Splicing and the evolution of proteins in mammals.

It is often supposed that a protein's rate of evolution and its amino acid content are determined by the function and anatomy of the protein. Here we examine an alternative possibility, namely that the requirement to specify in the unprocessed RNA, in the vicinity of intron-exon boundaries, information necessary for removal of introns (e.g., exonic splice enhancers) affects both amino acid usage and rates of protein evolution. We find that the majority of amino acids show skewed usage near intron-exon boundaries, and that differences in the trends for the 2-fold and 4-fold blocks of both arginine and leucine show this to be owing to effects mediated at the nucleotide level. More specifically, there is a robust relationship between the extent to which an amino acid is preferred/avoided near boundaries and its enrichment/paucity in splice enhancers. As might then be expected, the rate of evolution is lowest near intron-exon boundaries, at least in part owing to splice enhancers, such that domains flanking intron-exon junctions evolve on average at under half the rate of exon centres from the same gene. In contrast, the rate of evolution of intronless retrogenes is highest near the domains where intron-exon junctions previously resided. The proportion of sequence near intron-exon boundaries is one of the stronger predictors of a protein's rate of evolution in mammals yet described. We conclude that after intron insertion selection favours modification of amino acid content near intron-exon junctions, so as to enable efficient intron removal, these changes then being subject to strong purifying selection even if nonoptimal for protein function. Thus there exists a strong force operating on protein evolution in mammals that is not explained directly in terms of the biology of the protein.

Phosphatidylethanolamine critically supports internalization of cell-penetrating protein C inhibitor.

Although their contribution remains unclear, lipids may facilitate noncanonical routes of protein internalization into cells such as those used by cell-penetrating proteins. We show that protein C inhibitor (PCI), a serine protease inhibitor (serpin), rapidly transverses the plasma membrane, which persists at low temperatures and enables its nuclear targeting in vitro and in vivo. Cell membrane translocation of PCI necessarily requires phosphatidylethanolamine (PE). In parallel, PCI acts as a lipid transferase for PE. The internalized serpin promotes phagocytosis of bacteria, thus suggesting a function in host defense. Membrane insertion of PCI depends on the conical shape of PE and is associated with the formation of restricted aqueous compartments within the membrane. Gain- and loss-of-function mutations indicate that the transmembrane passage of PCI requires a branched cavity between its helices H and D, which, according to docking studies, precisely accommodates PE. Our findings show that its specific shape enables cell surface PE to drive plasma membrane translocation of cell-penetrating PCI.

Les groupes de parole de prévention de la récidive au sein des SPIP: une évolution centrée sur la gestion du risque, entre théorie et adaptation pratique

En France, les différentes réorientations pénales et les missions confiées au Service Pénitentiaire d'Insertion et de Probation (SPIP) placent l'évaluation des risques de récidive et leur prévention au centre de la pratique professionnelle des Conseillers Pénitentiaires d'Insertion et de Probation (CPIP). Les récentes évolutions législatives des missions des SPIP, les mutations identitaires et des pratiques qu'elles impliquent -en particulier les Groupes de Paroles de Prévention de la Récidive (GPPR)-, caractérisent une évolution centrée sur la gestion du risque. Partant de critiques dans la littérature sur la notion de gestion du risque de récidive dans les pratiques pénales et de ce qu'elle induit dans les modes d'appréhension des sujets et dans les interventions professionnelles, l'article met en relation les réorientations vers une gestion du risque telles qu'elles peuvent apparaître dans les textes, missions et référentiel du SPIP, avec une évaluation des pratiques professionnelles centrées sur les GPPR intégrés au sein des SPIP. Y a-t-il infiltration et remodelage des pratiques ? Si c'est bien le cas, on examine où se situe le niveau pertinent de cette influence et du réaménagement des pratiques.

Evolutionary origin and functions of retrogene introns.

