On the pH dependence of protein stability

This paper treats the free energy contribution of ionizable groups to protein stability. A method is presented for the calculation of the pH dependence of the denaturation free energy of a protein, which yields results that can be compared directly to experiment. The first step in the treatment is the determination of the average charges of all the ionizable groups in both the folded and unfolded protein. An expression due to Tanford then relates the pH dependence of the unfolding free energy to the difference in net charge between the two states. In order to determine absolute rather than relative unfolding free energies, it is necessary to calculate the total contribution of ionizable groups to protein stability at some reference pH. This is accomplished through a statistical mechanical treatment similar to the one used previously in the calculation of pKas. The treatment itself is rigorous but it suffers from uncertainties in the pKa calculations. Nevertheless, the overall shape of experimentally observed plots of denaturation free energy as a function of pH are reasonably well reproduced by the calculations. A number of general conclusions that arise from the analysis are: (1) knowledge of titration curves and/or effective pKa values of ionizable groups in proteins is sufficient to calculate the pH dependence of the denaturation free energy with respect to some reference pH value. However, in order to calculate the absolute contribution of ionizable groups to protein stability, it is necessary to also know the intrinsic pKa of each group. This is defined as the pKa of a group in a hypothetical state of the protein where all other groups are neutral. (2) Due to desolvation effects, ionizable groups destabilize proteins, although the effect is strongly dependent on pH. There are however, strongly stabilizing pairwise Coulombic interactions on the surface of proteins. (3) Plots of stability versus pH should not be interpreted in terms of a group whose pKa corresponds to the titration midpoint, but rather to a group with different pKas (that correspond approximately to the titration end points) in each state. (4) Any residual structure in the GuHCl-denatured state of proteins appears to have little effect on the pH dependence of stability. (5) pH-dependent unfolding, for example to the "molten globule" state, appears due to individual groups with anomalous pKas whose locations on the protein surface may determine the nature of the unfolded state.     

Three‐dimensional numerical modelling of the flushing process of the Kali Gandaki hydropower reservoir

Sediments filling reservoirs is a common problem in the world today, with an estimated 1% of the capacity of hydropower reservoirs being lost annually through sedimentation. One of the most used techniques for reducing this problem is reservoir flushing. During a flood, the water level is drawn down, causing increased velocities, therefore facilitating erosion and sediment transport. During the flushing, water from the reservoir will be lost, resulting in significant economic implications for the reservoir owner. The success of reservoir flushing depends on several parameters, including water discharge, sediment properties and reservoir geometry. This study describes the use of Computational Fluid Dynamics (CFD) as a modern method to predict the reservoir flushing process. A three‐dimensional numerical model (SSIIM 2), with an adaptive, non‐orthogonal and unstructured grid has been used. Through the application of special modified algorithms (e.g., wetting/drying, free water surface), numerical modelling of sediment movement can be an alternative for planning and optimizing the flushing process for complex reservoir geometries. The numerical model was tested against data from a physical model study of the Kali Gandaki hydropower reservoir in Nepal. The total quantity of flushed out sediments, and the bed deformation in six cross‐sections, were compared, highlighting a good correspondence between the results. These include the cross‐sectional shape of a 90‐degree bend, for which secondary currents influenced the results. The study indicates that numerical models might become a useful tool for reservoir flushing predictions.     

Penetration of fluorescent homologous serum proteins into the wall of the aorta in rats with acute angiotensin hypertension

A few hours of acute angiotensin hypertension in rats increased the permeability of the thoracic part of the aorta for plasma components. The permeability, which was demonstrated by means of homologous circulating fluorescent serum proteins, seemed to be diffuse rather than focal. The fluorescent proteins penetrated into the whole thickness of the aortic wall, but were to a great extent deposited in the subendothelial space and the most luminal part of the tunica media. The deposition took place in the greater part of the circumference of the aortic wall. These results are in agreement with the insudative theory of atherogenesis, and the initial stage seems to be a "damming back" of some of the serum or plasma proteins for deposition in the subendothelial space and the most luminal part of the tunica media.     

Appropriate Material Properties for Advective–Diffusive Solute Flux in Membrane Soil

A generalized advective–diffusive equation for describing electrolytic solute transport in fine-grained soil (clay) membranes is presented. Clarification is made between the current theory and the widely cited coupled-flow theory by Yeung and Mitchell. Results of recently published experimental data are evaluated to demonstrate that the effective diffusion coefficient associated with Fick’s first law is not an appropriate independent material property for solute transport considerations in membrane soil. Three independent and experimentally attainable material properties are identified, specifically: osmotic efficiency, membrane diffusion coefficient, and hydraulic conductivity. Simple physical experiments by which these properties may be measured are described.     

