Optimal foraging area: Size and allocation of search effort

A model is derived for the optimal spatial allocation of foraging effort for an animal returning with food to a central place in a uniform habitat. The forager is assumed to maximize its yield of food during a given period. Foraging effort is expended on search for food, and on transportation to the central place. It is shown that the allocation of search has been optimal if and only if the “marginal cost” of additional food is equal throughout the foraging area when the period has elapsed. The model is used to predict the optimal area radius and allocation of search time. With realistic parameter values, the optimal time per unit area roughly decreases linearly with the distance from the central place. The influence of food density and forager characteristics is examined.     

Gene transfer among bacteria under conditions of nutrient depletion in simulated and natural aquatic environments

Abstract Gene transfer among microorganisms has been well demonstrated in laboratory microcosms and in situ, under non-limiting nutrient conditions. The literature contains conflicting opinions, however, as to whether such processes could occur in the absence of nutrients. This review summarises the evidence for the occurrence of gene transfer by conjugation, transformation and transduction among non-growing bacteria in nutrient depleted environments. Conjugation by selftransmissible, or by non-selftransmissible but mobilisable, plasmids has been shown to occur among environmental isolates of Escherichia coli, Enterobacter cloacae, Pseudomonas aeruginosa and marine Vibrio strains. Transduction and transformation have been demonstrated in isolates of P. aeruginosa and marine Vibrio strains, respectively. It is possible that the mechanisms of these processes may be different in non-growing cells in nutrient depleted conditions, compared to those occurring in cells growing in rich media.     

The Function of Embryonic Stem Cell-expressed RAS (E-RAS), a Unique RAS Family Member,Correlates with Its Additional Motifs and Its Structural Properties

E-RAS is a member of the RAS family specifically expressed in embryonic stem cells, gastric tumors, and hepatic stellate cells. Unlike classical RAS isoforms (H-, N-, and K-RAS4B), E-RAS has, in addition to striking and remarkable sequence deviations, an extended 38-amino acid-long unique N-terminal region with still unknown functions. We investigated the molecular mechanism of E-RAS regulation and function with respect to its sequence and structural features. We found that N-terminal extension of E-RAS is important for E-RAS signaling activity. E-RAS protein most remarkably revealed a different mode of effector interaction as compared with H-RAS, which correlates with deviations in the effector-binding site of E-RAS. Of all these residues, tryptophan 79 (arginine 41 in H-RAS), in the interswitch region, modulates the effector selectivity of RAS proteins from H-RAS to E-RAS features.     

Paralogy and the Centre of Origin Concept

Ancestral area methodology, applied to finding the centre of origin, conflicts with most cladistic biogeographic methods since it uses, not reduces, paralogy. A new term, area cladistics, is herein proposed as an efficient paralogy-free (or reduced) method under the three-item philosophy that currently exists with other methods under the broad term cladistic biogeography.     

aRNA-longSAGE: a new approach to generate SAGE libraries from microdissected cells

Large-scale gene expression analyses of microdissected primary tissue are still difficult because generally only a limited amount of mRNA can be obtained from microdissected cells. The introduction of the T7-based RNA amplification technique was an important step to reduce the amount of RNA needed for such analyses. This amplification technique produces amplified antisense RNA (aRNA), which so far has precluded its direct use for serial analysis of gene expression (SAGE) library production. We describe a method, termed ‘aRNA-longSAGE’, which is the first to allow the direct use of aRNA for standard longSAGE library production. The aRNA-longSAGE protocol was validated by comparing two aRNA-longSAGE libraries with two Micro-longSAGE libraries that were generated from the same RNA preparations of two different cell lines. Using a conservative validation approach, we were able to verify 68% of the differentially expressed genes identified by aRNA-longSAGE. Furthermore, the identification rate of differentially expressed genes was roughly twice as high in our aRNA-longSAGE libraries as in the standard Micro-longSAGE libraries. Using our validated aRNA-longSAGE protocol, we were able to successfully generate longSAGE libraries from as little as 40 ng of total RNA isolated from 2000–3000 microdissected pancreatic ductal epithelial cells or cells from pancreatic intraepithelial neoplasias.     

