Comparative analysis of cancer genes in the human and chimpanzee genomes

Background: Cancer is a major medical problem in modern societies. However, the incidence of this disease in non-human primates is very low. To study whether genetic differences between human and chimpanzee could contribute to their distinct cancer susceptibility, we have examined in the chimpanzee genome the orthologous genes of a set of 333 human cancer genes. Results: This analysis has revealed that all examined human cancer genes are present in chimpanzee, contain intact open reading frames and show a high degree of conservation between both species. However, detailed analysis of this set of genes has shown some differences in genes of special relevance for human cancer. Thus, the chimpanzee gene encoding p53 contains a Pro residue at codon 72, while this codon is polymorphic in humans and can code for Arg or Pro, generating isoforms with different ability to induce apoptosis or interact with p73. Moreover, sequencing of the BRCA1 gene has shown an 8 Kb deletion in the chimpanzee sequence that prematurely truncates the co-regulated NBR2 gene. Conclusion: These data suggest that small differences in cancer genes, as those found in tumor suppressor genes, might influence the differences in cancer susceptibility between human and chimpanzee. Nevertheless, further analysis will be required to determine the exact contribution of the genetic changes identified in this study to the different cancer incidence in non-human primates.

Evaluation of the chicken transcriptome by SAGE of B cells and the DT40 cell line

Background: The understanding of whole genome sequences in higher eukaryotes depends to a large degree on the reliable definition of transcription units including exon/intron structures, translated open reading frames (ORFs) and flanking untranslated regions. The best currently available chicken transcript catalog is the Ensembl build based on the mappings of a relatively small number of full length cDNAs and ESTs to the genome as well as genome sequence derived in silico gene predictions.Results: We use Long Serial Analysis of Gene Expression (LongSAGE) in bursal lymphocytes and the DT40 cell line to verify the quality and completeness of the annotated transcripts. 53.6% of the more than 38,000 unique SAGE tags (unitags) match to full length bursal cDNAs, the Ensembl transcript build or the genome sequence. The majority of all matching unitags show single matches to the genome, but no matches to the genome derived Ensembl transcript build. Nevertheless, most of these tags map close to the 3' boundaries of annotated Ensembl transcripts.Conclusions: These results suggests that rather few genes are missing in the current Ensembl chicken transcript build, but that the 3' ends of many transcripts may not have been accurately predicted. The tags with no match in the transcript sequences can now be used to improve gene predictions, pinpoint the genomic location of entirely missed transcripts and optimize the accuracy of gene finder software.

Towards the Fully Automatic Merging of Lexical Resources: A Step Forward

This article reports on the results of the research done towards the fully automatically merging of lexical resources. Our main goal is to show the generality of the proposed approach, which have been previously applied to merge Spanish Subcategorization Frames lexica. In this work we extend and apply the same technique to perform the merging of morphosyntactic lexica encoded in LMF. The experiments showed that the technique is general enough to obtain good results in these two different tasks which is an important step towards performing the merging of lexical resources fully automatically.

Education as a mirror of Spanish society: challenges and policies towards multiple diversity

The ways in which the dominant cultural majority frames the educationalsystem determine perceptions of its own identity and understandings ofthe ‘other.’ In this article I take a political approach, by examining themanagement of cultural diversity within Spanish education policies, treating“education as the mirror of society”. This article analyzes Spanish challengesand policies approaches towards the management of immigrationrelated diversity in education. The main finding is that there is not one approach,but several, due to both the decentralized character of the educationsystem and the multiplicity of diversity that is at stake (i.e. language,religion, culture etc.)

Cross National Contact Strategies

Using paradata gathered from the 11-nation Survey of Health, Ageing and Retirement in Europe (SHARE), this paper examines the impact of the first contact attempt and the first contact properties, respectively, on contact and response efficiency using logistic multilevel models. We find that despite the different sample frames and interviewer compensation structure between countries, there are no considerable country effects with respect to making contact, once interviewer effects are controlled. Moreover, results point to an increased efficiency associated with evenings especially on Sundays, at least on the very first contact attempt. For attempts that result in initial contact, Saturday afternoons are most likely to eventually lead to completed interviews, followed by initial contact on weekdays during the daytime. We hypothesize that this may be due to the SHARE sample being composed of people aged 50 and over.

