Project description:Complex microbial metabolism is key to taste formation in high-quality fish sauce during fermentation. To guide quality supervising and targeted regulation, we analyzed the function of microbial flora during fermentation based on a previous metagenomic database. Most of the identified genes involved in metabolic functions showed an upward trend in abundance during fermentation. In total, 571 proteins extracted from fish sauce at different fermentation stages were identified. The proteins were mainly derived from Halanaerobium, Psychrobacter, Photobacterium, and Tetragenococcus. Functional annotation showed 15 pathways related to amino acid metabolism, including alanine, aspartate, glutamate, and histidine metabolism; lysine degradation; and arginine biosynthesis.
Project description:In order to identify the genes induced by different bacterial cells, which may contain different types of pathogen associated molecular patterns (PAMPs), high-throughput gene expression analyses using Agilent custom-oligo DNA microarray containingon 9,573 probes constructed for Japanese flounder Paralichthys olivaceus were conducted. A number of genes showed significant changes in mRNA levels. However, there are no significant difference in a manner of the changes among the different bacterial cell treatments. The genes significantly induced by the treatments included well-known immune-related genes such as granulocyte-colony stimulation factor, haptoglobin, hepcidin. The kidney were isolated from the formalin killed cells (FKCs) intraperitoneal injected Japanese flounder, Paralichthys olivaceus using the four formalin-killed cells, Edwardsiella tarda strain 54, Lactococcus garviae strain EH8706, Streptococcus iniae strain 02 and Vibrio anguillarum strain H775-3, respectively. Fishes were administered by an intraperitoneal injection using the 1.0 x 10^7 to 1.0 x 10^8 cells of FKCs. After 6 hours from a injection, fish kidney was isolated. We also isolated phosphate-bufferd seline injected fish kidney as a control. We analyzed a four samples in control. We also analyze a three samples in FKC injected fish (16 hybridization).
Project description:Clonal communities of single celled organisms, such as bacterial or fungal colonies and biofilms, are spatially structured, with subdomains of cells experiencing differing environmental conditions. In the development of such communities, cell specialization is not only important to respond and adapt to the local environment but has the potential to increase the fitness of the clonal community through division of labor. Here, we examine colony development in a yeast strain (F13) that produces colonies with a highly structured “ruffled” phenotype in the colony periphery and an unstructured “smooth” phenotype in the colony center. We demonstrate that in the F13 genetic background deletions of transcription factors can either increase (dig1 deletion, sfl1 deletion) or decrease (tec1deletion) the degree of colony structure. We identify genes responding additively and non-additively to the genotype and spatiotemporal factors and cluster these genes into a number of different expression patterns, including patterns that correlate closely with the degree of colony structure in each sample and include genes with known roles in the development of colony structure. Individual deletion of 26 genes sampled from different clusters identified 5 with strong effects on colony morphology (BUD8, CIS3, FLO11, MSB2 and SFG1), all of which eliminated or greatly reduced the structure of the F13 outer region.