Protein quality and quantity influence the effect of dietary fat on weight gain and tissue partitioning via host-microbiota changes.

We investigated how protein quantity (10%-30%) and quality (casein and whey) interact with dietary fat (20%-55%) to affect metabolic health in adult mice. Although dietary fat was the main driver of body weight gain and individual tissue weight, high (30%) casein intake accentuated and high whey intake reduced the negative metabolic aspects of high fat. Jejunum and liver transcriptomics revealed increased intestinal permeability, low-grade inflammation, altered lipid metabolism, and liver dysfunction in casein-fed but not whey-fed animals. These differential effects were accompanied by altered gut size and microbial functions related to amino acid degradation and lipid metabolism. Fecal microbiota transfer confirmed that the casein microbiota increases and the whey microbiota impedes weight gain. These data show that the effects of dietary fat on weight gain and tissue partitioning are further influenced by the quantity and quality of the associated protein, primarily via effects on the microbiota.

Physiological and transcriptional response to drought stress among bioenergy grass Miscanthus species.

BACKGROUND: Miscanthus is a commercial lignocellulosic biomass crop owing to its high biomass productivity, resilience and photosynthetic capacity at low temperature. These qualities make Miscanthus a particularly good candidate for temperate marginal land, where yields can be limited by insufficient or excessive water supply. Differences in response to water stress have been observed among Miscanthus species, which correlated to origin. In this study, we compared the physiological and molecular responses among Miscanthus species under excessive (flooded) and insufficient (drought) water supply in glasshouse conditions. RESULTS: A significant biomass loss was observed under drought conditions in all genotypes. M. x giganteus showed a lower reduction in biomass yield under drought conditions compared to the control than the other species. Under flooded conditions, biomass yield was as good as or better than control conditions in all species. 4389 of the 67,789 genes (6.4%) in the reference genome were differentially expressed during drought among four Miscanthus genotypes from different species. We observed the same biological processes were regulated across Miscanthus species during drought stress despite the DEGs being not similar. Upregulated differentially expressed genes were significantly involved in sucrose and starch metabolism, redox, and water and glycerol homeostasis and channel activity. Multiple copies of the starch metabolic enzymes BAM and waxy GBSS-I were strongly up-regulated in drought stress in all Miscanthus genotypes, and 12 aquaporins (PIP1, PIP2 and NIP2) were also up-regulated in drought stress across genotypes. CONCLUSIONS: Different phenotypic responses were observed during drought stress among Miscanthus genotypes from different species, supporting differences in genetic adaption. The low number of DEGs and higher biomass yield in flooded conditions supported Miscanthus use in flooded land. The molecular processes regulated during drought were shared among Miscanthus species and consistent with functional categories known to be critical during drought stress in model organisms. However, differences in the regulated genes, likely associated with ploidy and heterosis, highlighted the value of exploring its diversity for breeding.

Clinical presentation and immune characteristics in first-lactation Holstein-Friesian cows following intramammary infection with genotypically distinct Staphylococcus aureus strains.

Staphylococcus aureus is an important cause of bovine mastitis, and intramammary infections caused by this pathogen are often characterized as mild, chronic, or persistent. The strains of Staph. aureus associated with mastitis belong to several distinct bovine-adapted bacterial lineages. Studies of host-pathogen interactions have demonstrated that significant differences exist between Staph. aureus strains and lineages in their ability to internalize and to elicit expression of chemokines and pro-inflammatory mediators in bovine cells in vitro. To determine the effect of bacterial strain on the response to intramammary infection in vivo, 14 disease-free, first-lactation cows were randomly allocated to 2 groups and challenged with Staph. aureus strain MOK023 (belonging to CC97) or MOK124 (belonging to CC151). Clinical signs of infection, as well as somatic cell count (SCC), bacterial load, IL-8 and IL-1ß in milk, anti-Staph. aureus IgG in milk and serum, anti-Staph. aureus IgA in milk, and white blood cell populations in milk and blood were monitored for 30 d after the challenge. Cows infected with MOK023 generally developed subclinical mastitis, whereas cows infected with MOK124 generally developed clinical mastitis. Milk yield was reduced to a greater extent in response to infection with MOK124 compared with MOK023 in the first week of the study. Significantly higher SCC, IL-8, and IL-1ß in milk as well as higher anti-Staph. aureus IgG and IgA in milk and anti-Staph. aureus IgG in serum were also observed in response to MOK124 compared with the response to MOK023. Higher proportions of neutrophils were observed in milk of animals infected with MOK124 than in animals infected with MOK023. Higher neutrophil concentration in blood was also observed in the MOK124 group compared with the MOK023 group. Overall, the results indicate that the outcome of mastitis mediated by Staph. aureus is strain dependent.

