Anti-biofilm compounds derived from marine sponges

Bacterial biofilms are surface-attached communities of microorganisms that are protected by an extracellular matrix of biomolecules. In the biofilm state, bacteria are significantly more resistant to external assault, including attack by antibiotics. In their native environment, bacterial biofilms underpin costly biofouling that wreaks havoc on shipping, utilities, and offshore industry. Within a host environment, they are insensitive to antiseptics and basic host immune responses. It is estimated that up to 80% of all microbial infections are biofilm-based. Biofilm infections of indwelling medical devices are of particular concern, since once the device is colonized, infection is almost impossible to eliminate. Given the prominence of biofilms in infectious diseases, there is a notable effort towards developing small, synthetically available molecules that will modulate bacterial biofilm development and maintenance. Here, we highlight the development of small molecules that inhibit and/or disperse bacterial biofilms specifically through non-microbicidal mechanisms. Importantly, we discuss several sets of compounds derived from marine sponges that we are developing in our labs to address the persistent biofilm problem. We will discuss: discovery/synthesis of natural products and their analogues-including our marine sponge-derived compounds and initial adjuvant activity and toxicological screening of our novel anti-biofilm compounds.     

Variability in the performance of juvenile Chinook salmon is explained primarily by when and where they resided in estuarine habitats

Estuarine habitats provide rearing opportunities for the juvenile life stage of anadromous fishes. Because survival is positively correlated with juvenile performance, these estuarine habitats play an important role in population abundance and productivity. To provide information for the recovery of several depressed stocks of Chinook salmon in the Columbia River Basin, we sought to identify the factors that explain variability in performance. Using otolith‐derived estimates of juvenile somatic growth rate as an index of recent performance, we observed a negative nonlinear relationship between growth rate and day of year, and a decreasing and increasing trend of growth rate over the 8 years of this study and distance from the river mouth respectively. Using a generalised linear modelling approach, we found that variability in juvenile somatic growth rate was best explained by where and when individuals were collected, their body size, contaminant loads, stock of origin, and whether a fish was hatchery produced or unmarked. Lastly, we argue that a considerable improvement to the growth rate of juveniles in estuarine habitats is physiologically possible. The results of this 8‐year study provide a baseline of the performance of juvenile Chinook salmon to evaluate habitat restoration programs and to compare against future anthropogenic conditions.     

Intra‐household constraints on educational attainment in rural households in Papua New Guinea

This paper examines intra‐household and socio‐cultural factors leading to differential outcomes in educational attainment by gender and birth order amongst smallholder oil palm households in Papua New Guinea. Not all children share equitably in the household resources allocated to education: females have lower average education levels than males, and high birth order children have higher education attainment than lower birth order siblings, indicating preferential parental investment in sons and early born children. The findings demonstrate that despite households having regular access to relatively high incomes from oil palm and residing in close proximity to schools, primary school net enrolment rates remain significantly lower than those for East Asia and the Pacific region, and the millennium development goal of universal primary education has not been met. This finding is likely to be the result of a combination of intra‐household factors including gender power imbalances, low parental education levels, the agency of youth in educational decision‐making and the weakening attraction of education as a means of improving income‐earning potential.     

The pathogenesis of paraesophageal empyema in dogs and constancy of radiographic and computed tomography signs are linked to involvement of the mediastinal serous cavity

