Buffering an Acidic Stream in New Hampshire with a Silicate Mineral

Ground and pelletized Wollastonite (Wo; CaSiO₃) was added to a 50‐m reach of an anthropogenically acidified stream within the Hubbard Brook Experimental Forest, New Hampshire, to evaluate its buffering and restoration potential. The Wo was highly effective in raising the pH, acid‐neutralizing capacity (ANC), dissolved inorganic carbon (DIC), and Ca²⁺ concentrations of the stream water, but during the short duration of the experiment had no discernable effect on the stream biota. After initial, spike‐like fluctuations in pH and concentrations of ANC, DIC, and Ca²⁺, the relatively slow dissolution rates of the Wo dampened extreme concentrations and contributed to relatively long‐lasting (4 months) amelioration of streamwater acidity. Changes in concentrations of Ca²⁺, dissolved Si, ANC, and DIC were inversely related to streamflow. After several high, stream‐discharge events, concentrations quickly and consistently returned to pre‐event conditions.     

The structural basis for substrate and inhibitor selectivity of the anthrax lethal factor

Recent events have created an urgent need for new therapeutic strategies to treat anthrax. We have applied a mixture-based peptide library approach to rapidly determine the optimal peptide substrate for the anthrax lethal factor (LF), a metalloproteinase with an important role in the pathogenesis of the disease. Using this approach we have identified peptide analogs that inhibit the enzyme in vitro and that protect cultured macrophages from LF-mediated cytolysis. The crystal structures of LF bound to an optimized peptide substrate and to peptide-based inhibitors provide a rationale for the observed selectivity and may be exploited in the design of future generations of LF inhibitors.     

Nonenzymatic biotinylation of a biotin carboxyl carrier protein: unusual reactivity of the physiological target lysine

Enzyme-catalyzed addition of biotin to proteins is highly specific. In any single organism one or a small number of proteins are biotinylated and only a single lysine on each of these proteins is modified. A detailed understanding of the structural basis for the selective biotinylation process has not yet been elucidated. Recently certain mutants of the Escherichia coli biotin protein ligase have been shown to mediate "promiscuous" biotinylation of proteins. It was suggested that the reaction involved diffusion of a reactive activated biotin intermediate, biotinoyl-5'-AMP, with nonspecific proteins. In this work the reactivity of this chemically synthesized intermediate toward the natural target of enzymatic biotinylation, the biotin carboxyl carrier protein, was investigated. The results indicate that the intermediate does, indeed, react with target protein, albeit at a significantly slower rate than the enzyme-catalyzed process. Surprisingly, analysis of the products of nonenzymatic biotinylation indicates that of five lysine residues in the protein only the physiological target side chain is modified. These results indicate that either the environment of this lysine residue or its intrinsic properties render it highly reactive to nonenzymatic biotinylation mediated by biotinoyl-5'-AMP. This reactivity may be important for its selective biotinylation in vivo.     

The effects of host plant species on adult oviposition and larval performance of the aphid predator Aphidoletes aphidimyza

1. Although preference–performance relationships in insects are typically studied in a bi-trophic context, it is well known that host plants can affect both the preference and performance of natural enemies of herbivorous insects. 2. This study presents evidence from field and laboratory studies that two species of milkweeds, the putatively less defended Asclepias incarnata and the putatively more defended Asclepias syriaca, differentially affect adult oviposition and larval performance in Aphidoletes aphidimyza, an aphid-feeding predatory midge, independent of aphid density. 3. Host plant species affected predatory fly larvae abundance by a factor of 50 in the field and a factor of 8 in the laboratory. Larval and adult emergence rates in our laboratory studies provided strong evidence for reduced performance on A. syriaca. Oviposition in choice and no-choice settings provided some evidence for preference for A. incarnata, and a potentially suppressive effect of A. syriaca. 4. The results provide limited support for the hypothesis that natural selection can lead to positive correlations between adult oviposition preferences and larval performance upon various food sources, even when predatory insects oviposit onto host plants of their herbivorous prey. 5. Preference and performance are not perfectly aligned in this system, however, because ovipositing females do not reject A. syriaca entirely. Potential explanations for mismatches between preference and performance in this system include the neural constraints associated with being a generalist, adaptive time-limited foraging strategies, and unique evolutionary histories of laboratory colonies compared with wild insects.     

