Fear of the dark: substrate preference in Amazonian tadpoles

acta ethologica - Due to the importance of camouflage to avoid detection by predators, predation pressure can cause coupled evolution of skin colour and preference for substrate colour. Individuals...     

Potential of the predatory mite Amblydromalus zannoui to control pest mites on Jatropha curcas

Amblydromalus zannoui Sourassou, Sarmento and Moraes is a phytoseiid mite of the limonicus group described from central Brazil from leaves of physic nut, Jatropha curcas L. (Malpighiales: Euphorbiaceae), a plant potentially useful as a source of biofuel. This plant is often attacked by the mites Polyphagotarsonemus latus (Banks) (Prostigmata: Tarsonemidae) and Tetranychus bastosi Tuttle, Baker and Sales (Prostigmata: Tetranychidae). The objectives of this work were to evaluate the predation rate of A. zannoui on those phytophagous mites, to assess its life cycle on these prey and on pollen of Ricinus communis L. (Euphorbiaceae), and to determine its attraction to physic nut leaves infested by P. latus or T. bastosi. Amblydromalus zannoui attacked more nymphs and adults than eggs of P. latus, and more eggs and larvae than adults of T. bastosi. The life table parameters suggest that A. zannoui performs better on P. latus (r_m: 0.20, R_o: 18.77; λ: 1.23) and pollen (r_m: 0.18, R_o: 23.32, λ: 1.18). The predator seems to be attracted to plants with P. latus, but attraction was not clear cut for plants with T. bastosi. The results suggested that A. zannoui is a potential control agent to be used against P. latus on physic nut plants, and that R. communis pollen can be used as supplementary food to maintain the predator population in the absence of prey.

     

Drivers of the beta diversity of spider assemblages in southern Brazilian temporary wetlands

1. The composition of local assemblages is assembled by an interplay of species sorting, mass effects and dispersal limitation processes. The contributions of assembly processes to metacommunity structure can change with ecosystem type and specificities of the study area. Spider composition is influenced by environmental features such as habitat structure and climate, and also by spatial distances between patches. However, little is known about the roles of assembly processes in spider metacommunity structure in wetlands. 2. The beta diversity patterns of spider assemblages were assessed in 24 temporary wetlands distributed along a latitudinal gradient in southern Brazil. The study also assessed the individual correspondence of beta diversity (and its turnover and richness components) with dissimilarities in habitat structure and climate, as well as with geographic distances, using Mantel and partial Mantel correlation tests and multivariate correlograms. 3. Turnover was the most important component of spider beta diversity. Mantel tests detected significant correlations of spider beta diversity with habitat structure. Partial Mantel tests detected significant relationships only between spider beta diversity (and the richness component) and geographic distances. Additionally, spider composition was more similar than chance on smaller scales. 4. These results evidenced a complex interplay of assembly processes explaining spider metacommunity structure in temporary wetlands. Although species-sorting processes associated with habitat structure were important in structuring local spider composition, mass effects and dispersal limitation across climatic zones played an important role on a broader scale.     

Individual–resource networks reveal distinct fruit preferences of selective individuals from a generalist population of the Helmeted Manakin

Ecological studies traditionally assume that generalist populations are homogeneous in the use of food resources, but empirical evidence supports that intraspecific differences in morphology, physiology and behaviour affect foraging decisions and promote diet variation among individuals. Furthermore, the temporal availability of resources may shape the dynamics of population trophic niche, which ultimately depends on individual niches. In this study, we investigated the seasonal changes in individual-based networks between the Helmeted Manakin Antilophia galeata, a generalist frugivorous bird, and fruiting plants, following theoretical models of interindividual diet variation based on the Optimal Diet Theory. Selective individuals were the majority of the generalist population of the Helmeted Manakin. Our results suggest that the structure of the individual-resource networks varied seasonally. We found that modularity was higher than expected by chance in the wet season, when fruit availability was also higher. In the dry season, modules disappeared and the network became more nested. These findings are consistent with the Distinct Preference Model of diet variation. We suggest that downscaling ecological networks to the individual level may reveal emergent properties that, albeit existent, are not evident in species–resources networks.     

Hierarchical genetic and spatial structure among varieties and populations of Hymenaea stigonocarpa (Fabaceae) in Brazilian savannah

Tree Genetics & Genomes - Tree breeders must almost always address multiple traits. That entails choosing selection methods and weighing up known or assumed economic-worth functions for traits....     