Determination of 42 mycotoxins in oats using a mechanically assisted QuEChERS sample preparation and UHPLC-MS/MS detection.

A method was developed and validated for the simultaneous determination of 42 mycotoxins in oats. The method includes all the mycotoxins listed under Commission Regulation 1881/2006 and Commission Recommendation 165/2013, the emerging mycotoxins (beauvericin, alternariol, alternariol-methyl-ether and enniatins), and two masked metabolites, namely deoxynivalenol-3-glucoside and T-2-glucoside. The method also focuses on a wide range of analytes of toxicological interest. The sample preparation involved extraction with an aqueous acetic acid solution and acetonitrile, followed by QuEChERS with mechanically assisted vibrational shaking. No further clean-up steps were employed, and analysis was performed using ultra-high performance liquid chromatography coupled to tandem mass spectrometry (UHPLC-MS/MS). Trueness ranged between 78% and 158%, while precision ranged from 1.7% to 49.9% under within-laboratory reproducibility conditions. Beside the high degree of accuracy and sample throughput provided, the method can be applied to a large number of compounds currently not regulated, thus generating knowledge and for risk assessment purposes.

Purulent vaginal discharge diagnosed in pasture-based Holstein-Friesian cows at 21 days postpartum is influenced by previous lactation milk yield and results in diminished fertility.

In a subset of dairy cows, prolonged pathological uterine inflammation results in purulent vaginal discharge (PVD), which can have negative consequences for both fertility and milk production. However, unlike for intensive systems, analysis of the effects of PVD in predominantly pasture-based herds is limited. The objective of this study was to assess the effect of PVD in spring-calving, pasture-based dairy cows on production and reproduction indices, stratified according to previous full-lactation milk yield. We assessed clinical disease as defined by vaginal mucus score (VMS) in 440 Holstein-Friesian cows from 5 farms. Cows were categorized as healthy (VMS 0) or having PVD (VMS 1-3) at 21 d postpartum. We recorded 305-d milk, milk protein, and milk fat yields (kg) before and after disease diagnosis, as well as fertility data, such as services per conception and the calving-conception period (CCP). Using SAS 9.4 (SAS Institute Inc., Cary, NC), we analyzed data using PROC MIXED, PROC PHREG, and PROC LOGISTIC to determine the least squares means differences and hazard and odds ratios between the groups, respectively. Overall, a 60% prevalence of PVD was recorded at 21 d postpartum. Milk yield and milk constituents were similar between all VMS categories and between healthy cows and cows with PVD. Although cows in the 4 VMS categories had statistically similar CCP, cows with PVD had a significantly longer CCP than healthy cows on average (9 d). The hazard ratio for cows with PVD was 0.66, indicating a 34% higher risk of a prolonged CCP than healthy cows. Odds ratio analysis determined that cows with PVD were 3 times more likely not to conceive at all, twice as likely not to conceive at first service, twice as likely not to conceive by 100 d postpartum, and 3 times more likely to fail to conceive before 150 d postpartum compared with healthy cows. Cows were retrospectively categorized as having low or high milk yield, based on whether they were above or below the median 305-d milk yield of the study population (6,571 kg) in the lactation before vaginal mucus scoring. Based on a univariate odds ratio, high-yield cows were 1.6 times more likely to present with PVD in the subsequent lactation. The number of services per conception did not differ between healthy and PVD cows in the low- and high-yield groups. In the high-yield group, cows with PVD were 4.9 times more likely not to conceive, 2.7 times more likely to require multiple services to conceive, 2.1 times more likely to remain not pregnant by 100 d postpartum, and 4.4 times more likely to remain not pregnant by 150 d postpartum. The CCP was also significantly longer in cows with PVD than their healthy counterparts (115.9 ± 4.9 and 104 ± 7.4 d, respectively). In conclusion, PVD significantly increased the CCP in all cows, but to a greater extent in cows with a high milk yield in the lactation before disease diagnosis.

