is an evolutionarily novel feeding habit. Here, we found that the astacin metalloprotease Ppa-NAS-6 is required for the predatory killing by P. pacificus. Ppa-nas-6 mutants were defective in predation-associated characteristics, specifically the tooth morphogenesis and tooth movement during predation. Comparison of expression patterns and rescue experiments of nas-6 in P. pacificus and C. elegans suggested that alteration of the spatial expression patterns of NAS-6 may be vital for acquiring predation-related traits. Reporter analysis of the Ppa-nas-6 promoter in C. elegans revealed that the alteration in expression patterns was caused by evolutionary changes in cis- and trans-regulatory elements. This study suggests that the co-option of a metalloprotease is involved in an evolutionarily novel feeding morphology.
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Affiliation(s)
- Yuuki Ishita
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Ageha Onodera
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Taisuke Ekino
- School of Agriculture, Meiji University, Kawasaki 214-8571, Japan
| | - Takahiro Chihara
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
- Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Misako Okumura
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
- Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
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5
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Sikora RA, Helder J, Molendijk LPG, Desaeger J, Eves-van den Akker S, Mahlein AK. Integrated Nematode Management in a World in Transition: Constraints, Policy, Processes, and Technologies for the Future. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:209-230. [PMID: 37186900 DOI: 10.1146/annurev-phyto-021622-113058] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Plant-parasitic nematodes are one of the most insidious pests limiting agricultural production, parasitizing mostly belowground and occasionally aboveground plant parts. They are an important and underestimated component of the estimated 30% yield loss inflicted on crops globally by biotic constraints. Nematode damage is intensified by interactions with biotic and abiotic factors constraints: soilborne pathogens, soil fertility degradation, reduced soil biodiversity, climate variability, and policies influencing the development of improved management options. This review focuses on the following topics: (a) biotic and abiotic constraints, (b) modification of production systems, (c) agricultural policies, (d) the microbiome, (e) genetic solutions, and (f) remote sensing. Improving integrated nematode management (INM) across all scales of agricultural production and along the Global North-Global South divide, where inequalities influence access to technology, is discussed. The importance of the integration of technological development in INM is critical to improving food security and human well-being in the future.
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Affiliation(s)
| | - Johannes Helder
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands
| | | | - Johan Desaeger
- Institute of Food and Agricultural Sciences, Department of Entomology and Nematology, Gulf Coast Research and Education Center, University of Florida, Wimauma, Florida, USA
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6
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Freires IA, Morelo DFC, Soares LFF, Costa IS, de Araújo LP, Breseghello I, Abdalla HB, Lazarini JG, Rosalen PL, Pigossi SC, Franchin M. Progress and promise of alternative animal and non-animal methods in biomedical research. Arch Toxicol 2023; 97:2329-2342. [PMID: 37394624 DOI: 10.1007/s00204-023-03532-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/24/2023] [Indexed: 07/04/2023]
Abstract
Cell culture and invertebrate animal models reflect a significant evolution in scientific research by providing reliable evidence on the physiopathology of diseases, screening for new drugs, and toxicological tests while reducing the need for mammals. In this review, we discuss the progress and promise of alternative animal and non-animal methods in biomedical research, with a special focus on drug toxicity.
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Affiliation(s)
- Irlan Almeida Freires
- Department of Biosciences, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil.
| | - David Fernando Colon Morelo
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | | | | | | | | | - Henrique Ballassini Abdalla
- Laboratory of Neuroimmune Interface of Pain Research, São Leopoldo Mandic Institute and Research Center, Campinas, SP, Brazil
| | - Josy Goldoni Lazarini
- Department of Biosciences, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil
| | - Pedro Luiz Rosalen
- Department of Biosciences, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil
- Graduate Program in Biological Sciences, Federal University of Alfenas, Alfenas, Brazil
| | | | - Marcelo Franchin
- School of Dentistry, Federal University of Alfenas, Alfenas, Brazil
- Bioactivity and Applications Lab, Department of Biological Sciences, Faculty of Science and Engineering, School of Natural Sciences, University of Limerick, Limerick, Ireland
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7
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Kaiser M. Connectomes: from a sparsity of networks to large-scale databases. Front Neuroinform 2023; 17:1170337. [PMID: 37377946 PMCID: PMC10291062 DOI: 10.3389/fninf.2023.1170337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
The analysis of whole brain networks started in the 1980s when only a handful of connectomes were available. In these early days, information about the human connectome was absent and one could only dream about having information about connectivity in a single human subject. Thanks to non-invasive methods such as diffusion imaging, we now know about connectivity in many species and, for some species, in many individuals. To illustrate the rapid change in availability of connectome data, the UK Biobank is on track to record structural and functional connectivity in 100,000 human subjects. Moreover, connectome data from a range of species is now available: from Caenorhabditis elegans and the fruit fly to pigeons, rodents, cats, non-human primates, and humans. This review will give a brief overview of what structural connectivity data is now available, how connectomes are organized, and how their organization shows common features across species. Finally, I will outline some of the current challenges and potential future work in making use of connectome information.
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Affiliation(s)
- Marcus Kaiser
- NIHR Nottingham Biomedical Research Centre, School of Medicine, University of Nottingham, Nottingham, United Kingdom
- Sir Peter Mansfield Imaging Centre, School of Medicine, University of Nottingham, Nottingham, United Kingdom
- School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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8
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Wrobel CJJ, Schroeder FC. Repurposing degradation pathways for modular metabolite biosynthesis in nematodes. Nat Chem Biol 2023; 19:676-686. [PMID: 37024728 PMCID: PMC10559835 DOI: 10.1038/s41589-023-01301-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 02/24/2023] [Indexed: 04/08/2023]
Abstract
Recent studies have revealed that Caenorhabditis elegans and other nematodes repurpose products from biochemical degradation pathways for the combinatorial assembly of complex modular structures that serve diverse signaling functions. Building blocks from neurotransmitter, amino acid, nucleoside and fatty acid metabolism are attached to scaffolds based on the dideoxyhexose ascarylose or glucose, resulting in hundreds of modular ascarosides and glucosides. Genome-wide association studies have identified carboxylesterases as the key enzymes mediating modular assembly, enabling rapid compound discovery via untargeted metabolomics and suggesting that modular metabolite biosynthesis originates from the 'hijacking' of conserved detoxification mechanisms. Modular metabolites thus represent a distinct biosynthetic strategy for generating structural and functional diversity in nematodes, complementing the primarily polyketide synthase- and nonribosomal peptide synthetase-derived universe of microbial natural products. Although many aspects of modular metabolite biosynthesis and function remain to be elucidated, their identification demonstrates how phenotype-driven compound discovery, untargeted metabolomics and genomic approaches can synergize to facilitate the annotation of metabolic dark matter.
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Affiliation(s)
- Chester J J Wrobel
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.
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9
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Pereira FB, González-Solís D. Review of the parasitic nematodes of marine fishes from off the American continent. Parasitology 2022; 149:1928-1941. [PMID: 36076284 PMCID: PMC11010509 DOI: 10.1017/s0031182022001287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/29/2022] [Accepted: 08/31/2022] [Indexed: 12/29/2022]
Abstract
The ichthyofauna of the Atlantic and Pacific coasts off the American continent is very rich. Consequently, a high biodiversity of nematodes parasitizing these vertebrates is also expected. Currently, data on nematode parasites of marine fish off the Americas are fragmented. A review of all adult nematode species reported parasitizing marine fish from off the American continent is herein presented, as well as comments on their patterns of diversity, life cycles and advances in the taxonomic and phylogenetic knowledge. A total of 209 valid species, 19 species inquirendae and 6 dubious records have been recorded, the majority from the fish taxa Eupercaria and Perciformes. The families Sciaenidae, Serranidae and Lutjanidae, as well as the tropical and temperate Atlantic waters, exhibited the highest records of parasitic nematodes. The Cucullanidae, Philometridae and Cystidicolidae were the most speciose families of nematodes, which may be related to technological advances and relatively recent efforts of taxonomists, resulting in description of new taxa and the resolution of taxonomic problems. Numerous taxonomic questions still need resolution and, even though genetic data have been important for this process, the database is very scarce. This is the first review on all currently known nematode species parasitizing marine fish off the Americas and may serve as an important basis of reference for future approaches on these organisms.
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Affiliation(s)
- Felipe B. Pereira
- Department of Parasitology, Institute of Biological Sciences, Federal University of Minas Gerais, Av. Antonio Carlos, 6627, Pampulha, CEP 31270-901, Belo Horizonte, MG, Brazil
| | - David González-Solís
- El Colegio de la Frontera Sur, Unidad Chetumal, Av. Centenario km 5.5, C.P. 77014, Chetumal, Quintana Roo, Mexico
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10
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Langridge PD, Garcia Diaz A, Chan JY, Greenwald I, Struhl G. Evolutionary plasticity in the requirement for force exerted by ligand endocytosis to activate C. elegans Notch proteins. Curr Biol 2022; 32:2263-2271.e6. [PMID: 35349791 PMCID: PMC9133158 DOI: 10.1016/j.cub.2022.03.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/28/2022] [Accepted: 03/08/2022] [Indexed: 10/18/2022]
Abstract
The conserved transmembrane receptor Notch has diverse and profound roles in controlling cell fate during animal development. In the absence of ligand, a negative regulatory region (NRR) in the Notch ectodomain adopts an autoinhibited confirmation, masking an ADAM protease cleavage site;1,2 ligand binding induces cleavage of the NRR, leading to Notch ectodomain shedding as the first step of signal transduction.3,4 In Drosophila and vertebrates, recruitment of transmembrane Delta/Serrate/LAG-2 (DSL) ligands by the endocytic adaptor Epsin, and their subsequent internalization by Clathrin-mediated endocytosis, exerts a "pulling force" on Notch that is essential to expose the cleavage site in the NRR.4-6 Here, we show that Epsin-mediated endocytosis of transmembrane ligands is not essential to activate the two C. elegans Notch proteins, LIN-12 and GLP-1. Using an in vivo force sensing assay in Drosophila,6 we present evidence (1) that the LIN-12 and GLP-1 NRRs are tuned to lower force thresholds than the NRR of Drosophila Notch, and (2) that this difference depends on the absence of a "leucine plug" that occludes the cleavage site in the Drosophila and vertebrate Notch NRRs.1,2 Our results thus establish an unexpected evolutionary plasticity in the force-dependent mechanism of Notch activation and implicate a specific structural element, the leucine plug, as a determinant.
