Power to detect risk alleles using genome-wide tag SNP panels

Advances in high-throughput genotyping and the International HapMap Project have enabled association studies at the whole-genome level. We have constructed whole-genome genotyping panels of over 550,000 (HumanHap550) and 650,000 (HumanHap650Y) SNP loci by choosing tag SNPs from all populations genotyped by the International HapMap Project. These panels also contain additional SNP content in regions that have historically been overrepresented in diseases, such as nonsynonymous sites, the MHC region, copy number variant regions and mitochondrial DNA. We estimate that the tag SNP loci in these panels cover the majority of all common variation in the genome as measured by coverage of both all common HapMap SNPs and an independent set of SNPs derived from complete resequencing of genes obtained from SeattleSNPs. We also estimate that, given a sample size of 1,000 cases and 1,000 controls, these panels have the power to detect single disease loci of moderate risk (λ ~ 1.8–2.0). Relative risks as low as λ ~ 1.1–1.3 can be detected using 10,000 cases and 10,000 controls depending on the sample population and disease model. If multiple loci are involved, the power increases significantly to detect at least one locus such that relative risks 20%–35% lower can be detected with 80% power if between two and four independent loci are involved. Although our SNP selection was based on HapMap data, which is a subset of all common SNPs, these panels effectively capture the majority of all common variation and provide high power to detect risk alleles that are not represented in the HapMap data.     

The Evaluation of Biomarkers of Physical Activity on Stress Resistance and Wellness

Physical activity can improve health as well as reduce stress and the risk of developing several widespread diseases. However, there exists no accepted standard biomedical examination-method for stress evaluation. The purpose of this study was to investigate the effect of regular physical activity on stress and wellness as well as the evaluation of potential biomarkers in this field. This study included 105 people (mean age = 36.57 ± 1.4 years) who were randomly assigned into the exercise group 1 (EG-1) (n = 41), the exercise group 2 (EG-2) (n = 30), and the control group (CG) (n = 34). Measurements of stress and wellness were obtained by Multiscan BC-OXI before and after experimental period. This device presents a multifrequency segmental body composition 3D analyser with digital pulse oximeter. The key indicators of stress as well as for wellness were significantly improved in the EG-1. Parasympathetic activity showed significant changes as potential stress biomarker. Statistically significant gender differences were not observed in the comparable groups. The results suggest that the stress resistance and well-being significantly improved in the EG-1 due to regular physical activity. However, further research is necessary to determine effects of physical activity on integral health indicators.

     

Occurrence of Amblycerus species in Cordia trichotoma seeds and their influence on germination

Forest species can have their seeds damaged by granivorous insects, especially by those in their larval stage. In this context, this study aims to report the occurrence of Amblycerus species in Cordia trichotoma seeds, to describe their main damage to seeds and effects on germination, as well as their associated hymenopteran parasitoids. Therefore, seven trees were selected in the municipality of Taquaruçu do Sul, RS, Brazil. Fruits were collected weekly from the medium third of the tree crown, from the beginning of their formation until total dehiscence. To examine the damage caused by granivorous insects within the fruits, 15 fruits from each tree were sectioned with a scalpel. Furthermore, 10 fruits from each tree were stored individually in clear plates to verify the occurrence and identification of granivorous insect species. Evidence of the damage caused to seeds was verified through the germination test by comparing preserved and damaged seeds, with four repetitions of 25 seeds each. The species Amblycerus longesuturalis and Amblycerus profaupar (Chrysomelidae: Bruchinae) were found associated with fruits of C. trichotoma. Female insects predominantly laid eggs on the superior part between the marcescent calyx and the fruit, and larvae perforated the fruit tegument to start consuming seed embryos and reserves. Bruquine larvae are parasitized by Hymenoptera of Bracon, Mirax, Omeganastatus and Triapsis genera. In conclusion, the germination of C. trichotoma seeds is significantly affected by emergence orifices caused by granivorous species.     

Synthesis and biological evaluation of conformationally restricted derivatives of tryptophan as NK1/NK2 ligands

Chemical modifications on the NK₁ competitive antagonist L-732,138, with a view to creating a dual NK₁/NK₂ ligand, led to the tryptophan derivative 1 possessing the protected Gly-Leu sequence of the C-terminus of substance P and neurokinin A. Modifications in the nature of the carbamate function increased the selectivity for the NK₁ receptor, whereas the inclusion of the indole moiety in -carboline or carbazole rings decreased the affinity for both receptors. Free indolylmethyl and Cbz carbamate groups were shown to be essential for NK₂ affinity.     

