Identification, sequencing and mutagenesis of the gene for a d-carbamoylase from Agrobacterium radiobacter

Abstract A clone positive for d-carbamoylase activity (2.7 kb Hin dIII- Bam H1 DNA fragment) was obtained by screening a genomic library of Agrobacterium radiobacter in Escherichia coli . This DNA fragment contains an open reading frame of 912 bp which is predicted to encode a peptide of 304 amino acids with a calculated molecular mass of 34247 Da. The d-carbamoylase gene. named cauA , was placed under the control of T7 RNA-dependent promoter and expressed in E. coli BL21 (DE3). After induction with isopropyl-thio-β-d-galactopyranoside, the synthesis of d-carbamoylase in E. coli reached about 40% of the total protein. The expressed protein was shown to possess a molecular mass, on SDS-PAGE, of 36 kDa and showed an enhanced allowed us to establish that a Pro¹⁴→Leu¹⁴ exchange leads to an inactive enzyme species, while a Cys²⁷⁹→Ser²⁷⁹ exchange did not impair the functional properties of the enxyme.     

Filter and deposit: a potential role of freshwater mussels in ecosystem functioning associated with enhanced macroinvertebrate assemblage structure in a Neotropical river

Hydrobiologia - Mussels provide important ecological functions in freshwater ecosystems but the associations between Amazonian mussels, macroinvertebrate assemblage and habitat quality remain...     

Molecular phylogeny of mangrove oysters (Crassostrea) from Brazil

As a result of phenotypic plasticity, the cupped oysters (Crassostrea)are difficult to identify by means of their morphology. However,molecular DNA markers are a useful means of discriminating amongthese species. Cupped oysters are one of the most widely culturedmarine invertebrates and correct species identification is importantin aquaculture. Moreover, the molecular phylogeny of the genusCrassostrea and the subfamily Crassostreinae is still not clear.In order to identify the Brazilian cupped oysters and to clarifythe phylogenetic relationships of these species, we sequenceda fragment of mitochondrial DNA (16S rRNA gene) from 120 specimenscollected at nine different sites distributed along the Braziliancoast. The results identified two native species of oyster:Crassostrea gasar, from the Amazon to the Parnaíba delta;and Crassostrea rhizophorae, from the northeast (Fortim) tothe south of Brazil. An exotic Crassostrea species, closelyrelated to Indo-Pacific Crassostrea, was found in one locationin the north of Brazil. Crassostrea showed monophyly and theAtlantic oysters are clearly separated from the Indo-Pacificcluster. (Received 30 May 2006; accepted 12 April 2007)     

Greater macroinvertebrate diversity and freshwater mussel density in meander margins of an Amazon river

Meanders are complex aquatic environments exhibiting different flow and sediment characteristics that influence macroinvertebrate distribution. Differences in macroinvertebrate composition, freshwater mussel density (mainly Castalia ambigua Lamarck, 1819) and habitat variables were investigated, using uni‐ and multivariate analyses, in two zones, the margin and thalweg, of the meanders of a 7‐km stretch of a morphologically unaltered tropical alluvial lowland river. Clear differences were found between meander zones, with greater taxonomic and functional diversity of macroinvertebrates and greater freshwater mussel densities in the meander margin. A total of 12 families of macroinvertebrates were exclusive to the meander margin, and macroinvertebrate indicators of zones were Philopotamidae and Leptoceridae (meander margin) and Chironomidae and Elmidae (meander thalweg). In the meander margin, there were no differences in macroinvertebrate abundance, and taxonomic and functional group diversity among areas with low, medium and high mussel density. Macroinvertebrate abundance did not vary between zones, but in both, abundance was associated with lower pH and higher electrical conductivity. Low shear velocity, which stabilises the river bed, high organic matter content and percentage silt in the meander margin were associated with higher taxonomic and functional macroinvertebrate diversity, as well as the presence of freshwater mussels. Natural unaltered meanders are spatially heterogeneous in both habitat and biodiversity and, similar to restored meanders, support greater macroinvertebrate taxonomic and functional diversity, as well as maintain freshwater mussel beds, mainly by stabilising the river bed. The meander margin may also be important for attracting mussel host fish that feed on macroinvertebrates and aid mussel dispersal. Thus, the meander margins, and other similar riparian habitats with low shear velocity, for example, side channels and pools, have potentially high conservation value and should be afforded due protection.     