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Affiliation(s)
- Paul D Langridge
- Department of Genetics and Development, Columbia University, New York, NY 10027, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, New York, NY 10027, USA.
| | | | - Jessica Yu Chan
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Iva Greenwald
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
| | - Gary Struhl
- Department of Genetics and Development, Columbia University, New York, NY 10027, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, New York, NY 10027, USA.
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11
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Nematode epibionts on skin of the Florida manatee, Trichechus manatus latirostris. Sci Rep 2021; 11:1211. [PMID: 33441692 PMCID: PMC7806751 DOI: 10.1038/s41598-020-79879-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 12/03/2020] [Indexed: 11/25/2022] Open
Abstract
A survey for the presence of nematodes on the skin of the native Florida manatee, Trichechus manatus latirostris from Crystal River, Florida was conducted during annual manatee health assessments. A putative isolate of Cutidiplogaster manati (Diplogastridae) and two other nematodes belonging to the same family were recovered from mid-dorsal tail skin-scrapings from all sampled winter-collected healthy wild adult manatees during two successive years (2018–2019). Qualitative abundance estimates of these three species of diplogastrid nematodes suggest that an average wild Florida manatee adult might possess between 30,000 and 120,000 nematodes on its tail dorsum and that the entire body dorsum including the tail might possess 160,000–640,000 nematodes in roughly equal ratios. Attempts to culture these nematodes on a variety of different culture media were unsuccessful but examination of the mouth (stomatal) morphology suggests specialized feeding on microbes such as diatoms or predation on other nematodes. No skin lesions were observed during the 2018–2019 samplings suggesting that under normal conditions these nematodes are highly specialized free-living epibionts of the skin that are tightly bound to this niche and horizontally transferred between individual manatees in an analogous fashion to human skin mites (Demodex folliculorum and D. brevis). Molecular phylogenetic inferences using sequences of near full length SSU and D2–D3 expansion segments of LSU rRNA genes revealed a putative new morphospecies in Cutidiplogaster sister to C. manati that was monophyletic with several named Mononchoides species, and another putative new morphospecies that formed a clade with several undescribed species similar in appearance to Mononchoides as well as Tylopharyx, Eudiplogasterium, Paroigolaimella and Sachsia.
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12
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Nematode Identification Techniques and Recent Advances. PLANTS 2020; 9:plants9101260. [PMID: 32987762 PMCID: PMC7598616 DOI: 10.3390/plants9101260] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 01/02/2023]
Abstract
Nematodes are among the most diverse but least studied organisms. The classic morphology-based identification has proved insufficient to the study of nematode identification and diversity, mainly for lack of sufficient morphological variations among closely related taxa. Different molecular methods have been used to supplement morphology-based methods and/or circumvent these problems with various degrees of success. These methods range from fingerprint to sequence analyses of DNA- and/or protein-based information. Image analyses techniques have also contributed towards this success. In this review, we highlight what each of these methods entail and provide examples where more recent advances of these techniques have been employed in nematode identification. Wherever possible, emphasis has been given to nematodes of agricultural significance. We show that these alternative methods have aided nematode identification and raised our understanding of nematode diversity and phylogeny. We discuss the pros and cons of these methods and conclude that no one method by itself provides all the answers; the choice of method depends on the question at hand, the nature of the samples, and the availability of resources.
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13
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Ortega A, Olivares-Bañuelos TN. Neurons and Glia Cells in Marine Invertebrates: An Update. Front Neurosci 2020; 14:121. [PMID: 32132895 PMCID: PMC7040184 DOI: 10.3389/fnins.2020.00121] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/30/2020] [Indexed: 12/18/2022] Open
Abstract
The nervous system (NS) of invertebrates and vertebrates is composed of two main types of cells: neurons and glia. In both types of organisms, nerve cells have similarities in biochemistry and functionality. The neurons are in charge of the synapse, and the glial cells are in charge of important functions of neuronal and homeostatic modulation. Knowing the mechanisms by which NS cells work is important in the biomedical area for the diagnosis and treatment of neurological disorders. For this reason, cellular and animal models to study the properties and characteristics of the NS are always sought. Marine invertebrates are strategic study models for the biological sciences. The sea slug Aplysia californica and the squid Loligo pealei are two examples of marine key organisms in the neurosciences field. The principal characteristic of marine invertebrates is that they have a simpler NS that consists of few and larger cells, which are well organized and have accessible structures. As well, the close phylogenetic relationship between Chordata and Echinodermata constitutes an additional advantage to use these organisms as a model for the functionality of neuronal cells and their cellular plasticity. Currently, there is great interest in analyzing the signaling processes between neurons and glial cells, both in vertebrates and in invertebrates. However, only few types of glial cells of invertebrates, mostly insects, have been studied, and it is important to consider marine organisms' research. For this reason, the objective of the review is to present an update of the most relevant information that exists around the physiology of marine invertebrate neuronal and glial cells.
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Affiliation(s)
- Arturo Ortega
- Laboratorio de Neurotoxicología, Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
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14
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Weinstein DJ, Allen SE, Lau MCY, Erasmus M, Asalone KC, Walters-Conte K, Deikus G, Sebra R, Borgonie G, van Heerden E, Onstott TC, Bracht JR. The genome of a subterrestrial nematode reveals adaptations to heat. Nat Commun 2019; 10:5268. [PMID: 31754114 PMCID: PMC6872716 DOI: 10.1038/s41467-019-13245-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 10/24/2019] [Indexed: 12/16/2022] Open
Abstract
The nematode Halicephalobus mephisto was originally discovered inhabiting a deep terrestrial aquifer 1.3 km underground. H. mephisto can thrive under conditions of abiotic stress including heat and minimal oxygen, where it feeds on a community of both chemolithotrophic and heterotrophic prokaryotes in an unusual ecosystem isolated from the surface biosphere. Here we report the comprehensive genome and transcriptome of this organism, identifying a signature of adaptation: an expanded repertoire of 70 kilodalton heat-shock proteins (Hsp70) and avrRpt2 induced gene 1 (AIG1) proteins. The expanded Hsp70 genes are transcriptionally induced upon growth under heat stress, and we find that positive selection is detectable in several members of this family. We further show that AIG1 may have been acquired by horizontal gene transfer (HGT) from a rhizobial fungus. Over one-third of the genes of H. mephisto are novel, highlighting the divergence of this nematode from other sequenced organisms. This work sheds light on the genomic basis of heat tolerance in a complete subterrestrial eukaryotic genome. The nematode Halicephalobus mephisto has been found more than 1 km underground and can tolerate high heat and low oxygen. Here Weinstein et al. report the genome and transcriptome of H. mephisto and identify genomic innovations that likely are responsible for its tolerance to heat.
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Affiliation(s)
| | - Sarah E Allen
- Biology Department, American University, Washington, DC, 20016, USA.,Biology Department, Cornell University, Ithaca, NY, 14853, USA
| | - Maggie C Y Lau
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA.,Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, No. 28, Luhuitou Road, Sanya, 572000, Hainan Province, P.R. China
| | - Mariana Erasmus
- UFS/TIA Saense Platform, Department of Microbial, Biochemical, and Food Biotechnology, University of the Free State, Bloemfontein, 9301, South Africa
| | | | | | - Gintaras Deikus
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Esta van Heerden
- UFS/TIA Saense Platform, Department of Microbial, Biochemical, and Food Biotechnology, University of the Free State, Bloemfontein, 9301, South Africa.,North West University, Private Bag X6001, Potchefstroom, 2520, South Africa
| | - Tullis C Onstott
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA
| | - John R Bracht
- Biology Department, American University, Washington, DC, 20016, USA.
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15
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Gogarten JF, Calvignac-Spencer S, Nunn CL, Ulrich M, Saiepour N, Nielsen HV, Deschner T, Fichtel C, Kappeler PM, Knauf S, Müller-Klein N, Ostner J, Robbins MM, Sangmaneedet S, Schülke O, Surbeck M, Wittig RM, Sliwa A, Strube C, Leendertz FH, Roos C, Noll A. Metabarcoding of eukaryotic parasite communities describes diverse parasite assemblages spanning the primate phylogeny. Mol Ecol Resour 2019; 20:204-215. [PMID: 31600853 DOI: 10.1111/1755-0998.13101] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/02/2019] [Accepted: 10/07/2019] [Indexed: 11/28/2022]
Abstract
Despite their ubiquity, in most cases little is known about the impact of eukaryotic parasites on their mammalian hosts. Comparative approaches provide a powerful method to investigate the impact of parasites on host ecology and evolution, though two issues are critical for such efforts: controlling for variation in methods of identifying parasites and incorporating heterogeneity in sampling effort across host species. To address these issues, there is a need for standardized methods to catalogue eukaryotic parasite diversity across broad phylogenetic host ranges. We demonstrate the feasibility of a metabarcoding approach for describing parasite communities by analysing faecal samples from 11 nonhuman primate species representing divergent lineages of the primate phylogeny and the full range of sampling effort (i.e. from no parasites reported in the literature to the best-studied primates). We detected a number of parasite families and regardless of prior sampling effort, metabarcoding of only ten faecal samples identified parasite families previously undescribed in each host (x̅ = 8.5 new families per species). We found more overlap between parasite families detected with metabarcoding and published literature when more research effort-measured as the number of publications-had been conducted on the host species' parasites. More closely related primates and those from the same continent had more similar parasite communities, highlighting the biological relevance of sampling even a small number of hosts. Collectively, results demonstrate that metabarcoding methods are sensitive and powerful enough to standardize studies of eukaryotic parasite communities across host species, providing essential new tools for macroecological studies of parasitism.