Retroposed genes (retrogenes) originate via the reverse transcription of mature messenger RNAs from parental source genes and are therefore usually devoid of introns. Here, we characterize a particular set of mammalian retrogenes that acquired introns upon their emergence and thus represent rare cases of intron gain in mammals. We find that although a few retrogenes evolved introns in their coding or 3' untranslated regions (untranslated region, UTR), most introns originated together with untranslated exons in the 5' flanking regions of the retrogene insertion site. They emerged either de novo or through fusions with 5' UTR exons of host genes into which the retrogenes inserted. Generally, retrogenes with introns display high transcription levels and show broader spatial expression patterns than other retrogenes. Our experimental expression analyses of individual intron-containing retrogenes show that 5' UTR introns may indeed promote higher expression levels, at least in part through encoded regulatory elements. By contrast, 3' UTR introns may lead to downregulation of expression levels via nonsense-mediated decay mechanisms. Notably, the majority of retrogenes with introns in their 5' flanks depend on distant, sometimes bidirectional CpG dinucleotide-enriched promoters for their expression that may be recruited from other genes in the genomic vicinity. We thus propose a scenario where the acquisition of new 5' exon-intron structures was directly linked to the recruitment of distant promoters by these retrogenes, a process potentially facilitated by the presence of proto-splice sites in the genomic vicinity of retrogene insertion sites. Thus, the primary role and selective benefit of new 5' introns (and UTR exons) was probably initially to span the often substantial distances to potent CpG promoters driving retrogene transcription. Later in evolution, these introns then obtained additional regulatory roles in fine tuning retrogene expression levels. Our study provides novel insights regarding mechanisms underlying the origin of new introns, the evolutionary relevance of intron gain, and the origin of new gene promoters.

Genome organization and gene expression shape the transposable element distribution in the Drosophila melanogaster euchromatin.

The distribution of transposable elements (TEs) in a genome reflects a balance between insertion rate and selection against new insertions. Understanding the distribution of TEs therefore provides insights into the forces shaping the organization of genomes. Past research has shown that TEs tend to accumulate in genomic regions with low gene density and low recombination rate. However, little is known about the factors modulating insertion rates across the genome and their evolutionary significance. One candidate factor is gene expression, which has been suggested to increase local insertion rate by rendering DNA more accessible. We test this hypothesis by comparing the TE density around germline- and soma-expressed genes in the euchromatin of Drosophila melanogaster. Because only insertions that occur in the germline are transmitted to the next generation, we predicted a higher density of TEs around germline-expressed genes than soma-expressed genes. We show that the rate of TE insertions is greater near germline- than soma-expressed genes. However, this effect is partly offset by stronger selection for genome compactness (against excess noncoding DNA) on germline-expressed genes. We also demonstrate that the local genome organization in clusters of coexpressed genes plays a fundamental role in the genomic distribution of TEs. Our analysis shows that-in addition to recombination rate-the distribution of TEs is shaped by the interaction of gene expression and genome organization. The important role of selection for compactness sheds a new light on the role of TEs in genome evolution. Instead of making genomes grow passively, TEs are controlled by the forces shaping genome compactness, most likely linked to the efficiency of gene expression or its complexity and possibly their interaction with mechanisms of TE silencing.

A trap system for the isolation of amino acid sequences inducing GPI anchor addition.

We designed a trap system to isolate different amino acid sequences which could target proteins to the cell surface via GPI anchor transfer. This selection procedure is based on the insertion of various sequences which regenerate a functional GPI anchor signal sequence and therefore provoke re-expression at the surface of a reporter molecule. Using this trap for cell surface targeting sequences, we could show the importance of the defined elements essential for GPI anchor addition. Such a system could be used for an exhaustive analysis of the carboxyl terminus structural requirements for GPI membrane anchoring.

Caval collapse during cardiopulmonary bypass: a reproducible bench model.

