How does habitat complexity affect ant foraging success? A test using functional measures on three continents

Habitat complexity can mediate key processes that structure local assemblages through effects on factors such as competition, predation and foraging behaviour. While most studies address assemblage responses to habitat complexity within one locality, a more global approach allows conclusions with greater independence from the phylogenetic constraints of the target assemblages, thus allowing greater generality. We tested the effects of natural and manipulated habitat complexities on ant assemblages from South Africa, Australia and Sweden, in order to determine if there were globally consistent responses in how functional measures of foraging success are regulated by habitat complexity. Specifically, we considered how habitat complexity affected ant foraging rates including the speed of discovery and rate of monopolisation. We also tested if habitat complexity affected the body size index, a size-related morphological trait, of ants discovering resources and occupying and monopolising the resources after 180 min. Ants were significantly slower to discover baits in the more complex treatments, consistent with predictions that they would move more slowly through more complex environments. The monopolisation index was also lower in the more complex treatments, suggesting that resources were more difficult to defend. Our index of ant body size showed trends in the predicted direction for complexity treatments. In addition, ants discovering, occupying and monopolising resources were smaller in simple than in complex natural habitats. Responses of discovering ants to resources in natural habitats were clear in only one of three regions. Consistent with our predictions, habitat complexity thus affected functional measures of the foraging success of ants in terms of measures of discovery and monopolisation rates and body size traits of successful ants. However, patterns were not always equally clear in manipulative and mensurative components of the study.     

Non-native interactions play an effective role in protein folding dynamics

Systematic Monte Carlo simulations of simple lattice models show that the final stage of protein folding is an ordered process where native contacts get locked (i.e., the residues come into contact and remain in contact for the duration of the folding process) in a well‐defined order. The detailed study of the folding dynamics of protein‐like sequences designed as to exhibit different contact energy distributions, as well as different degrees of sequence optimization (i.e., participation of non‐native interactions in the folding process), reveals significant differences in the corresponding locking scenarios—the collection of native contacts and their average locking times, which are largely ascribable to the dynamics of non‐native contacts. Furthermore, strong evidence for a positive role played by non‐native contacts at an early folding stage was also found. Interestingly, for topologically simple target structures, a positive interplay between native and non‐native contacts is observed also toward the end of the folding process, suggesting that non‐native contacts may indeed affect the overall folding process. For target models exhibiting clear two‐state kinetics, the relation between the nucleation mechanism of folding and the locking scenario is investigated. Our results suggest that the stabilization of the folding transition state can be achieved through the establishment of a very small network of native contacts that are the first to lock during the folding process.     

CD23 Sheddase A Disintegrin and Metalloproteinase 10 (ADAM10) Is Also Required for CD23 Sorting into B Cell-derived Exosomes

The low affinity receptor for IgE, CD23, is the natural regulator of IgE synthesis, and understanding both the synthesis and the catabolism of CD23 are, thus, important issues. Membrane CD23 is cleaved by a disintegrin and metalloproteinase 10 (ADAM10) and this cleavage influences the ability of CD23 to regulate IgE. In contrast to the belief that cleavage is a cell surface event, endosomal neutralization with NH₄Cl was found to dramatically reduce CD23 cleavage, suggesting that the majority of CD23 cleavage occurred subsequent to internalization in the endosomal pathway and not at the cell surface. In line with this, full-length CD23 was shown to be sorted in an ADAM10-dependent manner into exosomes. Greatly increased ADAM10-mediated CD23 cleavage was seen at endosomal pH. Additionally, the stalk region of CD23 was found to interact with ADAM10 and ADAM10 binding of CD23 was found to be protease independent. SPR analysis of the interaction indicated about a 10-fold increase in the R_max at endosomal pH (pH 5.8) compared with pH 7.4, whereas the affinity of the interaction was not significantly changed. The R_max change, combined with the increased cleavage at endosomal pH, indicates greater accessibility of the CD23 stalk region for ADAM10 at the lower pH. These results indicate a model where CD23 internalization results in ADAM10-dependent incorporation into exosomes, followed by partial cleavage of CD23 by ADAM10 prior to being released from the cell. The increased cleavage at endosomal pH also has implications for other ADAM10 substrates.     