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Affiliation(s)
- Jan F Gogarten
- Project Group 3: Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute Berlin, Berlin, Germany.,Viral Evolution, Robert Koch-Institute Berlin, Berlin, Germany
| | - Sébastien Calvignac-Spencer
- Project Group 3: Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute Berlin, Berlin, Germany.,Viral Evolution, Robert Koch-Institute Berlin, Berlin, Germany
| | - Charles L Nunn
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA.,Duke Global Health Institute, Duke University, Durham, NC, USA
| | - Markus Ulrich
- Project Group 3: Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute Berlin, Berlin, Germany
| | - Nasrin Saiepour
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
| | - Henrik Vedel Nielsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Tobias Deschner
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Claudia Fichtel
- Behavioral Ecology & Sociobiology Unit, German Primate Center, Goettingen, Germany.,Leibniz Science Campus Primate Cognition, Goettingen, Germany
| | - Peter M Kappeler
- Behavioral Ecology & Sociobiology Unit, German Primate Center, Goettingen, Germany.,Leibniz Science Campus Primate Cognition, Goettingen, Germany.,Department of Sociobiology/Anthropology, Johann-Friedrich-Blumenbach Institute for Zoology, Georg-August University, Goettingen, Germany
| | - Sascha Knauf
- Neglected Tropical Diseases Work Group, Infection Biology Unit, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
| | - Nadine Müller-Klein
- Department of Behavioral Ecology, University of Goettingen, Goettingen, Germany
| | - Julia Ostner
- Leibniz Science Campus Primate Cognition, Goettingen, Germany.,Department of Behavioral Ecology, University of Goettingen, Goettingen, Germany.,Research Group Primate Social Evolution, German Primate Center - Leibniz Institute for Primate Research, Goettingen, Germany
| | - Martha M Robbins
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Somboon Sangmaneedet
- Department of Pathobiology, Faculty of Veterinary Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Oliver Schülke
- Leibniz Science Campus Primate Cognition, Goettingen, Germany.,Department of Behavioral Ecology, University of Goettingen, Goettingen, Germany.,Research Group Primate Social Evolution, German Primate Center - Leibniz Institute for Primate Research, Goettingen, Germany
| | - Martin Surbeck
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Roman M Wittig
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Ivory Coast
| | | | - Christina Strube
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Fabian H Leendertz
- Project Group 3: Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute Berlin, Berlin, Germany
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany.,Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
| | - Angela Noll
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
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16
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Genomic Analyses Identify Novel Molecular Signatures Specific for the Caenorhabditis and other Nematode Taxa Providing Novel Means for Genetic and Biochemical Studies. Genes (Basel) 2019; 10:genes10100739. [PMID: 31554175 PMCID: PMC6826867 DOI: 10.3390/genes10100739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/06/2019] [Accepted: 09/17/2019] [Indexed: 11/20/2022] Open
Abstract
The phylum Nematoda encompasses numerous free-living as well as parasitic members, including the widely used animal model Caenorhabditis elegans, with significant impact on human health, agriculture, and environment. In view of the importance of nematodes, it is of much interest to identify novel molecular characteristics that are distinctive features of this phylum, or specific taxonomic groups/clades within it, thereby providing innovative means for diagnostics as well as genetic and biochemical studies. Using genome sequences for 52 available nematodes, a robust phylogenetic tree was constructed based on concatenated sequences of 17 conserved proteins. The branching of species in this tree provides important insights into the evolutionary relationships among the studied nematode species. In parallel, detailed comparative analyses on protein sequences from nematodes (Caenorhabditis) species reported here have identified 52 novel molecular signatures (or synapomorphies) consisting of conserved signature indels (CSIs) in different proteins, which are uniquely shared by the homologs from either all genome-sequenced Caenorhabditis species or a number of higher taxonomic clades of nematodes encompassing this genus. Of these molecular signatures, 39 CSIs in proteins involved in diverse functions are uniquely present in all Caenorhabditis species providing reliable means for distinguishing this group of nematodes in molecular terms. The remainder of the CSIs are specific for a number of higher clades of nematodes and offer important insights into the evolutionary relationships among these species. The structural locations of some of the nematodes-specific CSIs were also mapped in the structural models of the corresponding proteins. All of the studied CSIs are localized within the surface-exposed loops of the proteins suggesting that they may potentially be involved in mediating novel protein–protein or protein–ligand interactions, which are specific for these groups of nematodes. The identified CSIs, due to their exclusivity for the indicated groups, provide reliable means for the identification of species within these nematodes groups in molecular terms. Further, due to the predicted roles of these CSIs in cellular functions, they provide important tools for genetic and biochemical studies in Caenorhabditis and other nematodes.
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17
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Karabinos A, Schünemann J, Parry DAD. Promiscuous Dimerization Between the Caenorhabditis elegans IF Proteins and a Hypothesis to Explain How Multiple IFs Persist Over Evolutionary Time. J Mol Evol 2019; 87:221-230. [PMID: 31407015 DOI: 10.1007/s00239-019-09904-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 08/01/2019] [Indexed: 11/28/2022]
Abstract
Our previous calculations of ionic interactions indicated that the Caenorhabditis elegans intermediate filament (IF) IFA proteins, in addition to IFA/IFB-1 heterodimers, may also form homodimers. In order to prove the significance of these calculations, we analysed the dimerization potential of the IFA chains in blot overlays. Unexpectedly, we found here that the dimerization of the IFA-1 protein was of both homotypic and heterotypic nature, and involved all proteins immobilized on the membrane (IFA-1, IFA-2, IFA-4, IFB-1, IFB-2, IFC-1, IFC-2, IFD-1, IFD-2 and IFP-1). A similar interaction profile, though less complex, was observed for two biotinylated proteins (IFA-2 and IFA-4). These and previous results indicate that the IFA proteins are able to form many different heteropolymeric and homopolymeric complexes in the C. elegans tissue, but that only those triggered by the IFA-specific IFB-1 protein result in mature IFs. Moreover, the calculations of the possible ionic interactions between the individual rod sequences as well as their various deletion variants indicated a special role in this process for the middle part of the C. elegans IF coil 1B segment that is deleted in all vertebrate cytoplasmic IFs. We hypothesized here, therefore, that the striking promiscuity of the C. elegans IFs originally involved a nuclear lamin which, due to a two-heptad-long rod deletion, prevented formation of a functional lamin/cIF dimer. This, in concert with an efficient dimerization and a strict tissue-specific co-expression, may allow expansion and maintenance of the multiple Caenorhabditis IFs. A possible implication for evolution of chordate IFs proteins is also discussed.
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Affiliation(s)
- Anton Karabinos
- SEMBID,s.r.o.-Research Centre of Applied Biomedical Diagnostics, Magnezitarska 2/C, 04013, Kosice, Slovakia.
| | - Jürgen Schünemann
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Goettingen, Germany
| | - David A D Parry
- School of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
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18
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Brennan JJ, Gilmore TD. Evolutionary Origins of Toll-like Receptor Signaling. Mol Biol Evol 2019; 35:1576-1587. [PMID: 29590394 DOI: 10.1093/molbev/msy050] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Toll-like receptors (TLRs) are transmembrane pattern recognition receptors that are best known for their roles in innate immunity for the detection of and defense against microbial pathogens. However, TLRs also have roles in many nonimmune processes, most notably development. TLRs direct both immune and developmental programs by activation of downstream signaling pathways, often by activation of the NF-κB pathway. There are two primary TLR subtypes: 1) TLRs with multiple cysteine clusters in their ectodomain (mccTLRs) and 2) TLRs with a single cysteine cluster in their ectodomain (sccTLRs). For some time, it has been known that TLRs and the biological processes that they control are conserved in organisms from insects to mammals. However, genome and transcriptome sequencing has revealed that many basal metazoans also have TLRs and downstream NF-κB signaling components. In this review, we discuss what is known about the structure, biological function, and downstream signaling pathways of TLRs found in phyla from Porifera through Annelida. From these analyses, we hypothesize that mccTLRs emerged in the phylum Cnidaria, that sccTLRs evolved in the phylum Mollusca, and that TLRs have dual immune and developmental biological functions in organisms as ancient as cnidarians.
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19
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Risi G, Aguilera E, Ladós E, Suárez G, Carrera I, Álvarez G, Salinas G. Caenorhabditis elegans Infrared-Based Motility Assay Identified New Hits for Nematicide Drug Development. Vet Sci 2019; 6:vetsci6010029. [PMID: 30884899 PMCID: PMC6466232 DOI: 10.3390/vetsci6010029] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/05/2019] [Accepted: 03/11/2019] [Indexed: 12/17/2022] Open
Abstract
Nematode parasites have a profound impact on humankind, infecting nearly one-quarter of the world’s population, as well as livestock. There is a pressing need for discovering nematicides due to the spread of resistance to currently used drugs. The free-living nematode Caenorhabditis elegans is a formidable experimentally tractable model organism that offers key advantages in accelerating nematicide discovery. We report the screening of drug-like libraries using an overnight high-throughput C. elegans assay, based on an automated infrared motility reader. As a proof of concept, we screened the “Pathogen Box” library, and identical results to a previous screen using Haemonchus contortus were obtained. We then screened an in-house library containing a diversity of compound families. Most active compounds had a conjugation of an unsaturation with an electronegative atom (N, O, or S) and an aromatic ring. Importantly, we identified symmetric arylidene ketones and aryl hydrazine derivatives as novel nematicides. Furthermore, one of these compounds, (1E,2E)-1,2-bis(thiophen-3-ylmethylene)hydrazine, was active as a nematicide at 25 µm, but innocuous to the vertebrate model zebrafish at 50 µm. Our results identified novel nematicidal scaffolds and illustrate the value of C. elegans in accelerating nematicide discovery using a nonlabor-intensive automated assay that provides a simple overnight readout.
