Investigation of growth and stress tolerance characteristics of Cronobacter spp.

Cronobacter spp. are opportunistic pathogens which can be isolated from a wide variety of foods and environments. They are Gram negative, motile, non-spore forming, peritrichous rods of the Enterobacteriaceae family. This food-borne pathogen is associated with the ingestion of contaminated infant milk formula (IMF), causing necrotizing enterocolitis, sepsis and meningitis in neonatal infants. The work presented in this thesis involved the investigation and characterisation of a bank of Cronobacter strains for their ability to tolerate physiologically relevant stress conditions that are commonly encountered in the gastrointestinal tract. While all strains were able to endure the suboptimal conditions tested, noteworthy variations were observed between strains. A collection of these strains were Lux-tagged to determine if their growth could be tracked in IMF by measuring bioluminescence. The resulting strains could be easily and reproducibly monitored in real time by measuring light emission. Following this a transposon mutagenesis library was created in one of the Lux-tagged strains of Cronobacter sakazakii. This library was screened for mutants with affected growth in milk. The majority of mutants identified were associated with amino acid metabolism. The final section of this thesis identified genes involved in the tolerance of C. sakazakii to the milk derived antimicrobial peptide, Lactoferricin B (Lfcin B). This was achieved by creating a transposon mutagenesis library in C. sakazakii and screening for mutants with increased susceptibility to Lfcin B. Overall this thesis demonstrates the variation between Cronobacter strains. It also identifies genes required for growth of the bacteria in milk, as well as genes needed for antimicrobial peptide tolerance.

Exploiting the bioactive potential of marine sponge microbiota

Endospore-forming bacteria are often isolated from different marine sponges, but their abundance varies, and they are frequently missed by culture-independent studies. Within endospore-formers, Bacillus are renowned for the production of antimicrobials and other compounds of medical and industrial importance. Although this group has been well studied in many different environments, very little is known about the actual diversity and properties of sporeformers associated with marine sponges. Identification of the endospore-forming bacteria associated with the marine sponges; Haliclona simulans, Amphilectus fucorum and Cliona celata, has uncovered an abundant and diverse microbial population composed of Bacillus, Paenibacillus, Solibacillus, Halobacillus and Viridibacillus species. This diversity appears to be overlooked by other non-targeted approaches where spore-formers are masked by more dominant species within the ecosystem. In addition to the identification of two antibiotic resistant plasmids, this bank of sporeformers produce a range of bioactive compounds. New antimicrobial compounds are urgently needed to combat the spread of multidrug resistant pathogens, as few new options are entering the drug discovery pipelines for clinical trials. Based on the results of this project, endospore-formers associated with marine sponges may hold the answer. The power of coupling functional based assays with genomic approaches has enabled us to identify a novel class 1 lantibiotic, subtilomycin, which is active against several clinically relevant pathogens. Subtilomycin is encoded in the genomes of all the marine sponge B. subtilis isolates analysed. They cluster together phylogenetically and form a distinct group from other sequenced B. subtilis strains. Regardless of its potential clinical relevance, subtilomycin may be providing these strains with a specific competitive advantage(s) within the stringent confines of the marine sponge environment. This work has outlined the industrial and biotechnological potential of marine sponge endospore-formers which appear to produce a cocktail of bioactive compounds. Genome sequencing of specific marine sponge isolates highlighted the importance of mining extreme environments and habitats for new lead compounds with potential therapeutic applications.

A unified anatomy ontology of the vertebrate skeletal system.

The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO), to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish) and multispecies (teleost, amphibian) vertebrate anatomy ontologies. Previous differences between these terminologies prevented even simple queries across databases pertaining to vertebrate morphology. This module of upper-level and specific skeletal terms currently includes 223 defined terms and 179 synonyms that integrate skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system. The VSAO is designed to integrate with other ontologies, including the Common Anatomy Reference Ontology (CARO), Gene Ontology (GO), Uberon, and Cell Ontology (CL), and it is freely available to the community to be updated with additional terms required for research. Its structure accommodates anatomical variation among vertebrate species in development, structure, and composition. Annotation of diverse vertebrate phenotypes with this ontology will enable novel inquiries across the full spectrum of phenotypic diversity.

