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Background With the current technological advances in high-throughput biology, the necessity to develop tools that help to analyse the massive amount of data being generated is evident. A powerful method of inspecting large-scale data sets is gene set enrichment analysis (GSEA) and investigation of protein structural features can guide determining the function of individual genes. However, a convenient tool that combines these two features to aid in high-throughput data analysis has not been developed yet. In order to fill this niche, we developed the user-friendly, web-based application, PhenoFam. Results PhenoFam performs gene set enrichment analysis by employing structural and functional information on families of protein domains as annotation terms. Our tool is designed to analyse complete sets of results from quantitative high-throughput studies (gene expression microarrays, functional RNAi screens, etc.) without prior pre-filtering or hits-selection steps. PhenoFam utilizes Ensembl databases to link a list of user-provided identifiers with protein features from the InterPro database, and assesses whether results associated with individual domains differ significantly from the overall population. To demonstrate the utility of PhenoFam we analysed a genome-wide RNA interference screen and discovered a novel function of plexins containing the cytoplasmic RasGAP domain. Furthermore, a PhenoFam analysis of breast cancer gene expression profiles revealed a link between breast carcinoma and altered expression of PX domain containing proteins. Conclusions PhenoFam provides a user-friendly, easily accessible web interface to perform GSEA based on high-throughput data sets and structural-functional protein information, and therefore aids in functional annotation of genes.

The salamander is the only tetrapod that regenerates complex body structures throughout life. Deciphering the underlying molecular processes of regeneration is fundamental for regenerative medicine and developmental biology, but the model organism had limited tools for molecular analysis. We describe a comprehensive set of germline transgenic strains in the laboratory-bred salamander Ambystoma mexicanum (axolotl) that open up the cellular and molecular genetic dissection of regeneration.We demonstrate tissue-dependent control of gene expression in nerve, Schwann cells, oligodendrocytes, muscle, epidermis, and cartilage. Furthermore, we demonstrate the use of tamoxifen-induced Cre/loxP-mediated recombination to indelibly mark different cell types. Finally, we inducibly overexpress the cellcycle inhibitor p16INK4a, which negatively regulates spinal cord regeneration. These tissue-specific germline axolotl lines and tightly inducible Cre drivers and LoxP reporter lines render this classical regeneration model molecularly accessible.

Diploma thesis is focused on creation of educational materials supporting the education of biochemistry, specifically amino acids and proteins, at secondary level. At first the analysis of Czech chemistry textbooks concerning the two topics - amino acids and proteins was performed. The major problems found were related to the insufficient graphical representation of biomolecules, unsatisfactory motivational components and insufficient integration of the topic with biology or everyday life experience. The supporting educational materials, presented in this work, supplement the widely used chemistry textbooks. The materials includes a graphic oriented presentation, interactive animations demonstrating the process of denaturation and precipitating of proteins at macroscopic and molecular level, poster presenting the structural formulas of standard amino acids, 3D models of selected proteins, additional texts supporting the current topics concerning amino acids and proteins and the laboratory protocols for students. The presented support materials were evaluated at the secondary school conditions. They were tested in one class and the improvement of student's understanding of the topic was compared to the second class employing only the classical educational methods. The comparison of the results of...

