New Insights into the Interdependence between Amino Acid Stereochemistry and Protein Structure

To successfully design new proteins and understand the effects of mutations in natural proteins, we must understand the geometric and physicochemical principles underlying protein structure. The side chains of amino acids in peptides and proteins adopt specific dihedral angle combinations; however, we still do not have a fundamental quantitative understanding of why some side-chain dihedral angle combinations are highly populated and others are not. Here we employ a hard-sphere plus stereochemical constraint model of dipeptide mimetics to enumerate the side-chain dihedral angles of leucine (Leu) and isoleucine (Ile), and identify those conformations that are sterically allowed versus those that are not as a function of the backbone dihedral angles ? and ψ. We compare our results with the observed distributions of side-chain dihedral angles in proteins of known structure. With the hard-sphere plus stereochemical constraint model, we obtain agreement between the model predictions and the observed side-chain dihedral angle distributions for Leu and Ile. These results quantify the extent to which local, geometrical constraints determine protein side-chain conformations.     

Evolution of pre‐zygotic and post‐zygotic barriers to gene flow among three cryptic species within the Anastrepha fraterculus complex

Tropical tephritids are ideally suited for studies on population divergence and speciation because they include species groups undergoing rapid radiation, in which morphologically cryptic species and sister species are abundant. The fraterculus species group in the Neotropical genus Anastrepha is a case in point, as it is composed of a complex of up to seven A. fraterculus morphotypes proposed to be cryptic species. Here, we document pre‐ and post‐zygotic barriers to gene flow among adults of the Mexican A. fraterculus morphotype and three populations (Argentina, Brazil, and Peru) belonging to two separate morphotypes (Brazilian 1 and Peruvian). We unveiled three forms of pre‐zygotic reproductive isolation resulting in strong assortative mating. In field cages, free‐ranging male and female A. fraterculus displayed a strong tendency to form couples with members of the opposite sex belonging to their own morphotype, suggesting that male pheromone emission, courtship displays, or both intervene in shaping female choice before actual contact and coupling. In addition, males and females of the Peruvian morphotype became receptive and mated significantly later than adults of the Mexican and Brazilian 1 morphotypes. After contact, Mexican females exhibited greater mating discrimination than males when facing adults of the opposite sex belonging to either the Peruvian or the Brazilian 1 morphotype as evidenced by vigorous resistance to penetration once they had been forcefully mounted by heterotypic males. Forced copulations resulted in production of F1 hybrids that were either less viable (and partially fertile) than parental crosses or even sterile. Our results suggest that the Mexican morphotype is a distinct biological entity and that pre‐zygotic reproductive isolation through divergence in courtship or male‐produced pheromone and other mechanisms appear to evolve faster than post‐zygotic isolation in the fraterculus species group.     

Degradation of benzene, toluene, and xylene isomers by a bacterial consortium obtained from rhizosphere soil of Cyperus sp. grown in a petroleum-contaminated area

Increasing contamination of soil and groundwater with benzene, toluene, and xylene (BTX) due to activities of the chemical and oil refinery industry has caused serious environmental damage. Efficient methods are required to isolate and degrade them. Microorganisms associated with rhizosphere soil are considered efficient agents to remediate hydrocarbon contamination. In this study, we obtained a stabilized bacterial consortium from the rhizosphere soil of Cyperus sp. grown in a petroleum-contaminated field in Southern Mexico. This consortium was able to completely degrade BTX in 14 days. Bacteria isolated from the consortium were identified by 16S rRNA gene sequence analysis as Ralstonia insidiosa, Cellulomonas hominis, Burkholderia kururiensis, and Serratia marcescens. The BTX-degradation capacity of the bacterial consortium was confirmed by the detection of genes pheA, todC1, and xylM, which encoded phenol hydroxylase, toluene 1,2-dioxygenase, and xylene monooxygenase, respectively. Our results demonstrate feasibility of BTX biodegradation by indigenous bacteria that might be used for soil remediation in Southern Mexico.     

Environmental correlates of annual survival differ between two ecologically similar and congeneric owls

Understanding how survival is affected by the environment is essential to gain insight into population dynamics and the evolution of life‐history traits as well as to identify environmental selection pressures. However, we still have little understanding of the relative effect of different environmental factors and their interactions on demographic traits and population dynamics. Here we used two long‐term, individual‐based datasets on Tawny Owl Strix aluco (1981–2010) and Ural Owl S. uralensis (1986–2010) to undertake capture‐mark‐recapture analysis of annual survival of adult females in response to three biologically meaningful environmental variables and their two‐way interactions. Despite the similar ecology of these two species, their survival was associated with different and uncorrelated environmental drivers. The main correlate of Tawny Owl survival was an inverse association with snow depth (winter severity). For Ural Owl, high food (vole) abundance improved survival during years with deep snow, but was less important during years with little snow. In addition, Ural Owl survival was strongly density‐dependent, whereas Tawny Owl survival was not. Our findings advise caution in extrapolating demographic inferences from one species to another, even when they are very closely related and ecologically similar. Analyses including only one or few potential environmental drivers of a species' survival may lead to incomplete conclusions because survival may be affected by several factors and their interactions.     

