Duality of Coordinates and Matter Fields in Curved Spacetime

We show that there exists a duality between the local coordinates and the solutions of the Klein-Gordon equation in curved spacetime in the same sense as in the Minkowski spacetime. However, the duality in curved spacetime does not have the same generality as in flat spacetime and it holds only if the system satisfies certain constraints. We derive these constraints and the basic equations of duality and discuss the implications in the quantum theory.Comment: 14 pages, ReVTeX file. Comments added, to appear in Phys.Lett.

PDBpaint, a visualization webservice to tag protein structures with sequence annotations

SUMMARY: Protein features are often displayed along the linear sequence of amino acids that make up that protein, but in reality these features occupy a position in the folded protein's three-dimensional space. Mapping sequence features to known or predicted protein structures is useful when trying to deduce the function of those features and when evaluating sequence or structural predictions. To facilitate this goal we developed PDBpaint, a simple tool that displays protein sequence features gathered from bioinformatics resources on top of protein structures, which are displayed in an interactive window (using the Jmol Java viewer). PDBpaint can be used either with existing protein structures or with novel structures provided by the user. The current version of PDBpaint allows the visualization of annotations from Pfam, ARD (detection of HEATrepeats), UniProt, TMHMM2.0 and SignalP. Users can also add other annotations manually. Availability and Implementation: PDBpaint is accessible at http://cbdm.mdc-berlin.de/~pdbpaint. Code is available from http://sourceforge.net/projects/pdbpaint. The website was implemented in Perl, with all major browsers supported. CONTACT: [email protected]

A novel approach for protein subcellular location prediction using amino acid exposure

BACKGROUND: Proteins perform their functions in associated cellular locations. Therefore, the study of protein function can be facilitated by predictions of protein location. Protein location can be predicted either from the sequence of a protein alone by identification of targeting peptide sequences and motifs, or by homology to proteins of known location. A third approach, which is complementary, exploits the differences in amino acid composition of proteins associated to different cellular locations, and can be useful if motif and homology information are missing. Here we expand this approach taking into account amino acid composition at different levels of amino acid exposure. RESULTS: Our method has two stages. For stage one, we trained multiple Support Vector Machines (SVMs) to score eukaryotic protein sequences for membership to each of three categories: nuclear, cytoplasmic and extracellular, plus extra category nucleocytoplasmic, accounting for the fact that a large number of proteins shuttles between those two locations. In stage two we use an artificial neural network (ANN) to propose a category from the scores given to the four locations in stage one. The method reaches an accuracy of 68% when using as input 3D-derived values of amino acid exposure. Calibration of the method using predicted values of amino acid exposure allows classifying proteins without 3D-information with an accuracy of 62% and discerning proteins in different locations even if they shared high levels of identity. CONCLUSIONS: In this study we explored the relationship between residue exposure and protein subcellular location. We developed a new algorithm for subcellular location prediction that uses residue exposure signatures. Our algorithm uses a novel approach to address the multiclass classification problem. The algorithm is implemented as web server 'NYCE' and can be accessed at http://cbdm.mdc-berlin.de/~amer/nyce

On The Symplectic Two-Form of Gravity in Terms of Dirac Eigenvalues

The Dirac eigenvalues form a subset of observables of the Euclidean gravity. The symplectic two-form in the covariant phase space could be expressed, in principle, in terms of the Dirac eigenvalues. We discuss the existence of the formal solution of the equations defining the components of the symplectic form in this framework.Comment: misprints corrected, final interpretation of results give

Superpropagators for explicitly broken 3D-supersymmetric theories

A systematic algorithm to derive superpropagators in the case of either explicitly or spontaneously broken supersymmetric three-dimensional theories is presented. We discuss how the explicit breaking terms that are introduced at tree-level induce 1-loop radiative corrections to the effective action. We also point out that the renormalisation effects and the breaking-inducing-breaking mechanism become more immediate whenever we adopt the shifted superpropagators discussed in this letter.Comment: 6 pages, LaTex, references added. To appear in Phys.Lett.

