A Study of Raman Spectroscopy as a Clinical Diagnostic Tool for the Detection of Lynch Syndrome/Hereditary NonPolyposis Colorectal Cancer (HNPCC)

Lynch syndrome also known as hereditary non-polyposis colorectal cancer (HNPCC) is a highly penetrant hereditary form of colorectal cancer that accounts for approximately 3% of all cases. It is caused by mutations in DNA mismatch repair resulting in accelerated adenoma to carcinoma progression. The current clinical guidelines used to identify Lynch Syndrome (LS) are known to be too stringent resulting in overall underdiagnoses. Raman spectroscopy is a powerful analytical tool used to probe the molecular vibrations of a sample to provide a unique chemical fingerprint. The potential of using Raman as a diagnostic tool for discriminating LS from sporadic adenocarcinoma is explored within this thesis. A number of experimental parameters were initially optimized for use with formalin fixed paraffin embedded colonic tissue (FFPE). This has resulted in the development of a novel cost-effective backing substrate shown to be superior to the conventionally used calcium fluoride (CaF2). This substrate is a form of silanized super mirror stainless steel that was found to have a much lower Raman background, enhanced Raman signal and complete paraffin removal from FFPE tissues. Performance of the novel substrate was compared against CaF2 by acquiring large high resolution Raman maps from FFPE rat and human colonic tissue. All of the major histological features were discerned from steel mounted tissue with the benefit of clear lipid signals without paraffin obstruction. Biochemical signals were comparable to those obtained on CaF2 with no detectable irregularities. By using principal component analysis to reduce the dimensionality of the dataset it was then possible to use linear discriminant analysis to build a classification model for the discrimination of normal colonic tissue (n=10) from two pathological groups: LS (n=10) and sporadic adenocarcinoma (n=10). Using leaveone-map-out cross-validation of the model classifier has shown that LS was predicted with a sensitivity of 63% and a specificity of 89% - values that are competitive with classification techniques applied routinely in clinical practice

Columbia Chronicle (10/05/2009)

Student newspaper from October 5, 2009 entitled The Columbia Chronicle. This issue is 40 pages and is listed as Volume 45, Number 5. Cover story: Big losses, small gains Editor-in-Chief: Bethany Reinharthttps://digitalcommons.colum.edu/cadc_chronicle/1764/thumbnail.jp

Winona Daily News

https://openriver.winona.edu/winonadailynews/1651/thumbnail.jp

Columbia Chronicle (02/22/2010)

Student newspaper from February 22, 2010 entitled The Columbia Chronicle. This issue is 40 pages and is listed as Volume 45, Number 20. Cover story: \u27Avatar\u27 cinematographer re-visits campus Editor-in-Chief: Bethany Reinharthttps://digitalcommons.colum.edu/cadc_chronicle/1779/thumbnail.jp

Origin of dolomites and associated porosities in lower ordovician boat harbour formation carbonates, western Newfoundland, Canada

The Boat Harbour Formation constitutes the upper part of the Lower Ordovician St. George Group on the Northern Peninsula, western Newfoundland. It varies in thickness from 140 m at Main Brook to 96 m at Daniel’s Harbour (about 200km). Dolomitization of the carbonate sequence is more pervasive in the lower 30–40 m at Main Brook, whereas at Daniel’s Harbour the section is entirely dolomitized. Petrography suggests that the formation has been affected by three phases of dolomitization: earliest (near-surface/syn-sedimentary) phase is D1 dolomicrite, mid–burial phase D2 dolomite, and late stage D3 dolomite. The earliest (near-surface/syn-sedimentary) phase is D1 dolomicrite. The geochemical composition suggests that D1 was developed from fluids of a mixture of meteoric and marine waters at near-surface conditions. The mid–burial phase D2 dolomite consists of coarse planar sub–euhedral crystals that precipitated from hot fluids that circulated through crustal rocks with progressive burial. The late stage D3 dolomite has large and coarse non–planar crystals that exhibit sweeping extinction. In addition to its micro-thermometric data these factors suggest that it likely precipitated during deeper burial in pulses and from hot fluids. For porosity the data suggest that it is mainly associated with the mid–burial D2 dolomite. Intercrystalline porosity is the dominant type and it varies in the formation from <1 to 8 % at Main Brook and from 7 to 12 % at Daniel’s Harbour. Recrystallization to more stoichiometric dolomite is usually accompanied by characteristic textural and geochemical signatures. These signatures are primarily studied using multiple populations of crystals, comparison of modern and ancient dolomites, or from results of high temperature dolomite formation experiments. This approach is inadequate. Therefore study was done using multi proxy high resolution approaches to carry out imaging and ion microprobe elemental analyses of individual dolomite (burial) crystals viz: Scanning Electron Microscopy (SEM), SEM based cathodoluminescence (SEM-CL), Secondary Ion Mass Spectrometer (SIMS). This is to better understand geochemical variations across the crystal traverses and to constrain possible conditions of crystal growth. The study reveals multiple mechanisms of dolomite crystal growth within constrained diagenetic settings and also shows that recrystallization and episodes of dolomitization evidenced by multi-crystal population, are also apparent within dolomite crystals. Further to this, photo-luminescence (PhL) features of the dolomite crystals were obtained using epifluorescence microscope. Combined with SEM-CL, SIMS measured Mn, Fe and REE-Y content of zoned and unzoned dolomite crystal facies are correlated with their luminescence characters (Chapter Four). The study affirms that, at low concentrations (<200 ppm), the correlation of activators (Mn and REE) and quenchers (Fe) with occurrence and intensity of luminescence remains speculative. Broadly speaking, REE-Y content was too low to control luminescence and Fe could not be conclusively demonstrated to have caused quenching, using the employed methods. Morphology and genesis of nanopores and micro-inclusions hosted in intracrystalline areas of dolomites and their association/s with dolomite formation was investigated (Chapter Five). Burial dolomite samples of the Boat Harbour Formation were subjected to Broad Ion Beam (BIB) argon milling. Thereafter, Scanning Electron Microscope (SEM) was used to examine, at high resolution, micrometer to nanometer scale pores hosted in the crystals of the dolomites. Intracrystalline nanopores are abundant within the burial dolomite crystals. They are shown to have developed as a result of imperfection associated with the alignment process of crystallites’ agglomeration. This occurred during the formation of the dolomite’s major crystal face. Furthermore, the origin of mineral inclusions, ‘which are accidentals’ in intracrystalline nanopores is related to the mechanism of dolomitization that involves dissolution of precursor carbonate mineral (calcite or early dolomite) and precipitation of dolomite