Project description:To characterize the ecological interactions among S. cerevisiae strains coming from the same geographical area, we examined the fitness of two natural isolates from San Giovese grapes, alone or in competition, in synthetic wine must (SWM). We performed genome-wide analyses in order to identify the genes involved in yeast competition and cooperation. 2 samples and 4 replicates.
Project description:To characterize the ecological interactions among S. cerevisiae strains coming from the same geographical area, we examined the fitness of two natural isolates from San Giovese grapes, alone or in competition, in synthetic wine must (SWM). We performed genome-wide analyses in order to identify the genes involved in yeast competition and cooperation. 2 samples and 2 replicates.
Project description:The pir genes comprise the largest multi-gene family in Plasmodium, with members found in P. vivax, P. knowlesi and the rodent malaria species. Despite comprising up to 5% of the parasite genome, little is known about the functions of the proteins encoded by pir genes. P. chabaudi causes chronic infection in mice, which may be due antigenic variation. In this model, pir genes are called cirs and may be involved in this mechanism allowing evasion of host immune responses. We have annotated the cir repertoire and performed detailed bioinformatic characterization of the encoded CIR proteins. Two major sub-families were identified: A and B, which display different amino acid motifs, and are thus predicted to have undergone functional divergence. The expression of all cirs was analyzed via RNA sequencing and microarray. Up to 40% of cir genes were expressed in the parasite population during infection, including members of both sub-families. Dominant cir transcripts could also be identified. Finally, specific cir genes were expressed at different time points during the blood stages of infection. Together our data characterizing the cir genes and their expression throughout the intra-erythrocytic cycle of development indicate that CIR proteins are likely to be important for parasite survival in the host. P. chabaudi AS is a highly synchronous parasite for which development in the blood follows its hostM-bM-^@M-^Ys circadian rhythm. Twelve time-points were then collected; one every two hours, to cover the entire 24 h cycle of blood stage development. At the peak of parasitaemia, one mouse was sacrificed at each time point and thin blood films were made and stained with Giemsa for optical microscopy. The pan-rodent microarray was designed using the OligoRankPick program as previously described: Liew, K et al.2010, Defining species specific genome differences in malaria parasites. BMC genomics 11,128. The RNA preparation, Cy-dye coupling to cDNA, hybridization and slide scanning were performed as described by Bozdech and colleagues Bozdech, Z et al 2003, The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 1, E5.
Project description:The Del-Mar 14K chip was used to interrogate differential expression of transcripts in the white isthmus (WI) compared with the adjacent magnum (Mg) and uterine (Ut) segments of the hen oviduct. Differential expression of genes common to both comparisons (WI/Mg and WI/Ut) was detected for 204 annotated proteins. Of these, 58 genes were overexpressed in both WI/Mg and WI/Ut, and are therefore considered to be the most interesting candidates for WI - specific functions. Additionally, general analysis revealed 135 clones hybridizing to overexpressed transcripts (WI/Mg + WI/Ut), and corresponding to 102 NCBI annotatated non-redundant Gallus gallus gene ID~s. This combined analysis revealed that structural proteins highly over-expressed in white isthmus were collagen X (COL10A1), Fibrillin (FBN1) and Cysteine Rich Eggshell Membrane Protein (CREMP). In addition, genes encoding collagen-processing enzymes were over-expressed, as were proteins known to regulate disulfide cross-linking, suggesting that coordinated upregulation of gene networks in the white isthmus is associated with eggshell membrane fibre formation. IPA interactome analysis reinforces the key role of the estrogen receptor and SMAD3 in mediating gene regulation during eggshell membrane synthesis. These results will assist with development of selection strategies to improve eggshell quality and food safety of the table egg. Keywords: Laying hen, eggshell, oviduct, Isthmus expression, cDNA microarray, indirect cDNA labelling, Alexa Fluor dyes Keywords: Expression profiling by array A balanced block hybridization design (Dye switch) was used where half of the samples were labelled with AlexaM-BM-. 555 fluorescent dye and the other half with AlexaM-BM-. 647. A total of 16 microarray slides were used for hybridization to 32 samples that correspond to four tissue contrast (White isthmus versus magnum and uterus versus white isthmus).
Project description:We combined gene expression experiments in response to HDAC inhibitor Depsipeptide with DNA methylation level to assess gene reactivation arising from hypermethylated promoters. We did one experiment with 1 untreated and 1 treated batch of cells
Project description:In order to study the role of chromatin remodeling in transcriptional regulation associated with the progression of the P. falciparum intraerythrocytic development cycle (IDC), we mapped the temporal pattern of chromosomal association with histone H3 and H4 modifications using chromatin-immunoprecipitation coupled to microarray (ChIP-on-chip). Genome-wide distribution of 13 histone modifications for 6 h time points of the 48 h P. falciparum IDC was done using ChIP-on-chip and compared to corresponding transcriptional profiles across the genome
Project description:The microarray experiments were carried out using a long oligonucleotide DNA microarray that represent all 5363 P. falciparum genes with one oligonucleotide per 1.9kb of coding sequence on average (Hu et al. 2007). Total 247 microarray experiments were carried out including 29-drug treatment time courses with 20 compounds and corresponding untreated controls from different drug or inhibitor treatment. Data of each drug/inhibitor experiment were normalized using a linear normalization and background filtering as implemented by the NOMAD database (http://derisilab.ucsf.edu). Time-series sampling and experiments with synchronized ex vivo culturing parasites. Each experiment has treatment and controls, and starts at a specific time of post invasion. For an example of quinine treatment, the treatments start from late ring stage through trophozoite stage of the parasites. First, IC50 is determined by drug assay with synchronized parasites (5% parasiteomia and 2% RBC). Second, synchronized parasite cultures are splitted into 12 flasks (75ml culture/flask) for a 6 time-point time-series experiment. 6 flasks are treated with quinine (final concentration is IC50) and 6 flasks are negative controls. 1,2,4,6,8 and 10 hrs after the treatment, parasites in each flask were harvested for total RNA isolation and microarray hybridizaiton.
