Exploring patterns of interspecific variation in quantitative traits using sequential phylogenetic eigenvector regressions

A number of metrics have been developed for estimating phylogenetic signal in data and to evaluate correlated evolution, inferring broad-scale evolutionary and ecological processes. Here, we proposed an approach called phylogenetic signal-representation (PSR) curve, built upon phylogenetic eigenvector regression (PVR). In PVR, selected eigenvectors extracted from a phylogenetic distance matrix are used to model interspecific variation. In the PSR curve, sequential PVR models are fitted after successively increasing the number of eigenvectors and plotting their R(2) against the accumulated eigenvalues. We used simulations to show that a linear PSR curve is expected under Brownian motion and that its shape changes under alternative evolutionary models. The PSR area, expressing deviations from Brownian motion, is strongly correlated (r= 0.873; P < 0.01) with Blomberg's K-statistics, so nonlinear PSR curves reveal if traits are evolving at a slower or higher rate than expected by Brownian motion. The PSR area is also correlated with phylogenetic half-life under an Ornstein-Uhlenbeck process, suggesting how both methods describe the shape of the relationship between interspecific variation and time since divergence among species. The PSR curve provides an elegant exploratory method to understand deviations from Brownian motion, in terms of acceleration or deceleration of evolutionary rates occurring at large or small phylogenetic distances.     

The hypervariable domain of the mitochondrial control region in Atlantic spiny lobsters and its potential as a marker for investigating phylogeographic structuring

Atlantic spiny lobsters support major fisheries in northeastern Brazilian waters and in the Caribbean Sea. To avoid reduction in diversity and elimination of distinct stocks, understanding their population dynamics, including structuring of populations and genetic diversity, is critical. We here explore the potential of using the hypervariable domain in the control region of the mitochondrial DNA as a genetic marker to characterize population subdivision in spiny lobsters, using Panulirus argus as the species model. The primers designed on the neighboring conserved genes have amplified the entire control region (approx. 780 bases) of P. argus and other closely related species. Average nucleotide and haplotype diversity within P. argus were found to be high, and population structuring was hypothesized. The data suggest a division of P. argus into genetically different phylogeographic groups. The hypervariable domain seems to be useful for determining genetic differentiation of geographically distinct stocks of P. argus and other Atlantic spiny lobsters.     

Genetic distance estimates among single cross hybrids and correlation with specific combining ability and yield in corn double cross hybrids

The objective of the present study was to correlate the genetic distances (GD) of single cross hybrids with yield, heterosis and specific combining ability (SCA) in the double cross hybrid synthesis. For this, 10 single cross commercial hybrids were used from different companies, and all the possible double hybrids were synthesized by a complete dialell. The hybrids were assessed in 15 locations in the 2005/2006 agricultural season, using the randomized complete block design with three repetitions. DNA was extracted from the single cross hybrids and 20 simple sequence repeat primers were used, nine of which were linked to the quantitative trait loci. It was ascertained that the single hybrids were superior in general to the double cross hybrids and that yield was highly correlated with heterosis and SCA (r = 0.75 and 0.82, respectively). There was no significant correlation between yield and GD (r = 0.25), but this index was at the limit of significance. There was a medium correlation between GD and heterosis (r = 0.40) and GD and SCA (r = 0.38). The intergroup hybrids placed by genetic grouping were generally more productive than intragroup hybrids, and the hybrids with GD greater than 0.84 had the maximum heterosis and SCA. It was concluded that the markers were efficient in placing hybrids in different heterosis groups and were also useful in eliminating the most negative heterosis and SCA.     

