The Role of Fluorescence and Human Factors in Quantitative Transdermal Blood and Tissue Analysis Using NIR Raman Spectroscopy

This research is part of an ongoing project aimed at the application of combined near infrared (NIR) Raman and fluorescence spectroscopy to noninvasive in vivo blood analysis including but not limited to glucose monitoring. Coping with practicalities of human factors and exploring ways to obtain and use knowledge gained about autofluorescence to improve algorithms for blood and tissue analysis are the general goals of this research. Firstly, the study investigated the various sources of human factors pertinent to our concerns, such as fingerprints, turgor, skin hydration and pigmentation. We then introduced specialized in vivo apparatus including means for precise and reproducible placement of the tissues relative to the optical aperture, i.e., the position detector pressure monitor (PDPM). Based on solid instrumental performances, appropriate methodology is now provided for applying and maintaining pressure to keep surface tissues immobile during experiments while obtaining the desired blood content and flow. Secondly, in vivo human fingertip skin autofluorescence photobleaching under 200 mW 830 nm NIR irradiation is observed and it is characterized that: i) the majority of the photobleached fluorescence originates from static tissue not blood, ii) the bleaching (1/e point) occurs in 101-102 sec timescale, and also iii) a photobleached region remains bleached for at least 45 min but recovers completely within several hours. A corresponding extensive but not exhaustive in vitro systematic study narrowed down the major contributors of such fluorescence and bleaching to collagen, melanin, plasma and hemoglobin: two major static tissue constituents and two major blood proteins. Thirdly, we established that measuring the inelastic and elastic emissions simultaneously leads to a sensitive probe for volume changes of both red blood cells and plasma. An algorithm based on measurements obtained while performing research needed for this thesis, as well as some empirical calibration approaches, was presented. The calibrated algorithm showed real potential to track hematocrit variations in cardiac pulses, centrifugal loading, blood vessel blockage using tourniquet, and even during as subtle an occurrence as in a Valsalva maneuver. Finally, NIR fluorescence and photochemistry of pentosidine, a representative of the advanced glycation endproducts (AGEs) which accumulate with age and hyperglycemia, was studied. The results indicate that oxygen plays a pivotal role in its photobleaching process. We hypothesized and offered proofs showing that pentosidine is a 1O2 sensitizer that is also subject to attack by the 1O2 resulting in the photobleaching that is observed when probing tissue using NIR. The photobleaching reaction is kinetically first order in pentosidine and ground state oxygen, and in vivo effectively first order with NIR irradiation also

Structural basis of inter-domain electron transfer in Ncb5or, a redox enzyme implicated in diabetes and lipid metabolism

NADH cytochrome b5 oxidoreductase (Ncb5or) is a multi-domain redox enzyme found in all animal tissues and associated with the endoplasmic reticulum (ER). Ncb5or contains (from N-terminus to C terminus) a novel N-terminal region, the b5 domain (Ncb5or-b5), the CS domain, and the b5R domain (Ncb5or-b5R). Ncb5or-b5, the heme binding domain, is homologous to microsomal cytochrome b5 (Cyb5A) and belongs to cytochrome b5 superfamily. Ncb5or-b5R, the FAD (flavin adenine dinucleotide) binding domain, is homologous to cytochrome b5 reductase (Cyb5R3) and belongs to ferredoxin NADP+ reductase superfamily. Both superfamilies are of great biological significance whose members have important functions. The CS domain can be assigned into the heat shock protein 20 (HSP20, or p23) family, whose members are known to mediate protein-protein interactions. Ncb5or is unique in containing these domains and employing a novel sequence as the N-terminal region. Cyb5A and Cyb5R3 have been shown to form a complex to donate electrons to stearoyl-CoA desaturase (SCD) in fatty acid desaturation in vitro. Monounsaturated fatty acids are preferentially used in triglyceride synthesis for lipid storage. Mice with hepatic deletion of Cyb5A show no significant defect in lipid metabolism, whereas Ncb5or null mice exhibit diabetes, lipoatrophy and impaired SCD activity. We hypothesize that Ncb5or, as a fusion of both Cyb5A and Cyb5R3-like domains, serves as an alternative electron donor to SCD in vivo. Ncb5or-b5 shows unique structural and functional features, such as, low sequence homology to other family members, displacement of the second heme-ligating His residue, a decrease in the number of surface-charged residues, and a much lower redox potential at the heme center compared with Cyb5A. In order to understand how these differences between Ncb5or and Cyb5A contribute to their unique structural and functional properties in electron transfer, we solved the crystal structure of Ncb5or-b5 and performed kinetic assays by using various domain combinations. Our 1.25 Å crystal structure shows that Ncb5or-b5 has a general b5 fold. However, Ncb5or-b5 has a unique heme environment, namely the two heme-ligating His residues are nearly perpendicular to each other. The latter feature agrees with a large gmax value in electron paramagnetic resonance (EPR) spectra. This makes Ncb5or the first example with a tetragonally distorted heme environment in the cytochrome b5 superfamily. Lower density of charge on the surface of Ncb5or-b5 suggests weaker ionic interaction between Ncb5or-b5 and Ncb5or-b5R than that between Cyb5A and Cyb5R3. The lack of Ncb5or-b5/Ncb5or-b5R complex formation and lower rates of electron transfer than Cyb5A/Cyb5R3 are consistent with this hypothesis. Low affinity between Ncb5or-b5 and Ncb5or-b5R prompted a search for other factors that facilitate the inter-domain electron transfer. Specifically, the role of the N-terminal region, a region rich in random coils but with little homology to known proteins, was explored. A reductionist approach was used to test various domains of Ncb5or with kinetic assays and spectral analyses, such as circular dichroism and nuclear magnetic resonance. I have unveiled the role of the N-terminal region for the first time: the N-terminal region facilitates inter-domain electron transfer by cooperatively interacting with the CS domain and the heme center of Ncb5or-b5. The formation of tertiary structure in the N-terminal region is governed by the region from Gly22 through Trp37, especially Trp37, and this region is essential for electron transfer. This feature suggests a potential mechanism to facilitate the inter-domain electron transfer in Ncb5or