Synthesis and anti-Trypanosoma cruzi activity of naphthoquinone-containing triazoles: Electrochemical studies on the effects of the quinoidal moiety

In our continued search for novel trypanocidal compounds, twenty-six derivatives of para- and ortho-naphthoquinones coupled to 1,2,3-triazoles were synthesized. These compounds were evaluated against the infective bloodstream form of Trypanosoma cruzi, the etiological agent of Chagas disease. Compounds 17–24, 28–30 and 36–38 are described herein for the first time. Three of these novel compounds (28–30) were found to be more potent than the standard drug benznidazole, with IC₅₀/24 h values between 6.8 and 80.8 μM. Analysis of the toxicity to heart muscle cells led to LC₅₀/24 h of <125, 63.1 and 281.6 μM for 28, 29 and 30, respectively. Displaying a selectivity index of 34.3, compound 30 will be further evaluated in vivo. The electrochemical properties of selected compounds were evaluated in an attempt to find correlations with trypanocidal activity, and it was observed that more electrophilic quinones were generally more potent.     

Comparing galling insect richness among Neotropical savannas: effects of plant richness, vegetation structure and super-host presence

Plant species diversity maintains the stability of ecosystems and the diversity of consumer species such as insect herbivores. Considering that gall-inducing insects are highly specialized on their host plants and dependent on the occurrence, abundance and distribution of plants, we evaluated the diversity patterns of gall-inducing insect along Brazilian Neotropical savannas and the potential role of plant species richness, vegetation structure and super-host presence on determining these patterns. We found 1,882 individual plants that belonged to 64 different host plant species grouped in 31 families, associated to 112 galling insect species. The galling richness was positively influenced by plant species richness and the presence of the super-host genus Qualea (Vochysiaceae). Plant species richness explained 48 % of the galling richness and areas with presence of super-hosts had more than twice of galling species than areas where they were absent. On the other hand, we found no evidence that larger plants hosted more species of galling insects. We observed that for the diversity of galling insects in the Brazilian Cerrado, vegetation structure explained almost the same portion as plant richness, because structural variables did not have an effect on residuals of galling richness and plant richness regression. Our findings suggests that plant richness has a more important role on the mitigation of natural enemies and adaptive radiation of galling species, while structural aspects of the vegetation does not seem to have that effect. Furthermore, we show that the super-host taxa provide an increment in local galling richness because they present a great diversity of local number of gall morphospecies (i.e. alpha diversity) and the high turnover of morphospecies among different localities (i.e. beta diversity). Therefore we argue that the quality of resources (richness and super host presence) appears to be a most important factor for the diversity of galling insects in Neotropical systems, than the amount of resources.     

Haemosporidian parasitism in the blackcap Sylvia atricapilla in relation to spring arrival and body condition

Parasites can exert strong selection on hosts. Throughout the year migrants are exposed to different sets of parasites, which may affect life history traits such as migratory schedules. Here, we studied the relationship between parasite infection and arrival date of blackcaps Sylvia atricapilla to their breeding grounds in Germany throughout a period of six years (2007–2012). We used two data sets, one that included all blackcaps and one that included only recaptured birds. We assesed whether parasites influence spring arrival to breeding grounds, and for the recaptured data set, we analysed temporal variation in parasitism (i.e. infection status and parasitaemia) throughout the breeding season. We used both microscopy and PCR (a fragment of ? 479 bp of the mtDNA cyt b) to determine haemosporidian infection. Blackcaps were mostly infected with Haemoproteus parabelopolskyi (lineages SYAT01 and SYAT02). Infection status, but not parasitaemia, was constant through time for individual birds; meaning that once a bird is infected, it most likely will retain the infection for life. We found that infection by haemosporidian parasites has no relationship to arrival date in this blackcap population; however, infection by H. parabelopolskyi has a marginally significant effect on arrival date of recaptured blackcaps, somewhat delaying their arrival to breeding grounds. Birds captured later in the season were more likely to be infected than those from early spring, and parasitaemia was frequently lower in birds captured earlier in the season compared to those captured later (summer).