Oncogenic Notch Promotes Long-Range Regulatory Interactions within Hyperconnected 3D Cliques

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The strength of ecological subsidies across ecosystems: a latitudinal gradient of direct and indirect impacts on food webs

Material and energy flows among ecosystems can directly and indirectly drive ecosystem functions. Yet, how populations of consumers respond to allochthonous inputs at a macroecological scale is still unclear. Using a meta‐analysis spanning several biomes, we show that the abundance of recipient populations is 36–57% larger with increased allochthonous inputs. The strength of direct effects on the recipients of these inputs as well as the indirect effects on the consumers of these recipients (i.e. ascending indirect effects) are constant across a latitudinal gradient spanning subtropical, arid, temperate, boreal and arctic ecosystems. However, indirect effect on the in situ resources of the input recipient (i.e. descending indirect effects) decreases with latitude. Our results suggest that the influence of allochthonous inputs can vary across large‐scale gradients of ecosystem productivity and may be driven by the types of trophic interactions within recipient food webs.     

Spatial variations in Eulemur fulvus rufus and Lepilemur mustelinus densities in Madagascar

I present data on variations in Eulemur fulvus rufus and Lepilemur mustelinus densities as well as tree characteristics (height, diameter and stem frequency) between edge and interior forest habitats in southeastern Madagascar. Line transect surveys were conducted from June 2003 to November 2005 in edge and interior forest habitats in the Vohibola III Classified Forest. Although E. f. rufus densities were significantly lower in edge habitats than in interior habitats, density estimates for L. mustelinus did not differ significantly between habitats. Trees in edge habitats were significantly shorter, had smaller diameters and had lower stem frequencies (for those >25 cm in diameter) than trees in interior habitats. Spatial characteristics of food abundance and quality may explain lemur density patterns in Vohibola III. Low E. f. rufus densities may reduce seed dispersal in edge habitats, which has important consequences for the long-term viability of forest ecosystems in Madagascar.     

Systematic identification of SH3 domain-mediated human protein-protein interactions by peptide array target screening

Systematic identification of direct protein-protein interactions is often hampered by difficulties in expressing and purifying the corresponding full-length proteins. By taking advantage of the modular nature of many regulatory proteins, we attempted to simplify protein-protein interactions to the corresponding domain-ligand recognition and employed peptide arrays to identify such binding events. A group of 12 Src homology (SH) 3 domains from eight human proteins (Swiss-Prot ID: SRC, PLCG1, P85A, NCK1, GRB2, FYN, CRK) were used to screen a peptide target array composed of 1536 potential ligands, which led to the identification of 921 binary interactions between these proteins and 284 targets. To assess the efficiency of the peptide array target screening (PATS) method in identifying authentic protein-protein interactions, we examined a set of interactions mediated by the PLCgamma1 SH3 domain by coimmunoprecipitation and/or affinity pull-downs using full-length proteins and achieved a 75% success rate. Furthermore, we characterized a novel interaction between PLCgamma1 and hematopoietic progenitor kinase 1 (HPK1) identified by PATS and demonstrated that the PLCgamma1 SH3 domain negatively regulated HPK1 kinase activity. Compared to protein interactions listed in the online predicted human interaction protein database (OPHID), the majority of interactions identified by PATS are novel, suggesting that, when extended to the large number of peptide interaction domains encoded by the human genome, PATS should aid in the mapping of the human interactome.     

Functional and ecological correlates of ecologically-based dimorphisms in squamate reptiles

Sexual dimorphism in phenotypic traits associated with the useof resources is a widespread phenomenon throughout the animalkingdom. While ecological dimorphisms are often initially generatedby sexual selection operating on an animal's size, natural selectionis believed to maintain, or even amplify, these dimorphismsin certain ecological settings. The trophic apparatus of snakeshas proven to be a model system for testing the adaptive natureof ecological dimorphisms because head size is rarely undersexual selection and it limits the maximum ingestible size ofprey in these gape-limited predators. Significantly less attentionhas been paid to the evolution of ecological dimorphisms inlizards, however, which may be due to the fact that lizards’feeding apparatus can be under both sexual and natural selectionsimultaneously, making it difficult to formulate clear-cut hypothesesto distinguish between the influences of natural and sexualselection. In order to tease apart the respective influencesof natural selection and sexual selection on the feeding apparatusof squamates, we take an integrative approach to formulate twohypotheses for snakes and lizards, respectively: (1) For gape-limitedsnakes, we predict that natural selection will act to generatedifferences in maximum gape, which will translate into differencesin maximum ingestible prey size between the sexes. (2) For lizardswhich mechanically reduce their prey, we predict that the degreeof dimorphism in head size should be positively correlated tothe degree of dimorphism in bite force which, in turn, shouldbe correlated to dimorphism in aspects of size or hardness ofprey. Finally, we predict that functional differences in thefeeding apparatus of these animals will also be linked withdifferences in sex-based feeding behavior and with selectionof prey.     

Open syntaxin docks synaptic vesicles

Synaptic vesicles dock to the plasma membrane at synapses to facilitate rapid exocytosis. Docking was originally proposed to require the soluble N-ethylmaleimide–sensitive fusion attachment protein receptor (SNARE) proteins; however, perturbation studies suggested that docking was independent of the SNARE proteins. We now find that the SNARE protein syntaxin is required for docking of all vesicles at synapses in the nematode Caenorhabditis elegans. The active zone protein UNC-13, which interacts with syntaxin, is also required for docking in the active zone. The docking defects in unc-13 mutants can be fully rescued by overexpressing a constitutively open form of syntaxin, but not by wild-type syntaxin. These experiments support a model for docking in which UNC-13 converts syntaxin from the closed to the open state, and open syntaxin acts directly in docking vesicles to the plasma membrane. These data provide a molecular basis for synaptic vesicle docking.     

Spatial phylogenetics of the Chinese angiosperm flora provides insights into endemism and conservation

The flora of China is well known for its high diversity and endemism. Identifying centers of endemism and designating conservation priorities are essential goals for biodiversity studies. However, there is no comprehensive study from a rigorous phylogenetic perspective to understand patterns of diversity and endemism and to guide biodiversity conservation in China. We conducted a spatial phylogenetic analysis of the Chinese angiosperm flora at the generic level to identify centers of neo- and paleo-endemism. Our results indicate that: (i) the majority of grid cells in China with significantly high phylogenetic endemism (PE) were located in the mountainous regions; (ii) four of the nine centers of endemism recognized, located in northern and western China, were recognized for the first time; (iii) arid and semiarid regions in Northwest China were commonly linked to significant PE, consistent with other spatial phylogenetic studies worldwide; and (iv) six high-priority conservation gaps were detected by overlaying the boundaries of China's nature reserves on all significant PE cells. Overall, we conclude that the mountains of southern and northern China contain both paleo-endemics (ancient relictual lineages) and neo-endemics (recently diverged lineages). The areas we highlight as conservation priorities are important for broad-scale planning, especially in the context of evolutionary history preservation.