GacA-controlled activation of promoters for small RNA genes in Pseudomonas fluorescens.

The Gac/Rsm signal transduction pathway positively regulates secondary metabolism, production of extracellular enzymes, and biocontrol properties of Pseudomonas fluorescens CHA0 via the expression of three noncoding small RNAs, termed RsmX, RsmY, and RsmZ. The architecture and function of the rsmY and rsmZ promoters were studied in vivo. A conserved palindromic upstream activating sequence (UAS) was found to be necessary but not sufficient for rsmY and rsmZ expression and for activation by the response regulator GacA. A poorly conserved linker region located between the UAS and the -10 promoter sequence was also essential for GacA-dependent rsmY and rsmZ expression, suggesting a need for auxiliary transcription factors. One such factor involved in the activation of the rsmZ promoter was identified as the PsrA protein, previously recognized as an activator of the rpoS gene and a repressor of fatty acid degradation. Furthermore, the integration host factor (IHF) protein was found to bind with high affinity to the rsmZ promoter region in vitro, suggesting that DNA bending contributes to the regulated expression of rsmZ. In an rsmXYZ triple mutant, the expression of rsmY and rsmZ was elevated above that found in the wild type. This negative feedback loop appears to involve the translational regulators RsmA and RsmE, whose activity is antagonized by RsmXYZ, and several hypothetical DNA-binding proteins. This highly complex network controls the expression of the three small RNAs in response to cell physiology and cell population densities.

Mapping of the genes coding for the two major vaccinia virus core polypeptides.

We have mapped the genes coding for two major structural polypeptides of the vaccinia virus core by hybrid selection and transcriptional mapping. First, RNA was selected by hybridization to restriction fragments of the vaccinia virus genome, translated in vitro and the products were immunoprecipitated with antibodies against the two polypeptides. This approach allowed us to map the genes to the left hand end of the largest Hind III restriction fragment of 50 kilobase pairs. Second, transcriptional mapping of this region of the genome revealed the presence of the two expected RNAs. Both RNAs are transcribed from the leftward reading strand and the 5'-ends of the genes are separated by about 7.5 kilobase pairs of DNA. Thus, two genes encoding structural polypeptides with a similar location in the vaccinia virus particle are clustered at approximately 105 kilobase pairs from the left hand end of the 180 kilobase pair vaccinia virus genome.

Condition, disease and immune defence

Life-history traits and secondary sexual characters often demonstrate condition-dependence, and reproductive success thus ultimately appears to be determined by condition. Here we test the hypothesis that anti-parasite defence is condition-dependent and thus ultimately limits fitness. Animal hosts defend themselves against parasites by an efficient immune system that changes its activity level depending on level of infection. Since immune function is costly, as demonstrated by several field studies, we predicted that large immune defence organs should be maintained when the costs of an elevated immune response were reduced, or when the benefits were increased. Hence, the size of immune defence organs was predicted to increase in response to disease due to increased benefits of investment in immune function, and the; size was predicted to increase in response to high body condition because of reduced costs of investment in immune function. A comparative study of birds demonstrated that the size of the spleen was significantly increased among individuals suffering from parasitic infections and signs of disease as compared to healthy individuals. Furthermore, we found evidence for a positive association between spleen size and body condition. These findings are consistent with the hypothesised cost of immune function and hence a cost of anti-parasite defence.

Transcriptional profiling of Gram-positive Arthrobacter in the phyllosphere: induction of pollutant degradation genes by natural plant phenolic compounds.

Arthrobacter chlorophenolicus A6 is a Gram-positive, 4-chlorophenol-degrading soil bacterium that was recently shown to be an effective colonizer of plant leaf surfaces. The genetic basis for this phyllosphere competency is unknown. In this paper, we describe the genome-wide expression profile of A.chlorophenolicus on leaves of common bean (Phaseolus vulgaris) compared with growth on agar surfaces. In phyllosphere-grown cells, we found elevated expression of several genes known to contribute to epiphytic fitness, for example those involved in nutrient acquisition, attachment, stress response and horizontal gene transfer. A surprising result was the leaf-induced expression of a subset of the so-called cph genes for the degradation of 4-chlorophenol. This subset encodes the conversion of the phenolic compound hydroquinone to 3-oxoadipate, and was shown to be induced not only by 4-chlorophenol but also hydroquinone, its glycosylated derivative arbutin, and phenol. Small amounts of hydroquinone, but not arbutin or phenol, were detected in leaf surface washes of P.vulgaris by gas chromatography-mass spectrometry. Our findings illustrate the utility of genomics approaches for exploration and improved understanding of a microbial habitat. Also, they highlight the potential for phyllosphere-based priming of bacteria to stimulate pollutant degradation, which holds promise for the application of phylloremediation.

