Analysis of paternal lineages in Brazilian and African populations

The present-day Brazilian population is a consequence of the admixture of various peoples of very different origins, namely, Amerindians, Europeans and Africans. The proportion of each genetic contribution is known to be very heterogeneous throughout the country. The aim of the present study was to compare the male lineages present in two distinct Brazilian populations, as well as to evaluate the African contribution to their male genetic substrate. Thus, two Brazilian population samples from Manaus (State of Amazon) and Ribeirão Preto (State of São Paulo) and three African samples from Guinea Bissau, Angola and Mozambique were typed for a set of nine Y chromosome specific STRs. The data were compared with those from African, Amerindian and European populations. By using Y-STR haplotype information, low genetic distances were found between the Manaus and Ribeirão Preto populations, as well as between these and others from Iberia. Likewise, no significant distances were observed between any of the African samples from Angola, Mozambique and Guinea Bissau. Highly significant Rst values were found between both Brazilian samples and all the African and Amerindian populations. The absence of a significant Sub-Saharan African male component resulting from the slave trade, and the low frequency in Amerindian ancestry Y-lineages in the Manaus and Ribeirão Preto population samples are in accordance with the accentuated gender asymmetry in admixture processes that has been systematically reported in colonial South American populations.     

Aggregation pheromone of the agave weevil, Scyphophorus acupunctatus

The agave weevil, Scyphophorus acupunctatus Gyllenhal (Coleoptera: Curculionidae), is the most important insect pest of wild and cultivated agaves in the world. Combined gas chromatography‐electroantennography (GC‐EAD) analysis of male volatile extracts showed that four peaks elicited antennal responses from males and females. The peaks were identified by GC‐mass spectrometry (GC‐MS) as 2‐methyl‐4‐heptanol (1), 2‐methyl‐4‐octanol (2), 2‐methyl‐4‐heptanone (3), and 2‐methyl‐4‐octanone (4). Electroantennogram (EAG) recordings of both sexes to 0.01‐, 0.1‐, 1‐, and 10‐µg stimulus load of synthetic compounds showed that the dose of the tested compounds and weevil sex significantly influenced the antennal response of S. acupunctatus. However, there was no sexual dimorphism in the antennal responses to the four synthetic compounds evaluated because the EAG profiles revealed no interaction between doses by sex. Antennae of S. acupunctatus were most sensitive to compounds 2 and 4, reaching the threshold at a 0.01‐µg stimulus load. Weevil antennae were less sensitive to compounds 1 and 3, and the threshold response to these compounds was 0.1 µg. Behavioural evaluation of the synthetic compounds showed them to be attractive to both males and females in a Y‐tube olfactometer. Field experiments confirmed the laboratory results, showing that all components, singly or in blends, were attractive to the weevils. In general, traps baited with the quaternary blend of compounds 1–4 captured significantly more weevils than traps baited with males. However, compounds 3 and 4 were sufficient to obtain captures equivalent to those by the quaternary blend. The potential use of the aggregation pheromone in the development of a mass‐trapping programme as a viable pest management alternative for S. acupunctatus is discussed.     

Large-scale pathway-based analysis of bladder cancer genome-wide association data from five studies of European background

Pathway analysis of genome-wide association studies (GWAS) offer a unique opportunity to collectively evaluate genetic variants with effects that are too small to be detected individually. We applied a pathway analysis to a bladder cancer GWAS containing data from 3,532 cases and 5,120 controls of European background (n = 5 studies). Thirteen hundred and ninety-nine pathways were drawn from five publicly available resources (Biocarta, Kegg, NCI-PID, HumanCyc, and Reactome), and we constructed 22 additional candidate pathways previously hypothesized to be related to bladder cancer. In total, 1421 pathways, 5647 genes and ∼90,000 SNPs were included in our study. Logistic regression model adjusting for age, sex, study, DNA source, and smoking status was used to assess the marginal trend effect of SNPs on bladder cancer risk. Two complementary pathway-based methods (gene-set enrichment analysis [GSEA], and adapted rank-truncated product [ARTP]) were used to assess the enrichment of association signals within each pathway. Eighteen pathways were detected by either GSEA or ARTP at P≤0.01. To minimize false positives, we used the I² statistic to identify SNPs displaying heterogeneous effects across the five studies. After removing these SNPs, seven pathways (‘Aromatic amine metabolism’ [P_GSEA = 0.0100, P_ARTP = 0.0020], ‘NAD biosynthesis’ [P_GSEA = 0.0018, P_ARTP = 0.0086], ‘NAD salvage’ [P_ARTP = 0.0068], ‘Clathrin derived vesicle budding’ [P_ARTP = 0.0018], ‘Lysosome vesicle biogenesis’ [P_GSEA = 0.0023, P_ARTP<0.00012], ’Retrograde neurotrophin signaling’ [P_GSEA = 0.00840], and ‘Mitotic metaphase/anaphase transition’ [P_GSEA = 0.0040]) remained. These pathways seem to belong to three fundamental cellular processes (metabolic detoxification, mitosis, and clathrin-mediated vesicles). Identification of the aromatic amine metabolism pathway provides support for the ability of this approach to identify pathways with established relevance to bladder carcinogenesis.     

