Exploring the genome of Trypanosoma vivax through GSS and in silico comparative analysis.

A survey of the Trypanosoma vivax genome was carried out by the genome sequence survey (GSS) approach resulting in 1,086 genomic sequences. A total of 455 high-quality GSS sequences were generated, consisting of 331 non-redundant sequences distributed in 264 singlets and 67 clusters in a total of 135.5 Kb of the T.

Characterization of two Acanthoscelides obtectus alpha-amylases and their inactivation by wheat inhibitors.

Wheat alpha-amylase inhibitors represent an important tool in engineering crop plants against bean bruchids. Because Acanthoscelides obtectus is a devastating storage bean insect-pest, we attempted to purify and characterize its gut alpha-amylases, to study their interaction with active proteinaceous inhibitors. Two digestives alpha-amylases (AoA1 and AoA2) were purified from gut larvae, showing molecular masses of 30 and 45 kDa for each one, respectively.

[Evaluation of diabetic foot amputation rate].

In 1987, it was created the first portuguese Diabetic Foot Clinic in Oporto, at the Hospital Geral de Santo António. The distinction between neuropathic and ischaemic foot was the key stone to reduce drastically the rate of major amputations in the first two years of activity. Since then and until 1995 the rate of major amputations had stabilised around 8%.

Methyl jasmonate and yeast elicitor induce differential transcriptional and metabolic re-programming in cell suspension cultures of the model legume Medicago truncatula.

Exposure of cell suspension cultures of Medicago truncatula Gaerth. to methyl jasmonate (MeJA) resulted in up to 50-fold induction of transcripts encoding the key triterpene biosynthetic enzyme beta-amyrin synthase (betaAS; EC 5.4.

Metabolic profiling of Medicago truncatula cell cultures reveals the effects of biotic and abiotic elicitors on metabolism.

GC-MS-based metabolite profiling was used to analyse the response of Medicago truncatula cell cultures to elicitation with methyl jasmonate (MeJa), yeast elicitor (YE), or ultraviolet light (UV). Marked changes in the levels of primary metabolites, including several amino acids, organic acids, and carbohydrates, were observed following elicitation with MeJa. A similar, but attenuated response was observed following YE elicitation, whereas little response was observed following UV elicitation.

A proposed framework for the description of plant metabolomics experiments and their results.

The study of the metabolite complement of biological samples, known as metabolomics, is creating large amounts of data, and support for handling these data sets is required to facilitate meaningful analyses that will answer biological questions. We present a data model for plant metabolomics known as ArMet (architecture for metabolomics). It encompasses the entire experimental time line from experiment definition and description of biological source material, through sample growth and preparation to the results of chemical analysis.

Kidney and anemia in familial amyloidosis type I.

Background: Familial amyloid polyneuropathy (FAP) type I is caused by a mutated transthyretin (TTR V30M) and characterized by a sensorimotor and autonomic neuropathy. Renal, cardiac, and ocular abnormalities can also occur. Anemia has been described in previous reports, but its prevalence in Portuguese FAP patients is not precisely known.

Discovery of meaningful associations in genomic data using partial correlation coefficients.

Motivation: A major challenge of systems biology is to infer biochemical interactions from large-scale observations, such as transcriptomics, proteomics and metabolomics. We propose to use a partial correlation analysis to construct approximate Undirected Dependency Graphs from such large-scale biochemical data. This approach enables a distinction between direct and indirect interactions of biochemical compounds, thereby inferring the underlying network topology.

Integrative modelling of gene expression and cell metabolism.

The goal of modelling biochemical networks is to understand the system's behaviour (dynamics and control) of these networks in terms of the properties of the individual molecules. Most modelling approaches have dealt with either gene expression or cell metabolism. In light of the widespread use of robotic technologies in laboratories and improved computational power, it is now time to incorporate information from all biochemical levels--gene expression, protein interactions and metabolism--into integrated models.

myo-inositol oxygenase offers a possible entry point into plant ascorbate biosynthesis.

Two biosynthetic pathways for ascorbate (l-ascorbic acid [AsA]; vitamin C) in plants are presently known, the mannose/l-galactose pathway and an l-GalUA pathway. Here, we present molecular and biochemical evidence for a possible biosynthetic route using myo-inositol (MI) as the initial substrate. A MI oxygenase (MIOX) gene was identified in chromosome 4 (miox4) of Arabidopsis ecotype Columbia, and its enzymatic activity was confirmed in bacterially expressed recombinant protein.

