Project description:Phenotypic plasticity, the ability of one genotype to express different phenotypes in response to changing environmental conditions, is one of the most common phenomena characterising the living world and is not only relevant for the ecology but also for the evolution of species. Daphnia, the waterflea, is a textbook example for predator induced phenotypic plastic defences including changes in life-history, behaviour and morphology. However, the analysis of molecular mechanisms underlying these inducible defences is still in its early stages.<br><br>We exposed Daphnia magna to chemical cues of the predator Triops cancriformis to identify key processes underlying plastic defensive trait formation. D. magna is known to develop an array of morphological changes in the presence of T. cancriformis including changes of carapace morphology and cuticle hardening. To get a more comprehensive idea of this phenomenon, we studied four different genotypes originating from habitats with different predation history, reaching from predator-free to temporary habitats containing T. cancriformis.<br><br>We analysed the morphologies as well as proteomes of predator-exposed and control animals. Three genotypes showed morphological changes when the predator was present. Using a high-throughput proteomics approach, we found 294 proteins which were significantly altered in their abundance after predator exposure in a general or genotype dependant manner. Proteins connected to genotype dependant responses were related to the cuticle, protein synthesis and calcium binding whereas the yolk protein vitellogenin increased in abundance in all genotypes, indicating their involvement in a more general response. Furthermore, genotype dependant responses at the proteome level correlated well with local adaptation to Triops predation.<br><br>Altogether, our study provides new insights concerning genotype dependant and general molecular processes involved in predator-induced phenotypic plasticity in D. magna.
Project description:Antibody microarray based profiling of twelve urine samples.<br>3 healthy female<br>3 heatlhy male<br>3 female with pancreatic cancer<br>3 male with pancreatic cancer<br>
Project description:DNA binding profiling of endogenous HIF1A on proximal promoters in human HeLa cells exposed to 1% oxygen (hypoxia), using normoxic cells (21% oxygen) as reference.<br><br>Biological background: The Hypoxia Inducible Factor Family of transcription factors is proposed as the main orchestrator of the cellular response to hypoxia. HIFs are heterodimers of a HIF alpha and a HIF beta subunit. HIF alpha protein stability is regulated by oxygen-dependent proteasomal degradation, and hence HIFs are strongly stabilized in hypoxia.<br><br>Purpose of the study: a number of HIF1 ChIP-chip studies have been reported, employing various cell types, array platforms and HIF antibodies, and the overlap of HIF binding locations in these studies is relatively small. The aim of this study was to characterize HIF1 binding in an additional cell line (HeLa), and employing a different HIFalpha antibody.<br><br>Experimental design: We conducted a total of six hybridizations employing four biological replicates. For two biological replicates, we performed dye-swap technical replicate experiments.<br><br>Results summary: We identified 55 HIF binding locations in HeLa cells (FDR<2%). While this number is relatively low compared to previous studies, presumably due to limiting antibody sensitivity, the overlap with data from other cell lines is comparable to our HeLa data.
Project description:Within a study RNA samples of synovial fluid polymorphnuclear neutrophil granulocytes from 9 RA patients and of blood PMN from 4 healthy donors were analyzed for anti-apoptotic gene expression. The RNA samples were amplified and labelled red. Control samples (SigM5 cell culture) were labelled green. Each sample and control sample was co-hybrizated on a microarray with 780 inflammatory genes and 20 internal controls. Within the 19 anti-apoptotic genes tested, only the p21cip1waf1, CDKN1A, gene is significantly upregulated.
Project description:This study newly identified Tripelennamine (TA) as an inhibitor of yeast meiosis and sporulation. To examine if and how exposure of sporulating yeast cells to TA changes the meiotic transcriptional program cells were sporulated for 0, 4, and 8 hours in the presence or absence of 100 uM TA.
Project description:Gene expression analysis of S. coelicolor M145 wild type strain, and mutants delta0877 and delta 7173. RNA samples were extracted from 48 h culture samples during growth in flasks in defined mineral medium MG supplemented with 5% of yeast extract. Cy5 labelled genomic DNA was used as the common reference.
Project description:Gene expression profiling studies were performed at various times using a defined in vitro endothelial cell invasion assay system. Total RNA from invading cells was isolated at 0, 6, 12 and 18 hours and subjected to microarray analyses.
Project description:Lactobacillus casei Zhang is a probiotic bacterium isolated from koumiss in Inner Mongolia of China that has been commercially used as a starter in the manufacture of dairy products. To study the gene expression profiles of L. casei Zhang during growth in milk, a whole-genome microarray was used. Compared to L. casei Zhang grown to late logarithmic phase in milk, 61 genes were significantly up-regulated (>5 fold) in stationary phase, whereas 26 genes were down-regulated. Collectively, these data showed that the majority of the identified genes was involved in carbohydrate metabolism and energy production, followed by genes involved in nucleotide metabolism, inorganic ion transport, amino acid transport and metabolism, chaperone, etc. This study demonstrates the fundamental effects of cultural conditions on the transcriptome of L. casei Zhang. Moreover, it improves the understanding of the growth and survival mechanism of the bacterium during the late stage of milk fermentation. L. casei Zhang was grown in milk for 14h (late logarithmic phase) or 18h (stationary phase). 2 biological replicates each.