Complete Genome Sequence of Bacteriophage vB_Hercules_Set, Which Infects Enteric Pathogen Salmonella enterica Serovar Typhimurium.

We report the isolation, sequencing, and annotation of bacteriophage vB_Hercules_Set, a kuttervirus infecting human pathogen Salmonella enterica. vB_Hercules_Set was isolated from a slurry of soil and deli meat collected in New Hampshire in 2021. The genome length is 157,338 nucleotides, containing 210 protein-coding genes and five tRNAs.

An undergraduate genome research course using "big data".

The ability to analyze large data sets ("Big Data") is an increasingly important skill in modern science. In Biochemistry, the increased volume and velocity of data is particularly evident in the rapid expansion of biological databases. We present a modular bioinformatics course to survey the analysis of genomic data for advanced undergraduates. Research activities include genome scanning for endogenous retroviruses, annotating genomic sequences and a brief exploration of programming in R. A summative poster session was used to disseminate their work. This course is amenable to remote or online instruction. Supplemental materials provided include a schedule and outline. This article reports a session from the virtual international 2021 IUBMB/ASBMB workshop, "Teaching Science on Big Data."

Cross-species transcriptomic signatures identify mechanisms related to species sensitivity and common responses to nanomaterials.

Physico-chemical characteristics of engineered nanomaterials are known to be important in determining the impact on organisms but effects are equally dependent upon the characteristics of the organism exposed. Species sensitivity may vary by orders of magnitude, which could be due to differences in the type or magnitude of the biochemical response, exposure or uptake of nanomaterials. Synthesizing conclusions across studies and species is difficult as multiple species are not often included in a study, and differences in batches of nanomaterials, the exposure duration and media across experiments confound comparisons. Here three model species, Danio rerio, Daphnia magna and Chironomus riparius, that differ in sensitivity to lithium cobalt oxide nanosheets are found to differ in immune-response, iron-sulfur protein and central nervous system pathways, among others. Nanomaterial uptake and dissolution does not fully explain cross-species differences. This comparison provides insight into how biomolecular responses across species relate to the varying sensitivity to nanomaterials.

Energy Starvation in Daphnia magna from Exposure to a Lithium Cobalt Oxide Nanomaterial.

Growing evidence across organisms points to altered energy metabolism as an adverse outcome of metal oxide nanomaterial toxicity, with a mechanism of toxicity potentially related to the redox chemistry of processes involved in energy production. Despite this evidence, the significance of this mechanism has gone unrecognized in nanotoxicology due to the field's focus on oxidative stress as a universal─but nonspecific─nanotoxicity mechanism. To further explore metabolic impacts, we determined lithium cobalt oxide's (LCO's) effects on these pathways in the model organism Daphnia magna through global gene-expression analysis using RNA-Seq and untargeted metabolomics by direct-injection mass spectrometry. Our results show that a sublethal 1 mg/L 48 h exposure of D. magna to LCO nanosheets causes significant impacts on metabolic pathways versus untreated controls, while exposure to ions released over 48 h does not. Specifically, transcriptomic analysis using DAVID indicated significant enrichment (Benjamini-adjusted p ≤0.0.5) in LCO-exposed animals for changes in pathways involved in the cellular response to starvation (25 genes), mitochondrial function (70 genes), ATP-binding (70 genes), oxidative phosphorylation (53 genes), NADH dehydrogenase activity (12 genes), and protein biosynthesis (40 genes). Metabolomic analysis using MetaboAnalyst indicated significant enrichment (γ-adjusted p <0.1) for changes in amino acid metabolism (19 metabolites) and starch, sucrose, and galactose metabolism (7 metabolites). Overlap of significantly impacted pathways by RNA-Seq and metabolomics suggests amino acid breakdown and increased sugar import for energy production. Results indicate that LCO-exposed Daphnia respond to energy starvation by altering metabolic pathways, both at the gene expression and metabolite levels. These results support altered energy production as a sensitive nanotoxicity adverse outcome for LCO exposure and suggest negative impacts on energy metabolism as an important avenue for future studies of nanotoxicity, including for other biological systems and for metal oxide nanomaterials more broadly.

Dubious Heritage: Tobacco, History, and the Perils of Remembering the Rural Past .

In 1994 the Virginia legislature created a vehicle license plate to memorialize the state's long history of tobacco agriculture. Other states have likewise created plates to allow drivers to voice support for farmers. Like Virginia's "Tobacco Heritage" plate, many use traditional imagery and direct appeals to the history of agriculture. Given the United States' automobile culture, the plates are prominent, if small, works of public history that offer official sanction to a particular view of agriculture's past. In creating the license plate, the Virginia legislature valorized a particular telling of tobacco's past and is best understood as part of a much larger effort to employ history to deflect criticism of the tobacco industry. This effort, like the license plate, relied on simplified imagery that elided the complex history of tobacco in Virginia