Sting_RDB: a relational database of structural parameters for protein analysis with support for data warehousing and data mining

An effective strategy for managing protein databases is to provide mechanisms to transform raw data into consistent, accurate and reliable information. Such mechanisms will greatly reduce operational inefficiencies and improve one's ability to better handle scientific objectives and interpret the research results. To achieve this challenging goal for the STING project, we introduce Sting_RDB, a relational database of structural parameters for protein analysis with support for data warehousing and data mining. In this article, we highlight the main features of Sting_RDB and show how a user can explore it for efficient and biologically relevant queries. Considering its importance for molecular biologists, effort has been made to advance Sting_RDB toward data quality assessment. To the best of our knowledge, Sting_RDB is one of the most comprehensive data repositories for protein analysis, now also capable of providing its users with a data quality indicator. This paper differs from our previous study in many aspects. First, we introduce Sting_RDB, a relational database with mechanisms for efficient and relevant queries using SQL. Sting_rdb evolved from the earlier, text (flat file)-based database, in which data consistency and integrity was not guaranteed. Second, we provide support for data warehousing and mining. Third, the data quality indicator was introduced. Finally and probably most importantly, complex queries that could not be posed on a text-based database, are now easily implemented. Further details are accessible at the Sting_RDB demo web page: http://www.cbi.cnptia.embrapa.br/StingRDB.     

Simple and rapid method determination for metformin in human plasma using high performance liquid chromatography tandem mass spectrometry: application to pharmacokinetic studies

A rapid and simple method for quantitation of metformin (MET) in human plasma by HPLC-MS/MS was developed and validated. The sample preparation consists of plasma deproteinization using acetonitrile. The mobile phase consisted of water-acetonitrile and formic acid (55/45/0.048, v/v/%) and the run time was 3 min. A pursuit C(18) (100 mm x 2.0 mm i.d., 3 microm) column connected to a guard column MS-pursuit (0.20 mm x 0.20 mm i.d., 5 microm) was used. The range of the calibration curve was from 20 to 5000 ng/mL, the limit of quantitation being 20 ng/mL. The detection was performed on a mass spectrometer (ESI+), using metoprolol as internal standard. The calibration curves have r(2) values of 0.995 (CV=0.24%, n=10). The accuracy and precision were between 90.74 and 106.7% and coefficients of variations (CV) of 1.10 and 4.35%, respectively. The method was applied to determine the pharmacokinetic parameters: C(max) (1667.25 ng/mL) and T(max) (3.89 h).     

Bone-marrow mononuclear cell therapy of severe ischemic heart failure

We describe cell therapy for severe ischemic heart failure using transendocardial injection of autologous bone-marrow-derived mononuclear cells. The treated patients had significantly less heart failure and angina, sustained significant improvement of pumping power, exercise capacity, cardiac muscle irrigation, and blood supply to the body. Electrical and mechanical mappings of the myocardium before and after the therapy, and anatomopathological examination of the myocardium of one of the patients that had deceased of a stroke eleven months after the treatment indicated sustained neoangiogenesis and improvement of activity and quantity of cardiomyocytes in the injected regions. Post-hoc analyses of injected cell phenotype and improvement of myocardial function indicate that presence of CD8+ and CD56+ cells does not correlate with good prognostics, suggesting a possibility of cell selection. For 'no-option' severe cardiac patients, significant benefits of cell therapy and absence of adverse effects may justify the application of bone-marrow-derived cell therapy.     

A two-dimensional proteome reference map of Herbaspirillum seropedicae proteins

Herbaspirillum seropedicae is an endophytic diazotroph associated with economically important crops such as rice, sugarcane, and wheat. Here, we present a 2-D reference map for H. seropedicae. Using MALDI-TOF-MS we identified 205 spots representing 173 different proteins with a calculated average of 1.18 proteins/gene. Seventeen hypothetical or conserved hypothetical ORFs were shown to code for true gene products. These data will support the genome annotation process and provide a basis on which to undertake comparative proteomic studies.     

Cartography of an organelle

Peptide counting in mass spectrometry allows researchers to draw a quantitative proteomic map of the ER and Golgi.     

Regulation of autophagy as a therapy for immunosenescence-driven cancer and neurodegenerative diseases: The role of exercise

Aging is one of the risk factors for the development of low-grade inflammation morbidities, such as several types of cancer and neurodegenerative diseases, due to changes in the metabolism, hormonal secretion, and immunosenescence. The senescence of the immune system leads to improper control of infections and tissue damage increasing age-related diseases. One of the mechanisms that maintain cellular homeostasis is autophagy, a cell-survival mechanism, and it has been proposed as one of the most powerful antiaging therapies. Regular exercise can reestablish autophagy, probably through AMP-activated protein kinase activation, and help in reducing the age-related senescence diseases. Therefore, in this study, we discuss the effects of exercise training in immunosenescence and autophagy, preventing the two main age-related disease, cancer and neurodegeneration.     

Minimal evidence of interspecific hybridisation between the Yellow-billed Duck and introduced Mallard in central and northwestern South Africa

Hybridisation is the interbreeding of genetically distinct groups that can lead to introgression – an exchange of genetic material between species. Hybridisation is of conservation concern when an alien invasive species is involved, as it can lead to a loss of local genetic adaptations and genetic diversity. Hybridisation is a significant threat for many dabbling ducks where interbreeding with the closely related invasive Mallard Anas platyrhynchos is extremely common. Phenotypic evidence suggests that Mallard populations in South Africa hybridise with the indigenous Yellow-billed Duck Anas undulata. The aim of this study was to determine the incidence of hybridisation between Yellow-billed Ducks, occurring in central and northwestern South Africa, and introduced Mallards. Genetic variation between Mallards, Yellow-billed Ducks, and their inferred hybrids was assessed using mitochondrial and microsatellite DNA markers. All samples inferred to be hybrids based on the phenotype were found to have Yellowbilled Duck mitochondrial DNA and showed minimal evidence of admixture across the microsatellite markers. Thus, these results do not support the notion that hybridisation between Mallards and Yellow-billed Ducks is prevalent in central and northwestern South Africa. However, hybridisation could be occurring where Mallards are found in higher abundance, such as in the Western Cape Province. Therefore, continued monitoring of this potential hybridisation should be performed frequently and throughout South Africa.