OBJECTIVES: During open heart surgery, so-called atrial chatter, a phenomenon due to right atria and/or caval collapse, is frequently observed. Collapse of the cava axis during cardiopulmonary bypass (CPB) limits venous drainage and may result downstream in reduced pump flow on (lack of volume) and upstream in increased after-load (stagnation), which in turn may both result in reduced or even inadequate end-organ perfusion. The goal of this study was to reproduce venous collapse in the flow bench. METHODS: In accordance with literature for venous anatomy, a caval tree system is designed (polyethylene, thickness 0.061 mm), which receives venous inflow from nine afferent veins. With water as medium and a preload of 4.4 mmHg, the system has an outflow of 4500 ml/min (Scenario A). After the insertion of a percutaneous venous cannula (23-Fr), the venous model is continuously served by the afferent branches in a venous test bench and venous drainage is augmented with a centrifugal pump (Scenario B). RESULTS: With gravity drainage (siphon: A), spontaneously reversible atrial chatter can be generated in reproducible fashion. Slight reduction in the outflow diameter allows for generation of continuous flow. With augmentation (B), irreversible collapse of the artificial vena cava occurs in reproducible fashion at a given pump speed of 2300 ± 50 RPM and a pump inlet pressure of -112 mmHg. Furthermore, bubbles form at the cannula tip despite the fact that the entire system is immersed in water and air from the environment cannot enter the system. This phenomenon is also known as cavitation and should be avoided because of local damage of both formed blood elements and endothelium, as well embolization. CONCLUSIONS: This caval model provides a realistic picture for the limitations of flow due to spontaneously reversible atrial chatter vs irreversible venous collapse for a given negative pressure during CPB. Temporary interruption of negative pressure in the venous line can allow for recovery of venous drainage. This know-how can be used not only for testing different cannula designs, but also for further optimizing perfusion strategies.

Enclouage verrouillé du tibia [Interlocking nailing of the tibia]

Centromedullary nailing is a well-established method of treatment for diaphyseal long bone fractures. The indications have been broadened greatly since the introduction in 1974 of interlocking centromedullary nailing. The purpose of this paper is to review our first results with locked intramedullary nailing of the tibia. We report our experience with the first 19 cases of interlocking tibia nails (15 fractures, 1 delayed union, 2 pseudarthrosis, 1 osteotomy). On the extension table, the insertion of the nail and the placement of the interlocking screws did not cause any problem. In 3 cases, a proximal screw had to be removed within two weeks because of spontaneous displacement. Complications have been noticed in three patients (15.8%) (pulmonary embolism on day 1, and compartment syndrome two days later in one case, sciatic nerve neuroapraxia in the other two). The other patients have been mobilized 24 to 48 hours after surgery. 94% of the fractures were consolidated 4 months post-operatively, with no major deformation. Interlocking tibia nailing seems to be an attractive method in the treatment of certain fractures of the tibia. Early mobilisation and weight-bearing are provided. The indications, the technical aspects as well as the dangers of the method must be carefully respected in order to avoid complications and poor results.

MAR elements and transposons for improved transgene integration and expression.

Reliable and long-term expression of transgenes remain significant challenges for gene therapy and biotechnology applications, especially when antibiotic selection procedures are not applicable. In this context, transposons represent attractive gene transfer vectors because of their ability to promote efficient genomic integration in a variety of mammalian cell types. However, expression from genome-integrating vectors may be inhibited by variable gene transcription and/or silencing events. In this study, we assessed whether inclusion of two epigenetic control elements, the human Matrix Attachment Region (MAR) 1-68 and X-29, in a piggyBac transposon vector, may lead to more reliable and efficient expression in CHO cells. We found that addition of the MAR 1-68 at the center of the transposon did not interfere with transposition frequency, and transgene expressing cells could be readily detected from the total cell population without antibiotic selection. Inclusion of the MAR led to higher transgene expression per integrated copy, and reliable expression could be obtained from as few as 2-4 genomic copies of the MAR-containing transposon vector. The MAR X-29-containing transposons was found to mediate elevated expression of therapeutic proteins in polyclonal or monoclonal CHO cell populations using a transposable vector devoid of selection gene. Overall, we conclude that MAR and transposable vectors can be used to improve transgene expression from few genomic transposition events, which may be useful when expression from a low number of integrated transgene copies must be obtained and/or when antibiotic selection cannot be applied.

