Journal: bioRxiv

Article Title: The co-receptors Orco and Ir8a are required for coordinated expression of chemosensory genes in the antennae of the yellow fever mosquito, Aedes aegypti

doi: 10.1101/2025.04.23.650034

Figure Lengend Snippet: Updated transcriptome files and GAF files were constructed to include current annotations of chemoreceptors. Salmon pseudoalignment was performed to align trimmed reads to the transcriptome. TxImport and DESeq2 analysis were performed to identify differentially expressed genes. Heatmaps, Volcano Plots, and TopGO analysis were performed.

Article Snippet: The transcriptome mRNA library was constructed with the Illumina Truseq stranded mRNA library prep kit.

Techniques: Construct

Journal: FEMS Microbiology Ecology

Article Title: Unveiling detoxifying symbiosis and dietary influence on the Southern green shield bug microbiota

doi: 10.1093/femsec/fiae150

Figure Lengend Snippet: Transcriptome and metabolome of Pantoea sp. Nvir growing on M9 mineral medium with 100 µM NPA. (A) Pantoea sp. Nvir differential gene expression profile under growth with and without NPA. Pantoea was cultured in an M9 mineral salt medium supplemented with 100 µM NPA or an equimolar concentration of glycerol (control). Samples for RNA extraction (biological triplicates) were taken 2 h after NPA/glycerol supplementation. A heatmap shows differential gene expression (log 2 fold change; cutoff = 2; P < .05) in Pantoea cultures. (B) Mirror plot of observed MS2 feature (top), and MS2 of a commercially purchased 2-isopropylmalic acid standard (bottom) analysed under the same experimental parameters with LC-qToF-MS. (C) Simplified l -leucine biosynthesis pathway with chemical structures and corresponding chromatograms at 6 h after NPA or glycerol (control) supplementation. 3-hydroxy-3-methyl-2-oxobutanoate and 2-oxoisovalerate were putatively identified based on m/z value (in italics), whereas 2-isopropylmalate and leucine/isoleucine were identified using chemical standards. Data are represented as the mean of biological quadruplicates.

Article Snippet: Transcriptome libraries were constructed using the TruSeq® Stranded mRNA Library Prep protocol (Illumina) according to the manufacturer’s instructions.

Techniques: Gene Expression, Cell Culture, Concentration Assay, Control, RNA Extraction

Journal: bioRxiv

Article Title: Snake venom-inspired novel peptides protect Caenorhabditis elegans against paraquat-induced Parkinson’s pathology

doi: 10.1101/2024.06.01.596942

Figure Lengend Snippet: Proteomics analysis to show the expression of common and intracellular proteins among the treated groups of C. elegans. (a) Venn diagram showing common intracellular proteins among untreated (control) (CT), PT (PT) treated, and HNP pre-treated followed by PT-treated (PHNP) groups of C. elegans determined by LC/MS-MS analysis. (b) Scatter plot showing significantly upregulated (fold change>1.25) and downregulated (fold change <0.80) proteins in PT-treated C. elegans . FC: fold-change in expression determined by LC/MS-MS analysis. (c) Venn diagram showing common intracellular proteins among untreated (control) (CT) and only HNP-treated C. elegans determined by LC/MS-MS analysis. (d) Molecular network of custom peptide HNP-mediated neuroprotection. The interaction network of peptide HNP-regulated genes/proteins and interlinking pathways as determined by both transcriptomic and proteomic analyses.

Article Snippet: Following the manufacturer’s protocol, transcriptomic mRNA libraries were prepared using NEB (cat# E7770L kit) as previously described [ ].

Techniques: Expressing, Control, Liquid Chromatography with Mass Spectroscopy

Journal: bioRxiv

Article Title: Snake venom-inspired novel peptides protect Caenorhabditis elegans against paraquat-induced Parkinson’s pathology

doi: 10.1101/2024.06.01.596942

Figure Lengend Snippet:

Article Snippet: Following the manufacturer’s protocol, transcriptomic mRNA libraries were prepared using NEB (cat# E7770L kit) as previously described [ ].

Techniques: Control