1
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Fox BW, Ponomarova O, Lee YU, Zhang G, Giese GE, Walker M, Roberto NM, Na H, Rodrigues PR, Curtis BJ, Kolodziej AR, Crombie TA, Zdraljevic S, Yilmaz LS, Andersen EC, Schroeder FC, Walhout AJM. C. elegans as a model for inter-individual variation in metabolism. Nature 2022; 607:571-577. [PMID: 35794472 PMCID: PMC9817093 DOI: 10.1038/s41586-022-04951-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 06/08/2022] [Indexed: 01/11/2023]
Abstract
Individuals can exhibit differences in metabolism that are caused by the interplay of genetic background, nutritional input, microbiota and other environmental factors1-4. It is difficult to connect differences in metabolism to genomic variation and derive underlying molecular mechanisms in humans, owing to differences in diet and lifestyle, among others. Here we use the nematode Caenorhabditis elegans as a model to study inter-individual variation in metabolism. By comparing three wild strains and the commonly used N2 laboratory strain, we find differences in the abundances of both known metabolites and those that have not to our knowledge been previously described. The latter metabolites include conjugates between 3-hydroxypropionate (3HP) and several amino acids (3HP-AAs), which are much higher in abundance in one of the wild strains. 3HP is an intermediate in the propionate shunt pathway, which is activated when flux through the canonical, vitamin-B12-dependent propionate breakdown pathway is perturbed5. We show that increased accumulation of 3HP-AAs is caused by genetic variation in HPHD-1, for which 3HP is a substrate. Our results suggest that the production of 3HP-AAs represents a 'shunt-within-a-shunt' pathway to accommodate a reduction-of-function allele in hphd-1. This study provides a step towards the development of metabolic network models that capture individual-specific differences of metabolism and more closely represent the diversity that is found in entire species.
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Affiliation(s)
- Bennett W Fox
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Olga Ponomarova
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Yong-Uk Lee
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Gaotian Zhang
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Gabrielle E Giese
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Melissa Walker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Nicole M Roberto
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Huimin Na
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Pedro R Rodrigues
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Brian J Curtis
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Aiden R Kolodziej
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Timothy A Crombie
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Stefan Zdraljevic
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - L Safak Yilmaz
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.
| | - Albertha J M Walhout
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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2
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Lin JL, Kuo WL, Huang YH, Jong TL, Hsu AL, Hsu WH. Using Convolutional Neural Networks to Measure the Physiological Age of Caenorhabditis elegans. IEEE/ACM Trans Comput Biol Bioinform 2021; 18:2724-2732. [PMID: 32031946 DOI: 10.1109/tcbb.2020.2971992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Caenorhabditis elegans (C. elegans) is a popular and excellent model for studies of aging due to its short lifespan. Methods for precisely measuring the physiological age of C. elegans are critically needed, especially for antiaging drug screening and genetic screening studies. The effects of various antiaging interventions on the rate of aging in the early stage of the aging process can be determined based on the quantification of physiological age. However, in general, the age of C. elegans is evaluated via human visual inspection of morphological changes based on personal experience and subjective judgment. For example, the rate of motor activity decay has been used to predict lifespan in early- to mid-stage aging. Using image processing, the physiological age of C. elegans can be measured and then classified into periods or classes from childhood to elderhood (e.g., 3 periods comprising days 0-2, 4-6 and 10-12) by using texture entropy (Shamir, L. et al., 2009). Our dataset consists of 913 microscopic images of C. elegans, with approximately 60 images per day from day 1 to day 14 of adulthood. We present quantitative methods to measure the physiological age of C. elegans with convolution neural networks (CNNs), which can measure age with a granularity of days rather than periods. The methods achieved a mean absolute error (MAE) of less than 1 day for the measured age of C. elegans. In our experiments, we found that after training and testing our dataset, 5 popular CNN models, 50-layer residual network (ResNet50), InceptionV3, InceptionResNetV2, 16-layer Visual Geometry Group network (VGG16) and MobileNet, measured the physiological age of C. elegans with an average testing MAE of 1.58 days. Furthermore, based on the results, we propose two models, one model for linear regression analysis and the other model for logistic regression, that combine a CNN model and a new attribute: curved_or_straight. The linear regression analysis model achieved a test MAE of 0.94 days; the logistic regression model achieved an accuracy of 84.78 percent with an error tolerance of 1 day.
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3
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Clark JN, Prajapati G, Aldaco FK, Sokolich TJ, Keung SS, Austin SP, Valdés ÁA, LaMunyon CW. Functionally non-redundant paralogs spe-47 and spe-50 encode FB-MO associated proteins and interact with him-8. PLoS One 2020; 15:e0230939. [PMID: 33382704 PMCID: PMC7774929 DOI: 10.1371/journal.pone.0230939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 12/10/2020] [Indexed: 11/25/2022] Open
Abstract
The activation of C. elegans spermatids to crawling spermatozoa is affected by a number of genes including spe-47. Here, we investigate a paralog to spe-47: spe-50, which has a highly conserved sequence and expression, but which is not functionally redundant to spe-47. Phylogenetic analysis indicates that the duplication event that produced the paralogs occurred prior to the radiation of the Caenorhabditis species included in the analysis, allowing a long period for the paralogs to diverge in function. Furthermore, we observed that knockout mutations in both genes, either alone or together, have little effect on sperm function. However, hermaphrodites harboring both knockout mutations combined with a third mutation in the him-8 gene are nearly self-sterile due to a sperm defect, even though they have numerous apparently normal sperm within their spermathecae. We suggest that the sperm in these triple mutants are defective in fusing with oocytes, and that the effect of the him-8 mutation is unclear but likely due to its direct or indirect effect on local chromatin structure and function.
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Affiliation(s)
- Jessica N. Clark
- Department of Biological Sciences, Cal Poly Pomona, Pomona, California, United States of America
| | - Gaurav Prajapati
- Department of Biological Sciences, Cal Poly Pomona, Pomona, California, United States of America
| | - Fermina K. Aldaco
- Department of Biological Sciences, Cal Poly Pomona, Pomona, California, United States of America
| | - Thomas J. Sokolich
- Department of Biological Sciences, Cal Poly Pomona, Pomona, California, United States of America
| | - Steven S. Keung
- Department of Biological Sciences, Cal Poly Pomona, Pomona, California, United States of America
| | - Sarojani P. Austin
- Department of Biological Sciences, Cal Poly Pomona, Pomona, California, United States of America
| | - Ángel A. Valdés
- Department of Biological Sciences, Cal Poly Pomona, Pomona, California, United States of America
| | - Craig W. LaMunyon
- Department of Biological Sciences, Cal Poly Pomona, Pomona, California, United States of America
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4
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Cermak N, Yu SK, Clark R, Huang YC, Baskoylu SN, Flavell SW. Whole-organism behavioral profiling reveals a role for dopamine in state-dependent motor program coupling in C. elegans. eLife 2020; 9:e57093. [PMID: 32510332 PMCID: PMC7347390 DOI: 10.7554/elife.57093] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 06/07/2020] [Indexed: 11/13/2022] Open
Abstract
Animal behaviors are commonly organized into long-lasting states that coordinately impact the generation of diverse motor outputs such as feeding, locomotion, and grooming. However, the neural mechanisms that coordinate these distinct motor programs remain poorly understood. Here, we examine how the distinct motor programs of the nematode C. elegans are coupled together across behavioral states. We describe a new imaging platform that permits automated, simultaneous quantification of each of the main C. elegans motor programs over hours or days. Analysis of these whole-organism behavioral profiles shows that the motor programs coordinately change as animals switch behavioral states. Utilizing genetics, optogenetics, and calcium imaging, we identify a new role for dopamine in coupling locomotion and egg-laying together across states. These results provide new insights into how the diverse motor programs throughout an organism are coordinated and suggest that neuromodulators like dopamine can couple motor circuits together in a state-dependent manner.
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Affiliation(s)
- Nathan Cermak
- Picower Institute for Learning & Memory, Department of Brain & Cognitive Sciences, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Stephanie K Yu
- Picower Institute for Learning & Memory, Department of Brain & Cognitive Sciences, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Rebekah Clark
- Picower Institute for Learning & Memory, Department of Brain & Cognitive Sciences, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Yung-Chi Huang
- Picower Institute for Learning & Memory, Department of Brain & Cognitive Sciences, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Saba N Baskoylu
- Picower Institute for Learning & Memory, Department of Brain & Cognitive Sciences, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Steven W Flavell
- Picower Institute for Learning & Memory, Department of Brain & Cognitive Sciences, Massachusetts Institute of TechnologyCambridgeUnited States
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5
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Stroehlein AJ, Young ND, Gasser RB. Improved strategy for the curation and classification of kinases, with broad applicability to other eukaryotic protein groups. Sci Rep 2018; 8:6808. [PMID: 29717207 PMCID: PMC5931623 DOI: 10.1038/s41598-018-25020-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/12/2018] [Indexed: 12/20/2022] Open
Abstract
Despite the substantial amount of genomic and transcriptomic data available for a wide range of eukaryotic organisms, most genomes are still in a draft state and can have inaccurate gene predictions. To gain a sound understanding of the biology of an organism, it is crucial that inferred protein sequences are accurately identified and annotated. However, this can be challenging to achieve, particularly for organisms such as parasitic worms (helminths), as most gene prediction approaches do not account for substantial phylogenetic divergence from model organisms, such as Caenorhabditis elegans and Drosophila melanogaster, whose genomes are well-curated. In this paper, we describe a bioinformatic strategy for the curation of gene families and subsequent annotation of encoded proteins. This strategy relies on pairwise gene curation between at least two closely related species using genomic and transcriptomic data sets, and is built on recent work on kinase complements of parasitic worms. Here, we discuss salient technical aspects of this strategy and its implications for the curation of protein families more generally.
