Project description:Establishment of a tumor bank, consisting of blood samples of tumor patients and healthy people as controls. The blood samples will be collected systematically together with the corresponding clinical data. The biological samples, the clinical date together with prospective experimental date constitute the entity of the tumor bank.
Project description:During seed germination, desiccation tolerance is lost in the radicle with progressing radicle protrusion and seedling establishment. This process is accompanied by comprehensive changes of the metabolome and proteome. Germination of Arabidopsis seeds was investigated over 72 h with special focus on the heat-stable proteome including late embryogenesis abundant (LEA) proteins together with changes of primary metabolites. Six metabolites in dry seeds known to be important for seed longevity decreased during germination and seedling establishment, while all other metabolites increased simultaneously with activation of growth and development. Thermo-stable proteins were associated with a multitude of biological processes. In the heat-stable proteome a relatively similar proportion of fully ordered and fully intrinsically disordered proteins (IDP) was discovered. Highly disordered proteins were found to be associated with functional categories development, protein, RNA and stress. As expected, the majority of LEA proteins decreased during germination and seedling establishment. However, four germination-specific dehydrins were identified, not present in dry seeds. A network analysis of proteins, metabolites and amino acids generated during the course of germination revealed a highly connected LEA protein network.
Project description:Establishment of a tumor bank, consisting of tissue samples of tumor patients (benign and malign tumors) and healthy people as controls. The tissue samples will be collected systematically together with the corresponding clinical data. The biological samples, the clinical date together with prospective experimental date constitute the entity of the tissue tumor bank.
This tumor bank for tissue samples, together with our tumorbank for blood samples (NCT01763125) combined constitute the entity "Tumorbank".
| 2139890 | ecrin-mdr-crc
Project description:Slow seedling establishment of switchgrass
Project description:The developmental program of seed formation and seedling development requires not only tight regulation of cell division and metabolism but also the adaption of organelles in structure and function. Therefore, changes in organellar protein composition is one crucial factor in development. Of particular interest in plants is the switch to photoautotrophic growth, for which biosynthesis and degradation of lipid droplets (LDs) play a critical role. We present here a bottom-up proteomics study analyzing eight different developmental phases during silique development, seed germination and seedling establishment. We investigated both total protein fractions and LD-enriched fractions for each time point. The overall changes in the seed and seedling proteome during germination and seedling establishment monitored in this study present a rich resource for researchers interested in different questions of early seedling biology. The analysis of the proteome of LDs using LD-enrichment factors allowed the identification of four LD-associated protein families, which were subsequently confirmed by a cell biological approach. In addition to protein discovery, our dataset allows for the study of the dynamics of LD proteins throughout the developmental phases analyzed. We found that the relative levels of oleosin stay stable, while many other proteins accumulate on LDs at later stages of seedling establishment. The methodology described here is shown to be well suited for describing a comprehensive and quantitative view of the Arabidopsis proteome across time, with a particular focus on proteins associated with LDs.
Project description:The developmental program of seed formation and seedling development requires not only tight regulation of cell division and metabolism but also the adaption of organelles in structure and function. Therefore, changes in organellar protein composition is one crucial factor in development. Of particular interest in plants is the switch to photoautotrophic growth, for which biosynthesis and degradation of lipid droplets (LDs) play a critical role. We present here a bottom-up proteomics study analyzing eight different developmental phases during silique development, seed germination and seedling establishment. We investigated both total protein fractions and LD-enriched fractions for each time point. The overall changes in the seed and seedling proteome during germination and seedling establishment monitored in this study present a rich resource for researchers interested in different questions of early seedling biology. The analysis of the proteome of LDs using LD-enrichment factors allowed the identification of four LD-associated protein families, which were subsequently confirmed by a cell biological approach. In addition to protein discovery, our dataset allows for the study of the dynamics of LD proteins throughout the developmental phases analyzed. We found that the relative levels of oleosin stay stable, while many other proteins accumulate on LDs at later stages of seedling establishment. The methodology described here is shown to be well suited for describing a comprehensive and quantitative view of the Arabidopsis proteome across time, with a particular focus on proteins associated with LDs.