Formação Profissional e Empreendedorismo: O Caso do Centro de Juventude de S. Vicente

À medida que oportunidades de emprego para toda a vida escasseiam, altas taxas de desemprego têm despertado o interesse por empreendedorismo. A salvação passa a ser a empregabilidade, sendo a educação empreendedora apontada como uma das áreas chave para fazer com que todos descubram potencialidades inovadoras e criativas despertando comportamentos empreendedores. A inserção dos jovens no mercado de trabalho é neste momento um dos maiores problemas da ilha de São Vicente com 23,3% de desempregados numa população maioritariamente jovem (65,7%) segundo INE (Instituto Nacional de Estatística). É neste contexto marcado por instabilidade e incerteza, que o Centro de Juventude de São Vicente tem vindo a promover a formação profissional oferecendo cursos de curta duração visando a inserção sócio económica de jovens carenciados e em situação de risco. Com base num suporte teórico que revela a possibilidade de desenvolver o espírito empreendedor através do ensino, optou-se pela metodologia de estudo de caso para analisar de que forma o Centro de Juventude de São Vicente contribui na formação para a empregabilidade e/ou no despertar do espírito empreendedor. Os resultados revelam que o Centro está dando os primeiros passos nesse sentido e que terá um papel importante no estímulo e incentivo ao trabalho por conta própria através da formação profissional, desde que em estreita articulação com o IEFP (Instituto do Emprego e Formação Profissional) e o mercado de trabalho. Visando uma mudança de mentalidade tem propiciado aos jovens um contexto de estímulo à iniciativa sobretudo através do apoio psicológico e na busca de financiamento. While opportunities for lifetime jobs are decreasing, high unemployment rates have aroused the interest in entrepreneurship. Employability will be the solution, being entrepreneurial education pointed out as one of the key factors in finding out innovative and creative potentialities as well as in stimulating entrepreneurial behaviours. Inserting young people in the labour market is, at present, one of the biggest problems in S.Vicente, an island with 23,3% of unemployed in a population mostly constituted by young people (65,7%), according to INE (National Institute of Statistics). In this context characterised by instability and uncertainty, the Youth Centre in S.Vicente has been promoting professional training through short courses aimed at socioeconomic insertion of young people in vulnerable and risky situations. Based on a theoretical support which points out the possibility of developing entrepreneurial spirit through education, the case study methodology was selected in order to analyse how the Youth Centre contributes through its training courses to employability and/or entrepreneurial spirit. The results obtained indicate that the Centre is taking its first steps in this direction and will play an important role in encouraging self-employment, through professional training. This has to be carried out in close relationship with both IEFP (Institute of Employment and Professional Training) and the labour market. With a view to changing mentalities, the Centre has been providing young people with a context capable of stimulating initiative, especially by supplying psychological support and helping them find financing sources.

Improved immunogenicity against HIV-1 clade C antigens by using NYVAC-C with restored replication competence.

In order to improve the immunogenicity of currently available non-replicating pox virus HIV vaccine vectors, NYVAC was genetically modified through re-insertion of two host range genes (K1L and C7L), resulting in restored replicative capacity in human cells. In the present study these vectors, expressing either a combination of the HIV-1 clade C antigens Env, Gag, Pol, Nef, or a combination of Gal, Pol, Nef were evaluated for safety and immunogenicity in rhesus macaques, which were immunized at weeks 0, 4 and 12 either by scarification (conventional poxvirus route of immunization), intradermal or by intramuscular injection (route used in previous vaccine studies).Replication competent NYVAC-C-KC vectors induced higher HIV-specific responses, as measured by IFN- ELISpot assay, than the replication defective NYVAC-C vectors. Application through scarification only required one immunization to induce maximum HIV-specific immune responses. This method simultaneously induced relatively lower anti-vector responses. In contrast, two to three immunizations were required when the NYVAC-C-KC vectors were given by intradermal or intramuscular injection and this method tended to generate slightly lower responses. Responses were predominantly directed against Env in the animals that received NYVAC-C-KC vectors expressing HIV-1 Env, Gag, Pol, Nef, while Gag responses were dominant in the NYVAC-C-KC HIV-1 Gag, Pol, Nef immunized animals.The current study demonstrates that NYVAC replication competent vectors were well tolerated and showed increased immunogenicity as compared to replication defective vectors. Further studies are needed to evaluate the most efficient route of immunization and to explore the use of these replication competent NYVAC vectors in prime/boost combination with gp120 protein-based vaccine candidates. This studies was performed within the Poxvirus T-cell Vaccine Discovery Consortium (PTVDC) which is part of the CAVD program.