A new Saccharomyces cerevisiae strain with a mutant Smt3-deconjugating Ulp1 protein is affected in DNA replication and requires Srs2 and homologous recombination for its viability

The Saccharomyces cerevisiae Srs2 protein is involved in DNA repair and recombination. In order to gain better insight into the roles of Srs2, we performed a screen to identify mutations that are synthetically lethal with an srs2 deletion. One of them is a mutated allele of the ULP1 gene that encodes a protease specifically cleaving Smt3-protein conjugates. This allele, ulp1-I615N, is responsible for an accumulation of Smt3-conjugated proteins. The mutant is unable to grow at 37 degrees C. At permissive temperatures, it still shows severe growth defects together with a strong hyperrecombination phenotype and is impaired in meiosis. Genetic interactions between ulp1 and mutations that affect different repair pathways indicated that the RAD51-dependent homologous recombination mechanism, but not excision resynthesis, translesion synthesis, or nonhomologous end-joining processes, is required for the viability of the mutant. Thus, both Srs2, believed to negatively control homologous recombination, and the process of recombination per se are essential for the viability of the ulp1 mutant. Upon replication, mutant cells accumulate single-stranded DNA interruptions. These structures are believed to generate different recombination intermediates. Some of them are fixed by recombination, and others require Srs2 to be reversed and fixed by an alternate pathway.     

Exploring structural features of the interaction between the scorpion toxinCnErg1 and ERG K+ channels

The gamma-KTx-type scorpion toxins specific for K+ channels were found to interact with ERG channels on the turret region, while alpha-KTx3.2 Agitoxin-2 binds to the pore region of the Shaker K+ channel, and alpha-KTx5.3 BmP05 binds to the intermediate region of the small-conductance calcium-activated K-channel (SK(Ca)). In order to explore the critical residues for gamma-KTx binding, we determined the NMR structure of native gamma-KTx1.1 (CnErg1), a 42 amino acid residues scorpion toxin isolated from the venom of the Mexican scorpion Centruro?des noxius Hoffmann, and we used computational evolutionary trace (ET) analysis to predict possible structural and functional features of interacting surfaces. The 1H-NMR three-dimensional solution structure of native ergtoxin (CnErg1) was solved using a total of 452 distance constraints, 13 3J(NH-Halpha) and 10 hydrogen bonds. The structure is characterized by 2 segments of alpha-helices and a triple-stranded antiparallel beta-sheet stabilized by 4 disulfide bridges. The ET and structural analysis provided indication of the presence of two important amino acid residue clusters, one hydrophobic and the other hydrophilic, that should be involved in the surface contact between the toxin and the channel. Some features of the proposed interacting surface are discussed.     

The complete genomic organization of the human MUC6 and MUC2 mucin genes

The complete genomic organization of the two mucin genes MUC2 and MUC6 was obtained by comparison of new and published mRNA sequences with newly available human genomic sequence. The two genes are located 38.5 kb apart in a head-to-head orientation within a gene complex on chromosome 11p15.5. The N-terminal organization of MUC6 is highly similar to that of MUC2, containing the D1, D2, D', and D3 Von Willebrand factor domains followed by the large tandem repeat domains located in exons 31 and 30, respectively. MUC6 has a much smaller C-terminal domain (101 amino acids) encoded by 2 exons containing only the CK domain, compared with MUC2, which has a C-terminal domain of 859 amino acids containing the D4, C, D, and CK domains, encoded by 19 exons. The gene structures agreed partially but not completely with predictions from gene prediction programs.     

Complex spatial distribution and dynamics of an abundant Escherichia coli outer membrane protein, LamB

Advanced techniques for observing protein localization in live bacteria show that the distributions are dynamic. For technical reasons, most such techniques have not been applied to outer membrane proteins in Gram-negative bacteria. We have developed two novel live-cell imaging techniques to observe the surface distribution of LamB, an abundant integral outer membrane protein in Escherichia coli responsible for maltose uptake and for attachment of bacteriophage lambda. Using fluorescently labelled bacteriophage lambda tails, we quantitatively described the spatial distribution and dynamic movement of LamB in the outer membrane. LamB accumulated in spiral patterns. The distribution depended on cell length and changed rapidly. The majority of the protein diffused along spirals extending across the cell body. Tracking single particles, we found that there are two populations of LamB--one shows very restricted diffusion and the other shows greater mobility. The presence of two populations recalls the partitioning of eukaryotic membrane proteins between 'mobile' and 'immobile' populations. In this study, we have demonstrated that LamB moves along the bacterial surface and that these movements are restricted by an underlying dynamic spiral pattern.