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Published: Oct 06, 2023
Only some bacteria accumulate substantial amounts of polyphosphate (polyP). We thought that despite sequence divergence, polyP synthesis enzymes in these bacteria might have similar structures. We found this is sometimes true but doesn’t fully explain the phenomenon.
Connections
Supplements (2): Data - Zenodo • Code - GitHub
Published: Sep 22, 2023
It is commonly assumed that phenotypes arise from the cumulative effects of many independent genes. However, we show that by accounting for dependent and nonlinear biological relationships, we can generate models that predict phenotypes with great accuracy.
Connections
Supplements (2): Data - Zenodo • Code v1.0.1 - GitHub
Published: Aug 25, 2023
We implemented a lightweight method to identify viruses in 342 human brain bulk and single-cell sequencing data sets, and identified two glioblastoma cells from a single patient that contained deltapolyomavirus sequences.
Connections
Supplements (1): Code v1.0 - GitHub
Published: Aug 15, 2023
Hoping to find proteins that alter physiology in useful ways, we screened venom data sets for toxins fused to domains with additional functionality. We identified candidates, but struggled to infer any novel functions, and none seem well-conserved across venomous species.
Connections
Supplements (2): Code v2.0 - GitHub • Data - Zenodo
Published: Jul 20, 2023
We are interested in neuroactive metabolites that influence animal behavior. Some fungi have horizontally transferred neuroactive metabolite pathways between species. We used a horizontal gene transfer detection pipeline to screen for novel fungal genes tied to neuroactivity.
Connections
Supplements (1): Code v1.0 - GitHub
Published: Jul 19, 2023
We sampled cheese microbial communities to discover bacteriophages with unusual genome chemistries. We isolated 114 bacterial host strains and 17 phages, and identified one phage with a probable arabinose hypermodification of hydroxymethylcytosine.
Connections
Supplements (8): Raw short reads from 11 cheese communities and one virome - ENA • Taxonomic and functional analysis - MGnify • Raw long reads from one cheese community - ENA • Serratia phage 92A1, complete genome - GenBank • Arthrobacter phage 1191A, complete genome - GenBank • Phage genomes and host 16S data - Zenodo • Protocol - Enriching and isolating phages on agar plates - protocols.io • Protocol - Enriching and isolating phages in liquid culture - protocols.io
Published: Jun 23, 2023
We’re crossing C. reinhardtii and C. smithii algae for high-throughput genotype-phenotype mapping. In preparation, we’re comparing the parents to uncover unique species-specific phenotypes.
Published: Jun 15, 2023
Even with many tools available, categorizing species is tough. We used data from Raman spectroscopy, a form of label-free imaging, to infer phylogenetic patterns among several dozen diverse microbial taxa, offering a non-destructive and rapid way to dissect species relationships.
Connections
Supplements (1): Code v1.0 - GitHub
Published: Mar 29, 2023
Treating P. tricornutum cells with serine endopeptidases or certain cytoskeletal inhibitors induces the formation of cell wall-free protoplasts and suggests a novel role for actin and myosin in preventing protoplast formation.
Published: Dec 04, 2022
Long protrusions from several microalgal species appear to help cells move, capture prey, transport mitochondria and chloroplasts, and more. Are they filopodia that evolved abilities more like other actin- or microtubule-based structures, or are they something new?
Published: Oct 14, 2022
Quantifying movement is a powerful window into cellular functions. However, cells can generate movement through a variety of complex mechanisms. Here, we generate a flexible framework for comparing an especially variable type of motility: cellular crawling.
Connections
Supplements (1): Code v1.1 - GitHub
