Development of antimicrobial synbiotics using potentially-probiotic faecal isolates of Lactobacillus fermentum and Bifidobacterium longum

The aims of the present study were to investigate in vitro the antimicrobial activity of Lactobacillus fermentum and Bifidobacterium longum, isolated from faeces of healthy elderly individuals, against enterohaemorrhagic Escherichia coli (E. coli O157:H7) and enteropathogenic E. coli (E. coli O86), to determine the capability of the selected strains to tolerate acid and bile in vitro, to select suitable carbohydrates in order to enhance the growth and maximise antimicrobial activity of the putative probiotic organisms and examine the adhesion properties of the synbiotics. Antimicrobial activity of the putative probiotics and synbiotics was investigated by a microtitre method using cell-free culture supernatants (CFCS). Results of the antimicrobial assay showed that both putative probiotic strains produced compounds at pH 5 that lead to higher lag phases of both E. coli O157:H7 and E. coli O86. When half the quantity of cell-free culture supernatants of both probiotic strains was used at pH 5, B. longum maintained the same antimicrobial effect against both strains of E. coli, whereas L. fermentum lead to a higher lag phase of E. coli O86 only. Neutralization of the culture supernatants with alkali reduced the antimicrobial effect with only cell-free supernatant of L. fermentum causing lower maximum growth rates of E. coli O157:H7 and E. coli O86. L. fermentum appeared to be acid tolerant whereas B. longum was more susceptible to acid and both isolates were bile tolerant. A short chain fructooligosaccharide (scFOS) and an isomalto-oligosaccharide (IMO) proved to be the most effective substrates, enhancing antimicrobial activity for L. fermentum and B. longum respectively. The adhesion of the synbiotic combinations showed that L. fermentum, exhibited higher percentage of adhesion when grown on glucose and as a synbiotic combination with scFOS whereas B. longum exhibited lowest percentage of adhesion when grown on both glucose and IMO.

A comparative review of dimension reduction methods in approximate Bayesian computation

Approximate Bayesian computation (ABC) methods make use of comparisons between simulated and observed summary statistics to overcome the problem of computationally intractable likelihood functions. As the practical implementation of ABC requires computations based on vectors of summary statistics, rather than full data sets, a central question is how to derive low-dimensional summary statistics from the observed data with minimal loss of information. In this article we provide a comprehensive review and comparison of the performance of the principal methods of dimension reduction proposed in the ABC literature. The methods are split into three nonmutually exclusive classes consisting of best subset selection methods, projection techniques and regularization. In addition, we introduce two new methods of dimension reduction. The first is a best subset selection method based on Akaike and Bayesian information criteria, and the second uses ridge regression as a regularization procedure. We illustrate the performance of these dimension reduction techniques through the analysis of three challenging models and data sets.

Cashew cultivation, access to land and food security in Brong-Ahafo Region, Ghana: Preventing the intergenerational transmission of poverty

This research aimed to investigate the implications of changing agricultural land use from food production towards increased cashew cultivation for food security and poverty alleviation in Jaman North District, Brong-Ahafo Region of Ghana. Based on qualitative, participatory research with a total of 60 participants, the research found that increased cashew production had led to improvements in living standards for many farmers and their children over recent years. Global demand for cashew is projected to continue to grow rapidly in the immediate future and cashew-growing areas of Ghana are well placed to respond to this demand. Cashew farmers however were subject to price fluctuations in the value of Raw Cashew Nuts (RCN) due to unequal power relations with intermediaries and export buyer companies and global markets, in addition to other vulnerabilities that constrained the quality and quantity of cashew and food crops they could produce. The expansion of cashew plantations was leading to pressure on the remaining family lands available for food crop production, which community members feared could potentially compromise the food security of rural communities and the land inheritance of future generations.

