Palaeobiology of an extinct Ice Age mammal: Stable isotope and cementum analysis of giant deer teeth

The extinct giant deer, Megaloceros giganteus, is among the largest and most famous of the cervids. Megaloceros remains have been uncovered across Europe and western Asia. but the highest concentrations come from Irish bogs and caves Although Megaloceros has enjoyed a great deal of attention over the centuries, paleobiological study has focused oil morphometric and distributional work until now. This paper presents quantitative data that have implications for understanding its sudden extirpation in western Europe during a period of global climate change approximately 10.600 C-14 years ago (ca 12,500 calendar years BP). We report here the first stable isotope analysis of giant deer teeth. which we combine with dental cementum accretion in order to document age, diet and life-history seasonality from birth until death Enamel delta C-13 and delta O-18 measured in the second and third molars from seven individual giant deer Suggest a grass and forbbased diet supplemented with browse in a deteriorating. possibly water-stressed, environment, and a season of birth around spring/early summer Cementurm data indicate that the ages of the specimens ranged from 6.5 to 14 years and that they possessed mature antlers by autumn, similar to extant cervids. In addition. the possibility for combining these two techniques in future mammalian paleoccological studies is considered. The data presented in this study imply that Megoloceros would have indeed been vulnerable to extirpation during the terminal Pleistocene in Ireland. and this information is relevant to understanding the broader pattern of its extinction.

Population-based study reveals new risk-stratification biomarker panel for Barrett's esophagus

BACKGROUND & AIMS: The risk of progression of Barrett's esophagus (BE) to esophageal adenocarcinoma (EAC) is low and difficult to calculate. Accurate tools to determine risk are needed to optimize surveillance and intervention. We assessed the ability of candidate biomarkers to predict which cases of BE will progress to EAC or high-grade dysplasia and identified those that can be measured in formalin-fixed tissues. METHODS: We analyzed data from a nested case-control study performed using the population-based Northern Ireland BE Register (1993-2005). Cases who progressed to EAC (n = 89) or high-grade dysplasia =6 months after diagnosis with BE were matched to controls (nonprogressors, n = 291), for age, sex, and year of BE diagnosis. Established biomarkers (abnormal DNA content, p53, and cyclin A expression) and new biomarkers (levels of sialyl Lewis(a), Lewis(x), and Aspergillus oryzae lectin [AOL] and binding of wheat germ agglutinin) were assessed in paraffin-embedded tissue samples from patients with a first diagnosis of BE. Conditional logistic regression analysis was applied to assess odds of progression for patients with dysplastic and nondysplastic BE, based on biomarker status. RESULTS: Low-grade dysplasia and all biomarkers tested, other than Lewis(x), were associated with risk of EAC or high-grade dysplasia. In backward selection, a panel comprising low-grade dysplasia, abnormal DNA ploidy, and AOL most accurately identified progressors and nonprogressors. The adjusted odds ratio for progression of patients with BE with low-grade dysplasia was 3.74 (95% confidence interval, 2.43-5.79) for each additional biomarker and the risk increased by 2.99 for each additional factor (95% confidence interval, 1.72-5.20) in patients without dysplasia. CONCLUSIONS: Low-grade dysplasia, abnormal DNA ploidy, and AOL can be used to identify patients with BE most likely to develop EAC or high-grade dysplasia.