Expression of T cell receptor genes in the thymus: localization of transcripts in situ and comparison of mature and immature subsets.

We have analyzed the expression of T cell receptor (TcR) genes in the thymus using in situ RNA hybridizations with probes to the constant regions of the TcR alpha, beta, gamma and delta chains. Localization of transcripts revealed low TcR alpha mRNA levels in the thymus cortex and very low levels in the subcapsular region. In contrast, TcR beta message was very abundant in the cortex. TcR gamma or delta mRNA+ thymocytes showed a scattered, predominantly cortical localization. In contrast to gamma, TcR delta transcripts were abundant in the subcapsular region. Control experiments with sorted TcR alpha/beta or gamma/delta cells revealed a detection efficiency of 75%-85% for the respective TcR mRNA and data on TcR gene expression in mature, CD3+ thymocytes were consistent with previous reports. The analysis of immature, CD3- thymocyte subsets, however, revealed a virtual absence of TcR alpha transcripts and an unexpectedly high proportion of cells (14%-29%) expressing the gene for the TcR delta chain. The data are discussed in view of current models of lineage relationships in the thymus.

What kind of relationships between the evolution of pain, beliefs and bio-psycho-social complexity after a locomotor traumatism?

Introduction: Pain and beliefs have an influence on the patient's course in rehabilitation, pain causes fears and fears influence pain perception. The aim of this study is to understand pain and beliefs evolutions during rehabilitation taking into account of bio-psycho-social complexity.Patients and methods: 631 consecutive patients admitted in rehabilitation after a musculoskeletal traumatism were included and assessed at admission and at discharge. Pain was measured by VAS (Visual Analogical Scale), bio-psycho-social complexity by Intermed scale, and beliefs by judgement on Lickert scales. Four kinds of beliefs were evaluated: fear of a severe origin of pain, fear of movement, fear of pain and feeling of distress (loss of control). The association between the changes in pain and beliefs during the hospitalization was assessed by linear regressions.Results: After adjustment for gender, age, education and native language, patients with a decrease in pain during rehabilitation have higher probability of decreasing their fears. For the distress feeling, this relationship is weaker among bio-psycho-socially complex patients (odds-ratio 1.22 for each decreasing of 10mm/100 VAS) than among non-complex patients (OR 1.47). Patients with a pain decrease of 30% or more during hospitalization have higher probability of seeing their fears decrease, this relationship being stronger in complex patient for fear of a severe origin of pain.Discussion: The relationships between evolution of pain and beliefs move in the same direction. The higher a patient feels pain, the less they could be able to modify their dysfunctional beliefs. When the pain diminishes of 30% or more, the probability to challenge the beliefs is increased. The prognostic with regard to feeling of distress and fear of a severe origin of pain, is worse among bio-psycho-socially complex patients.

Genes mirror geography within Europe.

Understanding the genetic structure of human populations is of fundamental interest to medical, forensic and anthropological sciences. Advances in high-throughput genotyping technology have markedly improved our understanding of global patterns of human genetic variation and suggest the potential to use large samples to uncover variation among closely spaced populations. Here we characterize genetic variation in a sample of 3,000 European individuals genotyped at over half a million variable DNA sites in the human genome. Despite low average levels of genetic differentiation among Europeans, we find a close correspondence between genetic and geographic distances; indeed, a geographical map of Europe arises naturally as an efficient two-dimensional summary of genetic variation in Europeans. The results emphasize that when mapping the genetic basis of a disease phenotype, spurious associations can arise if genetic structure is not properly accounted for. In addition, the results are relevant to the prospects of genetic ancestry testing; an individual's DNA can be used to infer their geographic origin with surprising accuracy-often to within a few hundred kilometres.

Identification of a new cancer/testis gene family, CT47, among expressed multicopy genes on the human X chromosome.

