<p>  </p> <p>Sudden death syndrome (SDS) caused by <em>Fusarium virguliforme</em> is one of the top yield-reducing diseases of soybean. This disease results in a two-stage symptom development, root rot followed by foliar interveinal chlorosis and necrosis. Foliar symptoms typically appear late in the growing season [full pod to full seed (R4 to R6) reproductive growth stages]. Prior to foliar symptoms, a destructive technique is usually carried out to identify the root rot phase of SDS. This technique requires intensive crop scouting and an expert for accurate diagnosis. Therefore, a nondestructive technique is needed to diagnose SDS disease in the absence of visible foliar symptoms. Additionally, no soybean cultivar is completely resistant to SDS and no single method can completely manage this disease. So, an improved integrated approach is needed for SDS disease management. </p> <p>Foliar fungal diseases such as frogeye leaf spot (<em>Cercospora sojina</em> Hara), Septoria brown spot (<em>Septoria glycines</em> Hemmi), and Cercospora leaf blight (<em>Cercospora</em> spp.) are also economically important diseases of soybean. To limit the losses caused by these diseases, several management methods can be used including the application of foliar fungicide. However, due to the low foliar disease pressure that is observed most years, fungicide applications may not be warranted to be applied annually in Indiana. </p> <p>The objectives of this research were: 1) to assess the effectiveness and economic impact of integrated management strategies that include cultivar selection, seed treatment, and seeding rate on SDS in Indiana; 2) to pre-symptomatically and non-destructively detect SDS disease using hyperspectral measurements; and 3) to evaluate foliar fungicides on soybean foliar diseases and yield in Indiana. </p> <p>Results from this research support the use of a seed treatment to protect soybean roots from SDS infection and the use of a moderately resistant cultivar planted at a seeding rate of 346,535 seeds/ha to protect yield and maximize on net returns. This research also demonstrated the ability of hyperspectral reflectance to discriminate healthy from <em>F. virguliforme</em> infected soybean roots in the absence of foliar symptoms. In addition, results show that fungicide applications can reduce foliar disease over the nontreated control, but under low foliar disease risk, these fungicides did not significantly increase yield over the nontreated control. Altogether, these results will contribute to improved soybean disease management approaches in Indiana.</p>