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Affiliation(s)
- Andreas J Stroehlein
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia.
| | - Neil D Young
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Robin B Gasser
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia.
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6
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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Ryan CP, Brownlie JC, Whyard S. Hsp90 and Physiological Stress Are Linked to Autonomous Transposon Mobility and Heritable Genetic Change in Nematodes. Genome Biol Evol 2016; 8:3794-3805. [PMID: 28082599 PMCID: PMC5521727 DOI: 10.1093/gbe/evw284] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2016] [Indexed: 12/21/2022] Open
Abstract
Transposable elements (TEs) have been recognized as potentially powerful drivers of genomic evolutionary change, but factors affecting their mobility and regulation remain poorly understood. Chaperones such as Hsp90 buffer environmental perturbations by regulating protein conformation, but are also part of the PIWI-interacting RNA pathway, which regulates genomic instability arising from mobile TEs in the germline. Stress-induced mutagenesis from TE movement could thus arise from functional trade-offs in the dual roles of Hsp90. We examined the functional constraints of Hsp90 and its role as a regulator of TE mobility by exposing nematodes (Caenorhabditis elegans and Caenorhabditis briggsae) to environmental stress, with and without RNAi-induced silencing of Hsp90. TE excision frequency increased with environmental stress intensity at multiple loci in several strains of each species. These effects were compounded by RNAi-induced knockdown of Hsp90. Mutation frequencies at the unc-22 marker gene in the offspring of animals exposed to environmental stress and Hsp90 RNAi mirrored excision frequency in response to these treatments. Our results support a role for Hsp90 in the suppression of TE mobility, and demonstrate that that the Hsp90 regulatory pathway can be overwhelmed with moderate environmental stress. By compromising genomic stability in germline cells, environmentally induced mutations arising from TE mobility and insertion can have permanent and heritable effects on both the phenotype and the genotype of subsequent generations.
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Affiliation(s)
- Calen P. Ryan
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Anthropology, Northwestern University, Evanston, IL
| | - Jeremy C. Brownlie
- School of Biomolecular and Physical Sciences, Griffith University, Brisbane, Queensland, Australia
| | - Steve Whyard
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
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8
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Attreed M, Saied-Santiago K, Bülow HE. Conservation of anatomically restricted glycosaminoglycan structures in divergent nematode species. Glycobiology 2016; 26:862-870. [PMID: 26976619 PMCID: PMC5018047 DOI: 10.1093/glycob/cww037] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/04/2016] [Accepted: 03/08/2016] [Indexed: 11/14/2022] Open
Abstract
Heparan sulfates (HS) are glycosaminoglycans of the extracellular matrices and characterized by complex modification patterns owing to sulfations, epimerization, and acetylation. Distinct HS modification patterns have been shown to modulate protein-protein interactions during development in general and of the nervous system in particular. This has led to the heparan sulfate code hypothesis, which posits that specifically modified HS epitopes are distributed in a tissue and cell-specific fashion to orchestrate neural circuit formation. Whether an HS code exists in vivo, how specific or how evolutionarily conserved the anatomical distribution of an HS code may be has remained unknown. Here we conduct a systematic comparison of HS modification patterns in the nematode Caenorhabditis elegans using transgenic expression of 33 different HS-specific single chain variable fragment antibodies. We find that some HS modification patterns are widely distributed in the nervous system. In contrast, other HS modification patterns appear highly cell-specific in both non-neuronal and neuronal cells. Some patterns can be as restricted in their localization as to single neurites or synaptic connections between two neurons. This restricted anatomical localization of specific HS patterns can be evolutionarily conserved over a span of 80-100 million years in the divergent nematode species Caenorhabditis briggsae suggesting structural and, possibly functional conservation of glycosaminoglycan structures similar to proteins. These findings suggest a HS code with subcellularly localized, unique glycan identities in the nervous system.
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Affiliation(s)
| | | | - Hannes E Bülow
- Department of Genetics
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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9
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Vu V, Verster AJ, Schertzberg M, Chuluunbaatar T, Spensley M, Pajkic D, Hart GT, Moffat J, Fraser AG. Natural Variation in Gene Expression Modulates the Severity of Mutant Phenotypes. Cell 2015; 162:391-402. [PMID: 26186192 DOI: 10.1016/j.cell.2015.06.037] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 11/04/2014] [Accepted: 06/10/2015] [Indexed: 12/16/2022]
Abstract
Many mutations cause genetic disorders. However, two people inheriting the same mutation often have different severity of symptoms, and this is partly genetic. The effects of genetic background on mutant phenotypes are poorly understood, but predicting them is critical for personalized medicine. To study this phenomenon comprehensively and systematically, we used RNAi to compare loss-of-function phenotypes for ∼1,400 genes in two isolates of C. elegans and find that ∼20% of genes differ in the severity of phenotypes in these two genetic backgrounds. Crucially, this effect of genetic background on the severity of both RNAi and mutant phenotypes can be predicted from variation in the expression levels of the affected gene. This is also true in mammalian cells, suggesting it is a general property of genetic networks. We suggest that differences in the manifestation of mutant phenotypes between individuals are largely the result of natural variation in gene expression.
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Affiliation(s)
- Victoria Vu
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Adrian J Verster
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Michael Schertzberg
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Tungalag Chuluunbaatar
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Mark Spensley
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Djina Pajkic
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - G Traver Hart
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Jason Moffat
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Andrew G Fraser
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada.
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10
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Labocha MK, Jung SK, Aleman-Meza B, Liu Z, Zhong W. WormGender - Open-Source Software for Automatic Caenorhabditis elegans Sex Ratio Measurement. PLoS One 2015; 10:e0139724. [PMID: 26421844 PMCID: PMC4589236 DOI: 10.1371/journal.pone.0139724] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 09/16/2015] [Indexed: 11/19/2022] Open
Abstract
Fast and quantitative analysis of animal phenotypes is one of the major challenges of current biology. Here we report the WormGender open-source software, which is designed for accurate quantification of sex ratio in Caenorhabditis elegans. The software functions include, i) automatic recognition and counting of adult hermaphrodites and males, ii) a manual inspection feature that enables manual correction of errors, and iii) flexibility to use new training images to optimize the software for different imaging conditions. We evaluated the performance of our software by comparing manual and automated assessment of sex ratio. Our data showed that the WormGender software provided overall accurate sex ratio measurements. We further demonstrated the usage of WormGender by quantifying the high incidence of male (him) phenotype in 27 mutant strains. Mutants of nine genes (brc-1, C30G12.6, cep-1, coh-3, him-3, him-5, him-8, skr-1, unc-86) showed significant him phenotype. The WormGender is written in Java and can be installed and run on both Windows and Mac platforms. The source code is freely available together with a user manual and sample data at http://www.QuantWorm.org/. The source code and sample data are also available at http://dx.doi.org/10.6084/m9.figshare.1541248.
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Affiliation(s)
- Marta K. Labocha
- Department of BioSciences, Rice University, Houston, Texas, United States of America
| | - Sang-Kyu Jung
- Department of BioSciences, Rice University, Houston, Texas, United States of America
| | - Boanerges Aleman-Meza
- Department of BioSciences, Rice University, Houston, Texas, United States of America
| | - Zheng Liu
- Department of BioSciences, Rice University, Houston, Texas, United States of America
| | - Weiwei Zhong
- Department of BioSciences, Rice University, Houston, Texas, United States of America
- * E-mail:
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11
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Abstract
The roundworm Caenorhabditis elegans has risen to the status of a top model organism for biological research in the last fifty years. Among laboratory animals, this tiny nematode is one of the simplest and easiest organisms to handle. And its life outside the laboratory is beginning to be unveiled. Like other model organisms, C. elegans has a boom-and-bust lifestyle. It feasts on ephemeral bacterial blooms in decomposing fruits and stems. After resource depletion, its young larvae enter a migratory diapause stage, called the dauer. Organisms known to be associated with C. elegans include migration vectors (such as snails, slugs and isopods) and pathogens (such as microsporidia, fungi, bacteria and viruses). By deepening our understanding of the natural history of C. elegans, we establish a broader context and improved tools for studying its biology.