Transcriptome characterization and differentially expressed genes under flooding and drought stress in the biomass grasses Phalaris arundinacea and Dactylis glomerata.

BACKGROUND AND AIMS: Perennial grasses are a global resource as forage, and for alternative uses in bioenergy and as raw materials for the processing industry. Marginal lands can be valuable for perennial biomass grass production, if perennial biomass grasses can cope with adverse abiotic environmental stresses such as drought and waterlogging. METHODS: In this study, two perennial grass species, reed canary grass (Phalaris arundinacea) and cocksfoot (Dactylis glomerata) were subjected to drought and waterlogging stress to study their responses for insights to improving environmental stress tolerance. Physiological responses were recorded, reference transcriptomes established and differential gene expression investigated between control and stress conditions. We applied a robust non-parametric method, RoDEO, based on rank ordering of transcripts to investigate differential gene expression. Furthermore, we extended and validated vRoDEO for comparing samples with varying sequencing depths. KEY RESULTS: This allowed us to identify expressed genes under drought and waterlogging whilst using only a limited number of RNA sequencing experiments. Validating the methodology, several differentially expressed candidate genes involved in the stage 3 step-wise scheme in detoxification and degradation of xenobiotics were recovered, while several novel stress-related genes classified as of unknown function were discovered. CONCLUSIONS: Reed canary grass is a species coping particularly well with flooding conditions, but this study adds novel information on how its transcriptome reacts under drought stress. We built extensive transcriptomes for the two investigated C3 species cocksfoot and reed canary grass under both extremes of water stress to provide a clear comparison amongst the two species to broaden our horizon for comparative studies, but further confirmation of the data would be ideal to obtain a more detailed picture.

Growth under cold conditions in a wide perennial ryegrass panel is under tight physiological control.

BACKGROUND: Perennial ryegrass is a cool-season grass species from the family Poaceae and is widely cultivated in temperate regions because it exhibits rapid growth and establishment, and possesses high forage quality. The extension of the growing season in Ireland in spring and autumn is a breeding target to make farming more profitable since a grass-fed diet based on grazing is the cheapest way of nutrition for ruminants. METHODS: Fifty-seven perennial ryegrass accessions were screened for their ability to grow under typical Irish spring conditions as taken from long term temperature records in controlled climate chambers. They were grown in low temperature (8 °C/2 °C day/night) and control conditions (15 °C/8 °C day/night) in three consecutive independent experiments. Fresh weight, height, chlorophyll content and electrolyte leakage were measured, and these parameters were used to rank plant performance under low temperature growth conditions. RESULTS: The results showed that height, yield and electrolyte leakage are excellent measures for the impact of cold stress tolerance. Little variation in growth was seen under cold stress, but a wide variety of responses were observed under control conditions. DISCUSSION: Our results suggest that cold stress is under tight physiological control. Interestingly, the various genotypes responded differentially to more amenable control conditions, indicating that a quick response to more amenable growth conditions is a better target for breeding programmes.

Author Correction: Influence of soil moisture on codenitrification fluxes from a urea-affected pasture soil.