The meso-scale response of subarctic North Pacific seabird community structure to lower trophic level abundance and diversity

Understanding the mechanisms that structure communities and influence biodiversity are fundamental goals of ecology. To test the hypothesis that the abundance and diversity of upper-trophic level predators (seabirds) is related to the underlying abundance and diversity of their prey (zooplankton) and ecosystem-wide energy availability (primary production), we initiated a monitoring program in 2002 that jointly and repeatedly surveys seabird and zooplankton populations across a 7,500 km British Columbia-Bering Sea-Japan transect. Seabird distributions were recorded by a single observer (MH) using a strip-width technique, mesozooplankton samples were collected with a Continuous Plankton Recorder, and primary production levels were derived using the appropriate satellite parameters and the Vertically Generalized Production Model (Behrenfeld and Falkowski 1997). Each trophic level showed clear spatio-temporal patterns over the course of the study. The strongest relationship between seabird abundance and diversity and the lower trophic levels was observed in March/April ('spring') and significant relationships were also found through June/July ('summer'). No discernable relationships were observed during the September/October ('fall') months. Overall, mesozooplankton abundance and biomass explained the dominant portion of seabird abundance and diversity indices (richness, Simpson's Index, and evenness), while primary production was only related to seabird richness. These findings underscore the notion that perturbations of ocean productivity and lower trophic level ecosystem constituents influenced by climate change, such as shifts in timing (phenology) and synchronicity (match-mismatch), could impart far-reaching consequences throughout the marine food web.

High-resolution view of the spring bloom initiation and net community production in the Subantarctic Southern Ocean using glider data

In the Southern Ocean, there is increasing evidence that seasonal to subseasonal temporal scales, and meso- to submesoscales play an important role in understanding the sensitivity of ocean primary productivity to climate change. This drives the need for a high-resolution approach to re- solving biogeochemical processes. In this study, 5.5 months of continuous, high-resolution (3 h, 2 km horizontal resolution) glider data from spring to summer in the Atlantic Subantarctic Zone is used to investigate: (i) the mechanisms that drive bloom initiation and high growth rates in the region and (ii) the seasonal evolution of water column production and respiration. Bloom initiation dates were analysed in the context of upper ocean boundary layer physics highlighting sensitivities of different bloom detection methods to different environmental processes. Model results show that in early spring (September to mid-November) increased rates of net community production (NCP) are strongly affected by meso- to submesoscale features. In late spring/early summer (late-November to mid-December) seasonal shoaling of the mixed layer drives a more spatially homogenous bloom with maximum rates of NCP and chlorophyll biomass. A comparison of biomass accumulation rates with a study in the North Atlantic highlights the sensitivity of phytoplankton growth to fine-scale dynamics and emphasizes the need to sample the ocean at high resolution to accurately resolve phytoplankton phenology and improve our ability to estimate the sensitivity of the biological carbon pump to climate change.

Effect of habitat fragmentation on the macroinvertebrate infaunal communities associated with the seagrass Zostera marina

1. The effect of habitat fragmentation was investigated in two adjacent, yet separate, intertidal Zostera marina beds in the Salcombe Estuary, Devon, UK. The seagrass bed on the west bank comprised a continuous meadow of ca. 2.3 ha, whilst the bed on the east bank of the estuary was fragmented into patches of 6–9 m2.2. Three 10 cm diameter core samples for infaunal macroinvertebrates were taken from three stations within each bed. No significant difference was found in univariate community parameters between beds, or in measured seagrass parameters. However, multivariate analysis revealed a significant difference in community composition, due mainly to small changes in species abundance rather than differences in the species present.3. The species contributing most to the dissimilarity between the two communities were polychaetes generally associated with unvegetated habitats (e.g. Magelona mirabilis) and found to be more common in the fragmented bed.4. A significant difference in median grain size and sorting coefficient was recorded between the two beds, and median grain size was found to be the variable best explaining multivariate community patterns.5. The results of the study provide evidence for the effects of habitat fragmentation on the communities associated with seagrass beds, habitats which are of high conservation importance. As the infaunal community is perhaps intuitively the component least likely to be affected by fragmentation at the scale observed, the significant difference in community composition recorded has consequences for more sensitive and high-profile parts of the biota (e.g. fish), and thus for the conservation of seagrass habitats and their associated communities.

The Genetics of Postglacial Colonization and Peripherality in Northwestern Populations of the Spring Peeper, Pseudacris crucifer

