The main objectives of this study are to determine how various physical and chemical properties of geologic samples can be investigated by Fourier Transform InfraRed (FTIR) spectral analyses, and determine how each of these individual properties uniquely alter the mid-infrared spectrum. Of particular interest is how extraterrestrial samples differ (spectrally) from terrestrial samples, and how such findings can be applied to current and future missions to airless planetary bodies (such as Diviner Lunar Radiometer, aboard the Lunar Reconnaissance Orbiter, and the Mercury Thermal Radiometer on BepiColombo). As such, a range of geological samples have been analysed including terrestrial rocks (anorthosite, granite, grabbro etc.), mineral standards (common rock-forming minerals), lunar meteorites (from Miller Range, Antarctica), and Apollo 14, 15, and 16 soils. A new technique to analyse such samples has been developed and implemented as part of this study: FTIR spectral imaging of unconsolidated samples (powders and soils) to obtain modal mineralogy estimates. Such estimates are comparable to QEMSCAN analyses and spot point counting of the same samples. This is particularly relevant for the non-destructive analysis of Apollo soil samples (bulk and sieved fractions). Individual spectra of polished terrestrial and extraterrestrial samples have been obtained in preparation for the creation of a spectral database. Such samples also have coupled chemical composition information via Electron Probe MicroAnalysis (EPMA). To have a spectrum and an associated chemical composition for each mineral in a database is unique compared to other spectral databases. Analyses of lunar meteorites resulted in an understanding of how shock (caused by hypervelocity impacts) alters the physical and spectral properties of lunar minerals. FTIR microscopy of individual minerals and phases in the meteorites were coupled with optical and cathodoluminescence (CL) imaging to identify the level of shock obtained by each mineral and phase. The FTIR reflectance bands of plagioclase merge with increasing shock pressure until a single, low-reflectance broad peak is displayed by the most highly shocked plagioclase (>45 GPa), and a dark-red colour is present in CL images. FTIR and QEMSCAN analyses of Apollo regolith samples have provided an understanding of the spectral effects of bulk mineralogy, maturity (a measure of the time spent at the lunar surface), grain size, and mineral chemistry. Using such information, the modal mineralogy of each sample has been estimated, one of which had not previously been analysed for its modal mineralogy. Samples from the same Apollo missions present similar spectral features, meaning FTIR spectroscopy can be used to identify the origin of lunar soils. A weak correlation in maturity with a spectral feature termed the Christiansen Feature has been found for lunar samples. Related to maturity, FTIR spectra of individual agglutinates (a product of space weathering) have been obtained and the spectral properties of agglutinates (decreased %Reflectance values of the region sensitive to geological materials) resemble those of highly mature lunar soils.

It has been long known that algae have the potential to produce a diverse range of metabolic products including lipid and starch, which could be utilized as a fuel feedstock. Despite the capacity of algae to synthesize and store large amounts of lipids and starch, algae are not currently a commercially viable feedstock for biofuel. The metabolite storage in algae can depend on the availability of nutrients such that nutrient starvation can boost the storage of lipid and carbohydrate. These nutrient-status-induced changes in lipid and starch are underpinned by altered expression of several metabolite-related genes. However, many aspects of fatty acid and carbohydrate biosynthesis are not well understood. Furthermore, the genetic regulators of nutrient starvation-induced carbohydrate and lipid accumulation are unknown in microalgae. Therefore, this PhD focused on screening cultivation conditions, in particular Phosphorus (P) and Nitrogen (N) limited conditions that induce metabolic changes, evaluated a rapid microalgal screening method, which was used to identify putative metabolism regulators, and characterized in detail the role of one P-starvation regulator, called PSR1 (Phosphorus starvation response 1). For establishing suitable culture conditions, the microalga Chlamydomonas reinhardtii was cultured in five different P and N-limited conditions and screened for metabolic changes using Fourier transform infrared spectroscopy (FT-IR) at different phases of growth. The FT-IR spectral changes were visualized by multivariate statistical tools such as principal component analysis (PCA) and principal component-discriminant function analysis (PC-DFA). Clear clustering based on nutrient availability and metabolic changes demonstrates the potential and sensitivity of FT-IR in screening multiple culture conditions. The potential of FT-IR was further tested by screening mutant strains of C. reinhardtii that were defective in response to