Casey Dunn's laboratory in the Department of Ecology and Evolutionary Biology at Yale University.

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PhD (f/m/d)

Proposed model for the stepwise evolution of DELLA functions in the green lineage.

Environmental genomics has focused mainly on prokaryotes, leaving microbial eukaryote diversity poorly understood. Using ~20,000 mitochondrial genomes from 3,400 lake metagenomes worldwide, this study...

Plasmid construction underpins molecular biology and synthetic biology, yet validation is often limited to the inserted fragment rather than the whole plasmid, and around a third of laboratory-made pl...

The amoeba Incendiamoeba cascadensis demonstrates that eukaryotic life can withstand temperatures beyond what was thought possible and sheds light on molecular strategies for survival in extreme heat.

CRISPR-Cas provides RNA-mediated adaptive immunity, but how its first RNA-guided effector arose is unclear. In this study, we report the discovery of Viral Interference Programmable Repeat (VIPR) syst...

Efficient construction of phylogenetic consensus trees. Methods include strict, majority-rule, majority-rule (+), loose (combinable component / semi-strict), greedy, Adams, frequency difference, R*, a...

RAxML-NG is a widely used tool for maximum likelihood based phylogenetic inference. In the seven years since the last RAxML-NG publication, we have continuously improved and extended the code. Here, w...

Through your undergraduate and graduate-level teaching, and your research activities, you will contribute to the faculty’s pursuit of excellence. Furthermore, you will promote your discipline and actively participate in the daily activities of a renowned institution. As such, you will:

RAxML-NG is a widely used tool for maximum likelihood based phylogenetic inference. In the seven years since the last RAxML-NG publication, we have continuously improved and extended the code. Here, w...

Animal cells extensively remodel their cytoskeleton during differentiation and can notably switch between two major motility modes: flagellum-based swimming and actin-based crawling. We previously sho...

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This Community Page presents the 100 Diatom Genomes Project, which aims to sequence the genomes and transcriptomes of 100 diatom species across major lineages, life forms and ecological strategies. Th...

Abstract. Zygnematophytes emerged as the unexpected closest algal relatives of land plants despite their simple body plans, raising questions about the mor

MetaCAT is a computational framework to assess host–microbiome interaction via a combination of high-accuracy and efficient microbial genome reconstruction and metagenome-wide association studies with...

Force Remove Copilot, Recall and More in Windows 11 - zoicware/RemoveWindowsAI

Symbiotic relationships of microorganisms are predicted and cataloged with a machine learning tool.

RNA virus infection alters the landscape of diatom organic matter, temporally decoupling the viral shunt and the microbial loop.

Viral infection is a major yet poorly quantified driver of microbial interactions and biogeochemical fluxes in the ocean. In diatoms, which are key contributors to marine primary production, the extent to which viruses reprogram host cell metabolism and alter elemental cycling remains largely unresolved. Here, we investigated how infection by a lytic single-stranded RNA virus reshapes carbon (C) and nitrogen (N) fluxes in the ecologically relevant nanoplanktonic diatom Mediolabrus comicus. Using controlled infection experiments coupled with flow cytometry, electron microscopy, PAM fluorimetry, and stable isotope probing, we resolved infection-driven changes from the population to the cellular scale. Infection induced rapid optical shifts and cellular reorganization, including the formation of membrane-bound viral replication compartments. These changes coincided with early impairment of plastidial functions, as shown by disruption of photosystem II functionality and a concomitant decline in photosynthetic carbon fixation. In contrast, nitrogen uptake was maintained and strongly enhanced during late stages of infection, indicating sustained resource acquisition to support viral replication. This decoupling led to dynamic changes in cellular stoichiometry and, overall, to substantial reductions in population-level carbon and nitrogen assimilation due to growth inhibition. Together, these findings demonstrate that diatom RNA virus infection reshapes host carbon and nitrogen metabolism, with cascading effects on elemental cycling. Our results identify diatom RNA viruses as important drivers of marine biogeochemical processes, with implications for primary production and the fate of organic matter in the ocean. ### Competing Interest Statement The authors have declared no competing interest. Agence Nationale de la Recherche, https://ror.org/00rbzpz17, ANR-22-CE01-0018 BONUS Sorbonne Université, https://ror.org/02en5vm52, Institut de l'océan

Ctenophores and placozoans arose early in metazoan evolution and are characterized by traits associated with key aspects of animal evolution. Despite the evolutionary significance of ctenophores and placozoans, their RNA viromes are poorly understood. To determine the diversity and evolution of RNA virome in these organisms, particularly whether the viruses present with these ancient host lineages similarly occupy basal phylogenetic positions, we analysed publicly available transcriptome data from the Sequence Read Archive (SRA). Accordingly, we identified 26 putative novel viruses classified into 11 virus groups, including members of the families Flaviviridae and Chuviridae . The novel viruses clustered with those previously identified in vertebrates, invertebrates, plants and fungi. Notably, some virus sequences within the Flaviviridae , Chuviridae , Lispiviridae and Marnaviridae were highly divergent, branching deeply relative to their closest known relatives or forming distinct lineages, in some cases suggesting a divergence early in metazoan evolution. In contrast, viruses within the Birnaviridae , Endornaviridae , Mymonaviridae , Narnaviridae , Phasmaviridae, Orthomyxoviridae , Orthototiviridae , and some viruses within the Picornavirales , exhibited patterns consistent with more recent diversification and host jumping. In addition, RNA viruses were detected across multiple species and tissues within the Ctenophora (including whole organisms and embryos) and Placozoa, expanding their host range and highlighting a largely uncharacterized diversity. Together, these findings expand the known diversity and host range of several virus groups, and shed light on virus evolution in early metazoans, demonstrating both host jumping within aquatic environments and virus host-associations that may span the entirety of animal evolution. ### Competing Interest Statement The authors have declared no competing interest. Australian Research Council, DP240101313 National Health and Medical Research Council, GNT2017197

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R programming foundations for bioinformatics, data science, and data visualization - cxli233/Section-301-R-Programming-Intro