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Influence of soil moisture on codenitrification fluxes from a urea-affected pasture soil.

Intensively managed agricultural pastures contribute to N2O and N2 fluxes resulting in detrimental environmental outcomes and poor N use efficiency, respectively. Besides nitrification, nitrifier-denitrification and heterotrophic denitrification, alternative pathways such as codenitrification also contribute to emissions under ruminant urine-affected soil. However, information on codenitrification is sparse. The objectives of this experiment were to assess the effects of soil moisture and soil inorganic-N dynamics on the relative contributions of codenitrification and denitrification (heterotrophic denitrification) to the N2O and N2 fluxes under a simulated ruminant urine event. Repacked soil cores were treated with 15N enriched urea and maintained at near saturation (-1 kPa) or field capacity (-10 kPa). Soil inorganic-N, pH, dissolved organic carbon, N2O and N2 fluxes were measured over 63 days. Fluxes of N2, attributable to codenitrification, were at a maximum when soil nitrite (NO2-) concentrations were elevated. Cumulative codenitrification was higher (P = 0.043) at -1 kPa. However, the ratio of codenitrification to denitrification did not differ significantly with soil moisture, 25.5 ± 15.8 and 12.9 ± 4.8% (stdev) at -1 and -10 kPa, respectively. Elevated soil NO2- concentrations are shown to contribute to codenitrification, particularly at -1 kPa.

The efficacy of different cleaning and disinfection procedures to reduce Salmonella and Enterobacteriaceae in the lairage environment of a pig abattoir.

This study investigated several cleaning and disinfection protocols for their ability to eliminate Salmonella and to reduce levels of Enterobacteriaceae, within the lairage pens of a commercial pig abattoir. Eight protocols were evaluated in each of 12 lairage pens at the end of the slaughtering day on 3 occasions (36 pens/protocol): (P1) high-pressure cold water wash (herein referred to as high-pressure wash); (P2) high-pressure wash followed by a quaternary ammonium compound (QAC)-based disinfectant without rinsing; (P3) high-pressure wash followed by a chlorocresol-based disinfectant without rinsing; (P4) high-pressure wash followed by a sodium hydroxide/sodium hypochlorite detergent with rinsing; (P5) P4 followed by P2; (P6) P4 followed by P3; (P7) P5 with drying for 24-48h; and (P8) P6 with drying for 24-48h. Two floor swabs and one wall swab were taken from each lairage pen before and after each protocol was applied, and examined for the presence of Salmonella and enumeration of Enterobacteriaceae. High-pressure washing alone (P1) did not reduce the prevalence of Salmonella in the lairage pens. When high-pressure washing, the probability of detecting Salmonella following application of the chlorocresol-based disinfectant (P3) was lower than with the QAC-based disinfectant, P2 (14.2% versus 34.0%, respectively; p<0.05). The probability of detecting Salmonella after the combined use of detergent and the chlorocresol-based disinfectant (P6) was also lower than application of detergent followed by the QAC-based disinfectant, P5 (2.2% versus 17.1%, respectively; p<0.05). Drying of pens (P7 and P8) greatly reduced the probability of detecting Salmonella. Only 3.8% of swabs were Salmonella-positive 48h after cleaning with detergent and the QAC-based disinfectant (P7); while an eradication of Salmonella was achieved 24h after cleaning with detergent and the chlorocresol-based disinfectant, P8. A reduction in Enterobacteriaceae counts to below the limit of detection (LOD; 10CFU/cm2) was achieved following cleaning with detergent and disinfection with the chlorocresol-based disinfectant, regardless of drying (p<0.05), whereas, applying detergent and the QAC-based disinfectant (P7) did not reduce Enterobacteriaceae counts to below the LOD. Therefore ensuring that lairage pens are allowed to dry after intensive cleaning with detergent and a chlorocresol-based disinfectant is recommended as the most effective hygiene routine to eliminate Salmonella and reduce Enterobacteriaceae counts.