Immunotoxicity of aflatoxin B1: Impairment of the cell-mediated response to vaccine antigen and modulation of cytokine expression

Aflatoxin B1 (AFB1), a mycotoxin produced by Aspergillus flavus or A. parasiticus, is a frequent contaminant of food and feed. This toxin is hepatotoxic and immunotoxic. The present study analyzed in pigs the influence of AFB1 on humoral and cellular responses, and investigated whether the immunomodulation observed is produced through interference with cytokine expression. For 28 days, pigs were fed a control diet or a diet contaminated with 385, 867 or 1807 mu g pure AFB1/kg feed. At days 4 and 15, pigs were vaccinated with ovalbumin. AFB1 exposure, confirmed by an observed dose-response in blood aflatoxin-albumin adduct, had no major effect on humoral immunity as measured by plasma concentrations of total IgA, IgG and IgM and of anti-ovalbumin IgG. Toxin exposure did not impair the mitogenic response of lymphocytes but delayed and decreased their specific proliferation in response to the vaccine antigen, suggesting impaired lymphocyte activation in pigs exposed to AFB1. The expression level of pro-inflammatory (TNF-alpha, IL-1 beta, IL-6, IFN-gamma) and regulatory (IL-10) cytokines was assessed by real-time PCR in spleen. A significant up-regulation of all 5 cytokines was observed in spleen from pigs exposed to the highest dose of AFB1. In pigs exposed to the medium dose, IL-6 expression was increased and a trend towards increased IFN-gamma and IL-10 was observed. In addition we demonstrate that IL-6 impaired in vitro the antigenic- but not the mitogenic-induced proliferation of lymphocytes from control pigs vaccinated with ovalbumin. These results indicate that AFB1 dietary exposure decreases cell-mediated immunity while inducing an inflammatory response. These impairments in the immune response could participate in failure of vaccination protocols and increased susceptibility to infections described in pigs exposed to AFB1. (C) 2008 Elsevier Inc. All rights reserved.

The biology of habitat dominance; can microbes behave as weeds?

Competition between microbial species is a product of, yet can lead to a reduction in, the microbial diversity of specific habitats. Microbial habitats can resemble ecological battlefields where microbial cells struggle to dominate and/or annihilate each other and we explore the hypothesis that (like plant weeds) some microbes are genetically hard-wired to behave in a vigorous and ecologically aggressive manner. These 'microbial weeds' are able to dominate the communities that develop in fertile but uncolonized - or at least partially vacant - habitats via traits enabling them to out-grow competitors; robust tolerances to habitat-relevant stress parameters and highly efficient energy-generation systems; avoidance of or resistance to viral infection, predation and grazers; potent antimicrobial systems; and exceptional abilities to sequester and store resources. In addition, those associated with nutritionally complex habitats are extraordinarily versatile in their utilization of diverse substrates. Weed species typically deploy multiple types of antimicrobial including toxins; volatile organic compounds that act as either hydrophobic or highly chaotropic stressors; biosurfactants; organic acids; and moderately chaotropic solutes that are produced in bulk quantities (e.g. acetone, ethanol). Whereas ability to dominate communities is habitat-specific we suggest that some microbial species are archetypal weeds including generalists such as: Pichia anomala, Acinetobacter spp. and Pseudomonas putida; specialists such as Dunaliella salina, Saccharomyces cerevisiae, Lactobacillus spp. and other lactic acid bacteria; freshwater autotrophs Gonyostomum semen and Microcystis aeruginosa; obligate anaerobes such as Clostridium acetobutylicum; facultative pathogens such as Rhodotorula mucilaginosa, Pantoea ananatis and Pseudomonas aeruginosa; and other extremotolerant and extremophilic microbes such as Aspergillus spp., Salinibacter ruber and Haloquadratum walsbyi. Some microbes, such as Escherichia coli, Mycobacterium smegmatis and Pseudoxylaria spp., exhibit characteristics of both weed and non-weed species. We propose that the concept of nonweeds represents a 'dustbin' group that includes species such as Synodropsis spp., Polypaecilum pisce, Metschnikowia orientalis, Salmonella spp., and Caulobacter crescentus. We show that microbial weeds are conceptually distinct from plant weeds, microbial copiotrophs, r-strategists, and other ecophysiological groups of microorganism. Microbial weed species are unlikely to emerge from stationary-phase or other types of closed communities; it is open habitats that select for weed phenotypes. Specific characteristics that are common to diverse types of open habitat are identified, and implications of weed biology and open-habitat ecology are discussed in the context of further studies needed in the fields of environmental and applied microbiology.

