Prevotella copri and microbiota members mediate the beneficial effects of a therapeutic food for malnutrition

Microbiota-directed complementary food (MDCF) formulations have been designed to repair the gut communities of malnourished children. A randomized controlled trial demonstrated that one formulation, MDCF-2, improved weight gain in malnourished Bangladeshi children compared to a more calorically dense standard nutritional intervention. Metagenome-assembled genomes from study participants revealed a correlation between ponderal growth and expression of MDCF-2 glycan utilization pathways by Prevotella copri strains. To test this correlation, here we use gnotobiotic mice colonized with defined consortia of age- and ponderal growth-associated gut bacterial strains, with or without P. copri isolates closely matching the metagenome-assembled genomes. Combining gut metagenomics and metatranscriptomics with host single-nucleus RNA sequencing and gut metabolomic analyses, we identify a key role of P. copri in metabolizing MDCF-2 glycans and uncover its interactions with other microbes including Bifidobacterium infantis. P. copri-containing consortia mediated weight gain and modulated energy metabolism within intestinal epithelial cells. Our results reveal structure-function relationships between MDCF-2 and members of the gut microbiota of malnourished children with potential implications for future therapies.

Prevotella copri-related effects of a therapeutic food for malnutrition

Preclinical and clinical studies are providing evidence that the healthy growth of infants and children reflects, in part, healthy development of their gut microbiomes1-5. This process of microbial community assembly and functional maturation is perturbed in children with acute malnutrition. Gnotobiotic animals, colonized with microbial communities from children with severe and moderate acute malnutrition, have been used to develop microbiome-directed complementary food (MDCF) formulations for repairing the microbiomes of these children during the weaning period5. Bangladeshi children with moderate acute malnutrition (MAM) participating in a previously reported 3-month-long randomized controlled clinical study of one such formulation, MDCF-2, exhibited significantly improved weight gain compared to a commonly used nutritional intervention despite the lower caloric density of the MDCF6. Characterizing the 'metagenome assembled genomes' (MAGs) of bacterial strains present in the microbiomes of study participants revealed a significant correlation between accelerated ponderal growth and the expression by two Prevotella copri MAGs of metabolic pathways involved in processing of MDCF-2 glycans1. To provide a direct test of these relationships, we have now performed 'reverse translation' experiments using a gnotobiotic mouse model of mother-to-offspring microbiome transmission. Mice were colonized with defined consortia of age- and ponderal growth-associated gut bacterial strains cultured from Bangladeshi infants/children in the study population, with or without P. copri isolates resembling the MAGs. By combining analyses of microbial community assembly, gene expression and processing of glycan constituents of MDCF-2 with single nucleus RNA-Seq and mass spectrometric analyses of the intestine, we establish a principal role for P. copri in mediating metabolism of MDCF-2 glycans, characterize its interactions with other consortium members including Bifidobacterium longum subsp. infantis, and demonstrate the effects of P. copri-containing consortia in mediating weight gain and modulating the activities of metabolic pathways involved in lipid, amino acid, carbohydrate plus other facets of energy metabolism within epithelial cells positioned at different locations in intestinal crypts and villi. Together, the results provide insights into structure/function relationships between MDCF-2 and members of the gut communities of malnourished children; they also have implications for developing future prebiotic, probiotic and/or synbiotic therapeutics for microbiome restoration in children with already manifest malnutrition, or who are at risk for this pervasive health challenge.

Updates on metaQuantome Software for Quantitative Metaproteomics

metaQuantome is a software suite that enables the quantitative analysis, statistical evaluation. and visualization of mass-spectrometry-based metaproteomics data. In the latest update of this software, we have provided several extensions, including a step-by-step training guide, the ability to perform statistical analysis on samples from multiple conditions, and a comparative analysis of metatranscriptomics data. The training module, accessed via the Galaxy Training Network, will help users to use the suite effectively both for functional as well as for taxonomic analysis. We extend the ability of metaQuantome to now perform multi-data-point quantitative and statistical analyses so that studies with measurements across multiple conditions, such as time-course studies, can be analyzed. With an eye on the multiomics analysis of microbial communities, we have also initiated the use of metaQuantome statistical and visualization tools on outputs from metatranscriptomics data, which complements the metagenomic and metaproteomic analyses already available. For this, we have developed a tool named MT2MQ ("metatranscriptomics to metaQuantome"), which takes in outputs from the ASaiM metatranscriptomics workflow and transforms them so that the data can be used as an input for comparative statistical analysis and visualization via metaQuantome. We believe that these improvements to metaQuantome will facilitate the use of the software for quantitative metaproteomics and metatranscriptomics and will enable multipoint data analysis. These improvements will take us a step toward integrative multiomic microbiome analysis so as to understand dynamic taxonomic and functional responses of these complex systems in a variety of biological contexts. The updated metaQuantome and MT2MQ are open-source software and are available via the Galaxy Toolshed and GitHub.

ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework

The Earth Microbiome Project (EMP) aided in understanding the role of microbial communities and the influence of collective genetic material (the 'microbiome') and microbial diversity patterns across the habitats of our planet. With the evolution of new sequencing technologies, researchers can now investigate the microbiome and map its influence on the environment and human health. Advances in bioinformatics methods for next-generation sequencing (NGS) data analysis have helped researchers to gain an in-depth knowledge about the taxonomic and genetic composition of microbial communities. Metagenomic-based methods have been the most commonly used approaches for microbiome analysis; however, it primarily extracts information about taxonomic composition and genetic potential of the microbiome under study, lacking quantification of the gene products (RNA and proteins). On the other hand, metatranscriptomics, the study of a microbial community's RNA expression, can reveal the dynamic gene expression of individual microbial populations and the community as a whole, ultimately providing information about the active pathways in the microbiome.  In order to address the analysis of NGS data, the ASaiM analysis framework was previously developed and made available via the Galaxy platform. Although developed for both metagenomics and metatranscriptomics, the original publication demonstrated the use of ASaiM only for metagenomics, while thorough testing for metatranscriptomics data was lacking.  In the current study, we have focused on validating and optimizing the tools within ASaiM for metatranscriptomics data. As a result, we deliver a robust workflow that will enable researchers to understand dynamic functional response of the microbiome in a wide variety of metatranscriptomics studies. This improved and optimized ASaiM-metatranscriptomics (ASaiM-MT) workflow is publicly available via the ASaiM framework, documented and supported with training material so that users can interrogate and characterize metatranscriptomic data, as part of larger meta-omic studies of microbiomes.

ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework

The Human Microbiome Project (HMP) aided in understanding the role of microbial communities and the influence of collective genetic material (the 'microbiome') in human health and disease. With the evolution of new sequencing technologies, researchers can now investigate the microbiome and map its influence on human health. Advances in bioinformatics methods for next-generation sequencing (NGS) data analysis have helped researchers to gain an in-depth knowledge about the taxonomic and genetic composition of microbial communities. Metagenomic-based methods have been the most commonly used approaches for microbiome analysis; however, it primarily extracts information about taxonomic composition and genetic potential of the microbiome under study, lacking quantification of the gene products (RNA and proteins). Conversely, metatranscriptomics, the study of a microbial community's RNA expression, can reveal the dynamic gene expression of individual microbial populations and the community as a whole, ultimately providing information about the active pathways in the microbiome.  In order to address the analysis of NGS data, the ASaiM analysis framework was previously developed and made available via the Galaxy platform. Although developed for both metagenomics and metatranscriptomics, the original publication demonstrated the use of ASaiM only for metagenomics, while thorough testing for metatranscriptomics data was lacking.  In the current study, we have focused on validating and optimizing the tools within ASaiM for metatranscriptomics data. As a result, we deliver a robust workflow that will enable researchers to understand dynamic functional response of the microbiome in a wide variety of metatranscriptomics studies. This improved and optimized ASaiM-metatranscriptomics (ASaiM-MT) workflow is publicly available via the ASaiM framework, documented and supported with training material so that users can interrogate and characterize metatranscriptomic data, as part of larger meta-omic studies of microbiomes.

Hermaphroditism in the dash-and-dot goatfish Parupeneus barberinus

Presence of bisexual individuals and a sex-specific bimodal size distribution are suggestive of protogyny in the dash-and-dot goatfish Parupeneus barberinus, but the most parsimonious interpretation of histological analysis is juvenile hermaphroditism. This is the first report of hermaphroditism in the Mullidae.

Genotypic resistance testing in HIV-infected pregnant women in an urban setting

This study examines the utility of HIV genotypic resistance testing (GT) in pregnant women at their initial pregnancy evaluation. A retrospective medical record review of 50 consecutive HIV-infected pregnant women in whom GT was obtained in the Bronx, New York was conducted. Twenty-eight (56%) were antiretroviral experienced, including 12 on antiretroviral therapy (ART) at time of GT. Major mutations were found in 11 (24%) of 45 amplifiable GTs. Major resistance mutations were identified against nucleoside reverse transcriptase inhibitors (NRTIs) in six (13%) patients; against non-nucleoside reverse transcriptase inhibitors (NNRTIs) in eight (18%) patients, and against protease inhibitors in two (4%) patients. Duration of ART exposure was significantly associated with identification of resistance mutations by GT for NRTIs and NNRTIs ( P ≥0.05). Results of this study indicate that GT at presentation may have implications on the initial choice of ART in up to one-quarter of HIV-infected pregnant women, especially with current or prior antiretroviral use.

An empirical assessment of the focal species hypothesis

Biodiversity surrogates and indicators are commonly used in conservation management. The focal species approach (FSA) is one method for identifying biodiversity surrogates, and it is underpinned by the hypothesis that management aimed at a particular focal species will confer protection on co-occurring species. This concept has been the subject of much debate, in part because the validity of the FSA has not been subject to detailed empirical assessment of the extent to which a given focal species actually co-occurs with other species in an assemblage. To address this knowledge gap, we used large-scale, long-term data sets of temperate woodland birds to select focal species associated with threatening processes such as habitat isolation and loss of key vegetation attributes. We quantified co-occurrence patterns among focal species, species in the wider bird assemblage, and species of conservation concern. Some, but not all, focal species were associated with high levels of species richness. One of our selected focal species was negatively associated with the occurrence of other species (i.e., it was an antisurrogate)-a previously undescribed property of nominated focal species. Furthermore, combinations of focal species were not associated with substantially elevated levels of bird species richness, relative to levels associated with individual species. Our results suggest that although there is some merit to the underpinning concept of the FSA, there is also a need to ensure that actions are sufficiently flexible because management tightly focused on a given focal species may not benefit some other species, including species of conservation concern, such of which might not occur in species-rich assemblages.

Dimensional structure and course of post-traumatic stress symptomatology in World Trade Center responders

BACKGROUND

Post-traumatic stress disorder (PTSD) in response to the World Trade Center (WTC) disaster of 11 September 2001 (9/11) is one of the most prevalent and persistent health conditions among both professional (e.g. police) and non-traditional (e.g. construction worker) WTC responders, even several years after 9/11. However, little is known about the dimensionality and natural course of WTC-related PTSD symptomatology in these populations.