The mediastinal serous cavity is a normal anatomic space in the caudal mediastinum. Aims of this anatomic and case series study were to describe the signs of pathologic expansion of the mediastinal serous cavity observed during computed tomography (CT), review the underlying anatomy, perform a literature review, and evaluate the medical records of several dogs with mediastinal serous cavity empyema (paraesophageal empyema). The mesothelial lined mediastinal serous cavity is a cranial extension of the omental bursa, separated from the peritoneal cavity by the diaphragm, in the dorsal part of the caudal mediastinum, to the right of the esophagus, between the heart base and diaphragm. In five adult, large‐breed dogs with surgically and histologically confirmed paraesophageal empyema, macroscopic plant material was found at surgery in two dogs, adherence to adjacent lung was present in three different dogs, accessory lobectomy was performed in two dogs with subacute‐chronic pyogranulomatous pneumonia, and one dog had concurrent pyothorax and mediastinitis, but none had esophageal abnormalities. This study expands our understanding of the pathogenesis and basis for the imaging appearance of paraesophageal empyema in dogs by clarifying the underlying anatomic structures that direct development of this condition. The term empyema accurately describes this condition because the purulent material accumulates within an existing body cavity. The study also provides initial evidence that the development of paraesophageal empyema might be due to local extension of lung disease, such as foreign body migration or pneumonia. Computed tomography was helpful for diagnosis, assessing size, and determining the spread of disease.     

Probing cold dense nuclear matter

The protons and neutrons in a nucleus can form strongly correlated nucleon pairs. Scattering experiments, in which a proton is knocked out of the nucleus with high-momentum transfer and high missing momentum, show that in carbon-12 the neutron-proton pairs are nearly 20 times as prevalent as proton-proton pairs and, by inference, neutron-neutron pairs. This difference between the types of pairs is due to the nature of the strong force and has implications for understanding cold dense nuclear systems such as neutron stars.     

Improving estimates of population status and trend with superensemble models

Fishery managers must often reconcile conflicting estimates of population status and trend. Superensemble models, commonly used in climate and weather forecasting, may provide an effective solution. This approach uses predictions from multiple models as covariates in an additional “superensemble” model fitted to known data. We evaluated the potential for ensemble averages and superensemble models (ensemble methods) to improve estimates of population status and trend for fisheries. We fit four widely applicable data‐limited models that estimate stock biomass relative to equilibrium biomass at maximum sustainable yield (B/B_MSY). We combined these estimates of recent fishery status and trends in B/B_MSY with four ensemble methods: an ensemble average and three superensembles (a linear model, a random forest and a boosted regression tree). We trained our superensembles on 5,760 simulated stocks and tested them with cross‐validation and against a global database of 249 stock assessments. Ensemble methods substantially improved estimates of population status and trend. Random forest and boosted regression trees performed the best at estimating population status: inaccuracy (median absolute proportional error) decreased from 0.42 – 0.56 to 0.32 – 0.33, rank‐order correlation between predicted and true status improved from 0.02 – 0.32 to 0.44 – 0.48 and bias (median proportional error) declined from ?0.22 – 0.31 to ?0.12 – 0.03. We found similar improvements when predicting trend and when applying the simulation‐trained superensembles to catch data for global fish stocks. Superensembles can optimally leverage multiple model predictions; however, they must be tested, formed from a diverse set of accurate models and built on a data set representative of the populations to which they are applied.     

Authentication of coffee by means of PCR-RFLP analysis and lab-on-a-chip capillary electrophoresis

Coffee is one of the most important world food commodities, commercial trade consisting almost entirely of Arabica and Robusta varieties. The former is considered to be of superior quality and thus attracts a premium price. Methods to differentiate these coffee species could prove to be beneficial for the detection of either deliberate or accidental adulteration. This study describes a molecular genetics approach to differentiate Arabica and Robusta coffee beans. This employs a Polymerase Chain Reaction-Restriction Fragment Length Polymorphism to monitor a single nucleotide polymorphism within the chloroplastic genome. Samples were analyzed with a lab-on-a-chip capillary electrophoresis system. Coffee powder mixtures were analyzed with this technique, displaying a 5% limit of detection. The plastid copy number was found to be relatively constant across a wide range of bean samples, suggesting that this methodology can also be employed for the quantification of any adulteration of Arabica with Robusta beans.     

