Put Your Money Where Your Mouth Is: Reforming Organized Dentistry to Address Persistent Oral Health Disparities in the U.S.

The importance of oral health has been largely neglected from the conventional standards of healthcare in terms of public understanding & prioritization, the industrial infrastructure, and the scope of prevention & early-intervention services. Its adjunctive locus to the field of medicine has lead to the bifurcation of the oral cavity from the rest of the human body. As a result of this divide, there have been multiple factors that have allowed socially stratified oral health outcomes to manifest. This thesis examines the determinants of oral health disparities through a multidisciplinary lens (i.e. biology, public policy, infrastructure), and offers evidence of an adaptable public health intervention to shape public policy recommendations that can remedy the downstream effects of oral health inequity in the state of California and beyond

Data-mining the FlyAtlas online resource to identify core functional motifs across transporting epithelia

<p>Background Comparative analysis of tissue-specific transcriptomes is a powerful technique to uncover tissue functions. Our FlyAtlas.org provides authoritative gene expression levels for multiple tissues of Drosophila melanogaster (1). Although the main use of such resources is single gene lookup, there is the potential for powerful meta-analysis to address questions that could not easily be framed otherwise. Here, we illustrate the power of data-mining of FlyAtlas data by comparing epithelial transcriptomes to identify a core set of highly-expressed genes, across the four major epithelial tissues (salivary glands, Malpighian tubules, midgut and hindgut) of both adults and larvae.</p> <p>Method Parallel hypothesis-led and hypothesis-free approaches were adopted to identify core genes that underpin insect epithelial function. In the former, gene lists were created from transport processes identified in the literature, and their expression profiles mapped from the flyatlas.org online dataset. In the latter, gene enrichment lists were prepared for each epithelium, and genes (both transport related and unrelated) consistently enriched in transporting epithelia identified.</p> <p>Results: A key set of transport genes, comprising V-ATPases, cation exchangers, aquaporins, potassium and chloride channels, and carbonic anhydrase, was found to be highly enriched across the epithelial tissues, compared with the whole fly. Additionally, a further set of genes that had not been predicted to have epithelial roles, were co-expressed with the core transporters, extending our view of what makes a transporting epithelium work. Further insights were obtained by studying the genes uniquely overexpressed in each epithelium; for example, the salivary gland expresses lipases, the midgut organic solute transporters, the tubules specialize for purine metabolism and the hindgut overexpresses still unknown genes.</p> <p>Conclusion Taken together, these data provide a unique insight into epithelial function in this key model insect, and a framework for comparison with other species. They also provide a methodology for function-led datamining of FlyAtlas.org and other multi-tissue expression datasets.</p&gt

An integrative and systems biology approach to Drosophila melanogaster transcriptomes

The availability of fully sequenced genomes of the model organisms including Drosophila, and their subsequent annotation has afforded seamless opportunities for reverse genetics in a complex model organism. With the advent of DNA microarrays to assay the levels of tens of thousands of genes in a single sample, functional genomics has been significantly aided to understand the functions in systems context. These microarrays have been employed predominantly on the RNA samples that are extracted from the whole animals for example at different developmental stages or in response to external stimuli. However, these approaches relied on the expression patterns that represent the sum of transcription coming from all the organs, which do not estimate the tissue-specificity of transcription. The purpose of this thesis is to provide tissue-specific transcriptomes of Drosophila melanogaster that were generated as part of the large FlyAtlas project using Affymetrix Drosophila GeneChips® (or microarrays). These chips, one at a time interrogate the levels of 18,500 transcripts (that represent all known genes) using 18,880 distinct probe sets in a single, total RNA sample. For each tissue, four biological replicates were analysed using the chips and the normalised signal intensities were obtained that represent the relative levels of mRNA expression. Using the transcriptomes, a general analysis was performed for potential novel insights into tissue-specific functions (Chintapalli et al., 2007) (Chapter 3). Then, a comparative analysis of epithelial tissues was performed to understand how the epithelia are organised in terms of their transcriptomes (Chapter 4). The Malpighian tubules are the Drosophila epithelial counterparts of the human kidney. They show asymmetric organisation in the body cavity. FlyAtlas segment-specific tubule transcriptomes allowed the comparison of their potential functional similarities and differences, thus to understand the asymmetry in function (Chapter 5)(Chintapalli, 2012). This identified a human Best vitelliform macular dystrophy (BVMD) disease homolog, Best2 in only the anterior pair of tubules that have the morphologically and functionally distinct enlarged initial (or distal) segment, a storage organ for Ca2+. Bestrophins were accordingly selected as candidate genes to analyse organismal functions, and thus to validate previous two theories that implicated bestrophins as Ca2+-activated Clˉ channels and/or Ca2+ channel regulators (Chapter 6). The confocal microscopy analysis of bestrophin YFP fusion proteins revealed interesting and novel localisations of bestrophins, in that Best1 was found in the apical plasma membranes, Best2 localised to peroxisomes, Best3 and Best4 were found intracellular. The salt survival analysis showed that Best1 is essential in regulating extra salt levels in the body. Furthermore, the fluid secretion analysis showed Best1’s potential role in Ca2+-dependent Clˉ function. Interestingly, the flies with reduced levels of Best2 expression showed increased ability to survive on extra salt food; the basis for this was investigated further in Chapter 7. Best2 was also found abundant in the eyes than anywhere else in the head. A comparative analysis of anterior tubule- and eye-specific transcriptomes revealed a potential overlap of Ca2+ signaling components, in that the PLCβ signaling was one. A neuropeptide Ca2+ agonist, capa1 evoked secondary cytosolic Ca2+ responses were found high in Best2 knockdowns. A quantitative PCR (qPCR) analysis of candidate Ca2+ signaling and homeostasis genes in Best2 mutants revealed their gene expression upregulation, under control-fed and salt-fed conditions than their wildtype controls, fed on similar diet regimes. The norpA that encodes PLCβ was found significantly enriched in the mutants. Cyp6a23 is another gene that was highly upregulated in Best2 mutants; it is a Drosophila homologue of human Cyp11b, a Ca2+-responsive gene implicated in renal salt wasting. Upon the downregulation of Cyp6a23, flies became sensitive to salt diet feeding. Other genes investigated and found to be upregulated in the mutants include transient-receptor-potential (trp) Ca2+ channel and retinal degeneration C (rdgC). Together, these results strongly suggest Best2 as a potential Ca2+ channel regulator, and provide fascinating insight into bestrophin function. Peroxisomal localisation of Best2 in line with the implication that peroxisomes act as dynamic regulators of cell Ca2+ homeostasis led to another aspect of the project (Chapter 8). This study identified two peroxins that are most abundant in the tubules and play essential roles in the novel cyclic nucleotide-regulated peroxisomal Ca2+ sequestration and transport pathway and that are detrimental for peroxisome biogenesis and proliferation