Transposase and cointegrase: specialized transposition proteins of the bacterial insertion sequence IS21 and related elements.

The bacterial insertion sequence IS21 shares with many insertion sequences a two-step, reactive junction transposition pathway, for which a model is presented in this review: a reactive junction with abutted inverted repeats is first formed and subsequently integrated into the target DNA. The reactive junction occurs in IS21-IS21 tandems and IS21 minicircles. In addition, IS21 shows a unique specialization of transposition functions. By alternative translation initiation, the transposase gene codes for two products: the transposase, capable of promoting both steps of the reactive junction pathway, and the cointegrase, which only promotes the integration of reactive junctions but with higher efficiency. This review also includes a survey of the IS21 family and speculates on the possibility that other members present a similar transpositional specialization.

Frame detection over the semantic web

In the past, research in ontology learning from text has mainly focused on entity recognition, taxonomy induction and relation extraction. In this work we approach a challenging research issue: detecting semantic frames from texts and using them to encode web ontologies. We exploit a new generation Natural Language Processing technology for frame detection, and we enrich the frames acquired so far with argument restrictions provided by a super-sense tagger and domain specializations. The results are encoded according to a Linguistic MetaModel, which allows a complete translation of lexical resources and data acquired from text, enabling custom transformations of the enriched frames into modular ontology components.

Genometrics as an essential tool for the assembly of whole genome sequences: the example of the chromosome of Bifidobacterium longum NCC2705.

BACKGROUND: Analysis of the first reported complete genome sequence of Bifidobacterium longum NCC2705, an actinobacterium colonizing the gastrointestinal tract, uncovered its proteomic relatedness to Streptomyces coelicolor and Mycobacterium tuberculosis. However, a rapid scrutiny by genometric methods revealed a genome organization totally different from all so far sequenced high-GC Gram-positive chromosomes. RESULTS: Generally, the cumulative GC- and ORF orientation skew curves of prokaryotic genomes consist of two linear segments of opposite slope: the minimum and the maximum of the curves correspond to the origin and the terminus of chromosome replication, respectively. However, analyses of the B. longum NCC2705 chromosome yielded six, instead of two, linear segments, while its dnaA locus, usually associated with the origin of replication, was not located at the minimum of the curves. Furthermore, the coorientation of gene transcription with replication was very low. Comparison with closely related actinobacteria strongly suggested that the chromosome of B. longum was misassembled, and the identification of two pairs of relatively long homologous DNA sequences offers the possibility for an alternative genome assembly proposed here below. By genometric criteria, this configuration displays all of the characters common to bacteria, in particular to related high-GC Gram-positives. In addition, it is compatible with the partially sequenced genome of DJO10A B. longum strain. Recently, a corrected sequence of B. longum NCC2705, with a configuration similar to the one proposed here below, has been deposited in GenBank, confirming our predictions. CONCLUSION: Genometric analyses, in conjunction with standard bioinformatic tools and knowledge of bacterial chromosome architecture, represent fast and straightforward methods for the evaluation of chromosome assembly.

Type I signal peptidase from Leishmania is a target of the immune response in human cutaneous and visceral leishmaniasis.

The gene encoding type I signal peptidase (Lmjsp) has been cloned from Leishmania major. Lmjsp encodes a protein of 180 amino residues with a predicted molecular mass of 20.5 kDa. Comparison of the protein sequence with those of known type I signal peptidases indicates homology in five conserved domains A-E which are known to be important, or essential, for catalytic activity. Southern blot hybridisation analysis indicates that there is a single copy of the Lmjsp gene. A recombinant SPase protein and a synthetic peptide of the L. major signal peptidase were used to examine the presence of specific antibodies in sera from either recovered or active individuals of both cutaneous and visceral leishmaniasis. This evaluation demonstrated that sera from cutaneous and visceral forms of leishmaniasis are highly reactive to both the recombinant and synthetic signal peptidase antigens. Therefore, the Leishmania signal peptidase, albeit localised intracellularly, is a significant target of the Leishmania specific immune response and highlights its potential use for serodiagnosis of cutaneous and visceral leishmaniasis.

