Rapid Evolution of the Sequences and Gene Repertoires

Proteins secreted to the extracellular environment or to the periphery of the cell envelope, the secretome, play essential roles in foraging, antagonistic and mutualistic interactions. We hypothesize that arms races, genetic conflicts and varying selective pressures should lead to the rapid change of sequences and gene repertoires of the secretome. The analysis of 42 bacterial pan-genomes shows that secreted, and especially extracellular proteins, are predominantly encoded in the accessory genome, i.e. among genes not ubiquitous within the clade. Genes encoding outer membrane proteins might engage more frequently in intra-chromosomal gene conversion because they are more often in multi-genic families. The gene sequences encoding the secretome evolve faster than the rest of the genome and in particular at non-synonymous positions. Cell wall proteins in Firmicutes evolve particularly fast when compared with outer membrane proteins of Proteobacteria. Virulence factors are over-represented in the secretome, notably in outer membrane proteins, but cell localization explains more of the variance in substitution rates and gene repertoires than sequence homology to known virulence factors. Accordingly, the repertoires and sequences of the genes encoding the secretome change fast in the clades of obligatory and facultative pathogens and also in the clades of mutualists and free-living bacteria. Our study shows that cell localization shapes genome evolution. In agreement with our hypothesis, the repertoires and the sequences of genes encoding secreted proteins evolve fast. The particularly rapid change of extracellular proteins suggests that these public goods are key players in bacterial adaptation.

Novel Secretion Apparatus Maintains Spore Integrity and Developmental Gene Expression in Bacillus subtilis

Plos Genetics, 5(7): ARTe1000566

Establishing a high titer transient gene expression process in conditioned media for CHO-DG44 cells

Dissertação para obtenção do Grau de Mestre em Biotecnologia

Mitosis and protein Na-terminal acetylation

Dissertation presented to obtain the Ph.D degree in Developmental Biology

Gold nanoparticle-DNA conjugates for oligonucleotide vectorization towards gene silencing

Dissertação para obtenção do Grau de Mestre em Genética Molecular e Biomedicina

Mapping of a Leishmania major gene/locus that confers pentamidine resistance by deletion and insertion of transposable element

Pentamidine (PEN) is an alternative compound to treat antimony-resistant leishmaniasis patients, which cellular target remains unclear. One approach to the identification of prospective targets is to identify genes able to mediate PEN resistance following overexpression. Starting from a genomic library of transfected parasites bearing a multicopy episomal cosmid vector containing wild-type Leishmania major DNA, we isolated one locus capable to render PEN resistance to wild type cells after DNA transfection. In order to map this Leishmania locus, cosmid insert was deleted by two successive sets of partial digestion with restriction enzymes, followed by transfection into wild type cells, overexpression, induction and functional tests in the presence of PEN. To determine the Leishmania gene related to PEN resistance, nucleotide sequencing experiments were done through insertion of the transposon Mariner element of Drosophila melanogaster (mosK) into the deleted insert to work as primer island. Using general molecular techniques, we described here this method that permits a quickly identification of a functional gene facilitating nucleotide sequence experiments from large DNA fragments. Followed experiments revealed the presence of a P-Glycoprotein gene in this locus which role in Leishmania metabolism has now been analyzed.

Rapid turnover of Plasmodium falciparum var gene transcripts and genotypes during natural non-symptomatic infections

The var genes of Plasmodium falciparum code for the antigenically variant erythrocyte membrane proteins 1 (PfEMP1), a major factor for cytoadherence and immune escape of the parasite. Herein, we analyzed the var gene transcript turnover in two ongoing, non-symptomatic infections at sequential time points during two weeks. The number of different circulating genomes was estimated by microsatellite analyses. In both infections, we observed a rapid turnover of plasmodial genotypes and var transcripts. The rapidly changing repertoire of var transcripts could have been caused either by swift elimination of circulating var-transcribing parasites stemming from different or identical genetic backgrounds, or by accelerated switching of var gene transcription itself.