Hyperglucosylated adhesin‐derived peptides as antigenic probes in multiple sclerosis: Structure optimization and immunological evaluation

Peptides mimicking antigenic epitopes targeted by antibodies can be powerful tools to be used as antigen surrogates for the specific diagnosis and treatment of autoimmune diseases. Obtaining structural insights about the nature of peptide–antibody interaction in complex mixtures such as sera is a critical goal. In multiple sclerosis (MS), we previously demonstrated that the N‐linked β‐d ‐glucopyranosyl moieties (N‐Glc) containing epitopes in nontypeable Haemophilus influenzae adhesin C‐terminal portion HMW1(1205–1526) were essential for high‐affinity antibody binding in a subpopulation of MS patients. With the aim of developing peptide probes and assessing their binding properties to antibodies from sera of representative patients, we performed the systematic analysis of synthetic peptides based on HMW1(1347–1354) fragment bearing one or two N‐Glc respectively on Asn‐1349 and/or Asn‐1352. The N‐glucosylated nonapeptides efficiently bind to IgG antibodies, displaying IC₅₀ in the range 10^?8–10^?10 M by competitive indirect enzyme‐linked immunosorbent assay (ELISA) in three representative MS patient sera. We selected the di‐N‐glucosylated adhesin peptide Ac‐KAN (Glc)VTLN (Glc)TT‐NH₂ as the shortest sequence able to inhibit high‐avidity interaction with N‐Glc targeting IgM antibodies. Nuclear magnetic resonance (NMR)‐ and circular dichroism (CD)‐based characterization showed that the binding properties of these antigens could not be ascribed to structural differences induced by the presence of up to two N‐glucosyl moieties. Therefore, the antibody binding is not easily correlated to the position of the sugar or to a determined conformation in water.     

Plumage colour and the expression of stress‐related genes in gull chicks

In many bird populations, individuals show remarkable differences in feather colouration, which are often linked to individual differences in physiological traits, but the mechanisms maintaining this covariation are still unclear. Here, we investigate the variability of the melanic colouration in yellow‐legged gull Larus michahellis chicks. In this species, hatchlings show high variability in the number and colour intensity of black spots in their plumage. In gulls, last‐laid eggs receive less antioxidants but higher levels of androgens than first eggs. We first explored whether these remarkable differences within the clutch affect the feather melanisation during embryo development. Melanic colouration was not related to laying order, but nestling males were darker and had a larger spotted area than nestling females. In chicks hatching from first‐laid eggs, the spot size and spot lightness were negatively correlated. We also explored the effect of the developmental environment, through a cross‐fostering experiment, on the expression of five stress‐related genes (SOD2, ALKBH3, HSPA8, NLRC5 and TRIAP1) and their link with melanic colouration. Post‐hatching hierarchy did not affect the expression of any of the tested genes, but paler chicks showed reduced expression in some studied genes (SOD2, ALKBH3 and HSPA8) in comparison to darker chicks. Our results suggest that melanic chicks suffer less stress during development.     

