Coarse-grained molecular simulation of diffusion and reaction kinetics in a crowded virtual cytoplasm

We present a general-purpose model for biomolecular simulations at the molecular level that incorporates stochasticity, spatial dependence, and volume exclusion, using diffusing and reacting particles with physical dimensions. To validate the model, we first established the formal relationship between the microscopic model parameters (timestep, move length, and reaction probabilities) and the macroscopic coefficients for diffusion and reaction rate. We then compared simulation results with Smoluchowski theory for diffusion-limited irreversible reactions and the best available approximation for diffusion-influenced reversible reactions. To simulate the volumetric effects of a crowded intracellular environment, we created a virtual cytoplasm composed of a heterogeneous population of particles diffusing at rates appropriate to their size. The particle-size distribution was estimated from the relative abundance, mass, and stoichiometries of protein complexes using an experimentally derived proteome catalog from Escherichia coli K12. Simulated diffusion constants exhibited anomalous behavior as a function of time and crowding. Although significant, the volumetric impact of crowding on diffusion cannot fully account for retarded protein mobility in vivo, suggesting that other biophysical factors are at play. The simulated effect of crowding on barnase-barstar dimerization, an experimentally characterized example of a bimolecular association reaction, reveals a biphasic time course, indicating that crowding exerts different effects over different timescales. These observations illustrate that quantitative realism in biosimulation will depend to some extent on mesoscale phenomena that are not currently well understood.     

The effects of fire, local environment and time on ant assemblages in fens and forests

We investigated the effects of the abiotic environment, plant community composition and disturbance by fire on ant assemblages in two distinct habitat types in the Siskiyou Mountains in northern California and southern Oregon, USA. Sampling over 2 years in burned and unburned Darlingtonia fens and their adjacent upland forests, we found that the effects of disturbance by fire depended on habitat type. In forests, fire intensity predicted richness in ant assemblages in both years after the fire, and plant community composition predicted richness 2 years after the fire. No factors were associated with richness in the species‐poor fen ant assemblages. Species‐specific responses to both habitat type and disturbance by fire were idiosyncratic. Assemblage composition depended on habitat type, but not disturbance by fire, and the composition of each assemblage between years was more dissimilar in burned than unburned sites.     

Bayesian inference in ecology

Bayesian inference is an important statistical tool that is increasingly being used by ecologists. In a Bayesian analysis, information available before a study is conducted is summarized in a quantitative model or hypothesis: the prior probability distribution. Bayes’ Theorem uses the prior probability distribution and the likelihood of the data to generate a posterior probability distribution. Posterior probability distributions are an epistemological alternative to P‐values and provide a direct measure of the degree of belief that can be placed on models, hypotheses, or parameter estimates. Moreover, Bayesian information‐theoretic methods provide robust measures of the probability of alternative models, and multiple models can be averaged into a single model that reflects uncertainty in model construction and selection. These methods are demonstrated through a simple worked example. Ecologists are using Bayesian inference in studies that range from predicting single‐species population dynamics to understanding ecosystem processes. Not all ecologists, however, appreciate the philosophical underpinnings of Bayesian inference. In particular, Bayesians and frequentists differ in their definition of probability and in their treatment of model parameters as random variables or estimates of true values. These assumptions must be addressed explicitly before deciding whether or not to use Bayesian methods to analyse ecological data.     

Diversity of rotifers from northeastern U.S.A. bogs with new species records for North America and New England

In order to assess the effects of pollution on recruitment of brown trout (Salmo trutta f. fario L.) exposure experiments with brown trout early life stages were performed in two differently contaminated small streams near Stuttgart, southwest Germany, and in a control situation in the laboratory. Pollution in the more polluted stream is mainly due to effluents of municipal sewage treatment plants and to the influx of surface waters from areas of intense agriculture activity. Additionally, the water carries high particle loads, especially after rainfall events. Water quality of the less polluted stream is occasionally influenced by agriculture activity in the vicinity. For the exposure of trout early life stages incubators were used, which allowed frequent examinations without serious disturbance of the exposed organisms and thus the development could be monitored over time. Compared to the less polluted stream and the control, in the more polluted stream high mortality rates, the lowest hatching success, and lowest values for growth occurred. In the less polluted stream, mortality rates were comparably low in prehatching stages, but high in hatchlings and juveniles due to heavy infestations with protozoic ectoparasites Chilodonella cyprini (Moroff, 1902) and Ichthyobodo necator (Henneguy, 1883). However, pollution-related effects were not detected in this stream. Differences in developmental rates between the different treatments were correlated with different water temperatures in the two streams and the control. For the more polluted stream, previous studies have indicated embryotoxic potentials mediated by pollutants. The present study indicates that in this steam, additionally, fine solids which infiltrate stream gravels may seriously affect development of brown trout early life stages.     

