Bacillus anthracis: Molecular taxonomy, population genetics, phylogeny and patho-evolution

Bacillus anthracis, the etiological agent of anthrax, manifests a particular bimodal lifestyle. This bacterial species alternates between short replication phases of 20-40 generations that strictly require infection of the host, normally causing death, interrupted by relatively long, mostly dormant phases as spores in the environment. Hence, the B. anthracis genome is highly homogeneous. This feature and the fact that strains from nearly all parts of the world have been analysed for canonical single nucleotide polymorphisms (canSNPs) and variable number tandem repeats (VNTRs) has allowed the development of molecular epidemiological and molecular clock models to estimate the age of major diversifications in the evolution of B. anthracis and to trace the global spread of this pathogen, which was mostly promoted by movement of domestic cattle with settlers and by international trade of contaminated animal products. From a taxonomic and phylogenetic point of view, B. anthracis is a member of the Bacillus cereus group. The differentiation of B. anthracis from B. cereus sensu strict, solely based on chromosomal markers, is difficult. However, differences in pathogenicity clearly differentiate B. anthracis from B. cereus and are marked by the strict presence of virulence genes located on the two virulence plasmids pXO1 and pXO2, which both are required by the bacterium to cause anthrax. Conversely, anthrax-like symptoms can also be caused by organisms with chromosomal features that are more closely related to B. cereus, but which carry these virulence genes on two plasmids that largely resemble the B. anthracis virulence plasmids. (C) 2011 Elsevier B.V. All rights reserved.

Scales of Impact: Settlement History and Landscape Change in the Gordion Region, Central Anatolia

The expansion of agriculture in the Near East during the middle Holocene significantly altered the physical landscape. However, the relationship between the scale of agriculture and the magnitude and timing of the environmental impacts is not well known. The Gordion Regional Survey provides a novel dataset to compare settlement density during archaeological periods to rates of environmental disruption. Sediment samples from alluvial cores directly date the environmental disruption, which can be matched to period-specific settlement intensities in the watershed as constructed from archaeological survey ceramics. Degradation rates rose sharply within a millennium of the earliest Chalcolithic occupation. Early Bronze Age (EBA) land use induced the greatest rates of environmental degradation, although settlement density was relatively low on the landscape. The degradation rate subsequently decreased to one-third its early peak by the Iron Age, even as settlement intensity climbed. This trajectory reveals how complex interaction effects can amplify or subdue the responses of the landscape-land use system. Prior to settlement, landscape soil reservoirs were highly vulnerable, easily tipped by early agricultural expansion. Subsequent reduced rates of erosion are tied both to changes in sociopolitical organization and to depletion of the vulnerable soil supply.

High Solids Co-Digestion of Food and Landscape Waste and the Potential for Ammonia Toxicity

A pilot-scale study was completed to determine the feasibility of high-solids anaerobic digestion (HSAD) of a mixture of food and landscape wastes at a university in central Pennsylvania (USA). HSAD was stable at low loadings (2g COD/L-day), but developed inhibitory ammonia concentrations at high loadings (15g COD/L-day). At low loadings, methane yields were 232L CH4/kg COD fed and 229L CH4/kg VS fed, and at high loadings yields were 211L CH4/kg COD fed and 272L CH4/kg VS fed. Based on characterization and biodegradability studies, food waste appears to be a good candidate for HSAD at low organic loading rates; however, the development of ammonia inhibition at high loading rates suggests that the C:N ratio is too low for use as a single substrate. The relatively low biodegradability of landscape waste as reported herein made it an unsuitable substrate to increase the C:N ratio. Codigestion of food waste with a substrate high in bioavailable carbon is recommended to increase the C:N ratio sufficiently to allow HSAD at loading rates of 15g COD/L-day. Copyright 2014 Elsevier Ltd. All rights reserved.