A longitudinal study of carbon disclosure strategy: evidence from utility, energy and mining industries in the UK

The paper investigates how energy-intensive industries respond to the recent government-led carbon emission schemes through the content analysis of 306 annual and standalone reports of 25 UK listed companies from 2004 to 2012. This period of reporting captures the trend and development of corporate disclosures on carbon emissions after the launch of EU Emissions Trading Schemes (ETS) and Climate Change Act (CCA) 2008. It is found that in corresponding to strategic legitimacy theory, there is an increase in both the quality and quantity of carbon disclosures as a response to these initiatives. However, the change is gradual, which reflects in the achievement of peak disclosure period two years after the launch. It indicates that the new legislations have a lasting impact on the discourses rather than an immediate legitimacy threat from the perspective of institutional legitimacy theory. The results also show that carbon disclosures are an institutionalised practice as companies in the same industries and/or with same carbon trading account status appear to imitate and adopt the industry’s ‘best practice’ disclosure strategy to maintain legitimacy. The trend analysis suggests that the overall disclosure practice is still in its infant stage, especially in the reporting of quantitative and monetary items. The paper contributes to the social and environmental accounting literature by adopting both strategic and institutional view of legitimacy, which explains why carbon disclosures evolve in a specific way to meet the expectation of various stakeholders.

In vitro colonic metabolism of coffee and chlorogenic acid results in selective changes in human faecal microbiota growth

Coffee is a relatively rich source of chlorogenic acids (CGA), which, like other polyphenols are postulated to exert preventative effects against cardiovascular disease and type-2 diabetes. As a considerable proportion of ingested CGA reaches the large intestine, CGA may be capable of exerting beneficial effects in the large gut. Here we utilise a stirred, anaerobic, pH controlled, batch culture fermentation model of the distal region of the colon in order to investigate the impact of coffee and CGA on the growth of the human faecal microbiota. Incubation of the coffee with the human faecal microbiota led to the rapid metabolism of CGA (4h) and the production of dihydrocaffeic acid and dihydroferulic acid, whilst caffeine remained un-metabolised. The coffee with the highest levels of CGA (p<0.05, relative to the other coffees) induced a significant increase in Bifidobacterium spp. relative to the control at 10 hours post exposure (p<0.05). Similarly, an equivalent quantity of CGA (80.8mg; matched with that in high CGA coffee) induced a significant increase in Bifidobacterium spp. (p<0.05). CGA alone also induced a significant increase in the Clostridium coccoides-Eubacterium rectale group (p<0.05). This selective metabolism and subsequent amplification of specific bacterial populations could be beneficial to host health.

Effects of organic and conventional fertilizer treatments on host selection by the aphid parasitoid Diaeretiella rapae

The type and quantity of fertilizer supplied to a crop will differ between organic and conventional farming practices. Altering the type of fertilizer a plant is provided with can influence a plant’s foliar nitrogen levels, as well as the composition and concentration of defence compounds, such as glucosinolates. Many natural enemies of insect herbivores can respond to headspace volatiles emitted by the herbivores’ host plant in response to herbivory. We propose that manipulating fertilizer type may also influence the headspace volatile profiles of plants, and as a result, the tritrophic interactions that occur between plants, their insect pests and those pests’ natural enemies. Here, we investigate a tritrophic system consisting of cabbage plants, Brassica oleracea, a parasitoid, Diaeretiella rapae, and one of its hosts, the specialist cabbage aphid Brevicoryne brassicae. Brassica oleracea plants were provided with either no additional fertilization or one of three types of fertilizer: Nitram (ammonium nitrate), John Innes base or organic chicken manure. We investigated whether these changes would alter the rate of parasitism of aphids on those plants and whether any differences in parasitism could be explained by differences in attractivity of the plants to D. rapae or attack rate of aphids by D. rapae. In free-choice experiments, there were significant differences in the percentage of B. brassicae parasitized by D. rapae between B. oleracea plants grown in different fertilizer treatments. In a series of dual-choice Y-tube olfactometry experiments, D. rapae females discriminated between B. brassicae-infested and undamaged plants, but parasitoids did not discriminate between similarly infested plants grown in different fertilizer treatments. Correspondingly, in attack rate experiments, there were no differences in the rate that D. rapae attacked B. brassicae on B. oleracea plants grown in different fertilizer treatments. These findings are of direct relevance to sustainable and conventional farming practices.

