Genome-wide transposon insertion scanning of environmental survival functions in the polycyclic aromatic hydrocarbon degrading bacterium Sphingomonas wittichii RW1.

Sphingomonas wittichii RW1 is a dibenzofuran and dibenzodioxin-degrading bacterium with potentially interesting properties for bioaugmentation of contaminated sites. In order to understand the capacity of the microorganism to survive in the environment we used a genome-wide transposon scanning approach. RW1 transposon libraries were generated with around 22 000 independent insertions. Libraries were grown for an average of 50 generations (five successive passages in batch liquid medium) with salicylate as sole carbon and energy source in presence or absence of salt stress at -1.5 MPa. Alternatively, libraries were grown in sand with salicylate, at 50% water holding capacity, for 4 and 10 days (equivalent to 7 generations). Library DNA was recovered from the different growth conditions and scanned by ultrahigh throughput sequencing for the positions and numbers of inserted transposed kanamycin resistance gene. No transposon reads were recovered in 579 genes (10% of all annotated genes in the RW1 genome) in any of the libraries, suggesting those to be essential for survival under the used conditions. Libraries recovered from sand differed strongly from those incubated in liquid batch medium. In particular, important functions for survival of cells in sand at the short term concerned nutrient scavenging, energy metabolism and motility. In contrast to this, fatty acid metabolism and oxidative stress response were essential for longer term survival of cells in sand. Comparison to transcriptome data suggested important functions in sand for flagellar movement, pili synthesis, trehalose and polysaccharide synthesis and putative cell surface antigen proteins. Interestingly, a variety of genes were also identified, interruption of which cause significant increase in fitness during growth on salicylate. One of these was an Lrp family transcription regulator and mutants in this gene covered more than 90% of the total library after 50 generations of growth on salicylate. Our results demonstrate the power of genome-wide transposon scanning approaches for analysis of complex traits.

Plant species richness and environmental heterogeneity in a mountain landscape: effects of variability and spatial configuration

The loss of biodiversity has become a matter of urgent concern and a better understanding of local drivers is crucial for conservation. Although environmental heterogeneity is recognized as an important determinant of biodiversity, this has rarely been tested using field data at management scale. We propose and provide evidence for the simple hypothesis that local species diversity is related to spatial environmental heterogeneity. Species partition the environment into habitats. Biodiversity is therefore expected to be influenced by two aspects of spatial heterogeneity: 1) the variability of environmental conditions, which will affect the number of types of habitat, and 2) the spatial configuration of habitats, which will affect the rates of ecological processes, such as dispersal or competition. Earlier, simulation experiments predicted that both aspects of heterogeneity will influence plant species richness at a particular site. For the first time, these predictions were tested for plant communities using field data, which we collected in a wooded pasture in the Swiss Jura mountains using a four-level hierarchical sampling design. Richness generally increased with increasing environmental variability and "roughness" (i.e. decreasing spatial aggregation). Effects occurred at all scales, but the nature of the effect changed with scale, suggesting a change in the underlying mechanisms, which will need to be taken into account if scaling up to larger landscapes. Although we found significant effects of environmental heterogeneity, other factors such as history could also be important determinants. If a relationship between environmental heterogeneity and species richness can be shown to be general, recently available high-resolution environmental data can be used to complement the assessment of patterns of local richness and improve the prediction of the effects of land use change based on mean site conditions or land use history.

Integrated environmental research and networking of economy and information in rural areas of Finland

Selostus: Kestävän kehityksen integroidun tutkimuksen ja verkostotalouden teorian tutkimusmenetelmälliset ongelmat

Structural quality of soils cultivated with coffee and pasture in an environmental protection area

Studies of soils in Environmental Protection Areas (EPAs) are of great importance, because they are an essential component of ecosystems, directly interfering in environmental sustainability. The objective of this study was to evaluate the structural quality of soil cultivated with coffee and used as pasture in the Capituva's River microbasin, which is located in the Environmental Protection Area in Coqueiral, south of the state of Minas Gerais. Uniaxial compression test (preconsolidation test) and soil resistance to penetration were used. Undisturbed samples were taken from the surface layer (0-5 cm) of the soils in the area: a typic dystrophic Red Latosol (LVd - Oxisol), a typic eutrophic Red Argisol (PVe - Ultisol), and a typic dystrophic Haplic Cambisol (CXbd - Inceptisol). A significant linear positive correlation was observed between the results of the preconsolidation test and soil resistance to penetration. Load bearing capacity of soil could be estimated accordingly by means of penetration resistance for LVd, PVe, and CXbd. Cambisol - CXbd showed lower loading support capacity and resistance to penetration than LVd and PVe, due to the better crop management in this soil that resulted in higher physical quality which accounts for higher production and environmental sustainability.