Response of farmland biodiversity to the introduction of bioenergy crops: effects of local factors and surrounding landscape context

The recent growth in bioenergy crop cultivation, stimulated by the need to implement measures to reduce net CO emissions, is driving major land-use changes with consequences for biodiversity and ecosystem service provision. Although the type of bioenergy crop and its associated management is likely to affect biodiversity at the local (field) scale, landscape context and its interaction with crop type may also influence biodiversity on farms. In this study, we assessed the impact of replacing conventional agricultural crops with two model bioenergy crops (either oilseed rape Brassica napus or Miscanthus × giganteus) on vascular plant, bumblebee, solitary bee, hoverfly and carabid beetle richness, diversity and abundance in 50 sites in Ireland. We assessed whether within-field biodiversity was also related to surrounding landscape structure. We found that local- and landscape-scale variables correlated with biodiversity in these agricultural landscapes. Overall, the differences between the bioenergy crops and the conventional crops on farmland biodiversity were mostly positive (e.g. higher vascular plant richness in Miscanthus planted on former conventional tillage, higher solitary bee abundance and richness in Miscanthus and oilseed rape compared with conventional crops) or neutral (e.g. no differences between crop types for hoverflies and bumblebees). We showed that these crop type effects were independent of (i.e. no interactions with) the surrounding landscape composition and configuration. However, surrounding landscape context did relate to biodiversity in these farms, negatively for carabid beetles and positively for hoverflies. Although we conclude that the bioenergy crops compared favourably with conventional crops in terms of biodiversity of the taxa studied at the field scale, the effects of large-scale planting in these landscapes could result in very different impacts. Maintaining ecosystem functioning and the delivery of ecosystem services will require a greater understanding of impacts at the landscape scale to ensure the sustainable development of climate change mitigation measures.

Lovastatin biosynthesis depends on the carbon-nitrogen proportion: model development and controller design

Lovastatin biosynthesis depends on the relative concentrations of dissolved oxygen and the carbon and nitrogen resources. An elucidation of the underlying relationship would facilitate the derivation of a controller for the improvement of lovastatin yield in bioprocesses. To achieve this goal, batch submerged cultivation experiments of lovastatin production by Aspergillus flavipus BICC 5174, using both lactose and glucose as carbon sources, were performed in a 7 liter bioreactor and the data used to determine how the relative concentrations of lactose, glucose, glutamine and oxygen affected lovastatin yield. A model was developed based on these results and its prediction was validated using an independent set of batch data obtained from a 15-liter bioreactor using five statistical measures, including the Willmott index of agreement. A nonlinear controller was designed considering that dissolved oxygen and lactose concentrations could be measured online, and using the lactose feed rate and airflow rate as process inputs. Simulation experiments were performed to demonstrate that a practical implementation of the nonlinear controller would result in satisfactory outcomes. This is the first model that correlates lovastatin biosynthesis to carbon-nitrogen proportion and possesses a structure suitable for implementing a strategy for controlling lovastatin production.

Is there a common water-activity limit for the three domains of life?

