Using polymeric materials to generate an amplified response to molecular recognition events

Clinical and field-portable diagnostic devices require the detection of atto- to zeptomoles of biological molecules rapidly, easily and at low cost, with stringent requirements in terms of robustness and reliability. Though a number of creative approaches to this difficult problem have been reported, numerous unmet needs remain in the marketplace, particularly in resource-poor settings. Using rational materials design, we investigated harnessing the amplification inherent in a radical chain polymerization reaction to detect molecular recognition. Polymerization-based amplification is shown to yield a macroscopically observable polymer, easily visible to the unaided eye, as a result of as few as approximately 1,000 recognition events (10 zeptomoles). Design and synthesis of a dual-functional macromolecule that is capable both of selective recognition and of initiating a polymerization reaction was central to obtaining high sensitivity and eliminating the need for any detection equipment. Herein, we detail the design criteria that were used and compare our findings with those obtained using enzymatic amplification. Most excitingly, this new approach is general in that it is readily adaptable to facile detection at very low levels of specific biological interactions of any kind.     

PCR detection of soy ingredients in bread

Bread may contain soy ingredients to variable extends. The nature of this soy may be genetically modified, or the ingredient may cause allergic reactions in sensitive patients. PCR is a powerful tool to detect the presence of soy in food products. Major prerequisite for a PCR analysis is DNA of good quality and quantity. The persistence of soy DNA during bread making was evaluated using different amounts of different soy ingredients. Agarose gel electrophoresis of the samples taken during the baking process reveal that DNA is degraded, but subsequent PCR detection remains possible. Results, however, greatly depend on the type of ingredient and the amount present. Lower detection limits were obtained for full-fat and defatted soybean flours than those for toasted soybean flour and soy fibre samples. Samples taken at different places in the bread, however, reveal that sampling strategy may influence the PCR results.     

A meta-analysis on the effect of dietary application of exogenous fibrolytic enzymes on the performance of dairy cows

The aim of this study was to use meta-analytical methods to estimate effects of adding exogenous fibrolytic enzymes (EFE) to dairy cow diets on their performance and to determine which factors affect the response. Fifteen studies with 17 experiments and 36 observations met the study selection criteria for inclusion in the meta-analysis. The effects were compared by using random-effect models to examine the raw mean difference (RMD) and standardized mean difference between EFE and control treatments after both were weighted with the inverse of the study variances. Heterogeneity sources evaluated by meta-regression included experimental duration, EFE type and application rate, form (liquid or solid), and method (application to the forage, concentrate, or total mixed ration). Only the cellulase-xylanase (C-X) enzymes had a substantial number of observations (n = 13 studies). Application of EFE, overall, did not affect dry matter intake, feed efficiency but tended to increase total-tract dry matter digestibility and neutral detergent fiber digestibility (NDFD) by relatively small amounts (1.36 and 2.30%, respectively, or <0.31 standard deviation units). Application of EFE increased yields of milk (0.83 kg/d), 3.5% fat-corrected milk (0.55 kg/d), milk protein (0.03 kg/d), and milk lactose (0.05 kg/d) by moderate to small amounts (<0.30 standard deviation units). Low heterogeneity (I?² statistic <25%) was present for yields and concentrations of milk fat and protein and lactose yield. Moderate heterogeneity (I?² = 25 to 50%) was detected for dry matter intake, milk yield, 3.5% fat-corrected milk, and feed efficiency (kg of milk/kg of dry matter intake), whereas high heterogeneity (I?² > 50%) was detected for total-tract dry matter digestibility and NDFD. Milk production responses were higher for the C-X enzymes (RMD = 1.04 kg/d; 95% confidence interval: 0.33 to 1.74), but were still only moderate, about 0.35 standardized mean difference. A 24% numerical increase in the RMD resulting from examining only C-X enzymes instead of all enzymes (RMD = 1.04 vs. 0.83 kg/d) suggests that had more studies met the inclusion criteria, the C-X enzymes would have statistically increased the milk response relative to that for all enzymes. Increasing the EFE application rate had no effect on performance measures. Application of EFE to the total mixed ration improved only milk protein concentration, and application to the forage or concentrate had no effect. Applying EFE tended to increase dry matter digestibility and NDFD and increased milk yield by relatively small amounts, reflecting the variable response among EFE types.     

RE in Rural Nicaragua

Sunrise is taking on a whole new meaning in rural Nicaragua thanks to solar energy technologies. In a country where urban migration is gaining momentum (1%+ annually), renewable energy is gaining national acceptance for meeting and improving basic needs in rural areas. Lack of these basic needs is a major factor in poverty and poor health, resulting in urban flight in search of a better life and social services. Kathy Dickerson from the Global Health Alliance (GHA) describes the efforts of this U.S.-based non-profit organization to bring renewable energy, and opportunities, to rural villages in the region.     

