How many mountains can we mine? Assessing the regional degradation of central appalachian rivers by surface coal mining

Surface coal mining is the dominant form of land cover change in Central Appalachia, yet the extent to which surface coal mine runoff is polluting regional rivers is currently unknown. We mapped surface mining from 1976 to 2005 for a 19,581 km(2) area of southern West Virginia and linked these maps with water quality and biological data for 223 streams. The extent of surface mining within catchments is highly correlated with the ionic strength and sulfate concentrations of receiving streams. Generalized additive models were used to estimate the amount of watershed mining, stream ionic strength, or sulfate concentrations beyond which biological impairment (based on state biocriteria) is likely. We find this threshold is reached once surface coal mines occupy >5.4% of their contributing watershed area, ionic strength exceeds 308 μS cm(-1), or sulfate concentrations exceed 50 mg L(-1). Significant losses of many intolerant macroinvertebrate taxa occur when as little as 2.2% of contributing catchments are mined. As of 2005, 5% of the land area of southern WV was converted to surface mines, 6% of regional streams were buried in valley fills, and 22% of the regional stream network length drained watersheds with >5.4% of their surface area converted to mines.     

Combining fuzzy querying of imprecise data and predictive microbiology using category-based reasoning for prediction of the possible microbial spoilage in foods: application to Listeria monocytogenes

Various predictive models of microbial behavior have been created and extensive data collection has been done by numerous private or public laboratories. However, significant differences between predicted and observed values in foods have been observed and need to be stressed, understood and explained as much as possible. In this paper, we present a software tool (currently at the level of a prototype) able: (i) to store in a database all relevant information expressed on one hand as qualitative or quantitative data and on the other hand as precise or imprecise data; (ii) to retrieve the more relevant information from the database using queries where criteria may be expressed as fuzzy values in order to enhance the flexibility of the search: (iii) to compute, in addition to the nearest data, an estimation of searched values using statistical models. The architecture of this software tool is structured as a category-based reasoning system. Example queries about Listeria monocytogenes (L. monocytogenes) illustrate the functionalities of this tool.     

Effective use of nisin to control Bacillus and Clostridium spoilage of a pasteurized mashed potato product

Heat-resistant spore-forming bacteria such as Bacillus and Clostridium can survive and grow in cooked potato products. This situation represents both a public health problem and an economic problem. The natural food preservative nisin is used in heat-treated foods to prevent the growth of such bacteria. A cocktail of Clostridium sporogenes and Clostridium tyrobutyricum spores was inoculated into cooked mashed potatoes, which were vacuum packed, pasteurized, and incubated at 8 and 25 degrees C. The shelf life of the mashed potatoes at 25 degrees C was extended by at least 58 days with the addition 6.25 microg of nisin per g. At 8 degrees C, in control samples not containing nisin, the natural contaminant Bacillus grew, but the inoculated Clostridium strains did not until the temperature was raised to 20 degrees C after 39 days. No bacterial growth occurred in nisin-containing samples. The shelf life of the mashed potatoes was extended by at least 30 days with 6.25 microg of nisin per g. In trials involving a cocktail of Bacillus cereus and Bacillus subtilis strains, 6.25 microg of nisin per g extended the shelf life of mashed potato samples that were not vacuum packed by at least 27 days at 8 degrees C. At 25 degrees C, 25 microg of nisin per g extended shelf life by a similar period. Shelf life extension was also observed at lower nisin levels. Microbiological analysis of the mashed potato ingredients showed that a high spore level was associated with the onion powder. It is emphasized that the preservative and the ingredients must be well mixed to ensure good nisin efficacy. Nisin remained at effective levels after pasteurization, and good retention was observed throughout the shelf life of the mashed potatoes.     

Future developments in assisted reproduction in humans

The advent of human in vitro fertilization (IVF) over 30 years ago has made the oocyte and preimplantation embryo uniquely accessible. This accessibility has given rise to new micromanipulation techniques, such as intracytoplasmic sperm injection for treatment of male infertility, as well as embryo biopsy for preimplantation diagnosis of both genetic disease and aneuploidy, a major cause of early embryo demise and miscarriage. In the UK, average pregnancy rates after IVF and embryo transfer are < 25%, even after transfer of several embryos. Unfortunately, a third of these pregnancies involve multiple gestations. Research is currently focusing on methods to improve IVF success rates while reducing twin and triplet pregnancies and their associated increased morbidity and mortality. One approach is to develop screening methods to identify the most viable embryos, so that transfer of fewer healthy embryos will result in a higher proportion of singleton pregnancies. Screening methods include optimizing culture conditions for prolonged culture and selection of viable blastocysts for transfer, or embryo biopsy and aneuploidy screening. Assisted reproduction is also increasingly important in other branches of medicine: survival rates for cancer sufferers are improving continually and there is now a significant need for approaches to preserve fertility after sterilizing chemo-and radiotherapy treatment. Techniques for cryopreserving male and female gametes or gonadal tissue are being developed, although systems to grow and mature these gametes are in their infancy. Finally, there are also concerns regarding the safety of these new assisted reproductive technologies.     