Identification of the Anabaena sp. strain PCC7120 cyanophycin synthetase as suitable enzyme for production of cyanophycin in gram-negative bacteria like Pseudomonas putida and Ralstonia eutropha

The cyanophycin synthetase gene cphA1 encoding the major cyanophycin synthetase (CphA) of Anabaena sp. strain PCC7120 was expressed in Escherichia coli conferring so far the highest specific CphA activity to E. coli (6.7 nmol arginine per min and mg protein). CphA1 and cphA genes of Synechocystis sp. strains PCC6803 and PCC6308 and Synechococcus strain MA19 were also expressed in wild types and polyhydroxyalkanoate-negative (PHA) mutants of Pseudomonas putida and Ralstonia eutropha. Recombinant strains of these bacteria expressing cphA1 accumulated generally more cyanophycin (23.0 and 20.0% of cellular dry matter, CDM, respectively) than recombinants expressing any other cphA (6.8, 9.0, or 15.8% of CDM for P. putida strains and 7.3, 12.6, or 14.1% of CDM for R. eutropha). Furthermore, PHA-negative mutants of P. putida (9.7, 10.0, 17.5, or 24.0% of CDM) and R. eutropha (8.9, 13.8, 16.0, or 22.0% of CDM) accumulated generally more cyanophycin than the corresponding PHA-positive parent strains (6.8, 9.0, 15.8, and 23.0% of CDM for P. putida strains and 7.3, 12.6, 14.1, or 20.0% of CDM for R. eutropha strains). Recombinant strains of Gram-positive bacteria (Bacillus megaterium, Corynebacterium glutamicum) were not suitable for cyanophycin production due to accumulation of less cyanophycin and retarded release of cyanophycin. PHA-negative mutants of P. putida and R. eutropha expressing cphA1 of Anabaena sp. strain PCC7120 are therefore preferred candidates for industrial production of cyanophycin.     

Comparative Epidemiology of Three Virus Diseases on Zucchini Squash

Zucchini yellow mosaic virus (ZYMV), Papaya ringspot virus – type W (PRSV‐W) and Zucchini lethal chlorosis virus (ZLCV) cause important diseases on zucchini squash crops in Brazil. ZYMV and PRSV‐W belong to the genus Potyvirus and are transmitted by aphids, whereas ZLCV belongs to Tospovirus and is transmitted by the thrips Frankliniella zucchini. These three viruses may occur simultaneously in the field, and the epidemiology of the corresponding diseases may be determined by interactions among viruses, hosts and vectors. In this work, the progress of the diseases caused by these viruses was studied over a temporal and geographic range for three planting seasons (PS). For the lethal chlorosis (ZLCV), a monomolecular model was found to be the best fit for the data, though only during the third PS. For data collected during the first two PS, the Gompertz model was found to fit the data best. The spatial distribution of disease indicated disease aggregation at the end of the crop cycle. For the yellow mosaic (ZYMV), the model that best fit in the 1st PS was the logistic and in the 2nd and 3rd PS was monomolecular. The spatial pattern of the disease was random when the disease incidence was low but aggregated when the disease incidence was high. The common mosaic (PRSV‐W) showed the lowest incidence in all three PS. An exponential model was the best fit for data collected during all PS, and the spatial pattern of the disease was random. Interactions among the three viruses apparently did not result in changes in the epidemiology of the diseases. Removal of sources of inoculum and planting at an unfavourable time for reproduction of virus vectors are the two main measures recommended for the control of these diseases. The use of insecticide is indicated only for the control of the F. zucchini.     

Western diet leads to aging-related tumorigenesis via activation of the inflammatory,UPR, and EMT pathways

Among the principal causative factors for the development of complications related to aging is a diet rich in fats and sugars, also known as the Western diet. This diet advocates numerous changes that might increase the susceptibility to initiate cancer and/or to create a tissue microenvironment more conducive to the growth of malignant cells, thus favoring the progression of cancer and metastasis. Hypercaloric diets in general lead to oxidative stress generating reactive oxygen species and induce endoplasmic reticulum stress. Our results demonstrate that mice bearing tumors fed with a Western diet presented bigger tumor mass with increased insulin sensitivity in these tissues. Several markers of insulin signaling, such as AKT phosphorylation and mTOR pathway, are promoted in tumors of Western diet-fed animals. This process is associated with increased macrophage infiltration, activation of unfolded protein response pathway, and initiation of epithelial–mesenchymal transition (EMT) process in these tumor tissues. Summing up, we propose that the Western diet accelerates the aging-related processes favoring tumor development.Subject terms: Melanoma, TOR signalling, Mechanisms of disease, Ageing