US 20 Proposed Dyersville Interchange Delaware and Dubuque Counties, IA, Environmental Assessment, February 2001

The Transportation Equity Act of the 21st Century (TEA-21) (23 CFR) mandated environmental streamlining in order to improve transportation project delivery without compromising environmental protection. In accordance with TEA-21, the environmental review process for this project has been documented as a Streamlined Environmental Assessment (EA). This document addresses only those resources or features that apply to the project. This allowed study and discussion of resources present in the study area, rather than expend effort on resources that were either not present or not impacted. Although not all resources are discussed in the EA, they were considered during the planning process and are documented in the Streamlined Resource Summary, shown in Appendix A. The following table shows the resources considered during the environmental review for this project. The first column with a check means the resource is present in the project area. The second column with a check means the impact to the resource warrants more discussion in this document. The other listed resources have been reviewed and are included in the Streamlined Resource Summary.

Pedochronology and development of peat bog in the environmental protection area pau-de-fruta - Diamantina, Brazil

In the region of the Serra do Espinhaço Meridional, peat bog is formed in hydromorphic environments developed in sunken areas on the plain surfaces with vegetation adapted to hydromorphic conditions, favoring the accumulation and preservation of organic matter. This pedoenvironment is developed on the regionally predominant quartzite rocks. Peat bog in the Environmental Protection Area - APA Pau-de-Fruta, located in the watershed of Córrego das Pedras, Diamantina,Brazil, was mapped and three representative profiles were morphologically characterized and sampled for physical, chemical and microbiological analyses. The organic matter was fractionated into fulvic acid (FA), humic acids (HA) and humin (H). Two profiles were sampled to determine the radiocarbon age and δ13C. The structural organization of the three profiles is homogeneous. The first two layers consist of fibric, the two subsequent of hemic and the four deepest of sapric peat, showing that organic matter decomposition advances with depth and that the influence of mineral materials in deeper layers is greater. Physical properties were homogeneous in the profiles, but varied in the sampled layers. Chemical properties were similar in the layers, but the Ca content, sum of bases and base saturation differed between profiles. Contents of H predominated in the more soluble organic matter fractions and were accumulated at a higher rate in the surface and deeper layers, while HA levels were higher in the intermediate and FA in the deeper layers. Microbial activity did not vary among profiles and was highest in the surface layers, decreasing with depth. From the results of radiocarbon dating and isotope analysis, it was inferred that bog formation began about 20 thousand years ago and that the vegetation of the area had not changed significantly since then.

When information can save lives: the duty to warn relatives about sudden cardiac death and environmental risks.

In certain cases of sudden death, forensic experts may discover during an investigation or autopsy that family members of the deceased are also at risk of harm-from genetic disease, for instance. But do they have a duty to warn them? Looking at similar duties of physicians and researchers to warn third parties of risk suggests they do.

Kinetic parameters of soil β-glucosidase response to environmental temperature and moisture regimes

Soil β-glucosidase participates in the final step of cellulose biodegradation. It is significant in the soil C cycle and is used as an indicator of the biological fertility of soil. However, the response of its kinetic parameters to environmental temperature and moisture regimes is not well understood. This study tested the β-glucosidase response in the main agricultural soils (black soil, albic soil, brown soil, and cinnamon soil) of Northeast China. Incubation tests were conducted to measure the kinetic parameters Km, Vmax or Vmax/Km of soil β-glucosidase at environmental temperatures of 10, 20 and 30 ºC and at 10, 20 and 30 % soil moisture content. The insensitive response of the kinetic parameters to temperature changes indicates that soil β-glucosidase was present primarily in immobilized form. The significant response of the kinetic parameters of soil β-glucosidase to soil moisture rather than to environmental temperatures suggests that the catalytic ability of soil β-glucosidase was sensitive to changing soil moisture regimes.

Clonal deletion and the fate of autoreactive thymocytes that survive negative selection.