Social and ecological drivers of success in agri-environment schemes: the roles of farmers and environmental context

1. Agri-environment schemes remain a controversial approach to reversing biodiversity losses, partly because the drivers of variation in outcomes are poorly understood. In particular, there is a lack of studies that consider both social and ecological factors. 2. We analysed variation across 48 farms in the quality and biodiversity outcomes of agri-environmental habitats designed to provide pollen and nectar for bumblebees and butterflies or winter seed for birds. We used interviews and ecological surveys to gather data on farmer experience and understanding of agri-environment schemes, and local and landscape environmental factors. 3. Multimodel inference indicated social factors had a strong impact on outcomes and that farmer experiential learning was a key process. The quality of the created habitat was affected positively by the farmer’s previous experience in environmental management. The farmer’s confidence in their ability to carry out the required management was negatively related to the provision of floral resources. Farmers with more wildlife-friendly motivations tended to produce more floral resources, but fewer seed resources. 4. Bird, bumblebee and butterfly biodiversity responses were strongly affected by the quantity of seed or floral resources. Shelter enhanced biodiversity directly, increased floral resources and decreased seed yield. Seasonal weather patterns had large effects on both measures. Surprisingly, larger species pools and amounts of semi-natural habitat in the surrounding landscape had negative effects on biodiversity, which may indicate use by fauna of alternative foraging resources. 5. Synthesis and application. This is the first study to show a direct role of farmer social variables on the success of agri-environment schemes in supporting farmland biodiversity. It suggests that farmers are not simply implementing agri-environment options, but are learning and improving outcomes by doing so. Better engagement with farmers and working with farmers who have a history of environmental management may therefore enhance success. The importance of a number of environmental factors may explain why agri-environment outcomes are variable, and suggests some – such as the weather – cannot be controlled. Others, such as shelter, could be incorporated into agri-environment prescriptions. The role of landscape factors remains complex and currently eludes simple conclusions about large-scale targeting of schemes.

Short communication: estimation of the financial benefit of using Jersey milk at different inclusion rates for Cheddar cheese production using partial budgeting

Partial budgeting was used to estimate the net benefit of blending Jersey milk in Holstein-Friesian milk for Cheddar cheese production. Jersey milk increases Cheddar cheese yield. However, the cost of Jersey milk is also higher; thus, determining the balance of profitability is necessary, including consideration of seasonal effects. Input variables were based on a pilot plant experiment run from 2012 to 2013 and industry milk and cheese prices during this period. When Jersey milk was used at an increasing rate with Holstein-Friesian milk (25, 50, 75, and 100% Jersey milk), it resulted in an increase of average net profit of 3.41, 6.44, 8.57, and 11.18 pence per kilogram of milk, respectively, and this additional profit was constant throughout the year. Sensitivity analysis showed that the most influential input on additional profit was cheese yield, whereas cheese price and milk price had a small effect. The minimum increase in yield, which was necessary for the use of Jersey milk to be profitable, was 2.63, 7.28, 9.95, and 12.37% at 25, 50, 75, and 100% Jersey milk, respectively. Including Jersey milk did not affect the quantity of whey butter and powder produced. Althoug further research is needed to ascertain the amount of additional profit that would be found on a commercial scale, the results indicate that using Jersey milk for Cheddar cheese making would lead to an improvement in profit for the cheese makers, especially at higher inclusion rates.

Stimulation of "stress-regulated" mitogen-activated protein kinases (stress-activated protein kinases/c-Jun N-terminal kinases and p38-mitogen-activated protein kinases) in perfused rat hearts by oxidative and other stresses.

"Stress-regulated" mitogen-activated protein kinases (SR-MAPKs) comprise the stress-activated protein kinases (SAPKs)/c-Jun N-terminal kinases (JNKs) and the p38-MAPKs. In the perfused heart, ischemia/reperfusion activates SR-MAPKs. Although the agent(s) directly responsible is unclear, reactive oxygen species are generated during ischemia/reperfusion. We have assessed the ability of oxidative stress (as exemplified by H2O2) to activate SR-MAPKs in the perfused heart and compared it with the effect of ischemia/reperfusion. H2O2 activated both SAPKs/JNKs and p38-MAPK. Maximal activation by H2O2 in both cases was observed at 0.5 mM. Whereas activation of p38-MAPK by H2O2 was comparable to that of ischemia and ischemia/reperfusion, activation of the SAPKs/JNKs was less than that of ischemia/reperfusion. As with ischemia/reperfusion, there was minimal activation of the ERK MAPK subfamily by H2O2. MAPK-activated protein kinase 2 (MAPKAPK2), a downstream substrate of p38-MAPKs, was activated by H2O2 to a similar extent as with ischemia or ischemia/reperfusion. In all instances, activation of MAPKAPK2 in perfused hearts was inhibited by SB203580, an inhibitor of p38-MAPKs. Perfusion of hearts at high aortic pressure (20 kilopascals) also activated the SR-MAPKs and MAPKAPK2. Free radical trapping agents (dimethyl sulfoxide and N-t-butyl-alpha-phenyl nitrone) inhibited the activation of SR-MAPKs and MAPKAPK2 by ischemia/reperfusion. These data are consistent with a role for reactive oxygen species in the activation of SR-MAPKs during ischemia/reperfusion.