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Affiliation(s)
- Gastón Risi
- Worm Biology Laboratory, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay.
| | - Elena Aguilera
- Grupo de Química Medicinal, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay.
| | - Enrique Ladós
- Worm Biology Laboratory, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay.
| | - Gonzalo Suárez
- Área Farmacología, Departamento de Fisiología, Facultad de Veterinaria, Universidad de la República, Montevideo 11600, Uruguay.
| | - Inés Carrera
- Worm Biology Laboratory, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay.
- Departamento de Ciencias Farmacéuticas, Área Farmacología, Facultad de Química, Universidad de la República, Montevideo 11800, Uruguay.
| | - Guzmán Álvarez
- Laboratorio de Moléculas Bioactivas-CENUR Litoral Norte, Universidad de la República, Paysandú 60000, Uruguay.
| | - Gustavo Salinas
- Worm Biology Laboratory, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay.
- Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo 11400, Uruguay.
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20
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Paschinger K, Yan S, Wilson IBH. N-glycomic Complexity in Anatomical Simplicity: Caenorhabditis elegans as a Non-model Nematode? Front Mol Biosci 2019; 6:9. [PMID: 30915340 PMCID: PMC6422873 DOI: 10.3389/fmolb.2019.00009] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 02/12/2019] [Indexed: 12/28/2022] Open
Abstract
Caenorhabditis elegans is a genetically well-studied model nematode or "worm"; however, its N-glycomic complexity is actually baffling and still not completely unraveled. Some features of its N-glycans are, to date, unique and include bisecting galactose and up to five fucose residues associated with the asparagine-linked Man2-3GlcNAc2 core; the substitutions include galactosylation of fucose, fucosylation of galactose and methylation of mannose or fucose residues as well as phosphorylcholine on antennal (non-reducing) N-acetylglucosamine. Only some of these modifications are shared with various other nematodes, while others have yet to be detected in any other species. Thus, C. elegans can be used as a model for some aspects of N-glycan function, but its glycome is far from identical to those of other organisms and is actually far from simple. Possibly the challenges of its native environment, which differ from those of parasitic or necromenic species, led to an anatomically simple worm possessing a complex glycome.
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Affiliation(s)
| | - Shi Yan
- Institut für Parasitologie, Veterinärmedizinische Universität, Wien, Austria
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21
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Liposome-based transfection enhances RNAi and CRISPR-mediated mutagenesis in non-model nematode systems. Sci Rep 2019; 9:483. [PMID: 30679624 PMCID: PMC6345965 DOI: 10.1038/s41598-018-37036-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 11/28/2018] [Indexed: 11/09/2022] Open
Abstract
Nematodes belong to one of the most diverse animal phyla. However, functional genomic studies in nematodes, other than in a few species, have often been limited in their reliability and success. Here we report that by combining liposome-based technology with microinjection, we were able to establish a wide range of genomic techniques in the newly described nematode genus Auanema. The method also allowed heritable changes in dauer larvae of Auanema, despite the immaturity of the gonad at the time of the microinjection. As proof of concept for potential functional studies in other nematode species, we also induced RNAi in the free-living nematode Pristionchus pacificus and targeted the human parasite Strongyloides stercoralis.
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22
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Almeida MV, Andrade-Navarro MA, Ketting RF. Function and Evolution of Nematode RNAi Pathways. Noncoding RNA 2019; 5:E8. [PMID: 30650636 PMCID: PMC6468775 DOI: 10.3390/ncrna5010008] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/07/2019] [Accepted: 01/08/2019] [Indexed: 12/11/2022] Open
Abstract
Selfish genetic elements, like transposable elements or viruses, are a threat to genomic stability. A variety of processes, including small RNA-based RNA interference (RNAi)-like pathways, has evolved to counteract these elements. Amongst these, endogenous small interfering RNA and Piwi-interacting RNA (piRNA) pathways were implicated in silencing selfish genetic elements in a variety of organisms. Nematodes have several incredibly specialized, rapidly evolving endogenous RNAi-like pathways serving such purposes. Here, we review recent research regarding the RNAi-like pathways of Caenorhabditis elegans as well as those of other nematodes, to provide an evolutionary perspective. We argue that multiple nematode RNAi-like pathways share piRNA-like properties and together form a broad nematode toolkit that allows for silencing of foreign genetic elements.
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Affiliation(s)
| | - Miguel A Andrade-Navarro
- Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany.
- Faculty of Biology, Johannes Gutenberg Universität, 55122 Mainz, Germany.
| | - René F Ketting
- Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany.
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23
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A tale of three kingdoms: members of the Phylum Nematoda independently acquired the detoxifying enzyme cyanase through horizontal gene transfer from plants and bacteria. Parasitology 2018; 146:445-452. [PMID: 30301483 DOI: 10.1017/s0031182018001701] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Horizontal gene transfer (HGT) has played an important role in the evolution of nematodes. Among candidate genes, cyanase, which is typically found only in plants, bacteria and fungi, is present in more than 35 members of the Phylum Nematoda, but absent from free-living and clade V organisms. Phylogenetic analyses showed that the cyanases of clade I organisms Trichinella spp., Trichuris spp. and Soboliphyme baturini (Subclass: Dorylaimia) represent a well-supported monophyletic clade with plant cyanases. In contrast, all cyanases found within the Subclass Chromadoria which encompasses filarioids, ascaridoids and strongyloids are homologous to those of bacteria. Western blots exhibited typical multimeric forms of the native molecule in protein extracts of Trichinella spiralis muscle larvae, where immunohistochemical staining localized the protein to the worm hypodermis and underlying muscle. Recombinant Trichinella cyanase was bioactive where gene transcription profiles support functional activity in vivo. Results suggest that: (1) independent HGT in parasitic nematodes originated from different Kingdoms; (2) cyanase acquired an active role in the biology of extant Trichinella; (3) acquisition occurred more than 400 million years ago (MYA), prior to the divergence of the Trichinellida and Dioctophymatida, and (4) early, free-living ancestors of the genus Trichinella had an association with terrestrial plants.
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24
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Haag ES, Fitch DHA, Delattre M. From "the Worm" to "the Worms" and Back Again: The Evolutionary Developmental Biology of Nematodes. Genetics 2018; 210:397-433. [PMID: 30287515 PMCID: PMC6216592 DOI: 10.1534/genetics.118.300243] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 08/03/2018] [Indexed: 12/13/2022] Open
Abstract
Since the earliest days of research on nematodes, scientists have noted the developmental and morphological variation that exists within and between species. As various cellular and developmental processes were revealed through intense focus on Caenorhabditis elegans, these comparative studies have expanded. Within the genus Caenorhabditis, they include characterization of intraspecific polymorphisms and comparisons of distinct species, all generally amenable to the same laboratory culture methods and supported by robust genomic and experimental tools. The C. elegans paradigm has also motivated studies with more distantly related nematodes and animals. Combined with improved phylogenies, this work has led to important insights about the evolution of nematode development. First, while many aspects of C. elegans development are representative of Caenorhabditis, and of terrestrial nematodes more generally, others vary in ways both obvious and cryptic. Second, the system has revealed several clear examples of developmental flexibility in achieving a particular trait. This includes developmental system drift, in which the developmental control of homologous traits has diverged in different lineages, and cases of convergent evolution. Overall, the wealth of information and experimental techniques developed in C. elegans is being leveraged to make nematodes a powerful system for evolutionary cellular and developmental biology.
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Affiliation(s)
- Eric S Haag
- Department of Biology, University of Maryland, College Park, Maryland 20742
| | | | - Marie Delattre
- Laboratoire de Biologie Moléculaire de la Cellule, CNRS, INSERM, Ecole Normale Supérieure de Lyon, 69007, France
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25
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Choudhury A, Nadler SA. Phylogenetic Relationships of Spiruromorph Nematodes (Spirurina: Spiruromorpha) In North American Freshwater Fishes. J Parasitol 2018; 104:496-504. [DOI: 10.1645/17-195] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Anindo Choudhury
- Division of Natural Science, St. Norbert College, 100 Grant Street, DePere, Wisconsin 54115
| | - Steven A. Nadler
- Department of Entomology and Nematology, One Shields Avenue, University of California–Davis, Davis, California 95616-8668
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26
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C. elegans as a model in developmental neurotoxicology. Toxicol Appl Pharmacol 2018; 354:126-135. [PMID: 29550512 DOI: 10.1016/j.taap.2018.03.016] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 02/28/2018] [Accepted: 03/12/2018] [Indexed: 12/22/2022]
Abstract
Due to many advantages Caenorhabditis elegans (C. elegans) has become a preferred model of choice in many fields, including neurodevelopmental toxicity studies. This review discusses the benefits of using C. elegans as an alternative to mammalian systems and gives examples of the uses of the nematode in evaluating the effects of major known neurodevelopmental toxins, including manganese, mercury, lead, fluoride, arsenic and organophosphorus pesticides. Reviewed data indicates numerous similarities with mammals in response to these toxins. Thus, C. elegans studies have the potential to predict possible effects of developmental neurotoxicants in higher animals, and may be used to identify new molecular pathways behind neurodevelopmental disruptions, as well as new toxicants.