Role of the DHH1 Gene in the Regulation of Monocarboxylic Acids Transporters Expression in Saccharomyces cerevisiae

Previous experiments revealed that DHH1, a RNA helicase involved in the regulation of mRNA stability and translation, complemented the phenotype of a Saccharomyces cerevisiae mutant affected in the expression of genes coding for monocarboxylic-acids transporters, JEN1 and ADY2 (Paiva S, Althoff S, Casal M, Leao C. FEMS Microbiol Lett, 1999, 170∶301–306). In wild type cells, JEN1 expression had been shown to be undetectable in the presence of glucose or formic acid, and induced in the presence of lactate. In this work, we show that JEN1 mRNA accumulates in a dhh1 mutant, when formic acid was used as sole carbon source. Dhh1 interacts with the decapping activator Dcp1 and with the deadenylase complex. This led to the hypothesis that JEN1 expression is post-transcriptionally regulated by Dhh1 in formic acid. Analyses of JEN1 mRNAs decay in wild-type and dhh1 mutant strains confirmed this hypothesis. In these conditions, the stabilized JEN1 mRNA was associated to polysomes but no Jen1 protein could be detected, either by measurable lactate carrier activity, Jen1-GFP fluorescence detection or western blots. These results revealed the complexity of the expression regulation of JEN1 in S. cerevisiae and evidenced the importance of DHH1 in this process. Additionally, microarray analyses of dhh1 mutant indicated that Dhh1 plays a large role in metabolic adaptation, suggesting that carbon source changes triggers a complex interplay between transcriptional and post-transcriptional effects.

Edifício do Terminal de Cruzeiros do Porto de Leixões: Acompanhamento dos trabalhos de Fundações e Estruturas de Suporte.

Infraestrutura com mais de um século de história, o Porto de Leixões encontra-se em fase de renovação com a criação de um emblemático Edifício de Terminal de Cruzeiros. Obra de arquitetura arrojada, o edifício é implantado em condições geológico-geotécnicas adversas e na convivência com o efeito da água do mar e das respetivas marés. O presente relatório é relativo a um Estágio realizado na obra numa fase de execução dos trabalhos de fundações e de contenções periféricas (ensecadeira). Apresentam-se as soluções sugeridas em projeto, as soluções apresentadas inicialmente pelo construtor e as alternativas a estas, propostas já durante a obra. Descrevem-se as diferentes soluções, identificando os equipamentos, recursos humanos e procedimentos envolvidos. Comparam-se os respetivos rendimentos e custos. Apresenta-se o Plano de Instrumentação e de Monitorização implementado em obra. Descreve-se em pormenor o trabalho realizado pelo estagiário, em obra, no decurso do estágio.

Training and discovering corpus-based data driven exercices in english teaching (L2/FL) to native speakers of portuguese (L1)

Project submitted as part requirement for the degree of Masters in English teaching,

Clinical and Pathological Findings in Women with Fabry Disease

Introduction. Fabry disease is a rare metabolic disorder caused by the genetic deficiency of the lysosomal hydrolase alpha-galactosidase A, located on chromosome X. Females with the defective gene are more than carriers and can develop a wide range of symptoms. Nevertheless, disease symptoms generally occur later and are less severe in women than in men. The enzyme deficiency manifests as a glycosphingolipidosis with progressive accumulation of glycosphingolipids and deposit of inclusion bodies in lysosomes giving a myelinlike appearance. Patients and Methods. Records of renal biopsies performed on adults from 1st January 2008 to 31st August 2011, were retrospectively examined at the Renal Pathology Laboratory. We retrieved biopsies diagnosed with Fabry disease and reviewed clinical and laboratory data and pathology findings. Results. Four female patients with a mean age of 49.3±4.5 (44-55) years were identified. The mean proteinuria was 0.75±0.3 g/24h (0.4-1.2) and estimated glomerular filtration rate (CKD EPI equation) was 71±15.7 ml/min/1.73m2 (48-83). Three patients experienced extra-renal organ involvement (cerebrovascular, cardiac, dermatologic, ophthalmologic and thyroid) with distinct severity degrees. Leukocyte α-GAL A activity was below normal range in the four cases but plasma and urinary enzymatic activity was normal. Light microscopy showed predominant vacuolisation of the podocyte cytoplasm and darkly staining granular inclusions on paraffin and plastic-embedded semi-thin sections. Electron microscopy showed in three patients the characteristic myelin-like inclusions in the podocyte cytoplasm and also focal podocyte foot process effacement. In one case the inclusions were also present in parietal glomerular cells, endothelial cells of peritubular capillary and arterioles. Conclusion. Clinical signs and symptoms are varied and can be severe among heterozygous females with Fabry disease. Intracellular accumulation of glycosphingolipids is a characteristic histologic finding of Fabry nephropathy. Since this disease is a potentially treatable condition, its early identification is imperative. We should consider it in the differential diagnosis of any patient presenting with proteinuria and/or chronic kidney disease, especially if there is a family history of kidney disease.