nutrient starvation. Nine lines with mutation in one or more of the PSR1, SNRK2.1 or SNRK2.2 genes and a wild type were screened by FT-IR for P and N starvation-induced metabolic changes. PCA, PC-DFA and predictive partial least squares discriminant analysis (PLS-DA) of FT-IR spectra, clearly distinguished wild type from mutant strains and clustered mutants with similar genetic backgrounds, demonstrating the potential of FT-IR to detect and differentiate specific genetic traits. The changes in lipid and carbohydrate profile under nutrient stress and in the different strains were validated by biochemical analysis and liquid chromatography-mass spectrometry (LC-MS).This thesis demonstrated that PSR1 is an important regulator of neutral lipid and starch biosynthesis. Transcriptomic analysis on wild type and psr1 mutant under P-starvation was performed to identify transcripts induced by P-starvation that were mis-regulated in psr1. Mainly transcripts encoding starch and triacylglycerol enzymes were affected. To further evaluate the role of PSR1 in regulating lipid and starch metabolism, complementation of psr1 and overexpression by PSR1 was performed. The P-starvation phenotype was clearly rescued in the complementation lines, and overexpression lines showed increased expression of P homeostasis genes and increased Pi accumulation in cells, with an increase in total starch content and number of starch granules. Clear increases in expression of key starch biosynthesis genes such as soluble starch synthase (SSS1, SSS5) and starch phosphorylase (SP1) was observed, which correlated with increased starch content in the overexpression lines. A carbon shift was observed as a decrease in neutral lipid was coupled with the increase in starch content. All together these findings suggest that PSR1 is a key transcriptional regulator of global metabolism, and demonstrated successful transcriptional engineering of microalgae.

Introdução: Nos últimos anos, procedimentos cirúrgicos envolvendo a glândula tireoide têm aumentado em todo o mundo, bem como a incidência de neoplasias malignas sem, no entanto, se observar aumento da taxa de mortalidade. Muitas técnicas foram propostas para alcançar um diagnóstico pré-operatório acurado em doenças da tireoide. As técnicas de espectroscopia de FTIV (Infravermelho por transformada de Fourier) já apresentam evidências na caracterização de múltiplos tecidos, entre eles a glândula tireoide, tendo como vantagem sua rapidez e preservação do tecido analisado. O estudo de novas técnicas na diferenciação dos nódulos tireoidianos pode auxiliar na seleção de pacientes que serão submetidos ao tratamento cirúrgico adequado, evitando o sobretratamento. Objetivos: Caracterizar os tecidos tireoidianos sadios e patológicos à luz da espectroscopia de infravermelho (IV), testar a viabilidade do método de espectroscopia no IV em diferenciar tecidos patologicamente alterados da glândula tireoide comparativamente aos achados espectroscópicos encontrados em tecidos sadios. Casuística e Métodos: Os pacientes foram selecionados no Serviço de Cirurgia de Cabeça e Pescoço do Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo (HCFMRP-USP), no período de 2014 a 2015. A amostra foi composta por 44 pacientes de ambos os sexos, com idade acima de 18 anos, com indicação de tireoidectomia. Quarenta e quatro amostras de nódulos em tireoide e 44 de tecidos normais foram analisadas por espectroscopia no IV utilizando-se um espectrômetro Nicolet 380 - Nicolet USA® em tecidos a fresco. A análise foi realizada definindo-se as áreas de cada banda, utilizando-se para os cálculos o programa OriginPro 8.6.0 (OriginLab Corporation Northrampton, MA 01060 USA). A seguir, efetuou-se a normalização pela banda a 1240 cm-1. A comparação das áreas foi calculada por meio do teste t- Student com p<0,05. Após o cálculo das médias realizou-se avaliação de derivadas de segunda ordem do espectro para se evidenciarem as posições de cada banda de absorção. Realizou-se, também, a análise de cada banda aplicando o teste t-Student para amostras pareadas e amostras independentes; e o teste de Wilcoxon para amostras pareadas e para comparação de duas amostras independentes. Resultados: O espectro IV de cada peça foi obtido, sendo expresso em função da absorbância e dos números de onda no IV médio (4000 - 900 cm-1). O presente estudo demonstrou que na análise do tecido tireoidiano pela espectroscopia no IV é possível diferenciar os nódulos benignos do tecido sadio, com diferença significativa na área da banda B entre tecido sadio e bócio, que corresponde a 1452,90 cm-1 no tecido sadio (Proteínas e Lipídeos) e 1069,80 cm-1 no bócio (DNA); e também diferença estatisticamente significativa entre os tecidos normal e carcinoma para largura na banda C, onde a largura foi maior no tecido com carcinoma do que no tecido normal. Conclusões: A espectroscopia no IV é capaz de diferenciar os tecidos tireoidianos patologicamente alterados da glândula tireoide comparativamente aos achados em tecidos tireoidianos sadios. Concluiu-se que nos pacientes com doença nodular benigna da glândula tireoide é possível diferenciar