Project description:We sampled lake-type and riverine sockeye in the pristine natural habitats of Aniakchak National Monument and Preserve, Alaska USA.
Project description:We sampled lake-type and riverine sockeye in the pristine natural habitats of Aniakchak National Monument and Preserve, Alaska USA. Samples were taken on the same day and close proximite in time. We sampled 17 riverine individuals from Albert Johnson Creek and 13 individuals from Surprise Lake. cDNA from a single individual on the Cy5 was compared with a reference of aRNA on the Cy3.
Project description:Triplets of Lactobacullus plantarum strains were isolated from nine contrasting habitats. Without any passage through other culture media, isolation and cultivation were on model media that strictly reproduced the chemical and physical conditions and stressors of the habitats of origin. Here, we demonstrated how L. plantarum regulates and shapes its transcriptome in response to contrasting habitats. Firstly, multivariate clustering analysis of transcriptional data (RNA-Seq), complemented with metabolomics and phenomics, grouped the strains according to the habitats of origin. Subsequently, selected strains from each habitat switched to repeated cultivation on MRS medium and transcriptomes homogenized into a unique cluster. Adaptation to this common medium mainly relied on activation of genes for phage- and prophage-related proteins and transposases. Finally, the comparison of growth across model media and with respect to MRS medium showed that 44% of the overall 3,112 gene transcripts changed depending on the specific habitat. Regulation and shaping of transcriptomes mainly concerned carbohydrate acquisition, pyruvate catabolism, proteolytic system and amino acid, lipid and inorganic ion transport and metabolism, with contrasting responses for contrasting habitats. Pathways reconstruction demonstrated how the large genome size of L. plantarum imparts transcriptome and metabolic flexibility as the basic mechanism for a nomadic lifestyle.
Project description:Purpose: Study transcriptome differences between biofilm, planktonic and stationary cultures. Methods: Total mRNA from in vitro cultures was extracted and sequenced using Ion Torrent PGM sequencer. Results: Characteristic transcriptomic profile was observed for biofilm, planktonic and stationary cultures. Biofilm and planktonic were similar biological states. Conclusions: Results suggest that H. parasuis F9 has more active metabolism during biofilm or planktonic growth when compared to stationary culture. Some identified membrane-related genes could play an important role in biofilm life.
Project description:The primary mammary epithelial cells of riverine buffalo were exposed to thermal stress condition at 42C for one hour. The cells were subsequently allowed to recover at 37C and harvested at different time intervals (30 min to 48 h) along with control samples (un-stressed). The study has identified several genes from different functional classes and biological pathways which could be termed as heat responsive in buffalo MEC
Project description:To combat dental implant-associated infections, there is a need for novel materials which effectively inhibit bacterial biofilm formation. In the present study, a titanium surface functionalization based on the “slippery liquid-infused porous surfaces” (SLIPS) principle was analyzed in an oral flow chamber system. The immobilized liquid layer was stable over 13 days of continuous flow. With increasing flow rates, the surface exhibited a significant reduction in attached biofilm of both the oral initial colonizer Streptococcus oralis and an oral multi-species biofilm composed of S. oralis, Actinomyces naeslundii, Veillonella dispar and Porphyromonas gingivalis. Using single cell force spectroscopy, reduced bacterial adhesion forces on the lubricant layer could be measured. Gene expression patterns in biofilms on SLIPS, on control surfaces and planktonic cultures were also compared. For this purpose, the genome of S. oralis strain ATCC® 9811TM was sequenced using PacBio Sequel technology. Even though biofilm cells showed clear changes in gene expression compared to planktonic cells, no differences could be detected between bacteria on SLIPS and on control surfaces. Therefore, it can be concluded that the ability of liquid-infused titanium to repel biofilms is solely due to weakened bacterial adhesion to the underlying liquid interface.
Project description:PA3225 is a LysR-type transcriptional regulator, and the ΔPA3225 deletion mutant is more resistant to various antibiotics than the wild-type PA14 strain in both planktonic and biofilm cells. In order to characterise the regulon of PA3225, we compared the transcriptomes of biofilm and planktonic ΔPA3225 to biofilm and planktonic PA14 wild-type by RNA-seq.
Project description:Interactions between human keratinocytes and secreted factors from Staphylococcus aureus biofilm and planktonic cultures were investigated using microarray analysis. Relative to planktonic secreted factors, biofilm secreted factors up regulated cytokine and chemokine genes in keratinocytes. Genes associated with DNA damage and oxidative stress were also induced in keratinocytes treated with secreted factors from S. aureus biofilm. Here we show that secreted factors from S. aureus planktonic (PCM) and biofilm (BCM) cultures differentially impact several aspects of wound healing processes.