Evaluating gull diets: a comparison of conventional methods and stable isotope analysis

ABSTRACT Samples such as regurgitated pellets and food remains have traditionally been used in studies of bird diets, but these can produce biased estimates depending on the digestibility of different foods. Stable isotope analysis has been developed as a method for assessing bird diets that is not biased by digestibility. These two methods may provide complementary or conflicting information on diets of birds, but are rarely compared directly. We analyzed carbon and nitrogen stable isotope ratios of feathers of Glaucous Gull (Larus hyperboreus) chicks from eight breeding colonies in northern Alaska, and used a Bayesian mixing model to generate a probability distribution for the contribution of each food group to diets. We compared these model results with probability distributions from conventional diet samples (pellets and food remains) from the same colonies and time periods. Relative to the stable isotope estimates, conventional analysis often overestimated the contributions of birds and small mammals to gull diets and often underestimated the contributions of fish and zooplankton. Both methods gave similar estimates for the contributions of scavenged caribou, miscellaneous marine foods, and garbage to diets. Pellets and food remains therefore may be useful for assessing the importance of garbage relative to certain other foods in diets of gulls and similar birds, but are clearly inappropriate for estimating the potential impact of gulls on birds, small mammals, or fish. However, conventional samples provide more species‐level information than stable isotope analysis, so a combined approach would be most useful for diet analysis and assessing a predator's impact on particular prey groups.     

Direct measurements of the kinematics and dynamics of bat flight

Experimental measurements and analysis of the flight of bats are presented, including kinematic analysis of high-speed stereo videography of straight and turning flight, and measurements of the wake velocity field behind the bat. The kinematic data reveal that, at relatively slow flight speeds, wing motion is quite complex, including a sharp retraction of the wing during the upstroke and a broad sweep of the partially extended wing during the downstroke. The data also indicate that the flight speed and elevation are not constant, but oscillate in synchrony with both the horizontal and vertical movements of the wing. PIV measurements in the transverse (Trefftz) plane of the wake indicate a complex 'wake vortex' structure dominated by a strong wing tip vortex shed from the wing tip during the downstroke and either the wing tip or a more proximal joint during the upstroke. Data synthesis of several discrete realizations suggests a 'cartoon' of the wake structure during the entire wing beat cycle. Considerable work remains to be done to confirm and amplify these results.     

Divergence thresholds and divergent biodiversity estimates: can metabarcoding reliably describe zooplankton communities?

DNA metabarcoding is a promising method for describing communities and estimating biodiversity. This approach uses high‐throughput sequencing of targeted markers to identify species in a complex sample. By convention, sequences are clustered at a predefined sequence divergence threshold (often 3%) into operational taxonomic units (OTUs) that serve as a proxy for species. However, variable levels of interspecific marker variation across taxonomic groups make clustering sequences from a phylogenetically diverse dataset into OTUs at a uniform threshold problematic. In this study, we use mock zooplankton communities to evaluate the accuracy of species richness estimates when following conventional protocols to cluster hypervariable sequences of the V4 region of the small subunit ribosomal RNA gene (18S) into OTUs. By including individually tagged single specimens and “populations” of various species in our communities, we examine the impact of intra‐ and interspecific diversity on OTU clustering. Communities consisting of single individuals per species generated a correspondence of 59–84% between OTU number and species richness at a 3% divergence threshold. However, when multiple individuals per species were included, the correspondence between OTU number and species richness dropped to 31–63%. Our results suggest that intraspecific variation in this marker can often exceed 3%, such that a single species does not always correspond to one OTU. We advocate the need to apply group‐specific divergence thresholds when analyzing complex and taxonomically diverse communities, but also encourage the development of additional filtering steps that allow identification of artifactual rRNA gene sequences or pseudogenes that may generate spurious OTUs.