Canopy and litter ant assemblages share similar climate–species density relationships

Tropical forest canopies house most of the globe''s diversity, yet little is known about global patterns and drivers of canopy diversity. Here, we present models of ant species density, using climate, abundance and habitat (i.e. canopy versus litter) as predictors. Ant species density is positively associated with temperature and precipitation, and negatively (or non-significantly) associated with two metrics of seasonality, precipitation seasonality and temperature range. Ant species density was significantly higher in canopy samples, but this difference disappeared once abundance was considered. Thus, apparent differences in species density between canopy and litter samples are probably owing to differences in abundance–diversity relationships, and not differences in climate–diversity relationships. Thus, it appears that canopy and litter ant assemblages share a common abundance–diversity relationship influenced by similar but not identical climatic drivers.     

Surface Covering of Downed Logs: Drivers of a Neglected Process in Dead Wood Ecology

Many species use coarse woody debris (CWD) and are disadvantaged by the forestry-induced loss of this resource. A neglected process affecting CWD is the covering of the surfaces of downed logs caused by sinking into the ground (increasing soil contact, mostly covering the underside of the log), and dense overgrowth by ground vegetation. Such cover is likely to profoundly influence the quality and accessibility of CWD for wood-inhabiting organisms, but the factors affecting covering are largely unknown. In a five-year experiment we determined predictors of covering rate of fresh logs in boreal forests and clear-cuts. Logs with branches were little covered because they had low longitudinal ground contact. For branchless logs, longitudinal ground contact was most strongly related to estimated peat depth (positive relation). The strongest predictor for total cover of branchless logs was longitudinal ground contact. To evaluate the effect on cover of factors other than longitudinal ground contact, we separately analyzed data from only those log sections that were in contact with the ground. Four factors were prominent predictors of percentage cover of such log sections: estimated peat depth, canopy shade (both increasing cover), potential solar radiation calculated from slope and slope aspect, and diameter of the log (both reducing cover). Peat increased cover directly through its low resistance, which allowed logs to sink and soil contact to increase. High moisture and low temperatures in pole-ward facing slopes and under a canopy favor peat formation through lowered decomposition and enhanced growth of peat-forming mosses, which also proved to rapidly overgrow logs. We found that in some boreal forests, peat and fast-growing mosses can rapidly cover logs lying on the ground. When actively introducing CWD for conservation purposes, we recommend that such rapid covering is avoided, thereby most likely improving the CWD''s longevity as habitat for many species.     

Statistical modeling of biomedical corpora: mining the Caenorhabditis Genetic Center Bibliography for genes related to life span

Background  

The statistical modeling of biomedical corpora could yield integrated, coarse-to-fine views of biological phenomena that complement discoveries made from analysis of molecular sequence and profiling data. Here, the potential of such modeling is demonstrated by examining the 5,225 free-text items in the Caenorhabditis Genetic Center (CGC) Bibliography using techniques from statistical information retrieval. Items in the CGC biomedical text corpus were modeled using the Latent Dirichlet Allocation (LDA) model. LDA is a hierarchical Bayesian model which represents a document as a random mixture over latent topics; each topic is characterized by a distribution over words.     

The shape of human gene family phylogenies

Background  

The shape of phylogenetic trees has been used to make inferences about the evolutionary process by comparing the shapes of actual phylogenies with those expected under simple models of the speciation process. Previous studies have focused on speciation events, but gene duplication is another lineage splitting event, analogous to speciation, and gene loss or deletion is analogous to extinction. Measures of the shape of gene family phylogenies can thus be used to investigate the processes of gene duplication and loss. We make the first systematic attempt to use tree shape to study gene duplication using human gene phylogenies.     