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Affiliation(s)
- Lise Frézal
- Institute of Biology of Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Paris, France
| | - Marie-Anne Félix
- Institute of Biology of Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Paris, France
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12
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Petrella LN. Natural variants of C. elegans demonstrate defects in both sperm function and oogenesis at elevated temperatures. PLoS One 2014; 9:e112377. [PMID: 25380048 PMCID: PMC4224435 DOI: 10.1371/journal.pone.0112377] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 10/14/2014] [Indexed: 01/07/2023] Open
Abstract
The temperature sensitivity of the germ line is conserved from nematodes to mammals. Previous studies in C. briggsae and Drosophila showed that isolates originating from temperate latitudes lose fertility at a lower temperature than strains originating from tropical latitudes. In order to investigate these relationships in C. elegans, analysis of the fertility of 22 different wild-type isolates of C. elegans isolated from equatorial, tropical and temperate regions was undertaken. It was found that there are significant temperature, genotype and temperature × genotype effects on fertility but region of isolation showed no significant effect on differences in fertility. For most isolates 100% of the population maintained fertility from 20°C to 26°C, but there was a precipitous drop in the percentage of fertile hermaphrodites at 27°C. In contrast, all isolates show a progressive decrease in brood size as temperature increases from 20°C to 26°C, followed by a brood size near zero at 27°C. Temperature shift experiments were performed to better understand the causes of high temperature loss of fertility. Males up-shifted to high temperature maintained fertility, while males raised at high temperature lost fertility. Down-shifting males raised at high temperature generally did not restore fertility. This result differs from that observed in Drosophila and suggested that in C. elegans spermatogenesis or sperm function is irreversibly impaired in males that develop at high temperature. Mating and down-shifting experiments with hermaphrodites were performed to investigate the relative contributions of spermatogenic and oogenic defects to high temperature loss of fertility. It was found that the hermaphrodites of all isolates demonstrated loss in both spermatogenic and oogenic germ lines that differed in their relative contribution by isolate. These studies uncovered unexpectedly high variation in both the loss of fertility and problems with oocyte function in natural variants of C. elegans at high temperature.
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Affiliation(s)
- Lisa N. Petrella
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, United States of America
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13
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Abstract
Ribosomal loci represent a major tool for investigating environmental diversity and community structure via high-throughput marker gene studies of eukaryotes (e.g. 18S rRNA). Since the estimation of species' abundance is a major goal of environmental studies (by counting numbers of sequences), understanding the patterns of rRNA copy number across species will be critical for informing such high-throughput approaches. Such knowledge is critical, given that ribosomal RNA genes exist within multi-copy repeated arrays in a genome. Here we measured the repeat copy number for six nematode species by mapping the sequences from whole genome shotgun libraries against reference sequences for their rRNA repeat. This revealed a 6-fold variation in repeat copy number amongst taxa investigated, with levels of intragenomic variation ranging from 56 to 323 copies of the rRNA array. By applying the same approach to four C. elegans mutation accumulation lines propagated by repeated bottlenecking for an average of ~400 generations, we find on average a 2-fold increase in repeat copy number (rate of increase in rRNA estimated at 0.0285-0.3414 copies per generation), suggesting that rRNA repeat copy number is subject to selection. Within each Caenorhabditis species, the majority of intragenomic variation found across the rRNA repeat was observed within gene regions (18S, 28S, 5.8S), suggesting that such intragenomic variation is not a product of selection for rRNA coding function. We find that the dramatic variation in repeat copy number among these six nematode genomes would limit the use of rRNA in estimates of organismal abundance. In addition, the unique pattern of variation within a single genome was uncorrelated with patterns of divergence between species, reflecting a strong signature of natural selection for rRNA function. A better understanding of the factors that control or affect copy number in these arrays, as well as their rates and patterns of evolution, will be critical for informing estimates of global biodiversity.
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Affiliation(s)
- Holly M. Bik
- Union Council Davis Genome Center, University of California Davis, Davis, California, United States of America
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, United States of America
| | - David Fournier
- Department of Computer Science, University of New Hampshire, Durham, New Hampshire, United States of America
| | - Way Sung
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, United States of America
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - R. Daniel Bergeron
- Department of Computer Science, University of New Hampshire, Durham, New Hampshire, United States of America
| | - W. Kelley Thomas
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, United States of America
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14
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Laing R, Kikuchi T, Martinelli A, Tsai IJ, Beech RN, Redman E, Holroyd N, Bartley DJ, Beasley H, Britton C, Curran D, Devaney E, Gilabert A, Hunt M, Jackson F, Johnston SL, Kryukov I, Li K, Morrison AA, Reid AJ, Sargison N, Saunders GI, Wasmuth JD, Wolstenholme A, Berriman M, Gilleard JS, Cotton JA. The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery. Genome Biol 2013; 14:R88. [PMID: 23985316 PMCID: PMC4054779 DOI: 10.1186/gb-2013-14-8-r88] [Citation(s) in RCA: 252] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 06/27/2013] [Accepted: 08/28/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The small ruminant parasite Haemonchus contortus is the most widely used parasitic nematode in drug discovery, vaccine development and anthelmintic resistance research. Its remarkable propensity to develop resistance threatens the viability of the sheep industry in many regions of the world and provides a cautionary example of the effect of mass drug administration to control parasitic nematodes. Its phylogenetic position makes it particularly well placed for comparison with the free-living nematode Caenorhabditis elegans and the most economically important parasites of livestock and humans. RESULTS Here we report the detailed analysis of a draft genome assembly and extensive transcriptomic dataset for H. contortus. This represents the first genome to be published for a strongylid nematode and the most extensive transcriptomic dataset for any parasitic nematode reported to date. We show a general pattern of conservation of genome structure and gene content between H. contortus and C. elegans, but also a dramatic expansion of important parasite gene families. We identify genes involved in parasite-specific pathways such as blood feeding, neurological function, and drug metabolism. In particular, we describe complete gene repertoires for known drug target families, providing the most comprehensive understanding yet of the action of several important anthelmintics. Also, we identify a set of genes enriched in the parasitic stages of the lifecycle and the parasite gut that provide a rich source of vaccine and drug target candidates. CONCLUSIONS The H. contortus genome and transcriptome provide an essential platform for postgenomic research in this and other important strongylid parasites.
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Affiliation(s)
- Roz Laing
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, 464 Bearsden Road, Glasgow, Scotland, G61 1QH, UK
| | - Taisei Kikuchi
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Division of Parasitology, Department of Infectious Disease, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692 Japan
| | - Axel Martinelli
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Isheng J Tsai
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Division of Parasitology, Department of Infectious Disease, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692 Japan
| | - Robin N Beech
- Institute of Parasitology, Macdonald Campus, McGill University, 21,111 Lakeshore Road, Ste. Anne de Bellevue, Québec, Canada H9X 3V9
| | - Elizabeth Redman
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, Faculty of Veterinary Medicine, 3330 Hospital Drive NW, Calgary, Alberta, Canada T2N 1N4
| | - Nancy Holroyd
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - David J Bartley
- Disease Control, Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Midlothian, EH26 0PZ, UK
| | - Helen Beasley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Collette Britton
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, 464 Bearsden Road, Glasgow, Scotland, G61 1QH, UK
| | - David Curran
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, Faculty of Veterinary Medicine, 3330 Hospital Drive NW, Calgary, Alberta, Canada T2N 1N4
| | - Eileen Devaney
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, 464 Bearsden Road, Glasgow, Scotland, G61 1QH, UK
| | - Aude Gilabert
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, Faculty of Veterinary Medicine, 3330 Hospital Drive NW, Calgary, Alberta, Canada T2N 1N4
| | - Martin Hunt
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Frank Jackson
- Disease Control, Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Midlothian, EH26 0PZ, UK
| | - Stephanie L Johnston
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, 464 Bearsden Road, Glasgow, Scotland, G61 1QH, UK
| | - Ivan Kryukov
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, Faculty of Veterinary Medicine, 3330 Hospital Drive NW, Calgary, Alberta, Canada T2N 1N4
| | - Keyu Li
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, Faculty of Veterinary Medicine, 3330 Hospital Drive NW, Calgary, Alberta, Canada T2N 1N4
| | - Alison A Morrison
- Disease Control, Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Midlothian, EH26 0PZ, UK
| | - Adam J Reid
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Neil Sargison
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Veterinary Centre, Roslin, Midlothian EH25 9RG, Scotland, UK
| | - Gary I Saunders
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, 464 Bearsden Road, Glasgow, Scotland, G61 1QH, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - James D Wasmuth
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, Faculty of Veterinary Medicine, 3330 Hospital Drive NW, Calgary, Alberta, Canada T2N 1N4
| | - Adrian Wolstenholme
- Department of Infectious Diseases and Center for Tropical and Emerging Global Disease, University of Georgia, Athens, Georgia 30602, USA
| | - Matthew Berriman
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - John S Gilleard
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, Faculty of Veterinary Medicine, 3330 Hospital Drive NW, Calgary, Alberta, Canada T2N 1N4
| | - James A Cotton
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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15
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Brown AEX, Yemini EI, Grundy LJ, Jucikas T, Schafer WR. A dictionary of behavioral motifs reveals clusters of genes affecting Caenorhabditis elegans locomotion. Proc Natl Acad Sci U S A 2013; 110:791-6. [PMID: 23267063 PMCID: PMC3545781 DOI: 10.1073/pnas.1211447110] [Citation(s) in RCA: 167] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Visible phenotypes based on locomotion and posture have played a critical role in understanding the molecular basis of behavior and development in Caenorhabditis elegans and other model organisms. However, it is not known whether these human-defined features capture the most important aspects of behavior for phenotypic comparison or whether they are sufficient to discover new behaviors. Here we show that four basic shapes, or eigenworms, previously described for wild-type worms, also capture mutant shapes, and that this representation can be used to build a dictionary of repetitive behavioral motifs in an unbiased way. By measuring the distance between each individual's behavior and the elements in the motif dictionary, we create a fingerprint that can be used to compare mutants to wild type and to each other. This analysis has revealed phenotypes not previously detected by real-time observation and has allowed clustering of mutants into related groups. Behavioral motifs provide a compact and intuitive representation of behavioral phenotypes.