Effect of UV irradiation on organic matter extracted from treated Ohio River water studied through the use of electrospray mass spectrometry

Ohio River water was treated by settling, sand filtration, and granular activated carbon filtration. It was then irradiated by low-pressure (monochromatic) and medium-pressure (polychromatic) UV lamps to investigate the effects of UV irradiation on the extracted organic matter (EOM). When the EOM, collected by solid phase extraction cartridges, was analyzed by conventional UV spectroscopy and size exclusion chromatography (SEC), no significant changes in the EOM were revealed for various UV doses. Positive and negative electrospray ionization mass spectrometry (ESI-MS) of the EOM produced mass spectra that vary significantly with UV dose. The UV dosage conditions also appear to affect the reactivity of the EOM to subsequent chlorination. The magnitude of the spectral changes is generally greater for medium-pressure lamps than for low pressure and increases with UV exposure. Based on the observed MS peaks, the changes may be due to the presence of lignin, resulting perhaps from photooxidation and/or photo rearrangement of macromolecules in the sample. When chlorination is used for secondary disinfection, these results suggest that it may be important to consider the effects of UV irradiation on the organic matter in the water before applying UV disinfection technology to a particular source water.     

Attachment and biofilm formation by Escherichia coli O157:H7 at different temperatures, on various food-contact surfaces encountered in beef processing

Escherichia coli O157:H7 attached to beef-contact surfaces found in beef fabrication facilities may serve as a source of cross-contamination. This study evaluated E. coli O157:H7 attachment, survival and growth on food-contact surfaces under simulated beef processing conditions. Stainless steel and high-density polyethylene surfaces (2 × 5 cm) were individually suspended into each of three substrates inoculated (6 log CFU/ml or g) with E. coli O157:H7 (rifampicin-resistant, six-strain composite) and then incubated (168 h) statically at 4 or 15 °C. The three tested soiling substrates included sterile tryptic soy broth (TSB), unsterilized beef fat-lean tissue (1:1 [wt/wt]) homogenate (10% [wt/wt] with sterile distilled water) and unsterilized ground beef. Initial adherence/attachment of E. coli O157:H7 (0.9 to 2.9 log CFU/cm²) on stainless steel and high-density polyethylene was not affected by the type of food-contact surface but was greater (p < 0.05) through ground beef. Adherent and suspended E. coli O157:H7 counts increased during storage at 15 °C (168 h) by 2.2 to 5.4 log CFU/cm² and 1.0 to 2.8 log CFU/ml or g, respectively. At 4 °C (168 h), although pathogen levels decreased slightly in the substrates, numbers of adherent cells remained constant on coupons in ground beef (2.4 to 2.5 log CFU/cm²) and increased on coupons in TSB and fat-lean tissue homogenate by 0.9 to 1.0 and 1.7 to 2.0 log CFU/cm², respectively, suggesting further cell attachment. The results of this study indicate that E. coli O157:H7 attachment to beef-contact surfaces was influenced by the type of soiling substrate and temperature. Notably, attachment occurred not only at a temperature representative of beef fabrication areas during non-production hours (15 °C), but also during cold storage (4 °C) temperatures, thus, rendering the design of more effective sanitation programs necessary.     

Factors associated with carcass contamination by Campylobacter at slaughterhouse in cecal-carrier broilers

A study was conducted in 2009 to identify risk factors of Campylobacter spp. transmission from the digestive tract to the carcasses of standard broilers (slaughter age: 37 day, carcass weight: 1.3 kg on average). Counts of Campylobacter were performed on pools of 10 ceca and 10 neck-skins from 108 Campylobacter ceca-positive batches in three slaughterhouses. Technical and health data also was collected on the broilers: age, size, carcass weight (mean and standard deviation), condemnation rate, mortality rate and nature of treatment during the rearing period.Cecal counts varied from 4.8 to 10.2 log₁₀ cfu/g. In seventeen batches (15.7%), the skin count was below the detection limit. In the 91 batches with positive neck-skin test results, the counts varied from 2.0 to 5.2 log₁₀ cfu/g. Standard deviation of carcass weight, condemnation rate, slaughter rate and cecal count were significantly lower and growth rate higher in the 17 batches where neck-skin results were not detected positive. Multivariate analysis showed that batches with higher standard deviation of carcass weight were 5 to 9 fold more at risk of having detectable carcass contamination. Among the 91 positive neck-skin batches, only slaughter rate and cecal counts were found to have a significant but limited effect on the level of neck-skin contamination. As far as body weight homogeneity may be affected by disease, better health control can contribute to a reduction of the contamination of the broiler carcasses in Campylobacter carrier batches.     