Cancer/testis (CT) genes are normally expressed in germ cells only, yet are reactivated and expressed in some tumors. Of the approximately 40 CT genes or gene families identified to date, 20 are on the X chromosome and are present as multigene families, many with highly conserved members. This indicates that novel CT gene families may be identified by detecting duplicated expressed genes on chromosome X. By searching for transcript clusters that map to multiple locations on the chromosome, followed by in silico analysis of their gene expression profiles, we identified five novel gene families with testis-specific expression and >98% sequence identity among family members. The expression of these genes in normal tissues and various tumor cell lines and specimens was evaluated by qualitative and quantitative RT-PCR, and a novel CT gene family with at least 13 copies was identified on Xq24, designated as CT47. mRNA expression of CT47 was found mainly in the testes, with weak expression in the placenta. Brain tissue was the only positive somatic tissue tested, with an estimated CT47 transcript level 0.09% of that found in testis. Among the tumor specimens tested, CT47 expression was found in approximately 15% of lung cancer and esophageal cancer specimens, but not in colorectal cancer or breast cancer. The putative CT47 protein consists of 288 amino acid residues, with a C-terminus rich in alanine and glutamic acid. The only species other than human in which a gene homologous to CT47 has been detected is the chimpanzee, with the predicted protein showing approximately 80% identity in its carboxy terminal region.

A fish-specific transposable element shapes the repertoire of p53 target genes in zebrafish.

Transposable elements, as major components of most eukaryotic organisms' genomes, define their structural organization and plasticity. They supply host genomes with functional elements, for example, binding sites of the pleiotropic master transcription factor p53 were identified in LINE1, Alu and LTR repeats in the human genome. Similarly, in this report we reveal the role of zebrafish (Danio rerio) EnSpmN6_DR non-autonomous DNA transposon in shaping the repertoire of the p53 target genes. The multiple copies of EnSpmN6_DR and their embedded p53 responsive elements drive in several instances p53-dependent transcriptional modulation of the adjacent gene, whose human orthologs were frequently previously annotated as p53 targets. These transposons define predominantly a set of target genes whose human orthologs contribute to neuronal morphogenesis, axonogenesis, synaptic transmission and the regulation of programmed cell death. Consistent with these biological functions the orthologs of the EnSpmN6_DR-colonized loci are enriched for genes expressed in the amygdala, the hippocampus and the brain cortex. Our data pinpoint a remarkable example of convergent evolution: the exaptation of lineage-specific transposons to shape p53-regulated neuronal morphogenesis-related pathways in both a hominid and a teleost fish.

Early change in defence mechanisms and coping in short-term dynamic psychotherapy: relations with symptoms and alliance.

Several patient-related variables have already been investigated as predictors of change in psychodynamic psychotherapy. Defensive functioning is one of them. However, few studies have investigated adaptational processes, encompassing defence mechanisms and coping, from an integrative or comparative viewpoint. This study includes 32 patients, mainly diagnosed with adjustment disorder and undergoing time-limited psychodynamic psychotherapy lasting up to 40 sessions, and will focus on early change in defence and coping. Observer-rater methodology was applied to the transcripts of two sessions of the first part of the psychotherapeutic process. It is assumed that the contextual-relational variable of therapeutic alliance intervenes as moderator on change in adaptational processes. Results corroborated the hypothesis, but only for coping, whereas for defences, overall functioning remained stable over the first 20 sessions of psychotherapy. These results are discussed within the framework of disentangling processes underlying adaptation, i.e., related to issues on trait and state aspects, as well as the role of the therapeutic alliance.

Comparative genomics of chemosensory protein genes reveals rapid evolution and positive selection in ant-specific duplicates.

Gene duplications can have a major role in adaptation, and gene families underlying chemosensation are particularly interesting due to their essential role in chemical recognition of mates, predators and food resources. Social insects add yet another dimension to the study of chemosensory genomics, as the key components of their social life rely on chemical communication. Still, chemosensory gene families are little studied in social insects. Here we annotated chemosensory protein (CSP) genes from seven ant genomes and studied their evolution. The number of functional CSP genes ranges from 11 to 21 depending on species, and the estimated rates of gene birth and death indicate high turnover of genes. Ant CSP genes include seven conservative orthologous groups present in all the ants, and a group of genes that has expanded independently in different ant lineages. Interestingly, the expanded group of genes has a differing mode of evolution from the orthologous groups. The expanded group shows rapid evolution as indicated by a high dN/dS (nonsynonymous to synonymous changes) ratio, several sites under positive selection and many pseudogenes, whereas the genes in the seven orthologous groups evolve slowly under purifying selection and include only one pseudogene. These results show that adaptive changes have played a role in ant CSP evolution. The expanded group of ant-specific genes is phylogenetically close to a conservative orthologous group CSP7, which includes genes known to be involved in ant nestmate recognition, raising an interesting possibility that the expanded CSPs function in ant chemical communication.