METHOD

Data were analysed from 10 835 WTC responders, including 4035 police and 6800 non-traditional responders who were evaluated as part of the WTC Health Program, a clinic network in the New York area established by the National Institute for Occupational Safety and Health. Confirmatory factor analyses (CFAs) were used to evaluate structural models of PTSD symptom dimensionality; and autoregressive cross-lagged (ARCL) panel regressions were used to examine the prospective interrelationships among PTSD symptom clusters at 3, 6 and 8 years after 9/11.

RESULTS

CFAs suggested that five stable symptom clusters best represent PTSD symptom dimensionality in both police and non-traditional WTC responders. This five-factor model was also invariant over time with respect to factor loadings and structural parameters, thereby demonstrating its longitudinal stability. ARCL panel regression analyses revealed that hyperarousal symptoms had a prominent role in predicting other symptom clusters of PTSD, with anxious arousal symptoms primarily driving re-experiencing symptoms, and dysphoric arousal symptoms primarily driving emotional numbing symptoms over time.

CONCLUSIONS

Results of this study suggest that disaster-related PTSD symptomatology in WTC responders is best represented by five symptom dimensions. Anxious arousal symptoms, which are characterized by hypervigilance and exaggerated startle, may primarily drive re-experiencing symptoms, while dysphoric arousal symptoms, which are characterized by sleep disturbance, irritability/anger and concentration difficulties, may primarily drive emotional numbing symptoms over time. These results underscore the importance of assessment, monitoring and early intervention of hyperarousal symptoms in WTC and other disaster responders.

Trajectories of PTSD risk and resilience in World Trade Center responders: an 8-year prospective cohort study

BACKGROUND

Longitudinal symptoms of post-traumatic stress disorder (PTSD) are often characterized by heterogeneous trajectories, which may have unique pre-, peri- and post-trauma risk and protective factors. To date, however, no study has evaluated the nature and determinants of predominant trajectories of PTSD symptoms in World Trade Center (WTC) responders.

METHOD

A total of 10835 WTC responders, including 4035 professional police responders and 6800 non-traditional responders (e.g. construction workers) who participated in the WTC Health Program (WTC-HP), were evaluated an average of 3, 6 and 8 years after the WTC attacks.

RESULTS

Among police responders, longitudinal PTSD symptoms were best characterized by four classes, with the majority (77.8%) in a resistant/resilient trajectory and the remainder exhibiting chronic (5.3%), recovering (8.4%) or delayed-onset (8.5%) symptom trajectories. Among non-traditional responders, a six-class solution was optimal, with fewer responders in a resistant/resilient trajectory (58.0%) and the remainder exhibiting recovering (12.3%), severe chronic (9.5%), subsyndromal increasing (7.3%), delayed-onset (6.7%) and moderate chronic (6.2%) trajectories. Prior psychiatric history, Hispanic ethnicity, severity of WTC exposure and WTC-related medical conditions were most strongly associated with symptomatic trajectories of PTSD symptoms in both groups of responders, whereas greater education and family and work support while working at the WTC site were protective against several of these trajectories.

CONCLUSIONS

Trajectories of PTSD symptoms in WTC responders are heterogeneous and associated uniquely with pre-, peri- and post-trauma risk and protective factors. Police responders were more likely than non-traditional responders to exhibit a resistant/resilient trajectory. These results underscore the importance of prevention, screening and treatment efforts that target high-risk disaster responders, particularly those with prior psychiatric history, high levels of trauma exposure and work-related medical morbidities.

Comparison of microarray preprocessing methods

Data preprocessing in microarray technology is a crucial initial step before data analysis is performed. Many preprocessing methods have been proposed but none has proved to be ideal to date. Frequently, datasets are limited by laboratory constraints so that the need is for guidelines on quality and robustness, to inform further experimentation while data are yet restricted. In this paper, we compared the performance of four popular methods, namely MAS5, Li & Wong pmonly (LWPM), Li & Wong subtractMM (LWMM), and Robust Multichip Average (RMA). The comparison is based on the analysis carried out on sets of laboratory-generated data from the Bioinformatics Lab, National Institute of Cellular Biotechnology (NICB), Dublin City University, Ireland. These experiments were designed to examine the effect of Bromodeoxyuridine (5-bromo-2-deoxyuridine, BrdU) treatment in deep lamellar keratoplasty (DLKP) cells. The methodology employed is to assess dispersion across the replicates and analyze the false discovery rate. From the dispersion analysis, we found that variability is reduced more effectively by LWPM and RMA methods. From the false positive analysis, and for both parametric and nonparametric approaches, LWMM is found to perform best. Based on a complementary q-value analysis, LWMM approach again is the strongest candidate. The indications are that, while LWMM is marginally less effective than LWPM and RMA in terms of variance reduction, it has considerably improved discrimination overall.

Pack wounds of donkeys and mules in the Northern High Atlas and lowlands of Morocco

REASONS FOR PERFORMING STUDY

Wounds are one of the primary welfare concerns of working equids and are often related to harness or load-bearing packs.

OBJECTIVES

To identify and quantify factors associated with the presence of pack wounds in donkeys and mules working in the wood trade in the Midelt (Northern High Atlas) region of Morocco, and to compare wounds of these donkeys and mules to those working in other trades.

METHODS

The study population comprised equids working in the Midelt region involved in the wood trade. Comparison populations were comprised of equids working in other trades, in the same region and in Khemmiset region (lowlands of Central Morocco). Wounds were numbered and scored according to their severity. Questionnaires were used to gather data from owners, and objective data regarding the animal, berdaa (back-pack) and load were collected. Data were analysed using multilevel uniand multivariable regression models to allow for clustering of wound sites within an equid.