Archaea and Bacteria constitute a majority of life systems on Earth but have long been considered inferior to Eukarya in terms of solute tolerance. Whereas the most halophilic prokaryotes are known for an ability to multiply at saturated NaCl (water activity (a_w) 0.755) some xerophilic fungi can germinate, usually at high-sugar concentrations, at values as low as 0.650–0.605 a_w. Here, we present evidence that halophilic prokayotes can grow down to water activities of <0.755 for Halanaerobium lacusrosei (0.748), Halobacterium strain 004.1 (0.728), Halobacterium sp. NRC-1 and Halococcus morrhuae (0.717), Haloquadratum walsbyi (0.709), Halococcus salifodinae (0.693), Halobacterium noricense (0.687), Natrinema pallidum (0.681) and haloarchaeal strains GN-2 and GN-5 (0.635 a_w). Furthermore, extrapolation of growth curves (prone to giving conservative estimates) indicated theoretical minima down to 0.611 a_w for extreme, obligately halophilic Archaea and Bacteria. These were compared with minima for the most solute-tolerant Bacteria in high-sugar (or other non-saline) media (Mycobacterium spp., Tetragenococcus halophilus, Saccharibacter floricola, Staphylococcus aureus and so on) and eukaryotic microbes in saline (Wallemia spp., Basipetospora halophila, Dunaliella spp. and so on) and high-sugar substrates (for example, Xeromyces bisporus, Zygosaccharomyces rouxii, Aspergillus and Eurotium spp.). We also manipulated the balance of chaotropic and kosmotropic stressors for the extreme, xerophilic fungi Aspergillus penicilloides and X. bisporus and, via this approach, their established water-activity limits for mycelial growth (~0.65) were reduced to 0.640. Furthermore, extrapolations indicated theoretical limits of 0.632 and 0.636 a_w for A. penicilloides and X. bisporus, respectively. Collectively, these findings suggest that there is a common water-activity limit that is determined by physicochemical constraints for the three domains of life.

Ethanol-induced water stress and fungal growth

Fungal growth inhibition by ethanol was compared with that caused by five other agents of water stress (at 25, 40 and 42.5°C), using Aspergillus oryzae. Ethanol, KCl, glycerol, glucose, sorbitol, and polyethylene glycol 400 were incorporated into media at concentrations corresponding to water activity (a(w)) values in the range 1 to 0.75. Generally, as temperature increased there was a decrease in the a(w) value at which optimum growth occurred. The a(w) limit for growth on KCl, glycerol, glucose, sorbitol, or polyethylene glycol 400 media was about 0.85, regardless of temperature. However, the a(w) limit for growth on ethanol media varied between 0.97 and 0.99 a(w) and was temperature-dependent. Water stress accounted for up to 31, 18 and 6% of growth inhibition by ethanol at 25, 40, and 42.5°C, respectively. For media containing ethanol, the decrease in growth rate per unit of a(w) reduction was greater as temperature increased. However, ethanol-induced water stress remained constant regardless of temperature, suggesting that other inhibitory effects of ethanol are closely temperature- dependent. Water stress may account for considerably more than 30% of growth inhibition by ethanol in cells that remain metabolically active at higher ethanol concentrations.

Extraordinary solute-stress tolerance contributes to the environmental tenacity of mycobacteria

Mycobacteria are associated with a number of well-characterized diseases, yet we know little about their stress-biology in natural ecosystems. This study focuses on the isolation and characterization of strains from Yellowstone-(YNP) and Glacier-National-Parks (GNP; USA), the majority of those identified were Mycobacterium parascrofulaceum, Mycobacterium avium (YNP) or Mycobacterium gordonae (GNP). Generally, their temperature windows for growth were >60°C; selected isolates grew at super-saturated concentrations of hydrophobic stressors and at levels of osmotic stress and chaotropic activity (up to 13.4 kJkg-1) similar to, or exceeding, those for the xerophilic fungus Aspergillus wentii and solvent-tolerant bacterium Pseudomonas putida. For example, mycobacteria grew down to 0.800 water-activity indicating that they are, with the sole exception of halophiles, more xerotolerant than other bacteria (or any Archaea). Furthermore, the fatty-acid composition of Mycobacterium cells grown over a range of salt concentrations changed less than that of other bacteria, indicating a high level of resilience, regardless of the stress load. Cells of M. parascrofulaceum, M. smegmatis and M. avium resisted the acute, potentially lethal challenges from extremes of pH (<1; >13), and saturated MgCl2-solutions (5 M; 212 kJ kg-1 chaotropicity). Collectively, these findings challenge the paradigm that bacteria have solute tolerances inferior to those of eukaryotes.

