Effects of detergents on the secondary structures of prion protein peptides as studied by CD spectroscopy.

Pathogenic prion proteins (PrP(Sc)) are thought to be produced by alpha-helical to beta-sheet conformational changes in the normal cellular prion proteins (PrP(C)) located solely in the caveolar compartments. In order to inquire into the possible conformational changes due to the influences of hydrophobic environments within caveolae, the secondary structures of prion protein peptides were studied in various kinds of detergents by CD spectra. The peptides studied were PrP(129-154) and PrP(192-213); the former is supposed to assume beta-sheets and the latter alpha-helices, in PrP(Sc). The secondary structure analyses for the CD spectra revealed that in buffer solutions, both PrP(129-154) and PrP(192-213) mainly adopted random-coils (approximately 60%), followed by beta-sheets (30%-40%). PrP(129-154) showed no changes in the secondary structures even in various kinds of detergents such as octyl-beta-D-glucopyranoside (OG), octy-beta-D-maltopyranoside (OM). sodium dodecyl sulfate (SDS), Zwittergent 3-14 (ZW) and dodecylphosphocholine (DPC). In contrast, PrP(192-213) changed its secondary structure depending on the concentration of the detergents. SDS, ZW, OG and OM increased the alpha-helical content, and decreased the beta-sheet and random-coil contents. DPC also increased the alpha-helical content, but to a lesser extent than did SDS, ZW, OG or OM. These results indicate that PrP(129-154) has a propensity to adopt predominantly beta-sheets. On the other hand, PrP(192-213) has a rather fickle propensity and varies its secondary structure depending on the environmental conditions. It is considered that the hydrophobic environments provided by these detergents may mimic those provided by gangliosides in caveolae, the head groups of which consist of oligosaccharide chains containing sialic acids. It is concluded that PrP(C) could be converted into a nascent PrP(Sc) having a transient PrP(Sc) like structureunder the hydrophobic environments produced by gangliosides.     

Simplified methods for monitoring petroleum‐contaminated ground water and soil vapor

Portable meters and simplified gas Chromatographic (GC) techniques were investigated for monitoring volatile hydrocarbon (HC), CO₂, and O₂, concentrations in groundwater, exhaust gases, and soil vapor during in situ remediation using soil vapor extraction (SVE) and air sparging (AS). Results of groundwater samples analyzed in‐house using a headspace technique compared well to split samples analyzed by a certified analytical laboratory (r² = 0.94). SVE exhaust gas HC and CO₂ concentrations measured using a GT201 portable HC/O₂ meter and a RA‐411A meter (GasTech), respectively, were highly correlated with in‐house laboratory GC analyses (r² = 0.91). O₂ concentrations fell in a small range and meter analyses were not well correlated with laboratory analyses. Results of soil gas monitoring were not as well correlated as those for exhaust gases for HC, CO₂, or O₂, perhaps due to environmental conditions such as changes in relative humidity or the wider range of soil gas values. Overall, the meters were good indicators of vapor contamination, they greatly simplified estimates of total HC mass removal, and they allowed estimates of the biological contribution to contaminant removal during the remediation process.     

Cone penetrometer testing,hydropunch®, and borehole geophysics applications for environmental investigations

An effective groundwater monitoring system can be implemented by the combined utilization of cone penetrometer (CPT), HydroPunch^® sampling, and borehole geophysical methods. The combined techniques provide a cost‐effective method for the design of a groundwater monitoring system for geologists or hydrogeologists assessing a site. With the relatively high costs associated with determining groundwater quality for site assessments, coupled with regulatory agency compliance, these combined methods can provide an effective edge in an increasingly competitive environmental industry. CPT combined with HydroPunch sampling can delineate the horizontal and vertical extent and concentration of a contaminant plume, define the extent and thickness of a free product plume, define soil and aquifer characteristics, and aid in the proper selection of well location and screen placement. The use of borehole geophysics further enhances the interpretation provided from the CPT. The interpretation of borehole geophysics provides additional information about the deposition regime of the area of investigation and a more detailed investigation of the stratigraphy. The CPT and HydroPunch can be used in unconsolidated sediments, and HydroPunch sampling can be combined with a hollow‐stem auger system. Borehole geophysics can be run in almost any environment. CPT and borehole geophysics provide information on specific lithologic characteristics necessary to obtain a groundwater sample from vertically separated aquifers. The HydroPunch can obtain a discrete, chemically representative groundwater sample from the targeted aquifer. CPT and borehole geophysics can also be used to determine lithology and for correlation of equivalent stratas from one borehole or well to the next. Borehole geophysical interpretation also provides a means of determining not only the stratigraphy and lithology but also the aquifer parameters and the type of fluids in the aquifer. Hydrogeologic and geologic data obtained from using these three methods can be employed to maximize the cost‐effectiveness and design efficiency of a groundwater monitoring system. Proper location of wells and screened interval placements are determined by a coherent design process rather than by random chance. Two studies demonstrating the combined applications of CPT, HydroPunch, and borehole geophysics for the design and placement of groundwater monitoring wells are presented in the following discussion.     