Clonal deletion of autoreactive thymocytes is important for self-tolerance, but the intrathymic signals that induce clonal deletion have not been clearly identified. We now report that clonal deletion during negative selection required CD28-mediated costimulation of autoreactive thymocytes at the CD4(+)CD8(lo) intermediate stage of differentiation. Autoreactive thymocytes were prevented from undergoing clonal deletion by either a lack of CD28 costimulation or transgenic overexpression of the antiapoptotic factors Bcl-2 or Mcl-1, with surviving thymocytes differentiating into anergic CD4(-)CD8(-) double-negative thymocytes positive for the T cell antigen receptor αβ subtype (TCRαβ) that 'preferentially' migrated to the intestine, where they re-expressed CD8α and were sequestered as CD8αα(+) intraepithelial lymphocytes (IELs). Our study identifies costimulation by CD28 as the intrathymic signal required for clonal deletion and identifies CD8αα(+) IELs as the developmental fate of autoreactive thymocytes that survive negative selection.

Environmental sex reversal, Trojan sex genes, and sex ratio adjustment: conditions and population consequences.

Abstract The great diversity of sex determination mechanisms in animals and plants ranges from genetic sex determination (GSD, e.g. mammals, birds, and most dioecious plants) to environmental sex determination (ESD, e.g. many reptiles) and includes a mixture of both, for example when an individual's genetically determined sex is environmentally reversed during ontogeny (ESR, environmental sex reversal, e.g. many fish and amphibia). ESD and ESR can lead to widely varying and unstable population sex ratios. Populations exposed to conditions such as endocrine-active substances or temperature shifts may decline over time due to skewed sex ratios, a scenario that may become increasingly relevant with greater anthropogenic interference on watercourses. Continuous exposure of populations to factors causing ESR could lead to the extinction of genetic sex factors and may render a population dependent on the environmental factors that induce the sex change. However, ESR also presents opportunities for population management, especially if the Y or W chromosome is not, or not severely, degenerated. This seems to be the case in many amphibians and fish. Population growth or decline in such species can potentially be controlled through the introduction of so-called Trojan sex genes carriers, individuals that possess sex chromosomes or genes opposite from what their phenotype predicts. Here, we review the conditions for ESR, its prevalence in natural populations, the resulting physiological and reproductive consequences, and how these may become instrumental for population management.

Major environmental change and bonebed genesis prior to the Triassic-Jurassic mass extinction

We present new geochemical and sedimentological data from marginal marine strata of Penarth Bay, south Wales (UK) to elucidate the origin of widespread but enigmatic concentrations of vertebrate hard parts (bonebeds) in marine successions of Rhaetian age (late Triassic). Sedimentological evidence shows that the phosphatic constituents of the bonebeds were subjected to intense phosphatization in shallow current-dominated settings and subsequently reworked and transported basinward by storms. Interbedded organic-rich strata deposited under quiescent and poorly oxygenated conditions record enhanced phosphorus regeneration from sedimentary organic matter into the water column and probably provided the main source of phosphate required for heavy bonebed clast phosphatization. The stratigraphically limited interval showing evidence for oxygen depletion and accelerated P-cycling coincides with a negative 4% organic carbon isotope excursion, which possibly reflects supra-regional changes in carbon cycling and clearly predates the 'initial isotope excursion' characterizing many Triassic-Jurassic boundary strata. our data indicate that Rhaetian bonebeds are the lithological signature of profound, climatically driven changes in carbon cycling and redox conditions and support the idea of a multi-pulsed environmental crisis at the end of the Triassic, possibly linked to successive episodes of igneous activity in the central Atlantic Magmatic Province.

Automatic Mapping and Classification of Spatial Environmental Data

The paper deals with the development and application of the generic methodology for automatic processing (mapping and classification) of environmental data. General Regression Neural Network (GRNN) is considered in detail and is proposed as an efficient tool to solve the problem of spatial data mapping (regression). The Probabilistic Neural Network (PNN) is considered as an automatic tool for spatial classifications. The automatic tuning of isotropic and anisotropic GRNN/PNN models using cross-validation procedure is presented. Results are compared with the k-Nearest-Neighbours (k-NN) interpolation algorithm using independent validation data set. Real case studies are based on decision-oriented mapping and classification of radioactively contaminated territories.