A web services choreography scenario for interoperating bioinformatics applications

Background  

Very often genome-wide data analysis requires the interoperation of multiple databases and analytic tools. A large number of genome databases and bioinformatics applications are available through the web, but it is difficult to automate interoperation because: 1) the platforms on which the applications run are heterogeneous, 2) their web interface is not machine-friendly, 3) they use a non-standard format for data input and output, 4) they do not exploit standards to define application interface and message exchange, and 5) existing protocols for remote messaging are often not firewall-friendly. To overcome these issues, web services have emerged as a standard XML-based model for message exchange between heterogeneous applications. Web services engines have been developed to manage the configuration and execution of a web services workflow.     

Immobilized pH gradient-driven paper-based IEF: a new method for fractionating complex peptide mixtures before MS analysis

Introduction  

The vast difference in the abundance of different proteins in biological samples limits the determination of the complete proteome of a cell type, requiring fractionation of proteins and peptides before MS analysis.     

AlphaV-integrins mediate the mechanoprotective action of osteopontin in podocytes

Increased mechanical load in podocytes due to glomerular hypertension is one of the important factors leading to podocyte damage and chronic kidney disease. In previous studies, we have shown that mechanical stretch increases osteopontin (OPN) expression in podocytes and that exogenous OPN is mechanoprotective via facilitating cytoskeletal reorganization of podocytes. In the present study, we asked whether the mechanoprotective effect of OPN in podocytes is mediated through specific integrins and whether endogenous OPN of podocytes is required for mechanoprotection. Conditionally immortalized mouse podocytes and primary podocytes (PP) from OPN-/- and OPN+/+ mice were used. Cyclic biaxial mechanical stretch (0.5 Hz, 7% linear strain) was applied for up to 3 days. Stretch-induced cell loss was ～30% higher in OPN-/- PP compared with OPN+/+ PP. Increased cell loss of OPN-/- PP was rescued by OPN coating. Analysis of integrin expression by RT-PCR, application of RGD and SLAYGLR peptides and anti-integrin antibodies, small-interfering RNA knockdown of integrins, and application of kinase inhibitors identified αV-integrins (αVβ1, αVβ3, and αVβ5) to mediate the mechano-protective effect of OPN in podocytes involving focal adhesion kinase, Src, phosphatidylinositol 3-kinase, and mitogen-activated protein kinase. Our results demonstrate that endogenous OPN of podocytes plays a nonredundant role in podocyte adaptation to mechanical stretch, and that OPN signaling via α(V)-integrins may represent a relevant therapeutical target in podocytes.     

Gibberellin-like substances and indole type auxins in developing grains of normal- and high-lysine genotypes of barley

Changes in gibberellin-like activity and content of indole type auxins were investigated during grain development of the two high-lysine barley (Hordeum vulgare L.) genotypes Sv 73608 and Risø 1508, and their corresponding normal cultivars Mona and Bomi. A peak in gibberellin-like activity was found in developing grains of the normal cultivars about 18 days after anthesis, whereas the grains of the high-lysine genotypes showed a two to five times higher maximum about 3–4 days later. The auxin content of the cultivar Bomi showed a maximum between the 22nd and the 29th day after anthesis, whereas, throughout their development the grains of the mutant Risø 1508 exhibited only about ¹/10 of the maximum level of auxin found in the grains of Bomi. The normal cultivar Mona also displayed higher contents of auxin than the high-lysine genotypes Sv 73608, particularly at the later stages of grain growth, but the differences in concentration were considerable smaller than for the pair ‘Bomi’—‘Risø 1508’. It is suggested that auxins play an important role in the development of barley grains.     

Der Einfluß von Sauerstoff und Atmungsgiften auf die Auf-nahme und Speicherung saurer und basischer Farbstoffe durch die lebende Pflanzenzelle

Zusammenfassung Die Aufnahme und Speicherung der sulfosauren Farbstoffe Prontosil, Ponceau PR, Bordeauxrot und Brillantsulfoflavin FF durch Epidermis- und Mesophyllzellen von Blumenblättern ist von der Lebenstätigkeit der Zellen abhängig. In einer Stickstoffatmosphäre und bei Zugabe von Stoffwechselgiften unterbleibt eine Anfärbung.Bei gleicher Molarität wirken die untersuchten Stoffwechselgifte in folgender Reihe hemmend auf die Aufnahme und Speicherung sulfosaurer Farbstoffe: Natriumazid > Dinitrophenol > Monojodacetat > KCN. Die Urethane sind erst in höheren Konzentrationen wirksam.Die Parenchymzellen längs der Leitbündel zeichnen sich durch eine besonders ausgeprägte Speicherungsfähigkeit für sulfosaure Farbstoffe aus, die auch noch bei Sauerstoffspannungen und Giftkonzentrationen, die eine Vitalfärbung anderer Zellen bereits verhindern, in Erscheinung tritt.Die beiderseitigen Epidemien der Schuppenblätter vonAllium cepa lassen sich mit der Immersionsmethode mit Prontosil nicht vital färben, dies gelingt aber in Übereinstimmung mit den Befunden von E. Küster (1952) mit der Transpirationsmethode. Aber auch hier unterbleibt eine Anfärbung in einer Stickstoffatmosphäre trotz guter Transpirationsmöglichkeit.Aufnahme und Speicherung der basischen Farbstoffe Neutralrot und Nilblau werden weder durch Sauerstoffmangel noch durch Stoffwechselgifte gehemmt.In den Epidermiszellen und den Parenchymzellen längs der Leitbündel der Blumenblätter vonChrysanthemum leucanthemum undMatricaria chamomilla wird Brillantsulfoflavin FF in kristalliner Form im Zellsaft gespeichert.Herrn Prof. Dr. Friedl Weber zu seinem 70. Geburtstag gewidmet.     

Painting of defined chromosomal regions by in situ suppression hybridization of libraries from laser-microdissected chromosomes

"Painting" of defined chromosomal regions provides a powerful tool for cytogenetic analyses. Here, we demonstrate that chromosomal in situ suppression (CISS)-hybridization of DNA libraries derived by microcloning laser-microdissected chromosomal regions can be applied to achieve this goal. As an example, we used unbanded metaphase spreads from a female patient carrying a balanced translocation. t(1;7)(1qter----1p36::7q11----7qter). Fragments from the long arms of 130 translocation chromosomes were microdissected. After microcloning, human inserts with an average size of about 3 kb were pooled from 400 recombinant bacteriophage DNA clones and used as a complex probe set in CISS-hybridization experiments. This resulted in painting of the translocation chromosome along the region 7q35 to 1p31. Painted chromosomal subregions in normal chromosomes 1 and 7 were consistent with this finding. This approach may be used to perform painting of any chromosome regions for which microlibraries can be established. Possible applications include the definition of marker chromosomes in clinical and tumor cytogenetics and studies of chromosomal evolution, as well as studies of nuclear chromosome topography in animal and plant species.