Project description:Urothelial cell carcinoma of the bladder (UCC) is a common disease characterized by FGFR3 mutation. Whilst upregulation of this oncogene occurs most frequently in low-grade non-invasive tumors, recent data reveal increased FGFR3 expression characterizes a common sub-type of invasive UCC sharing genetic similarities with lobular breast cancer. These similarities include upregulation of the FOXA1 transcription factor and reduced expression of microRNAs-99a/100. We have previously identified direct regulation of FGFR3 by these two microRNAs and now search for further targets. Using a microarray meta-database we find potential FOXA1 regulation by microRNAs-99a/100. We confirm direct targeting of the FOXA1 3âUTR by microRNAs-99a/100 and also potential indirect regulation through microRNA-485-5p/SOX5/JUN-D/FOXL1 and microRNA-486/FOXO1a. In 292 benign and malignant urothelial samples, we find an inverse correlation between the expression of FOXA1 and microRNAs-99a/100 (r=-0.33 to -0.43, p<0.05). As for FGFR3 in UCC, tumors with high FOXA1 expression have lower rates of progression than those with low expression (Log rank p=0.009). Using global gene expression and CpG methylation profiling we find genotypic consequences of FOXA1 upregulation in UCC. These are associated with regional hypomethylation and near FOXA1 binding sites, and mirror patterns previously reported in FGFR3 mutant UCC. These include gene silencing through aberrant hypermethylation (e.g. IGFBP3) and affect genes that characterize lobular breast cancer (e.g. ERBB2, XBP1). In conclusion, we have identified microRNAs-99a/100 mediate a direct relationship between FGFR3 and FOXA1, and potentially facilitate cross talk between these pathways in UCC. Gene expression profiling of EJ Bladder cancer cells transfected with FOXA1 construct or with empty pUC19 vector.
Project description:TGF-β is a crucial cytokine participate in the interplay between the intermediate host and helminthes. TGF-β receptors were discovered in many cestode, and could bind the human TGF-β. However, the function of host TGF-β on the Echinococcus is still not elucidated, and this paper aim to explore the question at transcription level. Microarray analysis was used to investigate differential expression genes in protoscolices of Echinococcus granulosus cultured in the presence or absence of human TGF-β at different time points (4h, 8h and 24h) in vitro. A total of 523 genes were up- or down-regulated in response to TGF-β, compared with control group, 390 genes were up-regulated and 47 genes were down-regulated at 8h, and 376 genes were up-regulated and 19 genes were down-regulated at 12h, including 310 differential genes were regulated at both time point. Only 1 gene down-regulated at 4 h. Gene ontology (GO) analysis showed that the biological process of the up-regulated genes in protoscolex were predominantly involved in DNA packaging, nucleosome assembly, chromatin assembly, etc. And the cellular component gene were located in cell nucleus. TGF-β appeared to promote growth or development of the protoscolex by up-regulated the gene related with mitosis. In addition, the study also indicated that TGF-β has a multiple influence on the protoscolex, as reflected in the increased stimulation of gene expression of the ErbB signaling pathway, MAPK signaling pathway, Notch signaling pathway and VEGF signaling pathway. Isolated E. granulosus protoscoleces were treated with human TGF-β at different time points (4h, 8h and 24h) in vitro, and replicated 3 times. Each samples independently grown and harvested. And was extracted of total RNA using the TRIZOL Reagent according to the manufacturer's instructions. Gene-expression profiling was performed for each RNA sample separately on the GeneChip of Echinococcus granulosus Genome Array (Capitalbio) at CapitalBio Corporation (Beijing, China). The reference samples are protoscoleces treated by human TGF-β(0 h)
Project description:MicroRNA 21 (miR-21) has been implicated in various aspects of carcinogenesis. However, the function and molecular mechanism of miR-21 in cervical squamous carcinoma has not been studied. Using TaqMan quantitative real-time PCR and Northern blot, we confirmed that miR-21 is significantly overexpressed in human cervical squamous cancer tissues and cell lines. Remarkably, we showed that the level of miR-21 correlates with the nodal status and differentiation by ISH. Furthermore, we demonstrated that miR-21 regulates cervical squamous cells proliferation, apoptosis, and migration which are HPV16 positive. In order to identify the candidate target genes for miR-21, we used gene expression profiling. By luciferase reporter assay, we confirmed the CCL20 gene is one of its targets, which is relative to the HPV16 oncogenes E6 and E7. Our results suggest that miR-21 may be involved in the cervical squamous cell tumorigenesis. Total RNA of cells transfected with anti-miR-21 or scrambled RNA oligonucleotide was extracted using the TRIZOL Reagent according to the manufacturer's instructions. Gene-expression profiling was performed for each pooling RNA sample separately on the GeneChip_ Porcine Genome Array (Affymetrix) at CapitalBio Corporation (Beijing, China) in which GeneChip microarray service was certificated by Affymetrix.