Biology subjects

Stevens, L.

Publications and source records attributed to Stevens, L..

43 records · Page 3Linked to original sources

bioRxiv2019

The genome of Caenorhabditis bovis

The free-living nematode Caenorhabditis elegans is a key laboratory model for metazoan biology. C. elegans is also used as a model for parasitic nematodes despite being only distantly related to most parasitic species. All [~]65 Caenorhabditis species currently in culture are free-living with most having been isolated from decaying plant or fungal matter. Caenorhabditis bovis is a particularly unusual species, having been isolated several times from the inflamed ears of Zebu cattle in Eastern Africa where it is believed to be the cause of bovine parasitic otitis. C. bovis is therefore of particular interest to researchers interested in the evolution of nematode parasitism and in Caenorhabditis diversity. However, as C. bovis is not in laboratory culture, it remains little studied and details of its prevalence, role in bovine parasitic otitis and relationships to other Caenorhabditis species are scarce. Here, by sampling livestock markets and slaughterhouses in Western Kenya, we successfully reisolate C. bovis from the ear of adult female Zebu. We sequence the genome of C. bovis using the Oxford Nanopore MinION platform in a nearby field laboratory and use the data to generate a chromosome-scale draft genome sequence. We exploit this draft genome to reconstruct the phylogenetic relationships of C. bovis to other Caenorhabditis species and reveal the changes in genome size and content that have occurred during its evolution. We also identify expansions in several gene families that have been implicated in parasitism in other nematode species, including those associated with resistance to antihelminthic drugs. The high-quality draft genome and our analyses thereof represent a significant advancement in our understanding of this unusual Caenorhabditis species.

genomics↗

bioRxiv2019

AFM based elasticity of intestinal epithelium correlate with barrier function under drug action

Over the past few years, atomic force microscopy (AFM) has developed as a mature research tool for measuring the nanomechanical properties of tissue, cells and biological structures. The force spectroscopy mode of AFM allows the local elasticity of biological samples to be measured. The mechanical properties of cells are highly affected by homeostatic changes observed during disease. In the case of the intestine, the aetiology for some conditions is still unclear. To improve the clinical translation of pre-clinical models, a new and different approach could be to study cellular behaviour in health and disease from a mechanical point of view. Specifically, knowledge of changes in epithelial membranes in response to drugs is useful for interpreting both drug action and disease development. Here, we used human intestinal Caco-2 cells as a first step to record epithelial membrane elasticity measurements at the nanoscale using AFM. Three different drugs were selected to influence intestinal epithelium integrity by specifically targeting different functional aspects of the membrane, such as permeability and support. Results indicate a relationship between measured cell elasticity and cell viability markers, such as cellular toxicity and membrane barrier functions. Our work represents a proof-of-concept that cells suffer a particular change in elastic properties depending upon the mechanism of action of an applied drug. The following may provide an efficient approach for diagnosing intestinal pathologies and testing drugs for clinical use.\n\nSTATEMENT OF SIGNIFICANCEWe present evidence that epithelial membrane suffers a particular change in elastic properties depending upon the mechanism of action of an applied drug. These changes can be monitored over time using AFM technology and may provide an alternative and efficient approach for diagnosing intestinal pathologies and testing drugs for clinical use.

biophysics↗

bioRxiv2019

Analysis of meiosis in Pristionchus pacificus reveals plasticity in homolog pairing and synapsis within the nematode lineage

Meiosis is conserved across eukaryotes yet varies in the details of its execution. Here we describe a new comparative model system for molecular analysis of meiosis, the nematode Pristionchus pacificus, a distant relative of the widely studied model organism Caenorhabditis elegans. P. pacificus shares many anatomical and other features that facilitate analysis of meiosis in C. elegans. However, while C. elegans has lost the meiosis-specific recombinase Dmc1 and evolved a recombination-independent mechanism to synapse its chromosomes, P. pacificus expresses both DMC-1 and RAD-51. We find that SPO-11 and DMC-1 are required for stable homolog pairing, synapsis, and crossover formation, while RAD-51 is dispensable for these key meiotic processes. RAD-51 and DMC-1 localize sequentially to chromosomes during meiotic prophase and show nonoverlapping functions. We also present a new genetic map for P. pacificus that reveals a crossover landscape very similar to that of C. elegans, despite marked divergence in the regulation of synapsis and crossing-over between these lineages.

cell biology↗

bioRxiv2019

Evolution of Yin and Yang isoforms of a chromatin remodeling subunit results in the creation of two genes