RESULTS

Analysis showed an overall pack wound prevalence of 54% (n=80/147). The most common site was the withers. Equids working in the wood trade were at increased risk of suffering pack wounds. Equids in the lowland study population were at increased risk of developing pack wounds, and donkeys were at increased risk of suffering pack wounds compared to mules both overall and within the wood trade. Other factors affecting the prevalence of wounds included the cleanliness of the berdaa and the frequency and distances of work imposed on the equid.

CONCLUSION

Pack wounds in donkeys and mules are common in the 2 study regions of Morocco and appear to be associated with work factors including the trade the equids work in, the frequency and distances of work imposed and cleanliness of the pack. Donkeys are more susceptible than mules to developing pack wounds.

POTENTIAL RELEVANCE

These results allow recommendations to be made to owners of equids that may decrease the prevalence of wounds and, therefore, improve welfare and working capability of these equids. Research is required to identify reasons for regional difference in prevalence of pack wounds in equids not working in the wood trade.

136. SPECIFICITY STUDIES ON THE IMMUNOSUPPRESSIVE AND CYTOTOXIC ACTIVITIES OF LYSOPHOSPHATIDYLCHOLINES (LPCs) OF GONADAL ORIGIN

The immunosuppressive activity of ovarian follicular fluid and testicular interstitial fluid is due to the presence of several LPCs, but the specificity of this inhibition is a potential source of controversy, as these molecules also possess lytic activity. In the following study, we compared the immunosuppressive and cytotoxic activities of the two most abundant gonadal LPCs, 1-palmitoyl-sn-glycero-3-phosphocholine (16:0aLPC) and 1-oleoyl-sn-glycero-3-phosphocholine (18:1aLPC), together with a number of related lysophospholipids (LPs), using a T-cell activation inhibition assay and an ovarian granulosa cell viability assay. Both the immunosuppressive and cytotoxic activities of the LPCs were blocked by serum (>5%) and serum albumin (>5mg/ml) in vitro. In the absence of serum proteins, the most immunosuppressive LPCs were 16:0aLPC, 18:0aLPC, 18:1aLPC and platelet activating factor (PAF; 1-O-palmitoyl-2-O-acetyl-sn-glycero-3-phosphocholine) with IC50 values of 1.2-4.3 μM. Curiously, PAF was the LPC most cytotoxic to granulosa cells (IC50 10 μM). The other immunosuppressive LPCs exhibited cytotoxicity within the range of 40-50 μM, i.e. at doses 10–50-fold higher than their immunosuppressive concentrations. Comparison of LPs of different structures indicated that optimal immunosuppression is related to a phosphocholine, but not serine, ethanolamine or phosphate group, at sn-3, and an ester- or ether-linked fatty acid of chain length C16-C18 at sn-1. Acetylation of sn-2, as in PAF, had only minor effects on immunosuppressive activity, but greatly increased cytotoxicity. These data establish that inhibition of activated T-cells is not a direct consequence of the cytotoxicity of these molecules, although some structural features that contribute to lytic activity, such as fatty acid chain length, overlap with the ability to confer immunosuppression. On the basis of these data, we propose that the effects of LPCs on T-cell proliferation may not be mediated by a specific lock-and-key receptor, but rather by a direct interaction with the cell membrane at concentrations significantly below their lytic concentrations.

Contrasting mammal responses to vegetation type and fire

The response of terrestrial mammals and arboreal marsupials to past burning history as well as a year prior to, and then for 4 years after, a major wildfire in 2003 at Booderee National Park, Jervis Bay Territory was quantified. The present study encompassed extensive repeated surveys at a set of 109 replicated sites stratified by vegetation type and fire history. It was found that most species exhibited significant differences in presence and abundance between major vegetation types. Detections of long-nosed bandicoot (Perameles nasuta) increased significantly in all vegetation types surveyed, in both burnt and unburnt areas. Temporal patterns in captures of three species of small mammals (bush rat (Rattus fuscipes), swamp rat (Rattus lutreolus) and brown antechinus (Antechinus stuartii)) showed a trend for lower numbers of captures on burnt sites compared with unburnt sites. Three species of arboreal marsupials, common ringtail possum (Pseudocheirus peregrinus), greater glider (Petauroides volans) and common brushtail possum (Trichosurus vulpecula), were moderately common and all showed marked differences in abundance between vegetation types. Whereas P. peregrinus and P. volans exhibited a temporal decline between 2003 and 2006, T. vulpecula exhibited a general increase from 2003 levels. However, arboreal marsupial responses did not appear to be directly fire related.

Changes in survival characteristics ofDiplostomum spathaceumcercariae emerged from cadmium-exposedLymnaea stagnalis

The effect of exposingLymnaea stagnalis(Gastropoda: Pulmonata), infected withDiplostomum spathaceum(Trematoda: Diplostomatidae), to 100 μg l−1cadmium for 7 days on survival characteristics (survival, tail loss, decaudized cercarial life-span) of emerged cercariae was investigated. Exposure ofL. stagnalisto cadmium resulted in significantly increasedD. spathaceumcercarial survival and an inhibited tail loss compared to controls. The normal parallel relationship which exists over time between decreasing cercarial survival and increasing tail loss in controls was changed in cercariae from cadmium-exposed hosts with an increased proportion of cercarial deaths occurring without tail loss. The decaudized cercarial life-span over the survival period of the cercarial population did not significantly change. However comparisons between individuals decaudized during the initial 24 h time period with those which were decaudized during the final period of cercarial survival showed a significantly altered life span which did not occur in the control population. As a potential indicator of penetration ‘fitness’ comparisons were also undertaken between control and exposed cercariae decaudized during the initial 24 h time period, which revealed that the decaudized cercarial life-span from the exposed hosts was significantly different from controls. This may have important implications for the ability of cercariae to migrate through the tissues of their target host. The importance and relevance of these results to parasite transmission are discussed.

