Post-repolarization block of cloned sodium channels by saxitoxin: the contribution of pore-region amino acids.

Sodium channels expressed in oocytes exhibited isoform differences in phasic block by saxitoxin (STX). Neuronal channels (rat IIa co-expressed with beta 1 subunit, Br2a + beta 1) had slower kinetics of phasic block for pulse trains than cardiac channels (RHI). After the membrane was repolarized from a single brief depolarizing step, a test pulse at increasing intervals showed first a decrease in current (post-repolarization block) then eventual recovery in the presence of STX. This block/unblock process for Br2a + beta 1 was 10-fold slower than that for RHI. A model accounting for these results predicts a faster toxin dissociation rate and a slower association rate for the cardiac isoform, and it also predicts a shorter dwell time in a putative high STX affinity conformation for the cardiac isoform. The RHI mutation (Cys374-->Phe), which was previously shown to be neuronal-like with respect to high affinity tonic toxin block, was also neuronal-like with respect to the kinetics of post-repolarization block, suggesting that this single amino acid is important for conferring isoform-specific transition rates determining post-repolarization block. Because the same mutation determines both sensitivity for tonic STX block and the kinetics of phasic STX block, the mechanisms accounting for tonic block and phasic block share the same toxin binding site. We conclude that the residue at position 374, in the putative pore-forming region, confers isoform-specific channel kinetics that underlie phasic toxin block.     

Oleaginous yeast: a value-added platform for renewable oils

Yeast single cell oil (SCO) is a non-crop-based, renewable oil source that can be used for the production of bio-based oleochemicals. Stand-alone production of SCO for oleochemicals is currently not cost-competitive because lower-cost alternatives from petroleum and crop-based resources are available. Utilizing low-valued nutrient sources, implementing cost-efficient downstream processes and adopting biotechnological advancements such as systems biology and metabolic engineering could prove valuable in making an SCO platform a reality in the emerging bio-based economy. This review aims to consider key biochemical pathways for storage lipid synthesis, possible pathways for SCO yield improvement, previously used bioprocessing techniques for SCO production, challenges in SCO commercialization and advantages of adopting a renewable SCO platform.     

Whole-Genome Sequencing in Microbial Forensic Analysis of Gamma-Irradiated Microbial Materials

Effective microbial forensic analysis of materials used in a potential biological attack requires robust methods of morphological and genetic characterization of the attack materials in order to enable the attribution of the materials to potential sources and to exclude other potential sources. The genetic homogeneity and potential intersample variability of many of the category A to C bioterrorism agents offer a particular challenge to the generation of attributive signatures, potentially requiring whole-genome or proteomic approaches to be utilized. Currently, irradiation of mail is standard practice at several government facilities judged to be at particularly high risk. Thus, initial forensic signatures would need to be recovered from inactivated (nonviable) material. In the study described in this report, we determined the effects of high-dose gamma irradiation on forensic markers of bacterial biothreat agent surrogate organisms with a particular emphasis on the suitability of genomic DNA (gDNA) recovered from such sources as a template for whole-genome analysis. While irradiation of spores and vegetative cells affected the retention of Gram and spore stains and sheared gDNA into small fragments, we found that irradiated material could be utilized to generate accurate whole-genome sequence data on the Illumina and Roche 454 sequencing platforms.     

The unusual internal motion of the villin headpiece subdomain

The thermostable 36‐residue subdomain of the villin headpiece (HP36) is the smallest known cooperatively folding protein. Although the folding and internal dynamics of HP36 and close variants have been extensively studied, there has not been a comprehensive investigation of side‐chain motion in this protein. Here, the fast motion of methyl‐bearing amino acid side chains is explored over a range of temperatures using site‐resolved solution nuclear magnetic resonance deuterium relaxation. The squared generalized order parameters of methyl groups extensively spatially segregate according to motional classes. This has not been observed before in any protein studied using this methodology. The class segregation is preserved from 275 to 305 K. Motions detected in Helix 3 suggest a fast timescale of conformational heterogeneity that has not been previously observed but is consistent with a range of folding and dynamics studies. Finally, a comparison between the order parameters in solution with previous results based on solid‐state nuclear magnetic resonance deuterium line shape analysis of HP36 in partially hydrated powders shows a clear disagreement for half of the sites. This result has significant implications for the interpretation of data derived from a variety of approaches that rely on partially hydrated protein samples.     

