Public health and landfill sites

Landfill management is a complex discipline, requiring very high levels of organisation, and considerable investment. Until the early 1990’s most Irish landfill sites were not managed to modern standards. Illegal landfill sites are, of course, usually not managed at all. Landfills are very active. The traditional idea of ‘put it in the ground and forget about it’ is entirely misleading. There is a lot of chemical and biological activity underground. This produces complex changes in the chemistry of the landfill, and of the emissions from the site. The main emissions of concern are landfill gases and contaminated water (which is known as leachate). Both of these emissions have complex and changing chemical compositions, and both depend critically on what has been put into the landfill. The gases spread mainly through the atmosphere, but also through the soil, while the leachate (the water) spreads through surface waters and the local groundwater. Essentially all unmanaged landfills will discharge large volumes of leachate into the local groundwater. In sites where the waste accepted has been properly regulated, and where no hazardous wastes are present, there is a lot known about the likely composition of this leachate and there is some knowledge of its likely biological and health effects. This is not the case for poorly regulated sites, where the composition of the waste accepted is unknown. It is possible to monitor the emissions from landfills, and to reduce some of the adverse health and environmental effects of these. These emissions, and hence the possible health effects, depend greatly on the content of the landfill, and on the details of the local geology and landscape. There is insufficient evidence to demonstrate a clear link between cancers and exposure to landfill, however, it is noted that there may be an association with adverse birth outcomes such as low birth weight and birth defects. It should be noted, however, that modern landfills, run in strict accordance with standard operation procedures, would have much less impact on the health of residents living in proximity to the site

Cubic Curves, Finite Geometry and Cryptography

Some geometry on non-singular cubic curves, mainly over finite fields, is surveyed. Such a curve has 9,3,1 or 0 points of inflexion, and cubic curves are classified accordingly. The group structure and the possible numbers of rational points are also surveyed. A possible strengthening of the security of elliptic curve cryptography is proposed using a `shared secret' related to the group law. Cubic curves are also used in a new way to construct sets of points having various combinatorial and geometric properties that are of particular interest in finite Desarguesian planes.Comment: This is a version of our article to appear in Acta Applicandae Mathematicae. In this version, we have corrected a sentence in the third paragraph. The final publication is available at springerlink.com at http://www.springerlink.com/content/xh85647871215644

The genome sequence of <i>Trypanosoma brucei gambiense</i>, causative agent of chronic Human African Trypanosomiasis

&lt;p&gt;&lt;b&gt;Background:&lt;/b&gt; &lt;i&gt;Trypanosoma brucei gambiense&lt;/i&gt; is the causative agent of chronic Human African Trypanosomiasis or sleeping sickness, a disease endemic across often poor and rural areas of Western and Central Africa. We have previously published the genome sequence of a &lt;i&gt;T. b. brucei&lt;/i&gt; isolate, and have now employed a comparative genomics approach to understand the scale of genomic variation between &lt;i&gt;T. b. gambiense&lt;/i&gt; and the reference genome. We sought to identify features that were uniquely associated with &lt;i&gt;T. b. gambiense&lt;/i&gt; and its ability to infect humans.&lt;/p&gt; &lt;p&gt;&lt;b&gt;Methods and findings:&lt;/b&gt; An improved high-quality draft genome sequence for the group 1 &lt;i&gt;T. b. gambiense&lt;/i&gt; DAL 972 isolate was produced using a whole-genome shotgun strategy. Comparison with &lt;i&gt;T. b. brucei&lt;/i&gt; showed that sequence identity averages 99.2% in coding regions, and gene order is largely collinear. However, variation associated with segmental duplications and tandem gene arrays suggests some reduction of functional repertoire in &lt;i&gt;T. b. gambiense&lt;/i&gt; DAL 972. A comparison of the variant surface glycoproteins (VSG) in &lt;i&gt;T. b. brucei&lt;/i&gt; with all &lt;i&gt;T. b. gambiense&lt;/i&gt; sequence reads showed that the essential structural repertoire of VSG domains is conserved across &lt;i&gt;T. brucei&lt;/i&gt;.&lt;/p&gt; &lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; This study provides the first estimate of intraspecific genomic variation within &lt;i&gt;T. brucei&lt;/i&gt;, and so has important consequences for future population genomics studies. We have shown that the &lt;i&gt;T. b. gambiense&lt;/i&gt; genome corresponds closely with the reference, which should therefore be an effective scaffold for any &lt;i&gt;T. brucei&lt;/i&gt; genome sequence data. As VSG repertoire is also well conserved, it may be feasible to describe the total diversity of variant antigens. While we describe several as yet uncharacterized gene families with predicted cell surface roles that were expanded in number in &lt;i&gt;T. b. brucei&lt;/i&gt;, no &lt;i&gt;T. b. gambiense&lt;/i&gt;-specific gene was identified outside of the subtelomeres that could explain the ability to infect humans.&lt;/p&gt

