Project description:Cichlids fishes exhibit extensive phenotypic diversification and speciation. In this study we integrate transcriptomic and proteomic signatures from two cichlids species, identify novel open reading frames (nORFs) and perform evolutionary analysis on these nORF regions. We embark comparative transrcriptomics and proteogenomic analysis of two metabolically active tissues, the testes and liver, of two cichlid species Oreochromis niloticus (Nile tilapia, ON) and Pundamilia nyererei (Makobe Island, PN). Our results suggest that the time scale of speciation of the two species can be better explained by the evolutionary divergence of these nORF genomic regions.
Project description:Purpose: The goal of this study was to assess the differential gene expression between control and leptin treated pituitary rostral pars distalis' of the tilapia (Oreochromis mossambicus). Methods: Pituitary mRNA profiles from control (PBS) and leptin (100nM) treated tilapia (Oreochromis mossambicus) pituitary rostral pars disatalis were generated by deep sequencing using Illumina MiSeq. The sequence reads that passed quality filters were analyzed at the transcript abundance level using ANOVA (ANOVA) and BowTie2 followed by Cufflinks. Results: Differential gene expression identified 1995 genes that were differentially expressed in the pituitary rostral pars distalis treated with leptin compared to PBS treated controls. These genes were indicated to be functionally involved in numerous biological processes including glycolyiss. Conclusions: Our study represents the first detailed pituitary rostral pars distalis transcriptomes in the tilapia and identifies leptin as a major stimulator of glycolysis at the cellular level in teleost fishes.
Project description:Purpose: In an effort to better understand the mechanism of blue light inhibition in Staphylococcus aureus, a whole transcriptome analysis of S. aureus isolate BUSA2288 was performed using RNA-seq to analyze the differential gene expression in response to blue light exposure. Methods: RNA was extracted from S. aureus cultures pooled from 24 one ml well samples illuminated with a dose of 250 J/cm2 of 465 nm blue light, and from control cultures grown in the dark. Complementary DNA (cDNA) were generated from the RNA samples and then sequenced using the Illumina MiSeq Next Generation Sequencer. The combined results of 2 independent experiments were analyzed using the Pairwise Analysis tools in GeneSifter®. The genes were normalized by Mapped Reads using EdgeR statistics including a Benjamini and Hochberg false discovery rate correction. Quality was set at a minimum number of 10 reads and a p value of 0.05. The lower threshold for change was 5 fold. Results: Transcriptomic comparisons using a cutoff of 5 fold identified a total of 28 down-regulated genes and 6 up-regulated genes in the samples that were exposed to blue light. All but 6 of the differentially regulated genes fall into 8 functional categories: amino acid biosynthesis, cell envelope components, cellular processes, central intermediary metabolism, energy metabolism, protein synthesis, regulatory function, and transport and binding proteins. Five genes encode conserved proteins of unknown function. Conclusions: Blue light has been shown to be bactericidal against S. aureus and is a potential alternative therapy for antibiotic resistant organisms. The mechanism for the inactivation of bacteria is hypothesized to involve ROS. We have found evidence that supports this hypothesis that involves multiple pathways including essential metabolic pathways and known virulence pathways.
Project description:Dissolved oxygen (DO) in cultured water is one of the important environment factor in fish farming. Hypoxic environment affects fish growth, metabolism and immune system. Multi-omics integrative analysis helps to uncover the underlying molecular mechanisms. In this study, the 96h median lethal hypoxia (96h-LH50) for Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) was first analyzed by linear interpolation. We built control (5mg/l) and hypoxic stress (96h-LH50) groups, and extracted the liver tissues for high-throughput transcriptome and metabolome sequencing. The identification and quantification results of metabolites showed that a total of 19656 metabolites had been obtained, of which 10390 were annotated. There were 3028 differentially expressed (DE) metabolites, of which 1596 metabolites were up-regulated and 1432 metabolites were down-regulated. We obtained 2375 DE genes, of which 1201 genes were up-regulated and 1174 genes were down-regulated. We verified 8 DE genes by quantitative real-time PCR. Our finding reveals the changes in metabolites and genes expression of GIFT and facilitate the understanding of regulatory pathways under hypoxic stress, which will help reduce the damage caused by hypoxic stress during culture.
Project description:A promising alternative to antibiotics for treatment of Staphylococcus aureus infections is photodynamic inactivation (PDI), which employs a photosensitizer (PS) that produces cytotoxic reactive oxygen species (ROS) when exposed to molecular oxygen and antimicrobial blue light in the spectrum of 400-470 nm. Although the precise mechanistic basis of PDI has not been defined, the formation of ROS and free radicals that oxidize a number of cellular targets, including membrane lipids, damage to proteins and nucleic acids result in inactivation of essential cellular functions and subsequent cell death. Because PDI is non-selective and affects multiple cellular targets, development of resistance or tolerance to PDI has been considered to be unlikely and attempts to induce S. aureus resistance or tolerance upon repeated sub-lethal doses of PDI have not succeeded. However, multiple aspects of PDI suggest that development of tolerance is highly probable, in particular when PDI is used for treatment of infections where the environment at the infection site prevents penetration of PDI at a level sufficient to cause death of all bacteria and with tolerant phenotypes emerging from the surviving bacteria. In this study, we sought to identify the mechanisms that contribute to PDI tolerance in S. aureus. S. aureus HG003 and the isogenic HG003DmutSL strain with defects in DNA mismatch repair were used to evaluate the response of S. aureus and the roles of DNA mismatch repair and gene regulatory networks to repeated sublethal doses of PDI. Global transcriptome and genome analyses were used in an agnostic approach to identify the underlying transcriptional responses and genetic adaptations that occur as a result of repeated PDI and contribute to PDI tolerance. Our results reveal multiple metabolic, transport and cell wall biogenesis pathways that contribute to PDI tolerance, and a S. aureus regulatory gene likely responsible for the adaptive transcriptional response to PDI.