A new eigenfunction spatial analysis describing population genetic structure

Several methods of spatial analyses have been proposed to infer the relative importance of evolutionary processes on genetic population structure. Here we show how a new eigenfunction spatial analysis can be used to model spatial patterns in genetic data. Considering a sample of n local populations, the method starts by modeling the response variable (allele frequencies or phenotypic variation) against the eigenvectors sequentially extracted from a geographic distance matrix (n × n). The relationship between the coefficient of determination (R ²) of the models and the cumulative eigenvalues, which we named the spatial signal-representation (SSR) curve, can be more efficient than Moran’s I correlograms in describing different patterns. The SSR curve was also applied to simulated data (under distinct scenarios of population differentiation) and to analyze spatial patterns in alleles from microsatellite data for 25 local populations of Dipteryx alata, a tree species endemic to the Brazilian Cerrado. The SSR curves are consistent with previous phylogeographical patterns of the species, revealing combined effects of isolation-by-distance and range expansion. Our analyses demonstrate that the SSR curve is a useful exploratory tool for describing spatial patterns of genetic variability and for selecting spatial eigenvectors for models aiming to explain spatial responses to environmental variables and landscape features.     

Whole-Genome Regression and Prediction Methods Applied to Plant and Animal Breeding

Meiotic crossovers facilitate the segregation of homologous chromosomes and increase genetic diversity. The formation of meiotic crossovers was previously posited to occur via two pathways, with the relative use of each pathway varying between organisms; however, this paradigm could not explain all crossovers, and many of the key proteins involved were unidentified. Recent studies that identify some of these proteins reinforce and expand the model of two meiotic crossover pathways. The results provide novel insights into the evolutionary origins of the pathways, suggesting that one is similar to a mitotic DNA repair pathway and the other evolved to incorporate special features unique to meiosis.     

Quantitative Dissection of the Binding Contributions of Ligand Lysines of the Receptor-associated Protein (RAP) to the Low Density Lipoprotein Receptor-related Protein (LRP1)

Although lysines are known to be critical for ligand binding to LDL receptor family receptors, relatively small reductions in affinity have been found when such lysines have been mutated. To resolve this paradox, we have examined the specific binding contributions of four lysines, Lys-253, Lys-256, Lys-270, and Lys-289, in the third domain (D3) of receptor-associated protein (RAP), by eliminating all other lysine residues. Using D3 variants containing lysine subsets, we examined binding to the high affinity fragment CR56 from LRP1. With this simplification, we found that elimination of the lysine pairs Lys-253/Lys-256 and Lys-270/Lys-289 resulted in increases in K_d of 1240- and 100,000-fold, respectively. Each pair contributed additively to overall affinity, with 61% from Lys-270/Lys-289 and 39% from Lys-253/Lys-256. Furthermore, the Lys-270/Lys-289 pair alone could bind different single CR domains with similar affinity. Within the pairs, binding contributions of Lys-270 ≫ Lys-256 > Lys-253 ∼ Lys-289 were deduced. Importantly, however, Lys-289 could significantly compensate for the loss of Lys-270, thus explaining how previous studies have underestimated the importance of Lys-270. Calorimetry showed that favorable enthalpy, from Lys-256 and Lys-270, overwhelmingly drives binding, offset by unfavorable entropy. Our findings support a mode of ligand binding in which a proximal pair of lysines engages the negatively charged pocket of a CR domain, with two such pairs of interactions (requiring two CR domains), appropriately separated, being alone sufficient to provide the low nanomolar affinity found for most protein ligands of LDL receptor family members.     

