Plant response to N availability in permafrost-affected alpine wetlands in arid and semi-arid climate zones.

Nutrient cycling in alpine permafrost-affected wetlands remains insufficiently studied, as it is influenced by a complex network of interrelated climatic and environmental factors, at both regional and local scale. Therefore, we applied mathematical models to examine relationship between environmental factors and plant functional traits reflecting N availability in wetland communities developed under locally variable conditions in a geographic and climatic gradient of high-altitude habitats. Moreover, we assessed impact of local differences in soil chemistry on plant fractionation of N isotopes as a response to N availability.

Probe set filtering increases correlation between Affymetrix GeneChip and qRT-PCR expression measurements.

Background: Affymetrix GeneChip microarrays are popular platforms for expression profiling in two types of studies: detection of differential expression computed by p-values of t-test and estimation of fold change between analyzed groups. There are many different preprocessing algorithms for summarizing Affymetrix data. The main goal of these methods is to remove effects of non-specific hybridization, and to optimally combine information from multiple probes annotated to the same transcript.

Novel proteins regulated by mTOR in subependymal giant cell astrocytomas of patients with tuberous sclerosis complex and new therapeutic implications.

Subependymal giant cell astrocytomas (SEGAs) are rare brain tumors associated with tuberous sclerosis complex (TSC), a disease caused by mutations in TSC1 or TSC2, resulting in enhancement of mammalian target of rapamycin (mTOR) activity, dysregulation of cell growth, and tumorigenesis. Signaling via mTOR plays a role in multifaceted genomic responses, but its effectors in the brain are largely unknown. Therefore, gene expression profiling on four SEGAs was performed with Affymetrix Human Genome arrays.

Distance matrix-based approach to protein structure prediction.

Much structural information is encoded in the internal distances; a distance matrix-based approach can be used to predict protein structure and dynamics, and for structural refinement. Our approach is based on the square distance matrix D = [r(ij)(2)] containing all square distances between residues in proteins. This distance matrix contains more information than the contact matrix C, that has elements of either 0 or 1 depending on whether the distance r (ij) is greater or less than a cutoff value r (cutoff).

AAindex: amino acid index database, progress report 2008.

AAindex is a database of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids. We have added a collection of protein contact potentials to the AAindex as a new section. Accordingly AAindex consists of three sections now: AAindex1 for the amino acid index of 20 numerical values, AAindex2 for the amino acid substitution matrix and AAindex3 for the statistical protein contact potentials.

Ideal amino acid exchange forms for approximating substitution matrices.

We have analyzed 29 published substitution matrices (SMs) and five statistical protein contact potentials (CPs) for comparison. We find that popular, 'classical' SMs obtained mainly from sequence alignments of globular proteins are mostly correlated by at least a value of 0.9.

A minimal proteinlike lattice model: an alpha-helix motif.

A simple protein model of a four-helix bundle motif on a face-centered cubic lattice has been studied. Total energy of a conformation includes attractive interactions between hydrophobic residues, repulsive interactions between hydrophobic and polar residues, and a potential that favors helical turns. Using replica exchange Monte Carlo simulations we have estimated a set of parameters for which the native structure is a global minimum of conformational energy.

Inferring ideal amino acid interaction forms from statistical protein contact potentials.

We have analyzed 29 different published matrices of protein pairwise contact potentials (CPs) between amino acids derived from different sets of proteins, either crystallographic structures taken from the Protein Data Bank (PDB) or computer-generated decoys. Each of the CPs is similar to 1 of the 2 matrices derived in the work of Miyazawa and Jernigan (Proteins 1999;34:49-68). The CP matrices of the first class can be approximated with a correlation of order 0.

A simple lattice model that exhibits a protein-like cooperative all-or-none folding transition.

In a recent paper (D. Gront et al., Journal of Chemical Physics, Vol.

A minimal physically realistic protein-like lattice model: designing an energy landscape that ensures all-or-none folding to a unique native state.

A simple protein model restricted to the face-centered cubic lattice has been studied. The model interaction scheme includes attractive interactions between hydrophobic (H) residues, repulsive interactions between hydrophobic and polar (P) residues, and orientation-dependent P-P interactions. Additionally, there is a potential that favors extended beta-type conformations.