Genetic variation for parental effects on the propensity to gregarise in <Emphasis Type="Italic">Locusta migratoria</Emphasis>

Background  

Environmental parental effects can have important ecological and evolutionary consequences, yet little is known about genetic variation among populations in the plastic responses of offspring phenotypes to parental environmental conditions. This type of variation may lead to rapid phenotypic divergence among populations and facilitate speciation. With respect to density-dependent phenotypic plasticity, locust species (Orthoptera: family Acrididae), exhibit spectacular developmental and behavioural shifts in response to population density, called phase change. Given the significance of phase change in locust outbreaks and control, its triggering processes have been widely investigated. Whereas crowding within the lifetime of both offspring and parents has emerged as a primary causal factor of phase change, less is known about intraspecific genetic variation in the expression of phase change, and in particular in response to the parental environment. We conducted a laboratory experiment that explicitly controlled for the environmental effects of parental rearing density. This design enabled us to compare the parental effects on offspring expression of phase-related traits between two naturally-occurring, genetically distinct populations of Locusta migratoria that differed in their historical patterns of high population density outbreak events.     

Impact of peroxisome proliferator-activated receptors gamma and delta on adiposity in toddlers and preschoolers in the GENESIS Study

Peroxisome proliferator-activated receptor gamma (PPAR gamma) and peroxisome proliferator-activated receptor delta (PPAR delta) are promising candidate genes for obesity. Associations between adiposity-related phenotypes and genetic variation in PPAR gamma (Pro12Ala and C1431T), as well as PPAR delta (T+294C) were assessed in 2,102 Greek children aged 1-6 years, as part of a large-scale epidemiological study (Growth, Exercise and Nutrition Epidemiological Study In preSchoolers). In girls aged 3-4 years, the Ala12 allele was associated with higher mid-upper arm (P = 0.010) and hip (P = 0.005) circumferences, as well as subscapular (P = 0.008) and total skinfolds (P = 0.011) that explained 2.0, 3.7, 2.1, and 1.9% of the phenotypic variance, respectively, while the T1431 allele was associated with higher mean values for waist circumference (P = 0.018) and suprailiac skinfold (P = 0.017), genotype accounting for 1.6% of the variance in both phenotypes. No significant effects of PPAR delta T+294C polymorphism or the interaction of the PPAR delta and PPAR gamma variants on adiposity-related phenotypes were observed in any age group or gender. Haplotype-based analysis including both PPAR gamma polymorphisms revealed that in girls aged 3-4 years, the Ala-T haplotype was associated with higher waist (P = 0.014) and hip (P = 0.007) circumferences compared to the common Pro-C haplotype. The PPAR gamma Pro12Ala and C1431T polymorphisms are associated with increased adiposity during early childhood in a gender- and age-specific manner and independently of the PPAR delta T+294C polymorphism.     

Princeton_TIGRESS 2.0: High refinement consistency and net gains through support vector machines and molecular dynamics in double‐blind predictions during the CASP11 experiment

Protein structure refinement is the challenging problem of operating on any protein structure prediction to improve its accuracy with respect to the native structure in a blind fashion. Although many approaches have been developed and tested during the last four CASP experiments, a majority of the methods continue to degrade models rather than improve them. Princeton_TIGRESS (Khoury et al., Proteins 2014;82:794–814) was developed previously and utilizes separate sampling and selection stages involving Monte Carlo and molecular dynamics simulations and classification using an SVM predictor. The initial implementation was shown to consistently refine protein structures 76% of the time in our own internal benchmarking on CASP 7‐10 targets. In this work, we improved the sampling and selection stages and tested the method in blind predictions during CASP11. We added a decomposition of physics‐based and hybrid energy functions, as well as a coordinate‐free representation of the protein structure through distance‐binning distances to capture fine‐grained movements. We performed parameter estimation to optimize the adjustable SVM parameters to maximize precision while balancing sensitivity and specificity across all cross‐validated data sets, finding enrichment in our ability to select models from the populations of similar decoys generated for targets in CASPs 7‐10. The MD stage was enhanced such that larger structures could be further refined. Among refinement methods that are currently implemented as web‐servers, Princeton_TIGRESS 2.0 demonstrated the most consistent and most substantial net refinement in blind predictions during CASP11. The enhanced refinement protocol Princeton_TIGRESS 2.0 is freely available as a web server at http://atlas.engr.tamu.edu/refinement/ . Proteins 2017; 85:1078–1098. © 2017 Wiley Periodicals, Inc.     

A portable fiber-optic pesticide biosensor based on immobilized cholinesterase and sol-gel entrapped bromcresol purple for in-field use.

A fiber-optic biosensor for the detection and determination of the pesticides carbaryl and dichlorvos was developed. The sensing bioactive material was a three-layer sandwich. The enzyme cholinesterase was immobilized on the outer layer, consisting of hydrophilic modified polyvinylidenefluoride membrane. The membrane was in contact with an intermediate sol-gel layer that incorporated bromcresol purple, deposited on an inner glass disk. The sensor operated in a static mode at room temperature and the rate of the inhibited reaction served as an analytical signal. Calibration curves were obtained for carbaryl and dichlorvos, with useful concentration ranges 0.11-8.0 mg l(-1) for carbaryl and 5.0-30 microg l(-1) for dichlorvos. The respective detection limits were 108 microg l(-1) and 5.2 microg l(-1). The method reproducibility was in the order of +/-3-5%. The method was successfully applied to the detection and determination of these pesticides in real water samples, without sample preparation steps. Recovery experiments were made and the accuracy of the method was 94.9%. No enzyme regeneration steps were applied and the sensor lifetime was 3 weeks (30% activity reduction). The bioactive mini sandwich can easily be replaced by simply unscrewing the terminal holding ring of the probe and placing a new sandwich, before the sensor is ready for use.     

