Expression profile of ACC-overexpressed wild type yeast strain
ABSTRACT: Individualized outcome prediction classifiers were successfully constructed through expression profiling of 1918 genes connected with lipid metabolism in yeast strain overexpressed of fatty acid biosynthesis gene In the study presented here, expression profiles of wild type and ACC-overexpressed wild type yeast strain were well-clustered by profiles- and gene similarities. It was analyzed the gene expression profile of ACC-overexpressing as compared with those of wild type. The expression levels between wild type(WT) and ACC-overexpressed wild type(ACC) were compared individually three times.
Project description:Although the majority of previous work on campylobacteriosis has centered on the species Campylobacter jejuni, Campylobacter coli, the sister group to C. jejuni, is also a significant problem, but remains a much less studied organism. The purpose of this study was to develop and apply an expanded 16 locus MLST genotyping scheme to a large collection of C. coli isolates sampled from a wide range of host species, and to complete microarray comparative genomic hybridizations for these same strains, in order to: (1) determine whether host specific clones, genotypes, or clonal complexes are evident and (2) evaluate whether there are particular genes comprising the dispensable portion of the C. coli genome that are more commonly associated with certain host species. Genotyping and ClonalFrame analyses of the expanded MLST data suggest that (1) host preferred groups have tended to evolve in the diversification of C. coli, (2) this has happened repeatedly, at different times, throughout the evolutionary history of the species, and (3) recombination has played varying roles in the diversification of the different groups. Concomitant with the information on evolutionary history derived from the MLST data, the microarray data suggests that a combination of common ancestry in some cases and lateral gene transfer in others are behind a tendency for sets of genes to be common to isolates derived from particular hosts. Keywords: comparative genomic hybridization Combimatrix CustomArray™ 4X2K was used in this study. This array is divided into 4 sectors, each of which contains 2,240 in situ synthesized oligonucleotide probes (spots) with the same probe design and layout. Based on the sequence of Campylobacter coli strain RM2228, oligonucleotide probes were designed to have a similar annealing temperature of 56ºC and a length 35-40 bp. Two separate designs were used in this study; both included 100 control probes (20 negative controls with sequences from plant and phage, each with 5 replicate spots) as well as loci from the RM2228 genome. Because of the strict criteria for probe design, not all ORFs could be covered in this analysis. The first design included 1942 of the 1967 protein coding genes described in the unfinished sequence of C. coli strain RM2228. The second-generation design was based on genes that were not clearly present (loci with low intensity or no hybridization for at least one strain) in the hybridization results involving the first design. The second design included additional two or five probes, separated from one another in order to span the entire gene, for these 615 ambiguous loci, synthesized in situ to occupy the 2,240 independent microarray spots. Replicate microarrays were hybridized for every 65 strains tested in this study.
Project description:Petunia is an excellent model system, especially for genetic, physiological and molecular studies. Thus far, however, genome-wide expression analysis has been rarely applied because of the lack of sequence information. We applied next-generation sequencing to generate, through de novo read assembly, a large catalogue of transcripts for Petunia axillaris and Petunia inflata. On the basis of the transcriptome of each species, comprehensive microarray chips for gene expression analysis were established and used for the analysis of global- and organ-specific gene expression in both species. In addition, microarray analysis was applied to explore the molecular basis of the seed coat defects in Petunia hybrida mutants, homozygous for a null allele of the AN11 gene, encoding a WDR transcription regulator. Among the transcripts differentially expressed in an11 seeds compared to wild type, many expected targets of AN11 were found but also several interesting new candidates that might play a role in morphogenesis of the seed coat. Our results validate the combination of next-generation sequencing with microarray analyses strategies to identify the transcriptome of two petunia species without previous knowledge of their genome, and to develop comprehensive chips as useful tools for the analysis of gene expression in P. axillaris, P. inflata and P. hybrida. The manuscript describes the creation by next generation sequencing of a large catalogue of the transcriptome of the two Petunia species, that are considered to represent the natural material from which the breeders selected their varieties. This submission represents the transcriptome component of study. The high throughput sequencing data were submitted to SRA (accession numbers: SRA027293, SRP004866.1, SRX036999.2, SRX036998.2).
