Project description:For aquaculture of carnivorous marine species to continue to expand, dietary fish oil must be replaced with more sustainable vegetable oil alternatives. Most vegetable oils are rich in n-6 polyunsaturated fatty acids (PUFA), specifically 18:2n-6, and their inclusion in feeds reduces the n-3/n-6 PUFA ratio of the fish flesh potentially compromising its nutritional quality. Few vegetable oils are rich in n-3 PUFA but one of these, Camelina oil (CO) is unique in that, in addition to high 18:3n-3 and a high n-3/n-6 PUFA ratio, it also contains substantial levels of C20 and C22 monoenes, similar to fish oil. Cod (initial weight ~0.8 Kg) were fed for 10 weeks with diets in which fish oil was replaced with graded amounts (0 M-bM-^@M-^S 100%) of CO. Growth performance, feed efficiency and fish biometric indices (HSI and VSI) was not significantly affected by increasing dietary CO. Lipid levels of liver tended to increase and those of flesh, decrease, with increasing dietary CO although the data were largely not statistically significant. Reflecting the diet, tissue n-3 long-chain PUFA (LC-PUFA) levels significantly decreased whereas levels of 18:3n-3 and 18:2n-6 increased with increasing inclusion of dietary CO. Dietary replacement of FO by Camelina oil did not appear to induce major metabolic changes in cod intestinal tissue, but rather potentially affected rates of cellular proliferation and death as well as induce changes in the structural properties of the intestinal muscle, most likely leading to different rates of tissue regeneration and/or repair, as well as changes in contractile activity or mechanical characteristics. Our results do not allow us to conclude on the underlying biological reasons explaining these molecular effects but given the important role of the intestine in overall nutrient absorption, further attention should be given to this organ in the future when examining effects of fish oil replacement by vegetable oils.
Project description:We designed a group of probes for detection of known and some putative E. coli sRNAs and included them in a commercial microarray containing a standard set of probes developed by Agilent Technologies for hybridization with E. coli transcripts. To assess the potential of the re-designed microarray to detect E. coli sRNAs, RNA profiling experiments were performed with total RNA extracted from E. coli MG1655 cells in log phase, grown in rich (Luria-Bertani) and minimall (M9/Glucose) media. The microarray data obtained indicate that many sRNAs could yield reasonably strong signals (i.e. considerably above the background). With few exceptions (such as SraA, IstR-1, OmrA, RseX and DicF), nearly all known trans-encoded sRNAs annotated in several databases including EcoCyc, RNAMap and BSRD were detected. The expression patterns of some transcripts were further validated by Northern blot analysis.
Project description:Trancriptional response of pediocin exposure of V583 and V583 expressing immunity (petAIM), and the transcriptional response of petAIM compared to both V583 and V583 containing the vector pet.
Project description:In this experiment we used a custom microarray (accession number A-MTAB-550) to compare the expression of known and predicted sRNAs together with the expression of genes of the standard set of microarray probes of Agilent Technologies in E. coli grown to late exponential phase in minimal media supplemented with glucose and pyruvate respectively as the only carbon source.
Project description:The experiments were aimed at comparison of gene expression patterns of Escherichia coli pcnB mutant (IBPC903) lacking functional poly(A) polymerase I with its isogenic wild-type (N3433) strain grown in Luria-Bertani (LB) by using custom microarrays with improved detection of E. coli sRNAs.
Project description:Little is known about cell survival in the presence of reducing reagents, likewise changing the redox state of living organisms and, therefore potentially conferring a negative effect on respiration and major metabolic pathways. We employed Escherichia coli as a model organism to analyze its responses to sublethal concentrations of sodium sulfite, one of the common food preservatives used for inhibition of microbial growth. We found that partial inhibition of E. coli growth by sodium sulfite was accompanied by profound changes in gene expression. Besides affecting major metabolic pathways, these changes apparently led to reduced production of flagellar proteins, thus potentially impacting cell motility. Concomitantly, E. coli upregulated a number of genes involved in repair of macromolecules and antisense control.
Project description:To understand the relationship between gene expression and capsule formation, H99 cells were cultured overnight at 37ºC in the following eight conditions: low iron medium with or without both 500 mM ethylenediaminetetraacetic acid (EDTA) and 10 mM bathophenanthroline disulfonate (BPDS); phosphate-buffered saline (PBS) with or without 10% v/v fetal bovine serum; Dulbecco's Modified Eagle's Medium (from Sigma) in ambient air or 5% CO2; and Littman's medium with either 0.01 µg/ml or 1 µg/ml thiamine. All samples were hybridized against a common reference pool of total RNA. Three biological replicates were performed for each growth condition, with the exception of growth in DMEM.
Project description:Immunostimulatory CpG ODN trigger an innate immune response characterized by the rapid production of pro-inflammatory cytokines and chemokines, an effect that persists for days to weeks in vivo. Previous studies established that gene up-regulation is maximal 3 hr after CpG ODN treatment of normal mice {Klaschik et al. JLB 2009}. The immunostimulatory activity of CpG ODN is blocked by the addition of immunosuppressive ODN expressing multiple TTAGGG motifs. To clarify the mechanism underlying this suppression, changes in gene expresssion were evaluated by microarray in mice treated with 400 ìg of CpG ODN + 400 ìg of suppressive ODN. Data from 4 independent biological replicates/time point and treatment group and 6 untreated controls were used for all statistical analyses. A reference design was used. Reference cDNA vs. sample cDNA were hybridized to same array.