Chemical and biological approaches to enhance the bacteriophage as a probe in molecular recognition

The aim of the work presented in this thesis was to explore the structural and molecular features of a filamentous bacteriophage for incorporation in biosensing platforms. To tune the bacteriophage surface as a scaffold for molecular recognition, chemical and biological protocols aimed at controlling and enhancing its intrinsic properties were developed. A key part of the work was aimed at anchoring bacteriophage particles by one-end to surfaces, and on labelling its viral capsid with dyes, antibodies and DNA molecules. The tolerance of the bacteriophage for modifications, as well its simplicity and robustness, makes it an attractive probe for biosensors. Furthermore, the filamentous structure of the bacteriophage was demonstrated to be a valuable feature in both microscopy- and spectroscopy-based biosensors. The ability of the bacteriophage to align under flow was considered as a simple, yet efficient approach for the detection of wall shear stress and pathogenic bacteria. A novel method to detect wall shear stress (WSS) was developed by using a fluorescently decorated bacteriophage particle anchored by one-end to a surface. The response of this filamentous nanosensor to flow variations was tracked under a microscope, and gave valuable information on the shear flow of a fluid passing over a surface. Using a custom-made analysis tool and an algorithm, we were able to derive the wall shear stress on the point of attachment of the nanosensor, using endothelial cells as a model system. The proof-of-concept to this work highlighted how a simple bacteriophage construct can be use as a nanosensor for imaging and mapping flow. Linear dichroism (LD) spectroscopy also explores the high aspect ratio of the filamentous bacteriophage. Linear Diagnostics Ltd., a startup company in Birmingham, exploits the natural LD properties of the bacteriophage and integrated it with a biosensing platform targeting pathogenic bacteria. The work reported in this thesis mainly focused on developing alternative approaches that could improve the biosensor sensitivity and simplicity, by modifying the bacteriophage scaffold, further demonstrating its versatility

PALAEOCLIMATIC EVOLUTION IN LOUTRA ARIDEAS CAVE (ALMOPIA SPELEOPARK, MACEDONIA, N. GREECE) BY STABLE ISOTOPIC ANALYSIS OF FOSSIL BEAR BONES AND TEETH

Carbon and oxygen stable isotope values (δ13C, δ18O) were obtained from structural carbonate in the bioapatite of bear bones (Ursus ingressus) from Loutra Arideas cave, Almopia Speleopark, Macedonia, N. Greece. Samples of Late Pleistocene bear bones were studied for palaeoclimatic reconstruction of the area. The age range of the fossil layers is from 32ka BP to a maximum of 38ka BP. Generally, the palaeoclimatic proxy is correlated with literature data for climatic variations in the area during Late Pleistocene, whereas dietary behavior was investigated taking into account possible diagenetic processes that may have affected the carbonate matrix of the bones

The Frequent Items Problem in Online Streaming under Various Performance Measures

In this paper, we strengthen the competitive analysis results obtained for a fundamental online streaming problem, the Frequent Items Problem. Additionally, we contribute with a more detailed analysis of this problem, using alternative performance measures, supplementing the insight gained from competitive analysis. The results also contribute to the general study of performance measures for online algorithms. It has long been known that competitive analysis suffers from drawbacks in certain situations, and many alternative measures have been proposed. However, more systematic comparative studies of performance measures have been initiated recently, and we continue this work, using competitive analysis, relative interval analysis, and relative worst order analysis on the Frequent Items Problem.Comment: IMADA-preprint-c

The impact of vascular burden on late-life depression.

Small vessel pathology and microvascular lesions are no longer considered as minor players in the fields of cognitive impairment and mood regulation. Although frequently found in cognitively intact elders, both neuroimaging and neuropathological data revealed the negative impact on cognitive performances of their presence within neocortical association areas, thalamus and basal ganglia. Unlike cognition, the relationship between these lesions and mood dysregulation is still a matter of intense debate. Early studies focusing on the role of macroinfarct location in the occurrence of post-stroke depression (PSD) led to conflicting data. Later on, the concept of vascular depression proposed a deleterious effect of subcortical lacunes and deep white matter demyelination on mood regulation in elders who experienced the first depressive episode. More recently, the chronic accumulation of lacunes in thalamus, basal ganglia and deep white matter has been considered as a strong correlate of PSD. We provide here a critical overview of neuroimaging and neuropathological sets of evidence regarding the affective repercussions of vascular burden in the aging brain and discuss their conceptual and methodological limitations. Based on these observations, we propose that the accumulation of small vascular and microvascular lesions constitutes a common neuropathological platform for both cognitive decline and depressive episodes in old age

