Evolutionary dynamics of Rh2 opsins in birds demonstrate an episode of accelerated evolution in the New World warblers (Setophaga)

Low rates of sequence evolution associated with purifying selection can be interrupted by episodic changes in selective regimes. Visual pigments are a unique system in which we can investigate the functional consequences of genetic changes, therefore connecting genotype to phenotype in the context of natural and sexual selection pressures. We study the RH2 and RH1 visual pigments (opsins) across 22 bird species belonging to two ecologically convergent clades, the New World warblers (Parulidae) and Old World warblers (Phylloscopidae) and evaluate rates of evolution in these clades along with data from 21 additional species. We demonstrate generally slow evolution of these opsins: both Rh1 and Rh2 are highly conserved across Old World and New World warblers. However, Rh2 underwent a burst of evolution within the New World genus Setophaga, where it accumulated substitutions at 6 amino acid sites across the species we studied. Evolutionary analyses revealed a significant increase in d_N/d_S in Setophaga, implying relatively strong selective pressures to overcome long‐standing purifying selection. We studied the effects of each substitution on spectral tuning and found they do not cause large spectral shifts. Thus, substitutions may reflect other aspects of opsin function, such as those affecting photosensitivity and/or dark–light adaptation. Although it is unclear what these alterations mean for colour perception, we suggest that rapid evolution is linked to sexual selection, given the exceptional plumage colour diversification in Setophaga.     

The evaluation of novel chromogenic substrates for the detection of lipolytic activity in clinical isolates of Staphylococcus aureus and MRSA from two European study groups

Pinellia ternata , a traditional Chinese herb that has been used in China for over 1000 years, is susceptible to a soft rot disease, which may cause major loss of yield. The use of bacteria as potential antagonists against Pectobacterium carotovorum SXR1, the causal agent of the disease on P. ternata , was evaluated. Altogether, 1107 candidate bacteria were isolated from the rhizosphere and surface-sterilized plants of P. ternata . In Petri dish tests, 55 isolates inhibited the growth of strain SXR1, and 21 of these reduced the disease development on P. ternata slices by over 50%. Four selected antagonists significantly reduced the disease incidence on tissue culture seedlings, and also prevented the disease on the transplants. Agonist P-Y2-2 yielded a good prevention level of 81.9%. The four antagonists rapidly colonized the tissue culture seedlings and transplants, whereas greater populations of the antagonists (10⁷–10⁹ CFU g⁻¹ fresh tissues) were observed in the seedlings and in the preinoculated transplants than in those inoculated during transplanting. The use of pathogen-free tissue culture seedlings pre-inoculated with antagonist may provide a strategy for production of P. ternata plantlets resistant to soft rot disease. This is the first report on the efficacy of biocontrol agents against pathogens on P. ternata .     

Release of phylogenetic constraints through low resource heterogeneity: the case of gall-inducing sawflies

Abstract. 1. A group of six unusual sawfly species, which do not conform to the phylogenetic constraints hypothesis as it has been applied to sawflies, was examined in natural populations. All species were in the genus Pontania (Hymenoptera: Tenthredinidae), which induce galls on leaves of willow species (Salicaceae). An understanding of these non‐conformist species was important as a test of the validity of the general hypothesis. 2. The six species of sawfly, Pontania mandshurica, P. cf. arcticornis, P. aestiva, P. arcticornis, P. pacifica, and P. nr. pacifica, showed no oviposition preference for long, vigorous shoots, in contrast to 37 documented tenthredinid species that have demonstrated such a preference. Rather, the non‐conformist species attacked the shortest shoot length classes more frequently and larval establishment in galls was successful. 3. The evident escape from the phylogenetic constraint, which commonly limits sawfly attack to the most vigorous shoots in a willow population, resulted from low apparent heterogeneity of the resources exploited by these Pontania species. At the time of female oviposition, shoots and leaves were too uniform to allow discrimination by females among shoot length classes, resulting in random, or near random attack of shoots. 4. The unusual relative uniformity of resources to which sawflies were exposed resulted from several characteristics. (1) Females emerged early relative to shoot growth phenology, making discrimination among shoot length and vigour difficult or impossible. (2) Low heterogeneity in leaf length resulted in resource similarity independent of shoot length. (3) Abscission of leaves occurred after emergence of larvae from leaf galls so that differential abscission of leaves in relation to shoot length became irrelevant. (4) In some cases, low variance in shoot lengths was evident in old ramets lacking long, vigorous shoots. Probably as a result of low resource heterogeneity, larvae survived well across all shoot length classes, revealing no ovipositional preference and larval performance linkage related to the exploitation of the longest shoot length classes in a population of willows, as in the conformist species. Therefore, larval survival did not provide positive feedback on female preferential behaviour for long shoots, as in the conformist species studied.     

METABOLIC ASPECTS OF THERMOGENESIS IN MALE CONES OF FIVE CYCAD SPECIES

High starch concentrations in the sporophylls of male cones of five species of cycad and their depletion during their heat-producing phase of development suggest that starch is a major fuel source for thermogenesis in these plants. Carbon-13/carbon-12 ratio analyses of respired CO₂, starch, and lipids in a male cone of one of these species, Macrozamia moorei F. Muell., indicate that although starch is a major contributor to respiration, lipids are also an important respiratory substrate.     