Population gene introgression and high genome plasticity for the zoonotic pathogen Streptococcus agalactiae

The influence that bacterial adaptation (or niche partitioning) within species has on gene spillover and transmission among bacteria populations occupying different niches is not well understood. Streptococcus agalactiae is an important bacterial pathogen that has a taxonomically diverse host range making it an excellent model system to study these processes. Here we analyze a global set of 901 genome sequences from nine diverse host species to advance our understanding of these processes. Bayesian clustering analysis delineated twelve major populations that closely aligned with niches. Comparative genomics revealed extensive gene gain/loss among populations and a large pan-genome of 9,527 genes, which remained open and was strongly partitioned among niches. As a result, the biochemical characteristics of eleven populations were highly distinctive (significantly enriched). Positive selection was detected and biochemical characteristics of the dispensable genes under selection were enriched in ten populations. Despite the strong gene partitioning, phylogenomics detected gene spillover. In particular, tetracycline resistance (which likely evolved in the human-associated population) from humans to bovine, canines, seals, and fish, demonstrating how a gene selected in one host can ultimately be transmitted into another, and biased transmission from humans to bovines was confirmed with a Bayesian migration analysis. Our findings show high bacterial genome plasticity acting in balance with selection pressure from distinct functional requirements of niches that is associated with an extensive and highly partitioned dispensable genome, likely facilitating continued and expansive adaptation

From international health to global health: how to foster a better dialogue between empirical and normative disciplines.

BACKGROUND: Public health recommendations are usually based on a mixture of empirical evidence and normative arguments: to argue that authorities ought to implement an intervention that has proven effective in improving people's health requires a normative position confirming that the authorities are responsible for improving people's health. While public health (at the national level) is based on a widely accepted normative starting point - namely, that it is the responsibility of the state to improve people's health - there is no widely accepted normative starting point for international health or global health. As global health recommendations may vary depending on the normative starting point one uses, global health research requires a better dialogue between researchers who are trained in empirical disciplines and researchers who are trained in normative disciplines. DISCUSSION: Global health researchers with a background in empirical disciplines seem reluctant to clarify the normative starting point they use, perhaps because normative statements cannot be derived directly from empirical evidence, or because there is a wide gap between present policies and the normative starting point they personally support. Global health researchers with a background in normative disciplines usually do not present their work in ways that help their colleagues with a background in empirical disciplines to distinguish between what is merely personal opinion and professional opinion based on rigorous normative research. If global health researchers with a background in empirical disciplines clarified their normative starting point, their recommendations would become more useful for their colleagues with a background in normative disciplines. If global health researchers who focus on normative issues used adapted qualitative research guidelines to present their results, their findings would be more useful for their colleagues with a background in empirical disciplines. Although a single common paradigm for all scientific disciplines that contribute to global health research may not be possible or desirable, global health researchers with a background in empirical disciplines and global health researchers with a background in normative disciplines could present their 'truths' in ways that would improve dialogue. This paper calls for an exchange of views between global health researchers and editors of medical journals

Virulence related sequences: insights provided by comparative genomics of Streptococcus uberis of differing virulence

Background: Streptococcus uberis, a Gram-positive, catalase-negative member of the family Streptococcaceae is an important environmental pathogen responsible for a significant proportion of subclinical and clinical bovine intramammary infections. Currently, the genome of only a single reference strain (0140J) has been described. Here we present a comparative analysis of complete draft genome sequences of an additional twelve S. uberis strains. Results: Pan and core genome analysis revealed the core genome common to all strains to be 1,550 genes in 1,509 orthologous clusters, complemented by 115-246 accessory genes present in one or more S. uberis strains but absent in the reference strain 0140J. Most of the previously predicted virulent genes were present in the core genome of all 13 strains but gene gain/loss was observed between the isolates in CDS associated with clustered regularly interspaced short palindromic repeats (CRISPRs), prophage and bacteriocin production. Experimental challenge experiments confirmed strain EF20 as non-virulent; only able to infect in a transient manner that did not result in clinical mastitis. Comparison of the genome sequence of EF20 with the validated virulent strain 0140J identified genes associated with virulence, however these did not relate clearly with clinical/non-clinical status of infection. Conclusion: The gain/loss of mobile genetic elements such as CRISPRs and prophage are a potential driving force for evolutionary change. This first “whole-genome” comparison of strains isolated from clinical vs non-clinical intramammary infections including the type virulent vs non-virulent strains did not identify simple gene gain/loss rules that readily explain, or be confidently associated with, differences in virulence. This suggests that a more complex dynamic determines infection potential and clinical outcome not simply gene content