Influence of cadmium exposure on the incidence of first intermediate host encystment by Echinoparyphium recurvatum cercariae in Lymnaea peregra

The effect of cadmium exposure of the snail first intermediate host Lymnaea peregra on the incidence of encystment of Echinoparyphium recurvatum (Digenea: Echinostomatidae) cercariae without emergence from the snail was investigated. Exposure to 100 μg l−1 Cd for 72 h caused a significant increase in the incidence of first host encystment when compared to controls. In addition, autometallographic staining of E. recurvatum daughter rediae and developing cercariae showed that there was metal accumulation within their body tissues. The significance of these findings to parasite transmission in metal-polluted environments is discussed.

Toxicity of cadmium and zinc mixtures to the decaudized cercarial life span ofDiplostomum spathaceum

The effects of cadmium and zinc mixtures at concentrations ranging from 0.1 to 10,000 μg l−1on the life-span of decaudized cercarial bodies (cercariae that have shed their tails) ofDiplostomum spathaceum(Trematoda: Diplostomatidae) was investigated. Cercariae were exposed to metal mixtures of equal and unequal concentrations, and a low-dose pre-treatment followed by a high-dose exposure mixtures. Metal mixtures demonstrated variable effects on decaudized cercariae either by increasing or reducing their life-span compared to single metal exposures dependent on concentration and the type of mixed metal treatment. Prolonged exposure to equal metal mixtures at low concentrations (0.1–100 μg l−1) resulted in a reduction in the life-span of decaudized cercariae at 0.1 and 100 μg l−1in those individuals decaudized during the initial 24 h exposure period compared with those decaudized during the final 24 h period of cercarial survival, whilst in controls there was no significant life-span change between the two time periods. Decaudized cercariae which were exposed to low concentrations (0.1–100 μg l−1) of equal metal mixtures were also evaluated for their role as an indicator of larval ‘fitness’ for migrating through the tissues of their target fish host for those individuals decaudized during the initial 24 h exposure period, and demonstrated only a limited change in their life-span compared to control and single metal exposures. The importance of metal mixtures in parasite establishment in the fish host is discussed.

Optimisation and parallelisation strategies for Monte Carlo simulation of HIV infection

In recent years, the study of immune response behaviour through mathematical and computational models has attracted considerable efforts. The dynamics of key cell types, and their interactions, has been a primary focus in terms of building a picture of how the immune system responds to a threat. Discrete methods, based on lattice Monte-Carlo (MC) models, with their flexibility and relative simplicity have previously been used to model the immune system behaviour. However, due to speed and memory constraints, large-scale simulations cannot be done on a single computer. Key issues in the reduction of simulation time are code optimisation and code parallelisation. In this paper, optimisation and parallelisation solutions are discussed, with reference to existing MC simulation code for dynamics of HIV infection.

Longevity in wild populations of the squirrel glider Petaurus norfolcensis

Petaurus norfolcensis were trapped between December 1996 and April 2005 at 3 sites in south-eastern Australia. In 2005 nine individuals marked in previous years were captured. Age estimates at first capture were based on body mass, tooth wear and pouch condition. Most recaptured individual were propertly assigned to the correct age category (>3 years), but the age of 2 were underestimated. This indicates uncertainty in using physical characteristics, chiefly wear of upper incisors, to estimate age in P. norfolcensis.One individual captured in 2005 was over 7 years 9 months old. This compares to captive P. breviceps and P. australis records of 9 years and 16 years respectively.

Case Study Part 1: How to calculate appropriate deterministic long-term toxicity to exposure ratios (TERs) for birds and mammals

In the European Union, first-tier assessment of the long-term risk to birds and mammals from pesticides is based on calculation of a deterministic long-term toxicity/exposure ratio (TER(lt)). The ratio is developed from generic herbivores and insectivores and applied to all species. This paper describes two case studies that implement proposed improvements to the way long-term risk is assessed. These refined methods require calculation of a TER for each of five identified phases of reproduction (phase-specific TERs) and use of adjusted No Observed Effect Levels (NOELs) to incorporate variation in species sensitivity to pesticides. They also involve progressive refinement of the exposure estimate so that it applies to particular species, rather than generic indicators, and relates spraying date to onset of reproduction. The effect of using these new methods on the assessment of risk is described. Each refinement did not necessarily alter the calculated TER value in a way that was either predictable or consistent across both case studies. However, use of adjusted NOELs always reduced TERs, and relating spraying date to onset of reproduction increased most phase-specific TERs. The case studies suggested that the current first-tier TER(lt )assessment may underestimate risk in some circumstances and that phase-specific assessments can help identify appropriate risk-reduction measures. The way in which deterministic phase-specific assessments can currently be implemented to enhance first-tier assessment is outlined.

Case Study Part 2: Probabilistic modelling of long-term effects of pesticides on individual breeding success in birds and mammals

Long term exposure of skylarks to a fictitious insecticide and of wood mice to a fictitious fungicide were modelled probabilistically in a Monte Carlo simulation. Within the same simulation the consequences of exposure to pesticides on reproductive success were modelled using the toxicity-exposure-linking rules developed by R.S. Bennet et al. (2005) and the interspecies extrapolation factors suggested by R. Luttik et al. (2005). We built models to reflect a range of scenarios and as a result were able to show how exposure to pesticide might alter the number of individuals engaged in any given phase of the breeding cycle at any given time and predict the numbers of new adults at the season's end.

