S100A12 porcina é um membro da família das proteínas S100, um grupo de pequenas proteínas ligantes de cálcio caracterizado pela presença de dois motivos “EF-hand”. Estas proteínas estão envolvidas em diversos eventos celulares, como a regulação da fosforilação protéica, atividade enzimática, tamponamento de Ca+2, processos inflamatórios e a polimerização de filamentos intermediários. Adicionalmente, algumas dessas proteínas podem ligar Zn+2, o qual pode afetar a ligação do íon Ca+2, particularmente para as proteínas S100. Neste trabalho, a seqüência gênica que codifica a proteína S100A12 porcina foi obtida por meio da construção de um gene sintético usando códons preferenciais para E.coli, permitindo a produção recombinante de grandes quantidades da proteína. Um estudo termodinâmico da estabilidade estrutural foi realizado, assim como a interação da proteína recombinante com íons divalentes usando técnicas de dicroísmo circular (CD) e fluorescência extrínseca. A desnaturação e renaturação induzidas por uréia ou temperatura indicam que se trata de um processo reversível e que a ligação dos íons Zn+2 e ou Ca+2 à rS100A12 aumenta sua estabilidade. A interação da sonda ANS com a proteína na presença de seus ligantes expõe superfícies hidrofóbicas podendo assim facilitar sua interação com macromoléculas alvo. Analisados em conjunto, os resultados obtidos indicam que S100A12 porcina é capaz de assumir diferentes conformações as quais podem estar correlacionadas com sua função fisiológica. / Porcine S100A12 is a member of S100 family, a small acidic calcium-binding proteins group characterized by the presence of two EF-hand motifs. These proteins are involved in many cellular events as the regulation of protein phosphorylation, enzymatic activity, Ca+2 homeostasis, inflammatory processes and intermediate filament polymerization. In addition, some of these proteins can bind Zn+2, which can affect the binding of Ca+2 particularly to S100 proteins. In this study, the gene sequence encoding S100A12 was obtained by the synthetic gene approach using E. coli codon bias allowing the recombinant production of large amounts of the protein. We report here a thermodynamic study on the structural stability of this recombinant protein and its interaction with divalent ions using circular dichroism and extrinsic fluorescence. The folding/unfolding induced by urea or temperature indicated a reversible process and the binding of Zn+2 or Zn+2 and Ca+2 to S100A12 increasing its stability. The interaction of the ANS probe with the protein in the ligant presence can lead to exposition of hydrofobic regions allowing its interaction with target macromolecules. Taken together, the results indicated that porcine S100A12 may assume different conformations that could be correlated to its physiological function.

Orientador: Patricia Sabino de Matos / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Ciencias Medicas / Made available in DSpace on 2018-08-09T15:50:12Z (GMT). No. of bitstreams: 1 Padrao_InesLiguori_D.pdf: 2489921 bytes, checksum: 62e17012ad64cca8cff1b95a7a39190e (MD5) Previous issue date: 2007 / Resumo: Adenomas hipofisários (AH) são neoplasias epiteliais geralmente bem diferenciadas e benignas. Manifestam-se clinicamente com sintomas de excesso ou redução hormonal e/ou de massa intracraniana. São classificados conforme aspecto macroscópico/radiológico (macro x microadenomas; invasivos x não invasivos), status funcional (funcionantes x não funcionantes), citológico (acidófilos, basófilos e cromófobos) e imunoistoquímicos/ultraestruturais (somatotropinomas, prolactinomas, orticotropinomas, tireotropinomas, gonadotropinomas e de células nulas). Entre as heterogêneas formas de apresentação, evolução e manifestações clínicas, adenomas invasivos e macroadenomas não invasivos são os que limitam o tratamento cirúrgico, com recidivas determinantes de morbidade endócrina e /ou neurológica. Variantes agressivas e não agressivas podem exibir aspecto histológico semelhante, motivando