Analysis of microbial diversity in polluted and non-polluted soils : a comparison of genetic, functional and culture based techniques

The examination of the microbial communities from different soils was conducted by means of a polyphasic approach utilising traditional culturing methods, taxonomic analysis (DGGE) and potential metabolic activity assays (Biolog). To examine how representative the Biolog assay was of the total bacterial community DGGE analysis of selected wells from Biolog Gram positive and Gram negative plates which were incubated over 96 hours. The results indicated a considerable enrichment effect of the microbial community in comparison with the original soil community. Taxonomic analysis of Biolog wells identified Pseudomonas species as the dominant microorganism present. Despite this enrichment effect Biolog analysis could still be used to provide a reproducible measure of potential metabolic activity in the soil and to analyse temporal changes. A wet sieving technique was used to examine the location of specific bacterial groups in Warwick soil. Wet sieving allowed reproducible separation of the soil into six different sized water-stable aggregates. The community analysis of these different sized soil fractions indicated that actinomycetes were located in higher numbers in the larger soil particles. Whereas pseudomonads were found in higher numbers in the smaller soil particles. Each aggregate fraction had a distinct and different microbial community. Correlations were found between the taxonomic diversity, culturable plate counts and metabolic potential. The polyphasic approach was used to compare Warwick soil with polluted and non- polluted Doncaster soils obtained from a coal spoil site. Soil fractionation analysis established that different microbial communities were present in the polluted and non- polluted soil fractions. The polluted soil had reduced genetic diversity, metabolic activity, fewer culturable propagules, and a very different soil particle distribution pattern when compared with the two non-polluted soils. Microcosms containing differing proportions of Warwick and Doncaster polluted soil were prepared to study the impact of pollutants on soil microbial communities. Microcosms containing high proportions of polluted soil resulted in the reduction of microbial potential activity, taxonomic diversity and culturable numbers. In the microcosm systems containing low proportions of polluted soil, potential metabolic activity was stimulated; this was also reflected in changes in the genetic diversity. Community analysis techniques were used to monitor a bioremediation field trial with industrial collaborators BG pic. (formerly British Gas). This field trial involved five soil treatment pits containing a complex mixture of polyaromatic hydrocarbons compounds, subjected to varying conditions designed to stimulate biodegradation rates. Analysis identified dominant bacterial groups present in the bioremediation treatment pits and provided a rigorous evaluation of the microbial diversity present. A combination of microbial analysis with physical and chemical data (provided by BG pic.) allowed the identification of treatments providing the highest rates of bioremediation. Polyaromatic hydrocarbon degradation in the different treatment pits did correlate with the highest potential metabolic activity, genetic diversity and culturable numbers

Spectral Properties and Synchronization in Coupled Map Lattices

Spectral properties of Coupled Map Lattices are described. Conditions for the stability of spatially homogeneous chaotic solutions are derived using linear stability analysis. Global stability analysis results are also presented. The analytical results are supplemented with numerical examples. The quadratic map is used for the site dynamics with different coupling schemes such as global coupling, nearest neighbor coupling, intermediate range coupling, random coupling, small world coupling and scale free coupling.Comment: 10 pages with 15 figures (Postscript), REVTEX format. To appear in PR

Stability of a neural network model with small-world connections

Small-world networks are highly clustered networks with small distances among the nodes. There are many biological neural networks that present this kind of connections. There are no special weightings in the connections of most existing small-world network models. However, this kind of simply-connected models cannot characterize biological neural networks, in which there are different weights in synaptic connections. In this paper, we present a neural network model with weighted small-world connections, and further investigate the stability of this model.Comment: 4 pages, 3 figure

Urine selenium concentration is a useful biomarker for assessing population level selenium status

Plasma selenium (Se) concentration is an established population level biomarker of Se status, especially in Se-deficient populations. Previously observed correlations between dietary Se intake and urinary Se excretion suggest that urine Se concentration is also a potentially viable biomarker of Se status. However, there are only limited data on urine Se concentration among Se-deficient populations. Here, we test if urine is a viable biomarker for assessing Se status among a large sample of women and children in Malawi, most of whom are likely to be Se-deficient based on plasma Se status. Casual (spot) urine samples (n = 1406) were collected from a nationally representative sample of women of reproductive age (WRA, n =741) and school aged children (SAC, n=665) across Malawi as part of the 2015/16 Demographic and Health Survey. Selenium concentration in urine was determined using inductively coupled plasma mass spectrometry (ICP-MS). Urinary dilution corrections for specific gravity, osmolality, and creatinine were applied to adjust for hydration status. Plasma Se status had been measured for the same survey participants. There was between-cluster variation in urine Se concentration that corresponded with variation in plasma Se concentration, but not between households within a cluster, or between individuals within a household. Corrected urine Se concentrations explained more of the between-cluster variation in plasma Se concentration than uncorrected data. These results provide new evidence that urine may be used in the surveillance of Se status at the population level in some groups. This could be a cost-effective option if urine samples are already being collected for other assessments, such as for iodine status analysis as in the Malawi and other national Demographic and Health Surveys