Determination Of Aldehydes In Particulate Matter Using Gas Chromatography-Mass Spectrometry

A gas chromatographic-mass spectrometric (GC-MS) method has been developed for the determination of a broad range of aldehydes (including, hydroxylated and aromatic aldehydes) in particulate matter (PM). In this method, the aldehydes are derivatized with O-2, 3, 4, 5-pentafluorobenzyl hydroxylamine hydrochloride (PFBHA) using various solvents for extraction and derivatization including acetonitrile, water, methanol, and acetonitrile/dichloromethane/methanol. An ACN/DCM/MeOH mixture with sonication was shown to be optimal as it increased the derivatization efficiency in addition to efficient extraction for all tested aldehydes. The optimal derivatization conditions were determined and then tested on a variety of oxy-PAHs which resulted in a complete derivatization of carboxaldehydes but only incomplete derivatization of quinonic species. Application of the extraction protocol to wood smoke (WS) PM and comparison to the traditional EPA buffer method resulted in higher recoveries (up to 150%) of several aldehydes. This artifact was shown to be due to the presence of organics like syringol and levoglucosan in WS PM at higher concentrations and not be caused by which were not due to completeness/incompleteness of the analyte derivatization. This effect was attributed to a matrix-assisted response enhancement, i.e., loss of analytes upon injection due to its adsorption, which may be masked by organics as blocking agents. Further application of the optimized method to particulate matter in GC-MS EI and NCI methods resulted in identification of up to 30 compounds. The NCI method proved to be more sensitive, with up to 28 compound detected with LODs in a range of 0.06 µg – 1.47 µg and comparable quantities (mean ± SD) of aldehydes in all concentrations of WS PM used. By contrast, the EI method was shown to be less sensitive, with only 16 compounds being detected

Flexible armor inspired from natural fish scales and osteoderms

The skins of armadillo, rhinoceros, and fish display interesting combinations of resistance to penetration, flexibility, and light weight. These armors are made of stiff and hard plates of finite size (tiles or scales), embedded in soft tissues. The plates are orders of magnitude harder and stiffer than the soft tissues to resist penetration, but they can also move relative to each other to provide compliance. Here, we have implemented these bio-inspired principles in an artificial system consisting of small hexagonal glass plates resting on a soft silicone substrate. -Compared with a continuous layer of glass, the flexural stresses in our segmented armor were greatly reduced, and as a result the puncture resistance was up to 70% higher. We also duplicated the robustness of natural armor: as opposed to pristine glass which is entirely destroyed by sharp puncture, damage in our segmented armor was confined to only one hexagonal plate. The structure and mechanics of this system can be translated to armor-grade materials for high-performance flexible, light-weight, puncture resistant, and robust protective systems

Design, Fabrication, and Programming of an Acoustic Property Measuring System for Ultrasound in the MHz Range

Accurate measurement of acoustic material properties for various microfluidic devices is essential for optimal device design. In this project, a continuation of the design of a novel microfluidic channel for in situ removal of photocurable polydimethylsiloxane (PDMS-a silicone), an apparatus was designed to measure the speed of sound through various liquids and solids. The apparatus was designed to hold piezoelectric transducers (pulser/receiver) and sample using the program AutoCAD™, fabricated on a three axis CNC mill, and tested by coupling input and output signals to an oscilloscope whose data was analyzed through algorithms implemented in MatLab™. The setup was calibrated and tested using the NIST standard with various glycerol and water solutions, and had an error of within 2%. Additionally, further acoustic properties such as attenuation, acoustic impedance, and material properties such as the modulus of elasticity are calculable with the same device, as well as reflection and transmission coefficients with minor modification