Tissue-specific RNA-seq defines genes governing male tail tip morphogenesis in C. elegans.

Caenorhabditis elegans males undergo sex-specific tail tip morphogenesis (TTM) under the control of the DM-domain transcription factor DMD-3. To find genes regulated by DMD-3, we performed RNA-seq of laser-dissected tail tips. We identified 564 genes differentially expressed (DE) in wild-type males versus dmd-3(-) males and hermaphrodites.

Morphologically defined substages of tail morphogenesis in C. elegans males.

Background: Sex-specific morphogenesis occurs in Caenorhabditis elegans in the vulva of the hermaphrodite and in the male tail during the last larval stage. Temporal progression of vulva morphogenesis has been described in fine detail. However, a similar precise description of male tail morphogenesis was lacking.

Morphologically defined substages of tail morphogenesis in males.

Background: Sex-specific morphogenesis occurs in in the vulva of the hermaphrodite and in the male tail during the last larval stage. Temporal progression of vulva morphogenesis has been described in fine detail. However, a similar precise description of male tail morphogenesis was lacking.

Tissue-specific RNA-seq defines genes governing male tail tip morphogenesis in .

males undergo sex-specific tail tip morphogenesis (TTM) under the control of the transcription factor DMD-3. To find genes regulated by DMD-3, We performed RNA-seq of laser-dissected tail tips. We identified 564 genes differentially expressed (DE) in wild-type males vs.

Homologies and evolution of male tail characters in rhabditid and diplogastrid nematodes.

A major question in evolutionary biology is how often the same developmental events, mechanisms and genes are reused in the recurrent evolution of similar phenotypes. If this happens frequently, it would suggest that evolution is often constrained by developmental genetic mechanisms. To help address this question, we used adherens junction staining and laser ablation to analyze the development underlying several features of nematode male tails have evolved recurrently.

Pellioditis pelhamensis n. sp. (Nematoda: Rhabditidae) and Pellioditis pellio (Schneider, 1866), earthworm associates from different subclades within Pellioditis (syn. Phasmarhabditis Andrássy, 1976).

Recently, much attention has been focused on a group of rhabditid nematodes called Phasmarhabditis, a junior synonym of Pellioditis, as a promising source of biocontrol agents for invasive slugs. Pellioditis pelhamensis n. sp.

nematodes colonize ephemeral resource patches in neotropical forests.

Factors shaping the distribution and abundance of species include life-history traits, population structure, and stochastic colonization-extinction dynamics. Field studies of model species groups help reveal the roles of these factors. Species of nematodes are highly divergent at the sequence level but exhibit highly conserved morphology, and many of these species live in sympatry on microbe-rich patches of rotten material.

Laser Microdissection for Species-Agnostic Single-Tissue Applications.

Single-cell methodologies have revolutionized the analysis of the transcriptomes of specific cell types. However, they often require species-specific genetic "toolkits," such as promoters driving tissue-specific expression of fluorescent proteins. Further, protocols that disrupt tissues to isolate individual cells remove cells from their native environment (e.

hlh-12, a gene that is necessary and sufficient to promote migration of gonadal regulatory cells in Caenorhabditis elegans, evolved within the Caenorhabditis clade.

Specialized cells of the somatic gonad primordium of nematodes play important roles in the final form and function of the mature gonad. Caenorhabditis elegans hermaphrodites are somatic females that have a two-armed, U-shaped gonad that connects to the vulva at the midbody. The outgrowth of each gonad arm from the somatic gonad primordium is led by two female distal tip cells (fDTCs), while the anchor cell (AC) remains stationary and central to coordinate uterine and vulval development.

EUAdb: A resource for COVID-19 test development and comparison.

Due to the sheer number of COVID-19 (coronavirus disease 2019) cases there is a need for increased world-wide SARS-CoV-2 testing capability that is both efficient and effective. Having open and easy access to detailed information about these tests, their sensitivity, the types of samples they use, etc. would be highly useful to ensure their reproducibility, to help clients compare and decide which tests would be best suited for their applications, and to avoid costs of reinventing similar or identical tests.

EUAdb: a resource for COVID-19 test development.

Due to the sheer number of COVID-19 (coronavirus disease 2019) cases, the prevalence of asymptomatic cases and the fact that undocumented cases appear to be significant for transmission of the causal virus, SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), there is an urgent need for increased SARS-CoV-2 testing capability that is both efficient and effective1. In response to the growing threat of the COVID-19 pandemic in February, 2020, the FDA (US Food and Drug Administration) began issuing Emergency Use Authorizations (EUAs) to laboratories and commercial manufacturers for the development and implementation of diagnostic tests[1]. So far, the gold standard assay for SARS-CoV-2 detection is the RT-qPCR (real-time quantitative polymerase chain reaction) test[2].