Genes can encode multiple isoforms, broadening their functions and providing a molecular substrate to evolve phenotypic diversity. Evolution of isoform function is a potential route to adapt to new environments. Here we show that de novo, beneficial alleles in the nurf-1 gene fixed in two laboratory strains of C. elegans after isolation from the wild in 1951, before methods of cryopreservation were developed. nurf-1 encodes an ortholog of BPTF, a large (>300kD) multidomain subunit of the NURF chromatin remodeling complex. Using CRISPR-Cas9 genome editing and transgenic rescue, we demonstrate that in C. elegans, nurf-1 has split into two, largely non-overlapping isoforms (NURF-1.B and NURF-1.D, which we call Yin and Yang) that share only two of 26 exons. Both isoforms are essential for normal gametogenesis but have opposite effects on male/female gamete differentiation. Reproduction in hermaphrodites, which involves production of both sperm and oocytes, requires a balance of these opposing Yin and Yang isoforms. Transgenic rescue and genetic position of the fixed mutations suggest that different isoforms are modified in each laboratory strain. In a related clade of Caenorhabditis nematodes, the shared exons have duplicated, resulting in the split of the Yin and Yang isoforms into separate genes, each containing approximately 200 amino acids of duplicated sequence that has undergone accelerated protein evolution following the duplication. Associated with this duplication event is the loss of two additional nurf-1 transcripts, including the long-form transcript and a newly identified, highly expressed transcript encoded by the duplicated exons. We propose these lost transcripts are non-functional biproducts necessary to transcribe the Yin and Yang transcripts in the same cells. Our work suggests that evolution of nurf-1 isoforms in nematodes creates adaptive conflict that can be resolved by the creation of new, independent genes.

evolutionary biology↗

bioRxiv2018

Comparative genomics of ten new Caenorhabditis species

The nematode Caenorhabditis elegans has been central to the understanding of metazoan biology. However, C. elegans is but one species among millions and the significance of this important model organism will only be fully revealed if it is placed in a rich evolutionary context. Global sampling efforts have led to the discovery of over 50 putative species from the genus Caenorhabditis, many of which await formal species description. Here, we present species descriptions for ten new Caenorhabditis species. We also present draft genome sequences for nine of these new species, along with a transcriptome assembly for one. We exploit these whole-genome data to reconstruct the Caenorhabditis phylogeny and use this phylogenetic tree to dissect the evolution of morphology in the genus. We show unexpected complexity in the evolutionary history of key developmental pathway genes. The genomic data also permit large scale analysis of gene structure, which we find to be highly variable within the genus. These new species and the associated genomic resources will be essential in our attempts to understand the evolutionary origins of the C. elegans model.

evolutionary biology↗

bioRxiv2018

Evolutionary analysis implicates RNA polymerase II pausing and chromatin structure in nematode piRNA biogenesis

Piwi-interacting RNAs (piRNAs) control transposable elements widely across metazoans but have rapidly evolving biogenesis pathways. In Caenorhabditis elegans, almost all piRNA loci are found within two 3Mb clusters on Chromosome IV. Each piRNA locus possesses an upstream motif that recruits RNA polymerase II to produce a [~]28 nt precursor transcript. Here, we use comparative epigenomics across nematodes to gain insight into piRNA biogenesis. We show that the piRNA upstream motif is derived from core promoter elements controlling snRNA biogenesis. We describe two alternative modes of piRNA organisation in nematodes: in C. elegans and closely related nematodes, piRNAs are clustered within repressive H3K27me3 chromatin, whilst in other species, typified by Pristionchus pacificus, piRNAs are distributed genome-wide within introns of actively transcribed genes. In both groups, piRNA production depends on downstream sequence signals associated with RNA polymerase II pausing, which synergise with the chromatin environment to control piRNA precursor transcription.

genomics↗

bioRxiv2017

Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus

Tardigrada, a phylum of meiofaunal organisms, have been at the center of discussions of the evolution of Metazoa, the biology of survival in extreme environments, and the role of horizontal gene transfer in animal evolution. Tardigrada are placed as sisters to Arthropoda and Onychophora (velvet worms) in the superphylum Ecdysozoa by morphological analyses, but many molecular phylogenies fail to recover this relationship. This tension between molecular and morphological understanding may be very revealing of the mode and patterns of evolution of major groups. Similar to bdelloid rotifers, nematodes and other animals of the water film, limno-terrestrial tardigrades display extreme cryptobiotic abilities, including anhydrobiosis and cryobiosis. These extremophile behaviors challenge understanding of normal, aqueous physiology: how does a multicellular organism avoid lethal cellular collapse in the absence of liquid water? Meiofaunal species have been reported to have elevated levels of HGT events, but how important this is in evolution, and in particular in the evolution of extremophile physiology, is unclear. To address these questions, we resequenced and reassembled the genome of Hypsibius dujardini, a limno-terrestrial tardigrade that can undergo anhydrobiosis only after extensive pre-exposure to drying conditions, and compared it to the genome of Ramazzottius varieornatus, a related species with tolerance to rapid desiccation. The two species had contrasting gene expression responses to anhydrobiosis, with major transcriptional change in H. dujardini but limited regulation in R. varieornatus. We identified few horizontally transferred genes, but some of these were shown to be involved in entry into anhydrobiosis. Whole-genome molecular phylogenies supported a Tardigrada+Nematoda relationship over Tardigrada+Arthropoda, but rare genomic changes tended to support Tardigrada+Arthropoda.

genomics↗