Article
Multidisciplinary Sciences
Bryan A. Martinez, Matthew S. Gill
Summary: We previously characterized a truncated isoform of the C. elegans insulin-like receptor, DAF-2B, which modifies insulin / insulin-like growth factor signaling-dependent processes and sequesters insulin-like peptides. In this study, we show that DAF-2B is also important for starvation resistance and enhances survival in starved first stage larvae. The expression of DAF-2B from the hypodermis promotes survival under starvation conditions.
Article
Multidisciplinary Sciences
Jadiel A. Wasson, Gareth Harris, Sabine Keppler-Ross, Trisha J. Brock, Abdul R. Dar, Rebecca A. Butcher, Sylvia E. J. Fischer, Konstantinos Kagias, Jon Clardy, Yun Zhang, Susan E. Mango
Summary: This study reveals that social cues can influence maternal provisioning to offspring in Caenorhabditis elegans through a neuron and neuropeptide. Parental FMRFamide-like peptide signaling affects offspring's oxidative stress resistance and gene silencing, indicating a previously unknown pathway for intergenerational communication. Loss of social cues in the parental environment is shown to stimulate stress responses across generations.
Article
Genetics & Heredity
Julia Wittes, Iva Greenwald
Summary: This study investigates the enzymatic activities of DAF-18/PTEN and their connection to specific phenotypes by analyzing missense mutants. The results show that transgenes expressing putative lipid phosphatase-deficient or putative protein phosphatase-deficient forms are unable to complement a daf-18 null allele. The endogenous missense mutant alleles also fail to maintain developmental quiescence and do not complement each other. Additionally, the homozygous missense mutants have a more severe phenotype than the null mutant. These findings complicate the interpretation of genetic assays to associate specific enzymatic activities with specific phenotypes.
G3-GENES GENOMES GENETICS
(2022)
Article
Environmental Sciences
Antoine Karengera, Cong Bao, Joost A. G. Riksen, H. Pieter J. van Veelen, Mark G. Sterken, Jan E. Kammenga, Albertinka J. Murk, Inez J. T. Dinkla
Summary: The study showed that exposure of Caenorhabditis elegans to hydrophilic compounds in water resulted in significantly altered gene transcription levels, potentially indicating toxicity risks of environmental contaminants. Different gene expression changes were observed for different genotoxicants, suggesting the potential of nematode gene expression profiling in uncovering mechanisms of chemical compound toxicity.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2021)
Article
Biochemistry & Molecular Biology
Gaotian Zhang, Ye Wang, Erik C. Andersen
Summary: This study provides a large-scale characterization of STR variation in wild C. elegans strains, revealing the association of STR diversity with genomic features, genetic divergence, and selection signatures. It also identifies background-dependent and fitness-dependent STR mutations, as well as the genome-wide association between STR variation and organismal phenotypic variation.
Article
Biochemistry & Molecular Biology
Gaotian Zhang, Erik C. Andersen
Summary: This study conducted a genome-wide analysis using expression and short tandem repeat (STR) variation data from wild Caenorhabditis elegans strains, and identified expression STRs (eSTRs) that have regulatory effects on gene expression variation. The study revealed specific regulatory mechanisms of eSTRs, such as their effects on splicing sites and alternative splicing efficiency. It also demonstrated that differential expression of antioxidant genes and oxidative stresses can contribute to higher mutation rates of STRs.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Infectious Diseases
Swarupa Mallick, Neha Mishra, Bedanta Kumar Barik, Vidya Devi Negi
Summary: This study aims to explore the development of C. elegans dauer larvae upon Salmonella Typhimurium infection and investigate the role of bacterial genes in regulating the worm's behavioral plasticity. The results revealed that the deletion of the fepB gene in the Salmonella strain reduced pathogenicity and bacterial burden in the worm's gut without damaging the pharynx. The fepB mutant strain enhanced the worm's immune responses and activated dauer signaling via the TGF-beta pathway, leading to increased dauer formation.
JOURNAL OF INFECTION
(2022)
Article
Genetics & Heredity
Travis Kyani-Rogers, Alison Philbrook, Ian G. McLachlan, Steven W. Flavell, Michael P. O'Donnell, Piali Sengupta
Summary: Developmental experiences play a critical role in shaping adult physiology and behavior. In the nematode Caenorhabditis elegans, transient dauer arrest during development affects gene expression profiles and chemoreceptor levels, leading to altered behavioral preferences in adult worms. Specifically, postdauer adults exhibit enhanced attraction to food-related attractive odorants, which is correlated with the upregulation of the diacetyl receptor ODR-10. This study suggests that developmental experiences can be encoded at the level of olfactory receptor regulation, allowing C. elegans to modulate its behavioral preferences based on current and past experiences.
Article
Microbiology
Hengzhi Shi, Xiaocui Huang, Xueqiu Chen, Yi Yang, Zhao Wang, Yimin Yang, Fei Wu, Jingru Zhou, Chaoqun Yao, Guangxu Ma, Aifang Du
Summary: Hypobiosis is a crucial life-cycle adaptation for parasitic nematodes to survive under adverse conditions. The gene acox-1 plays an essential role in the larval development of Haemonchus contortus, a parasitic nematode employing hypobiosis as a survival mechanism. Understanding the function of acox-1 and associated fatty acid oxidation provides insights into developmental regulation and potential intervention targets for parasitic nematodes of socioeconomic importance.