Unterhalb des Interleukin 3 (Il-3) Rezeptors sind zwei Ras-abhängige Signalwege beschrieben, die entweder zur Aktivierung von C-Raf oder von PI3-Kinase (PI3K)/Proteinkinase B (PKB, AKT) führen und Wachstum und Überleben vermitteln. Frühere Untersuchungen des Mechanismus, über den C-Raf Apoptose unterdrückt, zeigten die Notwendigkeit einer Anwesenheit der zytoplasmatischen Kinase an den Mitochondrien. Diese Translokation konnte entweder durch Überexpression des antiapoptotischen Proteins Bcl-2 oder aber durch Fusion der Kinase mit dem mitochondriellen Protein Mas p70 erreicht werden. Aktiviertes mitochondriell gebundenes C-Raf ist nicht in der Lage ERK1 und ERK2 zu aktivieren, vermag aber durch Inaktivierung des proapoptotischen Bcl-2 Familienmitgliedes BAD Apoptose zu unterdrücken. Ungeachtet dieser Ergebnisse deuteten andere genetische und biochemische Untersuchungen auch auf eine Bedeutung der Raf Effektoren MEK und ERK in der Unterdrückung des programmierten Zelltodes hin. Im Rahmen dieser Arbeit wurde daher die Bedeutung von MEK und MEK-abhängigen Signalwegen für das zelluläres Überleben untersucht. Wir nutzten für diese Untersuchungen überwiegend die Il-3 abhängige Zelllinie 23D. MEK war essentiell für das zelluläre Überleben und Wachstum nach Stimulation durch Il-3. Eine konstitutiv aktive MEK1 Mutante verzögerte signifikant das Einsetzen der Apoptose nach Entzug des Wachstumsfaktors, während eine dominant negative Mutante den Zelltod akzelerierte. In der Fibroblastenzelllinie NIH 3T3 unterdrückte eine konstitutiv aktive Mutante von ERK2, ähnlich effektiv wie onkogenes MEK, durch Doxorubicin induzierten Zelltod. Diese Beobachtung lässt auf einen, das Überleben der Zelle vermittelnden, Signalweg von MEK schließen, der zur Aktivierung von ERK führt. Der protektive Effekt von aktiviertem MEK in 32D Zellen wurde durch MEK- und PI3K-abhängige Mechanismen vermittelt. Die dabei beobachtete Aktivierung von PI3K führt zur Phosphorylierung und Aktivierung von AKT. Die Abhängigkeit von MEK und PI3K Signalwegen konnte auch für den Schutz von 32D Zellen vor Apoptose durch onkogenes C-Raf gezeigt werden. Diese Befunde ließen sich ebenso in der Il-3 abhängigen pro-B Zelllinie BaF3 verifizieren, was darauf schließen lässt, dass die Rekrutierung von MEK/ERK im antiapoptotischen Signalweg von aktiviertem Raf ein allgemeingültiger Mechanismus ist. Dass in diesem antiapoptotischen Signalweg von C-Raf auch der PI3K Effektor AKT notwendig ist zeigten weitere Untersuchungen, in denen eine dominant negative Mutante von AKT den protektiven Effekt von aktiviertem C-Raf inhibierte, während eine konstitutiv aktive Form von AKT einen synergistischen Effekt mit C-Raf in der Unterdrückung der Apoptose hatte. Diese Daten zeigen einen, zelluläres Überleben vermittelnden Effekt von Raf, der durch MEK und AKT vermittelt wird. / Two Ras effector pathways leading to the activation of C-Raf and phosphatidylinositol 3-kinase (PI3K) have been implicated in the survival signaling by the interleukin 3 (IL-3) receptor. Analysis of apoptosis suppression by C-Raf demonstrated the requirement for mitochondrial translocation of the kinase in this process. This could be achieved either by overexpression of the antiapoptotic protein Bcl-2 or by targeting C-Raf to the mitochondria via fusion to the mitochondrial protein Mas p70. Mitochondrially active C-Raf is unable to activate extracellular signal-related kinase 1 (ERK1) and ERK2 but suppresses cell death by inactivating the proapoptotic Bcl-2 family member BAD. However, genetic and biochemical data also have suggested a role for the C-Raf effector module MEK-ERK in apoptosis suppression. We thus tested for MEK requirement in cell survival signaling using the interleukin 3 (IL-3)-dependent cell line 32D. MEK is essential for survival and growth in the presence of IL-3. Upon growth factor withdrawal the expression of constitutively active MEK1 mutants significantly delays the onset of apoptosis, whereas the presence of a dominant negative mutant accelerates cell death. Survival signaling by MEK most likely results from the activation of ERKs since expression of a constitutively active form of ERK2 was as effective in protecting NIH 3T3 fibroblasts against doxorubicin-induced cell death as oncogenic MEK. The survival effect of activated MEK in 32D cells is achieved by both MEK- and PI3K-dependent mechanisms and results in the activation of PI3K and in the phosphorylation of AKT. MEK and PI3K dependence is also observed in 32D cells protected from apoptosis by oncogenic C-Raf. Additionally, we also could extend these findings to the IL-3-dependent pro-B-cell line BaF3, suggesting that recruitment of MEK is a common mechanism for survival signaling by activated Raf. Requirement for the PI3K effector AKT in this process is further demonstrated by the inhibitory effect of a dominant negative AKT mutant on Raf-1-induced cell survival. Moreover, a constitutively active form of AKT synergizes with Raf-1 in apoptosis suppression. In summary these data strongly suggest a Raf effector pathway for cell survival that is mediated by MEK and AKT.