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- Incidence of maple syrup urine disease in PortugalPublication . Quental, Sofia; Vilarinho, Laura; Martins, Esmeralda; Teles, Elisa Leão; Rodrigues, Esmeralda; Diogo, Luísa; Garcia, Paula; Eusébio, Filomena; Gaspar, Ana; Sequeira, Sílvia; Amorim, António; Prata, Maria JoãoMaple syrup urine disease is an autosomal recessive disorder of branched-chain amino acids metabolism with a worldwide frequency of 1/185,000 live newborns. In Portugal, the incidence of the disease has not been assessed. Based on the review of the cases diagnosed by tandem mass spectrometry an incidence of 1/86,800 live newborns was estimated in Portugal, indicating that the disease is more frequent in this country than reported in most populations.
- Private dysferlin exon skipping mutation (c.5492G>A) with a founder effect reveals further alternative splicing involving exons 49-51Publication . Santos, Rosário; Oliveira, Jorge; Vieira, Emília; Coelho, Teresa; Carneiro, António Leite; Evangelista, Teresinha; Dias, Cristina; Fortuna, Ana; Geraldo, Argemiro; Negrão, Luís; Guimarães, António; Bronze-da-Rocha, ElsaThe allelic muscle disorders known as limb-girdle muscular dystrophy type 2B (LGMD2B), Miyoshi myopathy and distal anterior compartment myopathy result from defects in dysferlin—a sarcolemma-associated protein involved in membrane repair. Mutation screening in the dysferlin gene (DYSF) enabled the identification of seven Portuguese patients presenting the variant c.5492G4A, which was observed to promote skipping of exon 49 (p.Gly1802ValfsX17). Several residually expressed products of alternative splicing also involving exons 50 and 51 were detected in the leukocytes and muscle of both patients and normal controls. Quantitative transcript analysis confirmed these results and revealed that D49/D50 transcripts were predominant in blood. Although the patients were apparently unrelated, the c.5492G4A mutation was found in linkage disequilibrium with a particularly rare haplotype in the population, corroborating the hypothesis of a common origin. Despite the presence of the same mutation on the same haplotype background, onset of the disease was heterogeneous, with either proximal or distal muscle involvement.
- Proteomics uncovering possible key players in F508del-CFTR processing and traffickingPublication . Gomes-Alves, Patrícia; Penque, DeborahThe achievement and maintenance of a protein native conformation is a very complex cellular process involving a multitude of key factors whose contribution to a successful folding remains to be elucidated. On top of this, it is known that correct folding is crucial for proteins to play their normal role and, consequently, for the maintenance of cellular homeostasis or proteostasis. If the folding process is affected, the protein is unable to achieve its native conformation, compromising its life and function, and a pathological condition may arise. Protein-misfolding diseases are characterized by either formation of protein aggregates that are toxic to the cell (gain-of-toxic-function diseases) or by an incorrect processing of proteins, which leads to a deficiency in protein activity (loss-of-function diseases). In this article we have focused on proteomics advances in the molecular knowledge of protein-misfolding diseases with direct impact on possible key players in F508del-CFTR processing and trafficking.
- Clinical relevance and diversity of two homologous genes encoding glycosyltransferases in Helicobacter pyloriPublication . Oleastro, Mónica; Andrea, Santos; Cordeiro, Rita; Nunes, Baltazar; Mégraud, Francis; Ménard, ArmelleHelicobacter pylori is known to be a major cause of peptic ulceration. The jhp0562 gene, encoding a glycosyltransferase involved in the synthesis of the lipopolysaccharide, was associated with peptic ulcer disease (PUD) in children. The beta-(1,3)-galactosyltransferase [beta-(1,3)GalT] gene (jhp0563), involved in Lewis (Le) antigen expression, is highly similar to jhp0562. The clinical significance and diversity of both genes were examined by PCR and sequencing of clinical strains (n = 117) isolated from children with PUD (n = 57) and nonulcer dyspepsia (NUD; n = 60). The prevalence of the jhp0562 gene was significantly higher in strains with a more-virulent profile (strains positive for the cag pathogenicity island [PAI], vacA sl allele, babA, homB, phase-variable gene oipA "on" [i.e., functional], and hopQ I allele). The distribution of genotypes according to clinical outcome showed that the presence of jhp0562 represented one of the greatest risks for the development of PUD. Moreover, the triple-positive genotype for the cag PAI, jhp0562, and homB provided the best discriminatory model for distinguishing PUD and NUD outcomes in children. Sequence and in vitro expression analyses of jhp0562 showed the presence of a complete open reading frame, while the beta-(1,3)GalT gene was shown to be a phase-variable gene. The regular presence of jhp0562 in strains with a truncated beta-(1,3)GalT gene suggests that jhp0562 may also be implicated in the regulation of Le antigen expression. Overall, the results of this study suggest that the jhp0562 gene is of great clinical relevance, being a useful comarker for severe H. pylori-related disease and contributing to host adaptation.
