Project description:Proteome and secretome of the extremotolerant rock black fungus Knufia chersonesos and its nonmelanized spontaneous mutant were analyzed following the fungus growth under LSSMG in rotating bioreactors (High Aspect Ratio Vessels; HARV). Tandem Mass Tags (TMS)-based quantitative shotgun proteomics was applied to compare gravity to microgravity conditions as well as to elucidate differences in the response between wild type and mutant strain.
Project description:Relentless mining operations have destroyed our environment significantly. Soil inhabiting microbes play a significant role in ecological restoration of these areas. Microbial weathering processes like chemical dissolution of rocks significantly promotes the soil properties and enhances the rock to soil ratio respectively. Earlier studies have reported that bacteria exhibit efficient rock-dissolution abilities by releasing organic acids and other chemical elements from the silicate rocks. However, rock-dissolving mechanisms of the bacterium remain to be unclear till date. Thus, we have performed rock-dissolution experiments followed by genome and transcriptome sequencing of novel Pseudomonas sp.NLX-4 strain to explore the efficiency of microbe-mediated habitat restoration and its molecular mechanisms underlying this biological process. Results obtained from initial rock dissolution experiments revealed that Pseudomonas sp. NLX-4 strain efficiently accelerates the dissolution of silicate rocks by secreting amino acids, exopolysaccharides, and organic acids with elevated concentrations of potassium, silicon and aluminium elements. The rock dissolution experiments of NLX-4 strain exhibited an initial increase in particle diameter variation values between 0-15 days and decline after 15 days-time respectively. The 6,771,445-base pair NLX-4 genome exhibited 63.21 GC percentage respectively with a total of 6041 protein coding genes. Genome wide annotations of NLX-4 strain exhibits 5045-COG, 3996-GO, 5342-InterPro, 4386-KEGG proteins respectively Transcriptome analysis of NLX-4 cultured with/without silicate rocks resulted in 539 (288-up and 251-down) differentially expressed genes (DEGs). Fifteen DEGs encoding for siderophore transport, EPS and amino acids synthesis, organic acids metabolism, and bacterial resistance to adverse environmental conditions were highly up-regulated by cultured with silicate rocks. This study has not only provided a new strategy for the ecological restoration of rock mining areas, but also enriched the applicable bacterial and genetic resources.
Project description:The extremotolerant rock-associated black fungus Knufia chersonesos and its nonmelanized spontaneous mutant were selected for a proteomic-based screening towards polyesterases. A non-labeling shotgun analysis of the secretome was performed to compare control and treatment condition (PBAT added to the cultivation media) as well as Wt and Mut.
Project description:This SuperSeries is composed of the following subset Series: GSE38456: Characterizing gene regulatory networks in the brain of largemouth bass inhabiting rivers containing high levels of methyl-mercury (lab study) GSE38458: Characterizing gene regulatory networks in the brain of largemouth bass inhabiting rivers containing high levels of methyl-mercury (field study) Refer to individual Series
Project description:During plant life, roots support beneficial associations with soil inhabiting microbes, mainly fungi and bacteria. Increasing evidence suggests that plant-associated microorganisms can promote plant growth and expand immune functions of the plant host. The beneficial entomopathogenic fungus Beauveria bassiana colonizes plant tissues in an asymptomatic way, triggering poorly characterized plant metabolic changes, which negatively affect both pest insects and plant pathogens. B. bassiana has an extremely broad host spectrum, including tomato (Solanum lycopersicum L.). In order to obtain a great overall snapshot of molecular events regulating tomato-B. bassiana interaction, plant proteome and hormonome changes induced over the time by the fungus have been in-depth analyzed by using a combination of high throughput profiling techniques and bioinformatics tools. The proteomics data highlighted interesting molecular pathways affected by B. bassiana related to primary and secondary metabolism and plant growth. Additionally, downregulation of a member of the endochitinase family and upregulation of calcium channel and transporter proteins suggested well-established plant-fungus symbiosis. The molecular pathways linked to protein/amino acids turn-over and to the biosynthesis of energy compounds shed some light on the strategies exploited by the plant to get the most out of the beneficial interaction in improving growth and development.
Project description:Rho-associated coiled-coil kinase (ROCK) protein is a central kinase that regulates numerous cellular functions, including cellular polarity, motility, proliferation and apoptosis. Here, we demonstrate that ROCK has antiviral properties and inhibition of its activity results in enhanced propagation of human cytomegalovirus (HCMV). We show that during HCMV infection ROCK1 translocates to the nucleus and concentrates in the nucleolus were it co-localizes with the stress related chaperone, heat shock cognate 71 kDa protein (Hsc70) . Gene expression measurements showed that inhibition of ROCK activity does not affect the cellular stress response. We further demonstrate that inhibition of myosin, one of the central targets of ROCK, also increases HCMV propagation, implying that the anti-viral activity of ROCK might be mediated by activation of the actomyosin network. Finally, we demonstrate that inhibition of ROCK results in increased levels of the tegument protein UL32 and of viral DNA in the cytoplasm, suggesting ROCK activity hinders the efficient egress of HCMV particles out of the nucleus. Altogether our findings illustrate ROCK activity restricts HCMV propagation and suggest this inhibitory effect may be mediated by suppression of capsid egress out of the nucleus.
Project description:Deep sequencing of mRNA from the rock pigeon Analysis of ploy(A)+ RNA of different specimens: heart and liver from the rock pigeon (Danish Tumbler, Oriental Frill and Racing)