Project description:During germination and early seedling development plants rely entirely on their seed storage compounds to provide energy and precursors for the synthesis of macromolecular structures such as cell walls until the seedling has emerged from the soil and photosynthesis can be established. Lupin seeds use proteins as their major storage compounds, accounting for up to 40% of the seed dry weight. Lupins are therefore a valuable complement to soy as a source of plant protein for human and animal nutrition. However, knowledge on protein and amino acid metabolism during germination and seedling establishment in lupin plants is still limited. The aim of this study was to elucidate how storage protein metabolism is coordinated with other metabolic processes to meet the requirements of the growing seedling. In a quantitative approach, we analyzed seedling growth, as well as alterations in biomass composition, the proteome, and metabolite profiles during germination and seedling establishment in Lupinus albus. The reallocation of nitrogen resources from seed storage proteins to functional seed proteins was mapped based on a manually curated functional protein annotation database. Although classified as a protein crop, Lupinus albus does not use amino acids as a primary resource during germination. The predominant role of the stored proteins is to act as a nitrogen resource for vigorous post-germinative growth. The degradation of storage lipids and carbohydrates is sufficient to meet the energy requirements for early seedling establishment until the onset of photosynthesis. However, our results suggest that during germination fatty acid and amino acid metabolism may be integrated at the level of malate synthase to combine stored carbon from lipids and proteins into gluconeogenesis.
Project description:In Arabidopsis mature seeds, the onset of the embryo-to-seedling transition is nonautonomously controlled, being blocked by endospermic abscisic acid (ABA) release under unfavorable conditions. Mature embryos lack an impermeable cuticle, unlike seedlings, consistent with their endospermic ABA uptake capability. Seedling cuticle formation occurs after germination rather than during embryogenesis. Mature endosperm removal prevents seedling cuticle formation and seed reconstitution by endosperm grafting onto embryos shows that the endosperm promotes seedling cuticle development. Grafting different endosperm and embryo mutant combinations, together with biochemical, microscopy and mass spectrometry approaches, reveals that endospermic release of Tyrosyl Sulfate Transferase (TPST)-sulfated CIF2 and PSY1 peptides promotes seedling cuticle development. Endosperm-deprived embryos produced nonviable seedlings bearing numerous developmental defects, in a manner unrelated to embryo nourishment, all restored by exogenously provided endosperm. Hence, seedling establishment is nonautonomous, requiring the mature endosperm.
Project description:Establishment and molecular characterization of 239 peritoneally-metastatic cancer cell lines from 170 patients’ ascites in 11 kinds of cancers mainly consisted of gastric, pancreatic, and ovarian cancer. We performed comparative transcriptome analyses using microarrays between our established cancer cell lines and cell-bank derived cancer cell lines
Project description:Seed germination involves transition from desiccation tolerance to sensitivity during early stages of seedling establishment accompanied by comprehensive changes of metabolome and proteome. Germination of Arabidopsis seeds was investigated over 72 h with special focus on the heat-stable proteome including late embryogenesis abundant (LEA) proteins together with changes of primary metabolites. Six metabolites in dry seeds important for seed longevity decreased during germination and seedling establishment, while all other metabolites increased simultaneously with activation of growth and development. In the heat stable proteome an almost equal fractioning of ordered and intrinsically disordered proteins (IDP) was discovered. Highly disordered proteins were assigned to functional bins development, protein, RNA and stress. Thermal stable proteins were related to a multitude of active biological processes. The majority of LEA proteins decreased during germination and seedling establishment in parallel to reduced desiccation tolerance. Five germination specific dehydrins were identified most likely providing stress tolerance. Network analysis of common proteins and metabolites over all time points revealed a tight network of LEA proteins with five hub LEAs with high connectivity. Connections to proteins such as Rubisco large subunit and seed storage proteins were discovered. Insights into the heat-stable proteome – metabolome network during seed germination are provided.