Transcriptomic response of maize primary roots to low temperatures at seedling emergence.

BACKGROUND: Maize (Zea mays) is a C4 tropical cereal and its adaptation to temperate climates can be problematic due to low soil temperatures at early stages of establishment. METHODS: In the current study we have firstly investigated the physiological response of twelve maize varieties, from a chilling condition adapted gene pool, to sub-optimal growth temperature during seedling emergence. To identify transcriptomic markers of cold tolerance in already adapted maize genotypes, temperature conditions were set below the optimal growth range in both control and low temperature groups. The conditions were as follows; control (18 °C for 16 h and 12 °C for 8 h) and low temperature (12 °C for 16 h and 6 °C for 8 h). Four genotypes were identified from the condition adapted gene pool with significant contrasting chilling tolerance. RESULTS: Picker and PR39B29 were the more cold-tolerant lines and Fergus and Codisco were the less cold-tolerant lines. These four varieties were subjected to microarray analysis to identify differentially expressed genes under chilling conditions. Exposure to low temperature during establishment in the maize varieties Picker, PR39B29, Fergus and Codisco, was reflected at the transcriptomic level in the varieties Picker and PR39B29. No significant changes in expression were observed in Fergus and Codisco following chilling stress. A total number of 64 genes were differentially expressed in the two chilling tolerant varieties. These two varieties exhibited contrasting transcriptomic profiles, in which only four genes overlapped. DISCUSSION: We observed that maize varieties possessing an enhanced root growth ratio under low temperature were more tolerant, which could be an early and inexpensive measure for germplasm screening under controlled conditions. We have identified novel cold inducible genes in an already adapted maize breeding gene pool. This illustrates that further varietal selection for enhanced chilling tolerance is possible in an already preselected gene pool.

Effect of strategic administration of an encapsulated blend of formic acid, citric acid, and essential oils on Salmonella carriage, seroprevalence, and growth of finishing pigs.

Controlling Salmonella at farm level can act as the first line of defence in reducing salmonellosis from pork. This study investigated the efficacy of an encapsulated blend of formic acid, citric acid, and essential oils (FormaXOL™) administered to finisher pigs for 28days prior to slaughter in controlling Salmonella shedding on a commercial farm with a history of high Salmonella seroprevalence. Fourteen pens of 8-10 pigs/pen were randomly assigned to a control (finisher diet without additive) or a treatment group (the same diet with 4kg/t of FormaXOL™) for 28 days. Faeces were collected from each pig on days 0, 14, and 28, while on day 29 blood, caecal digesta and ileocaecal-mesenteric lymph nodes were collected at slaughter. Pigs were weighed at the start and end of the trial, feed intake was recorded, and carcass quality parameters were recorded at slaughter. On day 14, Salmonella shedding was reduced in the treatment compared to the control group (27.9% versus 51.7% probability of detecting Salmonella in faeces, respectively; p=0.001). However, on day 28, no reduction was observed (20.6% versus 35.9% probability of detecting Salmonella in faeces, respectively; p=0.07). Interestingly, Salmonella shedding rates in the treated pigs remained stable throughout the trial compared to the control group. This suggests that the feed additive prevented additional pigs from acquiring the Salmonella infection. A lower Salmonella seroprevalence was detected at slaughter in the treatment compared to the control group using the 40% optical density cut-off (64.5% versus 88.5%, respectively; p=0.01). However, no significant differences in Salmonella recovery rates were observed in the caecal digesta or lymph nodes between treated and control groups. Treated pigs had a lower feed intake than pigs fed the control diet (p=0.001); however, average daily gain and feed conversion efficiency were not affected by treatment (p=0.45 and 0.55, respectively). Consequently, supplementing the diet with FormaXOL™ for 28days increased the feed cost per kg of live-weight gain by €0.08. Overall, results suggest that strategic administration of an encapsulated blend of formic acid, citric acid, and essential oils, to finishing pigs for 28days prior to slaughter has potential to prevent increased Salmonella shedding at certain time points as well as seroprevalence. However, this additive did not lower intestinal carriage, nor did it reduce seroprevalence to below the cut-off used for the high Salmonella risk category in Ireland (50%) or improve growth performance.