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Affiliation(s)
- André E. X. Brown
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Eviatar I. Yemini
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Laura J. Grundy
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Tadas Jucikas
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - William R. Schafer
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
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16
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Abstract
The nematode (worm) C. elegans is one of the widely studied animal model organisms in biology. It develops through 4 larval stages (L1-L4) in 2 to 3 days before becoming a young adult. Biological assays involving C. elegans frequently require a large number of animals that are appropriately staged and exhibit a similar behaviour. We have developed a new method to synchronize animals that relies on the electrotactic response (electric field-induced motion) of C. elegans to sort them in parallel based on their age, size and phenotype. By using local electric field traps in a microfluidic device, we can efficiently sort worms from a mixed culture in a semi-continuous flow manner (with a minimum throughput of 78 worms per minute per load-run) and obtain synchronized populations of animals. In addition to sorting larvae, our device can also distinguish between young and old adults efficiently. Unlike fluorescent based sorting systems that use active imaging based feedback, this method is passive and automatic and uses the innate behaviour of the worm. Considering that the entire procedure takes only a few minutes to run and is cost-effective, it promises to simplify and accelerate experiments requiring homogeneous cultures of worms as well as to facilitate isolation of mutants that have abnormal electrotaxis. More importantly, our method of isolating and separating worms using locomotion as a defining characteristic promises development of advanced microfluidics-based systems to study the neuronal basis of movement-related defects in worms and facilitate high-throughput chemical screening and drug discovery.
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Affiliation(s)
- Pouya Rezai
- JHE-212B, Department of Mechanical Engineering, McMaster University, 1280 Main Street West. Hamilton, ON L8S 4L7, Canada
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17
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Duveau F, Félix MA. Role of pleiotropy in the evolution of a cryptic developmental variation in Caenorhabditis elegans. PLoS Biol 2012; 10:e1001230. [PMID: 22235190 PMCID: PMC3250502 DOI: 10.1371/journal.pbio.1001230] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 11/18/2011] [Indexed: 12/20/2022] Open
Abstract
Using vulval phenotypes in Caenorhabditis elegans, the authors show that cryptic genetic variation can evolve through selection for pleiotropic effects that alter fitness, and identify a cryptic variant that has conferred enhanced fitness on domesticated worms under laboratory conditions. Robust biological systems are expected to accumulate cryptic genetic variation that does not affect the system output in standard conditions yet may play an evolutionary role once phenotypically expressed under a strong perturbation. Genetic variation that is cryptic relative to a robust trait may accumulate neutrally as it does not change the phenotype, yet it could also evolve under selection if it affects traits related to fitness in addition to its cryptic effect. Cryptic variation affecting the vulval intercellular signaling network was previously uncovered among wild isolates of Caenorhabditis elegans. Using a quantitative genetic approach, we identify a non-synonymous polymorphism of the previously uncharacterized nath-10 gene that affects the vulval phenotype when the system is sensitized with different mutations, but not in wild-type strains. nath-10 is an essential protein acetyltransferase gene and the homolog of human NAT10. The nath-10 polymorphism also presents non-cryptic effects on life history traits. The nath-10 allele carried by the N2 reference strain leads to a subtle increase in the egg laying rate and in the total number of sperm, a trait affecting the trade-off between fertility and minimal generation time in hermaphrodite individuals. We show that this allele appeared during early laboratory culture of N2, which allowed us to test whether it may have evolved under selection in this novel environment. The derived allele indeed strongly outcompetes the ancestral allele in laboratory conditions. In conclusion, we identified the molecular nature of a cryptic genetic variation and characterized its evolutionary history. These results show that cryptic genetic variation does not necessarily accumulate neutrally at the whole-organism level, but may evolve through selection for pleiotropic effects that alter fitness. In addition, cultivation in the laboratory has led to adaptive evolution of the reference strain N2 to the laboratory environment, which may modify other phenotypes of interest. Robustness is a property of biological systems that ensures the production of reproducible phenotypes in spite of underlying environmental, stochastic, and genetic variability. A consequence of robustness is that potentially functional genetic variation is free to accumulate in natural populations because it is buffered at the phenotypic level. Even if this so-called “cryptic” genetic variation has no obvious effects under standard conditions, it may become phenotypically expressed upon major genetic or environmental perturbations. Here we used the model organism Caenorhabditis elegans to identify genetic variations involved in the cryptic evolution of vulval cell fate induction between wild strains. We found that a mutation in the essential nath-10 gene not only contributes to cryptic genetic variation in the vulval system, but also affects key life history traits that are expected to be under a strong selective pressure (brood size, age at sexual maturity, sperm number and rate of progeny production). Indeed, an allele of nath-10 that emerged during the laboratory domestication of C. elegans about 50 years ago confers a strong competitive advantage over the ancestral allele under laboratory conditions. A genetic variation that is cryptic for a robust trait can therefore affect more sensitive phenotypes and thus evolve under selection.
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18
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Arellano-Carbajal F, Briseño-Roa L, Couto A, Cheung BHH, Labouesse M, de Bono M. Macoilin, a conserved nervous system-specific ER membrane protein that regulates neuronal excitability. PLoS Genet 2011; 7:e1001341. [PMID: 21437263 PMCID: PMC3060067 DOI: 10.1371/journal.pgen.1001341] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Accepted: 02/16/2011] [Indexed: 12/27/2022] Open
Abstract
Genome sequence comparisons have highlighted many novel gene families that are conserved across animal phyla but whose biological function is unknown. Here, we functionally characterize a member of one such family, the macoilins. Macoilins are characterized by several highly conserved predicted transmembrane domains towards the N-terminus and by coiled-coil regions C-terminally. They are found throughout Eumetazoa but not in other organisms. Mutants for the single Caenorhabditis elegans macoilin, maco-1, exhibit a constellation of behavioral phenotypes, including defects in aggregation, O₂ responses, and swimming. MACO-1 protein is expressed broadly and specifically in the nervous system and localizes to the rough endoplasmic reticulum; it is excluded from dendrites and axons. Apart from subtle synapse defects, nervous system development appears wild-type in maco-1 mutants. However, maco-1 animals are resistant to the cholinesterase inhibitor aldicarb and sensitive to levamisole, suggesting pre-synaptic defects. Using in vivo imaging, we show that macoilin is required to evoke Ca²(+) transients, at least in some neurons: in maco-1 mutants the O₂-sensing neuron PQR is unable to generate a Ca²(+) response to a rise in O₂. By genetically disrupting neurotransmission, we show that pre-synaptic input is not necessary for PQR to respond to O₂, indicating that the response is mediated by cell-intrinsic sensory transduction and amplification. Disrupting the sodium leak channels NCA-1/NCA-2, or the N-,P/Q,R-type voltage-gated Ca²(+) channels, also fails to disrupt Ca²(+) responses in the PQR cell body to O₂ stimuli. By contrast, mutations in egl-19, which encodes the only Caenorhabditis elegans L-type voltage-gated Ca²(+) channel α1 subunit, recapitulate the Ca²(+) response defect we see in maco-1 mutants, although we do not see defects in localization of EGL-19. Together, our data suggest that macoilin acts in the ER to regulate assembly or traffic of ion channels or ion channel regulators.
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Affiliation(s)
| | - Luis Briseño-Roa
- Medical Research Council–Laboratory of Molecular Biology, Cambridge, United Kingdom
- * E-mail: (LB-R); (MdB)
| | - Africa Couto
- Medical Research Council–Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Benny H. H. Cheung
- Medical Research Council–Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Michel Labouesse
- Institute of Genetics and Molecular and Cellular Biology, Illkirch, France
| | - Mario de Bono
- Medical Research Council–Laboratory of Molecular Biology, Cambridge, United Kingdom
- * E-mail: (LB-R); (MdB)
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19
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Affiliation(s)
- Anita G. Fernandez
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10003 USA
- Department of Biology, Fairfield University, Fairfield, CT 06824 USA
| | - Emily K. Mis
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10003 USA
| | - Bastiaan O.R. Bargmann
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10003 USA
| | - Kenneth D. Birnbaum
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10003 USA
| | - Fabio Piano
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10003 USA
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20
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Giurumescu CA, Sternberg PW, Asthagiri AR. Predicting phenotypic diversity and the underlying quantitative molecular transitions. PLoS Comput Biol 2009; 5:e1000354. [PMID: 19360093 PMCID: PMC2661366 DOI: 10.1371/journal.pcbi.1000354] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2008] [Accepted: 03/10/2009] [Indexed: 11/19/2022] Open
Abstract
During development, signaling networks control the formation of multicellular
patterns. To what extent quantitative fluctuations in these complex networks may
affect multicellular phenotype remains unclear. Here, we describe a
computational approach to predict and analyze the phenotypic diversity that is
accessible to a developmental signaling network. Applying this framework to
vulval development in C. elegans, we demonstrate that
quantitative changes in the regulatory network can render ∼500
multicellular phenotypes. This phenotypic capacity is an order-of-magnitude
below the theoretical upper limit for this system but yet is large enough to
demonstrate that the system is not restricted to a select few outcomes. Using
metrics to gauge the robustness of these phenotypes to parameter perturbations,
we identify a select subset of novel phenotypes that are the most promising for
experimental validation. In addition, our model calculations provide a layout of
these phenotypes in network parameter space. Analyzing this landscape of
multicellular phenotypes yielded two significant insights. First, we show that
experimentally well-established mutant phenotypes may be rendered using
non-canonical network perturbations. Second, we show that the predicted
multicellular patterns include not only those observed in C.