Accounting for size‐specific predation improves our ability to predict the strength of a trophic cascade

Predation can influence the magnitude of herbivory that grazers exert on primary producers by altering both grazer abundance and their per capita consumption rates via changes in behavior, density‐dependent effects, and size. Therefore, models based solely on changes in abundance may miss key components of grazing pressure. We estimated shifts in grazing pressure associated with changes in the abundance and per capita consumption rates of sea urchins triggered by size‐selective predation by sea otters (Enhydra lutris). Field surveys suggest that sea otters dramatically decreased the abundance and median size of sea urchins. Furthermore, laboratory experiments revealed that kelp consumption by sea urchins varied nonlinearly as a function of urchin size such that consumption rates increased to the 0.56 and 0.68 power of biomass for red and green urchins, respectively. This reveals that shifts in urchin size structure due to size‐selective predation by sea otters alter sea urchin per capita grazing rates. Comparison of two quantitative models estimating total consumptive capacity revealed that a model incorporating shifts in urchin abundance while neglecting urchin size structure overestimated grazing pressure compared to a model that incorporated size. Consequently, incorporating shifts in urchin size better predicted field estimates of kelp abundance compared to equivalent models based on urchin abundance alone. We provide strong evidence that incorporating size‐specific parameters increases our ability to describe and predict trophic interactions.     

Are the metabolomic responses to folivory of closely related plant species linked to macroevolutionary and plant–folivore coevolutionary processes?

The debate whether the coevolution of plants and insects or macroevolutionary processes (phylogeny) is the main driver determining the arsenal of molecular defensive compounds of plants remains unresolved. Attacks by herbivorous insects affect not only the composition of defensive compounds in plants but also the entire metabolome. Metabolomes are the final products of genotypes and are constrained by macroevolutionary processes, so closely related species should have similar metabolomic compositions and may respond in similar ways to attacks by folivores. We analyzed the elemental compositions and metabolomes of needles from three closely related Pinus species with distant coevolutionary histories with the caterpillar of the processionary moth respond similarly to its attack. All pines had different metabolomes and metabolic responses to herbivorous attack. The metabolomic variation among the species and the responses to folivory reflected their macroevolutionary relationships, with P. pinaster having the most divergent metabolome. The concentrations of terpenes were in the attacked trees supporting the hypothesis that herbivores avoid plant individuals with higher concentrations. Our results suggest that macroevolutionary history plays important roles in the metabolomic responses of these pine species to folivory, but plant–insect coevolution probably constrains those responses. Combinations of different evolutionary factors and trade‐offs are likely responsible for the different responses of each species to folivory, which is not necessarily exclusively linked to plant–insect coevolution.     

Extending bioacoustic monitoring of birds aloft through flight call localization with a three‐dimensional microphone array

Bioacoustic localization of bird vocalizations provides unattended observations of the location of calling individuals in many field applications. While this technique has been successful in monitoring terrestrial distributions of calling birds, no published study has applied these methods to migrating birds in flight. The value of nocturnal flight call recordings can increase with the addition of three‐dimensional position retrievals, which can be achieved with adjustments to existing localization techniques. Using the time difference of arrival method, we have developed a proof‐of‐concept acoustic microphone array that allows the three‐dimensional positioning of calls within the airspace. Our array consists of six microphones, mounted in pairs at the top and bottom of three 10‐m poles, arranged in an equilateral triangle with sides of 20 m. The microphone array was designed using readily available components and costs less than $2,000 USD to build and deploy. We validate this technique using a kite‐lofted GPS and speaker package, and obtain 60.1% of vertical retrievals within the accuracy of the GPS measurements (±5 m) and 80.4% of vertical retrievals within ±10 m. The mean Euclidian distance between the acoustic retrievals of flight calls and the GPS truth was 9.6 m. Identification and localization of nocturnal flight calls have the potential to provide species‐specific spatial characterizations of bird migration within the airspace. Even with the inexpensive equipment used in this trial, low‐altitude applications such as surveillance around wind farms or oil platforms can benefit from the three‐dimensional retrievals provided by this technique.