Novel broad host range shuttle vectors for expression in Escherichia coli, Bacillus subtilis and Pseudomonas putida

Novel shuttle vectors named pEBP were constructed to allow the gene expression in different bacterial hosts including Escherichia coli, Bacillus subtilis and Pseudomonas putida. These vectors share the inducible promoters P(T7) and P(Xyl) and a cos site to enable packaging of plasmid DNA into phage, and carry different multiple cloning sites and antibiotic resistance genes. Vector pEBP41 generally replicates episomally while pEBP18 replicates episomally in Gram-negative bacteria only, but integrates into the chromosome of B. subtilis. Plasmid copy numbers determined for E. coli and P. putida were in the range of 5-50 per cell. The functionality of pEBP18 and pEBP41 was confirmed by expression of two lipolytic enzymes, namely lipase A from B. subtilis and cutinase from the eukaryotic fungus Fusarium solani pisi in three different host strains. Additionally, we report here the construction of a T7 RNA polymerase-based expression strain of P. putida.     

Age-related increase in xanthine oxidase activity in human plasma and rat tissues

This study assessed the role of xanthine oxidase in vascular ageing. A positive correlation between xanthine oxidase activity and age was found in human plasma. Similar results were found in rat plasma. Xanthine oxidase expression and activity in homogenates from the aortic wall were significantly higher in samples from old rats than in their young counterparts (p<0.01). In rat skeletal muscle homogenates both xanthine oxidase expression and activity showed a similar age-related profile. Superoxide production by xanthine oxidase in aortic rings was higher in aged rats. Uric acid, the final product of xanthine oxidase has been proposed as a risk factor for coronary heart disease and an independent marker of worse prognosis in patients with moderate-to-severe chronic heart failure. These results give a possible explanation for this correlation and underscore the role of xanthine oxidase in ageing.     

Complex phylogeographic history of central African forest elephants and its implications for taxonomy

Background

The mitochondrial genomes of snakes are characterized by an overall evolutionary rate that appears to be one of the most accelerated among vertebrates. They also possess other unusual features, including short tRNAs and other genes, and a duplicated control region that has been stably maintained since it originated more than 70 million years ago. Here, we provide a detailed analysis of evolutionary dynamics in snake mitochondrial genomes to better understand the basis of these extreme characteristics, and to explore the relationship between mitochondrial genome molecular evolution, genome architecture, and molecular function. We sequenced complete mitochondrial genomes from Slowinski's corn snake (Pantherophis slowinskii) and two cottonmouths (Agkistrodon piscivorus) to complement previously existing mitochondrial genomes, and to provide an improved comparative view of how genome architecture affects molecular evolution at contrasting levels of divergence.

Results

We present a Bayesian genetic approach that suggests that the duplicated control region can function as an additional origin of heavy strand replication. The two control regions also appear to have different intra-specific versus inter-specific evolutionary dynamics that may be associated with complex modes of concerted evolution. We find that different genomic regions have experienced substantial accelerated evolution along early branches in snakes, with different genes having experienced dramatic accelerations along specific branches. Some of these accelerations appear to coincide with, or subsequent to, the shortening of various mitochondrial genes and the duplication of the control region and flanking tRNAs.

Conclusion

Fluctuations in the strength and pattern of selection during snake evolution have had widely varying gene-specific effects on substitution rates, and these rate accelerations may have been functionally related to unusual changes in genomic architecture. The among-lineage and among-gene variation in rate dynamics observed in snakes is the most extreme thus far observed in animal genomes, and provides an important study system for further evaluating the biochemical and physiological basis of evolutionary pressures in vertebrate mitochondria.     

An ADAM metalloprotease is a Cry3Aa Bacillus thuringiensis toxin receptor

Bacillus thuringiensis insecticidal proteins toxic action relies on the interaction with receptor molecules on insect midgut target cells. Here, we describe an ADAM metalloprotease as a novel type of B. thuringiensis toxin receptor on the basis of the following data: (i) by ligand blot and N-terminal analysis, we detected a Colorado potato beetle Cry3Aa toxin binding molecule that shares homology with an ADAM10 metalloprotease; (ii) Colorado potato beetle brush border membrane vesicles display ADAM activity since it cleaves an ADAM fluorogenic substrate; (iii) Cry3Aa acts as a competitor of the cleavage of the ADAM fluorogenic substrate; (iv) Cry3Aa sequence contains the recognition motif R(345)FQPGYYGND(354) present in ADAM10 substrates. Accordingly, a peptide representative of the recognition motif localized within loop 1 of Cry3Aa domain II (Ac-F(341)HTRFQPGYYGNDSFN(358)-NH(2)) effectively prevented Cry3Aa proteolytic processing and nearly abolished pore formation, evidencing the functional significance of the Cry3Aa-ADAM interaction in relation to this toxin mode of action.