Patch selection by wintering white-tailed deer : consequences for eastern hemlock regeneration at local and landscape scales

Tsuga canadensis (eastern hemlock) is a highly shade-tolerant, late-successional, and long-lived conifer species found throughout eastern North America. It is most often found in pure or nearly pure stands, because highly acidic and nutrient poor forest floor conditions are thought to favor T. canadensis regeneration while simultaneously limiting the establishment of some hardwood species with greater nutrient requirements. Once a common species, T. canadensis is currently experiencing widescale declines across its range. The hemlock woolly adelgid (Adelges tsugae) is decimating the population across its eastern distribution. Across the Upper Great Lakes region, where the adelgid is currently being held at bay by cold winter temperatures, T. canadensis has been experiencing failures in regeneration attributed, in part, to herbivory by white-tailed deer (Odocoileus virginianus). Deer utilize T. canadensis stands as winter habitat in areas of high snow depth. Tsuga canadensis, once a major component of these forests, currently exists at just a fraction of its pre-settlement abundance due to historic logging and contemporary forest management practices, and what remains is found in small remnant patches surrounded by second- and third-growth deciduous forests. The deer population across the region, however, is likely double that of pre-European settlement times. In this dissertation I explore the relationship between white-tailed deer use of T. canadensis as winter habitat and the effect this use is having on regeneration and forest succession. For this research I quantified stand composition and structure and abiotic variables of elevation and snow depth in 39 randomly selected T. canadensis stands from across the western Upper Peninsula of Michigan. I also quantified composition and the configuration of the landscapes surrounding these stands. I measured relative deer use of T. canadensis stands as pellet group piles deposited in each stand during each of three consecutive winters, 2005-06, 2006-07, and 2007-08. The results of this research suggest that deer use of T. canadensis stands as winter habitat is influenced primarily by snow depth, elevation, and the composition and configuration of the greater landscapes surrounding these stands. Specifically, stands with more heterogeneous landscapes surrounding them (i.e., a patchy mosaic of conifer, deciduous, and open cover) had higher relative deer use than stands surrounded by homogenous deciduous forest cover. Additionally, the intensity of use and the number of stands used was greater in years with higher average snow depth. Tsuga canadensis regeneration in these stands was negatively associated with deer use and Acer saccharum (sugar maple) basal area. Of the 39 stands, 17 and 22 stands had no T. canadensis regeneration in small and large sapling categories, respectively. Acer saccharum was the most common understory tree species, and the importance of A. saccharum in the understory (stems < 10 cm dbh) of the stands was positively associated with overstory A. saccharum dominance. Tsuga canadensis establishment was associated with high-decay coarse woody debris and moss, and deciduous leaf litter inputs in these stands may be limiting access to these important microsites. Furthermore, A. saccharum is more tolerant to the effects of deer herbivory than T. canadensis, giving A. saccharum a competitive advantage in stands being utilized as winter habitat by deer. My research suggests that limited microsite availability, in conjunction with deer herbivory, may be leading to an erosion in T. canadensis patch stability and an altered successional trajectory toward one of A. saccharum dominance, an alternately stable climax species.

Spatial and temporal analysis of land cover and landscape structure change in Zagros Forests

The Zagros oak forests in Western Iran are critically important to the sustainability of the region. These forests have undergone dramatic declines in recent decades. We evaluated the utility of the non-parametric Random Forest classification algorithm for land cover classification of Zagros landscapes, and selected the best spatial and spectral predictive variables. The algorithm resulted in high overall classification accuracies (>85%) and also equivalent classification accuracies for the datasets from the three different sensors. We evaluated the associations between trends in forest area and structure with trends in socioeconomic and climatic conditions, to identify the most likely driving forces creating deforestation and landscape structure change. We used available socioeconomic (urban and rural population, and rural income), and climatic (mean annual rainfall and mean annual temperature) data for two provinces in northern Zagros. The most correlated driving force of forest area loss was urban population, and climatic variables to a lesser extent. Landscape structure changes were more closely associated with rural population. We examined the effects of scale changes on the results from spatial pattern analysis. We assessed the impacts of eight years of protection in a protected area in northern Zagros at two different scales (both grain and extent). The effects of protection on the amount and structure of forests was scale dependent. We evaluated the nature and magnitude of changes in forest area and structure over the entire Zagros region from 1972 to 2009. We divided the Zagros region in 167 Landscape Units and developed two measures— Deforestation Sensitivity (DS) and Connectivity Sensitivity (CS) — for each landscape unit as the percent of the time steps that forest area and ECA experienced a decrease of greater than 10% in either measure. A considerable loss in forest area and connectivity was detected, but no sudden (nonlinear) changes were detected at the spatial and temporal scale of the study. Connectivity loss occurred more rapidly than forest loss due to the loss of connecting patches. More connectivity was lost in southern Zagros due to climatic differences and different forms of traditional land use.