Sea-air flux of CO2 in the Caribbean Sea estimated using in situ and remote sensing data

Empirical relationships between sea surface carbon dioxide fugacity (fCO₂^sw) and sea surface temperature (SST) were applied to datasets of remotely sensed SST to create fCO₂^sw fields in the Caribbean Sea. SST datasets from different sensors were used, as well as the SST fields created by optimum interpolation of bias corrected AVHRR data. Empirical relationships were derived using shipboard fCO₂^sw data, in situ SST data, and SST data from the remote sensing platforms. The results show that the application of a relationship based on shipboard SST data, on fields of remotely sensed SST yields biased fCO₂^sw values. This bias is reduced if the fCO₂^sw-SST relationships are derived using the same SST data that are used to create the SST fields. The fCO₂^sw fields found to best reproduce observed fCO₂^sw are used in combination with wind speed data from QuikSCAT to create weekly maps of the sea-air CO₂ flux in the Caribbean Sea in 2002. The region to the SW of Cuba was a source of CO₂ to the atmosphere throughout 2002, and the region to the NE was a sink during winter and spring and a source during summer and fall. The net uptake of CO₂ in the region was doubled when potential skin layer effects on fCO₂^sw were taken into account.     

Prevalence, distribution, and diversity of Listeria monocytogenes in retail environments, focusing on small establishments and establishments with a history of failed inspections

Despite growing concerns about cross-contamination of ready-to-eat foods with Listeria monocytogenes, our knowledge about the ecology and transmission of L. monocytogenes in retail establishments has remained limited. We conducted a cross-sectional study to characterize the prevalence, distribution, and subtype diversity of L. monocytogenes in 120 New York State retail deli establishments that were hypothesized to present an increased risk for environmental L. monocytogenes contamination (i.e., small establishments and establishments with a history of failed New York State Agriculture and Markets inspections). Analysis of these data along with previously reported data for 121 predominantly larger retail establishments in New York State identified establishment size, geographic location, and inspection history as significant predictors of L. monocytogenes presence and prevalence. The odds of an establishment being L. monocytogenes positive were approximately twice as high for large establishments, establishments located in New York City, or establishments with poor inspection history (as compared with establishments without these attributes), even though correlation between location and inspection history complicated interpretation of results. Within an establishment, L. monocytogenes was significantly more prevalent on nonfood contact surfaces than on food contact surfaces; prevalence was particularly high for floors and in floor drains, sinks, the dairy case, and milk crates. L. monocytogenes subtype diversity differed between sites, with lineage I isolates significantly associated with nonfood contact surfaces and lineage II isolates significantly associated with food contact surfaces. Isolates belonging to the same ribotype were often found dispersed across multiple sites within an operation.     

Shot-noise limited,supercontinuum-based optical coherence tomography

We present the first demonstration of shot-noise limited supercontinuum-based spectral domain optical coherence tomography (SD-OCT) with an axial resolution of ...     

Mechanisms and Kinetics of Liquid Silicon Oxidation During Industrial Refining

During oxidative ladle refining (OLR) of silicon, the metal surface is partly oxidized, resulting in the formation of a condensed silica fume (SiO₂). This fugitive emission of silica represents a potential health hazard to the workers in the silicon and ferrosilicon industry. In the current work, industrial measurement campaigns aimed at recording the fume generation during OLR were performed at the Elkem Salten plant in Norway. The measured amounts of silica produced were 2.5–5.1?kg/h, depending on the gas flow rate in the refining process. The rate of silica production correlates with the total flow rate and amount of air in the purge gas, and increases as the flow rate increases. The results of this work suggest that fume generation during OLR primarily results from oxidation of the exposed metal surface, with oxygen transport from the surrounding atmosphere to the metal surface being the limiting factor. Other identified mechanisms of SiO₂ formation were splashing of the metal and/or oxidation of SiO gas carried with the refining purge gas.     

Apple,Carrot, and Hibiscus Edible Films Containing the Plant Antimicrobials Carvacrol and Cinnamaldehyde Inactivate Salmonella Newport on Organic Leafy Greens in Sealed Plastic Bags

The objective of this study was to investigate the antimicrobial effects of carvacrol and cinnamaldehyde incorporated into apple, carrot, and hibiscus‐based edible films against Salmonella Newport in bagged organic leafy greens. The leafy greens tested included organic Romaine and Iceberg lettuce, and mature and baby spinach. Each leafy green sample was washed, dip inoculated with S. Newport (10⁷ CFU/mL), and dried. Each sample was put into a Ziploc® bag. Edible films pieces were put into the Ziploc bag and mixed well. The bags were sealed and stored at 4 °C. Samples were taken at days 0, 3, and 7 for enumeration of survivors. On all leafy greens, 3% carvacrol films showed the best bactericidal effects against Salmonella. All 3 types of 3% carvacrol films reduced the Salmonella population by 5 log₁₀ CFU/g at day 0 and 1.5% carvacrol films reduced Salmonella by 1 to 4 log₁₀ CFU/g at day 7. The films with 3% cinnamaldehyde showed 0.5 to 3 log reductions on different leafy greens at day 7. The films with 0.5% and 1.5% cinnamaldehyde and 0.5% carvacrol also showed varied reductions on different types of leafy greens. Edible films were the most effective against Salmonella on Iceberg lettuce. This study demonstrates the potential of edible films incorporated with carvacrol and cinnamaldehyde to inactivate S. Newport on organic leafy greens.