elegans, but also those occurring exclusively in other species of the
Caenorhabditis genus. This result demonstrates that
quantitative diversification of a common regulatory network is indeed
demonstrably sufficient to generate the phenotypic differences observed across
three major species within the Caenorhabditis genus. Using our
computational framework, we systematically identify the quantitative changes
that may have occurred in the regulatory network during the evolution of these
species. Our model predictions show that significant phenotypic diversity may be
sampled through quantitative variations in the regulatory network without
overhauling the core network architecture. Furthermore, by comparing the
predicted landscape of phenotypes to multicellular patterns that have been
experimentally observed across multiple species, we systematically trace the
quantitative regulatory changes that may have occurred during the evolution of
the Caenorhabditis genus. The diversity of metazoan life forms that we experience today arose as
multicellular systems continually sampled new phenotypes that withstood ever
changing selective pressures. This phenotypic diversification is driven by
variations in the underlying regulatory network that instructs cells to form
multicellular patterns and structures. Here, we computationally construct the
phenotypic diversity that may be accessible through quantitative tuning of the
regulatory network that drives multicellular patterning during C.
elegans vulval development. We show that significant phenotypic
diversity may be sampled through quantitative variations without overhauling the
core regulatory network architecture. Furthermore, by comparing the predicted
landscape of phenotypes to multicellular patterns that have been experimentally
observed across multiple species, we systematically deduce the quantitative
molecular changes that may have transpired during the evolution of the
Caenorhabditis genus.
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Affiliation(s)
- Claudiu A. Giurumescu
- Division of Chemistry and Chemical Engineering, California Institute of
Technology, Pasadena, California, United States of America
| | - Paul W. Sternberg
- Division of Biology, California Institute of Technology, Pasadena,
California, United States of America
| | - Anand R. Asthagiri
- Division of Chemistry and Chemical Engineering, California Institute of
Technology, Pasadena, California, United States of America
- * E-mail:
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21
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Blaise BJ, Giacomotto J, Elena B, Dumas ME, Toulhoat P, Ségalat L, Emsley L. Metabotyping of Caenorhabditis elegans reveals latent phenotypes. Proc Natl Acad Sci U S A 2007; 104:19808-12. [PMID: 18077412 PMCID: PMC2148380 DOI: 10.1073/pnas.0707393104] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2007] [Indexed: 01/22/2023] Open
Abstract
Assigning functions to every gene in a living organism is the next challenge for functional genomics. In fact, 85-90% of the 19,000 genes of the nematode Caenorhabditis elegans genome do not produce any visible phenotype when inactivated, which hampers determining their function, especially when they do not belong to previously characterized gene families. We used (1)H high-resolution magic angle spinning NMR spectroscopy ((1)H HRMAS-NMR) to reveal the latent phenotype associated to superoxide dismutase (sod-1) and catalase (ctl-1) C. elegans mutations, both involved in the elimination of radical oxidative species. These two silent mutations are significantly discriminated from the wild-type strain and from each other. We identify a metabotype significantly associated with these mutations involving a general reduction of fatty acyl resonances from triglycerides, unsaturated lipids being known targets of free radicals. This work opens up perspectives for the use of (1)H HRMAS-NMR as a molecular phenotyping device for model organisms. Because it is amenable to high throughput and is shown to be highly informative, this approach may rapidly lead to a functional and integrated metabonomic mapping of the C. elegans genome at the systems biology level.
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Affiliation(s)
- Benjamin J. Blaise
- *Centre de Resonance Magnétique Nucléaire à Très Hauts Champs and Laboritoire de Chimie, Ecole Normale Supérieure de Lyon/Centre National de la Recherche Scientifique, Université de Lyon, 69364 Lyon, France
| | - Jean Giacomotto
- Centre de Génétique Moléculaire et Cellulaire, Unité Mixte de Recherche 5534, Centre National de la Recherche Scientifique/Université Lyon 1, Bâtiment Mendel, 43, Boulevard du 11 Novembre, 69622 Villeurbanne Cedex, France; and
| | - Bénédicte Elena
- *Centre de Resonance Magnétique Nucléaire à Très Hauts Champs and Laboritoire de Chimie, Ecole Normale Supérieure de Lyon/Centre National de la Recherche Scientifique, Université de Lyon, 69364 Lyon, France
| | - Marc-Emmanuel Dumas
- *Centre de Resonance Magnétique Nucléaire à Très Hauts Champs and Laboritoire de Chimie, Ecole Normale Supérieure de Lyon/Centre National de la Recherche Scientifique, Université de Lyon, 69364 Lyon, France
| | - Pierre Toulhoat
- *Centre de Resonance Magnétique Nucléaire à Très Hauts Champs and Laboritoire de Chimie, Ecole Normale Supérieure de Lyon/Centre National de la Recherche Scientifique, Université de Lyon, 69364 Lyon, France
- Institut National de L'Environnement Industriel et des Risques, Parc Technologique Alata, BP2, 60550 Verneuil en Halatte, France
| | - Laurent Ségalat
- Centre de Génétique Moléculaire et Cellulaire, Unité Mixte de Recherche 5534, Centre National de la Recherche Scientifique/Université Lyon 1, Bâtiment Mendel, 43, Boulevard du 11 Novembre, 69622 Villeurbanne Cedex, France; and
| | - Lyndon Emsley
- *Centre de Resonance Magnétique Nucléaire à Très Hauts Champs and Laboritoire de Chimie, Ecole Normale Supérieure de Lyon/Centre National de la Recherche Scientifique, Université de Lyon, 69364 Lyon, France
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22
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Fairbairn DJ, Cavallaro AS, Bernard M, Mahalinga-Iyer J, Graham MW, Botella JR. Host-delivered RNAi: an effective strategy to silence genes in plant parasitic nematodes. Planta 2007; 226:1525-33. [PMID: 17653759 DOI: 10.1007/s00425-007-0588-x] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2007] [Accepted: 07/02/2007] [Indexed: 05/16/2023]
Abstract
Root-knot nematodes (Meloidogyne spp.) are obligate, sedentary endoparasites that infect many plant species causing large economic losses worldwide. Available nematicides are being banned due to their toxicity or ozone-depleting properties and alternative control strategies are urgently required. We have produced transgenic tobacco (Nicotiana tabacum) plants expressing different dsRNA hairpin structures targeting a root-knot nematode (Meloidogyne javanica) putative transcription factor, MjTis11. We provide evidence that MjTis11 was consistently silenced in nematodes feeding on the roots of transgenic plants. The observed silencing was specific for MjTis11, with other sequence-unrelated genes being unaffected in the nematodes. Those transgenic plants able to induce silencing of MjTis11, also showed the presence of small interfering RNAs. Even though down-regulation of MjTis11 did not result in a lethal phenotype, this study demonstrates the feasibility of silencing root-knot nematode genes by expressing dsRNA in the host plant. Host-delivered RNA interference-triggered (HD-RNAi) silencing of parasite genes provides a novel disease resistance strategy with wide biotechnological applications. The potential of HD-RNAi is not restricted to parasitic nematodes but could be adapted to control other plant-feeding pests.
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Affiliation(s)
- David J Fairbairn
- Department of Botany, School of Integrative Biology, University of Queensland, Brisbane, QLD 4072, Australia
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23
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Gutierrez A, Sommer RJ. Functional diversification of the nematode mbd2/3 gene between Pristionchus pacificus and Caenorhabditis elegans. BMC Genet 2007; 8:57. [PMID: 17725827 PMCID: PMC2000911 DOI: 10.1186/1471-2156-8-57] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2007] [Accepted: 08/28/2007] [Indexed: 01/10/2023] Open
Abstract
Background Several members of the Methyl-Binding Domain protein family link DNA methylation with chromatin remodeling complexes in vertebrates. Amongst the four classes of MBD proteins, MBD2/3 is the most highly conserved and widespread in metazoans. We have previously reported that an mbd2/3 like gene (mbd-2) is encoded in the genomes of the nematodes Pristionchus pacificus, Caenorhabditis elegans and Caenorhabditis briggsae. RNAi knock-down of mbd-2 in the two Caenorhabditis species results in varying percentages of lethality. Results Here, we report that a general feature of nematode MBD2/3 proteins seems to be the lack of a bona fide methyl-binding domain. We isolated a null allele of mbd-2 in P. pacificus and show that Ppa-mbd-2 mutants are viable, fertile and display a fully penetrant egg laying defect. This egg laying defect is partially rescued by treatment with acetylcholine or nicotine suggesting a specific function of this protein in vulval neurons. Using Yeast-two-hybrid screens, Ppa-MBD-2 was found to associate with microtubule interacting and vesicle transfer proteins. Conclusion These results imply that MBD2/3 proteins in nematodes are more variable than their relatives in insects and vertebrates both in structure and function. Moreover, nematode MBD2/3 proteins assume functions independent of DNA methylation ranging from the indispensable to the non-essential.
