Project description:Comparison of wild type and heterozygote and homozygote chico mutants ( Clancy, et al. Extension of Life-Span by Loss of CHICO, a Drosophila Insulin Receptor Substrate Protein. Science 292 (5514), 104.) on Affymetrix Drosophila2 GeneChip. The flies (Drosophila melanogaster) are 7 day old adult females.
Project description:Plants and rhizosphere microbes rely closely on each other, with plants supplying carbon to bacteria in root exudates, and bacteria mobilizing soil-bound phosphate for plant nutrition. When the phosphate supply becomes limiting for plant growth, the composition of root exudation changes, affecting rhizosphere microbial communities and microbially-mediated nutrient fluxes. To evaluate how plant phosphate deprivation affects rhizosphere bacteria, Lolium perenne seedlings were root-inoculated with Pseudomonas aeruginosa 7NR, and grown in axenic microcosms under different phosphate regimes (330 uM vs 3-6 uM phosphate). The effect of biological nutrient limitation was examined by DNA microarray studies of rhizobacterial gene expression.
Project description:Time-dependent gene expression patterns during development and antibiotic production on solid growth medium (SMM) comparing a M600 bldA deletion mutant with wild-type M600 of S.coelicolor A3(2). Eight time points matched in all three replicates of both wild-type and mutant were picked to span the entire Streptomyces growth curve.
Project description:Fusarium spp. are fungal pathogens of humans and plants. Fusarium oxysporum and Fusarium solani are important species isolated from infections such as onychomycosis, fungal keratitis, invasive infections, and disseminated diseases. These pathologies have a very difficult therapeutic management and poor therapeutic responses, especially in patients with disseminated infection. Little information is available regarding the molecular mechanisms responsible for antifungal resistance in these fungi. methods: In this study, we performed a quantitative analysis of the transcriptional profile of F. oxysporum and F. solani, challenged with amphotericin B (AMB) and posaconazole (PSC) using RNA-seq. Quantitative real-time reverse transcription PCR (qRT-PCR) was used to validate the results results: Several genes related to mechanisms of antifungal resistance such as efflux pumps, ergosterol pathway synthesis, and responses to oxidative stress were found. Genes such as ERG11, ERG5, the Major Facilitator Superfamily (MFS), thioredoxin, and different dehydrogenase genes may explain the reduced susceptibility of Fusarium spp. against azoles and the possible mechanisms that may play an important role in induced resistance against polyenes. conclusions: Important differences in the levels of transcriptional expression were found between F. oxysporum and F. solani exposed to the two different antifungal treatments. Knowledge on the gene expression profiles and gene regulatory networks in Fusarium spp. during exposure to antifungal compounds, may help to identify possible molecular targets for the development of novel, better, and more specific therapeutic compounds. profile transcriptional of Fusarium spp changed to antifungal treatments in vitro
Project description:Investigation of whole genome gene expression level changes in response to different light conditions of the H. jecorina CBS999.97(MAT1-2) parental strain (W) and the deletion strain delta-env1 (E). These two strains were grown on malt extract agar(Merck) at 25℃ in four different conditions: (1) 24L: constant light illumination (24L); (2) 12L12D: in a 12h light/dark cycle and then 6h light illumination; (3) 12D12L: in a 12h dark/light cycle and then 6h constant darknes; (4) 24D: constant darkness. The wild-type strain is potent for sexual development in 12D12L, 12L12D and 24D, whereas the delta-env1 mutant undergo sexual development only in 24D. By contrast, the wild-type strain is female sterile in 24L, and the delta-env1 mutant is female sterile in 12D12L, 12L12D and 24D. Our results reveal that conidation-specific genes, mating locus gene, h-type maitng pheromone genes, and genes invovled in processing and secretion of h-type mating pheromone are significantly upregulated in all four female sterile conditions (W-24L, E-12L12D, E-12D12L and E-24L). We used two biological replicates of two H. jecorina CBS999.97 (MAT1-2) strains, wild-type (W) and delta-env(E) on the cellophane-covered malt extract agar (MEA) plate at 25℃ for 7.25 days.
Project description:A self-designed Trichoderma high density oligonuclotide (HDO) microarray (Roche-NimbleGen, Inc., Madison, WI, USA) was constructed in a similar way than a previous Trichoderma HDO microarray (Samolski et al., 2009). The microarray was composed of 392,779 60-mer probes designed against 13,443 EST-derived transcripts (Trichochip-1) and the genomes of T. atroviride (11,100 genes) and T. virens (11,643 genes). The Trichochip-1 ESTs were obtained from 28 cDNA libraries from eight different species (representing the biodiversity of this genus: T. harzianum, T. atroviride, T. asperellum, T. viride, T. longibrachiatum, T. virens, T. stromaticum and T. aggresivum), under a wide range of growth conditions, including biocontrol-related conditions and different nutritional situations (Vizcaíno et al., 2006). The Trichochip1 EST database was generated in the TrichoEST project funded by the EU (QLK3-CT-2002-02032). Confrontations were carried out between the T. harzianum T34 or nox1 overexpressed transformant Tnox5 and P. ultimum. Agar plugs cut from the growing edge of a 4-day colony of Trichoderma and Pythium were placed 2 cm from the border on the opposite side of the same petri plates containing PDA covered with sterile cellophane sheets. Dual cultures were allowed to grow at 25 ºC and mycelia were collected from the interaction zone in confrontations between P. ultimum and T. harzianum T34 or Tnox5 strains. Seven PDA plates were used for each condition considered and RNAs were extracted and the corresponding cDNAs were use to hybridize by triplicate the Trichoderma HDO microarray.
Project description:Brassica napus leaves(18 days old) were inoculated by Sclerotinia sclerotiorum with leaves harvested after 12, 24 and 48 h. Arabidopsis thaliana full-genome 70mer microarray representing at least 23,686 genes were used.
Project description:Genomic and proteomic characterization of the Aspergillus niger isolate, JSC-093350089, collected from U.S. segment surfaces of the International Space Station (ISS) is reported, along with a comparison to the experimentally established strain ATCC 1015. Whole-genome sequencing of JSC-093350089 revealed enhanced genetic variance when compared to publicly available sequences of A. niger strains. Analysis of the isolate’s proteome revealed significant differences in the molecular phenotype of JSC-093350089, including increased abundance of proteins involved in the A. niger starvation response, oxidative stress resistance, cell wall integrity and modulation, and nutrient acquisition. Together, these data reveal the existence of a distinct strain of A. niger onboard the ISS and provide insight into the molecular phenotype that is selected for by melanized fungal species inhabiting spacecraft environments.
Project description:Microarray analysis was used to compare gene expression of Aspergillus fumigatus under two different sporulation temperatures, 17oC and 32oC, with an emphasis on genes encoding known or putative allergens of the fungus. The objective of the study was to investigate whether allergenic potencies of A. fumigatus spores produced under different sporulation temperatures would be influenced by temperature-dependent transcriptional regulation of allergenicity genes. Non-sporulating liquid culture of Aspergillus fumigatus was harvested and divided equally onto two sets of potato dextrose agar plates, one set for incubation at 17oC, the other for incubation at 32oC. After 48 hours of incubation, RNA was harvested from both sets of sporulating cultures, reverse-transcribed into dye-coupled cDNA and hybridized onto microarrays for analysis of gene expression. For each experiment, extracted RNA from the two cultures were hybridized onto two dye-swap technical replicate arrays. A total of three separate experiments were conducted for biological triplicates, for a total of six hybridizations.