o tecido sadio do bócio com significância estatística, bem como também diferenciar nódulos malignos do tecido sadio por meio da espectroscopia no IV. / Introduction: In recent years, surgical procedures involving the thyroid gland have increased worldwide, as well as the incidence of malignant neoplasia without, however, observing an increase in the mortality rate. Many techniques have been proposed to achieve an accurate preoperative diagnosis in thyroid diseases. The FTIR spectroscopy techniques already present evidence in the characterization of multiple tissues, among them the thyroid gland, having as an advantage its rapidity and preservation of the tissue analyzed. The study of new techniques in the differentiation of thyroid nodules can help in the selection of patients who will undergo the appropriate surgical treatment avoiding overtreatment. Objectives: To characterize healthy and pathological thyroid tissues in the light of infrared spectroscopy, to test the viability of the infrared spectroscopy method in differentiating pathologically altered tissues from the thyroid gland compared to the spectroscopic findings found in healthy tissues. Casuistic and methods: Patients were selected at the Head and Neck Surgery Service of the Hospital of Clinics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto-SP, Brazil, from 2014 to 2015. The sample consisted of 44 patients of both sexes, aged over 18 years, oriented about their participation in the study and with indication of thyroidectomy. The analysis was performed by defining the areas of each band, using the program OriginPro 8.6.0 (OriginLab Corporation Northrampton, MA 01060 USA). The band was then normalized to 1240 cm -1. The mean area was calculated using the Student t-test with p<0.05. After the calculation of the averages, the second-order derivative of the spectrum was evaluated to show the positions of each absorption band. We also performed the analysis of each band by applying the t-Student test for paired samples, Wilcoxon test for paired samples, Student\'s t-test for independent samples and the Wilcoxon test for comparison of two independent samples. Results: The infrared spectrum of each piece was obtained, being expressed as a function of absorbance and wave numbers in the mean IR (4000 - 900 cm -1). The present study demonstrated that in the analysis of thyroid tissue by infrared spectroscopy, we can differentiate benign nodules from healthy tissue, with a significant difference in the area of the B-band between healthy tissue and goiter, which corresponds to 1452.90 cm -1 in healthy tissue (Proteins and Lipids) and 1069.80 cm -1 in goiter (DNA) and also a significant difference in width between normal thyroid tissue and carcinoma of the C band. Conclusions: Infrared spectroscopy is able to differentiate pathologically altered thyroid tissues from the thyroid gland compared to findings in healthy thyroid tissues. After the analysis of the results it was possible to conclude that in patients with benign nodular disease of the thyroid gland it is possible to differentiate healthy goiter tissue with statistical significance, as well as it is possible to differentiate malignant nodules from healthy tissue through infrared spectroscopy

Depression is one of the most commonly seen psychiatric diseases in the population in recent years. Treatment of depression is mainly carried out by psychiatric drugs. In the past few years, agomelatine which is released to the market with a trade name, Valdoxane, has been thought to have far less side effects due to its non-addictive nature, not having trouble when the drug is quitted, and also due to its property of binding only to the specific receptor that the drug interacts with. The action mechanism of agomelatine on the membrane structure has not been clarified yet, for instance, no study has been found in the literature about the interaction of agomelatin with the lipids of biological membranes. In this current study, the interaction of agomelatine with the model membranes of dipalmitoylphosphatidylcholine (DPPC), dipalmitoylphosphatidylgylcerol (DPPG) and sphingomyelin (SM) is examined by Fourier transform infrared spectroscopy (FTIR) and Differential scanning calorimetry (DSC). DSC and FTIR studies show that, agomelatine shifts the phase transition temperature of DPPC and DPPG multilamellar membrane to the lower degrees, however, it shifts the phase transition temperature of SM membrane to the higher degrees. Agomelatine addition increases the lipid order of the DPPC and SM liposome, whereas, it decreases the lipid order of DPPG liposome. Moreover this drug enhances the membrane fluidity among all types of liposome studied. The increase of v lipid order and increase of fluidity at DPPC and SM liposome indicates domain formation upon drug addition (Vest et al., 2004). This was also confirmed by DSC studies. Agomelatine enhances H bonding capacity of all types of liposomes have been studied. However it has different effects on glycerol backbones of the DPPC and DPPG liposomes. At low agomelatine concentrations the increase in the frequency values indicates