Simultaneously estimating food web connectance and structure with uncertainty

1. Food web models explain and predict the trophic interactions in a food web, and they can infer missing interactions among the organisms. The allometric diet breadth model (ADBM) is a food web model based on the foraging theory. In the ADBM, the foraging parameters are allometrically scaled to body sizes of predators and prey. In Petchey et al. (Proceedings of the National Academy of Sciences, 2008; 105: 4191), the parameterization of the ADBM had two limitations: (a) the model parameters were point estimates and (b) food web connectance was not estimated.
2. The novelty of our current approach is: (a) We consider multiple predictions from the ADBM by parameterizing it with approximate Bayesian computation, to estimate parameter distributions and not point estimates. (b) Connectance emerges from the parameterization, by measuring model fit using the true skill statistic, which takes into account prediction of both the presences and absences of links.
3. We fit the ADBM using approximate Bayesian computation to 12 observed food webs from a wide variety of ecosystems. Estimated connectance was consistently greater than previously found. In some of the food webs, considerable variation in estimated parameter distributions occurred and resulted in considerable variation (i.e., uncertainty) in predicted food web structure.
4. These results lend weight to the possibility that the observed food web data is missing some trophic links that do actually occur. It also seems likely that the ADBM likely predicts some links that do not exist. The latter could be addressed by accounting in the ADBM for additional traits other than body size. Further work could also address the significance of uncertainty in parameter estimates for predicted food web responses to environmental change.

     

Induction of Nitrate Reductase and Peroxidase Activity in the Seedlings of Normal and High Lysine Maize

Steady state levels of in vivo nitrate reductase activity in the endosperm, scutella, roots and shoots of maize seedlings were higher in normal maize than those in high lysine maize. Activity of peroxidase in the roots, however, was higher in the high lysine cultivar. The nitrate reductase activity increased with the supply of nitrate in all parts of the seedlings of both cultivars, although the rates of increment in the endosperm were lower than those in scutella, roots and shoots. In relation to substrate concentration, a saturation was achieved at 5 to 10 mM of nitrate except in the endosperm, where activity increased slowly up to 100 mM at least. Final levels of enzyme activity were significantly higher in the scutella of normal than in that of high lysine seedlings. In vitro enzyme activity in the roots also increased with the supply of nitrate in both cultivars, reaching maximum at 5 to 10 mM nitrate.     

Biocompatible nanoparticles trigger rapid bacteria clustering

This study reveals an exciting phenomenon of stimulated bacteria clustering. Rapid aggregation and microbial arrest are shown to occur in Escherichia coli solutions of neutral pH when chitosan nanoparticles with positive zeta potential are added. Because chitosan nanoparticles can easily be dispersed in aqueous buffers, the rapid clustering phenomenon requires only minuscule nanoparticle concentrations and will be critical in developing new methods for extricating bacterial pathogens. This work establishes the dominant role of electrostatic attraction in bacteria‐nanoparticle interactions by varying the nanoparticle zeta potential from highly positive to strongly negative values, and by exploring concentration effects. For strongly negative nanoparticles, no clusters form, while aggregates are small and loose at intermediate conditions. In addition, optical density measurements indicate that over 90% of the suspended bacteria flocculate within seconds of being mixed with chitosan nanoparticles of a highly positive surface charge. Finally, the nanoparticles are significantly more efficient as a clustering agent compared to an equal mass of molecular chitosan in solution, as the bacteria‐nanoparticle clusters formed are substantially larger. The bacteria‐nanoparticle aggregation effect demonstrated here promises a rapid separation method for aiding pathogen detection and for flocculation of bacteria in fermentation processes. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Stereochemistry of Actinomycin–DNA Binding

The three dimensional structure of a crystalline complex containing actino-mycin D and deoxyguanosine has shed light on the stereochemistry of actino-mycin binding to DNA. The phenoxa-zone ring system of actinomycin intercalates into the DNA helix, while deoxyguanosine residues interact with both cyclic peptides through specific hydrogen bonds.     

Involvement of Riboflavin in UV-A and White Light-induced Synthesis of Anthocyanin in Sorghum bicolor

Synthesis of anthocyanin in isolated mesocotyls of Sorghum bicolor(var. Vidisha 60–1) is promoted by the external feedingof riboflavin (FMN) under white and UV-A light. Potassium iodide,salicylhydroxamic acid and sodium azide, which are known tointerfere with the photoreactions of riboflavin, inhibit thesynthesis of anthocyanin induced by white and UV-A light. Thisinhibition is reversed by riboflavin and there is a direct interactionbetween the inhibitors and riboflavin. It is concluded thatriboflavin is the major photoreceptor for the induction of anthocyaninsynthesis in Sorghum bicolor by white and UV-A light. Key words: Sorghum, anthocyanin, riboflavin, UV-A     

Bait shyness of two gerbils, Tatera indica indica Hardwicke and Meriones hurrianae Jerdon

Two rodents, Tatera indica indica Hardwicke and Meriones hurrianae Jerdon, developed aversion to zinc phosphide after one day's exposure to a sublethal dose. The poison shyness persisted for at least 115 and 35 days, respectively.     

Isolating Influenza RNA from Clinical Samples Using Microfluidic Oil-Water Interfaces

The effective and robust separation of biomolecules of interest from patient samples is an essential step in diagnostic applications. We present a platform for the fast extraction of nucleic acids from clinical specimens utilizing paramagnetic PMPs, an oil-water interface, a small permanent magnet and a microfluidic channel to separate and purify captured nucleic acids from lysate in less than one minute, circumventing the need for multiple washing steps and greatly simplifying and expediting the purification procedure. Our device was able to isolate influenza RNA from clinical nasopharyngeal swab samples with high efficiency when compared to the Ambion® MagMAX^TM Viral RNA Isolation Kit, sufficiently separating nucleic acid analytes from PCR-inhibiting contaminants within the lysate while also critically maintaining high integrity of the viral genome. We find that this design has great potential for rapid, efficient and sensitive nucleic acid separation from patient sample.