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Affiliation(s)
- Arturo Gutierrez
- Max-Planck Institute for Developmental Biology, Department for Evolutionary Biology, Spemannstrasse 37, D-72076 Tübingen, Germany
| | - Ralf J Sommer
- Max-Planck Institute for Developmental Biology, Department for Evolutionary Biology, Spemannstrasse 37, D-72076 Tübingen, Germany
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24
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Abstract
Four species in the ELEGANS group of subgenus the Caenorhabditis are distinguished by two very different mating systems: androdioecy in C. elegans and Caenorhabditis briggsae with males and self-fertilizing hermaphrodites and dioecy in Caenorhabditis remanei and Caenorhabditis sp. strain CB5161 with males and females. Using chemotaxis assays, we demonstrate that females secrete a potent sex pheromone that attracts males from a distance, whereas hermaphrodites do not. The female sex pheromone is not species-specific, with males of all four species attracted to both the C. remanei and Caenorhabditis sp. female sex pheromones. The pheromone is, however, sex-specific, with only females secreting the pheromone and attracting only males. Furthermore, the sex pheromone is stage-specific, with female secretion and male detection of the pheromone beginning near adulthood. Females lose their attractiveness immediately after mating but regain it several hours after mating ceases. Finally, the female somatic gonad is required for sex-pheromone production, and the male-specific cephalic neurons (CEM) are required for male response.
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Affiliation(s)
- J. R. Chasnov
- Departments of *Mathematics and
- To whom correspondence may be addressed. E-mail: or
| | - W. K. So
- Biology, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - C. M. Chan
- Biology, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - K. L. Chow
- Biology, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- To whom correspondence may be addressed. E-mail: or
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25
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Alkharouf NW, Klink VP, Matthews BF. Identification of Heterodera glycines (soybean cyst nematode [SCN]) cDNA sequences with high identity to those of Caenorhabditis elegans having lethal mutant or RNAi phenotypes. Exp Parasitol 2007; 115:247-58. [PMID: 17052709 DOI: 10.1016/j.exppara.2006.09.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2006] [Revised: 09/05/2006] [Accepted: 09/06/2006] [Indexed: 10/24/2022]
Abstract
The soybean cyst nematode (SCN; Heterodera glycines) is a devastating obligate parasite of Glycine max (soybean) causing one billion dollars in losses to the US economy per year and over ten billion dollars in losses worldwide. While much is understood about the pathology of H. glycines, its genome sequence is not well characterized or fully sequenced. We sought to create bioinformatic tools to mine the H. glycines nucleotide database. One way is to use a comparative genomics approach by anchoring our analysis with an organism, like the free-living nematode Caenorhabditis elegans. Unlike H. glycines, the C. elegans genome is fully sequenced and is well characterized with a number of lethal genes identified through experimental methods. We compared an EST database of H. glycines with the C. elegans genome. Our goal was identifying genes that may be essential for H. glycines survival and would serve as an automated pipeline for RNAi studies to both study and control H. glycines. Our analysis yielded a total of nearly 8334 conserved genes between H. glycines and C. elegans. Of these, 1508 have lethal phenotypes/phenocopies in C. elegans. RNAi of a conserved ribosomal gene from H. glycines (Hg-rps-23) yielded dead and dying worms as shown by positive Sytox fluorescence. Endogenous Hg-rps-23 exhibited typical RNA silencing as shown by RT-PCR. However, an unrelated gene Hg-unc-87 did not exhibit RNA silencing in the Hg-rps-23 dsRNA-treated worms, demonstrating the specificity of the silencing.
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Affiliation(s)
- Nadim W Alkharouf
- United States Department of Agriculture, ARS, Soybean Genomics and Improvement Laboratory, Beltsville, MD 20705-2350, USA
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26
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Schmitz C, Kinge P, Hutter H. Axon guidance genes identified in a large-scale RNAi screen using the RNAi-hypersensitive Caenorhabditis elegans strain nre-1(hd20) lin-15b(hd126). Proc Natl Acad Sci U S A 2007; 104:834-9. [PMID: 17213328 PMCID: PMC1783400 DOI: 10.1073/pnas.0510527104] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The navigation of axons toward their targets is a highly dynamic and precisely regulated process during nervous system development. The molecular basis of this navigation process is only partly understood. In Caenorhabditis elegans, we isolated the RNAi-hypersensitive strain nre-1(hd20) lin-15b(hd126), which allows us to phenocopy axon guidance defects of known genes by feeding RNAi. We used this mutant strain to systematically screen 4,577 genes on chromosomes I and III for axon guidance phenotypes. We identified 93 genes whose down-regulation led to penetrant ventral cord fasciculation defects or motoneuron commissure outgrowth defects. These genes encode various classes of proteins, ranging from secreted or putative cell surface proteins to transcription factors controlling gene expression. A majority of the genes is evolutionary conserved and previously uncharacterized. In addition, we found axon guidance functions for known genes like pry-1, a component of the Wnt-signaling pathway, and ced-1, a receptor required for the engulfment of neurons undergoing apoptosis during development. Our screen provides insights into molecular pathways operating during the generation of neuronal circuits and provides a basis for a more detailed analysis of gene networks regulating axon navigation.
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Affiliation(s)
- Caroline Schmitz
- Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Parag Kinge
- Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Harald Hutter
- Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
- To whom correspondence should be addressed at the present address:
Simon Fraser University, Burnaby, BC, Canada V5A 1S6. E-mail:
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27
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Herrmann M, Mayer WE, Sommer RJ. Nematodes of the genus Pristionchus are closely associated with scarab beetles and the Colorado potato beetle in Western Europe. ZOOLOGY 2006; 109:96-108. [PMID: 16616467 DOI: 10.1016/j.zool.2006.03.001] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2005] [Revised: 12/22/2005] [Accepted: 01/27/2006] [Indexed: 11/26/2022]
Abstract
Evolutionary developmental biology examines how changes in developmental programmes give rise to developmental and, ultimately, morphological novelty. To this end, comparisons of related but distinct organisms have to be performed. The diplogastrid nematode Pristionchus pacificus has been developed as a satellite system for a detailed comparison of various developmental processes to the model organism Caenorhabditis elegans, a rhabditid nematode. In addition to developmental and genetic studies, a genomic platform has been established to analyse the biology of this organism. However, only little is known about where and how Pristionchus pacificus and its relatives live in the wild. Here we show that nematodes of the genus Pristionchus live in close association with scarabaeoid beetles and the Colorado potato beetle. In total, we generated 371 isogenic female lines from 4242 beetles collected at 25 sampling sites all over Europe. Isogenic female lines were subjected to sequence analysis and mating experiments for species determination. The 371 isolates fell into six species. Two hermaphroditic species account for about 60% of the collected nematodes. We found Pristionchus maupasi almost exclusively on cockchafers and Pristionchus entomophagus predominantly on dung beetles. Colorado potato beetles carried the gonochoristic species Pristionchus uniformis, which was only rarely observed on scarabaeoid beetles. We describe the initial evidence for the association of Pristionchus nematodes with beetles and provide a phylogeny based on sequence analysis of the small subunit ribosomal RNA gene.
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Affiliation(s)
- Matthias Herrmann
- Max Planck Institute for Developmental Biology, Department of Evolutionary Biology, Spemannstrasse 37-39, D-72076 Tübingen, Germany
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28
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Ning F, Delhomme D, LeCun Y, Piano F, Bottou L, Barbano PE. Toward automatic phenotyping of developing embryos from videos. IEEE Trans Image Process 2005; 14:1360-71. [PMID: 16190471 DOI: 10.1109/tip.2005.852470] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We describe a trainable system for analyzing videos of developing C. elegans embryos. The system automatically detects, segments, and locates cells and nuclei in microscopic images. The system was designed as the central component of a fully automated phenotyping system. The system contains three modules 1) a convolutional network trained to classify each pixel into five categories: cell wall, cytoplasm, nucleus membrane, nucleus, outside medium; 2) an energy-based model, which cleans up the output of the convolutional network by learning local consistency constraints that must be satisfied by label images; 3) a set of elastic models of the embryo at various stages of development that are matched to the label images.
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Affiliation(s)
- Feng Ning
- Courant Institute of Mathematical Sciences, New York University, New York, NY 10003, USA.
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29
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Abstract
The most extensive phylogenetic analysis carried out to date, including 11 complete genomes, is shown to support the Ecdysozoa hypothesis in the open-ended debate of the Coelomata-Ecdysozoa evolutionary problem. Background The issue of whether coelomates form a single clade, the Coelomata, or whether all animals that moult an exoskeleton (such as the coelomate arthropods and the pseudocoelomate nematodes) form a distinct clade, the Ecdysozoa, is the most puzzling issue in animal systematics and a major open-ended subject in evolutionary biology. Previous single-gene and genome-scale analyses designed to resolve the issue have produced contradictory results. Here we present the first genome-scale phylogenetic evidence that strongly supports the Ecdysozoa hypothesis. Results Through the most extensive phylogenetic analysis carried out to date, the complete genomes of 11 eukaryotic species have been analyzed in order to find homologous sequences derived from 18 human chromosomes. Phylogenetic analysis of datasets showing an increased adjustment to equal evolutionary rates between nematode and arthropod sequences produced a gradual change from support for Coelomata to support for Ecdysozoa. Transition between topologies occurred when fast-evolving sequences of Caenorhabditis elegans were removed. When chordate, nematode and arthropod sequences were constrained to fit equal evolutionary rates, the Ecdysozoa topology was statistically accepted whereas Coelomata was rejected. Conclusions The reliability of a monophyletic group clustering arthropods and nematodes was unequivocally accepted in datasets where traces of the long-branch attraction effect were removed. This is the first phylogenomic evidence to strongly support the 'moulting clade' hypothesis.