Evolution and function of CAG/polyglutamine repeats in protein-protein interaction networks

Expanded runs of consecutive trinucleotide CAG repeats encoding polyglutamine (polyQ) stretches are observed in the genes of a large number of patients with different genetic diseases such as Huntington's and several Ataxias. Protein aggregation, which is a key feature of most of these diseases, is thought to be triggered by these expanded polyQ sequences in disease-related proteins. However, polyQ tracts are a normal feature of many human proteins, suggesting that they have an important cellular function. To clarify the potential function of polyQ repeats in biological systems, we systematically analyzed available information stored in sequence and protein interaction databases. By integrating genomic, phylogenetic, protein interaction network and functional information, we obtained evidence that polyQ tracts in proteins stabilize protein interactions. This happens most likely through structural changes whereby the polyQ sequence extends a neighboring coiled-coil region to facilitate its interaction with a coiled-coil region in another protein. Alteration of this important biological function due to polyQ expansion results in gain of abnormal interactions, leading to pathological effects like protein aggregation. Our analyses suggest that research on polyQ proteins should shift focus from expanded polyQ proteins into the characterization of the influence of the wild-type polyQ on protein interactions

mBISON: Finding miRNA target over-representation in gene lists from ChIP-sequencing data

BACKGROUND: Over-representation of predicted miRNA targets in sets of genes regulated by a given transcription factor (e.g. as defined by ChIP-sequencing experiments) helps to identify biologically relevant miRNA targets and is useful to get insight into post-transcriptional regulation. FINDINGS: To facilitate the application of this approach we have created the mBISON web-application. mBISON calculates the significance of over-representation of miRNA targets in a given non-ranked gene set. The gene set can be specified either by a list of genes or by one or more ChIP-seq datasets followed by a user-defined peak-gene association procedure. mBISON is based on predictions from TargetScan and uses a randomization step to calculate False-Discovery-Rates for each miRNA, including a correction for gene set specific properties such as 3'UTR length. The tool can be accessed from the following web-resource: http://cbdm.mdc-berlin.de/~mgebhardt/cgi-bin/mbison/home . CONCLUSION: mBISON is a web-application that helps to extract functional information about miRNAs from gene lists, which is in contrast to comparable applications easy to use by everyone and can be applied on ChIP-seq data directly

Ideias sobre evolução de professores de biologia em formação inicial

O conceito de evolução biológica é considerado um elemento integrador tanto nas pesquisas biológicas como no ensino de biologia. Entretanto, as pesquisas na área de Ensino de Biologia evidenciam as dificuldades em ensinar e apreender esse conceito e na utilização do mesmo como elemento integrador na aprendizagem de conceitos biológicos. Desse modo, este trabalho objetiva investigar a concepção de evolução biológica de alunos ao longo de um curso de Ciências Biológicas em uma Universidade do Estado do Paraná – Brasil. Os dados indicaram o aumento do grau de complexidade das respostas no processo de formação do curso de ciências biológicas analisado, mas também a persistência de respostas finalistas e superficiais ao longo de todos os anos do curso

La población del dolmen de Aizibita (Cirauqui, Navarra). Avance de la analítica aplicada a los restos óseos humanos

Se avanza el resultado del análisis de los restos humanos procedentes de la primera campaña de la excavación en esta estructura megalítica de la Cuenca Media del Ebro. La identificación del número de individuos, alguna patología detectada, y la edad de muerte, establecida en función del desarrollo de los dientes observados, son los resultados más llamativos

Update of the G2D tool for prioritization of gene candidates to inherited diseases

G2D (genes to diseases) is a web resource for prioritizing genes as candidates for inherited diseases. It uses three algorithms based on different prioritization strategies. The input to the server is the genomic region where the user is looking for the disease-causing mutation, plus an additional piece of information depending on the algorithm used. This information can either be the disease phenotype (described as an online Mendelian inheritance in man (OMIM) identifier), one or several genes known or suspected to be associated with the disease (defined by their Entrez Gene identifiers), or a second genomic region that has been linked as well to the disease. In the latter case, the tool uses known or predicted interactions between genes in the two regions extracted from the STRING database. The output in every case is an ordered list of candidate genes in the region of interest. For the first two of the three methods, the candidate genes are first retrieved through sequence homology search, then scored accordingly to the corresponding method. This means that some of them will correspond to well-known characterized genes, and others will overlap with predicted genes, thus providing a wider analysis. G2D is publicly available at http://www.ogic.ca/projects/g2d_2