- Allelic Diversity among Helicobacter pylori Outer Membrane Protein Genes homB and homA Generated by RecombinationPublication . Oleastro, Mónica; Cordeiro, Rita; Ménard, Armelle; Gomes, João PauloRecombination is one of the main mechanisms contributing to Helicobacter pylori genomic variability. homB and homA are paralogous genes coding for H. pylori outer membrane proteins (OMPs). Both genes display allelic variation yielded by polymorphisms of the genes’ middle regions, with six different alleles. This study used bioinformatic and statistical analyses to evaluate whether the allelic diversity of homB and homA is generated by recombination. A detailed molecular analysis of the most prevalent homB allelic variant was also performed to establish its molecular profile. The two most prevalent homB and homA allelic variants resulted from interallelic homologous recombination between the rarest allelic variants of each gene, with a crossover point localized in the middle of the genes, containing the allelic region. Molecular analysis of the most prevalent homB allele revealed a geographic partition among Western and East Asian strains, more noticeable for the 5 and 3 homB regions than for the middle allelic regions. In conclusion, the diversity of the 5 and 3 homB regions reflect the strains’ geographical origin, and variants likely occur via the accumulation of single nucleotide polymorphisms. On the other hand, homologous recombination seems to play an important role in the diversification of the highly polymorphic homB and homA allele-defining regions, where the most prevalent alleles worldwide result from genomic exchange between the rarest variants of each gene, suggesting that the resulting combinations confer biological advantages to H. pylori. This phenomenon illustrates an evolutionary scenario in which recombination appears to be associated with ecological success.
- Occurrence of patulin in apple-based-foods in PortugalPublication . Barreira, Maria João; Alvito, Paula; Almeida, Cristina M.M.An analytic procedure based on high-performance liquid chromatography with solid-phase extraction and UV detection (SPE–HPLC–UV) was validated and used to analyse 144 apple-based-foods, including 68 apple juices (32 clear and 36 cloudy) and 76 homogenised apple purees marketed in Portugal. Patulin was detected in 33 samples (23%) with values ranging from 1.2 lg/kg to 42 lg/kg. Patulin was not detected in the analysed infant drinks but its presence was quantified in five homogenised apple puree (7%) labelled as being intended for infants and young children consumption. A higher incidence of positive samples was detected in cloudy juices (67%) when compared with clear ones (13%). When the production mode is considered, the incidence of positive samples was 20% and 24% for products of organic and conventional origin, respectively. This is the first study on the occurrence of patulin in apple-basedfoods in Portugal, including baby food.
- Incorrect DNA methylation of the DAZL promoter CpG island associates with defective human spermPublication . Navarro-Costa, Paulo; Nogueira, Paulo; Carvalho, Marta; Leal, Fernanda; Cordeiro, Inês; Calhaz-Jorge, Carlos; Gonçalves, João; Plancha, Carlos E.Background: Successful gametogenesis requires the establishment of an appropriate epigenetic state in developing germ cells. Nevertheless, an association between abnormal spermatogenesis and epigenetic disturbances in germline-specific genes remains to be demonstrated. Methods: In this study, the DNA methylation pattern of the promoter CpG island (CGI) of two germline regulator genes—DAZL and DAZ, was characterized by bisulphite genomic sequencing in quality-fractioned ejaculated sperm populations from normozoospermic (NZ) and oligoasthenoteratozoospermic (OAT) men. Results: OAT patients display increased methylation defects in the DAZL promoter CGI when compared with NZ controls. Such differences are recorded when analyzing sperm fractions enriched either in normal or defective germ cells (P , 0.001 in both cases). Significant differences in DNA methylation profiles are also observable when comparing the qualitatively distinct germ cell fractions inside the NZ and OAT groups (P ¼ 0.003 and P ¼ 0.007, respectively). Contrastingly, the unmethylation pattern of the DAZ promoter CGI remains correctly established in all experimental groups. Conclusions: An association between disrupted DNA methylation of a key spermatogenesis gene and abnormal human sperm is described here for the first time. These results suggest that incorrect epigenetic marks in germline genes may be correlated with male gametogenic defects.