Lignocellulose degradation mechanisms across the Tree of Life.

Organisms use diverse mechanisms involving multiple complementary enzymes, particularly glycoside hydrolases (GHs), to deconstruct lignocellulose. Lytic polysaccharide monooxygenases (LPMOs) produced by bacteria and fungi facilitate deconstruction as does the Fenton chemistry of brown-rot fungi. Lignin depolymerisation is achieved by white-rot fungi and certain bacteria, using peroxidases and laccases. Meta-omics is now revealing the complexity of prokaryotic degradative activity in lignocellulose-rich environments. Protists from termite guts and some oomycetes produce multiple lignocellulolytic enzymes. Lignocellulose-consuming animals secrete some GHs, but most harbour a diverse enzyme-secreting gut microflora in a mutualism that is particularly complex in termites. Shipworms however, house GH-secreting and LPMO-secreting bacteria separate from the site of digestion and the isopod Limnoria relies on endogenous enzymes alone. The omics revolution is identifying many novel enzymes and paradigms for biomass deconstruction, but more emphasis on function is required, particularly for enzyme cocktails, in which LPMOs may play an important role.The work of the teams at York, Portsmouth and Cambridge on development of ideas expressed in this review was supported by grants from BBSRC (BB/H531543/1, BB/L001926/1, BB/1018492/1, BB/K020358/1). The workshop was supported by a US Partnering grant from BBSRC (BB/G016208/1) to Cragg and a BBSRC/FAPESP grant to Bruce (BB/1018492/1). Watts was supported by Marie Curie FP7-RG 276948. Goodell acknowledges support from USDA Hatch Project S-1041 VA-136288. Distel acknowledges support from NSF Award IOS1442759 and NIH Award Number U19 TW008163. Beckham thanks the US Department of Energy Bioenergy Technologies Office for funding. We appreciated the hospitality of the Linnean Society in allowing us to meet in inspirational surroundings under portraits of Linnaeus, Darwin and Wallace.This is the final version of the article. It first appeared from Elsevier via http://dx.doi.org/10.1016/j.cbpa.2015.10.01

Spatial analysis of urine zinc (Zn) concentration for women of reproductive age and school age children in Malawi

Zinc (Zn) is an essential micronutrient, and Zn deficiency remains a major global public health challenge. Recognised biomarkers of population Zn status include blood plasma or serum Zn concentration and proxy data such as dietary Zn intake and prevalence of stunting. Urine Zn concentration is rarely used to assess population Zn status. This study assessed the value of urine Zn concentration as a biomarker of population Zn status using a nationally representative sample of non-pregnant women of reproductive age (WRA) and school-aged children (SAC) in Malawi. Spot (casual) urine samples were collected from 741 WRA and 665 SAC. Urine Zn concentration was measured by inductively coupled plasma mass spectrometry with specific gravity adjustment for hydration status. Data were analysed using a linear mixed model with a spatially correlated random effect for between-cluster variation. The effect of time of sample collection (morning or afternoon), and gender (for SAC), on urine Zn concentration were examined. There was spatial dependence in urine Zn concentration between clusters among SAC but not WRA, which indicates that food system or environmental factors can influence urine Zn concentration. Mapping urine Zn concentration could potentially identify areas where the prevalence of Zn deficiency is greater and thus where further sampling or interventions might be targeted. There was no evidence for differences in urine Zn concentration between gender (P = 0.69) or time of sample collection (P = 0.85) in SAC. Urine Zn concentration was greater in afternoon samples for WRA (P = 0.003). Relationships between urine Zn concentration, serum Zn concentration, dietary Zn intake, and potential food systems covariates warrant further study

An approach for the identification of targets specific to bone metastasis using cancer genes interactome and gene ontology analysis