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27
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Yan S, Vanbeselaere J, Jin C, Blaukopf M, Wöls F, Wilson IBH, Paschinger K. Core Richness of N-Glycans of Caenorhabditis elegans: A Case Study on Chemical and Enzymatic Release. Anal Chem 2017; 90:928-935. [PMID: 29182268 PMCID: PMC5757221 DOI: 10.1021/acs.analchem.7b03898] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Despite years of research, the glycome of the model nematode Caenorhabditis elegans is still not fully understood. Certainly, data over the years have indicated that this organism synthesizes unusual N-glycans with a range of galactose and fucose modifications on the Man2-3GlcNAc2 core region. Previously, up to four fucose residues were detected on its N-glycans, despite these lacking the fucosylated antennae typical of many other eukaryotes; some of these fucose residues are capped with hexose residues as shown by the studies of us and others. There have, though, been contrasting reports regarding the maximal number of fucose substitutions in C. elegans, which in part may be due to different methodological approaches, including use of either peptide:N-glycosidases F and A (PNGase F and A) or anhydrous hydrazine to cleave the N-glycans from glycopeptides. Here we compare the use of hydrazine with that of a new enzyme (rice PNGase Ar) and show that both enable release of glycans with more sugar residues on the proximal GlcNAc than previously resolved. By use of exoglycosidase sequencing, in conjunction with high-performance liquid chromatography (HPLC) and matrix-assisted laser desorption ionization time-of-flight tandem mass spectrometry (MALDI-TOF MS/MS), we now reveal that actually up to five fucose residues modify the core region of C. elegans N-glycans and that the α1,3-fucose on the reducing terminus can be substituted by an α-linked galactose. Thus, traditional PNGase F and A release may be insufficient for release of the more highly core-modified N-glycans, especially those occurring in C. elegans, but novel enzymes can compete against chemical methods in terms of safety, ease of cleanup, and quality of resulting glycomic data.
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Affiliation(s)
- Shi Yan
- Department für Chemie, Universität für Bodenkultur , 1190 Wien, Austria
| | | | - Chunsheng Jin
- Institutionen för Biomedicin, Göteborgs Universitet , 405 30 Göteborg, Sweden
| | - Markus Blaukopf
- Department für Chemie, Universität für Bodenkultur , 1190 Wien, Austria
| | - Florian Wöls
- Department für Chemie, Universität für Bodenkultur , 1190 Wien, Austria
| | - Iain B H Wilson
- Department für Chemie, Universität für Bodenkultur , 1190 Wien, Austria
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Do holocentric chromosomes represent an evolutionary advantage? A study of paired analyses of diversification rates of lineages with holocentric chromosomes and their monocentric closest relatives. Chromosome Res 2017; 26:139-152. [PMID: 29043597 DOI: 10.1007/s10577-017-9566-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 10/05/2017] [Accepted: 10/06/2017] [Indexed: 10/18/2022]
Abstract
Despite most of the cytogenetic research is focused on monocentric chromosomes, chromosomes with kinetochoric activity localized in a single centromere, several studies have been centered on holocentric chromosomes which have diffuse kinetochoric activity along the chromosomes. The eukaryotic organisms that present this type of chromosomes have been relatively understudied despite they constitute rather diversified species lineages. On the one hand, holocentric chromosomes may present intrinsic benefits (chromosome mutations such as fissions and fusions are potentially neutral in holocentrics). On the other hand, they present restrictions to the spatial separation of the functions of recombination and segregation during meiotic divisions (functions that may interfere), separation that is found in monocentric chromosomes. In this study, we compare the diversification rates of all known holocentric lineages in animals and plants with their most related monocentric lineages in order to elucidate whether holocentric chromosomes constitute an evolutionary advantage in terms of diversification and species richness. The results showed that null hypothesis of equal mean diversification rates cannot be rejected, leading us to surmise that shifts in diversification rates between holocentric and monocentric lineages might be due to other factors, such as the idiosyncrasy of each lineage or the interplay of evolutionary selections with the benefits of having either monocentric or holocentric chromosomes.
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Holz A, Streit A. Gain and Loss of Small RNA Classes-Characterization of Small RNAs in the Parasitic Nematode Family Strongyloididae. Genome Biol Evol 2017; 9:2826-2843. [PMID: 29036592 PMCID: PMC5737618 DOI: 10.1093/gbe/evx197] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2017] [Indexed: 12/24/2022] Open
Abstract
The nematode family Strongyloididae is of particular interest because it contains important parasites of medical and veterinary relevance. In addition, species of this family can form parasitic and free-living generations and it also occupies an interesting phylogenetic position within the nematodes. Nematodes differ in several ways from other taxa with respect to their small noncoding RNAs. Recent comparative studies revealed that there is also considerable variability within the nematodes. However, no Strongyloididae species or close relative was included in these studies. We characterized the small RNAs of two developmental stages of three different Strongyloididae species and compared them with the well-studied free-living nematodes Caenorhabditis elegans and Pristionchus pacificus. Strongyloididae have conserved and taxon-specific microRNAs, many of which are differentially regulated between the two developmental stages. We identified a novel class of around 27-nucleotide-long RNAs starting with 5'G or A, of which a large fraction have the potential to target transposable elements. These RNAs most likely have triphosphates at their 5' ends and are therefore presumably synthesized by RNA-dependent RNA polymerases. In contrast to C. elegans but similarly to some other nematode taxa, Strongyloididae have no Piwi-interacting RNAs, nor do their genomes encode Argonaute proteins of the Piwi family. Finally, we attempted but failed to detect circulating parasite small RNAs in the blood of hosts.
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Affiliation(s)
- Anja Holz
- Department of Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Adrian Streit
- Department of Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
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Abstract
Plant-parasitic nematodes cause considerable damage to global agriculture. The ability to
parasitize plants is a derived character that appears to have independently emerged
several times in the phylum Nematoda. Morphological convergence to feeding style has been
observed, but whether this is emergent from molecular convergence is less obvious. To
address this, we assess whether genomic signatures can be associated with plant parasitism
by nematodes. In this review, we report genomic features and characteristics that appear
to be common in plant-parasitic nematodes while absent or rare in animal parasites,
predators or free-living species. Candidate horizontal acquisitions of parasitism genes
have systematically been found in all plant-parasitic species investigated at the sequence
level. Presence of peptides that mimic plant hormones also appears to be a trait of
plant-parasitic species. Annotations of the few genomes of plant-parasitic nematodes
available to date have revealed a set of apparently species-specific genes on every
occasion. Effector genes, important for parasitism are frequently found among those
species-specific genes, indicating poor overlap. Overall, nematodes appear to have
developed convergent genomic solutions to adapt to plant parasitism.
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31
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Sallé G, Cortet J, Koch C, Gascogne T, Reigner F, Cabaret J. Ivermectin failure in the control of Oxyuris equi in a herd of ponies in France. Vet Parasitol 2016; 229:73-75. [PMID: 27809982 DOI: 10.1016/j.vetpar.2016.09.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 09/26/2016] [Accepted: 09/28/2016] [Indexed: 11/27/2022]
Abstract
Drug resistance in equine gastro-intestinal parasitic nematodes has been reported throughout the world. While the focus is usually put on cyathostomins, observations of macrocylic lactone failure against Oxyuris equi have accumulated over the last decade. Here we report the failure of ivermectin in the control of O. equi in an experimental Welsh pony herd. In a first trial, 6 ponies previously drenched with moxidectin and showing patent O. equi infections were administered ivermectin and subsequently monitored for O. equi egg excretion over one month. This trial demonstrated a failure of ivermectin to control O. equi egg excretion as half of ponies demonstrated recurrent egg excretion in the peri-anal region during 21days after treatment. One year later, six female Welsh ponies drenched with moxidectin demonstrated signs of itching and scratching in their peri-anal region with worms being found transiently in fecal materials three weeks later. Ponies were allocated to three treatment groups, i.e. ivermectin, pyrantel embonate and fenbendazole and monitored for egg excretion over five weeks. Fenbendazole and pyrantel embonate broke ivermectin suboptimal efficacy as soon as 8 and 14days respectively after treatment, while egg excretion remained constant throughout the 41-day long trial in the ivermectin-treated ponies. This is the first report of ivermectin failure against O. equi in France. In the absence of critical efficacy test, it remains unclear whether true resistance is at stake or if these observations confound a constitutive suboptimal efficacy of ivermectin against O. equi.
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Affiliation(s)
- Guillaume Sallé
- UMR1282 ISP, INRA, Université de Tours, 37380, Nouzilly, France.
| | - Jacques Cortet
- UMR1282 ISP, INRA, Université de Tours, 37380, Nouzilly, France
| | - Christine Koch
- UMR1282 ISP, INRA, Université de Tours, 37380, Nouzilly, France
| | - Thierry Gascogne
- UE1297 Physiologie Animale de l'Orfrasière, INRA, 37380, Nouzilly, France
| | - Fabrice Reigner
- UE1297 Physiologie Animale de l'Orfrasière, INRA, 37380, Nouzilly, France
| | - Jacques Cabaret
- UMR1282 ISP, INRA, Université de Tours, 37380, Nouzilly, France
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32
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Molecular evolution of the multiple calmodulin-like cal genes in C. elegans and in nematodes. Dev Genes Evol 2016; 226:355-67. [PMID: 27558386 DOI: 10.1007/s00427-016-0558-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 08/04/2016] [Indexed: 10/21/2022]
Abstract
Calmodulin (CaM) is a major EF hand containing intracellular calcium receptor in animals and plants; however, eukaryotes also express a number of related CaM-like proteins. We have previously characterized an embryonic phenotype of the single Caenorhabditis elegans CaM gene cmd-1, reported no visible RNAi phenotype for the four related cal-1 to cal-4 genes and started tissue-specific expression analyses of these proteins. In the present study, we analyzed evolutionary aspects of the previously reported CAL-1 to CAL-4 proteins, along with the four new CAL-5 to CAL-8 sequences retrieved from the worm database. Phylogenetic analyses suggest that all C. elegans CAL proteins arose from a CaM ancestor through repeated gene duplications, fusions and sequence divergence. The same holds, also, for the variable N-terminal extensions of the CAL-1 to CAL-4 proteins, which have evolved from the CaM-like core domain. We found 97 CAL homologs in different nematode clades and also detected two CAL-7-related sequences outside the nematodes. Moreover, the C. elegans-specific cal-6 gene, representing the most CaM-related sequence found in nematodes so far, harbours many deletions, insertions and sequence substitutions and is predicted, therefore, to be non-functional. These analyses provide an insight into a complex and dynamic origin of the multiple CAL genes in C. elegans and in nematodes and represent also a basis for further functional studies of these CaM-related sequences in nematodes.