- Novel large deletions in the human alpha-globin gene cluster: Clarifying the HS-40 long-range regulatory role in the native chromosome environmentPublication . Coelho, Andreia; Isabel, Picanço; Filomena, Seuanes; Seixas, Maria Teresa; Paula, FaustinoGlobin genes, which encode the protein subunits of hemoglobin (Hb), are organized in two different gene clusters and present a coordinated and differential pattern of expression during development. Concerning the human α-globin gene cluster (located at chromosome region 16p13.3), four upstream highly conserved elements known as multispecies conserved sequences (MCS-R1-4) or DNase I hypersensitive sites (HSs) are implicated in the long-range regulation of downstream gene expression. However, only the absence of the MCS-R2 site (HS-40) has proven to drastically downregulate the expression of those genes, and consequently, it has been regarded as the major and crucial distal regulatory element. In this study, Multiplex Ligation-dependent Probe Amplification was used to screen for deletions in the telomeric region of the short arm of chromosome 16, in an attempt to explain the α-thalassemia or the HbH disease present in a group of Portuguese patients. We report four novel and five uncommon deletions that remove the α-globin distal regulatory elements and/or the complete α-globin gene cluster. Interestingly, one of them occurred de novo and removes all HSs except HS-10, while other eliminates only the HS-40 site, the latter being replaced by the insertion of a 39 nucleotide orphan sequence. Our results demonstrate that HS-10 alone does not significantly enhance the α-globin gene expression. The absence of HS-40 in homozygosity, found in a patient with Hb H disease, strongly downregulates the expression of α-globin genes but it is not associated with a complete absence of α-globin chain production. The study of naturally occurring deletions in this region is of great interest to understand the role of each upstream regulatory element in the native human erythroid environment.
- A novel molecular method for identification of Oenococcus oeni and its specific detection in winePublication . Marques, Ana P.; Zé-Zé, Líbia; San-Romão, Maria Vitória; Tenreiro, RogérioOenococcus oeni is a species of lactic acid bacteria with economic interest in winemaking. Using both in silico and in vitro analyses, a molecular method was developed that allows the identification of O. oeni isolates and its detection from wine samples. The method is based on the amplification of 16S rRNA gene with universal primers followed by restriction with the endonuclease FseI, generating two fragments of 326 and 1233 bp. Among wine bacteria, the FseI recognition sequence is only found in the 16S rRNA gene of O. oeni, ensuring the specificity of the method. The use of Whatman FTA cards for DNA extraction and purification is an efficient and interesting alternative to current methods, as samples can be easily collected at wineries by a non-specialized technician, stored at room temperature and sent in a mail envelope to the analytical laboratory for processing. The proposed method, with a detection limit between 102 and 103 cfu/mL and a full turnaround time of ca. 8 h, ensures the rapid and reliable detection of O. oeni in wine samples during winemaking surveillance and wine quality control.
- Folding and rescue of a cystic fibrosis transmembrane conductance regulator trafficking mutant identified using human-murine chimeric proteinsPublication . Da Paula, Ana Carina; Sousa, Marisa; Xu, Zhe; Dawson, Elizabeth S.; Boyd, A. Christopher; Sheppard, David N.; Amaral, Margarida D.Impairment of the cystic fibrosis transmembrane conductance regulator (CFTR) Cl channel causes cystic fibrosis, a fatal genetic disease. Here, to gain insight into CFTR structure and function, we exploited interspecies differences between CFTR homologues using human (h)-murine (m) CFTR chimeras containing murine nucleotide-binding domains (NBDs) or regulatory domain on an hCFTR backbone. Among 15 hmCFTR chimeras analyzed, all but two were correctly processed, one containing part of mNBD1 and another containing part of mNBD2. Based on physicochemical distance analysis of divergent residues between human and murine CFTR in the two misprocessed hmCFTR chimeras, we generated point mutations for analysis of respective CFTR processing and functional properties. We identified one amino acid substitution (K584E-CFTR) that disrupts CFTR processing in NBD1. No single mutation was identified in NBD2 that disrupts protein processing. However, a number of NBD2 mutants altered channel function. Analysis of structural models of CFTR identified that although Lys584 interacts with residue Leu581 in human CFTR Glu584 interacts with Phe581 in mouse CFTR. Introduction of the murine residue (Phe581) in cis with K584E in human CFTR rescued the processing and trafficking defects of K584E-CFTR. Our data demonstrate that human-murine CFTR chimeras may be used to validate structural models of full-length CFTR. We also conclude that hmCFTR chimeras are a valuable tool to elucidate interactions between different domains of CFTR.