Distribution, relative abundance and movements of pallid sturgeon in the free-flowing Mississippi River

A multiyear study of pallid sturgeon distribution and relative abundance was conducted in the lower and middle Mississippi river (LMR and MMR, respectively). The LMR and MMR comprise the free‐flowing Mississippi River extending 1857 river kilometers (rkm) from its mouth at the Gulf of Mexico upstream to the mouth of the Missouri River. A total of 219 pallid sturgeon and 6018 shovelnose sturgeon was collected during the periods 1996–1997 and 2000–2006. Trotlines baited with worms were the primary collecting gear. The smallest pallid sturgeon captured on trotlines was 405 mm FL and the largest was 995 mm FL. Mean size of pallid sturgeon was statistically smaller in the Mississippi River below the Atchafalaya River near Baton Rouge, LA (621 mm FL). Mean abundance (catch per trotline night) of pallid sturgeon was highest at water temperatures around 10°C. There was a latitudinal trend in mean abundance of pallid and shovelnose sturgeon, but the pattern differed between species. Pallid sturgeon abundance was statistically (P < 0.05) higher (0.3 fish per trotline night) in the lower reach between the Atchafalaya River and New Orleans (rkm 154–507), and at the Chain of Rocks (COR), a low water dam near the mouth of the Missouri River. Pallid sturgeon abundance between these two locations was statistically the same (0.12–0.23). Shovelnose sturgeon abundance increased going upstream, but was disproportionally higher at the COR (22 fish per line compared with <6 fish per line in other reaches). Overall, the ratio between pallid and shovelnose sturgeon varied from a high of 1 : 6 at the lower reach, and gradually decreased upstream to a low of 1 : 77 at the COR. Based on differences in sturgeon abundance, size and habitat characteristics, the free‐flowing Mississippi River can be divided into two reaches in the MMR (i.e. COR is a separate location), and four reaches (i.e., including the Atchafalaya River) in the LMR where management goals may differ.     

Herbivore abundance and grazing intensity on a Caribbean coral reef

Herbivory is a primary factor in determining the structure of coral reef communities. Spatial variation among reef habitats in the intensity of herbivory has been documented, but underlying variation in species composition and abundance within the herbivore guild has received little attention. The distribution and relative abundances of herbivorous fishes and sea urchins across several habitats were studied on the Belizean barrier reef off the Caribbean coast of Central America. Marked variation in total herbivore density as well as major changes in the composition of the herbivore guild were found across reef habitats. Acanthurids (surgeonfishes) predominated in shallow areas (< 5 m) while scarids (parrotfishes) were dominant in deeper habitats. Significant differences among habitats in an experimental assay of grazing intensity were strongly correlated with herbivore abundance. The spatial distribution of herbivorous fishes across reef habitats does not appear to be simply explained by differences in reef topography, but may depend on complex interactions among proximity to nearby shelter, predator abundance, density of territorial competitors, and local availability of food resources.     

Analysis of murine S-glutathionyl hemoglobins and beta globin haplotype by dynamic capillary isoelectric focusing

Genetic variation in the number and reactivity of beta globin sulfhydryl groups causes variation in erythrocyte redox status in mouse populations. These experiments demonstrate the use of capillary isoelectric focusing for measuring endogenous S-glutathionyl hemoglobin and identifying mouse beta globin (Hbb) haplotype in inbred and outbred mouse strains with mono-cysteinyl or di-cysteinyl beta globins. Hbb haplotype can be readily determined in all strains based on characteristic differences in peak profiles or on peak mobility shift induced by thiol exchange with glutathione disulfide in vitro. This method could prove useful for in vivo study of factors that influence thiol protein modification.     

Issues associated with residual cell-substrate DNA in viral vaccines

The presence of some residual cellular DNA derived from the production-cell substrate in viral vaccines is inevitable. Whether this DNA represents a safety concern, particularly if the cell substrate is derived from a tumor or is tumorigenic, is unknown. DNA has two biological activities that need to be considered. First, DNA can be oncogenic; second, DNA can be infectious. As part of our studies to assess the risk of residual cell-substrate DNA in viral vaccines, we have established assays that can quantify the biological activities of DNA. From data obtained using these assays, we have estimated the risk of an oncogenic or an infectious event from DNA. Because these estimates were derived from the most sensitive assays identified so far, they likely represent worst-case estimates. In addition, methods that inactivate the biological activities of DNA can be assessed and estimations of risk reduction by these treatments can be made. In this paper, we discuss our approaches to address potential safety issues associated with residual cellular DNA from neoplastic cell substrates in viral vaccines, summarize the development of assays to quantify the oncogenic and infectivity activities of DNA, and discuss methods to reduce the biological activities of DNA.     

Engineered bromodomains to explore the acetylproteome

MS‐based analysis of the acetylproteome has highlighted a role for acetylation in a wide array of biological processes including gene regulation, metabolism, and cellular signaling. To date, anti‐acetyllysine antibodies have been used as the predominant affinity reagent for enrichment of acetyllysine‐containing peptides and proteins; however, these reagents suffer from high nonspecific binding and lot‐to‐lot variability. Bromodomains represent potential affinity reagents for acetylated proteins and peptides, given their natural role in recognition of acetylated sequence motifs in vivo. To evaluate their efficacy, we generated recombinant proteins representing all known yeast bromodomains. Bromodomain specificity for acetylated peptides was determined using degenerate peptide arrays, leading to the observation that different bromodomains display a wide array of binding specificities. Despite their relatively weak affinity, we demonstrate the ability of selected bromodomains to enrich acetylated peptides from a complex biological mixture prior to mass spectrometric analysis. Finally, we demonstrate a method for improving the utility of bromodomain enrichment for MS through engineering novel affinity reagents using combinatorial tandem bromodomain pairs.