Biomedical subjects

Mauricio Gonzalez

Publications and source records attributed to Mauricio Gonzalez.

3 recordsLinked to original sources

PubMed2006

JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow.

BACKGROUND: Expressed sequence tag (EST) analyses provide a rapid and economical means to identify candidate genes that may be involved in a particular biological process. These ESTs are useful in many Functional Genomics studies. However, the large quantity and complexity of the data generated during an EST sequencing project can make the analysis of this information a daunting task. RESULTS: In an attempt to make this task friendlier, we have developed JUICE, an open source data management system (Apache + PHP + MySQL on Linux), which enables the user to easily upload, organize, visualize and search the different types of data generated in an EST project pipeline. In contrast to other systems, the JUICE data management system allows a branched pipeline to be established, modified and expanded, during the course of an EST project. The web interfaces and tools in JUICE enable the users to visualize the information in a graphical, user-friendly manner. The user may browse or search for sequences and/or sequence information within all the branches of the pipeline. The user can search using terms associated with the sequence name, annotation or other characteristics stored in JUICE and associated with sequences or sequence groups. Groups of sequences can be created by the user, stored in a clipboard and/or downloaded for further analyses. Different user profiles restrict the access of each user depending upon their role in the project. The user may have access exclusively to visualize sequence information, access to annotate sequences and sequence information, or administrative access. CONCLUSION: JUICE is an open source data management system that has been developed to aid users in organizing and analyzing the large amount of data generated in an EST Project workflow. JUICE has been used in one of the first functional genomics projects in Chile, entitled "Functional Genomics in nectarines: Platform to potentiate the competitiveness of Chile in fruit exportation". However, due to its ability to organize and visualize data from external pipelines, JUICE is a flexible data management system that should be useful for other EST/Genome projects. The JUICE data management system is released under the Open Source GNU Lesser General Public License (LGPL). JUICE may be downloaded from http://genoma.unab.cl/juice_system/ or http://www.genomavegetal.cl/juice_system/.

Chromatography↗

PubMed2006

A mathematical model for copper homeostasis in Enterococcus hirae.

Copper is an essential micronutrient for life. It is required by a wide range of species, from bacteria to yeast, plants and mammals including humans. To prevent the consequences of the excess or deficit of copper, living organisms have developed molecular mechanisms that regulate the uptake, efflux, storage and use of the metal. However, the limits of homeostatic regulation are not known. Here, we take advantage of a simple biological mechanism involved in copper metabolism of Enterococcus hirae, to explore how the regulation is achieved by using a set of four proteins codified in the cop operon: two P-type ATP-ases copper transporters, one copper chaper-one and one Cu-response transcription factor. We propose a mathematical model, based on differential equations and the power-law formalism (see M.A. Savageau, Chaos 11(1) (2001) 142-159), for the behavior of the cop operon and we show that homeostasis is a result of transient dynamics. The results derived from the mathematical model allow to measure qualitatively the adaptability of the system to its environment. This detailed model has been possible thanks to the available experimental biological information provided in a sequence of recent works by Solioz and co-workers.

Computer Simulation↗

PubMed2004

Gene expression profiling in chronic copper overload reveals upregulation of Prnp and App.

The level at which copper becomes toxic is not clear. Several studies have indicated that copper causes oxidative stress; however, most have tested very high levels of copper exposure. We currently have only a limited understanding of the protective systems that operate in cells chronically exposed to copper. Additionally, the limits of homeostatic regulation are not known, making it difficult to define the milder effects of copper excess. Furthermore, a robust assay to facilitate the diagnosis of copper excess and to distinguish mild, moderate, and severe copper overload is needed. To address these issues, we have investigated the effects on steady-state gene expression of chronic copper overload in a cell culture model system using cDNA microarrays. For this study we utilized cells from genetic models of copper overload: fibroblast cells from two mouse mutants, C57BL/6-Atp7a(Mobr) and C57BL/6-Atp7a(Modap). These cell lines accumulate copper to abnormally high levels in normal culture media due to a defect in copper export from the cell. We identified 12 differentially expressed genes in common using our outlier identification methods. Surprisingly, our results show no evidence of oxidative stress in the copper-loaded cells. In addition, candidate components perhaps responsible for a copper-specific homeostatic response are identified. The genes that encode for the prion protein and the amyloid-beta precursor protein, two known copper-binding proteins, are upregulated in both cell lines.

Amyloid↗