Brain Aging in the Oldest-Old

Nonagenarians and centenarians represent a quickly growing age group worldwide. In parallel, the prevalence of dementia increases substantially, but how to define dementia in this oldest-old age segment remains unclear. Although the idea that the risk of Alzheimer's disease (AD) decreases after age 90 has now been questioned, the oldest-old still represent a population relatively resistant to degenerative brain processes. Brain aging is characterised by the formation of neurofibrillary tangles (NFTs) and senile plaques (SPs) as well as neuronal and synaptic loss in both cognitively intact individuals and patients with AD. In nondemented cases NFTs are usually restricted to the hippocampal formation, whereas the progressive involvement of the association areas in the temporal neocortex parallels the development of overt clinical signs of dementia. In contrast, there is little correlation between the quantitative distribution of SP and AD severity. The pattern of lesion distribution and neuronal loss changes in extreme aging relative to the younger-old. In contrast to younger cases where dementia is mainly related to severe NFT formation within adjacent components of the medial and inferior aspects of the temporal cortex, oldest-old individuals display a preferential involvement of the anterior part of the CA1 field of the hippocampus whereas the inferior temporal and frontal association areas are relatively spared. This pattern suggests that both the extent of NFT development in the hippocampus as well as a displacement of subregional NFT distribution within the Cornu ammonis (CA) fields may be key determinants of dementia in the very old. Cortical association areas are relatively preserved. The progression of NFT formation across increasing cognitive impairment was significantly slower in nonagenarians and centenarians compared to younger cases in the CA1 field and entorhinal cortex. The total amount of amyloid and the neuronal loss in these regions were also significantly lower than those reported in younger AD cases. Overall, there is evidence that pathological substrates of cognitive deterioration in the oldest-old are different from those observed in the younger-old. Microvascular parameters such as mean capillary diameters may be key factors to consider for the prediction of cognitive decline in the oldest-old. Neuropathological particularities of the oldest-old may be related to “longevity-enabling” genes although little or nothing is known in this promising field of future research

Ultrasound and dynamic functional imaging in vascular cognitive impairment and Alzheimer's disease

The vascular contributions to neurodegeneration and neuroinflammation may be assessed by magnetic resonance imaging (MRI) and ultrasonography (US). This review summarises the methodology for these widely available, safe and relatively low cost tools and analyses recent work highlighting their potential utility as biomarkers for differentiating subtypes of cognitive impairment and dementia, tracking disease progression and evaluating response to treatment in various neurocognitive disorders. METHODS: At the 9th International Congress on Vascular Dementia (Ljubljana, Slovenia, October 2015) a writing group of experts was formed to review the evidence on the utility of US and arterial spin labelling (ASL) as neurophysiological markers of normal ageing, vascular cognitive impairment (VCI) and Alzheimer's disease (AD). Original articles, systematic literature reviews, guidelines and expert opinions published until September 2016 were critically analysed to summarise existing evidence, indicate gaps in current knowledge and, when appropriate, suggest standards of use for the most widely used US and ASL applications. RESULTS: Cerebral hypoperfusion has been linked to cognitive decline either as a risk or an aggravating factor. Hypoperfusion as a consequence of microangiopathy, macroangiopathy or cardiac dysfunction can promote or accelerate neurodegeneration, blood-brain barrier disruption and neuroinflammation. US can evaluate the cerebrovascular tree for pathological structure and functional changes contributing to cerebral hypoperfusion. Microvascular pathology and hypoperfusion at the level of capillaries and small arterioles can also be assessed by ASL, an MRI signal. Despite increasing evidence supporting the utility of these methods in detection of microvascular pathology, cerebral hypoperfusion, neurovascular unit dysfunction and, most importantly, disease progression, incomplete standardisation and missing validated cut-off values limit their use in daily routine. CONCLUSIONS: US and ASL are promising tools with excellent temporal resolution, which will have a significant impact on our understanding of the vascular contributions to VCI and AD and may also be relevant for assessing future prevention and therapeutic strategies for these conditions. Our work provides recommendations regarding the use of non-invasive imaging techniques to investigate the functional consequences of vascular burden in dementia

Airborne sampling of aerosol particles: Comparison between surface sampling at Christmas Island and P-3 sampling during PEM-Tropics B

Bulk aerosol sampling of soluble ionic compounds from the NASA Wallops Island P-3 aircraft and a tower on Christmas Island during PEM-Tropics B provides an opportunity to assess the magnitude of particle losses in the University of New Hampshire airborne bulk aerosol sampling system. We find that most aerosol-associated ions decrease strongly with height above the sea surface, making direct comparisons between mixing ratios at 30 m on the tower and the lowest flight level of the P-3 (150 m) open to interpretation. Theoretical considerations suggest that vertical gradients of sea-salt aerosol particles should show exponential decreases with height. Observed gradients of Na+ and Mg2+, combining the tower observations with P-3 samples collected below 1 km, are well described by exponential decreases (r values of 0.88 and 0.87, respectively), though the curve fit underestimates average mixing ratios at the surface by 25%. Cascade impactor samples collected on the tower show that \u3e99% of the Na+ and Mg2+mass is on supermicron particles, 65% is in the 1–6 micron range, and just 20% resides on particles with diameters larger than 9 microns. These results indicate that our airborne aerosol sampling probes must be passing particles up to at least 6 microns with high efficiency. We also observed that nss SO42− and NH4+, which are dominantly on accumulation mode particles, tended to decrease between 150 and 1000 m, but they were often considerably higher at the lowest P-3 sampling altitudes than at the tower. This finding is presently not well understood