Structural insights into peptide self-assembly using photo-induced crosslinking experiments and discontinuous molecular dynamics

Determining the structure of the (oligomeric) intermediates that form during the self-assembly of amyloidogenic peptides is challenging because of their heterogeneous and dynamic nature. Thus, there is need for methodology to analyze the underlying molecular structure of these transient species. In this work, a combination of fluorescence quenching, photo-induced crosslinking (PIC) and molecular dynamics simulation was used to study the assembly of a synthetic amyloid-forming peptide, Aβ_16-22. A PIC amino acid containing a trifluormethyldiazirine (TFMD) group—Fmoc(TFMD)Phe—was incorporated into the sequence (Aβ*_16–22). Electrospray ionization ion-mobility spectrometry mass-spectrometry (ESI-IMS-MS) analysis of the PIC products confirmed that Aβ*_16–22 forms assemblies with the monomers arranged as anti-parallel, in-register β-strands at all time points during the aggregation assay. The assembly process was also monitored separately using fluorescence quenching to profile the fibril assembly reaction. The molecular picture resulting from discontinuous molecule dynamics simulations showed that Aβ_16-22 assembles through a single-step nucleation into a β-sheet fibril in agreement with these experimental observations. This study provides detailed structural insights into the Aβ_16-22 self-assembly processes, paving the way to explore the self-assembly mechanism of larger, more complex peptides, including those whose aggregation is responsible for human disease.     

Investigating measurements of fine particle (PM2.5) emissions from the cooking of meals and mitigating exposure using a cooker hood

There is growing awareness that indoor exposure to particulate matter with diameter ≤ 2.5 μm (PM_2.5) is associated with an increased risk of adverse health effects. Cooking is a key indoor source of PM_2.5 and an activity conducted daily in most homes. Population scale models can predict occupant exposures to PM_2.5, but these predictions are sensitive to the emission rates used. Reported emission rates are highly variable and are typically for the cooking of single ingredients and not full meals. Accordingly, there is a need to assess PM_2.5 emissions from the cooking of complete meals. Mean PM_2.5 emission rates and source strengths were measured for four complete meals. Temporal PM_2.5 concentrations and particle size distributions were recorded using an optical particle counter (OPC), and gravimetric sampling was used to determine calibration factors. Mean emission rates and source strengths varied between 0.54—3.7 mg/min and 15—68 mg, respectively, with 95% confidence. Using a cooker hood (apparent capture efficiency > 90%) and frying in non‐stick pans were found to significantly reduce emissions. OPC calibration factors varied between 1.5 and 5.0 showing that a single value cannot be used for all meals and that gravimetric sampling is necessary when measuring PM_2.5 concentrations in kitchens.     

Surface structure and quenching effects in BiFeO3-BaTiO3 ceramics

The structure and properties of Mn-doped 0.67BiFeO₃-0.33BaTiO₃ ceramics are systematically investigated with respect to the effects of annealing prior to rapid cooling by quenching in air. Air-quenching induces a change in crystal structure from pseudo-cubic to rhombohedral, with higher quenching temperatures leading to an increased rhombohedral distortion. These structural changes are correlated with the appearance of more well-defined ferroelectric domain configurations. It is shown that the surface preparation procedures for XRD measurements can induce significant changes in the peak profiles, indicating differences in crystal structure between the surface and bulk regions. Frequency dispersion in the temperature-dependent relative permittivity for the as-sintered sample is significantly reduced after quenching, accompanied by enhancement of the Curie point and improved temperature-stability of piezoelectric properties. It is proposed that the formation of defect clusters by A-site cation diffusion during cooling is circumvented by quenching, leading to the observed modification of structural distortion and ferroelectric properties.     

Cigarette characteristics,smoker characteristics,and the relationship to cigarette fires

Data were collected from eight cities on a wide range of cigarette and smoker characteristics for a sample of smokers. Of these, 564 smokers had had fires and were identified through fire department response to those fires, while the other 1,611 smokers had not had fires and were identified through a telephone sample survey of the communities. The characteristics analyzed included those that had shown evidence of a relationship to the risk of a cigarette-initiated fire, either in laboratory studies or in previous statistical analyses of fire experience.The smoker characteristics analyzed were household income, education, age, gender, and race. The cigarette characteristics analyzed were filter, tobacco column length, filter length, circumference, density, amount of tobacco, menthol, citrate, porosity, and pack type. In addition, a variable was used to control for the smoker's city.After controlling for all smoker characteristics and city, logistic regression modeling showed four cigarette characteristics to be significant: filter, filter length, porosity, and type of pack. Filter, filter length, and porosity all affect air intake, which, therefore, appears to be an important physical element in the combustion process associated with risk. Analysis limited to filtered cigarettes only showed the same characteristics to be significant, plus tobacco column length. Extension of the analysis to two-way interaction terms did not change any of the conclusions on which cigarette characteristics are important, but it did indicate that the role of pack type was different for men and women.Sensitivity analyses, shown in the appendix, supported the main conclusions that cigarette characteristics are significant after controlling for smoker characteristics and that the four specific cigarette characteristics—filter, filter length, porosity, and pack—are the ones that are significant. These analyses checked the impact of cluster sampling, sensitivity to missing data on smoker characteristics, and sensitivity to nonfire smoker cases with responses by people other than the smokers themselves.All this means that there are already cigarettes commercially available that exhibit a reduced propensity for ignition when one controls for smoker characteristics.This report was originally written as the final report in June 1993 as part of CPSC-P-91-1147 Contract Cigarette Fire Incident Study that the National Fire Protection Association conducted for the U.S. Consumer Product Safety Commission.Harwood, formerly with the Consumer Product Safety Commission, is retired.     