Spatial and Temporal Evolution of the Volcanics and Sediments of the Kenya Rift

New volumetric and mass flux estimates have been calculated for the Kenya Rift. Spatial and temporal histories for volcanic eruptions, lacustrine deposition, and hominin fossil sites are presented, aided by the compilation of a new digital geologic map. Distribution of volcanism over time indicates several periods of southward expansion followed by relative positional stasis. Volcanism occurs throughout the activated rift length, with no obvious abandonment as the rift system migrated. The main exception is a period of volcanic concentration around 10 Ma, when activity was constrained within 2° of the equator. Volumes derived from seismic data indicate a total volume of c. 310,000 km3 (2.47 x 1010 kg/yr ), which is significantly more than the map-derived volumes found here or published previously. Map-based estimates are likely affected by a bias against recognizing small volume events in the older record. Such events are, however, the main driver of erupted volume over the last 5 Ma. A technique developed here to counter this bias results in convergence of the two volume estimation techniques. Relative erupted composition over time is variable. Overall, the erupted material has a mafic to silicic ratio of 0.9:1. Basalts are distinctly more common in the Turkana region, which previously experienced Mesozoic rifting. Despite the near equal ratio of mafic to silicic products, the Kenya Rift otherwise fits the definition of a SLIP. It is proposed that the compositions would better fit the published definition if the Turkana region was not twice-rifted. Lacustrine sedimentation post-dates initial volcanism by about 5 million years, and follows the same volcanic trends, showing south and eastward migration over time. This sedimentation delay is likely related to timing of fault displacements. Evidence of hominin habitation is distinctly abundant in the northern and southern sections of the Kenya Rift, but there is an observed gap in the equatorial rift between 4 and 0.5 million years ago. After 0.5 Ma, sites appear to progress towards the equator. The pattern and timing of hominid site distributions suggests that the equatorial gap in habitation may be the result of active volcanic avoidance.

A comparison of pixel and object-based land cover classification. A case study of the Asmara region, Eritrea

In this paper we compare the performance of two image classification paradigms (object- and pixel-based) for creating a land cover map of Asmara, the capital of Eritrea and its surrounding areas using a Landsat ETM+ imagery acquired in January 2000. The image classification methods used were maximum likelihood for the pixel-based approach and Bhattacharyya distance for the object-oriented approach available in, respectively, ArcGIS and SPRING software packages. Advantages and limitations of both approaches are presented and discussed. Classifications outputs were assessed using overall accuracy and Kappa indices. Pixel- and object-based classification methods result in an overall accuracy of 78% and 85%, respectively. The Kappa coefficient for pixel- and object-based approaches was 0.74 and 0.82, respectively. Although pixel-based approach is the most commonly used method, assessment and visual interpretation of the results clearly reveal that the object-oriented approach has advantages for this specific case-study.

Automatic Labeling of Software Components and their Evolution using Log-Likelihood Ratio of Word Frequencies in Source Code

As more and more open-source software components become available on the internet we need automatic ways to label and compare them. For example, a developer who searches for reusable software must be able to quickly gain an understanding of retrieved components. This understanding cannot be gained at the level of source code due to the semantic gap between source code and the domain model. In this paper we present a lexical approach that uses the log-likelihood ratios of word frequencies to automatically provide labels for software components. We present a prototype implementation of our labeling/comparison algorithm and provide examples of its application. In particular, we apply the approach to detect trends in the evolution of a software system.

Opportunities and limits of the ecosystem services framework in capturing the cultural dimension of sustainable regional and landscape development in protected areas

With regard to protected areas, the concepts of ecosystem services and the cultural dimension of sustainable development (SD) are increasingly under debate. This contribution analyses the role of cultural aspects within the ecosystem services framework using the Millennium Ecosystem Assessment classification as a reference. The limits of the ecosystem services framework in capturing the cultural dimension are highlighted. Potential ways of strengthening the position of cultural values within this framework are discussed.