a decrease in the hydrogen bonding capacity of the glycerol skeleton of DPPC. In contrast, at high concentrations of agomelatine, a decrease in the frequency values was observed as an indicator of the enhancement of the hydrogen bonding capacity. So it enhances H-bonding capacity at gel phase but lowers it at liquid chrystalline phases. A progressive decreases in Tm was observed at DPPG and DPPC liposomes where it increased the Tm at SM. The pretransition peak is abolished and the Tm peak becomes broad, indicating a larger perturbation to the membrane. These observations indicate the possible interaction of agomelatine with the head group as well. The shoulder seen at the thermograms of DPPC and DPPC liposomes at high doses may indicate the lateral phase separation in to drug-rich and drug-poor domains (D&rsquo / Souza et al., 2009). These results may indicate that agomelatine is partially buried in the hydrocarbon core of the bilayer, interacting primarily with the C2-C8 methylene region of the hydrocarbon chains. All these results highlight the fact that agomelatine interacts around the head group in such a manner that it destabilizes the membrane architecture to a large extent.

The objectives of this study were to investigate the effects of autoclave heating on the rumen protein degradation characteristics of flaxseed (<i>Linum usitatissimum</i>, cv. Vimy), and to compare them to differences in diffuse reflectance infrared Fourier transform (DRIFT) and Synchrotron based Fourier transform infrared microspectroscopy (S-FTIR) measurements of the protein alpha-helix to beta-sheet ratios. Hierarchical cluster analysis (CLA) and principal components analysis (PCA) were also conducted to identify differences in the DRIFT spectra. Flaxseed samples were kept raw for control or autoclaved in batches at 120°C for 20, 40 or 60 min for treatments 1, 2 and 3, respectively. The rumen degradation kinetics of protein were measured along with the protein sub-fractions of the Cornell net carbohydrate and protein system (CNCPS), and chemical composition. Intestinal digestibility was determined using the three-step procedure outlined by Calsamiglia and Stern (1995). Protein supply to the small intestine was determined using the NRC (2001) and DVE/OEB models. The results showed that heating increased dry matter (DM) and ether extract (EE) content, while reducing neutral detergent fibre (NDF) and acid detergent fibre (ADF), with little numerical difference between the three treatments. Soluble crude protein (SCP) also decreased upon autoclaving with concomitant increases in non-protein nitrogen (NPN), neutral detergent insoluble nitrogen (NDIN) and acid detergent insoluble nitrogen (ADIN). The CNCPS protein sub-fractions with the greatest changes were the buffer-soluble true protein fraction (PB1) and the fraction representing buffer-insoluble true protein which is not bound to NDF (PB2) showing dramatic increases, indicating a decrease in the overall protein degradability. <i>In situ</i>experiments showed a reduction in effective degradable dry matter (EDDM) as well as a reduction in effective degradable crude protein (EDCP) without significant differences between the treatments. Intestinal digestibility of protein as estimated by the three-step procedure showed no changes upon autoclaving. Modeling results, with flaxseed as the only feed source, for absorbable ruminally-undegraded feed protein in the intestines using both the NRC (2001) and DVE/OEB systems showed increases as a consequence of the autoclave treatments but again there were no differences between the treatments. The degraded protein balance results showed for both the NRC (2001) and DVE/OEB models that both were decreased upon autoclave treatment. However, the values for the NRC (2001) model suggested a potential nitrogen (N) deficiency and, therefore potentially impaired microbial crude protein (MCP) production, whereas the values for the DVE/OEB system showed potential N excess and, therefore, possible loss from the rumen. DRIFT analysis of protein secondary structure ratios showed a decrease in the alpha-helix to beta-sheet ratio for the whole seed, whereas results from S-FTIR spot data for cotyledon tissue showed autoclaving had the opposite effect on the ratio. CLA and PCA were successfully used to make distinctions between the different treatment spectra and showed enhanced sensitivity upon selection of a smaller spectral window to include only the amide I and II portion of the IR spectrum. The results failed to demonstrate any differences between the autoclave treatments used in this study, and showed that autoclaving generally decreased effectively ruminal degradability of flaxseed protein. The results further indicated that autoclaving had a significant enough effect on the flaxseed to permit identification of the altered alpha-helix to beta-sheet ratio with the mid-IR spectrum, as well as differentiation between the treatments using PCA and CLA. PCA and CLA results suggest that mid-IR spectral methods are more sensitive than traditional methods when used to identify differences between the heat treatments.