Migrating concepts: Immigrant integration and the regulation of religious dress in France and Canada

Religion in general, and Islam in particular, has become one of the main focal points of policy-making and constitutional politics in many Western liberal states. This article proposes to examine the legal and political dynamics behind new regulations targeting individual religious practices of Muslims. Although one could presuppose that church-state relations or the understanding of secularism is the main factor accounting for either accommodation or prohibition of Muslim religious practices, I make the case that the policy frame used to conceptualize the integration of immigrants in each national context is a more significant influence on how a liberal state approaches the legal regulation of individual practices such as veiling. However, this influence must be assessed carefully since it may have different effects on the different institutional actors in charge of regulating religion, such as the Courts and the legislature. To assess these hypotheses I compare two countries, France and Canada, which are solid examples of two contrasting national policy frames for the integration of immigrants.

Avaliação dos Serviços VoIP em Links de Baixa Capacidade com Tráfego Compartilhado de Dados

Esta dissertação descreve os resultados das medições observadas em um dos Laboratórios de uma Operadora de Telecomunicações (LOP), onde foram avaliados e analisados alguns requisitos de QoS em redes de pacotes IP (Internet Protocol). Essas medições foram feitas no âmbito do objetivo desta dissertação que é avaliar formas de prover serviços VoIP (Voice over Internet Protocol) em redes de pacotes conforme a recomendação do padrão FRF.12. Essa rede é assim, uma rede de link de 512kbps que também provê serviços VoIP compartilhados, concorrentemente com dados e serviços multimídia. Dos ítens analisados destacam-se: Análise de Codecs; QoS (Quality Of Service) Diffserv; Compressão de cabeçalho RTP (Real Time Protocol) - cRTP; Fragmentação com intercalação - LFI; Comportamento da Rede em situações diversas; a adequação do software free Multi Generator (MGEN) de geração - medição - coleta de dados, em redes. A análise foi, essencialmente, em enlace Frame Relay nos CPE (Customer Premise Equipment), passando pelo Backbone IP VPN / MPLS Multicast, pois o Frame Relay Fórum v12 (FRF.12) dá suporte à intercalação de voz entre os pacotes de dados. O FRF.12 é indispensável, pois este esta dissertação tem como objetivo realizar um conjuntos de testes e medidas que avaliam a aplicação dos serviços VoIP em links de baixa capacidades com trafego de dados compartilhados. Para oferecer esse serviço e de qualidade é necessário fragmentar e intercalar frames de voz entre os pacotes de dados usando o FRF.12. Depois do estudo teórico das recomendações, normas de padronização internacional e dos fabricantes, foram realizados testes que resultam na validação prática de toda a teoria outrora analisada através de testes específicos que comprovam em definitivo a viabilidade das aplicações VoIP em uma rede de enlace de baixa velocidade. Feitos esses testes chegou-se a conclusão de que em determinados casos não se revela necessário nem preocupante o aumento da banda para se puder prover determinados serviços. Na sequência dos testes foram também avaliados o desempenho, a ocupação da banda e a eficácia dos equipamentos - softwares. Da bancada dos testes e medições, provou-se o seguinte: que de fato consegue-se melhor otimização da banda ao realizar compressão do cabeçalho cRTP; que de fato a fragmentação de pacote FTP (File Transfer Protocol) com intercalação de pacotes VoIP faz reduzir o delay e jitter1 para as aplicações de tempo real; que de fato a habilitação de QoS Intserv provê classificação e faz diferenciação dos tráfegos, e que o CODEC G729 apresenta melhor adequação em lidar com aplicações VoIP em routers2 CISCO, disponível em CRT (Centro de referência Tecnológica) de uma LOP.