An investigation of the potential of DIP-STR markers for DNA mixture analyses

The genetic characterization of unbalanced mixed stains remains an important area where improvement is imperative. In fact, using the standard tools of forensic DNA profiling (i.e., STR markers), the profile of the minor contributor in mixed DNA stains cannot be successfully detected if its quantitative share of DNA is less than 10% of the mixed trace. This is due to the fact that the major contributor's profile "masks" that of the minor contributor. Besides known remedies to this problem, such as Y-STR analysis, a new compound genetic marker that consists of a Deletion/Insertion Polymorphism (DIP) linked to a Short Tandem Repeat (STR) polymorphism, has recently been developed and proposed [1]. These novel markers are called DIP-STR markers. This paper compares, from a statistical and forensic perspective, the potential usefulness of these novel DIP-STR markers (i) with traditional STR markers in cases of moderately unbalanced mixtures, and (ii) with Y-STR markers in cases of female-male mixtures. This is done through a comparison of the distribution of 100,000 likelihood ratio values obtained using each method on simulated mixtures. This procedure is performed assuming, in turn, the prosecution's and the defence's point of view.

Metodologia de Análise de Investimentos em Sistemas e Tecnologias da Informação, pelas empresas caboverdeanas

O aumento da competitividade das empresas caboverdeanas impõe-se sobretudo por causa do momento histórico que particularmente o país atravessa. A graduação para país de rendimento médio, a adesão à Organização Mundial de Comércio e o estatuto de parceria especial com a União Europeia constituem razões de grande vulto para as empresas nacionais e outras que empreendem no mercado caboverdeano, definirem eficazmente e eficientemente os seus processos organizacionais de forma a atingirem patamares de produtividade e performance aos níveis internacionais. A envolvente externa às empresas caboverdeanas tem sido alvo de alterações profundas com a globalização dos mercados e o novo paradigma de economia baseada no conhecimento. Para que as empresas mantenham posições competitivas são muitos os desafios que terão que superar. Inexoravelmente, terão que reorganizar e redefinir os seus processos de negócio e suas estratégias de forma coerente. Os SI/TI constituem o factor potencial de reorganização e modernização, a alavanca de diferenciação competitiva e da concretização de negócios e resultados adicionais. O objectivo deste trabalho é o desenvolvimento e a validação de uma metodologia de enquadramento, análise e avaliação de investimentos em SI/TI. O procedimento proposto é fundamentado pela literatura e nas práticas das empresas cabo-verdianas e visa apoiar as empresas a atingirem estágios de performance e produtividade elevados, decorrentes da utilização optimizada dos recursos oferecidos pelos SI/TI. Porque elevadas somas de recursos financeiros são investidos em Sistemas e Tecnologias de Informação e nem todos os benefícios associados são quantificáveis e dado que os riscos associados são elevados, propõe-se com este trabalho um procedimento metodológico de apoio às empresas. Esta metodologia simplificada de análise de investimentos em Sistemas e Tecnologias da Informação propõe uma abordagem científica, sólida e objectiva de avaliação de investimentos em SI/TI, visando propiciar incremento do valor acrescentado dos produtos e/ou serviços das empresas. Os resultados obtidos a partir das análises quantitativas e qualitativas elaboradas permitem retratar a prática das empresas caboverdeanas no domínio de análise e avaliação de investimentos em SI/TI e gerar inferências importantes sobre o comportamento dos responsáveis empresariais e de SI/TI. The increase in competition by the Capeverdean companies is taking place mainly because of the historic moment the country is going through. The recent nomination of Cape Verde as a medium development country, the adhesion to the WCO (World Commerce Organization) and the special partnership with the European Union are relevant reasons for the national companies and others that operate in the Capeverdean market to define efficiently their organizational processes in order to reach levels of productivity and performance comparable to the international ones. The external component of the Capeverdean companies has been undergoing deep changes with market globalization and with the new economic paradigma based on kowledge. In order to maintain their competitive position there are many challenges to overcome. Surely and steadily, they will have to reorganize and redefine their business processes and strategies in a coherent way. The IS/IT (information systems / information technologies) constitute the potential factor of reorganization and modernization, the boost-lever that will produce competitive diferentiation and concretization of businesses and additional results. The main goal of this work is development and validation of a methology of insertion, analysis and evaluation of investments in the IS/IT. The proposed procedure is fundamented by the literature and practice of the Capeverdian companies, and aims at supporting these companies so that they can reach high stages of performance and productivity due to the correct use of the resources offered by the IS/IT. As high amounts of financial resources are invested in Information Systems and Tehnologies, and because of the fact that not all associated benefits may be quantified, and since the associated risks are high, with this work we propose a methodological procedure to support these companies. This simplified analysis methodology in Information and Technologies Systems proposes a sound and objective scientific approach to evaluate investments in IS/IT aiming at providing an increase of the added value of the products and/or services supplied by these companies. The incoming results from the quantitative and qualitative analyses made will allow portraying the practice of the capeverdean companies in the domain of analysis and evaluation of investments in IS/IT and generating important inferences on the behaviour of the executives and IS/IT.