The impact of migration on the marriage structure in Fontanigorda

Until World War II the economic activity of the inhabitants of the commune of Fontanigorda (Genova — Italy) was based on subsistence farming and temporary migration. Migration to France in search of work absorbed the excess active male population: the isonymy study shows that the migrants were recruited from all the families of the commune. After having left for Marseilles or the mine at St. Maime (in the Alps of Upper Provence), these young migrants returned to their home town to marry. This behaviour maintained a high degree of consanguinity, obscured by a false exogamy, at least until the turn of the century. After this period, lifelong migration completely modified the pattern of marriage structure bacause migration to France became definitive.     

Marmoset phylogenetics, conservation perspectives, and evolution of the mtDNA control region

Marmosets (genus Callithrix) are a diverse group of platyrrhine primates with 13-15 purported taxa, many of them considered endangered. Morphological analyses constitute most of the basis for recognition of these forms as distinct taxa. The purpose of this study was to provide a molecular view, based on mitochondrial control region sequences, of the evolutionary history of the marmosets, concomitant with a molecular phylogenetic perspective on species diversity within the group. An additional purpose was to provide the first comparative examination of a complete New World monkey control region sequence with those of other mammals. The phylogenetic analyses provide convincing support for a split between the Atlantic forest and Amazonian marmosets, with the inclusion of the pygmy marmoset (Cebuella pygmaea) at the base of the Amazonian clade. The earliest branch of the Atlantic forest group was C. aurita. In the Amazonian group, the analyses do not support the recognition of C. humeralifer and the recently described C mauesi as distinct taxa. They do, however, support a clear distinction between C. argentata and a strongly supported mixed clade of C. humeralifer and C. mauesi. In the Atlantic forest group, the phylogenetic tree suggests mixing between C. penicillata, C. kuhli, and possibly C. jacchus. Most of the sequence features characteristic of other mammal control regions were also evident in marmosets, with the exception that conserved sequence blocks (CSBs) 2 and 3 were not clearly identifiable. Tandem repeat units often associated with heteroplasmy in a variety of other mammals were not evident in the marmoset sequences.      

Improved high-performance liquid chromatographic determination with amperometric detection of α-amanitin in human plasma based on its voltammetric study

A sensitive and simple method is described for the selective determination in human plasma of α-amanitin, the most poisonous and prevalent toxin in the lethal fungi of species Amanita, using high-performance liquid chromatography with amperometric detection. After an extraction of plasma with disposable C₁₈ silica cartridges, the extracts were separated by isocratic reversed-phase chromatography using a macroporous poly(styrene—divinylbenzene) column and a mobile phase of 0.05 M phosphate buffer—acetonitrile (91:9) at the apparent pH of 9.5. Amperometric detection was performed by applying an oxidation potential as low as +350 mV (vs. Ag/AgCl) to a glassy carbon electrode, in a thin-layer flow-cell. The linear range for α-amanitin was 3–200 ng/ml, and the relative limit of detection in plasma was 2 ng/ml at a signal-to-noise ratio of 2. The intra-assay precision was evaluated at levels of 10 and 200 ng/ml; the coefficients of variation were 4.5 and 2.6% (n=5), respectively. Inter-assay coefficients of variation were 6.5 and 4.2% (n=5) for the same concentrations of toxin. These analytical conditions have been chosen on the basis of a preliminary in batch cyclic voltammetric investigation of α-, β- and γ-amanitins, which has allowed their oxidation process to be clarified and the pH dependence of their oxidation potentials to be determined. All three amanitins are oxidized at the same potential values, and adsorption onto the electrode surface of both reactant and products was found in all cases. This adsorption did not affect the signal recorded for α- and γ-amanitins at the amperometric detector, and for β-amanitin a stronger adsorption for the anodic product was found, which leads to a marked positive shift of the potential required for the oxidation of this isomer in the amperometric detector cell.     