Biases in comparative analyses of extinction risk: mind the gap

1. Comparative analyses are used to address the key question of what makes a species more prone to extinction by exploring the links between vulnerability and intrinsic species’ traits and/or extrinsic factors. This approach requires comprehensive species data but information is rarely available for all species of interest. As a result comparative analyses often rely on subsets of relatively few species that are assumed to be representative samples of the overall studied group. 2. Our study challenges this assumption and quantifies the taxonomic, spatial, and data type biases associated with the quantity of data available for 5415 mammalian species using the freely available life-history database PanTHERIA. 3. Moreover, we explore how existing biases influence results of comparative analyses of extinction risk by using subsets of data that attempt to correct for detected biases. In particular, we focus on links between four species’ traits commonly linked to vulnerability (distribution range area, adult body mass, population density and gestation length) and conduct univariate and multivariate analyses to understand how biases affect model predictions. 4. Our results show important biases in data availability with c.22% of mammals completely lacking data. Missing data, which appear to be not missing at random, occur frequently in all traits (14–99% of cases missing). Data availability is explained by intrinsic traits, with larger mammals occupying bigger range areas being the best studied. Importantly, we find that existing biases affect the results of comparative analyses by overestimating the risk of extinction and changing which traits are identified as important predictors. 5. Our results raise concerns over our ability to draw general conclusions regarding what makes a species more prone to extinction. Missing data represent a prevalent problem in comparative analyses, and unfortunately, because data are not missing at random, conventional approaches to fill data gaps, are not valid or present important challenges. These results show the importance of making appropriate inferences from comparative analyses by focusing on the subset of species for which data are available. Ultimately, addressing the data bias problem requires greater investment in data collection and dissemination, as well as the development of methodological approaches to effectively correct existing biases.

Legacy effects of grassland management on soil carbon to depth

The importance of managing land to optimise carbon sequestration for climate change mitigation is widely recognised, with grasslands being identified as having the potential to sequester additional carbon. However, most soil carbon inventories only consider surface soils, and most large scale surveys group ecosystems into broad habitats without considering management intensity. Consequently, little is known about the quantity of deep soil carbon and its sensitivity to management. From a nationwide survey of grassland soils to 1 m depth, we show that carbon in grasslands soils is vulnerable to management and that these management effects can be detected to considerable depth down the soil profile, albeit at decreasing significance with depth. Carbon concentrations in soil decreased as management intensity increased, but greatest soil carbon stocks (accounting for bulk density differences), were at intermediate levels of management. Our study also highlights the considerable amounts of carbon in sub-surface soil below 30cm, which is missed by standard carbon inventories. We estimate grassland soil carbon in Great Britain to be 2097 Tg C to a depth of 1 m, with ~60% of this carbon being below 30cm. Total stocks of soil carbon (t ha-1) to 1 m depth were 10.7% greater at intermediate relative to intensive management, which equates to 10.1 t ha-1 in surface soils (0-30 cm), and 13.7 t ha-1 in soils from 30-100 cm depth. Our findings highlight the existence of substantial carbon stocks at depth in grassland soils that are sensitive to management. This is of high relevance globally, given the extent of land cover and large stocks of carbon held in temperate managed grasslands. Our findings have implications for the future management of grasslands for carbon storage and climate mitigation, and for global carbon models which do not currently account for changes in soil carbon to depth with management.

Evaluating microfossil content of dental calculus from Brazilian sambaquis

To date, limited numbers of dental calculus samples have been analyzed by researchers in diverse parts of the world. The combined analyses of these have provided some general guidelines for the analysis of calculus that is non-destructive to archaeological teeth. There is still a need for a quantitative study of large numbers of calculus samples to establish protocols, assess the level of contamination, evaluate the quantity of microfossils in dental calculus, and to compare analysis results with the literature concerning the biology of calculus formation. We analyzed dental calculus from 53 teeth from four Brazilian sambaquis. Sambaquis are the shell-mounds that were established prehistorically along the Brazilian coast. The analysis of sambaqui dental calculi shows that there are relatively high concentrations of microfossils (phytoliths and starch), mineral fragments, and charcoal in dental calculus. Mineral fragments and charcoal are possibly contaminants. The largest dental calculi have the lowest concentrations of microfossils. Biologically, this is explained by individual variation in calculus formation between people. Importantly, starch is ubiquitous in dental calculus. The starch and phytoliths show that certainly Dioscorea (yam) and Araucaria angustifolia (Parana pine) were eaten by sambaqui people. Araceae (arum family), Ipomoea batatas (sweet potato) and Zea mays (maize) were probably in their diet. (C) 2009 Elsevier Ltd. All rights reserved.