Discovery of Novel Irreversible Inhibitors of Interleukin (IL)-2-inducible Tyrosine Kinase (Itk) by Targeting Cysteine 442 in the ATP Pocket

IL-2-inducible tyrosine kinase (Itk) plays a key role in antigen receptor signaling in T cells and is considered an important target for anti-inflammatory drug discovery. In order to generate inhibitors with the necessary potency and selectivity, a compound that targeted cysteine 442 in the ATP binding pocket and with an envisaged irreversible mode of action was designed. We incorporated a high degree of molecular recognition and specific design features making the compound suitable for inhaled delivery. This study confirms the irreversible covalent binding of the inhibitor to the kinase by x-ray crystallography and enzymology while demonstrating potency, selectivity, and prolonged duration of action in in vitro biological assays. The biosynthetic turnover of the kinase was also examined as a critical factor when designing irreversible inhibitors for extended duration of action. The exemplified Itk inhibitor demonstrated inhibition of both T_H1 and T_H2 cytokines, was additive with fluticasone propionate, and inhibited cytokine release from human lung fragments. Finally, we describe an in vivo pharmacodynamic assay that allows rapid preclinical development without animal efficacy models.     

The cowl does not make the monk: scarab beetle pollination of the Neotropical aroid Taccarum ulei (Araceae: Spathicarpeae)

Taccarum ulei (Araceae, Spathicarpeae) is a seasonal geophytic aroid, native to north‐eastern Brazil, that flowers during two months of the rainy season. Patterns of floral thermogenesis, pollination biology, and floral traits associated with pollination syndromes were studied and compared with those of other Araceae. Two species of cyclocephaline scarabs (Scarabaeidae, Cyclocephalini) were recognized as effective pollinators: Cyclocephala celata and Cyclocephala cearae. Larvae of an unidentified species of fruit fly (Melanoloma spp., Richardiidae, Diptera) were also frequently observed in inflorescences at various maturation stages, feeding on the connectives of male florets and fruits, and thus lowering the reproductive success of individual plants. Beetles were attracted by odoriferous inflorescences in the early evening of the first day of anthesis, during the female phase. The emission of attractive volatiles was coupled with intense thermogenic activity in the entire spadix, unlike other aroids in which only certain zones of the spadix heat up. Pollen release, which marks the beginning of the male phase on the subsequent evening, was not related to floral thermogenesis. Comparative multivariate analysis of the floral traits of T. ulei points to a beetle‐pollinated aroid, although some of the observed traits of the species are not common to other taxa sharing this pollination strategy. Such incongruence might be explained by the evolutionary history of the tribe Spathicarpeae and potential pollinator shifts. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ??, ??–??.     

Mutant strains of Pichia pastoris with enhanced secretion of recombinant proteins

Although Pichia pastoris is a popular protein expression system, it exhibits limitations in its ability to secrete heterologous proteins. Therefore, a REMI (restriction enzyme mediated insertion) strategy was utilized to select mutant beta-g alactosidase s upersecretion (bgs) strains that secreted increased levels of a β-galactosidase reporter. Many of the twelve BGS genes may have functions in intracellular signaling or vesicle transport. Several of these strains also appeared to contain a more permeable cell wall. Preliminary characterization of four bgs mutants showed that they differed in the ability to enhance the export of other reporter proteins. bgs13, which has a disruption in a gene homologous to Saccharomyces cerevisiae protein kinase C (PKC1), gave enhanced secretion of most recombinant proteins that were tested, raising the possibility that it has the universal super-secreter phenotype needed in an industrial production strain of P. pastoris.     

Cytogenetic characterization of the ant Trachymyrmex fuscus Emery, 1934 (Formicidae: Myrmicinae: Attini) with the description of a chromosomal polymorphism

