Credit of ecological interactions: A new conceptual framework to support conservation in a defaunated world

As defaunation spreads through the world, there is an urgent need for restoring ecological interactions, thus assuring ecosystem processes. Here, we define the new concept of credit of ecological interactions, as the number of interactions that can be restored in a focal area by species colonization or reintroduction. We also define rewiring time, as the time span until all the links that build the credit of ecological interactions of a focal area have become functional again. We expect that the credit will be gradually cashed following refaunation in rates that are proportional to (1) the abundance of the reintroduced species (that is expected to increase in time since release), (2) the abundance of the local species that interact with them, and (3) the traits of reintroduced species. We illustrated this approach using a theoretical model and an empirical case study where the credit of ecological interactions was estimated. This new conceptual framework is useful for setting reintroduction priorities and for evaluating the success of conservation initiatives that aim to restore ecosystem services.     

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....     

Olfactory responses of Anaphes nitens (Hymenoptera,Mymaridae) to host and habitat cues

The eucalyptus weevil, Gonipterus spp. Schoenherr, 1833 (Coleoptera, Curculionidae) is considered a major pest of eucalyptus plantations. In regions where control is achieved, success is usually brought by the action of the solitary egg parasitoid Anaphes nitens (Girault, 1928) (Hymenoptera, Mymaridae). Research was conducted to ascertain which cues might mediate female wasp host location and selection. In Petri dish arenas, females were attracted to Gonipterus platensis Marelli, 1927 egg capsules, to G. platensis mated female faeces and to leaves of Eucalyptus globulus Labillardière, 1799. Gas chromatography–mass spectrometry electroantennographic detection analysis was conducted using extracts obtained from leaves of E. globulus, from G. platensis egg capsules, as well as from adults of both sexes and their faeces, in order to detect and identify compounds perceived by the wasp's olfactory system. The parasitoids were shown to detect a wide range of compounds emitted by each one of these sources, and for 31 compounds, antennal response was confirmed by dose-response tests. Further behavioural trials were conducted in Petri dishes in order to decode the effect, on parasitoid behaviour, of selected compounds emitted by E. globulus and of the pheromones, emitted by the weevils on parasitoid behaviour. Attraction was observed to two compounds emitted by E. globulus, namely 1,8-cineole and γ-terpinene, and to the main component of the male sex/aggregation pheromone, cis-verbenol. To our knowledge, this is the first report of attraction of a parasitoid from the family Mymaridae to a component of its host's sexual/aggregation pheromone. Similarly, to other egg parasitoid species, A. nitens females are likely to use the host plant volatiles as long-range host location cues and to adopt the ‘infochemical detour’ strategy in order to get in the vicinity of their hosts.     

Fluorometric determination of isocitrate dehydrogenase (EC 1.1.1.42; 1; NADP+ dependent) in ruminant milk

The enzyme isocitrate dehydrogenase (EC 1.1.1.42; 1; NADP⁺ dependent) located in the mammary cell cytosol mediates the synthesis of the majority of reducing equivalents for the energetically demanding milk fat and cholesterol synthesis in mammary cell cytosol. The present article presents a novel fluorometric method for quantification of the activity of this enzyme (IDH) in ruminant milk without pretreatment of the sample. Further, 493 goat milk samples – harvested before, during and after a nutritional restriction – were analysed for IDH activity i) with addition of extra substrate (isocitrate), and ii) with the intrinsic isocitrate solely. The IDH activity ranged from 0.22 to 15.4 units [nano moles product/(ml * min)] (un-supplemented) and from 0.22 to 45.6 units (isocitrate supplemented). The IDH activity increased considerably in milk during the nutritional restriction period concomitant with the increase in the metabolite isocitrate concentration and somatic cell count and returned to the initial level shortly after restriction period. The present ‘high through-put’ analytical method may be beneficial in future studies to phenotype modifications in mammary energy metabolism and milk fat synthesis, for which IDH activity may be a biomarker.     

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.