Contamination of peanuts by secondary metabolites of certain fungi, namely aflatoxins present a great health hazard when exposed either at low levels for prolonged times (carcinogenic) or at high levels at once (poisonous). It is important to develop an accurate and rapid measurement technique to trace the aflatoxin and/or source fungi presence in peanuts. Thus, current research focused on development of vibrational spectroscopy based methods for detection and separation of contaminated peanut samples. Aflatoxin incidence, as a chemical contaminant in peanut paste samples, was investigated, in terms of spectral characteristics using FTIR-ATR. The effects of spectral pre-processing steps such as mean-centering, smoothing the 1st derivative and normalizing were studied. Logarithmic method was the best normalization technique describing the exponentially distributed spectral data. Spectral windows giving the best correlation with respect to increasing aflatoxin amount led to selection of fat associated spectral bands. Using the multivariate analysis tools, structural contributions of aflatoxins in peanut matrix were detected. The best region was decided as 3028-2752, 1800-1707, 1584-1424, and 1408-1127 cm-1 giving correlation coefficient for calibration (R2C), root mean square error for calibration (RMSEC) and root mean square error for prediction (RMSEP) of 98.6%, 7.66ppb and 19.5ppb, respectively. Applying the constructed partial least squares model, 95% of the samples were correctly classified while the percentage of false negative and false positive identifications were 16% and 0%, respectively. Aspergillus species of section Flavi and the black fungi, A. niger are the most common colonists of peanuts in nature and the majority of the aflatoxin producing strains are from section Flavi. Seed colonization by selected Aspergillus spp. was investigated by following the chemical alterations as a function of fungal growth by means of spectral readouts. FTIR-ATR was utilized to correlate spectral characteristics to mold density, and to separate Aspergillus at section, species and strain levels, threshold mold density values were established. Even far before the organoleptic quality changes became visually observable (~10,000 mold counts), FTIR distinguished the species of same section. Besides, the analogous secondary metabolites produced increased the similarity within the spectra even their spectral contributions were mostly masked by bulk peanut medium; and led to grouping of species producing the same mycotoxins together. Aflatoxigenic and non-aflatoxigenic strains of A. flavus and A. parasiticus were further studied for measurement capability of FTIR-ATR system in discriminating the toxic streams from just moldy and clean samples. Owing to increased similarity within the collected spectral data due to aflatoxin presence, clean samples (having aflatoxin level lower than 20 ppb, n=44), only moldy samples (having aflatoxin level lower than 300 ppb, n=28) and toxic samples (having aflatoxin level between 300-1200 ppb, n=23) were separated into appropriate classes (with a 100% classification accuracy). Photoacoustic spectroscopy (PAS) is a non-invasive technique and offers many advantages over more traditional ATR system, specifically, for in-field measurements. Even though the sample throughput time is longer compared to ATR measurements, intact seeds can be directly loaded into sample compartment for analysis. Compared to ATR, PAS is more sensitive to high moisture in samples, which in our case was not a problem since peanuts have water content less than 10%. The spectral ranges between: 3600-2750, 1800-1480, 1200-900 cm-1 were assigned as the key bands and full separation between Aspergillus spp. infected and healthy peanuts was obtained. However, PAS was not sensitive as ATR either in species level classification of Aspergillus invasion or toxic-moldy level separation. When run for separation of aflatoxigenic versus non-aflatoxigenic batches of samples, 7 out of 54 contaminated samples were misclassified but all healthy peanuts were correctly identified (15 healthy/ 69 total peanut pods). This study explored the possibility of using vibrational spectroscopy as a tool to understand chemical changes in peanuts and peanut products to Aspergillus invasion or aflatoxin contamination. The overall results of current study proved the potential of FTIR, equipped with either ATR or PAS, in identification, quantification and classification at varying levels of mold density and aflatoxin concentration. These results can be used to develop quality control laboratory methods or in field sorting devices. / Ph. D.

It was found that the measurements captured by confocal microscopy and scanning electron microscopy had a statistically significant difference for bovine tissue. There was not a statistically significant for porcine and poultry tissue. The intent of the study is to perform a comparative study to examine efficacy of two distinct technologies for a singular purpose: tissue surface roughness characterization. The two technologies compared are a confocal reflectance microscope and a scanning electron microscope. The comparison was made by comparing two surface roughness parameters [Ra and Rq] within ImageJ. The study examined three different animal species [porcine, bovine, and poultry] to highlight if different tissues presented alternative conclusions for the efficiency of either technology. Additional analysis was produced comparing two cutting methods [Kleen Kut versus conventional], as well as six different poultry processing technique combinations.

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Near infrared spectroscopy (NIR) has become increasingly widespread throughout various fields as an alternative method for efficiently phenotyping crops and plants at rates unparalleled by conventional means. With growing reliability, the convergence of NIR spectroscopy and modern machine learning represent a promising methodology offering unprecedented access to rapid, high throughput phenotyping at negligible costs, representing prospects that excite agronomists and plant physiologists alike. However, as is true of all emergent methodologies, progressive refinement towards optimization exposes potential flaws and raises questions, one of which is the cornerstone of this study. Spectroscopic determination of plant functional traits utilizes plants' morphological and biochemical properties to make predictions, and has been validated at the community (inter-family) and individual crop (intraspecific) levels alike, yielding equally reliable predictions at both scales, yet what lies amid these poles on the spectrum of taxonomic scale remains unexplored territory. In this study, we replicated the protocol used in studies of the aforementioned taxonomic scale extremes and applied it to an intermediate scale. Interestingly, we found that predictive models built upon hyperspectral reflectance data collected across three genera of woody plants: Cornus, Rhododendron, and Salix, yielded inconsistent predictions of varying accuracy within and across taxa. Identifying the potential cause(s) underlying variability in predictive power at this intermediate taxonomic scale may reveal novel properties of the methodology, potentially permitting further optimization through careful consideration.

