388 research outputs found
SOPHIA
The Iraqi Insurgency (2003–2011) has commonly been characterized as demonstrating the tendency for violence to cluster and diffuse at the local level. Recent research has demonstrated that insurgent attacks in Iraq cluster in time and space in a manner similar to that observed for the spread of a disease. The current study employs a variety of approaches common to the scientific study of criminal activities to advance our understanding of the correlates of observed patterns of the incidence and contagion of insurgent attacks. We hypothesize that the precise patterns will vary from one place to another, but that more attacks will occur in areas that are heavily populated, where coalition forces are active, and along road networks. To test these hypotheses, we use a fishnet to build a geographical model of Baghdad that disaggregates the city into more than 3000 grid cell locations. A number of logistic regression models with spatial and temporal lags are employed to explore patterns of local escalation and diffusion. These models demonstrate the validity of arguments under each of three models but suggest, overall, that risk heterogeneity arguments provide the most compelling and consistent account of the location of insurgency. In particular, the results demonstrate that violence is most likely at locations with greater population levels, higher density of roads, and military garrisons
Movement dynamics of the little brown bat (Myotis lucifugus) and the northern long-eared bat (Myotis septentrionalis) in Nova Scotia
92 leaves : ill., maps ; 29 cm.Includes abstract.Includes bibliographical references.Two resident bat species in Nova Scotia are the little brown bat (Myotis lucifugus), an aerial hawker, and the northern long-eared bat (M. septentrionalis), a forest gleaner. Little is known about their local movement patterns and response to deforestation in summer, and their migration between summering sites and swarming sites in fall. A study was conducted near a newly constructed wind farm in Nova Scotia, for which forest was cleared, to make inferences on variable, inter-specific effects of ecosystem alterations. A second study was conducted to make inferences on migration between summer- and swarming sites, using stable isotopes of carbon and nitrogen in bat fur. The results indicate that both species are impacted differently by deforestation due to their different foraging and roosting requirements. Migration in fall appears to be uniform in both species, where swarming sites are congregations of bats from several summering sites
Characterization of the AtsR/AtsT global regulatory pathway in Burkholderia ceocepacia
Phosphorylation cascades governed by two-component signal transduction systems provide key signalling mechanisms in bacteria, simple eukaryotes and higher plants, allowing them to translate signals into adaptive responses. These regulatory pathways consist of a transmembrane sensor protein that responds to an environmental cue leading to autophosphorylation, followed by the transfer of the phosphate to a cytoplasmic response regulator. Here, I study AtsR, a membrane-bound hybrid sensor kinase of Burkholderia cenocepacia, that negatively regulates quorum sensing related virulence factors such as biofilm, type 6-secretion and protease secretion. B. cenocepacia is a Gram-negative opportunistic pathogen which causes severe, chronic respiratory infections in patients with cystic fibrosis and other immunocompromised conditions. This bacterium is also pathogenic in animal, plant, nematode, and insect infection models, and can survive within amoebae and macrophages. Presumably, the ability to survive in various niches requires adaptability to deal with changing environments. I hypothesize that AtsR is part of a multi-protein phosphorelay pathway which plays a critical role in regulation of niche adaptation and survival of B. cenocepacia in different hosts. In this thesis, I investigated AtsR function by characterizing the role of critical functional residues within the individual domains of AtsR and identify its cognate response regulator AtsT as a key component of the AtsR phosphorelay pathway. Furthermore, subsets of genes that are directly regulated by the AtsR cognate response regulator were identified by Chromatin immunoprecipitation followed by next generation sequencing (ChIP-Seq) analysis and its corresponding consensus DNA binding site is determined. I also investigated the role of AtsR as a global regulator of B. cenocepacia pathogenicity in the Arabidopsis thaliana and Galleria mellonella infection models.