303. Further characterisation of lymphocyte-suppressing activity in gonadal fluids

Protection of the developing gametes from an autoimmune response within the testis and ovary is essential for reproductive success, and autoimmune infertility represents a failure of this protection. The gonads also represent favorable sites for grafts of foreign tissue, that is, they are ‘immunologically privileged’. The actual mechanisms responsible for testicular and ovarian immune privilege are poorly understood. However, it has been well established that testicular interstitial fluid and ovarian fluid have profound inhibitory effects on T-cell activation and proliferation in vitro. We have established previously that a partially purified preparation of the inhibitor, isolated from bovine follicular fluid, suppresses proliferation in an in vitro T-cell activation assay, through induction of T-cell anergy and/or atypical apoptosis. Addition of increasing doses of normal fetal calf serum and/or bovine serum albumin blocks the actions of the inhibitor and progressively increases the ED50 of the assay. It has also been shown that stimulating the T-cells with phorbol-12-myristate-13-acetate (PMA) in place of a polyclonal mitogenic stimulus such as phytohaemagglutinin bypasses the anergic effects of the inhibitor. These results suggest that the activity of the inhibitor may be negatively regulated in the circulation and tissues by serum-derived proteins and other factors. These data also indicate that the inhibitor’s activity is mediated through a specific cellular pathway, most likely involving protein kinase C isotypes, which are activated by PMA. Further work will delineate the molecular pathways and mechanisms of serum regulation of the gonadal lymphocyte-suppressing activity, which may be exploited in the treatment of autoimmune diseases and for prevention of transplant rejection.

Toxicity of cadmium and zinc mixtures to cercarial tail loss in Diplostomum spathaceum (Trematoda:Diplostomidae)

The effects of cadmium and zinc mixtures on tail loss of the free-living cercarial stage of the parasitic fluke Diplostomum spathaceum were investigated at concentrations ranging from 0.1 to 10,000 microg/L. Cercariae were exposed to metal mixtures of equal concentrations, metal mixtures of unequal concentrations, and a low-dose pretreatment followed by high-dose exposure mixtures. Under control conditions as the cercarial population aged tail loss occurred naturally a few hours before death, with an increasing tail loss over time associated with a decrease in cercarial survival. Under all mixture exposures the period of tail loss was prolonged compared to single-metal exposures. In most test solutions this was associated with a similar increase in survival of cercariae. Inhibition of tail loss occurred in low concentrations (0.1-100 microg/L) of equal mixed exposures. In some unequal, and in all pretreatment mixture exposures, a significant stimulation of tail loss occurred compared to the pattern of decreasing survival over time within the cercarial population. The importance of toxic metal mixtures to cercarial tail loss and potential implications for successful parasite transmission are discussed.

Toxicity of anti-fouling biocides to encysted metacercariae of Echinoparyphium recurvatum (Digenea: Echinostomatidae) and their snail hosts

The toxicity of the anti-fouling biocides tributyltin (TBTO), copper, and Irgarol 1051 (irgarol) at a nominal concentration of 10 microg/l over a 30 day period were investigated against the viability of metacercarial cysts of the digenean parasite Echinoparyphium recurvatum resident within the body of two common freshwater snails, Lymnaea peregra and Physa fontinalis. Reduced parasite viability was found under most exposures in both snail species. However a greater effect of toxicant exposure was found in cysts within P. fontinalis compared to those in L. peregra. This was associated with an increased mortality of the host snail. Among all tested biocides, TBTO exposures induced the highest mortality to both the parasite and their hosts. These results suggest that parasite viability is interlinked with survival of the host snail. The mechanisms of differing toxicity between host species and its relevance to successful parasite transmission to the next host are discussed.

Ultrasonic sludge treatment for enhanced anaerobic digestion

Ultrasound is the term used to describe sound energy at frequencies above 20 kHz. High-powered ultrasound can be applied to a waste stream via purpose-designed tools in order to induce cavitation. This effect results in the rupture of cellular material and reduction of particle size in the waste stream, making the cells more amenable to downstream processing. sonix is a new technology utilising high-powered, concentrated ultrasound for conditioning sludges prior to further treatment. This paper presents recent results from a number of demonstration and full-scale plants treating thickened waste activated sludge (TWAS) prior to anaerobic digestion, therefore enhancing the process. The present studies have proved that the use of ultrasound to enhance anaerobic digestion can be achieved at full scale and effectively result in the TWAS (typically difficult to digest) behaving, after sonication, as if it were a "primary" sludge. The technology presents benefits in terms of increased biogas production, better solids reduction, improved dewatering characteristics of the digested sludge mixture and relatively short payback periods of two years or less subject to the site conditions and practices applicable at that time.

259.Identification of elevated levels of apoptosis among T-cells isolated from the rat testis

Protection of the developing gametes from attack by the immune system is essential for reproductive success. Autoimmune infertility represents a failure of this protection. Specific T-cell apoptosis is the main mechanism for control of antigen-specific immune responses. Studies were undertaken to investigate this regulatory process in adult rat testes. Flow cytometry was employed in conjunction with annexin-V/propidium iodide dual staining to identify apoptotic cells concurrent with CD3 staining to identify T-cells. CD3-positive cells isolated from the testicular interstitial tissue were shown to be 34.12���3.0% apoptotic (mean���s.e.m., n�=�3) at collection. This was consistently greater than the numbers of apoptotic CD3-positive cells isolated from lymph nodes (4.04���1.95%, n�=�2), spleen (16.77���4.73%, n�=�4) and peripheral blood (9.64���1.44%, n�=�2). These results also were confirmed by using T-cells purified with MACS microbeads against the pan T-cell marker OX52 to improve sample purity: 40% of isolated testicular T-cells and 3% lymph node T-cells were found to be undergoing apoptosis. The level of apoptosis among T-cells isolated from another non-lymphoid organ, the liver, was only 6%. It is hypothesised that the immunosuppressive milieu of the testis induces an increased level of apoptotic deletion among T-cells that gain entry into the testis and potentially threaten gamete viability. Further studies of the mechanism responsible for this elevated level of T-cell apoptosis in the testis will significantly enhance our knowledge of how testicular immune tolerance is maintained.