Saccharomyces cerevisiae exhibits an apoptotic response upon exposure to toxic metals such as cadmium (Cd) and copper (Cu). Preliminary findings indicate that this response is dependent –to some extent- on the presence of a fermentable carbon source, glucose. To investigate this dependency we monitored the apoptotic response to both metals in the presence and absence of glucose and have shown that glucose is absolutely necessary in order to induce apoptosis in yeast at least during the exposure to metal. We have also looked at the biochemical changes that are taking place in yeast when treated with Cd using Fourier Transform Infra-Red (FTIR) Spectroscopy. Our results suggest that there are definitive changes in cellular activities that are discernable at 1660-1640cm-1 (amide I), 1540-1510cm-1 (amide II) and 1140-1080cm-1(DNA absorption bands).

In this project, a new type of InP solar cell was investigated. The main idea is that light is converted to electrical current in p-i-n photodiodes formed in thin InP semiconductor nanowires epitaxially grown on an InP substrate. Two different types of samples were investigated. In the first sample type (series C03), the substrate was used as a common p-type electrode, whereas a short p-segment was included in all nanowires for the second sample type (B07). Current – voltage (I-V) characteristics with and without illumination were measured, as well as spectrally resolved photocurrents with and without bias. The main conclusion is that the p-i-n devices showed good rectifying behavior with an onset in photocurrent that agrees with the corresponding energy band gap of InP. An interesting observation was that in series B07 (with included p-segments) the photocurrent was determined by the band gap of hexagonal Wurtzite crystal structure, whereas series C03 (without p-segments) displayed a photocurrent dominated by the InP substrate which has a Zincblende crystal structure. We found that the overall short-circuit current was ten as large for the latter sample, stressing the importance of the substrate as a source of photocurrent.

El Virus de la Immunodeficiència Humana, VIH, és un virus amb envolta de la família Retroviridae. El primer pas en el procés d'infecció del virus és la seva entrada dins de la cèl·lula hoste. En el cas d'infecció de limfòcits T, primer es produeix el reconeixement del receptor CD4 del limfòcit per part de la proteïna gp120 del virus. Aquest proteïna està unida mitjançant interaccions de tipus febles a una altra proteïna de l'envolta lipídica del virus, la proteïna gp41. Aquesta proteïna és la responsable final de la fusió entre la membrana plasmàtica de la cèl·lula hoste i l'envolta lipídica del virus, permetent l'entrada d'aquest últim al citosol de la cèl·lula i iniciant el procés d'infecció.La proteïna gp41 presenta en el seu extrem amino terminal una seqüència molt hidrofòbica i rica en residus de glicina i alanina, la qual cosa fa que sigui conformacionalment polimòrfca, i que es coneix com pèptid de fusió. Un cop produït el reconeixement, la gp120 sofreix un canvi conformacional que es transmet a la gp41, de manera que el pèptid de fusió interacciona amb la membrana del limfòcit, desencadenant el procés de fusió.En el present treball s'ha estudiat la interacció de pèptids de fusió de la proteïna gp41 del VIH amb membranes model. Els resultats obtinguts han permès proposar un model cinètic dels diferents processos que tenen lloc durant la interacció d'aquests pèptids amb membranes model, contribuint de manera remarcable a resoldre una qüestió fins ara controvertida, referent al tipus d'estructura que adopta el pèptid de fusió quan interacciona amb les membranes i que desencadena la fusió. El treball també ha permès determinar la importància del potencial dipolar de membrana, un paràmetre físico-químic de les membranes, en aquests processos així com la importància de la presència de colesterol en les membranes model. Segons els resultats obtinguts, el pèptid de fusió primerament interaccionaria amb la membrana. Un cop unit a aquesta, el pèptid de fusió experimentaria un canvi conformacional, passant d'una barreja d'estructura helicoïdal, desordenada i de fulla ?, a més estrcutura ?, la qual finalment seria l'estructura responsable de la fusió. A més, el pèptid durant la interacció provocaria una desestabilització de la membrana, una agregació de membranes model i una deshidratació de la seva interfície aigua-lípid. El potencial dipolar de membrana, afectaria tan sols al procés d'unió del pèptid de fusió a les membranes, mentre que no afectaria al canvi conformacional ni a la fusió. Aquests últims estarien afectats per la hidratació de les membranes i/o per la seva fluïdesa, tal i com mostren els resultats obtinguts amb el colesterol. Finalment el treball ens ha permès formular la qüestió de si els agregats peptídics amorfs detectats en el cas dels pèptids de fusió del VIH podrien correspondre a un tipus conformacional més general, implicat en d'altres processos amb rellevància biològica, com l'efecte citotòxic dels pèptids amiloïdes relacionat amb certes malalties neurodegeneratives.El conexeixement dels processos moleculars de la infecció vírica podria permetre el disseny de noves estratègies farmacològiques que