Project description:Bifidobacteria represents one of the dominant group of microorganisms colonizing the intestine of infants. However, the genetic determinants supporting the establishment and the interaction with the human hosts are still largely unknown. Most commensal bacteria interacting with eukaryotic hosts express adhesive molecules on their surfaces that modulate interaction with host cell receptors or with soluble macromolecules. Whole genome transcription profiling of B. bifidum PRL2010, a strain isolated from infant stool, under in vitro as well as in vivo conditions revealed the expression of few common extracellular proteins among which type 1 pili encoding genes. To investigate the molecular mechanisms sustaining the interaction of PRL2010 strain with the human gut, we first explored the global genome transcription profiling of this strain in a in vitro human model such as in the presence of HT29 cell lines. The transcriptome was analyzed using a custom B. bifidum PRL2010 array representing the 90% of this organism’s protein coding genes. To better evaluate the conserved responses by B. bifidum, the in vivo transcriptomes were quantified against a diverse set of transcriptome patterns identified for in vitro laboratory cultures of the strain, i.e., B. bifidum responses after growth on an cell’s monolayers growth medium (DMEM); B.bifidum responses after growth on synthetic medium (MRS). Briefly, we analized five conditions, two of which are also used as references. Every experiment was performed in duplicate and in vivo condition was performed in quadruplicate.
Project description:In this study, we investigated the transcriptome of Bifidobacterium bifidum PRL2010 during in vitro growth by micro array technology. When B. bifidum PRL2010 was grown in liquid broth, 425 of the 1644 PRL2010 genes represented on the array were expressed in at least one of the three investigated growth phases, i.e., lag-, exponential and stationary phase. These transcriptional analyses identified a core in vitro transcriptome encompassing 150 genes, which resulted expressed in all phases. A proportion of the latter genes were further investigated as potential reference genes by Quantitative Real Time PCR (qRT-PCR) assays. Their expression stability was evaluated under different growth conditions, encompassing cultivation on different carbon sources, exposure to environmental stresses (thermal, acidic and osmotic) and growth phases. Our analyses validated six reference genes suitable for normalizing mRNA expression levels in qRT-PCR experiments applied to bifidobacteria. Transcriptional profiling of B.bifidum PRL2010 at different growth phases (lag phase, early exponential phase, late exponential phase, early stationary phase).
Project description:To obtain insights about the roles of VvMYB5a and VvMYB5b, here we perform complementation analyses using petunia regulatory mutants impaired in pigment accumulation in flower epidermis, proven to be a valid tool for gene functional studies. We created three transgenic petunia lines overexpressing VvMYB5a, VvMYB5b and VvMYBA1 and we compared petal transcriptomes of each overexpressors with the untransformed one.
Project description:In dairy ruminants transcriptome profiling has enabled the identification of genes, pathways and regulatory networks activated in mammary tissues during experimental infection by various pathogens, including E. coli, S. aureus and S. uberis. Information in goats are still low and many host-pathogen interaction mechanisms have to be explained. The objectives of the present study were (1) to identify the network of genes that becomes activated in caprine blood and milk somatic cells in early response towards a S. aureus challenge in order to better understand the local and sistemic response and (2) to search any difference in this immune response by using two animal groups belonging to a caprine reference family established based on founders with adverse SCC breeding values. Udders from ten healthy French Alpine goats were infected with S. aureus and samples of blood and milk cells were collected at 0, 24 and 30 hours after infection. Alterations in the transcriptome profile were investigated using a custom bovine DNA microarray containing 43.822 unique gene probes.
Project description:We have used cDNA-AFLP and microarray analyses to profile the response of the tomato meiotic anther transcriptome to moderate heat stress condition in Moneymaker or Falcorosso and HeatSet1 tomato genotype. Combimatrix microarray technology were applied to obtain a general overview of the gene expression in meiotic anthers of a tolerant and a sensitive tomato genotype. We analyzed three time points (0,2,and 6h) for each genotype. For each sample we performed three biological replicates.
Project description:The aim of this study was to determine the extent of the trxR regulon in the M1 serotype MGAS5005. Gold, Leday, McIver 2008 Keywords: Wild-type vs trxR- series contains MGAS5005 and MGAS5005.trxR (trxR-) from three independent isolations. cDNA ratios from these isolations as well as their dye swap included