Differential contribution to gene expression prediction of histone modifications at enhancers or promoters

The ChIP-seq signal of histone modifications at promoters is a good predictor of gene expression in different cellular contexts, but whether this is also true at enhancers is not clear. To address this issue, we develop quantitative models to characterize the relationship of gene expression with histone modifications at enhancers or promoters. We use embryonic stem cells (ESCs), which contain a full spectrum of active and repressed (poised) enhancers, to train predictive models. As many poised enhancers in ESCs switch towards an active state during differentiation, predictive models can also be trained on poised enhancers throughout differentiation and in development. Remarkably, we determine that histone modifications at enhancers, as well as promoters, are predictive of gene expression in ESCs and throughout differentiation and development. Importantly, we demonstrate that their contribution to the predictive models varies depending on their location in enhancers or promoters. Moreover, we use a local regression (LOESS) to normalize sequencing data from different sources, which allows us to apply predictive models trained in a specific cellular context to a different one. We conclude that the relationship between gene expression and histone modifications at enhancers is universal and different from promoters. Our study provides new insight into how histone modifications relate to gene expression based on their location in enhancers or promoters.     

Determination of bacterial cell surface hydrophobicity of single cells in cultures and in wastewater in situ

Bacterial cell surface hydrophobicity is one of the most important factors that influence bacterial adhesion. A new method, microsphere adhesion to cells, for measuring bacterial cell surface hydrophobicity was developed. Microsphere adhesion to cells is based on microscopic enumeration of hydrophobic, fluorescent microspheres attaching to the bacterial surface. Cell surface hydrophobicity estimated by microsphere adhesion to cells correlates well with adhesion of bacteria to hydrocarbons or hydrophobic interaction chromatography for a set of hydrophilic and hydrophobic bacteria (linear correlation coefficients, R², were 0.845 and 0.981 respectively). We also used microsphere adhesion to cells to investigate the in situ properties of individual free-living bacteria directly in activated sludge. Results showed that the majority of the bacteria were hydrophilic, indicating the importance of cell surface hydrophobicity for bacterial adhesion in sludge, and for the overall success of the wastewater treatment process.     

Chemical composition and alkaline phosphatase activity of nutrient-saturated and P-deficient cells of four marine dinoflagellates

Four marine dinoflagellates, Amphidinium carterae Hulburt, Ceratium tripos (O.F. Müll.) Nitzsch, Prorocentrum minimum (Pav.) J. Schiller, and Scrippsiella trochoidea (Stein) Loeblich III were grown as dilution cultures at 18°C, S = 29%. and 30 μE·m^?2·s^?1 at L:D = 14:10 h. In nutrient-saturated cultures, the growth rates (doubl·day^?1) ranged from 0.38 for Scrippsiella to 0.80 for Prorocentrum, and carbon content (pg·cell^?1) from 83 for Amphidinium to 6900 for Ceratium. The atomic $\text{N}\text{C}$ ratio was 0.13–0.15, but for Ceratium it was 0.088, because of its thick, cellulose theca. The atomic $\text{N}\text{P}$ ratio ranged from 12–13 for Ceratium and Scrippsiella to 15–17 for Prorocentrum and Amphidinium. Under P-deficient conditions (growth rate 39–70% of the maximum), cellular P decreased considerably, but so did N, so that the $\text{N}\text{P}$ ratio was only slightly affected. There was a concomitant increase in carbon content per cell of 1.2- to 1.7-fold. Alkaline phosphatase activity was virtually nil in nutrient-saturated cells, but was readily demonstrable in all species when P-deficient.     

Effects of the thermal environment on metabolism of deoxynivalenol and thermoregulatory response of sheep fed on corn silage grown at enriched atmospheric carbon dioxide and drought

Future livestock production is likely to be affected by both rising ambient temperatures and indirect effects mediated by modified growth conditions of feed plants such as increased atmospheric CO₂ concentrations and drought. Corn was grown at elevated CO₂ concentrations of 550?ppm and drought stress using free air carbon dioxide enrichment technology. Whole plant silages were generated and fed to sheep kept at three climatic treatments. Differential blood count was performed. Plasma DON and de-epoxy-DON concentration were measured. Warmer environment increased rectal and skin temperatures and respiration rates (p?<?0.001 each) but did not affect blood parameters and the almost complete metabolization of DON into de-epoxy-DON. Altered growth conditions of the corn fed did not have single effects on sheep body temperature measures and differential blood count. Though the thermoregulatory activity of sheep was influenced by the thermal environment, the investigated cultivation factors did not indicate considerable impacts on the analysed parameters.