Incorporation of micro-level analysis in strategic urban transport modelling: with a case study of the Greater Beijing

Many developing countries and regions are suffering from severe urban transport problems arising from accidents, congestion, air pollution, rising carbon intensity, and chronic under-funding of infrastructure and services. The problems make those cities the most polluted and often the least liveable. Strategic transport modelling has been recognised as an effective approach for developing and testing policy options, especially where it is integrated with land use planning and urban design. However, in most developing-country cities strategic transport modelling has been out of reach for practical policy use because of its sophisticated data and skill requirements, which currently imply unaffordable high costs and long durations for model development. This means that strategic urban transport modelling is the least available where it is needed most urgently. Meanwhile, the spread of smart data in mapping and urban activity monitoring has often been just as rapid in developing countries as in the developed. This has triggered new approaches in micro-level analyses of transport networks, personal movements and vehicles. In the most advanced cases, the new analyses have started to influence strategic modelling. The main hypothesis of this dissertation is that an incorporation of the micro-level smart data and analyses in strategic urban transport modelling will make it feasible to establish a sufficiently robust strategic transport model for evidence-based policy analysis with cost, time and skill thresholds that are close to being affordable in developing country cities. In order to test this main hypothesis, a number of novel model development tasks have been carried out which contribute to the field of applied urban modelling. This new approach aims to contribute to the transformation of the prevailing modus operandi where model development could not start in earnest until extensive data collection and skills training have been completed to a situation where a sufficiently robust model can be established cheaply and quickly to support on-going and incremental refinements. More specifically, new modelling tools have been developed as part of this dissertation using sparse GPS taxi traces to identify slow-moving and stopping traffic hotspots using an extended density-based spatial clustering algorithm that is tolerant of significant data noise, and to estimate congested road speeds (which used to be very costly and time-consuming to obtain if at all). The micro-level network, congested speeds and insights into the nature of the congested traffic have been incorporated into a MEPLAN-based strategic transport model interacting with a MEPLAN-based land use and travel demand model. This means that the strategic economic, social and environmental impacts of transport interventions can be tested in a robust way through accounting for the interactions among transport, land-use and background social-technical trends. A new approach to establish the medium to long term visions for alternative travel demand management and transport investment scenarios has been tested using this model. The methods and algorithms have been tested in a case study of the Greater Beijing region, which consists of the municipalities of Beijing and Tianjin together with the surrounding areas in the province of Hebei. The government’s data regulations of restricting overseas studies to using only publicly available data sources have made the case study ideal for testing the new approach. The potential of the new strategic urban transport model has been tested through a wide range of policy scenarios. The results suggest that the new approach developed in this dissertation has made it not only cheaper and faster to develop a robust model, but could also potentially fill a gap in the lack of medium to long term perspectives regarding major road and metro investments over the next two decades. Such analyses could be of critical importance in improving the performance of the transport system in terms of safety, economic efficiency, air quality and carbon reduction given the long lead times to plan and deliver transport infrastructure investments