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33
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A review of methods for nematode identification. J Microbiol Methods 2016; 138:37-49. [PMID: 27262374 DOI: 10.1016/j.mimet.2016.05.030] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 05/23/2016] [Accepted: 05/31/2016] [Indexed: 12/15/2022]
Abstract
Nematodes are non-segmented roundworms found in soil, aquatic environment, plants, or animals. Either useful or pathogenic, they greatly influence environmental equilibrium, human and animal health, as well as plant production. Knowledge on their taxonomy and biology are key issues to answer the different challenges associated to these organisms. Nowadays, most of the nematode taxonomy remains unknown or unclear. Several approaches are available for parasite identification, from the traditional morphology-based techniques to the sophisticated high-throughput sequencing technologies. All these techniques have advantages or drawbacks depending on the sample origin and the number of nematodes to be processed. This review proposes an overview of all newly available methods available to identify known and/or unknown nematodes with a specific focus on emerging high-throughput molecular techniques.
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Gasser RB, Schwarz EM, Korhonen PK, Young ND. Understanding Haemonchus contortus Better Through Genomics and Transcriptomics. ADVANCES IN PARASITOLOGY 2016; 93:519-67. [PMID: 27238012 DOI: 10.1016/bs.apar.2016.02.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Parasitic roundworms (nematodes) cause substantial mortality and morbidity in animals globally. The barber's pole worm, Haemonchus contortus, is one of the most economically significant parasitic nematodes of small ruminants worldwide. Although this and related nematodes can be controlled relatively well using anthelmintics, resistance against most drugs in common use has become a major problem. Until recently, almost nothing was known about the molecular biology of H. contortus on a global scale. This chapter gives a brief background on H. contortus and haemonchosis, immune responses, vaccine research, chemotherapeutics and current problems associated with drug resistance. It also describes progress in transcriptomics before the availability of H. contortus genomes and the challenges associated with such work. It then reviews major progress on the two draft genomes and developmental transcriptomes of H. contortus, and summarizes their implications for the molecular biology of this worm in both the free-living and the parasitic stages of its life cycle. The chapter concludes by considering how genomics and transcriptomics can accelerate research on Haemonchus and related parasites, and can enable the development of new interventions against haemonchosis.
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Affiliation(s)
- R B Gasser
- The University of Melbourne, Parkville, VIC, Australia
| | - E M Schwarz
- The University of Melbourne, Parkville, VIC, Australia; Cornell University, Ithaca, NY, United States
| | - P K Korhonen
- The University of Melbourne, Parkville, VIC, Australia
| | - N D Young
- The University of Melbourne, Parkville, VIC, Australia
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Kumarasingha R, Preston S, Yeo TC, Lim DSL, Tu CL, Palombo EA, Shaw JM, Gasser RB, Boag PR. Anthelmintic activity of selected ethno-medicinal plant extracts on parasitic stages of Haemonchus contortus. Parasit Vectors 2016; 9:187. [PMID: 27036205 PMCID: PMC4818492 DOI: 10.1186/s13071-016-1458-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 03/16/2016] [Indexed: 12/16/2022] Open
Abstract
Background Parasitic roundworms (nematodes) cause substantial morbidity and mortality in livestock animals globally, and considerable productivity losses to farmers. The control of these nematodes has relied largely on the use of a limited number of anthelmintics. However, resistance to many of these these anthelmintics is now widespread, and, therefore, there is a need to find new drugs to ensure sustained and effective treatment and control into the future. Methods Recently, we developed a screening assay to test natural, plant extracts with known inhibitory effects against the free-living worm Caenorhabditis elegans. Using this assay, we assessed here the effects of the extracts on motility and development of parasitic larval stages of Haemonchus contortus, one of the most important nematodes of small ruminants worldwide. Results The study showed that two of five extracts from Picria fel-terrae Lour. have a significant inhibitory effect (at concentrations of 3–5 mg/ml) on the motility and development of H. contortus larvae. Although the two extracts originated from the same plant, they displayed different levels of inhibition on motility and development, which might relate to the presence of various active constituents in these extracts, or the same constituents at different concentrations in distinct parts of the plant. Conclusions These results suggest that extracts from P. fel-terrae Lour. have promising anthelmintic activity and that more broadly, plant extracts are a potential rich source of anthelmintics to combat helminthic diseases.
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Affiliation(s)
- Rasika Kumarasingha
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Sarah Preston
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Tiong-Chia Yeo
- Sarawak Biodiversity Centre (SBC), KM 20 Jalan Borneo Heights, Semengoh, Locked Bag No. 3032, 93990, Kuching, Sarawak, Malaysia
| | - Diana S L Lim
- Sarawak Biodiversity Centre (SBC), KM 20 Jalan Borneo Heights, Semengoh, Locked Bag No. 3032, 93990, Kuching, Sarawak, Malaysia
| | - Chu-Lee Tu
- Sarawak Biodiversity Centre (SBC), KM 20 Jalan Borneo Heights, Semengoh, Locked Bag No. 3032, 93990, Kuching, Sarawak, Malaysia
| | - Enzo A Palombo
- Department of Chemistry and Biotechnology, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Victoria, 3122, Australia
| | - Jillian M Shaw
- Department of Health and Medical Sciences, Faculty of Health, Arts and Design, Swinburne University of Technology, Victoria, 3122, Australia
| | - Robin B Gasser
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Peter R Boag
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia. .,Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia.
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36
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Abstract
Be it their pervasiveness, experimental tractability or their impact on human health and agriculture, nematode–bacterium associations are far-reaching research subjects. Although the omics hype did not spare them and helped reveal mechanisms of communication and exchange between the associated partners, a huge amount of knowledge still awaits to be harvested from their study. Here, I summarize and compare the kind of research that has been already performed on the model nematode Caenorhabditis elegans and on symbiotic nematodes, both marine and entomopathogenic ones. The emerging picture highlights how complementing genetic studies with ecological ones (in the case of well-established genetic model systems such as C. elegans) and vice versa (in the case of the yet uncultured Stilbonematinae) will deepen our understanding of how microbial symbioses evolved and how they impact our environment. Nematode–bacterium associations are major research subjects. Complementing genetic studies with ecological ones is necessary to boost our understanding of how microbial symbioses evolved and how they impact the environment.
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Affiliation(s)
- Silvia Bulgheresi
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
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37
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Van Campenhout J, Vanreusel A, Van Belleghem S, Derycke S. Transcription, Signaling Receptor Activity, Oxidative Phosphorylation, and Fatty Acid Metabolism Mediate the Presence of Closely Related Species in Distinct Intertidal and Cold-Seep Habitats. Genome Biol Evol 2015; 8:51-69. [PMID: 26637468 PMCID: PMC4758239 DOI: 10.1093/gbe/evv242] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Bathyal cold seeps are isolated extreme deep-sea environments characterized by low species diversity while biomass can be high. The Håkon Mosby mud volcano (Barents Sea, 1,280 m) is a rather stable chemosynthetic driven habitat characterized by prominent surface bacterial mats with high sulfide concentrations and low oxygen levels. Here, the nematode Halomonhystera hermesi thrives in high abundances (11,000 individuals 10 cm−2). Halomonhystera hermesi is a member of the intertidal Halomonhystera disjuncta species complex that includes five cryptic species (GD1-5). GD1-5’s common habitat is characterized by strong environmental fluctuations. Here, we compared the transcriptomes of H. hermesi and GD1, H. hermesi’s closest relative. Genes encoding proteins involved in oxidative phosphorylation are more strongly expressed in H. hermesi than in GD1, and many genes were only observed in H. hermesi while being completely absent in GD1. Both observations could in part be attributed to high sulfide concentrations and low oxygen levels. Additionally, fatty acid elongation was also prominent in H. hermesi confirming the importance of highly unsaturated fatty acids in this species. Significant higher amounts of transcription factors and genes involved in signaling receptor activity were observed in GD1 (many of which were completely absent in H. hermesi), allowing fast signaling and transcriptional reprogramming which can mediate survival in dynamic intertidal environments. GC content was approximately 8% higher in H. hermesi coding unigenes resulting in differential codon usage between both species and a higher proportion of amino acids with GC-rich codons in H. hermesi. In general our results showed that most pathways were active in both environments and that only three genes are under natural selection. This indicates that also plasticity should be taken in consideration in the evolutionary history of Halomonhystera species. Such plasticity, as well as possible preadaptation to low oxygen and high sulfide levels might have played an important role in the establishment of a cold-seep Halomonhystera population.