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Affiliation(s)
- Hernán Dopazo
- Pharmacogenomics and Comparative Genomics Unit, Bioinformatics Department, Centro de Investigación Príncipe Felipe, Autopista del Saler 16, 46013 Valencia, Spain
| | - Joaquín Dopazo
- Functional Genomics Unit, Bioinformatics Department, Centro de Investigación Príncipe Felipe, Autopista del Saler 16, 46013 Valencia, Spain
- Functional Genomics Node, INB, Centro de Investigación Príncipe Felipe, Autopista del Saler 16, 46013 Valencia, Spain
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30
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Lee EY, Shim YH, Chitwood DJ, Hwang SB, Lee J, Paik YK. Cholesterol-producing transgenic Caenorhabditis elegans lives longer due to newly acquired enhanced stress resistance. Biochem Biophys Res Commun 2005; 328:929-36. [PMID: 15707967 DOI: 10.1016/j.bbrc.2005.01.050] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2004] [Indexed: 10/25/2022]
Abstract
Because Caenorhabditis elegans lacks several components of the de novo sterol biosynthetic pathway, it requires sterol as an essential nutrient. Supplemented cholesterol undergoes extensive enzymatic modification in C. elegans to form other sterols of unknown function. 7-Dehydrocholesterol reductase (DHCR) catalyzes the reduction of the Delta7 double bond of sterols and is suspected to be defective in C. elegans, in which the major endogenous sterol is 7-dehydrocholesterol (7DHC). We microinjected a human DHCR expression vector into C. elegans, which was then incorporated into chromosome by gamma-radiation. This transgenic C. elegans was named cholegans, i.e., cholesterol-producing C. elegans, because it was able to convert 7DHC into cholesterol. We investigated the effects of changes in sterol composition on longevity and stress resistance by examining brood size, mean life span, UV resistance, and thermotolerance. Cholegans contained 80% more cholesterol than the wild-type control. The brood size of cholegans was reduced by 40% compared to the wild-type control, although the growth rate was not significantly changed. The mean life span of cholegans was increased up to 131% in sterol-deficient medium as compared to wild-type. The biochemical basis for life span extension of cholegans appears to partly result from its acquired resistance against both UV irradiation and thermal stress.
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Affiliation(s)
- Eun-Young Lee
- Department of Biochemistry, Bioproducts Research Center and Yonsei Proteome Research Center, Yonsei University, 134 Shinchon-dong, Sudaemoon-ku, Seoul 120-749, Republic of Korea
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31
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Gutierrez A, Sommer RJ. Evolution of dnmt-2 and mbd-2-like genes in the free-living nematodes Pristionchus pacificus, Caenorhabditis elegans and Caenorhabditis briggsae. Nucleic Acids Res 2004; 32:6388-96. [PMID: 15576683 PMCID: PMC535690 DOI: 10.1093/nar/gkh982] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Whole genome sequencing of several metazoan model organisms provides a platform for studying genome evolution. How representative are the genomes of these model organisms for their respective phyla? Within nematodes, for example, the free-living soil nematode Caenorhabditis elegans is a highly derived species with unusual genomic characters, such as a reduced Hox cluster (Curr. Biol., 13, 37-40) and the absence of a Hedgehog signaling system. Here, we describe the recent loss of a DNA methyltransferase-2 gene (dnmt-2) in C.elegans. A dnmt-2-like gene is present in the satellite model organism Pristionchus pacificus, another free-living nematode that diverged from C.elegans 200-300 million years ago. In contrast, C.elegans, Caenorhabditis briggsae and P.pacificus all contain an mbd-2-like gene, which encodes another essential component of the methylation system of higher animals and fungi. Cel-mbd-2 is expressed throughout development and RNA interference (RNAi) experiments result in variable phenotypes. In contrast, Cbr-mbd-2 RNAi results in paralyzed larval or adult worms suggesting recent changes of gene function within the genus Caenorhabditis. We speculate that both genes were part of an ancestral DNA methylation system in nematodes and that gene loss and sequence divergence have abolished DNA methylation in C.elegans.
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Affiliation(s)
- Arturo Gutierrez
- Max-Planck-Institut für Entwicklungsbiologie, Abteilung Evolutionsbiologie, Spemannstrasse 37-39, D-72076 Tübingen, Germany
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32
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Abstract
This paper presents a method for automatic tracking of the head, tail, and entire body movement of the nematode Caenorhabditis elegans (C. elegans) using computer vision and digital image analysis techniques. The characteristics of the worm's movement, posture and texture information were extracted from a 5-min image sequence. A Random Forests classifier was then used to identify the worm type, and the features that best describe the data. A total of 1597 individual worm video sequences, representing wild type and 15 different mutant types, were analyzed. The average correct classification ratio, measured by out-of-bag (OOB) error rate, was 90.9%. The features that have most discrimination ability were also studied. The algorithm developed will be an essential part of a completely automated C. elegans tracking and identification system.
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Affiliation(s)
- Wei Geng
- Department of Electrical and Computer Engineering, University of California at San Diego, La Jolla, CA 92093-0407, USA.
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33
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Ami D, Natalello A, Zullini A, Doglia SM. Fourier transform infrared microspectroscopy as a new tool for nematode studies. FEBS Lett 2004; 576:297-300. [PMID: 15498551 DOI: 10.1016/j.febslet.2004.09.022] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2004] [Revised: 08/04/2004] [Accepted: 09/06/2004] [Indexed: 10/26/2022]
Abstract
We report the results of a microspectroscopy study on the Fourier transform infrared (FT-IR) absorption spectra of Caenorhabditis elegans, collected from the different parts of a single intact specimen--pharynx, intestine and tail regions. The principal absorption bands were assigned to the molecular species present in C. elegans, with an excellent reproducibility for the pharynx spectrum. These results enabled us to explore if FT-IR microspectroscopy could offer a new tool for nematode identification. As an example, the discrimination among four well characterised nematode taxa is reported. The FT-IR results completely match those obtained by Blaxter and colleagues through molecular biology [Nature 392 (1998) 71].
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Affiliation(s)
- Diletta Ami
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
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34
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Abstract
Protein kinases play a crucial role in the regulation of cellular functions. Various kinds of information about these molecules are important for understanding signaling pathways and organism characteristics. We have developed the Kinase Pathway Database, an integrated database involving major completely sequenced eukaryotes. It contains the classification of protein kinases and their functional conservation, ortholog tables among species, protein-protein, protein-gene, and protein-compound interaction data, domain information, and structural information. It also provides an automatic pathway graphic image interface. The protein, gene, and compound interactions are automatically extracted from abstracts for all genes and proteins by natural-language processing (NLP). The method of automatic extraction uses phrase patterns and the GENA protein, gene, and compound name dictionary, which was developed by our group. With this database, pathways are easily compared among species using data with more than 47,000 protein interactions and protein kinase ortholog tables. The database is available for querying and browsing at http://kinasedb.ontology.ims.u-tokyo.ac.jp/.
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Affiliation(s)
- Asako Koike
- Human Genome Center, Institute of Medical Science, University of Tokyo, Shirokane-dai, Minato-Ku, Tokyo 108-8639, Japan
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35
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Abstract
This study establishes a phylogenetic framework for the natural geographic isolates of the widely studied nematode species Caenorhabditis elegans. Virtually complete mitochondrial genomes are sequenced from 27 C. elegans natural isolates to characterize mitochondrial divergence patterns and to investigate the evolutionary history of the C. elegans hermaphrodite lineages. Phylogenetic analysis of mitochondrial sequences reveals the presence of two major C. elegans hermaphrodite clades (designated clade I and clade II). Fifty-six nuclear loci, widely distributed across the five autosomes and the X chromosome, are also analyzed in a subset of the C. elegans isolates to evaluate nuclear divergence patterns and the extent of mating between different strains. A comparison of the phylogenetic tree derived from mitochondrial data with the phylogenetic tree derived from nuclear data reveals only one inconsistency in the distribution of isolates into clades I and II, suggesting that mating between divergent C. elegans strains is an infrequent event in the wild.
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Affiliation(s)
- Dee R Denver
- Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri, USA.
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36
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Abstract
Sperm morphology evolves rapidly, resulting in an exceptional diversity of sperm size and shape across animal phyla. This swift evolution has been thought to prevent fertilizations between closely related species. Alternatively, recent correlative analyses suggest that competition among sperm from more than one male may cause sperm diversity, but these hypotheses have not been tested. Here, we test experimentally the effect of sperm competition on sperm-size evolution using the nematode Caenorhabditis elegans. This worm has a three day generation time, which allowed the study to cover many generations. Sperm volume increased nearly 20% over 60 generations in lines genetically induced to have high levels of sperm competition compared with those of control lines. These results show that sperm competition can and does cause morphological evolution of sperm and, therefore, can explain much of the diversity in sperm morphology.