Effect of feeding sodium butyrate in the late finishing period on Salmonella carriage, seroprevalence, and growth of finishing pigs.

Pork is an important source of human salmonellosis and low-cost on-farm control measures may provide a useful element in reducing the prevalence of this pathogen in food. This study investigated the effectiveness of dietary supplementation with sodium butyrate administered to finisher pigs for ∼4-weeks prior to slaughter to control Salmonella shedding on highly contaminated farms. Two trials (A and B) were conducted on two commercial pig farms, which had a history of high Salmonella seroprevalence. In both trials, pens (14 pens of 12 pigs/pen in Trial A and 12 pens of 12-17 pigs/pen in Trial B) were randomly assigned to a control (finisher feed without additive) or a treatment group (the same feed with 3kg sodium butyrate/t) for 24-28days, depending on the trial. Faeces were collected from each pig on days 0, 12 and 24/28, and blood, caecal digesta and ileocaecal/mesenteric lymph nodes were collected from the slaughterhouse. Pigs were weighed at the start and end of the trials, feed intake was recorded, and carcass quality parameters were recorded at slaughter. In Trial A, Salmonella shedding was reduced in the treatment compared to the control group at the end of the trial (30% versus 57% probability of detecting Salmonella in faeces, respectively; p<0.001). This reflected the serology results, with detection of a lower seroprevalence in the treatment compared to the control group using the 20% optical density cut-off (69.5% versus 89%; p=0.001). However, no effect on faecal shedding or seroprevalance was observed in Trial B, which may be explained by the detection of a concomitant infection with Lawsonia intracellularis. No significant differences in Salmonella recovery rates were observed in the caecal digesta or lymph nodes in either trial. Furthermore, feed intake, weight gain, and feed conversion efficiency (FCE) did not differ between groups (p>0.05) in either trial. Numerical improvements in weight gain and FCE were found with sodium butyrate treatment, which gave a cost benefit of €0.04/kg of live-weight gain. Overall, results suggest that strategic feeding of sodium butyrate, at 3kg/t of feed, to finishing pigs for 24-28days prior to slaughter was effective in reducing Salmonella shedding and seroprevalance but perhaps only in the absence of co-infection with other pathogens. However, sodium butyrate supplementation at this rate did not influence intestinal carriage, nor did it reduce seroprevalence to below the cut-off used for the high Salmonella risk category in Ireland (50%), or significantly improve growth performance.

A prototype of a novel cell phone application for tracking the vaccination coverage of children in rural communities.

Immunization saves millions of lives against vaccine-preventable diseases. Yet, 24 million children born every year do not receive proper immunization during their first year. UNICEF and WHO have emphasized the need to strengthen the immunization surveillance and monitoring in developing countries to reduce childhood deaths. In this regard, we present a software application called Jeev to track the vaccination coverage of children in rural communities. Jeev synergistically combines the power of smartphones and the ubiquity of cellular infrastructure, QR codes, and national identification cards. We present the design of Jeev and highlight its unique features along with a detailed evaluation of its performance and power consumption using the National Immunization Survey datasets. We are in discussion with a non-profit organization in Haiti to pilot test Jeev in order to study its effectiveness and identify socio-cultural issues that may arise in a large-scale deployment.

Salmonella occurrence and Enterobacteriaceae counts in pig feed ingredients and compound feed from feed mills in Ireland.