Assembly rules for New England ant assemblages

Community assembly rules specify patterns of species co-occurrence and morphology dictated by interspecific competition. We collected data on the occurrence of ground-foraging ant species in 22 ombrotrophic bogs and adjacent forest plots of New England to test two general assembly rules: reduced co-occurrence of species among communities, and even spacing of body sizes of species within communities. We used null models to generate random communities unstructured by competition and evaluated patterns at regional and local spatial scales. At the regional scale, species co-occurrence in forests, but not bogs, was less than expected by chance, whereas, at the local scale, co-occurrence in both habitats was not different from random. At the regional scale, spacing of body size distributions was random (in bogs) or aggregated (in forests). At the local scale, body size patterns were weakly segregated in bogs, but random or weakly aggregated in forests. In bogs, size ratio constancy was accompanied by greater generic diversity than expected. Although assembly rules were originally developed for vertebrate communities, they successfully explained some patterns in New England ant assemblages. However, the patterns were contingent on spatial scale, and were distinctly different for bog and forest communities, despite their close proximity and the presence of many shared species in both assemblages. The harsh physical conditions of bogs may act as a habitat filter that alters community assembly rules.     

L1 (LINE-1) retrotransposable elements provide a "fossil" record of the phylogenetic history of murid rodents

The single most difficult problem in phylogenetic analysis is deciding whether a shared taxonomic character is due to common ancestry or one that appeared independently due to convergence, parallelism, or reversion to an ancestral state. Mammalian L1 retrotransposons undergo periodic amplifications in which multiple copies of the elements are interspersed in the genome. Because these elements apparently are transmitted only by inheritance and are retained in the genome, a shared L1 amplification event can only be an inherited ancestral character. We propose that L1 amplification events can be an excellent tool for analyzing mammalian evolution and demonstrate here how we addressed several refractory problems in rodent systematics using L1 DNA as a taxonomic character.      

Behavior of adult and young grassland songbirds at fledging

The behavior of adults and young at the time of fledging is one of the least understood aspects of the breeding ecology of birds. Current hypotheses propose that fledging occurs either as a result of parent‐offspring conflict or nestling choice. We used video recordings to monitor the behavior of nestling and adult grassland songbirds at the time of fledging. We observed 525 nestlings from 166 nests of 15 bird species nesting in grasslands of Alberta, Canada, and Wisconsin, USA. Overall, 78% of nestlings used terrestrial locomotion for fledging and 22% used wing‐assisted locomotion. Species varied in propensity for using wing‐assisted locomotion when fledging, with nestling Grasshopper Sparrows (Ammodramus savannarum) and Henslow's Sparrows (Centronyx henslowii) often doing so (47% of fledgings) and nestling Song Sparrows (Melospiza melodia), Common Yellowthroats (Geothlypis trichas), and Chestnut‐collared Longspurs (Calcarius ornatus) rarely doing so (3.5% of fledgings). For 390 fledging events at 127 nests, camera placement allowed adults near nests to be observed. Of these, most young fledged (81.5%) when no adult was present at nests. Of 72 fledging events that occurred when an adult was either at or approaching a nest, 49 (68.1%) involved feeding. Of those 49 fledgings, 30 (62.1%) occurred when one or more nestlings jumped or ran from nests to be fed as an adult approached nests. The low probability of nestlings fledging while an adult was at nests, and the tendency of young to jump or run from nests when adults did approach nests with food minimize opportunities for parents to withhold food to motivate nestlings to fledge. These results suggest that the nestling choice hypothesis best explains fledging by nestlings of ground‐nesting grassland songbirds, and fledging results in families shifting from being place‐based to being mobile and spatially dispersed.     

Multiple sclerosis: urinary amine measurement for orthomolecular diagnosis

Urinary amines from 53 people who have multiple sclerosis and 58 controls have been separated and measured quantitatively by means of low-resolution ion-exchange procedure. Dependences on multiple sclerosis and on sex have been detected. The multiple-sclerosis-dependent pattern has been tested for diagnostic value by means of the weighted non-correlation index method.