Search results for "COD"
showing 10 items of 2985 documents
Genomic determinants of protein folding thermodynamics in prokaryotic organisms.
2004
Here we investigate how thermodynamic properties of orthologous proteins are influenced by the genomic environment in which they evolve. We performed a comparative computational study of 21 protein families in 73 prokaryotic species and obtained the following main results. (i) Protein stability with respect to the unfolded state and with respect to misfolding are anticorrelated. There appears to be a trade-off between these two properties, which cannot be optimized simultaneously. (ii) Folding thermodynamic parameters are strongly correlated with two genomic features, genome size and G+C composition. In particular, the normalized energy gap, an indicator of folding efficiency in statistical…
RNA nucleotide methylation
2011
Methylation of RNA occurs at a variety of atoms, nucleotides, sequences and tertiary structures. Strongly related to other posttranscriptional modifications, methylation of different RNA species includes tRNA, rRNA, mRNA, tmRNA, snRNA, snoRNA, miRNA, and viral RNA. Different catalytic strategies are employed for RNA methylation by a variety of RNA-methyltransferases which fall into four superfamilies. This review outlines the different functions of methyl groups in RNA, including biophysical, biochemical and metabolic stabilization of RNA, quality control, resistance to antibiotics, mRNA reading frame maintenance, deciphering of normal and altered genetic code, selenocysteine incorporation,…
Structural Characterization of Set1 RNA Recognition Motifs and their Role in Histone H3 Lysine 4 Methylation
2006
Departament de Bioquimica iBiologia Molecular, Universitatde Valencia, C/Dr Moliner 50,46100, Burjassot, SpainThe yeast Set1 histone H3 lysine 4 (H3K4) methyltransferase contains, inaddition to its catalytic SET domain, a conserved RNA recognition motif(RRM1). We present here the crystal structure and the secondary structureassignment in solution of the Set1 RRM1. Although RRM1 has the expectedβαββαβ RRM-fold, it lacks the typical RNA-binding features of thesemodules. RRM1 is not able to bind RNA by itself in vitro, but a constructcombining RRM1 with a newly identified downstream RRM2 specificallybinds RNA. Invivo,H3K4 methylation isnot affectedbyapoint mutation inRRM2 that preserves Set1 s…
Molecular volumes and surfaces of biomacromolecules via GEPOL: A fast and efficient algorithm
1990
A triangular tesselation approach to build up surfaces has been adapted to the study of biomolecules. By using a data-coded generic pentakisdodecahedron each atom is assigned a particular sphere whose radii are chosen according to any suitable property. Different types of surfaces have been adapted to this method: van der Waals, surface accessible, and Richard's molecular surface. A simple method is used to eliminate all triangles found at the intersection volume of the atomic spheres and a fast algorithm is employed to calculate the area of the envelope surface and the volume therein. The data about the surface are given by the coordinates of the center of each triangle, elementary surface…
Distributed evolutionary approach to data clustering and modeling
2014
In this article we describe a framework (DEGA-Gen) for the application of distributed genetic algorithms for detection of communities in networks. The framework proposes efficient ways of encoding the network in the chromosomes, greatly optimizing the memory use and computations, resulting in a scalable framework. Different objective functions may be used for producing division of network into communities. The framework is implemented using open source implementation of MapReduce paradigm, Hadoop. We validate the framework by developing community detection algorithm, which uses modularity as measure of the division. Result of the algorithm is the network, partitioned into non-overlapping co…
One-dimensional hydrodynamic modeling of coronal plasmas on transputer arrays
1990
Abstract We describe a concurrent implementation of the Palermo-Harvard hydrodynamic code on cost-effective and modularity expandable transputer arrays. We have tested the effectiveness of our approach by simulating an already well-studied compact solar-flare model on different transputer configurations and compared their performances with those of other machines. We have found that the speed of the concurrent program on a 16-T800 transputers array is ~1/9 of that of the equivalent code optimized for a CRAY X-MP/48. This work clearly shows that transputer-based arrays provide locally available high computing-power tools to extend the investigation of compact solar flares and similar astroph…
Attendibilità dei modelli per la valutazione dei moduli elastici delle murature suggeriti dalle norme tecniche
2012
In this paper the results of an experimental investigation aimed to the assessment of Young moduli, rigidity moduli and other mechanical properties for different types of masonry are shown. The mechanical characteristics predicted by models proposed by some technical codes were compared against experimental data. This study was motivated by the suggestion of the Masonry Standards Joint Committee's (MSJC) code that, while proposing the use of such models, acknowledges the lack of testing in support of their validation. The experimental investigation has included compressive tests on components (blocks and mortar), diagonal compressive tests and ordinary compressive tests (orthogonally to bed…
Selection on Coding Regions Determined Hox7 Genes Evolution
2003
The important role of Hox genes in determining the regionalization of the body plan of the vertebrates makes them invaluable candidates for evolutionary analyses regarding functional and morphological innovation. Gene duplication and gene loss led to a variable number of Hox genes in different vertebrate lineages. The evolutionary forces determining the conservation or loss of Hox genes are poorly understood. In this study, we show that variable selective pressures acted on Hox7 genes in different evolutionary lineages, with episodes of positive selection occurring after gene duplications. Tests for functional divergence in paralogs detected significant differentiation in a region known to …
Functional variants of 5S rRNA in the ribosomes of common sea urchin Paracentrotus lividus
2012
Abstract We have previously reported a molecular and cytogenetic characterization of three different 5S rDNA clusters in the sea urchin Paracentrotus lividus ; this study, performed at DNA level only, lends itself as starting point to verify that these clusters could contain transcribed genes, then, to demonstrate the presence of heterogeneity at functional RNA level, also. In the present work we report in P. lividus ribosomes the existence of several transcribed variants of the 5S rRNA and we associate all transcribed variants to the cluster to which belong. Our finding is the first demonstration of the presence of high heterogeneity in functional 5S rRNA molecules in animal ribosomes, a f…
Multiple Ig-like featuring genes divergent within and among individuals of the marine sponge Geodia cydonium.
1998
Abstract The receptor tyrosine kinase of the marine sponge Geodia cydonium features two extracellular Ig-like domains in which we recently documented RT-PCR polymorphism among individuals. Genomic-PCR analysis presented here revealed 14 unique sequences from four sponges, differing predominantly in the sequence of an intron which splits the Ig-like domains. Nevertheless, analysis of putative coding regions in 19 distinct clones (156–159 aa) from seven sponges revealed 69 positions of nucleotide substitutions, 67.6% of them non-synonymous, translating into 43 positions of divergent residues. Excluding aa deletions, these 19 sequences share pairwise aa identities of 89–99%. In three sponges, …