The purpose of this study was to assess the occurrence of non-typhoidal Salmonellae and Enterobacteriaceae counts in raw ingredients and compound feeds sampled from feed mills manufacturing pig diets. Between November 2012 and September 2013, feed ingredients (n=340) and compound pig feed (n=313) samples were collected from five commercial feed mills and one home compounder at various locations throughout Ireland. Feed ingredients included cereals, vegetable protein sources and by-products of oil extraction and ethanol production. The compound feeds included meal and pelleted feed for all stages of pig production. Samples were analysed for Salmonella using standard enrichment procedures. Recovered isolates were serotyped, characterised for antibiotic resistance and subtyped by multi locus variance analysis (MLVA). Total Enterobacteriaceae counts were also performed. Salmonella was recovered from 2/338 (0.6%) ingredients (wheat and soybean meal), at two of the six mills. Salmonella was also detected in 3/317 (0.95%) compound feeds including pelleted feed which undergoes heat treatment. All isolates recovered from feed ingredient and compound feed samples were verified as Salmonella enterica subsp. enterica serotype (4,[5],12:i:-) that lack the expression of flagellar Phase 2 antigens representing monophasic variants of Salmonella Typhimurium (4,[5],12:i:-). Isolates exhibited resistance to between two and seven antimicrobials. Two distinct MLVA profiles were observed, with the same profile recovered from both feed and ingredients, although these did not originate at the same mill. There was no relationship between the occurrence of Salmonella and a high Enterobacteriaceae counts but it was shown that Enterobacteriaceae counts were significantly lower in pelleted feed (heat treated) than in meal (no heat treatment) and that Enterobacteriaceae counts would be very useful indicator in HACPP programme. Overall, although the prevalence of Salmonella in pig feed and feed ingredients in the present study was low, even minor Salmonella contamination in feed has the potential to affect many herds and may subsequently cause human infection. Furthermore, the recovery of a recently emerged serovar with multi-antibiotic resistance is a potential cause for concern.

Pesticide occurrence in groundwater and the physical characteristics in association with these detections in Ireland.

This study explores the associations of pesticide occurrence in groundwater to geological characteristics of the monitoring points (MPs) contributing area. Pesticide analyses were undertaken during a 2-year groundwater monitoring campaign which generated 845 samples. MCPA and mecoprop were the most frequently detected pesticides in groundwater. Each MP (n = 158) had a specifically delineated zone of contribution (ZOC) and the dominant physical characteristics present from nine national datasets were recorded for each ZOC. Associations between detections in groundwater and the dominant physical characteristic in each MPs ZOC tested were then statistically analyzed using Fisher's exact test, logistic regression, and multiple logistic regression. The original physical characteristic datasets used that were associated with detections in groundwater were the type of MP, aquifer type, and Quaternary deposit type. Logistic regression revealed that springs, regionally important aquifer types, aquifers with a karstic flow regime, and alkaline Quaternary deposits in existence above karst aquifers in a MP's ZOC were more likely to have a pesticide detection in groundwater. Multiple regression from this exploratory work showed some mutual dependency between soil association, aquifer type, and the Geological Survey of Ireland groundwater vulnerability map. The combination of national monitoring data and physical attribute datasets can be used to explore key areas where groundwater is more vulnerable to pesticide contamination.

Insights into the low-temperature adaptation and nutritional flexibility of a soil-persistent Escherichia coli.

An understanding of the survival capacity of Escherichia coli in soil is critical for the evaluation of its role as a faecal indicator. Recent reports that E. coli can become long-term residents in maritime temperate soils have raised the question of how the organism survives and competes for niche space in the suboptimal soil environment. The ability of an environmental isolate to utilize 380 substrates was assessed together with that of a reference laboratory strain (E. coli K12) at both 15 and 37 °C. At 15 °C, the environmental strain could utilize 161 substrates, with only 67 utilizable by the reference strain, while at 37 °C, 239 and 223 substrates could be utilized by each strain respectively. An investigation into the cold response of the strains revealed that E. coli K12 was found to reduce the expression of biosynthetic proteins at 15 °C, while the environmental isolate seemed to switch on proteins involved in stress response, suggesting low-temperature adaptation in the latter. Taken together, the results indicate that the environmentally persistent E. coli strain is well adapted to use a wide range of nutrient sources at 15 °C and to direct its protein expression to maintain a relatively fast growth rate at low temperature.