Real‐time model based process monitoring of enzymatic biodiesel production

In this contribution we extend our modelling work on the enzymatic production of biodiesel where we demonstrate the application of a Continuous‐Discrete Extended Kalman Filter (a state estimator). The state estimator is used to correct for mismatch between the process data and the process model for Fed‐batch production of biodiesel. For the three process runs investigated, using a single tuning parameter, q_x = 2 × 10^?2 which represents the uncertainty in the process model, it was possible over the entire course of the reaction to reduce the overall mean and standard deviation of the error between the model and the process data for all of the five measured components (triglycerides, diglycerides, monoglycerides, fatty acid methyl esters, and free fatty acid). The most significant reduction for the three process runs, were for the monoglyceride and free fatty acid concentration. For those components, there was over a ten‐fold decrease in the overall mean error for the state estimator prediction compared with the predictions from the pure model simulations. It is also shown that the state estimator can be used as a tool for detection of outliers in the measurement data. For the enzymatic biodiesel process, given the infrequent and sometimes uncertain measurements obtained we see the use of the Continuous‐Discrete Extended Kalman Filter as a viable tool for real time process monitoring. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 31:585–595, 2015     

Pathway-Based Genome-Wide Association Studies for Plasma Triglycerides in Obese Females and Normal-Weight Controls

Pathway-based analysis as an alternative approach can provide complementary information to single-marker genome-wide association studies (GWASs), which always ignore the epistasis and does not have sufficient power to find rare variants. In this study, using genotypes from a genome-wide association study (GWAS), pathway-based association studies were carried out by a modified Gene Set Enrichment Algorithm (GSEA) method (GenGen) for triglyceride in 1028 unrelated European-American extremely obese females (BMI≥35kg/m²) and normal-weight controls (BMI<25kg/m²), and another pathway association analysis (ICSNPathway) was also used to verify the GenGen result in the same data. The GO0009110 pathway (vitamin anabolism) was among the strongest associations with triglyceride (empirical P<0.001); the result remained significant after FDR correction (P = 0.022). MMAB, an obesity-related locus, included in this pathway. The ABCG1 and BCL6 gene was found in several triglyceride-related pathways (empirical P<0.05), which were also replicated by ICSNPathway (empirical P<0.05, FDR<0.05). We also performed single-marked GWAS using PLINK for TG levels (log-transformed). Significant associations were found between ASTN2 gene SNPs and plasma triglyceride levels (rs7035794, P = 2.24×10⁻¹⁰). Our study suggested that vitamin anabolism pathway, BCL6 gene pathways and ASTN2 gene may contribute to the genetic variation of plasma triglyceride concentrations.     

A universal TagModule collection for parallel genetic analysis of microorganisms

Systems-level analyses of non-model microorganisms are limited by the existence of numerous uncharacterized genes and a corresponding over-reliance on automated computational annotations. One solution to this challenge is to disrupt gene function using DNA tag technology, which has been highly successful in parallelizing reverse genetics in Saccharomyces cerevisiae and has led to discoveries in gene function, genetic interactions and drug mechanism of action. To extend the yeast DNA tag methodology to a wide variety of microorganisms and applications, we have created a universal, sequence-verified TagModule collection. A hallmark of the 4280 TagModules is that they are cloned into a Gateway entry vector, thus facilitating rapid transfer to any compatible genetic system. Here, we describe the application of the TagModules to rapidly generate tagged mutants by transposon mutagenesis in the metal-reducing bacterium Shewanella oneidensis MR-1 and the pathogenic yeast Candida albicans. Our results demonstrate the optimal hybridization properties of the TagModule collection, the flexibility in applying the strategy to diverse microorganisms and the biological insights that can be gained from fitness profiling tagged mutant collections. The publicly available TagModule collection is a platform-independent resource for the functional genomics of a wide range of microbial systems in the post-genome era.     

Zero-sum allocational strategies determine the allometry of specific leaf area

? Premise of the study: Specific leaf area (SLA) is a critical component of the leaf economics spectrum, and many functional leaf traits have been empirically demonstrated to covary with SLA. However, a complete understanding of how change in leaf size influences SLA has not yet emerged. ? Methods: To help develop a more complete understanding of the determinants of variability in SLA, we present a covariation model of leaf allometry that predicts a zero-sum interdependence of leaf thickness, density, and surface area on leaf mass. We test the model's predictions on measurements of 900 leaves from 44 angiosperm species. ? Key results: We observe that "diminishing returns," the negative allometry (slope < 1) of surface area versus mass, does not hold universally across species. Rather, the scaling of SLA is linked to the relative allocation to thickness and density. Specifically, diminishing returns are observed when leaves grow thicker, more than their density decreases, with increasing mass. Finally, we confirm model predictions that the allometric dependence of area, thickness, and density on mass can be well approximated by a zero-sum allocational process. ? Conclusions: Our work adds to the growing body of evidence that allometric covariation is a hallmark of the scaling behavior of complex plant and leaf traits. Moreover, because our model makes predictions based on allocational constraints, it provides a foundation to understand how deviations from zero-sum tradeoffs in allocation to leaf thickness, density, or area determine the allometry of SLA and, ultimately, underlie adaptive strategies within and across plant species.