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Affiliation(s)
- Craig W LaMunyon
- Division of Biological Sciences, Florida Atlantic University, Davie 33314, USA.
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37
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Abstract
BACKGROUND The complete genomes of three animals have been sequenced by global research efforts: a nematode worm (Caenorhabditis elegans), an insect (Drosophila melanogaster), and a vertebrate (Homo sapiens). Remarkably, their relationships have yet to be clarified. The confusion concerns the enigmatic position of nematodes. Traditionally, nematodes have occupied a basal position, in part because they lack a true body cavity. However, the leading hypothesis now joins nematodes with arthropods in a molting clade, Ecdysozoa, based on data from several genes. RESULTS We tested the Ecdysozoa hypothesis with analyses of more than 100 nuclear protein alignments, under conditions that would expose biases, and found that it was not supported. Instead, we found significant support for the traditional hypothesis, Coelomata. Our result is robust to different rates of sequence change among genes and lineages, different numbers of taxa, and different species of nematodes. CONCLUSION We conclude that insects (arthropods) are genetically and evolutionarily closer to humans than to nematode worms.
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Affiliation(s)
- Jaime E Blair
- Astrobiology Research Center and Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kazuho Ikeo
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka-ken 411-8540, Japan
| | - Takashi Gojobori
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka-ken 411-8540, Japan
| | - S Blair Hedges
- Astrobiology Research Center and Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
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38
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Abstract
The organism about which most is known on a molecular level is a nematode, the free-living organism Caenorhabditis elegans. This organism has served as a reasonable model for the discovery of anthelmintic drugs and for research on the mechanism of action of anthelmintics. Useful information on mechanisms of anthelmintic resistance has also been obtained from studies on C. elegans. Unfortunately, there has not been a large-scale extension of genetic techniques developed in C. elegans to research on parasitic species of veterinary (or human) parasites. Much can be learned about the essentials of nematode biology by studying C. elegans, but discovering the basic biology of nematode parasitism can only be gained through comparative studies on multiple parasitic species.
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Affiliation(s)
- T G Geary
- Discovery Research, Pharmacia Animal Health, 7923-25-111, 7000 Portage Road, Kalamazoo, MI 49001-0199, USA.
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39
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Abstract
Much life-history theory assumes that alleles segregating in natural populations pleiotropically affect life-history traits. This assumption, while plausible, has rarely been tested directly. Here we investigate the genetic relationship between two traits often suggested to be connected by pleiotropy: maternal body size and fertility. We carry out a quantitative trait locus (QTL) analysis on two isolates of the free-living nematode Caenorhabditis elegans, and identify two body size and three fertility QTLs. We find that one of the fertility QTLs colocalizes with the two body size QTLs on Chromosome IV. Further analysis, however, shows that these QTLs are genetically separable. Thus, none of the five body size or fertility QTLs identified here shows detectable pleiotropy for the assayed traits. The evolutionary origin of these QTLs, possible candidate loci, and the significance for life-history evolution are discussed.
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Affiliation(s)
- C G Knight
- Department of Biology, Imperial College at Silwood Park, Ascot, Berkshire, United Kingdom
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40
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Abstract
Recent studies have introduced Oscheius sp. CEW1 as a third nematode species accessible to genetic analysis, joining the better known Caenorhabditis elegans and Pristionchus pacificus. A group of vulva-defective mutants in Oscheius has been identified, with defects not seen in C. elegans.
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Affiliation(s)
- R J Sommer
- Max-Planck Institute for Developmental Biology, Abteilung für Evolutionsbiologie, Spemannstrasse 37-39, D-72076,., Tübingen, Germany.
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41
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Abstract
The Caenorhabditis elegans genome sequence was surveyed for transcription factor and signaling gene families that have been shown to regulate development in a variety of species. About 10 to 25 percent of the genes in most of the gene families already have been genetically analyzed in C. elegans, about half of the genes detect probable orthologs in other species, and about 10 to 25 percent of the genes are, at present, unique to C. elegans. Caenorhabditis elegans is also missing genes that are found in vertebrates and other invertebrates. Thus the genome sequence reveals universals in developmental control that are the legacy of metazoan complexity before the Cambrian explosion, as well as genes that have been more recently invented or lost in particular phylogenetic lineages.
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Affiliation(s)
- G Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Department of Genetics, Harvard Medical School, Boston, MA 02114, USA.
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42
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Abstract
Caenorhabditis elegans is a rhabditid nematode. What relevance does this have for the interpretation of the complete genome sequence, and how will it affect the exploitation of the sequence for scientific and social ends? Nematodes are only distantly related to humans and other animal groups; will this limit the universality of the C. elegans story? Many nematodes are parasites; can knowledge of the C. elegans sequence aid in the prevention and treatment of disease?
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Affiliation(s)
- M Blaxter
- Institute of Cell, Animal, and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, UK
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43
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Blaxter ML, De Ley P, Garey JR, Liu LX, Scheldeman P, Vierstraete A, Vanfleteren JR, Mackey LY, Dorris M, Frisse LM, Vida JT, Thomas WK. A molecular evolutionary framework for the phylum Nematoda. Nature 1998; 392:71-5. [PMID: 9510248 DOI: 10.1038/32160] [Citation(s) in RCA: 1117] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nematodes are important: parasitic nematodes threaten the health of plants, animals and humans on a global scale; interstitial nematodes pervade sediment and soil ecosystems in overwhelming numbers; and Caenorhabditis elegans is a favourite experimental model system. A lack of clearly homologous characters and the absence of an informative fossil record have prevented us from deriving a consistent evolutionary framework for the phylum. Here we present a phylogenetic analysis, using 53 small subunit ribosomal DNA sequences from a wide range of nematodes. With this analysis, we can compare animal-parasitic, plant-parasitic and free-living taxa using a common measurement. Our results indicate that convergent morphological evolution may be extensive and that present higher-level classification of the Nematoda will need revision. We identify five major clades within the phylum, all of which include parasitic species. We suggest that animal parasitism arose independently at least four times, and plant parasitism three times. We clarify the relationship of C. elegans to major parasitic groups; this will allow more effective exploitation of our genetic and biological knowledge of this model species.
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Affiliation(s)
- M L Blaxter
- Institute of Cell, Animal and Population Biology, University of Edinburgh, UK.
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Baldwin JG, Frisse LM, Vida JT, Eddleman CD, Thomas WK. An evolutionary framework for the study of developmental evolution in a set of nematodes related to Caenorhabditis elegans. Mol Phylogenet Evol 1997; 8:249-59. [PMID: 9299229 DOI: 10.1006/mpev.1997.0433] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Nematodes are known to be a useful system for studies of comparative development. Here we perform a molecular phylogenetic analysis to allow for the independent interpretation of the developmental and morphological changes observed among a selected set of nematode species. Our molecular phylogenetic analysis is based on coding regions of the genes for RNA polymerase II, the small subunit rRNA and an expansion segment of the large subunit rRNA. Sequences were compared from five species in the family (Rhabditidae) that includes the developmental model organism Caenorhabditis elegans and from an outgroup taxon Aduncospiculum halicti (Diplogasterina). The phylogenetic analysis does not support the monophyly of the subfamily Mesorhabditinae and identifies the unnamed strain PS1010 as a sister taxon of C. elegans despite its morphologically divergent buccal capsule. On the basis of the inferred framework, we can begin to interpret the evolution of vulval development and of morphological differences among these nematode species.
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Affiliation(s)
- J G Baldwin
- Department of Nematology, University of California, Riverside, California 92521, USA
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Abstract
In vertebrate visual and olfactory systems, a cyclic nucleotide-gated channel couples receptor activation to electrical activity of the sensory neurons. The Caenorhabditis elegans tax-2 gene is required for some forms of olfaction, for chemosensation of salts, and for thermosensation. We show here that tax-2 encodes a predicted subunit of a cyclic nucleotide-gated channel that is expressed in olfactory, gustatory, and thermosensory neurons, implicating this channel in multiple sensory modalities. Some sensory neurons display axon outgrowth defects in tax-2 mutants. Thus, the channel has an unexpected role in sensory neuron development in addition to its role in sensation. Consistent with this proposed dual function, a Tax-2::GFP fusion protein is present both in sensory cilia and in sensory axons.
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Affiliation(s)
- C M Coburn
- Howard Hughes Medical Institute, Department of Anatomy, The University of California, San Francisco 94143-0452, USA
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Abstract
Methods are described for culturing large populations of age-synchronous Caenorhabditis elegans throughout the adult life span. Contamination of adult populations by progeny was prevented by constructing double-mutant strains that produce progeny at a frequency of less than .005 per adult at the nonpermissive temperature (25.5 degrees C). Of four double-mutant strains that we have characterized, three have wild-type life spans at 25.5 degrees. The other strain contains a mutant allele, age-1(hx542), that results in an increase in life span of 60% over wild type. All four strains produced sufficient numbers of progeny at the permissive temperature (20 degrees C) to generate populations containing 1-5 x 10(6) nematodes within two weeks. Age-synchronous young adult populations were produced using these strains and have been maintained as adults both in liquid culture and on agar medium. Procedures that reduce E. coli contamination by 30-fold in harvested samples of adults are also described.
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Affiliation(s)
- T J Fabian
- Institute for Behavioral Genetics, University of Colorado, Boulder
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