Bazant, Wojtek et al. (2019) International Worm Meeting "Exploring helminth gene expression data using WormBase ParaSite."

Bazant, Wojtek, Sternberg, Paul, Howe, Kevin, Berriman, Matthew, Rodgers, Faye, Le, Tuan

[International Worm Meeting, 2019]

WormBase ParaSite (http://parasite.wormbase.org) is a sister site to WormBase that aims to integrate, organise and present data for nearly all parasitic nematode and platyhelminth genomes. Five years on from the start of the project, we now include data for over 150 genomes, adding value by way of systematic and consistent functional annotation (e.g. protein domains and Gene Ontology terms), and comparative analysis (e.g. orthologues and paralogues). We provide several ways to explore the data, including genome and gene summary pages, text search, sequence search, a query wizard, bulk downloads, a choice of genome browsers, and a programmatic interface. We will describe recent updates to WormBase ParaSite. In particular, WBPS13 (released in spring 2019) includes a major update: a gene expression sub-portal. This has been underpinned by three key components of work: (a) curation of the majority of published helminth RNASeq studies, inferring the experimental design and standardising on sample labels and descriptions; (b) quantification of samples on a per-gene and per-transcript basis using a established tools; and (c) for selected studies, differential expression analysis. The results are made available via a number of new views in WormBase ParaSite, including a per-genome study explorer, and per-gene summaries of expression across all studies.

Paulini, Michael et al. (2019) International Worm Meeting "Supporting nematode research outside of Caenorhabditis."

Russel, Matthew, Williams, Gary, Paulini, Michael, Davis, Paul, Rodgers, Faye, Howe, Kevin

[International Worm Meeting, 2019]

WormBase (http://www.wormbase.org) is a central data repository for genetic and genomic data relating to C. elegans and other well studied nematodes. WormBase is also a founding member of the Alliance of Genome Resources (https://www.alliancegenome.org), an effort to align data representation and curation workflows between the major model organism databases (MODs). We will present an update on the curation of nematode genomes outside the Caenorhabditis genus, demonstrate how we use data-mining to add information from current and historical publications, and show examples of the use and benefit to the nematode community. The genome of Trichuris muris has been added by WormBase to act as a representative reference genome for Blaxter clade I group. WormBase have performed first-pass annotation of the genome and manual curation of selected gene structures, with the aim of helping with annotation efforts of closely related Trichuris species. We have also added an updated version of the Pristionchus pacificus genome. This represents the start of a formal collaboration between WormBase and pristionchus.org on the joint maintenance and curation of the reference annotation. Finally, the curation of the Brugia malayi genome is ongoing, and reference annotation provided by WormBase is being used by research groups to analyse the evolution of filarial nematodes and the diseases they cause.

Hart, Michael et al. (2015) International Worm Meeting "Age-related deterioration of neurons in male C. elegans."

Hart, Michael, Hobert, Oliver

[International Worm Meeting, 2015]

Aging neurons undergo changes in structural and functional integrity that result in neuronal dysfunction associated with both normal aging and neurodegenerative diseases. C. elegans provide a powerful model for studying the development of the nervous system, and have been instrumental in the study of pathways and processes involved in aging. Neurons in hermaphrodite C. elegans show mild morphological changes with increasing age, including neurite sprouting and branching, axon beading and defasciculation, and synapse deterioration (1, 2, 3). The nervous system of male C. elegans shares 294 neurons in common with hermaphrodites, but also contains 89 additional sex-specific neurons and a significantly more complex connectivity, resulting in the male-specific mating behavior (4). With these differences in mind, we analyzed aging male C. elegans for neuronal age-related changes. Using fluorescent neuronal reporters, we found that the posterior male nervous system can undergo dramatic age-related changes prior to death, including progressive axon denervation and degeneration, which is not seen in hermaphrodites. This male-specific neuronal degeneration occurs in different neuron types at different frequencies. We have identified neuron specification and signaling mutants that can rescue the age-related neuronal degeneration phenotype in males, independent of general tissue deterioration. We are currently testing the hypothesis that inherent excitability of the male-mating circuit may contribute to these male-specific age-related neuronal changes (5).1) Tank EM, Rodgers KE and Kenyon C. 2011, J. Neurosci 31(25):9279-9288. 2) Toth ML et al. 2012, J. Neurosci 32(26): 8778-8790. 3) Pan C-L et al. 2011, PNAS 108: 22 2010. 4) Jarrell TA et al. 2012, Science 337, 437. 5) Guo X et al. 2012, Neurobiol Aging 33(7):1483.