2024
Computational reassessment of RNA-seq data reveals key genes in active tuberculosis
Arya R, Shakya H, Chaurasia R, Kumar S, Vinetz J, Kim J. Computational reassessment of RNA-seq data reveals key genes in active tuberculosis. PLOS ONE 2024, 19: e0305582. PMID: 38935691, PMCID: PMC11210783, DOI: 10.1371/journal.pone.0305582.Peer-Reviewed Original ResearchConceptsMolecular Complex DetectionProtein-protein interactionsDeregulated genesGene OntologyRNA-seq dataGene Expression Omnibus (GEO) databaseIncreasing prevalence of multidrug-resistantGEO2R online toolPrevalence of multidrug resistancePathway enrichment analysisExpression levelsPatterns of variationGene expression levelsArea under curveInnate immune responseGene networksCore genesMicroarray datasetsSTRING databaseTranscript levelsEnrichment analysisGenesInterferon signalingInterferon-gamma signalingResponse to Mtb infection
2022
Structure–function analysis of cysteine residues in the plasmodium falciparum chitinase, PfCHT1
Kaur H, Garber L, Murphy JW, Vinetz JM. Structure–function analysis of cysteine residues in the plasmodium falciparum chitinase, PfCHT1. Protein Science 2022, 31: e4289. PMID: 35481637, PMCID: PMC8994504, DOI: 10.1002/pro.4289.Peer-Reviewed Original ResearchConceptsPutative chitin-binding domainChitin-binding domainPlasmodium ookinetesProtein-protein interactionsRecombinant protein productionIntermolecular protein-protein interactionsMosquito midgut invasionStructure-function analysisEnzymatic activityIntramolecular disulfide linkagesIntermolecular disulfide bondingChitin-containing peritrophic matrixParasite cladesMidgut invasionPeritrophic matrixCysteine residuesProtein productionChitinase activityBiochemical studiesDisulfide bondingUnpaired cysteineChitinaseMalaria parasitesE. coliMutants