The genus Trachymyrmex is a key group in the tribe Attini because of its close phylogenetic relationship to leaf-cutter ants, Acromyrmex and Atta. Cytogenetic data are only available for five taxa of Trachymyrmex, with chromosome numbers of 2n = 12, 18, 20 and 22, and morphology with predominantly metacentric chromosomes. The aim of the present study was to characterize the karyotype of the ant Trachymyrmex fuscus Emery, 1934, by means of the number and morphology of its chromosomes, heterochromatin pattern, CMA₃ and DAPI fluorochromes in the population of two nests collected at Paraopeba, state of Minas Gerais, Brazil. Nineteen females presented 2n = 18 chromosomes (16m + 2sm) and a single male presented n = 9 (8m + 1sm). A size chromosomal polymorphism involving the short arm of the submetacentric pair was confirmed by statistical analysis, with three character conditions: heterozygous SB (with a difference in size between the short arms), standard SS (smaller short arms) and homozygote BB (bigger short arms). In the first nest, both SB and SS workers were observed. The other nest contained heterozygous (SB), homozygous (BB), and a male carrying the B chromosome (larger size). The presence of heterochromatin on all centromeric and pericentromeric chromosomes of T. fuscus suggests that the size difference observed in the submetacentric pair in the SB and BB workers is not related to the heterochromatin but to a duplication of euchromatic regions through intra- or inter- chromosomal rearrangements. The fluorochrome CMA₃ matched the C-banding markings, indicating that the heterochromatin is rich in GC base pairs. As far as we know, this is the first chromosomal polymorphism reported in the tribe Attini.     

Variability and resistance mutations in the hepatitis C virus NS3 protease in patients not treated with protease inhibitors

The goal of treatment of chronic hepatitis C is to achieve a sustained virological response, which is defined as exhibiting undetectable hepatitis C virus (HCV) RNA levels in serum following therapy for at least six months. However, the current treatment is only effective in 50% of patients infected with HCV genotype 1, the most prevalent genotype in Brazil. Inhibitors of the serine protease non-structural protein 3 (NS3) have therefore been developed to improve the responses of HCV-infected patients. However, the emergence of drug-resistant variants has been the major obstacle to therapeutic success. The goal of this study was to evaluate the presence of resistance mutations and genetic polymorphisms in the NS3 genomic region of HCV from 37 patients infected with HCV genotype 1 had not been treated with protease inhibitors. Plasma viral RNA was used to amplify and sequence the HCV NS3 gene. The results indicate that the catalytic triad is conserved. A large number of substitutions were observed in codons 153, 40 and 91; the resistant variants T54A, T54S, V55A, R155K and A156T were also detected. This study shows that resistance mutations and genetic polymorphisms are present in the NS3 region of HCV in patients who have not been treated with protease inhibitors, data that are important in determining the efficiency of this new class of drugs in Brazil.     

Influence of Several Sources and Amounts of Iron on DNA, Lipid and Protein Oxidative Damage During Anaemia Recovery

Nanoparticles (NPs) in agricultural systems can potentially be used as appropriate candidate for change in growth, development, productivity, and quality of plants. In the present study, we assessed the effect of TiO₂ NP concentrations (0, 2, 5, and 10 ppm) on changes of membrane damage indexes like electrolyte leakage index (ELI) and malondialdehyde (MDA) during cold stress (CS) 4 °C in sensitive (ILC 533) and tolerant (Sel 11439) chickpea (Cicer arietinum L.) genotypes. Aggregation of NPs within the vacuole and chloroplast indicated absorbed NPs in seedlings. Bioaccumulation of NPs showed that, under thermal treatments, the sensitive genotype had more permeability to NPs compared to the tolerant one, and TiO₂ content was higher during CS compared to optimum temperature. Physiological indexes were positively affected by NP treatments during thermal treatments. TiO₂ NP treatments (especially 5 ppm) caused a decrease in ELI during thermal treatments, whereas ELI content under CS treatment increased at 0 ppm TiO₂ in both genotypes. Under thermal treatments, although the genotype 11439 showed lower accumulation of MDA than ILC 533 genotype, a significant decrease was observed in MDA content at 5 ppm TiO₂. Results showed that TiO₂ treatments not only did not induce oxidative damage in sensitive and tolerant chickpea genotypes but also alleviated membrane damage indexes under CS treatment. It was suggested for the first time that TiO₂ NPs improved redox status of the genotypes under thermal treatments. New findings possibly would reveal the use of NPs generally or TiO₂ NPs especially for increase of cold tolerance in crops.