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Molecular Station is THE largest network of researchers, scientists and science lovers anywhere!
Science, at bottom, is really anti-intellectual. It always distrusts pure reason, and demands the production of objective fact. ~H.L. Mencken, Minority Report: H.L. Mencken's Notebook, 1956
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Nuclear microenvironments and cancer.
J Cell Biochem. 2008 Jul 22;104(6):1949-1952
Authors: Stein GS, Davie JR, Knowlton JR, Zaidi SK
Nucleic acids and regulatory proteins are architecturally organized in nuclear microenvironments. The compartmentalization of regulatory machinery for gene expression, replication and repair, is obligatory for fidelity of biological control. Perturbations in the organization, assembly and integration of regulatory machinery have been functionally linked to the onset and progression of tumorigenesis. The combined application of cellular, molecular, biochemical and in vivo genetic approaches, together with structural biology, genomics, proteomics and bioinformatics, will likely lead to new approaches in cancer diagnostics and therapy. J. Cell. Biochem. 104: 1949-1952, 2008. (c) 2008 Wiley-Liss, Inc.
PMID: 18649350 [PubMed - as supplied by publisher]
Comparative 3'UTR Analysis Allows Identification of Regulatory Clusters that Drive Eph/ephrin Expression in Cancer Cell Lines.
PLoS ONE. 2008;3(7):e2780
Authors: Winter J, Roepcke S, Krause S, Müller EC, Otto A, Vingron M, Schweiger S
Eph receptors are the largest family of receptor tyrosine kinases. Together with their ligands, the ephrins, they fulfill multiple biological functions. Aberrant expression of Ephs/ephrins leading to increased Eph receptor to ephrin ligand ratios is a critical factor in tumorigenesis, indicating that tight regulation of Eph and ephrin expression is essential for normal cell behavior. The 3'-untranslated regions (3'UTRs) of transcripts play an important yet widely underappreciated role in the control of protein expression. Based on the assumption that paralogues of large gene families might exhibit a conserved organization of regulatory elements in their 3'UTRs we applied a novel bioinformatics/molecular biology approach to the 3'UTR sequences of Eph/ephrin transcripts. We identified clusters of motifs consisting of cytoplasmic polyadenylation elements (CPEs), AU-rich elements (AREs) and HuR binding sites. These clusters bind multiple RNA-stabilizing and destabilizing factors, including HuR. Surprisingly, despite its widely accepted role as an mRNA-stabilizing protein, we further show that binding of HuR to these clusters actually destabilizes Eph/ephrin transcripts in tumor cell lines. Consequently, knockdown of HuR greatly modulates expression of multiple Ephs/ephrins at both the mRNA and protein levels. Together our studies suggest that overexpression of HuR as found in many progressive tumors could be causative for disarranged Eph receptor to ephrin ligand ratios leading to a higher degree of tissue invasiveness.
PMID: 18648668 [PubMed - in process]
NEIBank: genomics and bioinformatics resources for vision research.
Mol Vis. 2008;14:1327-37
Authors: Wistow G, Peterson K, Gao J, Buchoff P, Jaworski C, Bowes-Rickman C, Ebright JN, Hauser MA, Hoover D
NEIBank is an integrated resource for genomics and bioinformatics in vision research. It includes expressed sequence tag (EST) data and sequence-verified cDNA clones for multiple eye tissues of several species, web-based access to human eye-specific SAGE data through EyeSAGE, and comprehensive, annotated databases of known human eye disease genes and candidate disease gene loci. All expression- and disease-related data are integrated in EyeBrowse, an eye-centric genome browser. NEIBank provides a comprehensive overview of current knowledge of the transcriptional repertoires of eye tissues and their relation to pathology.
PMID: 18648525 [PubMed - in process]
A comprehensive comparison of random forests and support vector machines for microarray-based cancer classification.
BMC Bioinformatics. 2008 Jul 22;9(1):319
Authors: Statnikov A, Wang L, Aliferis CF
ABSTRACT: BACKGROUND: Cancer diagnosis and clinical outcome prediction are among the most important emerging applications of gene expression microarray technology with several molecular signatures on their way toward clinical deployment. Use of the most accurate classification algorithms available for microarray gene expression data is a critical ingredient in order to develop the best possible molecular signatures for patient care. As suggested by a large body of literature to date, support vector machines can be considered "best of class" algorithms for classification of such data. Recent work, however, suggests that random forest classifiers may outperform support vector machines in this domain. RESULTS: In the present paper we identify methodological biases of prior work comparing random forests and support vector machines and conduct a new rigorous evaluation of the two algorithms that corrects these limitations. Our experiments use 22 diagnostic and prognostic datasets and show that support vector machines outperform random forests, often by a large margin. Our data also underlines the importance of sound research design in benchmarking and comparison of bioinformatics algorithms. CONCLUSIONS: We found that both on average and in the majority of microarray datasets, random forests are outperformed by support vector machines both in the settings when no gene selection is performed and when several popular gene selection methods are used.
PMID: 18647401 [PubMed - as supplied by publisher]
The central proline rich region of POB1/REPS2 plays a regulatory role in Epidermal Growth Factor Receptor endocytosis by binding to 14-3-3 and SH3 domain-containing proteins.
BMC Biochem. 2008 Jul 22;9(1):21
Authors: Tomassi L, Costantini A, Corallino S, Santonico E, Carducci M, Cesareni G, Castagnoli L
ABSTRACT: BACKGROUND: The human POB1/REPS2 (Partner of RalBP1) protein is highly conserved in mammals where it has been suggested to function as a molecular scaffold recruiting proteins involved in vesicular traffic and linking them to the actin cytoskeleton remodeling machinery. More recently POB1/REPS2 was found highly expressed in androgen-dependent prostate cancer cell lines, while one of its isoforms (isoform 2) is down regulated during prostate cancer progression. RESULTS: In this report we characterize the central proline rich domain of the protein and, for the first time, we describe its functional role in receptor endocytosis. We show that the ectopic expression of this domain has a dominant negative effect on the endocytosis of activated epidermal growth factor receptor (EGFR) while leaving transferrin receptor endocytosis unaffected. By a combination of different approaches (phage display, bioinformatics predictions, peptide arrays, mutagenic analysis, in vivo co-immunoprecipitation), we have identified two closely spaced binding motifs for 14-3-3 and for the SH3 containing proteins Amphiphysin II and Grb2. Differently from wild type, mutants that are altered in these motifs do not inhibit EGFR endocytosis, suggesting that they play a functional role in this process. CONCLUSIONS: Our findings are relevant to the characterization of the molecular mechanism underlying the involvement of POB1/REPS2, SH3 and14-3-3 proteins in receptor endocytosis, suggesting that 14-3-3 could work by bridging the EGF receptor and the scaffold protein POB1/REPS2.
PMID: 18647389 [PubMed - as supplied by publisher]
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