Combined mitochondrial and nuclear DNA sequences resolve the interrelations of the major Australasian marsupial radiations

Australasian marsupials include three major radiations, the insectivorous/carnivorous Dasyuromorphia, the omnivorous bandicoots (Peramelemorphia), and the largely herbivorous diprotodontians. Morphologists have generally considered the bandicoots and diprotodontians to be closely related, most prominently because they are both syndactylous (with the 2nd and 3rd pedal digits being fused). Molecular studies have been unable to confirm or reject this Syndactyla hypothesis. Here we present new mitochondrial (mt) genomes from a spiny bandicoot (Echymipera rufescens) and two dasyurids, a fat-tailed dunnart (Sminthopsis crassicaudata) and a northern quoll (Dasyurus hallucatus). By comparing trees derived from pairwise base-frequency differences between taxa with standard (absolute, uncorrected) distance trees, we infer that composition bias among mt protein-coding and RNA sequences is sufficient to mislead tree reconstruction. This can explain incongruence between trees obtained from mt and nuclear data sets. However, after excluding major sources of compositional heterogeneity, both the "reduced-bias" mt and nuclear data sets clearly favor a bandicoot plus dasyuromorphian association, as well as a grouping of kangaroos and possums (Phalangeriformes) among diprotodontians. Notably, alternatives to these groupings could only be confidently rejected by combining the mt and nuclear data. Elsewhere on the tree, Dromiciops appears to be sister to the monophyletic Australasian marsupials, whereas the placement of the marsupial mole (Notoryctes) remains problematic. More generally, we contend that it is desirable to combine mt genome and nuclear sequences for inferring vertebrate phylogeny, but as separately modeled process partitions. This strategy depends on detecting and excluding (or accounting for) major sources of non-historical signal, such as from compositional non-stationarity. [Base composition; combined data; marsupial; mitochondrial genome; phylogeny.].     

Effects of an agonist of gonadotrophin releasing hormone in cattle. I. Hormone concentrations and oestrous cycle length

Four trials were completed to study the effects of a single intramuscular injection of 5 μg of an agonist of gonadotrophin releasing hormone (Hoe 766) on plasma concentrations of LH and progesterone, and on oestrous cycle length in normally cycling dairy cows.The first trial (four cows) showed that a mid-cycle injection of Hoe 766 temporarily increases plasma LH from less than 5 ng/ml to over 20 ng/ml within 2.5 h. Average plasma progesterone concentrations ranged from 4.8 to 7.0 ng/ml compared to 3.3 ng/ml in the control animal.The second trial (22 cows) showed that an injection of Hoe 766 on Cycle Day 3, 6 or 9 (Oestrus = Cycle Day 0) increased average plasma progesterone concentrations during Cycle Days 13, 14 and 15 by 1.2 ng/ml. Each of three cows injected on Cycle Day 16 maintained plasma concentrations above 3.9 ng/ml until Cycle Day 19 and corpus luteum (CL) size was maintained until Cycle Day 21. Except for the group of cows injected on Cycle Day 3, all other groups had temporarily reduced concentrations of plasma progesterone when sampled 24 h after Hoe 766 administration.The third trial (216 cows) showed that a single injection of Hoe 766 made between Cycle Day 1 and 10 did not alter oestrous cycle length (21.5 vs 21.3 days). In contrast, in the fourth trial (371 cows), a single injection of Hoe 766 between Cycle Days 12 to 16 altered the distribution of cycle lengths of 17–29 days, the average cycle length and the incidence of ovulation without detected oestrus. Compared to matched control cows, fewer Hoe 766-treated cows were detected in oestrus (73.9% vs 90%), or had cycle lengths of less than 20 days (4.7% vs 22.2%). These effects were most pronounced among cows injected on Cycle Day 16 when only 51.7% were detected in oestrus and their average cycle length was 24.1 days.These effects were not due to the formation of a secondary CL. Rather, the injection of Hoe 766 stimulated CL function and appeared to prevent or delay normal luteolysis when administered from Cycle Day 12.