Parameter estimation in biochemical pathways: a comparison of global optimization methods.

Here we address the problem of parameter estimation (inverse problem) of nonlinear dynamic biochemical pathways. This problem is stated as a nonlinear programming (NLP) problem subject to nonlinear differential-algebraic constraints. These problems are known to be frequently ill-conditioned and multimodal.

Artificial gene networks for objective comparison of analysis algorithms.

Motivation: Large-scale gene expression profiling generates data sets that are rich in observed features but poor in numbers of observations. The analysis of such data sets is a challenge that has been object of vigorous research. The algorithms in use for this purpose have been poorly documented and rarely compared objectively, posing a problem of uncertainty about the outcomes of the analyses.

[Phenotypic evolution in adrenoleukodystrophy].

The X-linked adrenoleukodystrophy (ALD) is a genetic disease, caused by a defect mapped to Xq28. It is characterised by progressive demyelination of the cerebral white matter and adrenal insufficiency. The most important change that occurs is the accumulation of very long chain fatty acids (VLCFAs).

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.

Motivation: Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively.

Results: We summarize the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks. SBML is a software-independent language for describing models common to research in many areas of computational biology, including cell signaling pathways, metabolic pathways, gene regulation, and others.

Plant metabolomics: large-scale phytochemistry in the functional genomics era.

Metabolomics or the large-scale phytochemical analysis of plants is reviewed in relation to functional genomics and systems biology. A historical account of the introduction and evolution of metabolite profiling into today's modern comprehensive metabolomics approach is provided. Many of the technologies used in metabolomics, including optical spectroscopy, nuclear magnetic resonance, and mass spectrometry are surveyed.

Elderly patients on chronic hemodialysis: effect of the secondary hyperparathyroidism on the hemoglobin level.

In patients on chronic hemodialysis (CHD) hyperparathyroidism (HPTH) is associated with anemia and resistance to erythropoietin (EPO). This study included 86 CHD elderly pts (mean age 74.8 y, mean time on CHD = 50.

Intravenous propofol in the treatment of refractory headache.

We analyzed the results of treating patients who had chronic daily headaches that were refractory to standard medications with repetitive low-dose boluses of intravenous propofol (2,6-diisopropylphenol). Patients were treated over a 1-year period at Thomas Jefferson University Hospital. A total of 18 patients were treated a total of 21 times.

Gene networks: how to put the function in genomics.

An increasingly popular model of regulation is to represent networks of genes as if they directly affect each other. Although such gene networks are phenomenological because they do not explicitly represent the proteins and metabolites that mediate cell interactions, they are a logical way of describing phenomena observed with transcription profiling, such as those that occur with popular microarray technology. The ability to create gene networks from experimental data and use them to reason about their dynamics and design principles will increase our understanding of cellular function.

Quantifying gene networks with regulatory strengths.

A gene network is the collection of regulatory relationships between all genes in a genome. Gene networks are high-level descriptions of cellular biochemistry and show the phenomenological interactions between gene activities. These interactions are mediated by proteins and metabolites.

Metabolic control in integrated biochemical systems.

Traditional analyses of the control and regulation of steady-state concentrations and fluxes assume the activities of the enzymes to be constant. In living cells, a hierarchical control structure connects metabolic pathways to signal-transduction and gene-expression. Consequently, enzyme activities are not generally constant.

Linking the genes: inferring quantitative gene networks from microarray data.

Modern microarray technology is capable of providing data about the expression of thousands of genes, and even of whole genomes. An important question is how this technology can be used most effectively to unravel the workings of cellular machinery. Here, we propose a method to infer genetic networks on the basis of data from appropriately designed microarray experiments.

Emerging bioinformatics for the metabolome.

Metabolic profiling applied to functional genomics (metabolomics) is in an early stage of development. Here, the technologies used for metabolite profiling are briefly covered, illustrated by a few pioneering studies. Issues related to bioinformatics, namely data analysis, visualisation and archival, are the main focus of this review.

[Dog bite in a splenectomized patient].

We present a case of Capnocytophaga canimorsus fulminant infection linked to a dog bite in a splenectomized patient. Capnocytophaga canimorsus is a gram-negative rod that typically causes septicaemia with disseminated intravascular coagulation in both immunocompromised and immunocompetent hosts. It is associated with high mortality.