Biochemical Differences Between Products of the ADH Locus in Olive Fruit Fly (Bactrocera oleae)

Purified alcohol dehydrogenases from olive fruitflies of genotypes SS, II, and SI were biochemicallycompared. The enzymes were found to differ in thespecific activity, in the influence of pH andtemperature on activity, and in the affinity with differentsubstrate-alcohols. The probable relationships of thesefindings with the dramatic changes in allele frequenciesobserved when natural populations are introduced in the laboratory are discussed.     

Y chromosome haplogroups of elite Ethiopian endurance runners

Favourable genetic endowment has been proposed as part of the explanation for the success of East African endurance athletes, but no evidence has yet been presented. The Y chromosome haplogroup distribution of elite Ethiopian athletes (n=62) was compared with that of the general Ethiopian population (n=95) and a control group from Arsi (a region producing a disproportionate number of athletes; n=85). Athletes belonged to three groups: marathon runners (M; n=23), 5–km to 10–km runners (5–10K; n=21) and other track and field athletes (TF; n=18). DNA was extracted from buccal swabs and haplogroups were assigned after the typing of binary markers in multiplexed minisequencing reactions. Frequency differences between groups were assessed by using contingency exact tests and showed that Y chromosome haplogroups are not distributed amongst elite Ethiopian endurance runners in the same proportions as in the general population, with statistically significant (P<0.05) differences being found in four of the individual haplogroups. The geographical origins and languages of the athletes and controls suggest that these differences are less likely to be a reflection of population structure and that Y chromosome haplogroups may play a significant role in determining Ethiopian endurance running success.     

The “clustered structure” of the purines/pyrimidines distribution in DNA distinguishes systematically between coding and non-coding sequences

A method allowing to measure the inhomogeneous distribution of purines/pyrimidines in nucleotide sequences is developed. We show that this measure relates to the coding or non-coding character of the considered sequence. Coding sequences present a near to the random Pu or Py distribution. This property is shared by both protein-coding DNA and functional RNA-coding DNA. Non-coding sequences present a highly clustered inhomogeneity. We propose the hypothesis, corroborated with appropriate computer simulations, that this is due to the action of various transposition events accumulated for long time periods.     

Apex predatory sharks and crocodiles simultaneously scavenge a whale carcass

Scavenging is an important component to the overall ecology of consumers in virtually all ecosystems on Earth. Given the energetic benefits of foraging on these resource subsidies, opportunistic predators will adjust their behaviors accordingly to maximize access. One of the many consequences of large-scale scavenging opportunities is species interactions that are rarely observed in nature. Here we describe the first published record of predatory sharks (tiger sharks, Galeocerdo cuvier) and saltwater crocodiles (Crocodylus porosus) foraging together in space and time, as documented on a large whale carcass off Western Australia. We report on and discuss the behaviors of the sharks and crocodiles in the hope of shedding new light on the interactions between apex predators that are rarely seen together, but may overlap under specific contexts.     

Comparing naturalized alien plants and recipient habitats across an east–west gradient in the Mediterranean Basin

Aim To investigate alien plant species invasion levels in different habitats and alien species traits by comparing the naturalized flora in different areas of the same biogeographical region. Location Spain, Italy, Greece and Cyprus. Methods Comparison of floristic composition, species traits and recipient habitats of naturalized alien neophytes across an east–west gradient comprising four countries in the European Mediterranean basin. Results A total of 782 naturalized neophytes were recorded; only 30 species were present in all four countries. Although floristic similarity is low, the four alien floras share the same patterns of growth form (mostly herbs), life cycle (mostly perennials) and life form (mostly therophytes, hemicryptophytes and phanerophytes). The majority of the recipient habitats were artificial. Wetlands were the natural habitats, with the highest numbers of naturalized species. Floristic similarity analyses revealed: (1) the highest floristic similarity between Italy and Spain, both of which were more similar to Greece than to Cyprus; (2) two groups of floristic similarity between habitat categories in each country (Greece–Cyprus and Italy–Spain); (3) a higher degree of homogenization in the plant assemblages in different habitats in Greece and Cyprus and a lower degree of homogenization in those in Italy and Spain; and (4) a higher degree of homogenization in artificial and natural fresh‐water habitats than in the other natural habitats. Main conclusions The floristic similarity of naturalized neophytes between the four countries is low, although the overall analysis indicates that the western group (Italy–Spain) is separated from the eastern group (Greece–Cyprus). Similar patterns emerged regarding the life‐history traits and recipient habitats. The artificial habitats and the natural wet habitats are those that are invaded most and display the greatest homogenization in all four countries. Coastal habitats display a lower degree of homogenization but a high frequency of aliens. Dry shrubs and rocky habitats display a lower degree of homogenization and a low frequency of aliens.