Human LC3 and GABARAP subfamily members achieve functional specificity via specific structural modulations

ABSTRACT

Autophagy is a conserved adaptive cellular pathway essential to maintain a variety of physiological functions. Core components of this machinery are the six human Atg8 orthologs that initiate formation of appropriate protein complexes. While these proteins are routinely used as indicators of autophagic flux, it is presently not possible to discern their individual biological functions due to our inability to predict specific binding partners. In our attempts towards determining downstream effector functions, we developed a computational pipeline to define structural determinants of human Atg8 family members that dictate functional diversity. We found a clear evolutionary separation between human LC3 and GABARAP subfamilies and also defined a novel sequence motif responsible for their specificity. By analyzing known protein structures, we observed that functional modules or microclusters reveal a pattern of intramolecular network, including distinct hydrogen bonding of key residues (F52/Y49; a subset of HP2) that may directly modulate their interaction preferences. Multiple molecular dynamics simulations were performed to characterize how these proteins interact with a common protein binding partner, PLEKHM1. Our analysis showed remarkable differences in binding modes via intrinsic protein dynamics, with PLEKHM1-bound GABARAP complexes showing less fluctuations and higher number of contacts. We further mapped 373 genomic variations and demonstrated that distinct cancer-related mutations are likely to lead to significant structural changes. Our findings present a quantitative framework to establish factors underlying exquisite specificity of human Atg8 proteins, and thus facilitate the design of precise modulators.

Abbreviations: Atg: autophagy-related; ECs: evolutionary constraints; GABARAP: GABA type A receptor-associated protein; HsAtg8: human Atg8; HP: hydrophobic pocket; KBTBD6: kelch repeat and BTB domain containing 6; LIR: LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MD: molecular dynamics; HIV-1 Nef: human immunodeficiency virus type 1 negative regulatory factor; PLEKHM1: pleckstrin homology and RUN domain containing M1; RMSD: root mean square deviation; SQSTM1/p62: sequestosome 1; WDFY3/ALFY: WD repeat and FYVE domain containing 3     

Site-Specific Formation of A basic Lesions in DNA

Abstract

A method for the introduction of depurinated lesions in DNA is described, and is based on the formation of a covalent cross-link between an antisense oligonucleotide probe and the target DNA sequence followed by an unexpectedly mild thermal depurination.     

Surfactin reduces the adhesion of food-borne pathogenic bacteria to solid surfaces

Aims:  To investigate the effect of the biosurfactants surfactin and rhamnolipids on the adhesion of the food pathogens Listeria monocytogenes , Enterobacter sakazakii and Salmonella Enteritidis to stainless steel and polypropylene surfaces.
Methods and Results:  Quantification of bacterial adhesion was performed using the crystal violet staining technique. Preconditioning of surfaces with surfactin caused a reduction on the number of adhered cells of Ent. sakazakii and L. monocytogenes on stainless steel. The most significant result was obtained with L. monocytogenes where number of adhered cells was reduced by 10² CFU cm⁻². On polypropylene, surfactin showed a significant decrease on the adhesion of all strains. The adsorption of surfactin on polystyrene also reduces the adhesion of L. monocytogenes and Salm. Enteritidis growing cells. For short contact periods using nongrowing cells or longer contact periods with growing cells, surfactin was able to delay bacterial adhesion.
Conclusions:  The prior adsorption of surfactin to solid surfaces contributes on reducing colonization of the pathogenic bacteria.
Significance and Impact of the Study:  This is the first work investigating the effect of surfactin on the adhesion of the food pathogens L. monocytogenes , Ent. sakazakii and Salm. Enteritidis to polypropylene and stainless steel surfaces.     

Iron-histidine resonance raman band of deoxyheme proteins: effects of anharmonic coupling and glass-liquid phase transition

Weak anharmonic coupling of two soft molecular vibrations is shown to cause pronounced temperature dependence of the corresponding resonance Raman bands. The developed theory is used to interpret the temperature dependence of the iron-histidine band of deoxyheme proteins and model compounds. It is shown that anharmonic coupling of the iron-histidine and heme doming vibrations must cause pronounced broadening of the band, its asymmetry, and shift of its maximum to the red upon heating. It also can lead to a structured shape of this band at room temperature. Proper consideration of the anharmonic coupling allows simulation of the temperature dependence of the iron-histidine band shape of horse heart myoglobin in the temperature interval of 10-300 K, using the minimum number of necessary parameters. Analysis of this temperature dependence clearly shows that the iron-histidine band of deoxyheme proteins is sensitive to the glass-liquid phase transition in the protein hydration shell, which takes place at 160-190 K.     

Mapping the evolutionary twilight zone: molecular markers, populations and geography

Since evolutionary processes, such as dispersal, adaptation and drift, occur in a geographical context, at multiple hierarchical levels, biogeography provides a central and important unifying framework for understanding the patterns of distribution of life on Earth. However, the advent of molecular markers has allowed a clearer evaluation of the relationships between microevolutionary processes and patterns of genetic divergence among populations in geographical space, triggering the rapid development of many research programmes. Here we provide an overview of the interpretation of patterns of genetic diversity in geographical and ecological space, using both implicit and explicit spatial approaches. We discuss the actual or potential interaction of phylogeography, molecular ecology, ecological genetics, geographical genetics, landscape genetics and conservation genetics with biogeography, identifying their respective roles and their ability to deal with ecological and evolutionary processes at different levels of the biological hierarchy. We also discuss how each of these research programmes can improve strategies for biodiversity conservation. A unification of these research programmes is needed to better achieve their goals, and to do this it is important to develop cross‐disciplinary communication and collaborations among geneticists, ecologists, biogeographers and spatial statisticians.