Genomic, Biochemical, and Modeling Analyses of Asparagine Synthetases from Wheat.

Asparagine synthetase activity in cereals has become an important issue with the discovery that free asparagine concentration determines the potential for formation of acrylamide, a probably carcinogenic processing contaminant, in baked cereal products. Asparagine synthetase catalyses the ATP-dependent transfer of the amino group of glutamine to a molecule of aspartate to generate glutamate and asparagine. Here, asparagine synthetase-encoding polymerase chain reaction (PCR) products were amplified from wheat () cv.

Computational modelling of cancerous mutations in the EGFR/ERK signalling pathway.

Background: The Epidermal Growth Factor Receptor (EGFR) activated Extracellular-signal Regulated Kinase (ERK) pathway is a critical cell signalling pathway that relays the signal for a cell to proliferate from the plasma membrane to the nucleus. Deregulation of the EGFR/ERK pathway due to alterations affecting the expression or function of a number of pathway components has long been associated with numerous forms of cancer. Under normal conditions, Epidermal Growth Factor (EGF) stimulates a rapid but transient activation of ERK as the signal is rapidly shutdown.

Prediction of protein-protein interaction types using association rule based classification.

Background: Protein-protein interactions (PPI) can be classified according to their characteristics into, for example obligate or transient interactions. The identification and characterization of these PPI types may help in the functional annotation of new protein complexes and in the prediction of protein interaction partners by knowledge driven approaches.

Results: This work addresses pattern discovery of the interaction sites for four different interaction types to characterize and uses them for the prediction of PPI types employing Association Rule Based Classification (ARBC) which includes association rule generation and posterior classification.

A novel main chain motif in proteins bridged by cationic groups: the niche.

We have surveyed the bridging of pairs of main chain carbonyl oxygens by cations or by delta(+) hydrogens within hydrogen bonding groups. A three to four residue motif, which we call the niche, with characteristic phi,psi angles, is by far the commonest feature with this property. The niche accommodates atoms or groups that offer delta(+) charges, including water molecules or metal ions, as well as amines, guanidines, and other NH(2) groups.

Magnesium dietary manipulation and recovery of function following controlled cortical damage in the rat.

Previous research has shown that dietary magnesium (Mg2+) deficiency prior to injury worsens recovery of function and that systemic administration of Mg2+ pre or post-injury significantly improves functional recovery. The purpose of the present study was to determine if manipulations in dietary Mg2+ would alter functional recovery following unilateral cortical injuries. Two weeks prior to injury, rats were placed on a customized diet enriched with Mg2+, deficient in Mg2+, or on a standard Mg2+ diet.

Automatic generation of 3D motifs for classification of protein binding sites.

Background: Since many of the new protein structures delivered by high-throughput processes do not have any known function, there is a need for structure-based prediction of protein function. Protein 3D structures can be clustered according to their fold or secondary structures to produce classes of some functional significance. A recent alternative has been to detect specific 3D motifs which are often associated to active sites.

Predicting protein function by machine learning on amino acid sequences--a critical evaluation.

Background: Predicting the function of newly discovered proteins by simply inspecting their amino acid sequence is one of the major challenges of post-genomic computational biology, especially when done without recourse to experimentation or homology information. Machine learning classifiers are able to discriminate between proteins belonging to different functional classes. Until now, however, it has been unclear if this ability would be transferable to proteins of unknown function, which may show distinct biases compared to experimentally more tractable proteins.

Nicotinamide reduces acute cortical neuronal death and edema in the traumatically injured brain.

Previous studies have shown that administration of nicotinamide (Vitamin B(3)) in animal models of traumatic brain injury (TBI) and ischemia significantly reduced the size of infarction or injury and improved functional recovery. The present study evaluated the ability of nicotinamide to provide acute neuroprotection and edema reduction following TBI. Groups of rats were assigned to nicotinamide (500mg/kg) or saline (1.

A lock-and-key model for protein-protein interactions.

Motivation: Protein-protein interaction networks are one of the major post-genomic data sources available to molecular biologists. They provide a comprehensive view of the global interaction structure of an organism's proteome, as well as detailed information on specific interactions. Here we suggest a physical model of protein interactions that can be used to extract additional information at an intermediate level: It enables us to identify proteins which share biological interaction motifs, and also to identify potentially missing or spurious interactions.

Computational modelling of the receptor-tyrosine-kinase-activated MAPK pathway.

The MAPK (mitogen-activated protein kinase) pathway is one of the most important and intensively studied signalling pathways. It is at the heart of a molecular-signalling network that governs the growth, proliferation, differentiation and survival of many, if not all, cell types. It is de-regulated in various diseases, ranging from cancer to immunological, inflammatory and degenerative syndromes, and thus represents an important drug target.

GeneRank: using search engine technology for the analysis of microarray experiments.

Background: Interpretation of simple microarray experiments is usually based on the fold-change of gene expression between a reference and a "treated" sample where the treatment can be of many types from drug exposure to genetic variation. Interpretation of the results usually combines lists of differentially expressed genes with previous knowledge about their biological function. Here we evaluate a method--based on the PageRank algorithm employed by the popular search engine Google--that tries to automate some of this procedure to generate prioritized gene lists by exploiting biological background information.

TOPS: an enhanced database of protein structural topology.

The TOPS database holds topological descriptions of protein structures. These compact and highly abstract descriptions reduce the protein fold to a sequence of Secondary Structure Elements (SSEs) and three sets of pairwise relationships between them, hydrogen bonds relating parallel and anti- parallel beta strands, spatial adjacencies relating neighbouring SSEs, and the chiralities of selected supersecondary structures, including connections in betaalphabeta units and between parallel alpha helices. The database is used as a resource for visualizing folding topologies, fast topological pattern searching and structure comparison.