Artículos de revistas
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Esta colección incluye artículos de revistas de profesores de la Pontificia Universidad Católica de Chile, publicados en revistas nacionales y extranjeras.
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- ItemComparative protein structure modeling of genes and genomes(2000) Martí-Renom, M. A.; Stuart, A. C.; Fiser, A.; Sánchez, R.; Melo Ledermann, Francisco Javier; Sali, A.Comparative modeling predicts the three-dimensional structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target–template alignment, model building, and model evaluation. The number of protein sequences that can be modeled and the accuracy of the predictions are increasing steadily because of the growth in the number of known protein structures and because of the improvements in the modeling software. Further advances are necessary in recognizing weak sequence–structure similarities, aligning sequences with structures, modeling of rigid body shifts, distortions, loops and side chains, as well as detecting errors in a model. Despite these problems, it is currently possible to model with useful accuracy significant parts of approximately one third of all known protein sequences. The use of individual comparative models in biology is already rewarding and increasingly widespread. A major new challenge for comparative modeling is the integration of it with the torrents of data from genome sequencing projects as well as from functional and structural genomics. In particular, there is a need to develop an automated, rapid, robust, sensitive, and accurate comparative modeling pipeline applicable to whole genomes. Such large-scale modeling is likely to encourage new kinds of applications for the many resulting models, based on their large number and completeness at the level of the family, organism, or functional network.
- ItemScoring functions for protein structure prediction(2008) Melo Ledermann, Francisco Javier; Feytmans, E.; Schwede, Torsten; Peitsch, ManuelThe following sections are included: Introduction Structure and Components of Scoring Functions Contact Scoring Functions Distance-dependent Scoring Functions Accessible Surface Scoring Functions Combined Scoring Functions How is a Scoring Function Derived? Selection of Source Experimental Data Reference Systems How is a Scoring Function Used? Classical Overall Score Calculation Sequence space reference frame Structure space reference frame Classical Detailed Score Calculation Variations on Score Calculations Typical Applications of Scoring Functions in Protein Structure Prediction Fold Assessment Model Ranking Error Detection Folding and Molecular Simulations Other Applications of Scoring Functions Future Outlook Reference Systems and Atom Type Definitions Solvation Models Evolutionary Information Multivariate Scoring Functions Acknowledgements References
- ItemQuantitative analysis of wine yeast gene expression profiles under winemaking conditions(2005) Varela, C.; Cárdenas, J.; Melo Ledermann, Francisco Javier; Agosin T., EduardoWine fermentation is a dynamic and complex process in which the yeast cell is subjected to multiple stress conditions. A successful adaptation involves changes in gene expression profiles where a large number of genes are up- or downregulated. Functional genomic approaches are commonly used to obtain global gene expression profiles, thereby providing a comprehensive view of yeast physiology. We used SAGE to quantify gene expression profiles in an industrial strain of Saccharomyces cerevisiae under winemaking conditions. The transcriptome of wine yeast was analysed at three stages during the fermentation process, mid-exponential phase, and early- and late-stationary phases. Upon correlation with the yeast genome, we found three classes of transcripts: (a) sequences that corresponded to ORFs; (b) expressed sequences from intergenic regions; and (c) messengers that did not match the published reference yeast genome. In all fermentation phases studied, the most highly expressed genes related to energy production and stress response. For many pathways, including glycolysis, different transcript levels were observed during each phase. Different isoenzymes, including hexose transporters (HXT), were differentially induced, depending on the growth phase. About 10% of transcripts matched non-annotated ORF regions within the yeast genome and could correspond to small novel genes originally omitted in the first gene annotation effort. Up to 22% of transcripts, particularly at late-stationary phase, did not match any known location within the genome. As the available reference yeast genome was obtained from a laboratory strain, these expressed sequences could represent genes only expressed by an industrial yeast strain. Further studies are necessary to identify the role of these potential genes during wine fermentation.
- ItemA new multiplex PCR assay for the simultaneous detection of vancomycin-resistant enterococci from rectal swabs(2010) Benadof, D.; San Martín, M.; Aguirre, J.; Paredes, L.; Malig, R.; Melo Ledermann, Francisco Javier; Lehouque, G.Objectives This study describes the diagnostic performance of a recently available multiplex PCR-based kit for the simultaneous detection and identification of Enterococcus faecium, Enterococcus faecalis, vanA, vanB, vanC1 and vanC2/C3 genes, directly from rectal swabs constituting the most complete existing molecular assay currently available. Methods The diagnostic performance of this assay was evaluated by a multicenter study involving three independent public hospitals and consisted in the analysis of 187 rectal swabs from patients at high risk for vancomycin-resistant enterococci colonization. Results When bacteria culture was used as the gold standard, the sensitivity, specificity, positive and negative predicted values for the assay were 96.8%, 76.0%, 67.7% and 97.9%, respectively. When a composite reference standard consisting of culture and DNA sequencing of PCR products was used as the gold standard, the sensitivity, specificity, positive and negative predicted values for the PCR-based assay were 97.8%, 96.9%, 96.7% and 97.9%, respectively. Conclusions Based on these results, we conclude that this assay is considerably more sensitive than traditional microbiological methods for detecting vancomycin-resistant enterococci from rectal swabs. It is also much faster than culture. We believe that the implementation of this assay in routine clinical laboratories could help to reduce hospital-acquired vancomycin-resistant enterococci infections.
- ItemThe internal region leucine-rich repeat 6 of decorin interacts with low density lipoprotein receptor-related protein-1, modulates transforming growth factor (TGF)-β-dependent signaling, and inhibits TGF-β-dependent fibrotic response in skeletal muscles(2012) Cabello Verrugio, C.; Santander, C.; Cofré, C.; Acuña, M. J.; Melo Ledermann, Francisco Javier; Brandan, EnriqueDecorin is a small proteoglycan, composed of 12 leucine-rich repeats (LRRs) that modulates the activity of transforming growth factor type β (TGF-β) and other growth factors, and thereby influences proliferation and differentiation in a wide array of physiological and pathological processes, such as fibrosis, in several tissues and organs. Previously we described two novel modulators of the TGF-β-dependent signaling pathway: LDL receptor-related protein (LRP-1) and decorin. Here we have determined the regions in decorin that are responsible for interaction with LRP-1 and are involved in TGF-β-dependent binding and signaling. Specifically, we used decorin deletion mutants, as well as peptides derived from internal LRR regions, to determine the LRRs responsible for these decorin functions. Our results indicate that LRR6 and LRR5 participate in the interaction with LRP-1 and TGF-β as well as in its dependent signaling. Furthermore, the internal region (LRR6i), composed of 11 amino acids, is responsible for decorin binding to LRP-1 and subsequent TGF-β-dependent signaling. Furthermore, using an in vivo approach, we also demonstrate that the LRR6 region of decorin can inhibit TGF-β mediated action in response to skeletal muscle injury.