Pre-Calving and Calving Management Practices in Dairy Herds with a History of High or Low Bovine Perinatal Mortality.

Bovine perinatal mortality is an increasing problem in dairy industries internationally. The objective of this study was to determine the risk factors associated with high and low herd-level calf mortality. Thirty herds with a history of either high (case) or low (control) calf mortality were recruited. A herd-level questionnaire was used to gather information on management practices likely to impact bovine perinatal mortality. The questionnaire was divided into four subsections dealing with pre-calving (breeding, diet and body condition score, endemic infectious diseases) and calving factors. Most of the significant differences between case and control herds were found in calving management. For example, in case herds, pregnant cattle were less likely to be moved to the calving unit two or more days and more likely to be moved less than 12 hours pre-calving, they were also less likely to calve in group-calving facilities and their calves were more likely to receive intranasal or hypothermal resuscitation. These management procedures may cause social isolation and periparturient psychogenic uterine atony leading to dystocia, more weak calves requiring resuscitation and high perinatal calf mortality. The key finding is that calving, not pre-calving, management appears to be the most important area of concern in herds with high perinatal mortality.

Extraction efficiencies of heavy metals in hydroethanolic solvent from herbs of commerce.

Heavy metal contamination of herbal products is a major concern in the herbal and dietary supplement industry. Heavy metal exposure is well-documented to cause a variety of adverse human health effects and to negatively impact our environment. The Final Rule for Dietary Supplements for current good manufacturing practice regulation, 21 U.S. Food and Drug Administration Code of Federal Regulations 111, requires dietary supplement manufacturers to establish herbal purity limits for heavy metal contaminants considered safe for human consumption. Heavy metals may enter into the herbal manufacturing process via bioaccumulation from the harvest site or during postharvest processing phases, such as drying and/or liquid extraction. Traditionally, herbalists have used hydroethanolic solvents to extract herbal biomasses in pure food-grade ethanol-water combinations with solvent polarities capable of removing a wide range of hydrophilic and lipophilic constituents. The presented data demonstrate that hydroethanolic solvents are not completely efficient in the extraction of heavy metal accumulations from plant matrixes; and can act as an effective decontamination step in herbal product processing.

Long-term persistence and leaching of Escherichia coli in temperate maritime soils.

Enteropathogen contamination of groundwater, including potable water sources, is a global concern. The spreading on land of animal slurries and manures, which can contain a broad range of pathogenic microorganisms, is considered a major contributor to this contamination. Some of the pathogenic microorganisms applied to soil have been observed to leach through the soil into groundwater, which poses a risk to public health. There is a critical need, therefore, for characterization of pathogen movement through the vadose zone for assessment of the risk to groundwater quality due to agricultural activities. A lysimeter experiment was performed to investigate the effect of soil type and condition on the fate and transport of potential bacterial pathogens, using Escherichia coli as a marker, in four Irish soils (n = 9). Cattle slurry (34 tonnes per ha) was spread on intact soil monoliths (depth, 1 m; diameter, 0.6 m) in the spring and summer. No effect of treatment or the initial soil moisture on the E. coli that leached from the soil was observed. Leaching of E. coli was observed predominantly from one soil type (average, 1.11 +/- 0.77 CFU ml(-1)), a poorly drained Luvic Stagnosol, under natural rainfall conditions, and preferential flow was an important transport mechanism. E. coli was found to have persisted in control soils for more than 9 years, indicating that autochthonous E. coli populations are capable of becoming naturalized in the low-temperature environments of temperate maritime soils and that they can move through soil. This may compromise the use of E. coli as an indicator of fecal pollution of waters in these regions.