Project description:RNA-seq analysis of Pseudomonas sp OST1909 exposed to various preparations of naphthenic acids samples led to the identiifcation of many NA-induced genes.
Project description:This study provides comparative RNA-seq datasets for four freshwater bacterial isolates, Pseudomonas sp. FBCC-B13192, Herbaspirillum sp. FBCC-B12834, Pantoea sp. FBCC-B5559, and Micrococcus sp. FBCC-B5738, cultured under iron-replete (+100 uM FeCl3) and iron-limited (no FeCl3) conditions. Iron availability is a key factor influencing bacterial fitness, and iron limitation is known to activate siderophore biosynthesis, iron transport, and homeostasis pathways. A total of eight libraries generated in 2024 and 2025 were analyzed, comprising 349.9 million processed reads. Reference-guided mapping rates varied among strains, with higher mapping efficiency observed in Pseudomonas, Herbaspirillum, and Pantoea, while Micrococcus showed comparatively lower mapping rates under both conditions. Differential expression analysis revealed strain-specific responses to iron limitation. Genes related to pyoverdine and ferrichrome uptake were enriched in Pseudomonas and Herbaspirillum, enterobactin-associated pathways were prominent in Pantoea, and genes associated with siderophore production, heme utilization, and Fe-S cluster assembly were identified in Micrococcus. Raw sequencing data are available in the NCBI Sequence Read Archive under BioProject PRJNA1456794, and processed data are deposited in a public repository. These datasets provide a valuable resource for understanding bacterial adaptation to iron availability and for comparative transcriptomic analyses.
Project description:Hsp70 inhibition affects many signaling pathways. We established how these effects are translated into changes in gene expression. Hsp70 is a promising anti-cancer target, and several inhibitors of Hsp70 have been recently developed. Interest to Hsp70 inhibitors as drug prototypes is, however, somewhat hampered by potential similarity of their physiological effects to effects of already well-developed Hsp90 inhibitors. JG-98 series of inhibitors is unique in its ability to target an allosteric site in the ATPase domain of Hsp70, which disrupts its interaction with a co-chaperone Bag3 and affects a variety of signaling pathways important for cancer development and survival. Here, we used the Broad Institute Connectivity Map platform to evaluate physiological effects of JG-98, and found that these effects are dissimilar from effects of Hsp90 inhibitors, thus justifying further development of this compound series. Further, using gene expression data and ActivSignal IPAD platform, we identified pathways modulated by JG-98. Some of these pathways were affected by JG-98 in Bag3-dependent and some pathways in Bag3-independent manner, indicating multiple mechanisms of JG-98 action. Using pooled shRNA genetic screen, we established gene sets that modulate the response of cancer cells to JG-98. Based on genetic and gene expression information, we developed approaches to predict potent combinations of JG-98 with known drugs. These predictions were validated by demonstrating that proteasome, RNApol II, Akt and RTK inhibitors synergize with anti-cancer effects of JG-98. Overall, in this study we analyze unique effects of Hsp70 inhibitors of JG-98 series on cell physiology and define potential drug combinations for clinical use of these inhibitors.
