Crossfit analysis: a novel method to characterize the dynamics of induced plant responses

Background  

Many plant species show induced responses that protect them against exogenous attacks. These responses involve the production of many different bioactive compounds. Plant species belonging to the Brassicaceae family produce defensive glucosinolates, which may greatly influence their favorable nutritional properties for humans. Each responding compound may have its own dynamic profile and metabolic relationships with other compounds. The chemical background of the induced response is therefore highly complex and may therefore not reveal all the properties of the response in any single model.     

Classification-based comparison of pre-processing methods for interpretation of mass spectrometry generated clinical datasets

Background  

Mass spectrometry is increasingly being used to discover proteins or protein profiles associated with disease. Experimental design of mass-spectrometry studies has come under close scrutiny and the importance of strict protocols for sample collection is now understood. However, the question of how best to process the large quantities of data generated is still unanswered. Main challenges for the analysis are the choice of proper pre-processing and classification methods. While these two issues have been investigated in isolation, we propose to use the classification of patient samples as a clinically relevant benchmark for the evaluation of pre-processing methods.     

More robust detection of motifs in coexpressed genes by using phylogenetic information

Background  

Several motif detection algorithms have been developed to discover overrepresented motifs in sets of coexpressed genes. However, in a noisy gene list, the number of genes containing the motif versus the number lacking the motif might not be sufficiently high to allow detection by classical motif detection tools. To still recover motifs which are not significantly enriched but still present, we developed a procedure in which we use phylogenetic footprinting to first delineate all potential motifs in each gene. Then we mutually compare all detected motifs and identify the ones that are shared by at least a few genes in the data set as potential candidates.     

Evidence based guidelines for complex regional pain syndrome type 1

Background  

Treatment of complex regional pain syndrome type I (CRPS-I) is subject to discussion. The purpose of this study was to develop multidisciplinary guidelines for treatment of CRPS-I.     

Bacterial networking

A report of the ESF-EMBO Symposium Bacterial Networks (BacNet08), Sant Feliu de Guixols, Spain, 13-18 September 2008.     

mlstdbNet – distributed multi-locus sequence typing (MLST) databases

Background  

Multi-locus sequence typing (MLST) is a method of typing that facilitates the discrimination of microbial isolates by comparing the sequences of housekeeping gene fragments. The mlstdbNet software enables the implementation of distributed web-accessible MLST databases that can be linked widely over the Internet.     

Analysis of insulin-receptor phosphorylation sites in intact cells by two-dimensional phosphopeptide mapping.

Insulin stimulates the autophosphorylation of the partially purified insulin receptor initially on tyrosine residues 1146, 1150 and 1151. This is followed by increased autophosphorylation of tyrosine residues 1316, 1322 and two further residues, possibly tyrosine residues 953 and 960 or 972 [Tavaré & Denton (1988) Biochem. J. 252, 607-615]. In the present paper we have used two cell lines transfected with insulin-receptor cDNA (CHO.T and NIH 3T3 HIR3.5 cells) to assess which tyrosine residues are phosphorylated on the insulin receptor within intact cells. We show that: (1) insulin causes a rapid increase in phosphorylation of tyrosine residues 1146, 1150 and 1151 in both cell types; tyrosine residues 1316 and 1322 are also phosphorylated, but apparently to a lesser extent in NIH 3T3 HIR3.5 cells; (2) the sites that may correspond to tyrosine residues 953 and 960 or 972 appear to be very poorly phosphorylated in both intact cell types; (3) insulin also promotes a substantial and rapid increase in the phosphorylation of serine and threonine residues on insulin receptors on CHO.T cells; this results in the appearance of two phosphopeptides not evident in the maps of the solubilized receptor preparations autophosphorylated in vitro.     

Synergistic enhancement of type I and III collagen production in cultured fibroblasts by transforming growth factor-β and ascorbate

Transforming growth factor-β (TGF-β) is a prototype of a family of polypeptides that regulates cellular growth and phenotypic differentiation [(1986) Science 233, 532-534; (1987) Cell 49, 437-438]. TGF-β injection induces angiogenesis and fibrosis locally [(1986) Proc. Natl. Acad. Sci. USA 83, 4167-4171; (1987) Science 237, 1333-1336] and stimulates the synthesis of extracellular matrix proteins, fibronectin, collagens, and proteoglycans in vitro in many cell types [(1986) J. Biol. Chem. 261, 4337-4345; (1987) Biochem J. 247, 597-604]. Ascorbate is also known to induce collagen synthesis and to promote wound healing [(1988) J. Invest. Dermatol. 90, 420-424; (1986) Coll. Rel. Res. 6, 455-466]. We report that in cultured human skin fibroblasts, ascorbate and TGF-β synergistically enhance the biosynthesis of type I and III collagens and their steady-state mRNAs. TGF-β alone has no enhancing effect on type III collagen synthesis. The cooperation between ascorbate and TGF-β may be of significance in wound healing and in disorders of fibrosis.