Intercolony variation in reproductive skipping in the African penguin

In long‐lived species, reproductive skipping is a common strategy whereby sexually mature animals skip a breeding season, potentially reducing population growth. This may be an adaptive decision to protect survival, or a non‐adaptive decision driven by individual‐specific constraints. Understanding the presence and drivers of reproductive skipping behavior can be important for effective population management, yet in many species such as the endangered African penguin (Spheniscus demersus), these factors remain unknown. This study uses multistate mark‐recapture methods to estimate African penguin survival and breeding probabilities at two colonies between 2013 and 2020. Overall, survival (mean ± SE) was higher at Stony Point (0.82 ± 0.01) than at Robben Island (0.77 ± 0.02). Inter‐colony differences were linked to food availability; under decreasing sardine (Sardinops sagax) abundance, survival decreased at Robben Island and increased at Stony Point. Additionally, reproductive skipping was evident across both colonies; at Robben Island the probability of a breeder becoming a nonbreeder was ~0.22, versus ~0.1 at Stony Point. Penguins skipping reproduction had a lower probability of future breeding than breeding individuals; this lack of adaptive benefit suggests reproductive skipping is driven by individual‐specific constraints. Lower survival and breeding propensity at Robben Island places this colony in greater need of conservation action. However, further research on the drivers of inter‐colony differences is needed.     

Flux balance analysis in the production of clavulanic acid by Streptomyces clavuligerus

In this work, in silico flux balance analysis is used for predicting the metabolic behavior of Streptomyces clavuligerus during clavulanic acid production. To choose the best objective function for use in the analysis, three different optimization problems are evaluated inside the flux balance analysis formulation: (i) maximization of the specific growth rate, (ii) maximization of the ATP yield, and (iii) maximization of clavulanic acid production. Maximization of ATP yield showed the best predictions for the cellular behavior. Therefore, flux balance analysis using ATP as objective function was used for analyzing different scenarios of nutrient limitations toward establishing the effect of limiting the carbon, nitrogen, phosphorous, and oxygen sources on the growth and clavulanic acid production rates. Obtained results showed that ammonia and phosphate limitations are the ones most strongly affecting clavulanic acid biosynthesis. Furthermore, it was possible to identify the ornithine flux from the urea cycle and the α‐ketoglutarate flux from the TCA cycle as the most determinant internal fluxes for promoting clavulanic acid production. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:1226–1236, 2015     

Modeling activity patterns of wildlife using time‐series analysis

The study of wildlife activity patterns is an effective approach to understanding fundamental ecological and evolutionary processes. However, traditional statistical approaches used to conduct quantitative analysis have thus far had limited success in revealing underlying mechanisms driving activity patterns. Here, we combine wavelet analysis, a type of frequency‐based time‐series analysis, with high‐resolution activity data from accelerometers embedded in GPS collars to explore the effects of internal states (e.g., pregnancy) and external factors (e.g., seasonal dynamics of resources and weather) on activity patterns of the endangered giant panda (Ailuropoda melanoleuca). Giant pandas exhibited higher frequency cycles during the winter when resources (e.g., water and forage) were relatively poor, as well as during spring, which includes the giant panda's mating season. During the summer and autumn when resources were abundant, pandas exhibited a regular activity pattern with activity peaks every 24 hr. A pregnant individual showed distinct differences in her activity pattern from other giant pandas for several months following parturition. These results indicate that animals adjust activity cycles to adapt to seasonal variation of the resources and unique physiological periods. Wavelet coherency analysis also verified the synchronization of giant panda activity level with air temperature and solar radiation at the 24‐hr band. Our study also shows that wavelet analysis is an effective tool for analyzing high‐resolution activity pattern data and its relationship to internal and external states, an approach that has the potential to inform wildlife conservation and management across species.