Together, these studies identified a new regulatory network that highlights the importance of bacterial virulence and pathogenicity with careful consideration of the host. This work may provide an understanding at the molecular level of bacterial adaptation to ever changing niche environments
Monitoring population size, structure and change in Bechstein’s bat (Myotis bechsteinii): combined approaches using molecular and landscape ecology
The Bechstein’s bat, Myotis bechsteinii, is known as one of Britain’s most
elusive mammals. Critical information on the species is lacking, hindering
evidence-based conservation and management in a human-dominated
landscape. In this thesis, I used a combination of molecular and landscape
approaches to assess the genetic health and population genetic structure of M.
bechsteinii and understand how the British landscape affects the species
habitat and its connectivity. I also aimed to develop new molecular tools, such
as non-invasive genetic sampling and molecular ageing, which could then be
used to better monitor the species.
Data from nuclear markers (microsatellites) showed high levels of genetic
diversity and little inbreeding across the species range, though genetic diversity
was slightly lower in Britain than in mainland Europe. Bayesian and spatial
Principal Components (sPCA) analysis showed a clear separation between
British and European populations. This analysis also revealed that in Europe
the Italian population south of the Alps was found to constitute a different group
from other sites. In Britain, there was genetic structuring between the northern
and southern part of the species range. Despite there being little genetic
divergence in mitochondrial DNA (mtDNA) sequences throughout most of
Europe, the mtDNA patterns in Britain confirmed this separation of northern and
southern populations. Such genetic structuring within Britain — in the absence
of any obvious physical barriers — suggested that other features such as landuse
may limit gene-flow. To better understand how the species interacts with
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the British landscape, I used a landscape genetic approach, habitat suitability
modelling using presence-only data and a landscape connectivity analysis. The
negative association of M. bechsteinii presence with distance from woodland
was identified as the main variable determining habitat suitability, while the
landscape genetics results highlighted the importance of woodlands for gene
flow. M. bechsteinii habitat was highly fragmented and only showed good
connectivity if the species was able to disperse over 5,000 m. These results
subsequently highlight the importance of woodlands not only for providing
suitable habitat, but also in maintaining genetic connectivity between
populations.
Then, I investigated the use of non-invasive capture-mark-recapture (CMR) and
demographic history models to estimate the population size and changes of M.
bechsteinii. Bat droppings were collected below roosting sites of a single
colony. After species identification, the 123 droppings belonging to M.
bechsteinii were genotyped at nine DNA microsatellite loci in order to
differentiate all individuals. All microsatellites showed very low amplification
rates indicating low quality samples. However, at a larger scale, the use of
population demographic models to assess effective population size variation
using a dataset of 260 bats of the British population gave an estimate of the
effective population size of 6,569 (CI: 5,307-8,006) and suggested that the
British population of Myotis bechsteinii is stable and possibly expanding. Finally,
I developed an epigenetic assay to estimate the age of individual bats. For this,
I measured DNA methylation on bats of known age at seven CpG sites from
three genes. All CpG sites from the tested genes showed a significant
relationship between DNA methylation and age and provided reliable age
estimates.