Metastasis is one of the most enigmatic aspects of cancer pathogenesis and is a major cause of cancer-associated mortality. Secondary bone cancer (SBC) is a complex disease caused by metastasis of tumor cells from their primary site and is characterized by intricate interplay of molecular interactions. Identification of targets for multifactorial diseases such as SBC, the most frequent complication of breast and prostate cancers, is a challenge. Towards achieving our aim of identification of targets specific to SBC, we constructed a 'Cancer Genes Network', a representative protein interactome of cancer genes. Using graph theoretical methods, we obtained a set of key genes that are relevant for generic mechanisms of cancers and have a role in biological essentiality. We also compiled a curated dataset of 391 SBC genes from published literature which serves as a basis of ontological correlates of secondary bone cancer. Building on these results, we implement a strategy based on generic cancer genes, SBC genes and gene ontology enrichment method, to obtain a set of targets that are specific to bone metastasis. Through this study, we present an approach for probing one of the major complications in cancers, namely, metastasis. The results on genes that play generic roles in cancer phenotype, obtained by network analysis of 'Cancer Genes Network', have broader implications in understanding the role of molecular regulators in mechanisms of cancers. Specifically, our study provides a set of potential targets that are of ontological and regulatory relevance to secondary bone cancer.Comment: 54 pages (19 pages main text; 11 Figures; 26 pages of supplementary information). Revised after critical reviews. Accepted for Publication in PLoS ON

Directed Mammalian Gene Regulatory Networks Using Expression and Comparative Genomic Hybridization Microarray Data from Radiation Hybrids

Meiotic mapping of quantitative trait loci regulating expression (eQTLs) has allowed the construction of gene networks. However, the limited mapping resolution of these studies has meant that genotype data are largely ignored, leading to undirected networks that fail to capture regulatory hierarchies. Here we use high resolution mapping of copy number eQTLs (ceQTLs) in a mouse-hamster radiation hybrid (RH) panel to construct directed genetic networks in the mammalian cell. The RH network covering 20,145 mouse genes had significant overlap with, and similar topological structures to, existing biological networks. Upregulated edges in the RH network had significantly more overlap than downregulated. This suggests repressive relationships between genes are missed by existing approaches, perhaps because the corresponding proteins are not present in the cell at the same time and therefore unlikely to interact. Gene essentiality was positively correlated with connectivity and betweenness centrality in the RH network, strengthening the centrality-lethality principle in mammals. Consistent with their regulatory role, transcription factors had significantly more outgoing edges (regulating) than incoming (regulated) in the RH network, a feature hidden by conventional undirected networks. Directed RH genetic networks thus showed concordance with pre-existing networks while also yielding information inaccessible to current undirected approaches

Dietary mineral supplies in Malawi: spatial and socioeconomic assessment

Background Dietary mineral deficiencies are widespread globally causing a large disease burden. However, estimates of deficiency prevalence are often only available at national scales or for small population sub-groups with limited relevance for policy makers. Methods This study combines food supply data from the Third Integrated Household Survey of Malawi with locally-generated food crop composition data to derive estimates of dietary mineral supplies and prevalence of inadequate intakes in Malawi. Results We estimate that >50 % of households in Malawi are at risk of energy, calcium (Ca), selenium (Se) and/or zinc (Zn) deficiencies due to inadequate dietary supplies, but supplies of iron (Fe), copper (Cu) and magnesium (Mg) are adequate for >80 % of households. Adequacy of iodine (I) is contingent on the use of iodised salt with 80 % of rural households living on low-pH soils had inadequate dietary Se supplies compared to 55 % on calcareous soils; concurrent inadequate supplies of Ca, Se and Zn were observed in >80 % of the poorest rural households living in areas with non-calcareous soils. Prevalence of inadequate dietary supplies was greater in rural than urban households for all nutrients except Fe. Interventions to address dietary mineral deficiencies were assessed. For example, an agronomic biofortification strategy could reduce the prevalence of inadequate dietary Se supplies from 82 to 14 % of households living in areas with low-pH soils, including from 95 to 21 % for the poorest subset of those households. If currently-used fertiliser alone were enriched with Se then the prevalence of inadequate supplies would fall from 82 to 57 % with a cost per alleviated case of dietary Se deficiency of ~ US$ 0.36 year−1. Conclusions Household surveys can provide useful insights into the prevalence and underlying causes of dietary mineral deficiencies, allowing disaggregation by spatial and socioeconomic criteria. Furthermore, impacts of potential interventions can be modelled