Random analysis of amino acid pairs sensitive to variants in human coagulation factor IX precursor

In this study, we used a random approach to determine which amino acid pairs in human coagulation factor IX precursor are more sensitive to its 99 variants. The results show that the randomly unpredictable amino acid pairs are more sensitive to variants.     

A Regional Multiple-Stressor Rank-Based Ecological Risk Assessment for the Fjord of Port Valdez,Alaska

We conducted an ecological risk assessment of the marine environment of Port Valdez, a fjord in south-central Alaska. Because the assessment was regional rather than site-specific and contained a large number of different stressors in a variety of environments, we required a nontraditional method to estimate risks. We created a Relative Risk Model to rank and sum individual risks numerically within each subarea, from each source, and to each habitat. Application of this model involved division of Port Valdez into 11 subareas containing specific ecological and anthropogenic structures and activities. Within each subarea, the stressor sources were analyzed to estimate exposure of receptors within habitats leading to effects relevant to the chosen assessment endpoints. The subareas were analyzed and compared to form a Port-wide perspective of ecological risk. Available chemical concentrations from sediment and mussels collected from the Port were compared to various toxicological benchmarks as a partial confirmation of the risk analysis. An estimation of the risk of polycyclic aromatic hydrocarbons (PAHs) to marine invertebrates indicated low risk. The municipal boat harbor had the highest estimate, which reflected our relative risk rankings. The Relative Risk Model approach appears robust and has potential for use in situations where multiple stressors are of concern and for assessments covering broad geographic areas. In the Port Valdez assessment the approach provided relative risk rankings for chemical and physical stressors from various sources. But data were available for confirmation of risk estimates only for the chemical stressors. The rankings are relative, and extrapolation beyond the scenario in which they were developed is not warranted. Uncertainty is large, and the numerical scores collapse a multidimensional space into a single value. Use of just the numerical score out of context is more valid than with other indexes. The value of the approach lies in the relative rankings and the accounting of the components of the relative risk score.     

Tracking the acetate threshold using DO-transient control during medium and high cell density cultivation of recombinant Escherichia coli in complex media

DO-transient nutrient controllers use the dissolved oxygen signal to attempt acetate threshold tracking during fed-batch cultivation of recombinant E. coli. Here we apply DO-transient control to the production of Jembrana disease virus protein in complex Super Luria medium and compare performance against a high-limit pH-stat controller. For induction at medium cell density (harvest between 31 and 32.5 g dcw L) a total productivity of 0.27 g L h was achieved as compared to 0.24 g L h with the high-limit pH-stat. For induction at high cell density (harvest at 60 g dcw L), decreased productivity (0.12 g L h) was attributed to the effect of acetate accumulation on recombinant protein formation and a concomitant lowering of the critical growth rate. Our results suggest that complex media provides a difficult environment for the application of acetate threshold tracking DO-transient control because of difficulties in re-oxidizing acetate, and apparent localized production of acetate below the production threshold (as detected by the DO-transient controller as SPOUR(crit)). Configuring the DO-transient controller to avoid aggressive threshold probing is suggested as a means to improve performance and reduce acetate accumulation in complex media.     

Structure of diabolic acid-containing phospholipids isolated from Butyrivibrio sp.

The structures of the diabolic acid-containing phospholipids of Buryrivibrio S2 grown in the presence of palmitic acid have been investigated. Generally they consist of two conventional bacterial phospholipid or galactolipid structures linked by esterification through a single diabolic acid residue. The main lipid consists of the butyroyl ester of sn-1-alkenylglycero-3-phospho-1'-sn-glycerol joined in this way to the butyroyl ester of sn-1-alkenyl-3-galactosylglycerol by esterification of the vacant 2-hydroxy groups of the alkenyl-substituted glycerol molecules. A lipid that possess a palmitoyl group rather than one of the butyroyl groups of the latter structure has also been detected. The lipid occurring in the second highest concentration consists of two molecules of sn-1-alkenylglycero-3-phospho-sn-1'-glycerol butyroyl ester linked through diabolic acid in a similar manner to the main lipid. Other lipids with the latter structure either minus a butyroyl group or with palmitoyl group, instead of one of the buryroyl groups, exist as minor components.     

Evaluating the ability of regional models to predict local avian abundance

Spatial modeling over broad scales can potentially direct conservation efforts to areas with high species-specific abundances. We examined the performance of regional models for predicting bird abundance at spatial scales typically addressed in conservation planning. Specifically, we used point count data on wood thrush (Hylocichla mustelina) and blue-winged warbler (Vermivora cyanoptera) from 2 time periods (1995–1998 and 2006–2007) to evaluate the ability of regional models derived via Bayesian hierarchical techniques to predict bird abundance. We developed models for each species within Bird Conservation Region (BCR) 23 in the upper midwestern United States at 800-ha, 8,000-ha, and approximately 80,000-ha scales. We obtained count data from the Breeding Bird Survey and land cover data from the National Land Cover Dataset (1992). We evaluated predictions from the best models, as defined by an information-theoretic criterion, using point count data collected within an ecological subregion of BCR 23 at 131 count stations in the 1990s and again in 2006–2007. Competing (Deviance Information Criteria <5) blue-winged warbler models accounted for 67% of the variability and suggested positive associations with forest edge and proportion of forest at the 8,000-ha scale, and negative associations with forest patch area (800 ha) and wetness (800 ha and 80,000 ha). The regional model performed best for blue-winged warbler predicted abundances from point counts conducted in Iowa during 1995–1996 (r_s = 0.57; P = 0.14), the survey period that most closely aligned with the time period of data used for regional model construction. Wood thrush models exhibited positive correlations with point count data for all survey areas and years combined (r_s = 0.58, P ≤ 0.001). In comparison, blue-winged warbler models performed worse as time increased between the point count surveys and vintage of the model building data (r_s = 0.03, P = 0.92 for Iowa and r_s = 0.13, P = 0.51 for all areas, 2006–2007), likely related to the ephemeral nature of their preferred early successional habitat. Species abundance and sensitivity to changing habitat conditions seems to be an important factor in determining the predictive ability of regional models. Hierarchical models can be a useful tool for concentrating efforts at the scale of management units and should be one of many tools used by land managers, but we caution that the utility of such models may decrease over time for species preferring relatively ephemeral habitats if model inputs are not updated accordingly. © 2012 The Wildlife Society.     

THE INTERACTION OF CATIONIC LIPOSOMES CONTAINING ENTRAPPED HORSERADISH PEROXIDASE WITH CELLS IN CULTURE

Cationic liposomes composed of sphingomyelin, cholesterol, and stearylamine were prepared with horseradish peroxidase trapped inside. Stable particles were formed in which 10–12% of the enzymic activity appeared to be located at, or near, the outer surface of the liposome. Adsorption and uptake of liposomes by HeLa cells were followed cytochemically by electron microscopy and quantitated by enzyme assay and by the distribution and fate of particles labeled with [¹⁴C]cholesterol and [¹²⁵I]horseradish peroxidase. The particles were adsorbed by HeLa cells at least 300 times as efficiently as was free horseradish peroxidase. Many of the particles remained at the cell surface, but numerous membrane-bound cytoplasmic inclusions were observed to contain peroxidase-staining material. In addition, many areas of the cell membrane gave a positive staining reaction. It was concluded that many particles (presumably the larger ones) did not gain access to the interior of the cells, many were phagocytized, and some enzyme was transferred to the cell membrane, perhaps as a result of fusion of the liposomal membrane with the cell membrane.