podrien inhibir la entrada del virus a la cèl·lula. / The Human Immunodeficiency Virus, HIV, is an enveloped virus of the Retroviridae family. The first step in the sequence of events leading to the virus entry into the target cell is the binding of gp120 to the CD4 receptor on T-lymphocytes membranes. The gp120 protein is noncovalently associated to gp41 protein, which is the protein responsible of fusion between cellular and viral membranes, allowing virus entry in the target cell.The gp41 contains in its amino terminus a sequence rich in glycine and alanine residues, the so-called fusion peptide. Following the interaction of gp120 with the CD4 receptor, a series of conformational rearrangements takes place, which result in the interaction of the N-terminal part of gp41 with the cell membrane. This process has been described to trigger the fusion of the viral and the cellular membranes.In the present work we have studied the interaction of HIV gp41 fusion peptide with model membranes. The results obtained allow us to propose a kinetic model for the different steps that take place during interaction of fusion peptide with model membranes, contributing to resolve a controversial question about the secondary structure that adopts the fusion peptide upon interaction with membranes and that trigger membrane fusion. Results also allowed us to determine the significance of membrane dipole potential on the interaction of fusion peptides with the membranes, an effect which is due to the presence of cholesterol in the model membranes. The results showed that membrane fusion depends on the transformation of unordered and probably helical structures into ? aggregates structures and that such a conformational change occurs upon binding to the membrane. Moreover, this interaction would induce membrane destabilization, vesicle aggregation and the dehydration of the membrane surface. The membrane dipole potential would only affect the binding process but would not affect either the conformational change or the fusion. These two processes would be affected by surface membrane hydration and/or membrane fluidity. Finally this work allowed us hypothesize whether amorphous peptidic aggregates detected in the case of HIV fusion peptides would correspond to a more general structure, that could be involved in others relevant biological processes, such as the cytotoxic effect of amyloid peptides which is related with certain neurodegenerative diseases.The knowledge of molecular mechanisms underlying viral infection could facilitate the design of novel pharmacological strategies against the viral entry into the target cell.

The purpose of this work was to provide a better understanding of urea’s decomposition and byproduct formation in an SCR system on heavy trucks. In my experimental setup with TGA-DSC-FTIR (a combination of two thermal analysis methods and a method for gas phase detection), an FTIR method for urea in the gas phase was developed for the qualitative and quantitative determination of urea and its decomposition products. Chemicals such as urea, biuret, cyanuric acid and melamine of p.a. quality were used in this method development. Beforehand, there was no FTIR method available to detect these substances; hence, the aim of this work was to develop an FTIR method to understand the degradation chain of urea.  The combination of TGA and DSC was used for analysis of different samples, where urea, biuret, cyanuric acid and melamine in varying amounts have been weighted in for various experiments in order to study the temperature at which a phase transition or reaction occurs, i.e. the temperature at which substances begin to melt, vaporize, decompose and react. In combination with FTIR, information was obtained for the appearance of substances at various temperatures. With FTIR, we have been able to develop unique infrared spectra of substances and along with weight loss in TGA the calibration of different substances has been achieved. These calibrations have been combined together to develop an FTIR method, which has been used for detection of the substances in the ongoing study of the reaction pathways. In this study we also investigated the degradation chain of urea in the presence of metals. Austenitic and ferritic silencer materials with different surface roughness were analyzed to study whether the metals have a catalytic function or effect on the byproduct formation. Those experiments have shown that a higher amount of urea was decomposed in contact with metal surface, i.e. a larger amount of NH3 and HNCO was formed. Biuret studies in the presence of metals appeared to give a higher formation of urea over the rougher surfaces (a larger amount of biuret was decomposed over the rougher surfaces), while experiments with cyanuric acid revealed a higher HNCO formation over ferrite than over austenite, i.e. a larger amount of cyanuric acid was decomposed. By the chosen method, used in FTIR in combination with TGA-DSC, the following important reactions have been demonstrated:  Biuret decomposed to urea and HNCO; Urea decomposed into HNCO and NH3; formation of cyanuric acid from the decompositions of urea and biuret and finally decomposition of cyanuric acid into HNCO at a higher temperature.