Morphology and anatomy of inflorescence and inflorescence axis in Paepalanthus sect. Diphyomene Ruhland (Eriocaulaceae, Poales) and its taxonomic implications

Paepalanthus sect. Diphyomene has inflorescences arranged in umbels. The underlying bauplan seems however to be more complex and composed of several distinct subunits. Despite appearing superficially very similar, the morphology and anatomy of the inflorescences can supply useful information for the understanding of the phylogeny and taxonomy of the group. Inflorescences of Paepalanthus erectifolius, Paepalanthus flaccidus, Paepalanthus giganteus, and Paepalanthus polycladus were analyzed in regard to branching pattern and anatomy. In P. erectifolius, P. giganteus and P. polycladus the structure is a tribotryum, with terminal dibotryum, and with pherophylls bearing lateral dibotrya. In P. flaccidus, the inflorescence is a pleiobotryum, with terminal subunit, and without pherophylls. Secondary inflorescences may occur in all species without regular pattern. Especially when grown in sites without a pronounced seasonality, the distinction between enrichment zone (part of the same inflorescence) and new inflorescences may be obscured. The main anatomical features supplying diagnostic and phylogenetic information are as follows: (a) in the elongated axis, the thickness of the epidermal cell walls and the cortex size; (b) in the bracts, the quantity of parenchyma cells (c) in the scapes, the shape and the presence of a pith tissue. Therefore, P. sect. Diphyomene can be divided in two groups; group A is represented by P. erectifolius, P. giganteus and P. polycladus, and group B is represented by P. flaccidus. The differentiation is based in both, inflorescence structure and anatomy. Group A presents a life cycle and anatomical features similar to species of Actinocephalus. Molecular trees also point that these two groups are closely related. However, inflorescence morphology and blooming sequence are different. Species of group B present an inflorescence structure and anatomical features shared with many genera and species in Eriocaulaceae. The available molecular and morphology based phylogenies still do not allow a precise allocation of the group in the bulk of basal species of Paepalanthus collocated in P. sect. Variabiles. The characters described and used here supply however important information towards this goal. (C) 2009 Elsevier GmbH. All rights reserved.

Intranuclear crystalloids of Antarctic sea urchins as a biomarker for oil contamination

Because of human actions, biomarkers have become important to detect and mitigate pollution. This study showed that crystalloids can be a biomarker for analyses of low levels of water-soluble fractions of oil (WSF). Antarctic sea urchins (Sterechinus neumayeri) from regions free of pollution were exposed for 2, 5, 10 and 15 days at different levels of WSF (0.4, 0.8 and 1.2 ppm). No significant differences were observed in the phagocytic rates or the germicide capacity for the yeast Saccharomyces cerevisiae; however, there was a significant increase in the quantity of intranuclear iron crystalloids in phagocytic amoebocytes of urchins exposed to higher levels of WSF. This study characterizes histological alterations in crystalloids of S. neumayeri that could be used as a biomarker for oil contaminants, with a simple and inexpensive protocol.

Finite determinacy and Whitney equisingularity of map germs from C(n) to C(2n-1)

We show that a holomorphic map germ f : (C(n), 0) -> (C(2n-1), 0) is finitely determined if and only if the double point scheme D(f) is a reduced curve. If n >= 3, we have that mu(D(2)(f)) = 2 mu(D(2)(f)/S(2))+C(f)-1, where D(2)(f) is the lifting of the double point curve in (C(n) x C(n), 0), mu(X) denotes the Milnor number of X and C(f) is the number of cross-caps that appear in a stable deformation of f. Moreover, we consider an unfolding F(t, x) = (t, f(t)(x)) of f and show that if F is mu-constant, then it is excellent in the sense of Gaffney. Finally, we find a minimal set of invariants whose constancy in the family f(t) is equivalent to the Whitney equisingularity of F. We also give an example of an unfolding which is topologically trivial, but it is not Whitney equisingular.