Delecção 1p36 – A Síndrome Não Explica Tudo…

Introdução: A criança com co-morbilidade grave é um premente desafio diagnóstico, cujo sucesso depende de uma abordagem multi-disciplinar. A síndrome de delecção 1p36, microdelecção subtelomérica de apresentação clínica pleiotrópica e multissistémica, pode incluir atraso do desenvolvimento psicomotor, alterações cardíacas, neurológicas e gastrointestinais. Caso Clínico: Filha única de pais não consanguíneos, PNV sem vacinação anti pneumocócica, com múltiplos internamentos: choque cardiogénico com miocardiopatia dilatada (3M), sépsis a S. aureus e Streptococcus do grupo G (5M) e várias intercorrencias infecciosas (varicela, gastrenterite, bronquiolite, febre sem foco). Aos 22 meses é reinternada por choque séptico com falência multi-orgânica por Streptococcus pneumoniae (serotipo 23-F), complicada de osteomielite dos ossos do antebraço e abcesso abdominal com necessidade de cirurgia. Pelos antecedentes e gravidade desta sépsis pneumocócica investigou-se eventual imunodeficiência identificando-se asplenia, confirmada por corpos de Howell-Jolly, TC abdominal e laparotomia. Retrospectivamente, para além da miocardiopatia havia má progressão ponderal com dificuldades alimentares, atraso global do desenvolvimento psicomotor, dermatose eczematosa grave e hipereosinofilia (2.410-5.680/uL), investigada por Genética, Infecciologia e Doenças Metabólicas. O cariotipo revelou monossomia da região distal ao locus 1p36 – delecção 1p36. Cintigrafia com MIBG sem evidência de neuroblastoma (risco aumentado pela síndrome). O estudo metabólico foi negativo, à excepção de défice de L-carnitina, pelo que mantem suplementos estando em curso estudo molecular de CPT2 – gene associado a défice de carnitina, na localização 1p32. Quanto à hipereosinofilia, verificou-se IgE aumentada e biopsia óssea normal pelo que iniciou prednisolona 2mg/Kg/dia com resposta favorável, estando estudo molecular específico em curso. Discussão: No fenótipo da síndrome enquadram-se o atraso global do desenvolvimento, a miocardiopatia e dificuldades alimentares. A asplenia, hipereosinofilia e dermatose eczematosa graves, não associadas a esta síndrome e de etiologia ainda a esclarecer podem-se integrar eventualmente na delecção terminal do cromossoma 1. As alterações no cariotipo carecem ainda de caracterização do ponto de quebra centromérico através de array-CGH, teste com maior especificidade para avaliar a tradução clínica dos efeitos individuais e combinados dos genes envolvidos.

Amplification of the flgE gene provides evidence for the existence of a Brazilian borreliosis

INTRODUCTION: The symptoms of Brazilian borreliosis resemble the clinical manifestations of Lyme disease (LD). However, there are differences between the two in terms of epidemiological and laboratory findings. Primers usually employed to diagnose LD have failed to detect Borrelia strains in Brazil. OBJECTIVE: We aimed to identify the Brazilian Borrelia using a conserved gene that synthesizes the flagellar hook (flgE) of Borrelia burgdorferi sensu lato. METHOD: Three patients presenting with erythema migrans and positive epidemiological histories were recruited for the study. Blood samples were collected, and the DNA was extracted by commercial kits. RESULTS: The gene flgE was amplified from DNA of all selected patients. Upon sequencing, these positive samples revealed 99% homology to B. burgdorferi flgE. CONCLUSION: These results support the existence of borreliosis in Brazil. However, it is unclear whether this borreliosis is caused by a genetically modified B. burgdorferi sensu stricto or by a new species of Borrelia spp.

Acidose Tubular Renal Distal e Surdez Neurossensorial com Mutação no Gene ATP6V1B1

A acidose tubular renal distal é uma doença rara, caracterizada pela incapacidade na acidificação da urina, condicionando acidose metabólica hiperclorémica, hipocaliémia, hipercalciúria e nefrocalcinose, o que poderá causar atraso de crescimento, alteração do metabolismo ósseo e insuficiência renal crónica. A acidose tubular renal distal associada a surdez neurossensorial é uma doença de herança autossómica recessiva, causada por mutações do gene que codifica a subunidade B1 da H+ -ATPase (ATP6V1B1). Os autores relatam os casos de duas irmãs que apresentaram má progressão ponderal, alterações iónicas, do equilíbrio ácido base e surdez neurossensorial. Foi detectada em ambas as crianças a mutação homozigótica no gene ATP6V1B1. Com estes dois casos pretende -se destacar a importância de um diagnóstico precoce nesta patologia rara.