Evaluation of an alternative spectroscopic approach for aflatoxin analysis: Comparative analysis of food and feed samples with UPLC-MS/MS

Increasing research has highlighted the effects of changing climates on the occurrence and prevalence of toxigenic Aspergillus species producing aflatoxins. There is concern of the toxicological effects to human health and animal productivity following acute and chronic exposure that may affect the future ability to provide safe and sufficient food globally. Considerable research has focused on the detection of these toxins, based on the physicochemical and biochemical properties of the aflatoxin compounds, in agricultural products for human and animal consumption. As improvements in food security continue more regulations for acceptable levels of aflatoxins have arisen globally; the most stringent in Europe. These regulations are important for developing countries as aflatoxin occurrence is high significantly effecting international trade and the economy. In developed countries analytical approaches have become highly sophisticated, capable of attaining results with high precision and accuracy, suitable for regulatory laboratories. Regrettably, many countries that are affected by aflatoxin contamination do not have resources for high tech HPLC and MS instrumentation and require more affordable, yet robust equally accurate alternatives that may be used by producers, processors and traders in emerging economies. It is especially important that those companies wishing to exploit the opportunities offered by lucrative but highly regulated markets in the developed world, have access to analytical methods that will ensure that their exports meet their customers quality and safety requirements.

This work evaluates the ToxiMet system as an alternative approach to UPLC–MS/MS for the detection and determination of aflatoxins relative to current European regulatory standards. Four commodities: rice grain, maize cracked and flour, peanut paste and dried distillers grains were analysed for natural aflatoxin contamination. For B1 and total aflatoxins determination the qualitative correlation, above or below the regulatory limit, was good for all commodities with the exception of the dried distillers grain samples for B1 for which no calibration existed. For B1 the quantitative R² correlations were 0.92, 0.92, 0.88 (<250 μg/kg) and 0.7 for rice, maize, peanuts and dried distillers grain samples respectively whereas for total aflatoxins the quantitative correlation was 0.92, 0.94, 0.88 and 0.91. The ToxiMet system could be used as an alternative for aflatoxin analysis for current legislation but some consideration should be given to aflatoxin M1 regulatory levels for these commodities considering the high levels detected in this study especially for maize and peanuts

Fast and sensitive aflatoxin B1 and total aflatoxins ELISAs for analysis of peanuts, maize and feed ingredients

Aflatoxins are a group of carcinogenic compounds produced by Aspergillus fungi that can grow on different agricultural crops. Both acute and chronic exposure to these mycotoxins can cause serious illness. Due to the high occurrence of aflatoxins in crops worldwide fast and cost-effective analytical methods are required for the identification of contaminated agricultural commodities before they are processed into final products and placed on the market. In order to provide new tools for aflatoxin screening two prototype fast ELISA methods: one for the detection of aflatoxin B₁ and the other for total aflatoxins were developed. Seven monoclonal antibodies with unique high sensitivity and at the same time good cross-reactivity profiles were produced. The monoclonal antibodies were characterized and two antibodies showing IC₅₀ of 0.037 ng/mL and 0.031 ng/mL for aflatoxin B₁ were applied in simple and fast direct competitive ELISA tests. The methods were validated for peanut matrix as this crop is one of the most affected by aflatoxin contamination. The detection capabilities of aflatoxin B₁ and total aflatoxins ELISAs were 0.4 μg/kg and 0.3 μg/kg for aflatoxin B₁, respectively, which are one of the lowest reported values. Total aflatoxins ELISA was also validated for the detection of aflatoxins B₂, G₁ and G₂. The application of the developed tests was demonstrated by screening 32 peanut samples collected from the UK retailers. Total aflatoxins ELISA was further applied to analyse naturally contaminated maize porridge and distiller's dried grain with solubles samples and the results were correlated with these obtained by UHPLC-MS/MS method.