Biomedical subjects

Patricia Hernandez

Publications and source records attributed to Patricia Hernandez.

6 recordsLinked to original sources

PubMed2006

Protective effect of Mangifera indica L. polyphenols on human T lymphocytes against activation-induced cell death.

Activation-induced cell death (AICD) plays an important role in maintenance of peripheral lymphocyte homeostasis. Reactive oxygen species (ROS) combined with simultaneous calcium (Ca(2+)) influx into the cytosol are required for induction of AICD. The extract obtained from the stem bark of Mangifera indica L. has shown to protect T cells from in vitro AICD. This extract is rich in polyphenolic compounds, the three main components of which are mangiferin (MA), catechin (C) and epicatechin (EC). The present study has focused on the possible contribution of the polyphenols MA, C and EC to the demonstrated protective effect of M. indica extract on in vitro human T cell AICD. Our results show that these polyphenols diminished the increase of intracellular ROS and free Ca(2+) induced by T cell receptor (TCR) triggering. In addition, these polyphenols attenuated AICD. Our findings suggest that the T cell survival effect of M. indica extract is mediated, at least in part, by its main polyphenols.

Apoptosis↗

PubMed2006

Proteome informatics I: bioinformatics tools for processing experimental data.

Bioinformatics tools for proteomics, also called proteome informatics tools, span today a large panel of very diverse applications ranging from simple tools to compare protein amino acid compositions to sophisticated software for large-scale protein structure determination. This review considers the available and ready to use tools that can help end-users to interpret, validate and generate biological information from their experimental data. It concentrates on bioinformatics tools for 2-DE analysis, for LC followed by MS analysis, for protein identification by PMF, by peptide fragment fingerprinting and by de novo sequencing and for data quantitation with MS data. It also discloses initiatives that propose to automate the processes of MS analysis and enhance the quality of the obtained results.

Algorithms↗

PubMed2003

Trophic partitioning in tropical rain forest birds: insights from stable isotope analysis.

Bird communities reach their highest taxonomic and trophic diversity in tropical rain forest, but the use of different foraging strategies to meet food requirements in such competitive environments is poorly understood. Conventional dietary analyses are poorly suited to investigate dietary patterns in complex systems. We used stable carbon ((13)C/(12)C) and nitrogen ((15)N/(14)N) isotope analysis of whole blood to examine avian trophic patterns and sources of diet in the tropical rain forest of Los Tuxtlas, Veracruz, Mexico. We used stable nitrogen isotope analysis to delineate trophic levels, and stable carbon isotope analysis to distinguish the relative contribution of C-3 and CAM/C-4 ultimate sources of proteins to diets. There was large inter- and intraspecific variation in whole blood delta(13)C and delta(15)N values in 23 species of birds. Stable nitrogen isotope analysis separated birds into several trophic levels, including species that obtained their dietary protein mostly from plants, insects or a combination of both food sources. Stable carbon isotope analysis showed that most birds fed on C3-based foods but Stub-tailed Spadebills (Platyrinchus cancrominus) included C-3- and C-4/CAM-specialist individuals. Our analyses provided insights into the nutritional contribution of plant and animal sources of protein and distinguish their photosynthetic origin over relatively long average time periods.

Animals↗

PubMed2003

Popitam: towards new heuristic strategies to improve protein identification from tandem mass spectrometry data.

In recent years, proteomics research has gained importance due to increasingly powerful techniques in protein purification, mass spectrometry and identification, and due to the development of extensive protein and DNA databases from various organisms. Nevertheless, current identification methods from spectrometric data have difficulties in handling modifications or mutations in the source peptide. Moreover, they have low performance when run on large databases (such as genomic databases), or with low quality data, for example due to bad calibration or low fragmentation of the source peptide. We present a new algorithm dedicated to automated protein identification from tandem mass spectrometry (MS/MS) data by searching a peptide sequence database. Our identification approach shows promising properties for solving the specific difficulties enumerated above. It consists of matching theoretical peptide sequences issued from a database with a structured representation of the source MS/MS spectrum. The representation is similar to the spectrum graphs commonly used by de novo sequencing software. The identification process involves the parsing of the graph in order to emphasize relevant sections for each theoretical sequence, and leads to a list of peptides ranked by a correlation score. The parsing of the graph, which can be a highly combinatorial task, is performed by a bio-inspired algorithm called Ant Colony Optimization algorithm.

Algorithms↗

PubMed2002

Country response to HIV/AIDS: national health accounts on HIV/AIDS in Brazil, Guatemala, Honduras, Mexico and Uruguay.

National expenditures on HIV/AIDS were estimated as summary indicators to assess the country's response to HIV/AIDS. The methodology is based on a matrix system describing the level and flow of health expenditures on HIV/AIDS: an adaptation of the National Health Accounts methods. The expenditures were classified by source (public, private, international), by the use of funds (prevention, care), by object, and by type of provider institution. The results are reported in US dollars using the official exchange rate for the year of estimation. For international comparisons monetary units were adjusted by the purchasing power parity (US dollars PPP). National HIV/AIDS total expenditures were: Guatemala US dollars PPP29.5 million, Uruguay US dollars PPP 32.5 million, Mexico US dollars PPP 257 million, and Brazil US dollars PPP 587.4 million during 1998, and Honduras US dollars PPP 33.9 million for 1999. The total HIV/AIDS expenditures per capita for 1998 were: Brazil US dollars 2.69, Mexico US dollars 1.25, Guatemala US dollars 1.08, Uruguay US dollars 6.63, and Honduras US dollars 3.6 for 1999. The 1998 distribution of the total HIV/AIDS expenditures in prevention and care were, respectively, Brazil 10 and 80%, Guatemala 15 and 70%, Mexico 29 and 66%, Uruguay 36 and 51%, and Honduras 28 and 65% for 1999. The share of total expenditures on antiretroviral drugs ranged from 52% in Guatemala to 75% in Brazil, even when the estimated coverage of antiretroviral therapy was close to 10% in Guatemala and universal in Brazil. The estimated flow from international sources per capita in 1998 was Uruguay US dollars 0.03, Brazil US dollars 0.24, Guatemala US dollars 0.11, Mexico US dollars 0.01, and Honduras US dollars 1.04 in 1999. The data allow international comparisons and provide critical information to improve equity and efficiency in the allocation of scarce resources. The National HIV/AIDS Accounts also constitute a powerful tool to describe the country's response to HIV/AIDS.

Acquired Immunodeficiency Syndrome↗

PubMedDate not supplied

Automated protein identification by tandem mass spectrometry: issues and strategies.

Protein identification by tandem mass spectrometry (MS/MS) is key to most proteomics projects and has been widely explored in bioinformatics research. Obtaining good and trustful identification results has important implications for biological and clinical work. Although well matured, automated software identification of proteins from MS/MS data still faces a number of obstacles due to the complexity of the proteome or procedural issues of mass spectrometry data acquisition. Expected or unexpected modifications of the peptide sequences, polymorphisms, errors in databases, missed or non-specific cleavages, unusual fragmentation patterns, and single MS/MS spectra of multiple peptides of the same m/z are so many pitfalls for identification algorithms. A lot of research work has been carried out in recent years that yielded new strategies to handle a number of these issues. Multiple MS/MS identification algorithms are now available or have been theoretically described. The difficulty resides in choosing the most adapted method for each type of spectra being identified. This review presents an overview of the state-of-the-art bioinformatics approaches to the identification of proteins by MS/MS to help the reader doing the spade work of finding the right tools among the many possibilities offered.

Automation↗