Project description:NF-YC10 is a subunit of the NF-Y transcription factor complex in Arabidopsis thaliana. We identified NF-YC10 as an interactor of the transcription factor DREB2A, which binds to DRE and activate expression of target genes under heat and/or dehydration stress conditions. Transgenic Arabidopsis plants that overexpress NF-YC10 showed stronger expression of DREB2A target genes under heat stress and were more tolerant to heat stress tolerance than the vector control plants. We conducted a transcript profiling by microarray aiming to identify target genes of NF-YC10 under heat stress
Project description:To gain better insight into the molecular link between the post-mating transcriptional and morphological changes and the behavioral and physiological shift induced by copulation in An. gambiae females, we performed an in-depth transcriptional analysis of the female lower reproductive tract (LRT), comprising the atrium and the spermatheca, to identify the molecular pathways specifically regulated in these female reproductive tissues. We analyzed three time points post mating (3, 12 and 24 hours post mating) in order to capture transcriptional changes occurring within a broad time window after copulation. For each time point, tissues were collected from mated and age-matched virgin females and the transcriptional profile compared across 4 biological replicates using Agilent one-color microarrays.
Project description:For the detailed and sensitive detection of the responses to a specific treatment it is important to perform tissue or cell type specific analyses, but this is not easily achievable for the different leaf tissues. Here we developed a method termed MeSelect to effectively separate leaf epidermis, vascular and mesophyll cells basically without contamination from other tissues. The high yield of the MeSelect method allowed for tissue specific high-throughput proteome analyses after inhibition of the proteasome with Syringolin A and the affinity enrichment of polyubiquitylated proteins in epidermis, mesophyll and vasculature.
Project description:Solid-pseudopapillary neoplasm of pancreas (SPN), ductal adenocarcinoma (PCA), neuroendocrine tumor (NET) and non-neoplastic pancreas. comparison with gene expression of tumors and non-tumors To investigate the specific microRNA expression of SPN compared to other types of pancreatic tumor, we analyzed large-scale microRNA expressioin analysis to identify the molecular signature that may affect SPN tumorigenesis with mRNA expression profiles. Differentially expressed microRNAs were analyzed on SPNs, PCAs, NETs and Non-neoplastic tissues.
Project description:Background: It has been shown that intracellular pathogens hijack DC functions to evade immune defense mechanisms. In this study, we investigated the responses of human monocyte derived DCs to four intracellular bacteria, Tropheryma whipplei, Coxiella burnetii, Brucella abortus and Orientia tsutsugamushi, responsible for human infectious diseases and known to infect myeloid cells. Methods: Whole genome microarrays were assessed to define common and specific transcriptionnal responses to bacterial pathogen. Bacterial pathogen ability to affect DC maturation was assessed by measuring lymphoproliferation and endocytosis as well as phenotypic maturation markers (CD80, CD83, CD86 and HLA-DR) expression. Results: We found that Coxiella burnetii, Orientia tsutsugamushi and Brucella abortus induced DC maturation assessed through decreased endocytosis ability, triggering lymphoproliferation, surface expression of HLA class II molecules and phenotypic changes, whereas Tropheryma whipplei did not induce DC maturation. As revealed by microarray analysis, the response of DCs to these bacteria consisted of a core associated with the maturation of DCs and signatures specific for each pathogen. The core response represented 10% of genes modulated in response to pathogens and consisted of general cellular processes including nucleotide binding, protein transport, cell fraction, protein kinase, cell cycle, mitochondrial membrane and cytoskeleton. The specific transcriptional signature induced by C. burnetii is associated with the communication between innate and adaptive immune cells and DC maturation. B. abortus signature specifically involved arachidonic acid and lipooxygenase pathways and O. tsutsugamushi signature involved type I and type III IFN responses. Conclusion: This study demonstrates that intracellular bacteria use multifaceted pathways to induce DC maturation which may lead to unadapted immune response. The understanding of these pathways may be useful to improve our knowledge of bacterial recognition by the immune system but also intracellular bacterial diseases. IL4/GM-CSF monocyte-derived dendritic cells were stimulated by T. whipplei, B. abortus, C. burnetii, O. tsutsugamushi and LPS during 6 hours. Common and specific signatures were determined by comparison with uninfected DCs. moDCs (5.10^6) were plated in 6 well plates and stimulated with bacteria or LPS for 6 hours, and total RNA was extracted using the RNeasy minikit (Qiagen, adresse CA) and DNase treatment. The Agilent-014850 4X44k Human Whole Genome microarrays (Agilent Technologies, CA) representing 44,000 probes were used as recently described. Reverse transcription, sample labeling and hybridization were performed according to protocols specified by the manufacturer (One-Color Microarray-Based Gene Expression Analysis). Three samples per experimental condition were included in the analysis.