The objectives of this study were to investigate the effects of autoclave heating on the rumen protein degradation characteristics of flaxseed (<i>Linum usitatissimum</i>, cv. Vimy), and to compare them to differences in diffuse reflectance infrared Fourier transform (DRIFT) and Synchrotron based Fourier transform infrared microspectroscopy (S-FTIR) measurements of the protein alpha-helix to beta-sheet ratios. Hierarchical cluster analysis (CLA) and principal components analysis (PCA) were also conducted to identify differences in the DRIFT spectra. Flaxseed samples were kept raw for control or autoclaved in batches at 120°C for 20, 40 or 60 min for treatments 1, 2 and 3, respectively. The rumen degradation kinetics of protein were measured along with the protein sub-fractions of the Cornell net carbohydrate and protein system (CNCPS), and chemical composition. Intestinal digestibility was determined using the three-step procedure outlined by Calsamiglia and Stern (1995). Protein supply to the small intestine was determined using the NRC (2001) and DVE/OEB models. The results showed that heating increased dry matter (DM) and ether extract (EE) content, while reducing neutral detergent fibre (NDF) and acid detergent fibre (ADF), with little numerical difference between the three treatments. Soluble crude protein (SCP) also decreased upon autoclaving with concomitant increases in non-protein nitrogen (NPN), neutral detergent insoluble nitrogen (NDIN) and acid detergent insoluble nitrogen (ADIN). The CNCPS protein sub-fractions with the greatest changes were the buffer-soluble true protein fraction (PB1) and the fraction representing buffer-insoluble true protein which is not bound to NDF (PB2) showing dramatic increases, indicating a decrease in the overall protein degradability. <i>In situ</i>experiments showed a reduction in effective degradable dry matter (EDDM) as well as a reduction in effective degradable crude protein (EDCP) without significant differences between the treatments. Intestinal digestibility of protein as estimated by the three-step procedure showed no changes upon autoclaving. Modeling results, with flaxseed as the only feed source, for absorbable ruminally-undegraded feed protein in the intestines using both the NRC (2001) and DVE/OEB systems showed increases as a consequence of the autoclave treatments but again there were no differences between the treatments. The degraded protein balance results showed for both the NRC (2001) and DVE/OEB models that both were decreased upon autoclave treatment. However, the values for the NRC (2001) model suggested a potential nitrogen (N) deficiency and, therefore potentially impaired microbial crude protein (MCP) production, whereas the values for the DVE/OEB system showed potential N excess and, therefore, possible loss from the rumen. DRIFT analysis of protein secondary structure ratios showed a decrease in the alpha-helix to beta-sheet ratio for the whole seed, whereas results from S-FTIR spot data for cotyledon tissue showed autoclaving had the opposite effect on the ratio. CLA and PCA were successfully used to make distinctions between the different treatment spectra and showed enhanced sensitivity upon selection of a smaller spectral window to include only the amide I and II portion of the IR spectrum. The results failed to demonstrate any differences between the autoclave treatments used in this study, and showed that autoclaving generally decreased effectively ruminal degradability of flaxseed protein. The results further indicated that autoclaving had a significant enough effect on the flaxseed to permit identification of the altered alpha-helix to beta-sheet ratio with the mid-IR spectrum, as well as differentiation between the treatments using PCA and CLA. PCA and CLA results suggest that mid-IR spectral methods are more sensitive than traditional methods when used to identify differences between the heat treatments.