Estudi i implementació d’un mètode de reconstrucció 3D basat en SfM i registre de vistes 3D parcials

Aquest projecte es basarà en reconstruir una imatge 3D gran a partir d’una seqüència d’imatges 2D capturades per una càmera. Ens centrem en l’estudi de les bases matemàtiques de la visió per computador així com en diferents mètodes emprats en la reconstrucció 3D d’imatges. Per portar a terme aquest estudi s’utilitza la plataforma de desenvolupament MatLab ja que permet tractar operacions matemàtiques, imatges i matrius de gran tamany amb molta senzillesa, rapidesa i eficiència, per aquesta raó s’usa en moltes recerques sobre aquest tema. El projecte aprofundeix en el tema descrit anteriorment estudiant i implementant un mètode que consisteix en aplicar Structure From Motion (SFM) a pocs frames seguits obtinguts d’una seqüència d’imatges 2D per crear una reconstrucció 3D. Quan s’han creat dues reconstruccions 3D consecutives i fent servir un frame com a mínim en comú entre elles, s’aplica un mètode de registre d’estructures 3D, l’Iterative Closest Point (ICP), per crear una reconstrucció 3D més gran a través d’unir les diferents reconstruccions obtingudes a partir de SfM. El mètode consisteix en anar repetint aquestes operacions fins al final dels frames per poder aconseguir una reconstrucció 3D més gran que les petites imatges que s’aconsegueixen a través de SfM. A la Figura 1 es pot veure un esquema del procés que es segueix. Per avaluar el comportament del mètode, utilitzem un conjunt de seqüències sintètiques i un conjunt de seqüències reals obtingudes a partir d’una càmera. L’objectiu final d’aquest projecte és construir una nova toolbox de MatLab amb tots els mètodes per crear reconstruccions 3D grans per tal que sigui possible tractar amb facilitat aquest problema i seguir-lo desenvolupant en un futur

Is the person trade-off a valid method for allocating health care resources? Some caveats

The Person Trade-Off (PTO) is a methodology aimed at measuring thesocial value of health states. The rest of methodologies would measure individualutility and would be less appropriate for taking resource allocation decisions.However few studies have been conducted to test the validity of the method.We present a pilot study with this objective. The study is based on theresult of interviews to 30 undergraduate students in Economics. We judgethe validity of PTO answers by their adequacy to three hypothesis of rationality.First, we show that, given certain rationality assumptions, PTO answersshould be predicted from answers to Standard Gamble questions. This firsthypothesis is not verified. The second hypothesis is that PTO answersshould not vary with different frames of equivalent PTO questions. Thissecond hypothesis is also not verified. Our third hypothesis is that PTOvalues should predict social preferences for allocating resources betweenpatients. This hypothesis is verified. The evidence on the validity of themethod is then conflicting.

Sense and antisense transcripts in the histone H1 (HIS-1) locus of Leishmania major.

Histone H1 in the parasitic protozoan Leishmania is a developmentally regulated protein encoded by two genes, HIS-1.1 and HIS-1.2. These genes are separated by approximately 20 kb of sequence and are located on the same DNA strand of chromosome 27. When Northern blots of parasite RNA were probed with HIS-1 strand-specific riboprobes, we detected sense and antisense transcripts that were polyadenylated and developmentally regulated. When the HIS-1.2 coding region was replaced with the coding region of the neomycin phosphotransferase gene, antisense transcription of this gene was unaffected, indicating that the regulatory elements controlling antisense transcription were located outside of the HIS-1.2 gene, and that transcription in Leishmania can occur from both DNA strands even in the presence of transcription of a selectable marker in the complementary strand. A search for other antisense transcripts within the HIS-1 locus identified an additional transcript (SC-1) within the intervening HIS-1 sequence, downstream of adenine and thymine-rich sequences. These results show that gene expression in Leishmania is not only regulated polycistronically from the sense strand of genomic DNA, but that the complementary strand of DNA also contains sequences that could drive expression of open reading frames from the antisense strand of DNA. These findings suggest that the parasite has evolved in such a way as to maximise the transcription of its genome, a mechanism that might be important for it to maintain virulence.

Ambiguity seeking as a result of the status quo bias

Several factors affect attitudes toward ambiguity. What happens, however, when peopleare asked to exchange an ambiguous alternative in their possession for an unambiguousone? We present three experiments in which individuals preferred to retain the former.This status quo bias emerged both within- and between-subjects, with and withoutincentives, with different outcome distributions, and with endowments determined byboth the experimenter and the participants themselves. Findings emphasize the need toaccount for the frames of reference under which evaluations of probabilistic informationtake place as well as modifications that should be incorporated into descriptive modelsof decision making.