Glaciation over the Pleistocene induced dramatic range fluctuations for species across North America such that postglacial recolonization by southern refugial lineages has characterized the genetic structure of northern North American species. Based on the leading edge model of postglacial range expansion, dispersal and rapid population growth in these northern taxa is expected to produce vast areas of genetic homogeneity. Previous work on the widely distributed spring peeper (Pseudacris crucifer) revealed six distinct mitochondrial lineages that diverged between 3-11 mya, expanding and contracting with glacial cycles. Beginning 16,000 yBP, receding glaciers permitted Eastern lineage refugia residing in the southern Appalachians to migrate northward into the St. Lawrence Valley then westward through most of central Canada. Peripheral populations at the northwestern range limit of P. crucifer in central Manitoba are likely descended from this westward expanding Eastern lineage. According to the central-marginal hypothesis, founder effects from colonization as well as limited gene flow is expected to reveal genetic differentiation and lower genetic diversity in peripheral populations. The goal of my study is to further our understanding of peripheral range dynamics in peripheral Manitoba populations of P. crucifer by determining their genetic affinity and diversity relative to more central populations in Ontario and Minnesota. In this study I amplified and aligned cytochrome b sequences from sample sites across central Manitoba to reconstruct a Bayesian phylogeny for P. crucifer; additionally, microsatellite loci were genotyped to estimate genetic diversity. Results from this study affirmed Eastern lineage descent for peripheral Manitoba sites by aligning with Ontario. Initial colonization by the Interior lineage between glacial retreat and the appearance of arid vicariance events may explain the apparent introgression of non-Eastern lineages in Manitoba. However, genetic diversity measured in expected heterozygosity (H¬e) was not found to be significantly different in Manitoba genotypes. Greater isolation by distance and inbreeding relative to Ontario and Minnesota is likely the primary driver of genetic variation in these sites. Further sampling is necessary to generate a more complete genetic population structure for P. crucifer.

Training-induced changes in the pattern of triceps to biceps activation during reaching tasks after chronic and severe stroke

This exploratory study was undertaken to investigate the mechanisms that contributed to improvements in upper limb function following a novel training program. Surface electromyography (EMG) was used to examine training-induced changes in the pattern of triceps and biceps activation during reaching tasks in stroke survivors with severe paresis in the chronic stage of recovery. The EMG data were obtained in the context of a single blind randomised clinical trial conducted with 42 stroke survivors with minimal upper limb muscle activity and who were more than 6 months post-stroke. Of the 33 participants who completed the study, 10 received training of reaching using a non-robotic upper limb training device, the SMART Arm, with EMG triggered functional electrical stimulation (EMG-stim), 13 received training of reaching using the SMART Arm alone, and 10 received no intervention. Each intervention group engaged in 12 1-h training sessions over a 4-week period. Clinical and laboratory measures of upper limb function were administered prior to training (0 weeks), at completion (4 weeks) and 2 months (12 weeks) after training. The primary outcome measure was 'upper arm function' which is Item 6 of the Motor Assessment Scale (MAS). Laboratory measures consisted of two multijoint reaching tasks to assess 'maximum isometric force' and 'maximum distance reached'. Surface EMG was used to monitor triceps brachii and biceps brachii during the two reaching tasks. To provide a comparison with normal values, seven healthy adults were tested on one of the reaching tasks according to the same procedure. Study findings demonstrated a statistically significant improvement in upper limb function for stroke participants in the two training groups compared to those who received no training however no difference was found between the two training groups. For the reaching tasks, all stroke participants, when compared to normal healthy adults, exhibited lower triceps and biceps activation and a lower ratio of triceps to biceps activation. Following training, stroke participants demonstrated increased triceps activation and an increased ratio of triceps to biceps activation for the task that was trained. Better performance was associated with greater triceps activation and a higher ratio of triceps to biceps activation. The findings suggest that increased activation of triceps as an agonist and an improved coordination between triceps and biceps could have mediated the observed changes in arm function. The changes in EMG activity were small relative to the changes in arm function indicating that factors, such as the contribution of other muscles of reaching, may also be implicated.

Potential output in a rapidly developing economy: the case of China and a comparison with the United States and the European Union

The authors use a growth accounting framework to examine growth of the rapidly developing Chinese economy. Their findings support the view that, although feasible in the intermediate term, China's recent pattern of extensive growth is not sustainable in the long run. The authors believe that China will be able to sustain a growth rate of 8 to 9 percent for an extended period if it moves from extensive to intensive growth. They next compare potential growth in China with historical developments in the United States and the European Union. They discuss the differences in production structure and level of development across the three economies that may explain the countries' varied intermediate-term growth prospects. Finally, the authors provide an analysis of "green" gross domestic product and the role of natural resources in China's growth. © 2009, The Federal Reserve Bank of St. Louis.

Banking in Crisis: The Rise and Fall of British Banking Stability, 1800 to the Present

Can the lessons of the past help us to prevent another banking collapse in the future? This is the first book to tell the story of the rise and fall of British banking stability in the past two centuries, and it sheds new light on why banking systems crash and the factors underpinning banking stability. John Turner shows that there were only two major banking crises in Britain during this time: the crisis of 1825–6 and the Great Crash of 2007–8. Although there were episodic bouts of instability in the interim, the banking system was crisis-free. Why was the British banking system stable for such a long time and why did the British banking system implode in 2008? In answering these questions, the book explores the long-run evolution of bank regulation, the role of the Bank of England, bank rescues and the need to hold shareholders to account.