Toxicity of cadmium and zinc to the decaudised cercarial life-span of Diplostomum spathaceum (Trematoda: Diplostomidae)

The toxicity of cadmium and zinc at concentrations ranging from 0·1 to 10 000 μg/l to the life-span of decaudised cercarial bodies (cercariae that have shed their tails) of Diplostomum spathaceum was investigated. The effects of metal exposure at 3 temperatures (12, 20, and 25 °C) and 3 levels of water hardness (distilled water, soft water and hard water) were studied. In general, under most experimental conditions increasing metal concentrations reduced the life-span of decaudised cercariae. Increasing water hardness and decreasing water temperature caused an increase in the life-span of both control and metal exposed decaudised cercariae. However, at certain isolated metal concentrations, associated with a specific level of water hardness and temperature, increased survival above controls occurred. Differences in the relative toxicity of cadmium and zinc were dependent on the environmental conditions of exposure. The decaudised cercarial life-span under metal exposure was found to be generally independent of the overall cercarial survival and tail loss in most experimental conditions. Prolonged exposure to cadmium and zinc caused changes in the decaudised cercarial life-span when compared to individuals decaudised during the initial 24 h exposure period to those which were decaudised during the final 24 h period of cercarial survival. The validity of studying the decaudised cercarial life-span as an indicator of ‘fitness’ of larvae to migrate through the tissues of the target fish host, in terms of glycogen utilization, was assessed for those cercariae decaudised during the initial 24 h exposure period only. A limited reduction in the decaudised cercarial life-span during this period compared to controls was recorded, which may possibly indicate a reduced penetration ‘fitness’ of cercariae exposed to cadmium and zinc. The importance and relevance of these findings to parasite migration and establishment in the fish host are discussed.

Incorporation of in situ and biomarker assays in higher-tier assessment of the aquatic toxicity of insecticides

This study was designed to test the feasibility of integrating in situ, single species exposures and biomarker analysis into microcosm studies. Experimental ponds were dosed with pirimiphos methyl (PM) and lindane. C. riparius fourth instar larvae were deployed for 48h on nine separate occasions during the study period before and after treatment. Surviving larvae were analysed for acetylcholinesterase activity (AChE). Survival and biomarker data were compared to chironomid assemblage analysis by monitoring insects emerging from the microcosms. Survival of chironomids within the in situ systems commenced on day +16 after treatment with 31.6% and 53.3% survival in the lindane and PM treated ponds, respectively. In contrast, the first emergence from the microcosms occurred on days +27, in respect to lindane, and +59 for the PM treated ponds. Thus the in situ bioassay was able to demonstrate gradual reduction in toxicity within the sediment before this was evident from macroinvertebrate monitoring. Significant AChE inhibition was only detected on exposure to PM. Levels decreased from 75% on day +16 to 26% by day +29. The biomarker analysis confirmed that, by the end of the study, the insecticide was no longer exerting an effect. We discuss how the use of in situ bioassays could also aid comparison of microcosm studies by adding a standardized dimension.

Effects of cadmium and zinc toxicity on orientation behaviour of Echinoparyphium recurvatum (Digenea: Echinostomatidae) cercariae

The effects of cadmium and zinc toxicity on orientation behaviour (photo- and geo-taxis) of Echinoparyphium recurvatum cercariae was investigated at concentrations ranging from 10 to 1000 microg l(-1). Exposure to the toxicants at all metal concentrations caused a change in orientation to negative phototaxis and positive geotaxis during the submaximal dispersal phase (0.5 h cercarial age). Autometallography staining of cercariae exposed to 1000 microg l(-1) cadmium or zinc showed selective binding of heavy metals to tegumental surface sites associated with sensory receptors. The significance to parasite transmission of changes in cercarial orientation behaviour in metal polluted environments is discussed.

Toxicity of anti-fouling biocides to Parorchis acanthus (Digenea: Philophthalmidae) cercarial encystment

The toxicity of the anti-fouling biocides tributyltin (TBTO), copper, and Irgarol 1051 (irgarol) at nominal concentrations ranging from 10 to 10,000 microg l(-1) was investigated against the speed of encystment and successful formation of a protective cyst of the cercariae of Parorchis acanthus. For all biocide exposures, cercariae had a much slower rate of encystment and reduced cyst formation than controls. Exposure of the snail host Nucella lapillus for 7 d caused complete cessation of cercarial shedding in irgarol-exposed snails but had no effect on cercarial encystment from TBTO and copper-exposed snails. The mechanisms of toxicity of the biocides are briefly discussed.