Where is the ‘Social’ in Constructions of ‘Liveability’? Exploring Community,Social Interaction and Social Cohesion in Changing Urban Environments

Ongoing changes in the urban environment have renewed interest in the transformation of cities and suburbs as liveable places. This article examines the limitations inherent in a functional (objective) notion of liveability that commonly underpins government policy directions. Through an examination of key debates in the literature we consider how the delivery of the social (subjective) dimension of liveability, linked to community, social interaction and social cohesion, poses unique challenges for policy makers, urban planners and developers. We argue for a deeper understanding of the social constructs of liveability that acknowledges the complexity of changing urban environments in contemporary society.     

Biocatalytic detoxification of 2-chloroethyl ethyl sulfide

Rhodococcus rhodochrous IGTS8 (ATCC 53968) was shown to be capable of utilizing 2-chloroethyl ethyl sulphide (CEES) as the sole source of sulphur for microbial growth. 2-Chloroethanol and a compound tentatively identified as 2-chloroethanesulfinic acid have been detected as metabolites. This demonstrates that carbon—sulphur bonds were cleaved in CEES prior to hydrolysis of the chlorine atom. These data indicate that Rhodococcus rhodochrous IGTS8 may be useful for the biodetoxification of the chemical warfare agent mustard (2,2′ dichlorodiethyl sulphide).     

A new definition of threshold voltage in Tunnel FETs

This work reports on the physical definition and extraction of threshold voltage in Tunnel FETs (field effect transistors) based on numerical simulation data. It is shown that the Tunnel FET has the outstanding property of having two threshold voltages: one in terms of gate voltage, V_TG, and one in terms of drain voltage, V_TD. These threshold voltages can be physically defined based on the transition between a quasi-exponential dependence, and a linear dependence of the drain current on V_GS or V_DS, and by extension, on the saturation of the tunneling energy barrier width narrowing. The extractions of V_TG and V_TD are performed based on the transconductance change method in the double gate Tunnel FET with a high-k dielectric, and a systematic comparison with the constant current method is reported. The effect of gate length scaling on these Tunnel FETs’ threshold voltages, as well as the dependence of V_TG on applied drain voltage and V_TD on applied gate voltage, are investigated.     

Seasonal distribution of total and pathogenic Vibrio parahaemolyticus in Chesapeake Bay oysters and waters

The objectives of this study were to investigate the seasonal distribution of total and pathogenic Vibrio parahaemolyticus in the Chesapeake Bay oysters and waters, and to determine the degree of association between V. parahaemolyticus densities and selected environmental parameters. Oyster and water samples were collected monthly from three sites in Chesapeake Bay, Maryland from November 2004 through October 2005. During collection of samples, water temperature, salinity, turbidity, dissolved oxygen, pH, chlorophyll a, and fecal coliform levels in oysters were also determined. V. parahaemolyticus levels were enumerated by a quantitative direct-plating method followed by DNA colony hybridization; presence/absence was further determined by overnight broth enrichment followed by either standard colony isolation or real-time PCR. The thermolabile hemolysin (tlh) gene and thermostable direct hemolysin (tdh) gene were targeted for detection of total and pathogenic V. parahaemolyticus, respectively, for both direct plating and enrichment. The thermostable related hemolysin (trh) gene, which is a presumptive pathogenicity marker, was targeted only for the enrichment approach. By direct plating, colonies producing tlh signals were detected in 79% of oyster samples at densities ranging from 1.5x10(1) to 6.0x10(2) CFU/g. Pathogenic V. parahaemolyticus (tdh+) was detected in 3% (level was 10 CFU/g) of oyster samples while no V. parahaemolyticus was detected in water samples. By the enrichment approach with standard colony isolation, 67% of oyster and 55% of water samples (n=33) were positive for total V. parahaemolyticus, and all samples were negative for pathogenic V. parahaemolyticus. In contrast, enrichment followed by real-time PCR detected tlh, tdh and trh in 100%, 20% and 40% of oyster and 100%, 13% and 40% of water enrichments collected from June to October 2005, respectively. V. parahaemolyticus densities in oysters varied seasonally and were found to be positively correlated with water temperature, turbidity, and dissolved oxygen.     

Microbial diversity in Tunisian olive fermentation brine as evaluated by small subunit rRNA - Single strand conformation polymorphism analysis

The microbial diversity of a Tunisian olive fermentation brine was analysed using a culture-independent approach based on the polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP). SSCP patterns show a remarkably simple microbial community but higher for bacterial community than for the eukaryotic community. This study did not show the presence of archaeal populations. After PCR amplification, two small subunit (SSU) rRNA clone libraries of Bacteria and Eucarya populations were established. Three bacteria and only one eukaryotic phylotype were identified. Two dominant bacteria showed 100% phylogenetic similarity to the 16S rRNA sequences of Lactobacillus plantarum and Lactobacillus collinoides and represent 85% of bacterial community. The third bacteria phylotype was phylogenetically close related to the 16S rRNA sequence of a moderately halophilic bacterium belonging to the class gamma Proteobacteria. The dominant eukaryotic phylotype was identified as a Pichia membranaefaciens.