Utilising Creative Methodologies to Elicit the Views of Young Learners with Additional Needs in Literacy

The research described in this article aimed to explore and examine the dominant ‘assessment’ and ‘participation’ stories of upper-primary pupils with long-standing and marked literacy learning needs, their views on how their level of participation in the assessment and remediation of their additional needs might be increased and also how they perceive themselves as literacy learners. This qualitative small-scale study adopted a case study approach and utilised creative methodologies in the context of focus groups to investigate sensitively theviews and experiences of Key Stage 2 pupils with additional needs in literacy. The findings discussed here are based on the outcomes from the four Northern Irish schools that participated in the original cross-border (Northern Ireland/Republic of Ireland) study. Findings are discussed in the context of strategies for promotingholistic and empowering pathways for learners with additional needs in literacy.

The Klondike goldfields and Pleistocene environments of Beringia

The Klondike goldfields of Yukon, Canada, contain a key record of Pleistocene Beringia, the region of Alaska, Siberia, and Yukon that remained largely unglaciated during the late Cenozoic. A concentration of mining exposures, with relict permafrost that is locally more than 700,000 years old, provides exceptional preservation of paleoenvironmental archives and a new perspective on the nature of paleoenvironments during the Pleistocene. A critical feature is the stratigraphic association of distal tephra beds with these paleoenvironmental archives, which facilitates their regional correlation and, in many cases, provides independent ages for the paleoenvironmental assemblages. Paleoenvironmental analyses of fossil arctic ground-squirrel middens and buried vegetation indicate the presence of cryoxerophilous ("steppe-tundra") vegetation growing on well-drained substrates with deep active layers (seasonal thaw depths) during cold intervals of the Pleistocene. Studies of full-glacial paleosols and cryostratigraphic relations of associated ground ice indicate the importance of active loess deposition and surface vegetation cover in maintaining the functionally distinct mammoth-steppe biome, which supported grazing mega-fauna populations, including mammoth, horse, and bison.

Family caregiver views on patient-centred care at the end of life

Aim: The purpose of this study was to evaluate the patient-centredness of community palliative care from the perspective of family members who were responsible for the care of a terminally ill family member. Method: A survey questionnaire was mailed to families of a deceased family member who had been designated as palliative and had received formal home care services in the central west region of the Province of Ontario, Canada. Respondents reported on service use in the last four weeks of life; the Client-Centred Care Questionnaire (CCCQ) was used to evaluate the extent to which care was patient-centred. The accessibility instrument was used to assess respondent perception of access to care. Descriptive and inferential statistics were used for data analyses. Results: Of the 243 potential participants, 111 (46.0%) family caregivers completed the survey questionnaire. On average, respondents reported that they used five different services during the last four weeks of the care recipient's life. When asked about programme accessibility, care was also perceived as largely accessible and responsive to patients' changing needs (M=4.3 (SD=1.04)]. Most respondents also reported that they knew what service provider to contact if they experienced any problems concerning the care of their family member. However, this service provider was not consistent among respondents. Most respondents were relatively positive about the patient-centred care they received. There were however considerable differences between some items on the CCCQ. Respondents tended to provide more negative ratings concerning practical arrangement and the organization of care: who was coming, how often and when. They also rated more negatively the observation that service providers were quick to say something was possible when it was not the case. Bivariate analyses found no significant differences in CCCQ or accessibility domain scores by caregiver age, care recipient age, income, education and caregiver sex. Conclusions: Patient-centred care represents a service attribute that should be recognized as an important outcome to assess the quality of service delivery. This study demonstrates how this attribute can be evaluated in the provision of care. © 2011 The Authors. Scandinavian Journal of Caring Sciences © 2011 Nordic College of Caring Science.

Caregiving and its impact on families of the terminally ill

Changes in the health care system have meant that increasing numbers of the terminally ill receive the majority of their care at home. The purpose of this paper was to document patterns of informal and formal care provided to the terminally ill and assess the impact caregiving has on family members. One hundred and fifty-one family caregivers were recruited for interviews from two community-nursing agencies in an urban region of the province of Ontario, Canada. The majority of respondents 119 (79%) were the female spouses of the patient. The numbers of caregivers providing assistance in specific functional activities were: bathing, 133 (88%); mobility, 123 (81%); dressing and undressing, 114 (76%); toileting, 101 (67%), and assistance at night 97 (64%). Sixty-two (41%) respondents reported that they had been providing some form of caregiving for over one year. They also reported that physical demands in caregiving increased substantially during the last three months of the care recipient's life. As family caregivers provided more assistance in activities of daily living they were at greater risk of reporting high caregiver burden. The results of this paper identify the types of care provided by family caregivers of the terminally ill and the impact these demands have on the family caregiver.