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Affiliation(s)
- Jelle Van Campenhout
- Research Group Marine Biology, Biology Department, Ghent University, Belgium Department of Biology, Center for Molecular Phylogenetics and Evolution (CeMoFe), Ghent University, Biology Department, Belgium
| | - Ann Vanreusel
- Research Group Marine Biology, Biology Department, Ghent University, Belgium
| | - Steven Van Belleghem
- Terrestrial Ecology Unit, Biology Department, Ghent University, Belgium OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Sofie Derycke
- Research Group Marine Biology, Biology Department, Ghent University, Belgium OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
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38
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Wever CM, Farrington D, Dent JA. The Validation of Nematode-Specific Acetylcholine-Gated Chloride Channels as Potential Anthelmintic Drug Targets. PLoS One 2015; 10:e0138804. [PMID: 26393923 PMCID: PMC4578888 DOI: 10.1371/journal.pone.0138804] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 09/03/2015] [Indexed: 01/06/2023] Open
Abstract
New compounds are needed to treat parasitic nematode infections in humans, livestock and plants. Small molecule anthelmintics are the primary means of nematode parasite control in animals; however, widespread resistance to the currently available drug classes means control will be impossible without the introduction of new compounds. Adverse environmental effects associated with nematocides used to control plant parasitic species are also motivating the search for safer, more effective compounds. Discovery of new anthelmintic drugs in particular has been a serious challenge due to the difficulty of obtaining and culturing target parasites for high-throughput screens and the lack of functional genomic techniques to validate potential drug targets in these pathogens. We present here a novel strategy for target validation that employs the free-living nematode Caenorhabditis elegans to demonstrate the value of new ligand-gated ion channels as targets for anthelmintic discovery. Many successful anthelmintics, including ivermectin, levamisole and monepantel, are agonists of pentameric ligand-gated ion channels, suggesting that the unexploited pentameric ion channels encoded in parasite genomes may be suitable drug targets. We validated five members of the nematode-specific family of acetylcholine-gated chloride channels as targets of agonists with anthelmintic properties by ectopically expressing an ivermectin-gated chloride channel, AVR-15, in tissues that endogenously express the acetylcholine-gated chloride channels and using the effects of ivermectin to predict the effects of an acetylcholine-gated chloride channel agonist. In principle, our strategy can be applied to validate any ion channel as a putative anti-parasitic drug target.
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Affiliation(s)
- Claudia M. Wever
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | | | - Joseph A. Dent
- Department of Biology, McGill University, Montreal, Quebec, Canada
- * E-mail:
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39
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Zalucki O, Day R, Kottler B, Karunanithi S, van Swinderen B. Behavioral and electrophysiological analysis of general anesthesia in 3 background strains of Drosophila melanogaster. Fly (Austin) 2015; 9:7-15. [PMID: 26267354 DOI: 10.1080/19336934.2015.1072663] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
General anesthetics achieve behavioral unresponsiveness via a mechanism that is incompletely understood. The study of genetic model systems such as the fruit fly Drosophila melanogaster is crucial to advancing our understanding of how anesthetic drugs render animals unresponsive. Previous studies have shown that wild-type control strains differ significantly in their sensitivity to general anesthetics, which potentially introduces confounding factors for comparing genetic mutations placed on these wild-type backgrounds. Here, we examined a variety of behavioral and electrophysiological endpoints in Drosophila, in both adult and larval animals. We characterized these endpoints in 3 commonly used fly strains: wild-type Canton Special (CS), and 2 commonly used white-eyed strains, isoCJ1 and w(1118). We found that CS and isoCJ1 show remarkably similar sensitivity to isoflurane across a variety of behavioral and electrophysiological endpoints. In contrast, w(1118) is resistant to isoflurane compared to the other 2 strains at both the adult and larval stages. This resistance is however not reflected at the level of neurotransmitter release at the larval neuromuscular junction (NMJ). This suggests that the w(1118) strain harbors another mutation that produces isoflurane resistance, by acting on an arousal pathway that is most likely preserved between larval and adult brains. This mutation probably also affects sleep, as marked differences between isoCJ1 and w(1118) have also recently been found for behavioral responsiveness and sleep intensity measures.
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Affiliation(s)
- Oressia Zalucki
- a Queensland Brain Institute; The University of Queensland ; Brisbane , Queensland , Australia
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40
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Gordon KL, Arthur RK, Ruvinsky I. Phylum-Level Conservation of Regulatory Information in Nematodes despite Extensive Non-coding Sequence Divergence. PLoS Genet 2015; 11:e1005268. [PMID: 26020930 PMCID: PMC4447282 DOI: 10.1371/journal.pgen.1005268] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 05/09/2015] [Indexed: 11/28/2022] Open
Abstract
Gene regulatory information guides development and shapes the course of evolution. To test conservation of gene regulation within the phylum Nematoda, we compared the functions of putative cis-regulatory sequences of four sets of orthologs (unc-47, unc-25, mec-3 and elt-2) from distantly-related nematode species. These species, Caenorhabditis elegans, its congeneric C. briggsae, and three parasitic species Meloidogyne hapla, Brugia malayi, and Trichinella spiralis, represent four of the five major clades in the phylum Nematoda. Despite the great phylogenetic distances sampled and the extensive sequence divergence of nematode genomes, all but one of the regulatory elements we tested are able to drive at least a subset of the expected gene expression patterns. We show that functionally conserved cis-regulatory elements have no more extended sequence similarity to their C. elegans orthologs than would be expected by chance, but they do harbor motifs that are important for proper expression of the C. elegans genes. These motifs are too short to be distinguished from the background level of sequence similarity, and while identical in sequence they are not conserved in orientation or position. Functional tests reveal that some of these motifs contribute to proper expression. Our results suggest that conserved regulatory circuitry can persist despite considerable turnover within cis elements. To explore the phylogenetic limits of conservation of cis-regulatory elements, we used transgenesis to test the functions of enhancers of four genes from several species spanning the phylum Nematoda. While we found a striking degree of functional conservation among the examined cis elements, their DNA sequences lacked apparent conservation with the C. elegans orthologs. In fact, sequence similarity between C. elegans and the distantly related nematodes was no greater than would be expected by chance. Short motifs, similar to known regulatory sequences in C. elegans, can be detected in most of the cis elements. When tested, some of these sites appear to mediate regulatory function. However, they seem to have originated through motif turnover, rather than to have been preserved from a common ancestor. Our results suggest that gene regulatory networks are broadly conserved in the phylum Nematoda, but this conservation persists despite substantial reorganization of regulatory elements and could not be detected using naïve comparisons of sequence similarity.
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Affiliation(s)
- Kacy L. Gordon
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, Illinois, United States of America
- * E-mail: (KLG); (IR)
| | - Robert K. Arthur
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, United States of America
| | - Ilya Ruvinsky
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, Illinois, United States of America
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, United States of America
- * E-mail: (KLG); (IR)
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41
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Yan S, Brecker L, Jin C, Titz A, Dragosits M, Karlsson NG, Jantsch V, Wilson IBH, Paschinger K. Bisecting Galactose as a Feature of N-Glycans of Wild-type and Mutant Caenorhabditis elegans. Mol Cell Proteomics 2015; 14:2111-25. [PMID: 26002521 DOI: 10.1074/mcp.m115.049817] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Indexed: 01/15/2023] Open
Abstract
The N-glycosylation of the model nematode Caenorhabditis elegans has proven to be highly variable and rather complex; it is an example to contradict the existing impression that "simple" organisms possess also a rather simple glycomic capacity. In previous studies in a number of laboratories, N-glycans with up to four fucose residues have been detected. However, although the linkage of three fucose residues to the N,N'-diacetylchitobiosyl core has been proven by structural and enzymatic analyses, the nature of the fourth fucose has remained uncertain. By constructing a triple mutant with deletions in the three genes responsible for core fucosylation (fut-1, fut-6 and fut-8), we have produced a nematode strain lacking products of these enzymes, but still retaining maximally one fucose residue on its N-glycans. Using mass spectrometry and HPLC in conjunction with chemical and enzymatic treatments as well as NMR, we examined a set of α-mannosidase-resistant N-glycans. Within this glycomic subpool, we can reveal that the core β-mannose can be trisubstituted and so carries not only the ubiquitous α1,3- and α1,6-mannose residues, but also a "bisecting" β-galactose, which is substoichiometrically modified with fucose or methylfucose. In addition, the α1,3-mannose can also be α-galactosylated. Our data, showing the presence of novel N-glycan modifications, will enable more targeted studies to understand the biological functions and interactions of nematode glycans.
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Affiliation(s)
- Shi Yan
- From the ‡Department für Chemie, Universität für Bodenkultur, 1190 Wien, Austria
| | - Lothar Brecker
- §Institut für Organische Chemie, Universität Wien, 1090 Wien, Austria
| | - Chunsheng Jin
- ¶Institutionen för Biomedicin, Göteborgs universitet, 405 30 Göteborg, Sweden
| | - Alexander Titz
- From the ‡Department für Chemie, Universität für Bodenkultur, 1190 Wien, Austria
| | - Martin Dragosits
- From the ‡Department für Chemie, Universität für Bodenkultur, 1190 Wien, Austria
| | - Niclas G Karlsson
- ¶Institutionen för Biomedicin, Göteborgs universitet, 405 30 Göteborg, Sweden
| | - Verena Jantsch
- ‖Department für Chromosomenbiologie, Max F. Perutz Laboratories, Universität Wien, 1030 Wien, Austria
| | - Iain B H Wilson
- From the ‡Department für Chemie, Universität für Bodenkultur, 1190 Wien, Austria;
| | - Katharina Paschinger
- From the ‡Department für Chemie, Universität für Bodenkultur, 1190 Wien, Austria
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42
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Grencis RK. Immunity to Helminths: Resistance, Regulation, and Susceptibility to Gastrointestinal Nematodes. Annu Rev Immunol 2015; 33:201-25. [DOI: 10.1146/annurev-immunol-032713-120218] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Richard K. Grencis
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom;
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43
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Schwarz EM, Hu Y, Antoshechkin I, Miller MM, Sternberg PW, Aroian RV. The genome and transcriptome of the zoonotic hookworm Ancylostoma ceylanicum identify infection-specific gene families. Nat Genet 2015; 47:416-22. [PMID: 25730766 PMCID: PMC4617383 DOI: 10.1038/ng.3237] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Accepted: 02/05/2015] [Indexed: 12/19/2022]
Abstract
Hookworms infect over 400 million people, stunting and impoverishing them. Sequencing hookworm genomes and finding which genes they express during infection should help in devising new drugs or vaccines against hookworms. Unlike other hookworms, Ancylostoma ceylanicum infects both humans and other mammals, providing a laboratory model for hookworm disease. We determined an A. ceylanicum genome sequence of 313 Mb, with transcriptomic data throughout infection showing expression of 30,738 genes. Approximately 900 genes were upregulated during early infection in vivo, including ASPRs, a cryptic subfamily of activation-associated secreted proteins (ASPs). Genes downregulated during early infection included ion channels and G protein-coupled receptors; this downregulation was observed in both parasitic and free-living nematodes. Later, at the onset of heavy blood feeding, C-lectin genes were upregulated along with genes for secreted clade V proteins (SCVPs), encoding a previously undescribed protein family. These findings provide new drug and vaccine targets and should help elucidate hookworm pathogenesis.
