Project description:To examine the difference of the bovine cells between PBS and IFNT treatment, gene expression profiles were compared. The expressions of 902 genes were significantly higher in granulocytes with IFNT treament than those PBS treatment, whereas 1810 genes were lower (Fold change<1, P=0.05 or lower). The expressions of 555 genes were significantly higher in Bovine Endometrial Stromal cells (BES) with IFNT treatment than those PBS treatment, whereas 874 genes were lower (Fold change<1, P=0.05 or Low) Bovine granulocytes and BES were treated with PBS or IFNT
Project description:Bioelectrochemical systems employing mixed microbial communities as biocatalysts are gaining importance as potential renewable energy, bioremediation, or biosensing devices. While we are beginning to understand how individual microorganism species interact with an electrode as electron donor, not much is known about the interactions between different microbial species in a community. Here, we compare the bioelectrochemical performance of Shewanella oneidensis in a pure-culture and in a co-culture with the homolactic acid fermenter Lactococcus lactis. While S. oneidensis alone can only use lactate as electron donor for current production, the co-culture is able to convert glucose into current with a similar coulombic efficiency of approximately 17%, respectively. With (electro)-chemical analysis and transcription profiling, we found that the BES performance and S. oneidensis physiology were not significantly different whether grown as a pure- or co-culture. These co-culture experiments represent a first step in understanding microbial interactions in BES communities with the goal to design complex microbial communities, which specifically convert target substrates into electricity. Further, for the first time, we elucidated S. oneidensis gene expression with an electrode as the only electron acceptor. The expression pattern confirms many previous studies regarding the enzymatic requirements for electrode respiration, and it generates new hypotheses on the functions of proteins, which are so far not known to be involved in electrode respiration. The BES was either operated with S. oneidensis alone, fed with lactate, or it was operated with S. oneidensis and L. lactis with glucose as primary substrate. The basic medium was a modified M4 medium containing 0.5 g/L yeast extract, 0.5 g/L trypton and 5 g/L glycerol phosphate, besides the commen M4 incredients. S. oneidensis oxidizes lactate to acetate and electrons in a BES - the latter generate a current at a graphite anode. The anode biofilm was harvested after about 4 weeks of continuous BES operation and subjected to total RNA extraction.
Project description:Population dynamics of methanogenic genera was investigated in pilot anaerobic digesters. Cattle manure and two-phase olive mill wastes were codigested at a 3:1 ratio in two reactors operated at 37 ï¾°C and 55 ï¾°C. Other two reactors were run with either residue at 37 ï¾°C. Sludge DNA extracted from samples taken from all four reactors on days 4, 14 and 28 of digestion was used for hybridisation with the AnaeroChip, an oligonucleotide microarray targeting those groups of methanogenic archaea that are commonly found under mesophilic and thermophilic conditions (Franke-Whittle et al. 2009, in press, doi:10.1016/j.mimet.2009.09.017).
Project description:C-to-T base editing mediated by CRISPR/Cas9 base editors (BEs) needs a G/C-rich PAM and the editing fidelity is compromised by unwanted indels and non-C-to-T substitutions. We developed CRISPR/Cpf1-based BEs to recognize a T-rich PAM and induce efficient C-to-T editing with few indels and/or non-C-to-T substitutions. The requirement of editing fidelity in therapeutic-related trials necessitates the development of CRISPR/Cpf1-based BEs, which also facilitates base editing in A/T-rich regions.
Project description:Low concentrations of pharmaceutical compounds were shown to induce transcriptional responses in isolated microorganisms, which could have consequences on ecosystem dynamics. In order to test if these transcriptional responses could also be observed in complex river microbial communities, biofilm reactors were inoculated with water from two distinct rivers and supplemented with environmentally relevant doses of four pharmaceutical products (erythromycin-ER, gemfibrozil-GM, sulfamethazine-SN and sulfamethoxazole-SL). To follow the expression of functional genes, we constructed a 9,600 features anonymous DNA microarray platform onto which cDNA from the various biofilms was hybridized. The reactor design for biofilm development has been previously described (Lawrence et al., 2004; Lawrence et al., 2000). Two duplicate experiments were carried out, with reactors being inoculated with either water from the WC (nutrient rich) or the SSR (nutrient poor). Treatments consisted in the addition of various pharmaceutical compounds: 1 µg l-1 erythromycin (ER), 1 µg l-1 gemfibrozil (GM), 0.5 µg l-1 sulfamethazine (SN), 0.5 µg l-1 sulfamethoxazole (SL). Nothing was added to control reactors (CO). All treatments were replicated independently three times. A reference sample (composite sample from Wascana Creek reactors used to construct the microarray) was hybridized (Cy5) on each slide.
Project description:The present results provided an improved understanding of the changes in the microenvironment during the process of esophageal fibrosis, as well as novel potential targets for the treatment of esophageal fibrosis and BES.