Identification of Components of the Aggregation Pheromone of the Guam Strain of Coconut Rhinoceros Beetle,Oryctes rhinoceros,and Determination of Stereochemistry

The coconut rhinoceros beetle, Oryctes rhinoceros (Linnaeus 1758) (Coleoptera: Scarabaeidae: Dynastinae) (CRB), is endemic to tropical Asia where it damages both coconut and oil palm. A new invasion by CRB occurred on Guam in 2007 and eradication attempts failed using commonly applied Oryctes rhinoceros nudivirus (OrNV) isolates. This and subsequent invasive outbreaks were found to have been caused by a previously unrecognized haplotype, CRB-G, which appeared to be tolerant to OrNV. The male-produced aggregation pheromone of the endemic, susceptible strain of O. rhinoceros (CRB-S) was previously identified as ethyl 4-methyloctanoate. Following reports from growers that commercial lures containing this compound were not attractive to CRB-G, the aim of this work was to identify the pheromone of CRB-G. Initial collections of volatiles from virgin male and female CRB-G adults from the Solomon Islands failed to show any male- or female-specific compounds as candidate pheromone components. Only after five months were significant quantities of ethyl 4-methyloctanoate and 4-methyloctanoic acid produced by males but not by females. No other male-specific compounds could be detected, in particular methyl 4-methyloctanoate, 4-methyl-1-octanol, or 4-methyl-1-octyl acetate, compounds identified in volatiles from some other species of Oryctes. Ethyl 4-methyloctanoate elicited a strong electroantennogram response from both male and female CRB-G, but these other compounds, including 4-methyloctanoic acid, did not. The enantiomers of ethyl 4-methyloctanoate and 4-methyloctanoic acid were conveniently prepared by enzymatic resolution of the commercially-available acid, and the enantiomers of the acid, but not the ester, could be separated by gas chromatography on an enantioselective cyclodextrin phase. Using this approach, both ethyl 4-methyloctanoate and 4-methyloctanoic acid produced by male CRB-G were shown to be exclusively the (R)-enantiomers whereas previous reports had suggested male O. rhinoceros produced the (S)-enantiomers. However, re-examination of the ester and acid produced by male CRB-S from Papua New Guinea showed that these were also the (R)-enantiomers. In field trapping experiments carried out in the Solomon Islands, both racemic and ethyl (R)-4-methyloctanoate were highly attractive to both male and female CRB-G beetles. The (S)-enantiomer and the corresponding acids were only weakly attractive. The addition of racemic 4-methyloctanoic acid to ethyl 4-methyloctanoate did significantly increase attractiveness, but the addition of (R)- or (S)-4-methyloctanoic acid to the corresponding ethyl esters did not. Possible reasons for the difference in assignment of configuration of the components of the CRB pheromone are discussed along with the practical implications of these results.

     

Controlling harmful cyanobacterial blooms in a world experiencing anthropogenic and climatic-induced change

Harmful (toxic, food web altering, hypoxia generating) cyanobacterial algal blooms (CyanoHABs) are proliferating world-wide due to anthropogenic nutrient enrichment, and they represent a serious threat to the use and sustainability of our freshwater resources. Traditionally, phosphorus (P) input reductions have been prescribed to control CyanoHABs, because P limitation is widespread and some CyanoHABs can fix atmospheric nitrogen (N₂) to satisfy their nitrogen (N) requirements. However, eutrophying systems are increasingly plagued with non N₂ fixing CyanoHABs that are N and P co-limited or even N limited. In many of these systems N loads are increasing faster than P loads. Therefore N and P input constraints are likely needed for long-term CyanoHAB control in such systems. Climatic changes, specifically warming, increased vertical stratification, salinization, and intensification of storms and droughts play additional, interactive roles in modulating CyanoHAB frequency, intensity, geographic distribution and duration. In addition to having to consider reductions in N and P inputs, water quality managers are in dire need of effective tools to break the synergy between nutrient loading and hydrologic regimes made more favorable for CyanoHABs by climate change. The more promising of these tools make affected waters less hospitable for CyanoHABs by 1) altering the hydrology to enhance vertical mixing and/or flushing and 2) decreasing nutrient fluxes from organic rich sediments by physically removing the sediments or capping sediments with clay. Effective future CyanoHAB management approaches must incorporate both N and P loading dynamics within the context of altered thermal and hydrologic regimes associated with climate change.     

Corrosion of copper-coated used nuclear fuel containers due to oxygen trapped in a Canadian deep geological repository

The Nuclear Waste Management Organization is evaluating the safety and feasibility of the permanent disposal of used nuclear fuel in a deep geological repository. Their current design concept utilises copper-coated steel used fuel containers to isolate the waste from the environment. Immediately following repository closure, a finite quantity of O₂ will be trapped inside the repository and could cause some amount of oxic corrosion to the outer copper layer of the containers. On a per container basis, 13?mol of O₂ will be trapped in the repository rooms at the time of closure, based on reference design dimensions. This corresponds to a maximum depth of copper corrosion of 81?μm, assuming a uniform distribution. This work also considers the sensitivity of this oxic corrosion allowance to various hypothetical design changes to the repository that may occur before or during construction.