Effect of copper on the volatility of aroma compounds in a model mouth system

Copper is thought to influence aroma perception by affecting volatility of aroma compounds in the mouth through interaction with salivary components, especially proteins. Our objective was to identify the effect of copper on the volatility of aroma compounds and the role of copper-protein interaction in volatile chemistry in the mouth. Copper (2.5 mg/L) and four aroma compounds (hexanal, butyl acetate, 2-heptanone, and ethyl hexanoate, 0.5 microL/L each) were added to model systems containing water, electrolytes, and artificial saliva at different pH levels. Headspace concentration of each volatile was measured using SPME-GC analysis. Copper in the model systems increased headspace concentration of volatiles at pH 6.5, but no change in volatility was observed at pH 7.0. At pH 7.5, the presence of copper in the artificial saliva system containing mucin and alpha-amylase decreased headspace volatile concentration, whereas histatin did not cause any changes in volatility. Effect of copper on volatiles at pH 6.5 may be due to increased solubility of copper at lower pH. Salivary proteins seem to interact with copper at pH 7.5. The interaction may change configuration of binding sites for aroma compounds in mucin.     

Long-term alternative dairy manure management approaches enhance microbial biomass and activity in perennial forage grass

Removing solids from liquid dairy manure slurry reduces manure phosphorus (P) and increases the available (mineral) fraction of nitrogen (N) but also decreases the organic matter content of the manure. While this novel treatment reduces environmental concerns associated with excess N and P application to soils, it may also reduce microbial biomass and activity in soil. This study evaluated the long-term effects of this alternative manure treatment compared to more typical nutrient applications in a perennial grass sward (tall fescue, Festuca arundinacea Schreb.) on soil microbial biomass, community composition, hydrolytic enzyme activity, and forage yield. Nutrient treatments for this long-term field experiment in Agassiz, British Columbia, Canada were started in 2003. The treatments included liquid dairy manure slurry, liquid dairy manure with solids removed, commercial fertilizer, a combination of fertilizer and dairy manure, and a control. All treatments were applied at 400–600 kg total N ha^?1 year^?1 in four equal doses. Soil microbial community composition (phospholipid fatty acid analysis) and activity (hydrolytic enzyme activity) were determined several times during the 2013 and 2014 growing seasons to a depth of 15 cm. Time of sampling (date) had a strong influence on microbial biomass, community composition, and activity, while the response to soil properties and yield was more varied. All manure treatments (dairy manure slurry, liquid fraction, and the combination) increased microbial biomass (by 19–32%) and the potential activity of cellulose-degrading enzymes (by 31–47%) compared to commercial fertilizer and unamended plots. The commercial fertilizer and liquid fraction lowered fungal/bacterial ratios compared with both whole manure and unamended plots. Our results indicate that separating the solid from the liquid fraction of manure, to improve crop yield and reduce P loading, did not reduce microbial community size and activity and that all manure treatments increased microbial biomass and activity compared to mineral fertilizer application.     

Antioxidant properties of Fusarium head blight-resistant and -susceptible soft red winter wheat grains grown in Virginia

Fusarium head blight (FHB) has emerged as a major threat to wheat crops around the world, and it has been hypothesized that wheat antioxidants may play a role against Fusarium infections. The current study aimed to determine antioxidant properties of FHB-resistant wheat grains as compared to susceptible wheat. The wheat samples were collected from a single growing location (Warsaw, VA) and the same growing season. The results showed that both FHB-resistant and -susceptible wheat grains exerted strong radical scavenging activities against DPPH* radical [0.91-1.53 micromol of Trolox equivalents (TE)/g], peroxyl radical (15.5-24.5 micromol of TE/g), and hydroxyl radical (15.7-35.8 micromol of TE/g). Their total phenolic contents ranged from 888 to 1117 microg of gallic acid equivalents (GAE)/g. Five phenolic acids including ferulic, syringic, vanillic, caffeic, and p-coumaric acids were determined in soluble and insoluble fractions of wheat grains, altogether with a range of 219-389 microg/g. On average, the FHB-resistant wheat group showed significantly higher average values in DPPH* and hydroxyl radicals scavenging activities (30 and 41% higher, respectively) than the FHB-susceptible wheat group.