Differences in immunocontraceptive responses in white-tailed deer (Odocoileus virginianus) and goats (Capra hircus)

Thirteen deer (Odocoileus virginianus) and three goats (Capra hircus) were given an initial immunization of 300 microg porcine zona pellucida (PZP) combined with 50 mg synthetic trehalose dicorynomycolate ml(-1) (STDCM) in drakeol i.m. in the semitendinosus and semimembranosus muscles. This immunization was followed by two booster injections of 300 microg PZP, 2 weeks apart. The vaccinations were made from the same purified batch of PZP and lot of adjuvant. All the doses were made at the same time and injected on the same day. The immune response was quantified by measuring serum anti-PZP IgG antibody concentration by ELISA. The results showed that the mean serum IgG concentration of the deer increased from 0.000 +/- 0.003 to 0.083 +/- 0.023 absorbance units, whereas in the goats the mean IgG concentration increase was from 0.044 +/- 0.019 to 1.245 +/- 0.774 absorbance units. Both the goats and deer showed a significant increase in IgG concentration (P < 0.05) after the final booster injection compared with preimmune serum. The final goat IgG concentration was significantly (P < 0.05) higher than that of the deer. If PZP and Freund's adjuvant are administered to deer, immunocontraception is achieved, but the IgG concentration in the deer in this study did not appear to be compatible with immunocontraception.

Is there a relationship between soil and groundwater toxicity?

Part IIA of the Environmental Protection Act 1990 requires environmental regulators to assess the risk of contaminants leaching from soils into groundwater (DETR, 1999). This newly introduced legislation assumes a link between soil and groundwater chemistry, in which rainwater leaches contaminants from soil into the saturated zone. As the toxicity of both groundwater and overlying soils is dependent upon the chemicals present, their partitioning and their bioavailability, similar patterns of soil, leachates and groundwater toxicity should be observed at contaminated sites. Soil and groundwater samples were collected from different contaminated land sites in an urban area, and used to determine relationships between soil chemistry and toxicity, mobility of contaminants, and groundwater chemistry and toxicity. Soils were leached using water to mimic rainfall, and both the soils and leachates tested using bioassays. Soil bioassays were carried out using Eisenia fetida, whilst groundwater and leachates were tested using the Microtox test system and Daphnia magna 48 h acute tests. Analysis of the bioassay responses demonstrated that a number of the samples were toxic to test organisms, however, there were no significant statistical relationships between soil, groundwater and leachate toxicity. Nor were there significant correlations between soil, leachates and groundwater chemistry.

Cadmium toxicity and snail-digenean interactions in a population of Lymnaea spp

The toxicity of cadmium to a population of Lymnaea peregra and L. stagnalis naturally infected with a range of digeneans and collected from a number of sites in the lower Thames Valley, UK was investigated. Lymnaeid snails were exposed to 100 microg l-1 cadmium and the effects on host survival and emergence of cercariae recorded. Overwintered L. peregra, but not L. stagnalis, showed significantly reduced survival compared to seasonally infected snails, i.e. snails which have acquired an infection during the spring or summer. A significant increase in survival with increasing snail size was demonstrated for L. stagnalis and for seasonally infected L. peregra only. Only L. stagnalis infected with Diplostomum spathaceum and L. peregra infected individually with D. spathaceum, Sanguinicola inermis, Echinoparyphium recurvatum and Notocotylus attenuatus demonstrated a significantly reduced survival compared to laboratory-bred controls. The exposure of L. stagnalis to cadmium resulted in a significant reduction in the emergence of D. spathaceum over a 5-day period but cadmium-exposed L. peregra showed no difference in the emergence of E. recurvatum cercariae over a 3-day exposure period. The mechanisms and importance of metal toxicity to snail-digenean interactions are discussed.

The use of nest boxes by arboreal marsupials in the forests of the Central Highlands of Victoria

The results are reported of a nest-box study conducted in two locations in the mountain ash (Eucalyptus regnans) forests of the Central Highlands of Victoria (south-eastern Australia) to compare usage of different nest-box designs located at different heights in trees. A total of 96 nest boxes was established using a rigorous experimental design – two regions (Powelltown and Toolangi State Forests), two forest age classes (20-year post-logging regrowth and 60-year fire- and salvage-logging regrowth), two nest-box designs (large boxes with large entrance holes and small boxes with small entrance holes), and two heights at which nest boxes were attached to trees (3 m and 8 m above the ground). The study entailed setting out four nest boxes at each of 24 sites to meet the design criteria. Evidence of occupancy by vertebrates was recorded in a total of 19 of 96 boxes on 11 of 24 sites site during regular inspections over more than three years. Thirteen boxes were used by Leadbeater's possum (Gymnobelideus leadbeateri), six by the mountain brushtail possum (Trichosurus cunninghami) and seven by the common ringtail possum (Pseudocheirus peregrinus). The common ringtail possum and mountain brushtail possum were seen only in high–large boxes but Leadbeater's possum used all but the low–large boxes. There was evidence of spatial dependence in usage patterns, with all four boxes at a given site showing signs of eventually being occupied. Only two nest boxes located in mountain ash forest regenerating after the 1939 wildfires were occupied. Relatively limited use of nest boxes supports concerns about the use of a nest box over large scales and long timeframes as an effective recovery tool for species threatened by the loss and subsequent shortage in the numbers of naturally occurring hollows.

Toxicity of cadmium and zinc to encystment of Notocotylus attenuatus (Trematoda: Notocotylidae) cercariae

The toxicity of cadmium, zinc, and cadmium/zinc mixtures at concentration ranging from 100 to 10,000 microg/L was investigated against the encystment strategy of free-living metacercarial stages of the parasitic fluke Notocotylus attenuatus. Exposure of encysting cercariae caused a reduction in encystment by all metals at concentrations of 1000 microg/L or higher. The formation of cyst associations was reduced in all metal-polluted test solutions. In addition, there was an increase in the number of floating metacercariae (cysts formed when not in contact with any surface) at low metal concentrations. The effects of metal toxicity to encystment strategy and its influence on transmission to the target host are briefly discussed.