Regulation of the expression of Fit insect toxin locus genes in the root-associated biocontrol pseudomonad CHA0

The root-colonizing Pseudomonas fluorescens strain CHA0 is a biocontrol agent of soil-borne plant diseases caused by fungal and oomycete pathogens. Remarkably, this plant-beneficial pseudomonad is also endowed with potent insecticidal activity that depends on the production of a large protein toxin termed Fit (for P. fluorescens insecticidal toxin). In our present work, the genomic locus encoding the P. fluorescens insect toxin is subjected to a detailed molecular analysis. The Fit toxin gene fitD is flanked upstream by the fitABC genes and downstream by the fitE gene that encode the ABC transporter, membrane fusion, and outer membrane efflux components of a type I protein secretion system predicted to function in toxin export. The fitF, fitG, and fitH genes located downstream of fitE code for regulatory proteins having domain structures typical of signal transduction histidine kinases, LysR-type transcriptional regulators, and response regulators, respectively. The role of these insect toxin locus-associated control elements is being investigated with mutants defective for the regulatory genes and with GFP-based reporter fusions to putative promoter regions upstream of the transporter genes fitA and fitE, the toxin gene fitD, and the regulatory genes fitF and fitH. Our preliminary findings suggest that the three regulators interact with known global regulators of biocontrol factor expression to control Fit toxin expression and secretion.

Exploración bio - oceanológica básica del área Callao - Punta Aguja Crucero E-6503

Describe las condiciones bio-oceanológicas encontradas en la región Callao -Punta Aguja, durante el Crucero E-6503, admitiendo que hubo cambios en el régimen térmico de nuestro mar, ocasionados por el avance hacia el sur de aguas ecuatoriales con temperaturas de 26º -24º C y salinidades de 34.6 -34.1 º/00. Por otro lado demuestra que la corriente costanera se presentó en forma de una franja estrecha, variable de 10-40 millas de la costa con temperaturas de 22º - 19º C y salinidades alrededor de 34.9 º/00. Estas aguas presentaron su mayor ensanchamiento al norte de Huarmey hasta Pimentel.