Access, equity and social cohesion: evaluation of intersectoral strategies for people experiencing homelessness

Objective To understand and evaluate the work of intersectoral assistance on the insertion and the flow of people in situation of street with severe mental illness in public services of Mental Health. Method A case study developed from ten visits to a night shelter between March and April 2012. For data collection, the participant observation and semi-structured interviews were carried out with four sheltered individuals, as well as non-directive group interviews with five technicians of the social-assistance services. Results Were analyzed using Content Analysis and developing a Logic Model validated with the professionals involved. Conclusion The social assistance services are the main entry of this clientele in the public network of assistance services, and the Mental Health services have difficulty in responding to the specificities of the same clientele and in establishing intersectoral work.


The role of gene duplication in the origin and evolution of new biological functions

Abstract : Gene duplication is an essential source of material for the origin of genetic novelty and the evolution of lineage- or species-specific phenotypic traits. The reverse transcription of source gene mRNA followed by the genomic insertion of the resulting cDNA - retroposition - has provided the human genome with a significant number of gene copies during the last ~63 million years (MYA) of primate evolution. We estimated that at least 1 new functional gene (retrogene) per MYA emerged by retroposition in the primate lineage leading to humans. Using a combination of comparative sequencing and evolutionary simulations, we obtained strong evidence of functionality for 7 primate specific retrogenes. Most of these genes are specifically expressed in testis suggesting that retroposition has contributed with genetic raw material necessary for the evolution ofmale-specific functions in primates. We characterized CDC14Bretro (identified in the previous survey) that originated from the retroposition of a cell cycle gene - CDC14B - in the common ancestor of humans and apes. We demonstrate that CDC14Bretro experienced a period of intense positive selection in the African ape ancestor. By virtue of the amino acid substitutions that occurred during this period CDC 14Bretro adapted to a new subcellular compartment in African apes. Further analyses indicate that this subcellular shift reflects the evolution of anew functional role of CDC 14Bretro. Prompted by this result, we used yeast (Saccharomyces cerevisiae) to investigate on a global scale the extent of functional diversification of duplicate genes through the subcellular adaptation of their encoded proteins. We found that duplicate proteins frequently evolved new cellular localization patterns, either by partitioning of ancestral localizations ("sublocalization"), or more frequently by relocalization to previously unoccupied compartments ("neolocalization"). Interestingly, proteins involved in processes with a wider subcellular distribution more frequently evolved new localization patterns suggesting that subcellular localization changes are dependent on progenitor gene functions. Relocated proteins adapted to their new subcellular environments and evolved new functional roles through changes of their physio-chemical properties, expression levels, and interaction partners. Our work suggests an important role of subcellular adaptation for the emergence of new gene functions.