Project description:Phaeocystis is a globally distributed Prymnesiophyceae genus and usually forms massive harmful colony blooms, which impact marine ecosystem, mariculture, human health, and even threaten coastal nuclear power plant safety. However, the mechanisms behind the colony formation from the solitary cells remain poorly understood. Here, we investigated metabolic processes of both solitary and non-flagellated colonial cells of Phaeocystis globosa at different colonial bloom stages using a metaproteomic approach. Temperature was significantly correlated with Phaeocystis colony bloom formation, and the flagellated motile solitary cells with abundant flagellum-associated proteins, such as tubulin and dynein, were the exclusive cellular morphotype at the solitary cell stage featured with temperatures ≥ 21℃. When the temperature decreased to <21℃, tiny colonies appeared and the flagellum-associated proteins were identified lower abundances in both solitary and non-flagellated colonial cells, while proteins involved in biosynthesis, chain polymerization and aggregation of glycosaminoglycan (GAG), a key constituent of gelatinous matrix, were identified higher abundances, indicating the central role of active GAG biosynthesis during the colony formation. Furthermore, light utilization, carbon fixation, nitrogen assimilation, and amino acid and protein synthesis were also enhanced to provide sufficient energy and substrates for GAG biosynthesis. This study highlighted that temperature induced re-allocation of energy and substances toward GAG biosynthesis is essential for colony bloom formation of P. globosa.
Project description:We found that mainstream cigarette smoking (4 cigarettes/day, 5 days/week for 2 weeks using Kentucky Research Cigarettes 3R4F) resulted in >20% decrease in the percentage of normal Paneth cell population in Atg16l1 T300A mice but showed minimal effect in wildtype littermate control mice, indicating that Atg16l1 T300A polymorphism confers sensitivity to cigarette smoking-induced Paneth cell damage. We performed 16S rRNA sequencing to identify potential microbiota changes associated with Paneth cell defect in Atg16l1 T300A mice exposed to cigarette smoking. Female mice were used at 4-5 weeks of age. Cigarette smoking was performed using smoking chamber with the dosage and schedule as described above. The fecal samples from the mice were collected for 16S rRNA sequencing analysis after completing 6 weeks of smoking.
Project description:Iron-rich pelagic aggregates (iron snow) were collected directly onto silicate glass filters using an electronic water pump installed below the redoxcline. RNA was extracted and library preparation was done using the NEBNext Ultra II directional RNA library prep kit for Illumina. Data was demultiplied by GATC sequencing company and adaptor was trimmed by Trimgalore. After trimming, data was processed quality control by sickle and mRNA/rRNA sequences were sorted by SortmeRNA. mRNA sequences were blast against NCBI-non redundant protein database and the outputs were meganized in MEGAN to do functional analysis. rRNA sequences were further sorted against bacterial/archeal 16S rRNA, eukaryotic 18S rRNA and 10,000 rRNA sequences of bacterial 16S rRNA, eukaryotic 18S rRNA were subset to do taxonomy analysis.
Project description:IL22 induces antimicrobial peptides which influnce microbiota. We used 16s rRNA gene sequencing (16s DNA-seq) to analyze the microbiota with Fc or IL-22Fc treatment.
Project description:A phylogenetic microarray targeting 66 families described in the human gut microbiota has been developped aud used to monitor the gut microbiota's structure and diversity. The microarray format provided by Agilent and used in this study is 8x15K. A study with a total of 4 chips was realized. Arrays 1 and 2: Hybridization with 100ng of labelled 16S rRNA gene amplicons from a mock community sample and 250ng of labelled 16S rRNA gene amplicons from 1 faecal sample. Each Agilent-030618 array probe (4441) was synthetized in three replicates. Arrays 3 and 4: Hybridization with 250ng of labelled 16S rRNA gene amplicons from 2 faecal samples. Each Agilent-40558 array probe (4441) was synthetized in three replicates.
Project description:Comparison of probe-target dissociations of probe Eub338 and Gam42a with native RNA of P. putida, in vitro transcribed 16s rRNA of P. putida, in vitro transcribed 16S rRNA of a 2,4,6-trinitrotoluene contaminated soil and an uncontaminated soil sample. Functional ANOVA revealed no significant differences in the dissociation curves of probe Eub338 when hybridised to the different samples. On the opposite, the dissociation curve of probe Gam42a with native RNA of P. putida was significantly different than the dissociation curves obtained with in vitro transcribed 16S rRNA samples. Keywords: Microbial diversity, thermal dissociation analysis, CodeLink microarray