O Quadro Nacional de Bio-Segurança para Cabo Verde

A aplicação das biotecnologias é hoje considerada uma parte importante da solução aos problemas gerados pela insegurança alimentar e a redução da pobreza no mundo. Contudo, há necessidade da avaliação dos riscos reais associados à liberação dos Organismos Geneticamente Modificados (OGMs) desde que existe a possibilidade potencial de danos ao ambiente e à saúde humana, pela alteração da diversidade biológica. Face ao desenvolvimento acelerado da biotecnologia moderna e face ao desconhecimento das reais consequências das interacções dos OGMs com os diversos ecossistemas, a comunidade internacional adoptou o Protocolo de Cartagena sobre a Bio-segurança como um instrumento de prevenção dos riscos provenientes de produtos biotecnológicos. Este Protocolo é um instrumento jurídico internacional de cariz obrigatório adoptado pela Conferência das Partes aquando da Convenção “Quadro das Nações Unidas sobre a Diversidade Biológica (CDB)”, em 1992. A Convenção, reconhecendo o enorme potencial da biotecnologia moderna para a resolução dos problemas antes mencionados, objectiva “contribuir para assegurar um nível adequado de protecção para a transferência, manipulação e utilização segura dos organismos vivos modificados resultantes da biotecnologia moderna, e que possam ter efeitos adversos para a conservação e utilização sustentável da diversidade biológica, considerando igualmente os riscos para a saúde humana, e centrando-se especificamente nos movimentos transfronteiriços”. O governo de Cabo Verde, consciente da importância que se relaciona à protecção da biodiversidade das ilhas e da saúde pública contra os potenciais riscos dos OGMs, assinou, através do Decreto nº 11/2005 de 26 de Setembro, o Protocolo de Cartagena sobre a Bio-segurança. Com a ratificação do PCB, a 1 de Novembro de 2005, o país comprometeu-se a cumprir as exigências e obrigações do Protocolo, dentre as quais, a elaboração e materialização do O objectivo primário do Projecto para o desenvolvimento do Quadro Nacional de Bio-segurança ou, simplesmente, Projecto Nacional de Bio-segurança (PNB), é o de desenvolver um Quadro Nacional de Bio-segurança para CV, de acordo com as necessidades relevantes do protocolo de Cartagena, considerando principalmente que “cada parte deve tomar as medidas legais, administrativas e outras apropriadas para implementar suas obrigações sob o protocolo”. Para a implementação do Plano, Cabo Verde fez uma análise do cenário actual da biotecnologia e da Bio-segurança, propôs um quadro jurídico institucional Nacional e elaborou um plano de acção para implementação do Quadro Nacional de Bio-segurança (QNB). Este Quadro consiste num conjunto de instrumentos políticos, legais, administrativos e técnicos, próprios para atingir as necessidades relevantes do Protocolo de Cartagena. Especificamente, o quadro visa o estabelecimento de bases científicas e sistemas transparentes de tomada de decisão que habilitem o país a beneficiar dos potenciais benefícios da biotecnologia moderna, assegurando a máxima protecção do ambiente, saúde humana e animal dos potenciais riscos dessa biotecnologia; assegurar que a investigação, liberação e manuseio de produtos da biotecnologia moderna sejam desenvolvidos de forma a minimizar os potenciais riscos para o ambiente, saúde humana e animal e; assegurar o manuseio e o movimento transfronteiriço seguros de produtos derivados da biotecnologia moderna. Entretanto, embora o país não dispõe de nenhuma política que aborde a questão concreta da Bio-segurança, existem prioridades nacionais no contexto de objectivos maiores de desenvolvimento, como o desenvolvimento sustentável, conservação da biodiversidade, desenvolvimento agrícola, segurança alimentar, etc., sob os quais uma política de biotecnologia e Biosegurança no quadro do QNB será desenvolvida. Ela será alicerçada nas políticas existentes para os vários sectores, principalmente, nos domínios do ambiente (conservação da biodiversidade), da saúde pública, da agricultura (protecção fitossanitária e sanidade animal) e da pesca, embora a investigação neste domínio seja ainda incipiente. O desenvolvimento e a implementação do quadro nacional de Bio-segurança enfatizam e priorizam o reforço da capacitação institucional e técnico para o manuseamento dos OGMs, permitindo a adequação e reorganização das estruturas existentes. Não obstante, o país pode utilizar os produtos da biotecnologia moderna já disponíveis, em benefício da produção alimentar, da saúde humana e animal, do ambiente, do melhoramento do sector florestal, da pesca e da indústria. Para concretizar o plano, foi proposta a criação de um sistema administrativo e institucional composto por seis órgãos, nomeadamente, a Autoridade Nacional Competente, o Conselho Nacional de Bio-segurança; o Comité Regulador (CR) /Monitorização e Fiscalização; o Secretariado Técnico (ST); o Painel Técnico Científico (PTC) e; o Comité Público. Cada um desses órgãos tem funções específicas que vão desde a orientação das vertentes políticas do país até a sensibilização e educação do público no referente ao assunto. A proposta inclui uma Autoridade Nacional Competente única, sob a alçada do Ministério do Ambiente e Agricultura, como o órgão responsável pela autorização ou não da introdução/criação de OGMs, pela coordenação de todas as actividades ligadas à Bio-segurança; e pela recepção de pedidos de autorização e a gestão de notificações, sejam eles para importação, liberação, propagação ou comercialização; ou uso directo para a alimentação, derivado ou produtos do processamento de produtos alimentares, através do Secretariado Técnico. O diploma legislativo proposto estabelece as normas de segurança e mecanismos de fiscalização à importação, exportação, trânsito, produção, manipulação, manuseamento e utilização de organismos geneticamente modificados (OGM) e seus produtos, em conformidade com o princípio da precaução e tendo em vista a protecção da vida e a saúde do homem, dos animais e das plantas, bem como, o meio ambiente. As normas estabelecidas pelo diploma aplicam-se a todas as entidades públicas e privadas envolvidas na importação, exportação, trânsito, produção, manipulação, manuseamento e utilização de OGM e seus produtos, sem prejuízo do regime fixado para as operações de comércio externo de e para Cabo Verde e demais legislação aplicável. O diploma também não se aplica aos movimentos transfronteiriços de fármacos para seres humanos, que sejam OGM e seus produtos, e que estejam sujeitos a legislação específica. E finalmente, visando assegurar que o QNB para Cabo Verde seja cabalmente activo no país, foi concebido um plano de acção quinquenal para sua operacionalização. Este plano de acção consiste num conjunto de actividades que deverão ser adoptadas e realizadas nos próximos cinco anos, sendo estas: o estabelecimento de um quadro institucional e administrativo de Bio-segurança; estabelecimento de um sistema de consciencialização, educação e participação para bio-segurança; criação de capacidade local para o manuseio da biotecnologia; reforço da capacidade local institucional existente no domínio da biotecnologia/bio-segurança; estudo dos impactos da biotecnologia moderna na agricultura local (incluindo produção pecuária e aquacultura); manutenção do uso seguro de produtos farmacêuticos e alimentares como uma prioridade no domínio da saúde pública e; certificação de um conjunto de medidas e políticas efectivas que acompanhem as constantes mudanças.