Deep sampling of Hawaiian reveals high genetic diversity and admixture with global populations.

Hawaiian isolates of the nematode species have long been known to harbor genetic diversity greater than the rest of the worldwide population, but this observation was supported by only a small number of wild strains. To better characterize the niche and genetic diversity of Hawaiian and other species, we sampled different substrates and niches across the Hawaiian islands. We identified hundreds of new strains from known species and a new species, .

The Makorin and the lncRNA regulate to schedule sexual maturation of the nervous system.

Sexual maturation must occur on a controlled developmental schedule. In mammals, Makorin3 () and the miRNA regulators are key regulators of this process, but how they act is unclear. In , sexual maturation of the nervous system includes the functional remodeling of postmitotic neurons and the onset of adult-specific behaviors.

Comparative genomics of 10 new species.

The nematode has been central to the understanding of metazoan biology. However, 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 , many of which await formal species description.

The Long Non-Coding RNA lep-5 Promotes the Juvenile-to-Adult Transition by Destabilizing LIN-28.

Biological roles for most long non-coding RNAs (lncRNAs) remain mysterious. Here, using forward genetics, we identify lep-5, a lncRNA acting in the C. elegans heterochronic (developmental timing) pathway.

Genome Architecture and Evolution of a Unichromosomal Asexual Nematode.

Asexual reproduction in animals, though rare, is the main or exclusive mode of reproduction in some long-lived lineages. The longevity of asexual clades may be correlated with the maintenance of heterozygosity by mechanisms that rearrange genomes and reduce recombination. Asexual species thus provide an opportunity to gain insight into the relationship between molecular changes, genome architecture, and cellular processes.

Description of two three-gendered nematode species in the new genus Auanema (Rhabditina) that are models for reproductive mode evolution.

The co-existence of males, females and hermaphrodites, a rare mating system known as trioecy, has been considered as an evolutionarily transient state. In nematodes, androdioecy (males/hermaphrodites) as found in Caenorhabditis elegans, is thought to have evolved from dioecy (males/females) through a trioecious intermediate. Thus, trioecious species are good models to understand the steps and requirements for the evolution of new mating systems.

Makorin ortholog LEP-2 regulates LIN-28 stability to promote the juvenile-to-adult transition in Caenorhabditis elegans.

The heterochronic genes lin-28, let-7 and lin-41 regulate fundamental developmental transitions in animals, such as stemness versus differentiation and juvenile versus adult states. We identify a new heterochronic gene, lep-2, in Caenorhabditis elegans. Mutations in lep-2 cause a delay in the juvenile-to-adult transition, with adult males retaining pointed, juvenile tail tips, and displaying defective sexual behaviors.

A phylogeny and molecular barcodes for Caenorhabditis, with numerous new species from rotting fruits.

Background: The nematode Caenorhabditis elegans is a major laboratory model in biology. Only ten Caenorhabditis species were available in culture at the onset of this study. Many of them, like C.

A bow-tie genetic architecture for morphogenesis suggested by a genome-wide RNAi screen in Caenorhabditis elegans.

During animal development, cellular morphogenesis plays a fundamental role in determining the shape and function of tissues and organs. Identifying the components that regulate and drive morphogenesis is thus a major goal of developmental biology. The four-celled tip of the Caenorhabditis elegans male tail is a simple but powerful model for studying the mechanism of morphogenesis and its spatiotemporal regulation.

Phenotypic plasticity: different teeth for different feasts.

A polyphenism in the nematode Pristionchus pacificus involves the development of different feeding structures in response to an environmental cue, providing a genetic model species for investigating ecologically relevant phenotypic plasticity.

Evolution of early embryogenesis in rhabditid nematodes.

The cell-biological events that guide early-embryonic development occur with great precision within species but can be quite diverse across species. How these cellular processes evolve and which molecular components underlie evolutionary changes is poorly understood. To begin to address these questions, we systematically investigated early embryogenesis, from the one- to the four-cell embryo, in 34 nematode species related to C.

Evolutionary biology: patchy food may maintain a foraging polymorphism.

Two naturally-occurring alleles in the nematode Caenorhabditis elegans that differ by a single amino acid and cause striking differences in foraging behavior are probably maintained by selection in patchy environments.

Ecology of Caenorhabditis species.

Although several Caenorhabditis species are now studied in laboratories in great detail, the knowledge of the ecology of most Caenorhabditis species is scarce. In this chapter we present data on the habitat, animal associations, and geographical distribution of the eighteen described and five undescribed Caenorhabditis species currently known to science. The habitats of these species are very diverse, ranging from rotting cactus tissue to inflamed auditory canals of zebu cattle.