Direct injection high-performance liquid chromatographic method with electrochemical detection for the determination of ethanol and methanol in plasma using an alcohol oxidase reactor

A highly sensitive reversed-phase high-performance liquid chromatographic assay for ethanol and methanol in plasma, using a post-column enzymic reactor with electrochemical detection, has been developed. The alcohols, separated on the column, were converted by immobilized alcohol oxidase into their respective aldehydes with formation of stoichiometric amounts of hydrogen peroxide, detected via oxidation at a platinum electrode. As the chromatographic column, two glass cartridges (150 mm × 3 mm I.D.) in series, packed with 10-μm HEMA-S 1000^® packing, were used. Alcohol oxidase from Candida boidinii was immobilized onto HEMA-BIO 1000 VS-L (10 μm), packed in a 30 mm × 3 mm I.D. glass cartridge. The reaction product, hydrogen peroxide, was detected with an amperometric detector with a platinum electrode, operated at +500 mV vs. an Ag/AgCl reference electrode. A 20-μl volume of ten-fold diluted plasma was injected without any pre-treatment. Under the described conditions, methanol and ethanol were well resolved from each other and from the “front” of the chromatogram. The limit of detection was ca. 2.5 nmol for ethanol and 0.6 nmol for methanol in plasma, at a signal-to-noise ratio of 3. Excellent linearity was observed for ethanol, in the range 0.125–4 μg injected (r = 0.9999). In contrast, the response for methanol was markedly non-linear above 500 μg injected, presumably owing to progressive saturation of the reactor. The precision and accuracy of the assay were satisfactory, as was the reactor life (one month).     

Significant genetic differentiation among populations of Anomalocardia brasiliana (Gmelin, 1791): A bivalve with planktonic larval dispersion

Four Brazilian populations of Anomalocardia brasiliana were tested for mutual genetic homogeneity, using data from 123 sequences of the mtDNA cytochrome oxidase c subunit I gene. A total of 36 haplotypes were identified, those shared being H3 (Canela Island, Prainha and Acupe) and both H5 and H9 (Prainha and Acupe). Haplotype diversity values were high, except for the Camurupim population, whereas nucleotide values were low in all the populations, except for that of Acupe. Only the Prainha population showed a deviation from neutrality and the SSD test did not reject the demographic expansion hypothesis. Fst values showed that the Prainha and Acupe populations represent a single stock, whereas in both the Canela Island and Camurupim stocks, population structures are different and independent. The observed structure at Canela Island may be due to the geographic distance between this population and the remainder. The Camurupim population does not share any haplotype with the remaining populations in northeastern Brazil. The apparent isolation could be due to the rocky barrier located facing the mouth of the Mamanguape River. The results highlight the importance of wide-scale studies to identify and conserve local genetic diversity, especially where migration is restricted.     

Carbohydrate-deficient transferrin (CDT) as a marker of alcohol abuse: a critical review of the literature 2001-2005

The diagnosis of alcohol abuse based on objective data is a necessary requirement in both clinical and forensic environments. Among the different biomarkers of chronic alcohol abuse, carbohydrate-deficient transferrin (CDT) is world wide recognized as the most reliable indicator. However, several problems about the real meaning of CDT and the reliability of its use for the diagnosis of alcohol abuses are still open, as reported by numerous research articles and reviews. The present article presents a critical review of the literature on CDT appeared in the period from 2001 to 2005 (included). The article is organized in the following sections: (1) introduction, (2) definition and structure of human serum CDT, (3) pathomechanisms of the ethanol-induced CDT increase, (4) preanalysis, (5) analysis, (6) data interpretation, (7) review papers, (8) conclusions. As many as 127 papers appeared in the international literature and retrieved by the search engines PubMed and Scopus are quoted.