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This study investigates the possibility of using a time-resolved Fluorescence and Diffuse Reflectance Spectroscopy (tr-FRS) system to define tumour surgical margins of invasive ducal carcinoma of breast. UV excitation light was used for the fluorescence component and data was collected from the 370-550 nm range. A broadband source was used for diffuse reflectance collection and the emitted response was in the 400-800 nm range. 40 matched pair cases were collected from patients undergoing breast conservation surgeries. Histological analysis was performed on each sample to determine the fat and tumour content within each normal and tumour sample respectively. Statistical analysis was performed on the optical data to reveal biochemical changes in the endogenous fluorophores collagen, reduced nicotinamide adenine dinucleotide (NADH), and flavin adenine dinucleotide (FAD) as well as changes in absorption and scattering properties attributed to variances in absorber concentrations and cell density respectively. Statistical significant differences in collagen, NADH, and FAD lifetimes, collagen, NADH, FAD and NADH/FAD intensity, diffuse reflectance and reduced scatter coefficient were observed between tumour and normal breast samples. These significant factors were used in Principle Component Analysis model construction and a binary classification scheme using Soft Independent Modeling of Class Analogy (SIMCA) was used as a classification tool to predict unknown breast samples as either normal or tumour with specificity of 60% and sensitivity slightly over 50%. / Thesis / Master of Science (MSc)

Ammonium has been detected in and around several epithermal Au-Ag deposits, including those in Nevada, Japan, Argentina, Mexico, and New Zealand, using short-wave infrared (SWIR) reflectance spectroscopy. This study examined the distribution and occurrence of ammonium in three epithermal low-sulfidation vein-type deposits in the Hauraki goldfield of New Zealand: Martha (>6.7Moz Au, >42.1Moz Ag), Favona (>0.6Moz Au, >2.36Moz Ag), and the recently discovered Wharekirauponga (WKP; 0.42Moz Au, 0.8Moz Ag) deposit. The Martha and Favona auriferous quartz-adularia veins are hosted by late Miocene to Pliocene andesite, whereas auriferous veins at WKP are hosted by late Miocene to Pliocene rhyolite. The wallrock of all three deposits is altered to form quartz, illite, smectite, adularia, chlorite, and pyrite +/- kaolinite. Ammonium contents are enriched (>137 ppm) in wallrock samples from all three deposits and low (<94 ppm) in vein samples. Ammonium contents are higher at Favona (<10,675 ppm) than at Martha (<192 ppm) and WKP (<2,783 ppm). Leaching experiments using a 2N KCl solution show that most ammonium is in mineral structures (>90% at Favona, >80% at Martha, >70% at WKP). There is a positive correlation of ammonium contents with LOI (0.6 – 16.3 wt%) and with K2O (1.3 – 8.0 wt%) in all samples which suggest a hydrous potassium mineral as the major host of the ammonium. This is supported by the SWIR data obtained by previous workers of these samples where they show an absorption at ~1410 nm due to OH. At Favona, samples with high ammonium (>990 ppm) are reported to have significant absorption at ~2000 nm and ~2100 nm in the SWIR spectra likely due to ammonium. High ammonium contents (990 – 10,675 ppm) are found in rocks less than ~100m from the Favona vein which occur within an ammonium-bearing zone identified by previous workers based on SWIR. Samples outside of this zone contain low ammonium (107 – 301 ppm) with the smectite altered samples being the lowest. Ammonium contents within the hangingwall (1,827 – 10,675 ppm) of the Favona vein tend to be higher than in the footwall (990 – 4,301 ppm) and are highest within the most intensely illite altered rocks. At WKP, the intensely adularia +/- minor illite altered samples within 100m of the main East-Graben (EG) vein contain low ammonium (<200 ppm). The intensely illite altered samples away from the EG vein (>100m) have higher ammonium contents (200 – 800 ppm). This relationship of high ammonium contents to high illite abundance confirms illite as the major host of ammonium in these deposits. δ15N values for all samples (n=54) including near and far from auriferous veins range from +0.5 to +7.9 ‰, suggesting the derivation of most of the ammonium from the Jurassic greywacke basement or sediments intercalated within the volcanic rocks.