Article
Multidisciplinary Sciences
Sneha L. Koneru, Mark Hintze, Dimitris Katsanos, Michalis Barkoulas
Summary: This study addresses how genetic background modifies mutation expression, focusing on seam cell development in Caenorhabditis elegans isolates. It is demonstrated that a single amino acid deletion in a conserved heat shock protein HSP-110 in the CB4856 isolate can modify Wnt signaling and seam cell development, highlighting natural variation can shape phenotype expressivity.
NATURE COMMUNICATIONS
(2021)
Article
Cell Biology
Yujin Lee, Yoonji Jung, Dae-Eun Jeong, Wooseon Hwang, Seokjin Ham, Hae-Eun H. Park, Sujeong Kwon, Jasmine M. Ashraf, Coleen T. Murphy, Seung-Jae Lee
Summary: Genetic inhibition of the DAF-2/insulin/IGF-1 receptor in Caenorhabditis elegans can enhance immunocompetence in old age by up-regulating anti-aging transcription factors and preventing immune aging. This study may lead to the development of strategies against immune aging in humans, as many functions are conserved across phyla.
JOURNAL OF CELL BIOLOGY
(2021)
Article
Food Science & Technology
Yanan Wang, Jiachen Shi, Kun Liu, Yu Wang, Yongjiang Xu, Yuanfa Liu
Summary: This study investigated the effects of different edible oils on the aging process and lifespan of Caenorhabditis elegans. The results showed that teaseed oil (TO) could prolong lifespan and slow down aging by regulating lipid metabolism. Furthermore, there were significant differences in gene expression levels and metabolites between the control group and the TO group.
FOOD SCIENCE AND HUMAN WELLNESS
(2023)
Article
Multidisciplinary Sciences
Mercedes M. Perez-Jimenez, Jose M. Monje-Moreno, Ana Maria Brokate-Llanos, Monica Venegas-Caleron, Alicia Sanchez-Garcia, Paula Sansigre, Amador Valladares, Sara Esteban-Garcia, Irene Suarez-Pereira, Javier Vitorica, Jose Julian Rios, Marta Artal-Sanz, Angel M. Carrion, Manuel J. Munoz
Summary: The study demonstrates that loss of function of the steroid sulfatase sul-2 in Caenorhabditis elegans increases lifespan and ameliorates protein aggregation diseases, through mechanisms involving factors related to germline-mediated longevity. Sul-2 is predominantly expressed in sensory neurons, suggesting regulation by environmental cues.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Analytical
Seleipiri Charles, Guillaume Aubry, Han-Ting Chou, Annalise B. Paaby, Hang Lu
Summary: The article introduces a method for large-scale smFISH imaging using microfluidics to reduce labor intensity. By designing embryo traps and developing a protocol that allows for efficient chemical exchange of hundreds of C. elegans embryos simultaneously, the bottleneck of performing efficient reagent exchange on chip for large numbers of embryos is addressed. Additionally, the device design optimizes imaging throughput and allows for high-temporal-resolution studies, benefiting large-scale RNAi and drug screens beyond C. elegans embryos.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Sarah Clark, Hanbin Jeong, April Goehring, Yunsik Kang, Eric Gouaux
Summary: This study presents a detailed protocol for isolating membrane protein complexes from transgenic Caenorhabditis elegans. The genetically modified worms are grown abundantly using standard laboratory equipment, and purification conditions are optimized on a small scale using fluorescence-detection size-exclusion chromatography. The optimized conditions are then applied to a large-scale preparation, allowing for the purification of sufficient quantities of target proteins for structural, biochemical, and biophysical studies. The utility of this approach is demonstrated by successfully isolating membrane protein complexes from transgenic C. elegans.
Article
Multidisciplinary Sciences
Christopher M. Bellas, Declan C. Schroeder, Arwyn Edwards, Gary Barker, Alexandre M. Anesio
NATURE COMMUNICATIONS
(2020)
Article
Multidisciplinary Sciences
Mark Winfield, Amanda Burridge, Matthew Ordidge, Helen Harper, Paul Wilkinson, Danny Thorogood, Liz Copas, Keith Edwards, Gary Barker
Article
Biotechnology & Applied Microbiology
Sarah Raffan, Caroline Sparks, Alison Huttly, Lucy Hyde, Damiano Martignago, Andrew Mead, Steven J. Hanley, Paul A. Wilkinson, Gary Barker, Keith J. Edwards, Tanya Y. Curtis, Sarah Usher, Ondrej Kosik, Nigel G. Halford
Summary: This study successfully edited wheat lines using CRISPR/Cas9 technology to knock out the asparagine synthetase gene TaASN2, leading to a significant reduction in free asparagine concentration in the grain. These edits affected the concentrations of free asparagine, glutamine, glutamate, and aspartate in seeds across multiple generations.