Project description:Pancreatic ductal adenocarcinoma (PDAC) remains a lethal disease with a 5-year survival of 4%. A key hallmark of PDAC is extensive stromal involvement, which makes capturing precise tumor-specific molecular information difficult. Here, we have overcome this problem by applying blind source separation to a diverse collection of PDAC gene expression microarray data, which includes primary, metastatic, and normal samples. By digitally separating tumor, stroma, and normal gene expression, we have identified and validated two tumor-specific subtypes including a â€œbasal-like⬝ subtype which has worse outcome, and is molecularly similar to basal tumors in bladder and breast cancer. Furthermore, we define 'normal' and 'activated' stromal subtypes which are independently prognostic. Our results provide new insight into the molecular composition of PDAC which may be used to tailor therapies or provide decision support in a clinical setting where the choice and timing of therapies is critical. Analysis of the landscape of gene expression in pancreatic adenocarcinoma. Data include 145 primary and 61 metastatic PDAC tumors, 17 cell lines, 46 pancreas and 88 distant site adjacent normal samples. Arrays represent distinct samples. The SPOT column in the raw data file (linked to each sample record) contains Agilent feature extraction numbers (included in the 'GPL4133-20424.txt' linked to the platform records).
Project description:Obligate biotrophs such as the virulent powdery mildew Golovinomyces orontii alter plant host cellular architecture, metabolism, and defense in order to acquire nutrients while suppressing cell death and senescence. G. orontii exclusively infects epidermal cells of Arabidopsis with clearly defined stages of infection. Host factors mediating the powdery mildew (PM) interaction are often expressed in the mesophyll cells underlying the infected epidermal cells. Therefore, in order to identify Arabidopsis processes and regulators mediating this PM interaction, we used UV laser microdissection to isolate cells at the PM infection site for global expression profiling. As part of this process, we optimized and/or developed novel tissue preparation, RNA extraction and amplification, and quality control protocols resulting in highly correlated biological replicate data. We focused on the growth and reproduction stage of the PM infection (5 days post infection) when the number of reproductive structures, conidiophores, can be quantified. Site-specific profiling increased our sensitivity dramatically, allowing us to identify specific processes, process components, and their putative regulators hidden in previous whole leaf global expression analyses. For example, the known cell cycle regulator MYB3R4 exhibits altered expression at the site of infection, as do a subset of cell-cycle-associated genes. Furthermore, null myb3r4 mutants exhibit enhanced resistance to PM with reduced conidiophores per colony, suggesting cell cycle control plays an important role in the PM interaction. Experiment Overall Design: Arabidopsis whole leaves from wild type Columbia-0 and enhanced disease susceptibility mutant eds16-1, a null isochorismate synthase 1 (At1g74710) mutant were harvested at 5 days after Golovinomyces orontii infection, microwave-fixed, paraffin-embedded and sectioned. Groups of epidermal and mesophyll cells (~20 cells/group) surrounding the G. orontii infected epidermal cell were cut using a Leica AS laser microdissection (LMD) system. In parallel, groups of epidermal and mesophyll cells were collected from uninfected leaves at 5 days from wild type Arabidopsis. LMD-isolated cells, whole leaf, whole leaf amplified and tissue scrape samples were used for RNA extraction and hybridization to Affymetrix Arabidopsis ATH1 microarrays. Gene expression profiles were obtained for wild type from all samples and for ics1 mutant from LMD infected samples. The experiment includes 2 biological replicates.