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The findings presented in this thesis show that despite exhibiting high levels of
genetic diversity throughout its range, the genetic structure, habitat and
connectivity of M. bechsteinii populations is highly influenced by woodlands. It
also offers a novel method to monitor the species by developing an assay which
can provide information on the age structure of an entire colony from a single
sampling session. Such approaches are much needed in the field of
conservation and could in the future help preserve a wider range of species.Vincent Wildlife TrustWoodland TrustPeople's Trust for Endangered Specie
Assessing the health status of managed honeybee colonies (HEALTHY-B): a toolbox to facilitate harmonised data collection
Tools are provided to assess the health status of managed honeybee colonies by facilitating further harmonisation of data collection and reporting, design of field surveys across the European Union (EU) and analysis of data on bee health. The toolbox is based on characteristics of a healthy managed honeybee colony: an adequate size, demographic structure and behaviour; an adequate production of bee products (both in relation to the annual life cycle of the colony and the geographical location); and provision of pollination services. The attributes ‘queen presence and performance’, ‘demography of the colony’, ‘in-hive products’ and ‘disease, infection and infestation’ could be directly measured in field conditions across the EU, whereas ‘behaviour and physiology’ is mainly assessed through experimental studies. Analysing the resource providing unit, in particular land cover/use, of a honeybee colony is very important when assessing its health status, but tools are currently lacking that could be used at apiary level in field surveys across the EU. Data on ‘beekeeping management practices’ and ‘environmental drivers’ can be collected via questionnaires and available databases, respectively. The capacity to provide pollination services is regarded as an indication of a healthy colony, but it is assessed only in relation to the provision of honey because technical limitations hamper the assessment of pollination as regulating service (e.g. to pollinate wild plants) in field surveys across the EU. Integrating multiple attributes of honeybee health, for instance, via a Health Status Index, is required to support a holistic assessment. Examples are provided on how the toolbox could be used by different stakeholders. Continued interaction between the Member State organisations, the EU Reference Laboratory and EFSA is required to further validate methods and facilitate the efficient use of precise and accurate bee health data that are collected by many initiatives throughout the EU
Intelligent Sensor Networks
In the last decade, wireless or wired sensor networks have attracted much attention. However, most designs target general sensor network issues including protocol stack (routing, MAC, etc.) and security issues. This book focuses on the close integration of sensing, networking, and smart signal processing via machine learning. Based on their world-class research, the authors present the fundamentals of intelligent sensor networks. They cover sensing and sampling, distributed signal processing, and intelligent signal learning. In addition, they present cutting-edge research results from leading experts
Genetics of Halophilic Microorganisms
Halophilic microorganisms are found in all domains of life and thrive in hypersaline (high salt content) environments. These unusual microbes have been a subject of study for many years due to their interesting properties and physiology. Studies of the genetics of halophilic microorganisms (from gene expression and regulation to genomics) have provided understanding into the mechanisms of how life can exist at high salinity levels. Here, we highlight recent studies that advance the knowledge of biological function through examination of the genetics of halophilic microorganisms and their viruses
Functional genomics of commensal Lactobacilli
Catabolic flexibility affords a bacterium the ability to utilise different sugar sources as carbon for energy. This is important for commensal lactobacilli like Lactobacillus ruminis which can be exposed to a variety of carbohydrates in vivo. However, little is known about the fermentation capabilities, metabolic pathways, genetic diversity or potential survival mechanisms used by L. ruminis in vivo. A combination of in vitro and in silico techniques was used to identify the catabolic pathways of L. ruminis. I also compared 16 L. ruminis strains using a panel of biochemical and survival assays, genetically, whole genome sequencing and RNA sequencing. Multi locus sequence typing revealed that strains clustered according to their host sources. Transcriptome analysis by RNAseq of two motile strains under three growth conditions, including swarming, identified the up-regulation of carbohydrate-related genes under swarming conditions. This suggests that carbohydrate flexibility may have an uncharacterised role in L. ruminis swarming. Following on from the assessment of L. ruminis catabolic flexibility, the porcine diet was supplemented with galactooligosaccharides or L. ruminis ATCC 25644 plus galactooligosaccharides. Supplementation of the porcine diet with galactooligosaccharide had no effect on microbiota diversity. In contrast, the L. ruminis plus galactooligosaccharide treatment significantly reduced the microbiota diversity. Diet is a major factor that affects the diversity of the gut microbiota. In order to get a more thorough understanding of diet and gut health in animals such as racehorses and domesticated herbivores, I determined the core microbiota of animals consuming different feeds. Interestingly, the gut microbiota diversity correlated with the host phylogeny of the animal. The genome of Lactobacillus equi (2.19 Mb), isolated from a healthy Irish thoroughbred was also sequenced and annotated, and comprised 2,263 predicted genes. The large repertoire of predicted carbohydrate-related genes may offer L. equi an advantage in the complex and harsh hindgut environment. In summary, this thesis uses functional genomics to assess the effect that carbohydrates have on commensal lactobacilli and the microbiota as a whole
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