PLANT BIOTECHNOLOGY JOURNAL
(2021)
Article
Multidisciplinary Sciences
Helen Harper, Amanda Burridge, Mark Winfield, Adam Finn, Andrew Davidson, David Matthews, Stephanie Hutchings, Barry Vipond, Nisha Jain, Keith Edwards, Gary Barker
Summary: This study introduces a SNP identification pipeline that identifies 15 distinct genotypes from 50 sequenced SARS-CoV-2 samples, demonstrating the feasibility of using a genotyping panel for rapid, cost-effective, and reliable monitoring of SARS-CoV-2 variants.
Article
Geography, Physical
Gilda Varliero, Alexandra Holland, Gary L. A. Barker, Marian L. Yallop, Andrew G. Fountain, Alexandre M. Anesio
Summary: The study reveals that microbial communities in glaciers are influenced by spatial distribution and ice type. Significant differences in microbial communities exist in different types of ice, with englacial channels possibly playing a crucial role in microbial dispersion within glaciers and the shaping of glacial microbial communities.
JOURNAL OF GLACIOLOGY
(2021)
Article
Multidisciplinary Sciences
Gilda Varliero, Jared Wray, Cedric Malandain, Gary Barker
Summary: Phylo-Primer is a user-friendly platform designed to semi-automate the design of taxon-specific oligos, which can help researchers accurately design PCR primers to increase oligo taxon-specificity. The software is capable of effectively designing primers for specific genes, as well as checking and validating predesigned primers.
Article
Microbiology
Gilda Varliero, Alexandre M. Anesio, Gary L. A. Barker
Summary: The microbial succession in three Arctic proglacial systems was studied, showing an increasing diversity trend along the forefield chronosequence. The microbial trends were influenced by the distance from the ice edge and total nitrogen and total organic carbon concentrations in the soil of the proglacial systems.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Environmental Sciences
L. L. R. de Miranda, K. E. Harvey, A. Ahmed, S. C. Harvey
Summary: UV-filters are widely used in cosmetics and personal care products to protect the skin, and also in industrial products like paints and plastics. They can enter aquatic environments and have potential effects on marine species and human health. Challenges include removal of UV-filters and researching more environmentally friendly alternatives.
ENVIRONMENTAL MONITORING AND ASSESSMENT
(2021)
Article
Reproductive Biology
Lucy May Vining, Louisa J. Zak, Simon Crawford Harvey, Katie Evelyn Harvey
Summary: Cryopreservation of gametes and embryos is crucial for assisted reproductive technology and livestock reproduction. Freezing procedures may induce cell apoptosis, and inhibiting apoptosis could improve cryosurvival.
Article
Plant Sciences
Amanda J. Burridge, Mark O. Winfield, Paul A. Wilkinson, Alexandra M. Przewieslik-Allen, Keith J. Edwards, Gary L. A. Barker
Summary: In this study, the bread wheat genome was analyzed using exome capture and sequencing techniques, revealing variable regions and potential undocumented introgressions.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Sarah Raffan, Joseph Oddy, Andrew Mead, Gary Barker, Tanya Curtis, Sarah Usher, Christopher Burt, Nigel G. Halford
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Microbiology
Gilda Varliero, Muhammad Rafiq, Swati Singh, Annabel Summerfield, Fotis Sgouridis, Don A. Cowan, Gary Barker
Summary: This study collected permafrost samples from southwest Greenland to create a Cold-Adapted Predicted Protein (CAPP) database with over three million predicted proteins, which can provide information for protein engineering of cold-adapted enzymes in the future.
FEMS MICROBIOLOGY ECOLOGY
(2021)
Article
Veterinary Sciences
Giuseppe Silvestri, Claudia C. Rathje, Simon C. Harvey, Rebecca L. Gould, Grant A. Walling, Peter J. I. Ellis, Katie E. Harvey, Darren K. Griffin
Summary: Grading oocytes based on cumulus investment is a reliable method to predict in vitro maturation (IVM) success, with Grade A and B oocytes showing similar developmental potential. Recovery of oocytes is maximized by using an 18-gauge needle and 50 mmHg aspiration pressure.
VETERINARY MEDICINE AND SCIENCE
(2021)
Article
Plant Sciences
Alexandra M. Przewieslik-Allen, Paul A. Wilkinson, Amanda J. Burridge, Mark O. Winfield, Xiaoyang Dai, Mark Beaumont, Julie King, Cai-yun Yang, Simon Griffiths, Luzie U. Wingen, Richard Horsnell, Alison R. Bentley, Peter Shewry, Gary L. A. Barker, Keith J. Edwards
Summary: Bread wheat relatives provide a valuable source of novel alleles for breeding new cultivars due to their considerable genetic variation. Gene flow from relatives appears to have made a major contribution to genetic diversity in cultivar collections through introgressions and chromosomal rearrangements.
Article
Mathematical & Computational Biology
Paul A. Wilkinson, Alexandra M. Allen, Simon Tyrrell, Luzie U. Wingen, Xingdong Bian, Mark O. Winfield, Amanda Burridge, Daniel S. Shaw, Jan Zaucha, Simon Griffiths, Robert P. Davey, Keith J. Edwards, Gary L. A. Barker
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2020)