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Affiliation(s)
- Erich M Schwarz
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Yan Hu
- 1] Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA. [2] Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, USA
| | - Igor Antoshechkin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Melanie M Miller
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, USA
| | - Paul W Sternberg
- 1] Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA. [2] Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California, USA
| | - Raffi V Aroian
- 1] Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA. [2] Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, USA
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44
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Castagnone-Sereno P, Danchin EGJ. Parasitic success without sex – the nematode experience. J Evol Biol 2015; 27:1323-33. [PMID: 25105196 DOI: 10.1111/jeb.12337] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Asexual reproduction is usually considered as an evolutionary dead end, and difficulties for asexual lineages to adapt to a fluctuating environment are anticipated due to the lack of sufficient genetic plasticity. Yet, unlike their sexual congeners, mitotic parthenogenetic root-knot nematode species, Meloidogyne spp., are remarkably widespread and polyphagous, with the ability to parasitize most flowering plants. Although this may reflect in part the short-term stability of agricultural environments, the extreme parasitic success of these clonal species points them as an outstanding evolutionary paradox regarding current theories on the benefits of sex. The discovery that most of the genome of the clonal species M. incognita is composed of pairs of homologous but divergent segments that have presumably been evolving independently in the absence of sexual recombination has shed new light on this evolutionary paradox. Together with recent studies on other biological systems, including the closely related sexual species M. hapla and the ancient asexual bdelloid rotifers, this observation suggests that functional innovation could emerge from such a peculiar genome architecture, which may in turn account for the extreme adaptive capacities of these asexual parasites. Additionally, the higher proportion of transposable elements in M. incognita compared to M. hapla and other nematodes may also be responsible in part for genome plasticity in the absence of sexual reproduction. We foresee that ongoing sequencing efforts should lead soon to a genomic framework involving genetically diverse Meloidogyne species with various different reproductive modes. This will undoubtedly promote the entire genus as a unique and valuable model system to help deciphering the evolution of asexual reproduction in eukaryotes.
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45
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Markov GV, Baskaran P, Sommer RJ. The Same or Not the Same: Lineage-Specific Gene Expansions and Homology Relationships in Multigene Families in Nematodes. J Mol Evol 2014; 80:18-36. [DOI: 10.1007/s00239-014-9651-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 10/06/2014] [Indexed: 11/30/2022]
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46
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Landmann F, Foster JM, Michalski ML, Slatko BE, Sullivan W. Co-evolution between an endosymbiont and its nematode host: Wolbachia asymmetric posterior localization and AP polarity establishment. PLoS Negl Trop Dis 2014; 8:e3096. [PMID: 25165813 PMCID: PMC4148215 DOI: 10.1371/journal.pntd.0003096] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 07/03/2014] [Indexed: 01/07/2023] Open
Abstract
While bacterial symbionts influence a variety of host cellular responses throughout development, there are no documented instances in which symbionts influence early embryogenesis. Here we demonstrate that Wolbachia, an obligate endosymbiont of the parasitic filarial nematodes, is required for proper anterior-posterior polarity establishment in the filarial nematode B. malayi. Characterization of pre- and post-fertilization events in B. malayi reveals that, unlike C. elegans, the centrosomes are maternally derived and produce a cortical-based microtubule organizing center prior to fertilization. We establish that Wolbachia rely on these cortical microtubules and dynein to concentrate at the posterior cortex. Wolbachia also rely on PAR-1 and PAR-3 polarity cues for normal concentration at the posterior cortex. Finally, we demonstrate that Wolbachia depletion results in distinct anterior-posterior polarity defects. These results provide a striking example of endosymbiont-host co-evolution operating on the core initial developmental event of axis determination. Filarial nematodes are responsible for a number of neglected tropical diseases. The vast majority of these human parasites harbor the bacterial endosymbiont Wolbachia. Wolbachia are essential for filarial nematode survival and reproduction, and thus are a promising anti-filarial drug target. Understanding the molecular and cellular basis of Wolbachia-nematode interactions will facilitate the development of a new class of drugs that specifically disrupt these interactions. Here we focus on Wolbachia segregation patterns and interactions with the host cytoskeleton during early embryogenesis. Our studies indicate that centrosomes are maternally inherited in filarial nematodes resulting in a posterior microtubule-organizing center of maternal origin, unique to filarial nematodes. This microtubule-organizing center facilitates the concentration of Wolbachia at the posterior pole. We find that the microtubule motor dynein is required for the proper posterior Wolbachia localization. In addition, we demonstrate that Wolbachia rely on polarity signals in the egg for their preferential localization at the posterior pole. Conversely, Wolbachia are required for normal embryonic axis determination and Wolbachia removal leads to distinct anterior-posterior embryonic polarity defects. To our knowledge, this is the first example of a bacterial endosymbiont required for normal host embryogenesis.
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Affiliation(s)
- Frederic Landmann
- Department of Molecular, Cell and Developmental Biology, Sinsheimer Labs, University of California, Santa Cruz, California, United States of America
- Centre de Recherche de Biochimie Macromoléculaire, CNRS, Montpellier, France
- * E-mail:
| | - Jeremy M. Foster
- Molecular Parasitology, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Michelle L. Michalski
- Department of Biology and Microbiology, University of Wisconsin Oshkosh, Oshkosh, Wisconsin, United States of America
| | - Barton E. Slatko
- Molecular Parasitology, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - William Sullivan
- Department of Molecular, Cell and Developmental Biology, Sinsheimer Labs, University of California, Santa Cruz, California, United States of America
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47
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Borgo F, Ballestriero F, Ferrario C, Fortina MG. Hydrogen peroxide-mediated killing of Caenorhabditis elegans by Enterococcus italicus and Lactococcus garvieae isolated from food. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0924-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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48
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Koutsovoulos G, Makepeace B, Tanya VN, Blaxter M. Palaeosymbiosis revealed by genomic fossils of Wolbachia in a strongyloidean nematode. PLoS Genet 2014; 10:e1004397. [PMID: 24901418 PMCID: PMC4046930 DOI: 10.1371/journal.pgen.1004397] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 04/06/2014] [Indexed: 12/19/2022] Open
Abstract
Wolbachia are common endosymbionts of terrestrial arthropods, and are also found in nematodes: the animal-parasitic filaria, and the plant-parasite Radopholus similis. Lateral transfer of Wolbachia DNA to the host genome is common. We generated a draft genome sequence for the strongyloidean nematode parasite Dictyocaulus viviparus, the cattle lungworm. In the assembly, we identified nearly 1 Mb of sequence with similarity to Wolbachia. The fragments were unlikely to derive from a live Wolbachia infection: most were short, and the genes were disabled through inactivating mutations. Many fragments were co-assembled with definitively nematode-derived sequence. We found limited evidence of expression of the Wolbachia-derived genes. The D. viviparus Wolbachia genes were most similar to filarial strains and strains from the host-promiscuous clade F. We conclude that D. viviparus was infected by Wolbachia in the past, and that clade F-like symbionts may have been the source of filarial Wolbachia infections. Bovine lungworms are economically important nematode parasites of cattle. We have sequenced the genome of the bovine lungworm to provide information for drug and vaccine discovery. Within the lungworm genome we found extensive evidence of an ancient association between the lungworm and a bacterium called Wolbachia. The lungworm Wolbachia is now a “fossil” in the genome, but tells of an ancient infection. Association between lungworms, and related nematode worms, and Wolbachia was not known previously. We have used the lungworm Wolbachia sequence to explore the history of nematode-Wolbachia interactions, particularly the jumping of these symbionts between arthropods and nematodes.
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Affiliation(s)
- Georgios Koutsovoulos
- Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
| | - Benjamin Makepeace
- Institute of Infection and Global Health, The University of Liverpool, Liverpool, United Kingdom
| | - Vincent N. Tanya
- Institut de Recherche Agricole pour le Développement, Regional Centre of Wakwa, Ngaoundéré, Adamawa Region, Cameroon
| | - Mark Blaxter
- Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh, United Kingdom
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49
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Affiliation(s)
- Karin Kiontke
- Department of Biology, New York University, New York, NY 10003, USA
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50
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Meyer D, Williams PL. Toxicity testing of neurotoxic pesticides in Caenorhabditis elegans. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART B, CRITICAL REVIEWS 2014; 17:284-306. [PMID: 25205216 DOI: 10.1080/10937404.2014.933722] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The use of pesticides is ubiquitous worldwide, and these chemicals exert adverse effects on both target and nontarget species. Understanding the modes of action of pesticides, as well as quantifying exposure concentration and duration, is an important goal of clinicians and environmental health scientists. Some chemical exposures result in adverse effects on the nervous system. The nematode Caenorhabditis elegans (C. elegans) is a model lab organism well established for studying neurotoxicity, since the components of its nervous system are mapped and known, and most of its neurotransmitters correspond to human homologs. This review encompasses published studies in which C. elegans nematodes were exposed to pesticides with known neurotoxic actions. Endpoints measured include changes in locomotion, feeding behavior, brood size, growth, life span, and cell death. From data presented, evidence indicates that C. elegans can serve a role in assessing the effects of neurotoxic pesticides at the sublethal cellular level, thereby advancing our understanding of the mechanisms underlying toxicity induced by these chemicals. A proposed toxicity testing scheme for water-soluble chemicals is also included.
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Affiliation(s)
- Dean Meyer
- a Department of Environmental Health Science , College of Public Health, The University of Georgia , Athens , Georgia , USA
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