Saccharomyces cerevisiae S288C genome annotation: a working hypothesis

The S. cerevisiae genome is the most well-characterized eukaryotic genome and one of the simplest in terms of identifying open reading frames (ORFs), yet its primary annotation has been updated continually in the decade since its initial release in 1996 (Goffeau et al., 1996). The Saccharomyces Genome Database (SGD; www.yeastgenome.org) (Hirschman et al., 2006), the community-designated repository for this reference genome, strives to ensure that the S. cerevisiae annotation is as accurate and useful as possible. At SGD, the S. cerevisiae genome sequence and annotation are treated as a working hypothesis, which must be repeatedly tested and refined. In this paper, in celebration of the tenth anniversary of the completion of the S. cerevisiae genome sequence, we discuss the ways in which the S. cerevisiae sequence and annotation have changed, consider the multiple sources of experimental and comparative data on which these changes are based, and describe our methods for evaluating, incorporating and documenting these new data.     

Effect of pasture versus indoor feeding systems on quality characteristics,nutritional composition,and sensory and volatile properties of full-fat Cheddar cheese

The purpose of this study was to investigate the effects of pasture-based versus indoor total mixed ration (TMR) feeding systems on the chemical composition, quality characteristics, and sensory properties of full-fat Cheddar cheeses. Fifty-four multiparous and primiparous Friesian cows were divided into 3 groups (n = 18) for an entire lactation. Group 1 was housed indoors and fed a TMR diet of grass silage, maize silage, and concentrates; group 2 was maintained outdoors on perennial ryegrass only pasture (GRS); and group 3 was maintained outdoors on perennial ryegrass/white clover pasture (CLV). Full-fat Cheddar cheeses were manufactured in triplicate at pilot scale from each feeding system in September 2015 and were examined over a 270-d ripening period at 8°C. Pasture-derived feeding systems were shown to produce Cheddar cheeses yellower in color than that of TMR, which was positively correlated with increased cheese β-carotene content. Feeding system had a significant effect on the fatty acid composition of the cheeses. The nutritional composition of Cheddar cheese was improved through pasture-based feeding systems, with significantly lower thrombogenicity index scores and a greater than 2-fold increase in the concentration of vaccenic acid and the bioactive conjugated linoleic acid C18:2 cis-9,trans-11, whereas TMR-derived cheeses had significantly higher palmitic acid content. Fatty acid profiling of cheeses coupled with multivariate analysis showed clear separation of Cheddar cheeses derived from pasture-based diets (GRS or CLV) from that of a TMR system. Such alterations in the fatty acid profile resulted in pasture-derived cheeses having reduced hardness scores at room temperature. Feeding system and ripening time had a significant effect on the volatile profile of the Cheddar cheeses. Pasture-derived Cheddar cheeses had significantly higher concentrations of the hydrocarbon toluene, whereas TMR-derived cheese had significantly higher concentration of 2,3-butanediol. Ripening period resulted in significant alterations to cheese volatile profiles, with increases in acid-, alcohol-, aldehyde-, ester-, and terpene-based volatile compounds. This study has demonstrated the benefits of pasture-derived feeding systems for production of Cheddar cheeses with enhanced nutritional and rheological quality compared with a TMR feeding system.     

Interlaboratory comparison of real-time PCR protocols for quantification of general fecal indicator bacteria

The application of quantitative real-time PCR (qPCR) technologies for the rapid identification of fecal bacteria in environmental waters is being considered for use as a national water quality metric in the United States. The transition from research tool to a standardized protocol requires information on the reproducibility and sources of variation associated with qPCR methodology across laboratories. This study examines interlaboratory variability in the measurement of enterococci and Bacteroidales concentrations from standardized, spiked, and environmental sources of DNA using the Entero1a and GenBac3 qPCR methods, respectively. Comparisons are based on data generated from eight different research facilities. Special attention was placed on the influence of the DNA isolation step and effect of simplex and multiplex amplification approaches on interlaboratory variability. Results suggest that a crude lysate is sufficient for DNA isolation unless environmental samples contain substances that can inhibit qPCR amplification. No appreciable difference was observed between simplex and multiplex amplification approaches. Overall, interlaboratory variability levels remained low (<10% coefficient of variation) regardless of qPCR protocol.