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- ArticleLeonard SR, Mammel MK, Lacher DW, Elkins CA.PLoS One. 2016;11(12):e0167870.Consumption of fresh bagged spinach contaminated with Shiga toxin-producing Escherichia coli (STEC) has led to severe illness and death; however current culture-based methods to detect foodborne STEC are time consuming. Since not all STEC strains are considered pathogenic to humans, it is crucial to incorporate virulence characterization of STEC in the detection method. In this study, we assess the comprehensiveness of utilizing a shotgun metagenomics approach for detection and strain-level identification by spiking spinach with a variety of genomically disparate STEC strains at a low contamination level of 0.1 CFU/g. Molecular serotyping, virulence gene characterization, microbial community analysis, and E. coli core gene single nucleotide polymorphism (SNP) analysis were performed on metagenomic sequence data from enriched samples. It was determined from bacterial community analysis that E. coli, which was classified at the phylogroup level, was a major component of the population in most samples. However, in over half the samples, molecular serotyping revealed the presence of indigenous E. coli which also contributed to the percent abundance of E. coli. Despite the presence of additional E. coli strains, the serotype and virulence genes of the spiked STEC, including correct Shiga toxin subtype, were detected in 94% of the samples with a total number of reads per sample averaging 2.4 million. Variation in STEC abundance and/or detection was observed in replicate spiked samples, indicating an effect from the indigenous microbiota during enrichment. SNP analysis of the metagenomic data correctly placed the spiked STEC in a phylogeny of related strains in cases where the indigenous E. coli did not predominate in the enriched sample. Also, for these samples, our analysis demonstrates that strain-level phylogenetic resolution is possible using shotgun metagenomic data for determining the genomic relatedness of a contaminating STEC strain to other closely related E. coli.
- ArticleChen J, Mu X, Liu H, Yong Q, Ouyang X, Liu Y, Zheng L, Chen H, Zhai Y, Ma J, Meng L, Liu S, Zheng H.Sci Total Environ. 2024 Jan 10;907:167870.Bumblebees are essential pollinators of both wildflowers and crops and face multiple anthropogenic stressors, particularly the utilization of pesticides. Rotenone is an extensively applied neurotoxic pesticide that possesses insecticidal activities against a wide range of pests. However, whether environmentally realistic exposure levels of rotenone can damage neurons in bumblebee brains is still uncertain. Using single-cell RNA-seq, we revealed that rotenone induced cell-specific responses in bumblebee brains, emphasizing the disruption of energy metabolism and mitochondrial dysfunction in glial cells. Correspondingly, the gene regulatory network associated with neurotransmission was also suppressed. Notably, rotenone could specially reduce the number of dopaminergic neurons, impairing bumblebee's ability to fly and crawl. We also found impaired intestinal motility in rotenone-treated bumblebees. Finally, we demonstrated that many differentially expressed genes in our snRNA-seq data overlapped with rotenone-induced Parkinson's disease risk genes, especially in glial cells. Although rotenone is widely used owing to its hypotoxicity, we found that environmentally realistic exposure levels of rotenone induced disturbed glial energetics and locomotor dysfunction in bumblebees, which may lead to an indirect decline in this essential pollinator.
- ArticleRidha F, Kulandaisamy A, Michael Gromiha M.J Mol Biol. 2023 07 15;435(14):167870.Membrane protein complexes are crucial for a large variety of biological functions which are mainly dictated by their binding affinity. Due to the intricate nature of their structure, however, the binding affinity of membrane proteins is less explored compared to globular proteins. Mutations in these complexes affect their binding affinity, as well as impair critical functions, and may lead to diseases. Although experimental binding affinity data have expanded in the literature, they are dispersed and it is necessary to compile them into a reliable and comprehensive database. Hence, we developed MPAD (Membrane Protein complex binding Affinity Database), which contains experimental binding affinities of membrane protein-protein complexes and their mutants along with sequence, structure, and functional information, membrane-specific features, experimental conditions, as well as literature information. MPAD has an easy-to-use interface and options to build search queries, display, sort, download, and upload the data are among the other features available to users. This database can be used to understand the factors influencing the binding affinity in membrane proteins when compared to globular proteins as well as the impact of mutations on binding affinity, which may have potential applications to structure-based drug design. MPAD can be freely accessed at https://web.iitm.ac.in/bioinfo2/mpad.