Evolutionary genomics of a cold-adapted diatom: Fragilariopsis cylindrus

The Southern Ocean houses a diverse and productive community of organisms1, 2. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice3, 4, 5, 6, 7. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-adapted diatom from the Southern Ocean, Fragilariopsis cylindrus8, 9, based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO2. Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation. Divergent alleles may be involved in adaptation to environmental fluctuations in the Southern Ocean

Sequence of a complete chicken BG haplotype shows dynamic expansion and contraction of two gene lineages with particular expression patterns.

Many genes important in immunity are found as multigene families. The butyrophilin genes are members of the B7 family, playing diverse roles in co-regulation and perhaps in antigen presentation. In humans, a fixed number of butyrophilin genes are found in and around the major histocompatibility complex (MHC), and show striking association with particular autoimmune diseases. In chickens, BG genes encode homologues with somewhat different domain organisation. Only a few BG genes have been characterised, one involved in actin-myosin interaction in the intestinal brush border, and another implicated in resistance to viral diseases. We characterise all BG genes in B12 chickens, finding a multigene family organised as tandem repeats in the BG region outside the MHC, a single gene in the MHC (the BF-BL region), and another single gene on a different chromosome. There is a precise cell and tissue expression for each gene, but overall there are two kinds, those expressed by haemopoietic cells and those expressed in tissues (presumably non-haemopoietic cells), correlating with two different kinds of promoters and 5' untranslated regions (5'UTR). However, the multigene family in the BG region contains many hybrid genes, suggesting recombination and/or deletion as major evolutionary forces. We identify BG genes in the chicken whole genome shotgun sequence, as well as by comparison to other haplotypes by fibre fluorescence in situ hybridisation, confirming dynamic expansion and contraction within the BG region. Thus, the BG genes in chickens are undergoing much more rapid evolution compared to their homologues in mammals, for reasons yet to be understood.This is the final published version. It was originally published by PLOS in PLOS Genetics here: http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004417

Microplastics in brown trout (Salmo trutta Linnaeus, 1758) from an Irish riverine system

Rivers play an important role in the overall transport of microplastic pollution (1 μm to 5 mm), with fluvial dynamics expected to influence biotic interactions, particularly for fish. So far, there have been few assessments of microplastics in freshwater salmonids. The prevalence (i.e. percentage occurrence) and burden (i.e. abundance per fish) of microplastics were assessed in the gastrointestinal tracts (GITs) and stomach contents (SCs) of 58 brown trout Salmo trutta Linnaeus, 1758 sampled at six sites along the River Slaney catchment in south-east Ireland. Sites were divided into two classifications (high and low exposure) based on proximity to microplastic pollution sources, comprising three sites each. Analysis of biological traits (e.g. fish length) and diet was performed on the same fish to determine possible factors explaining microplastic burden. Microplastics were found in 72% of fish having been recovered from 66% of GITs (1.88 ± 1.53 MPs fish⁻1) and 28% of SCs (1.31 ± 0.48 MPs fish⁻1). Fibres were the dominant particle type recovered from GITs (67%) and SCs (57%) followed by fragments. No difference in median microplastic burden was observed between fish collected in high and low exposure sites. Microplastic burden was unrelated to fish fork length, while microplastic size distribution (100 ≤ 350 μm, 350 μm to ≤ 5 mm) was unrelated to S. trutta age class estimates. Furthermore, microplastic burden was not explained by dietary intake. Though further research is necessary, this study showed the presence of microplastics in wild S. trutta collected from an Irish riverine system, which could have further implications for top-level consumers that feed on the species, including humans. Further analysis is required to determine possible trophic linkages for the species, with respect to microplastics, and to assess the suitability of S. trutta for monitoring microplastics in river systems.ye