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C. elegans - A tribute to the legendary worm
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C. elegans - A tribute to the legendary worm

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (30 September 2019)

Special Issue Editor

Dr. Patrícia Maciel

E-Mail Website
Guest Editor
School of Medicine, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
Interests: neurogenetics; neurodegeneration; neurodevelopment
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue aims to illustrate the key scientific contributions of research teams worldwide using the nematode C. elegans as a model. This small, transparent animal has been the focus of attention of many researchers and enabled major advancements in the fields of cell biology, development, neurobiology, aging, metabolism, and gene expression regulation, among others, the relevance of which is highlighted by the three Nobel prizes awarded to date concerning C. elegans-based biological discoveries. More recently, this model organism has served as a platform for drug discovery. The review articles included in this Special Issue will provide an overview of developments to date in each field, in addition to the main challenges and emerging possibilities for future research.

Dr. Patrícia Maciel
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • model organism
  • nematode
  • cell biology
  • genetics
  • epigenetics
  • metabolism
  • neuroscience
  • aging
  • drug discovery
  • screening

Published Papers (2 papers)

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13 pages, 1728 KiB  
Article
Transcriptomic Profiling of DAF-7/TGFβ Pathway Mutants in C. elegans
by Muhan Hu, David Crossman, Jeevan K. Prasain, Michael A. Miller and Rosa A. Serra
Genes 2020, 11(3), 288; https://doi.org/10.3390/genes11030288 - 09 Mar 2020
Cited by 6 | Viewed by 3106
Abstract
The transforming growth factor beta superfamily encompasses a large family of ligands that are well conserved across many organisms. They are regulators of a number of physiological and pathological processes. The model nematode Caenorhabditis elegans has been instrumental in identifying key components of [...] Read more.
The transforming growth factor beta superfamily encompasses a large family of ligands that are well conserved across many organisms. They are regulators of a number of physiological and pathological processes. The model nematode Caenorhabditis elegans has been instrumental in identifying key components of the transforming growth factor beta (TGFβ) pathway. In C. elegans, the TGFβ homolog DAF-7 signals through the DAF-1 Type I and DAF-4 Type II receptors to phosphorylate downstream R-SMADs DAF-8 and DAF-14. These R-SMADs translocate into the nucleus to inhibit Co-SMAD DAF-3. Many of the roles of the canonical DAF-7 pathway, involving both DAF-1 and DAF-3, have been identified using targeted genetic studies. Few have assessed the global transcriptomic changes in response to these genes, especially in adult animals. In this study, we performed RNA sequencing on wild type, daf-1, and daf-1; daf-3 adult hermaphrodites. To assess the overall trends of the data, we identified differentially expressed genes (DEGs) and performed gene ontology analysis to identify the types of downstream genes that are differentially expressed. Hierarchical clustering showed that the daf-1; daf-3 double mutants are transcriptionally more similar to wild type than daf-1 mutants. Analysis of the DEGs showed a disproportionally high number of genes whose expression is increased in daf-1 mutants, suggesting that DAF-1 acts as a general repressor of gene expression in wild type animals. Gene ontology analysis of the DEGs produced many significantly enriched terms, including Molting Cycle, Response to Topologically Incorrect Protein, and Response to Biotic Stimulus. Understanding the direct and indirect targets of the DAF-7 TGFβ pathway through this RNA-seq dataset can provide insight into novel roles of the multifunctional signaling pathway, as well as identify novel genes that may participate in previously reported functions of TGFβ signaling. Full article
(This article belongs to the Special Issue C. elegans - A tribute to the legendary worm)
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23 pages, 7028 KiB  
Article
Genomic Analyses Identify Novel Molecular Signatures Specific for the Caenorhabditis and other Nematode Taxa Providing Novel Means for Genetic and Biochemical Studies
by Bijendra Khadka, Tonuka Chatterjee, Bhagwati P. Gupta and Radhey S. Gupta
Genes 2019, 10(10), 739; https://doi.org/10.3390/genes10100739 - 24 Sep 2019
Cited by 2 | Viewed by 3275
Abstract
The phylum Nematoda encompasses numerous free-living as well as parasitic members, including the widely used animal model Caenorhabditis elegans, with significant impact on human health, agriculture, and environment. In view of the importance of nematodes, it is of much interest to identify [...] Read more.
The phylum Nematoda encompasses numerous free-living as well as parasitic members, including the widely used animal model Caenorhabditis elegans, with significant impact on human health, agriculture, and environment. In view of the importance of nematodes, it is of much interest to identify novel molecular characteristics that are distinctive features of this phylum, or specific taxonomic groups/clades within it, thereby providing innovative means for diagnostics as well as genetic and biochemical studies. Using genome sequences for 52 available nematodes, a robust phylogenetic tree was constructed based on concatenated sequences of 17 conserved proteins. The branching of species in this tree provides important insights into the evolutionary relationships among the studied nematode species. In parallel, detailed comparative analyses on protein sequences from nematodes (Caenorhabditis) species reported here have identified 52 novel molecular signatures (or synapomorphies) consisting of conserved signature indels (CSIs) in different proteins, which are uniquely shared by the homologs from either all genome-sequenced Caenorhabditis species or a number of higher taxonomic clades of nematodes encompassing this genus. Of these molecular signatures, 39 CSIs in proteins involved in diverse functions are uniquely present in all Caenorhabditis species providing reliable means for distinguishing this group of nematodes in molecular terms. The remainder of the CSIs are specific for a number of higher clades of nematodes and offer important insights into the evolutionary relationships among these species. The structural locations of some of the nematodes-specific CSIs were also mapped in the structural models of the corresponding proteins. All of the studied CSIs are localized within the surface-exposed loops of the proteins suggesting that they may potentially be involved in mediating novel protein–protein or protein–ligand interactions, which are specific for these groups of nematodes. The identified CSIs, due to their exclusivity for the indicated groups, provide reliable means for the identification of species within these nematodes groups in molecular terms. Further, due to the predicted roles of these CSIs in cellular functions, they provide important tools for genetic and biochemical studies in Caenorhabditis and other nematodes. Full article
(This article belongs to the Special Issue C. elegans - A tribute to the legendary worm)
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