a investigação imunoistoquímica, genética e de biologia molecular, com o propósito de relacionar mecanismos de tumorigênese com o comportamento biológico desses tumores, como crescimento invasivo e recorrência. Objetivos Classificação e estudo da freqüência dos AH da amostra sob o ponto de vista funcional embasada na sintomatologia clínica; Classificação anatômica/neuroradiológica baseada no tamanho tumoral e grau de invasão, utilizando a gradação de Jules Hardy; Classificação e estudo da freqüência dos subtipos hormonais, utilizando o método imunoistoquímico. Correlacionar dados clínicos, anatômicos, imunoistoquímicos, com o grau de agressividade dos AH, buscando fatores de prognóstico utilizando marcadores de atividade proliferativa (Ki 67), alteração de gene supressor tumoral (p53 e menin), angiogênese (CD 34) e expressão de neuropeptídeo (Galanina). Material e métodos Avaliamos AH de 61 pacientes submetidos à ressecção cirúrgica, sob o ponto de vista clínico, anatômico/neuroradiológico e imunoistoquímico. Utilizamos a técnica imunoistoquímica: para a determinação dos diferentes subtipos hormonais e para o Ki 67 como marcador de proliferação, o p53 e menin como marcadores de supressão tumoral, CD34 para a avaliação da angiogênese e Galanina para avaliar a presença desse neuropeptídeo. Resultados A amostra está constituída por 57 (93,4%) macroadenomas (19 invasivos e 38 não invasivos) e 4 microadenomas não invasivos; a freqüência de invasão foi de 62,3%. Vinte e cinco (41%) AH são clinicamente funcionantes (13 somatotropinomas, 6 prolactinomas , 6 corticotropinomas) e 36 (59%) não funcionantes (32 AH silenciosos e 4 de células nulas). Macroadenomas invasivos não funcionantes predominaram em relação aos macroadenomas invasivos funcionantes (p= 0,014). Houve 54,09% de recidiva. A imunoistoquímica revelou expressão positiva para hormônio do crescimento (GH) em 18 AH, 10 AH expressaram prolactina (PRL), 12 positivos para corticotropina (ACTH), 17 para gonadotrofinas e 4 AH negativos para todos os hormônios. A sintomatologia endócrina incidiu em 42,62% dos casos e os sintomas neurológicos em 88%. Homens e mulheres foram igualmente afetados e a maioria dos AH estão distribuídos nas quarta e quinta décadas de vida. O Ki 67 foi positivo em 83,69% do total da amostra e a média desse índice foi 4,39% (variação de 0 ¿ 36,9%); entre os subtipos hormonais os AH com expressão positiva para GH, mono ou pluri-hormonais, apresentaram índice de proliferação significativamente maior em relação aos demais subtipos (p=0,001). Os macroadenomas funcionantes invasivos apresentaram maior índice de proliferação em relação aos macroadenomas não funcionantes invasivos (p = 0,0328). O p53 foi positivo em 60,65% do total da amostra e a média do índice de núcleos corados foi 1,23% (variação de 0 ¿ 16%). Não houve diferença significativa da expressão do p53 quanto à invasão, fenótipo hormonal, status funcional e recidiva, entretanto houve correlação positiva entre o índice de proliferação e o p53 (p = 0,0004). Quanto à angiogênese, o CD34 mostrou que a densidade microvascular (DMV) em AH é menor em relação ao tecido adeno-hipofisário normal. A Galanina (GAL) foi positiva em 57% dos casos; os AH negativos para a GAL apresentaram índices de DMV significativamente maior em relação aos GAL positivos (p = 0,0464). A imunoreação para menin foi positiva em 41 AH (67,21%), e negativa em 20 AH (32,7%). A grande variedade de expressão de menin, tanto na intensidade da coloração quanto na localização nuclear ou citoplasmática, dificultou a interpretação dos resultados, sendo necessários estudos genéticos comparativos que possam orientar essa interpretação dos dados obtidos. Conclusões A maior freqüência de AH não funcionantes desta amostra pode estar relacionada ao diagnóstico tardio. A expressão do Ki 67 não se associou à gradação de Hardy. Os macroadenomas funcionantes e invasivos apresentaram índice de proliferação maior do que os não funcionantes, podendo indicar comportamento mais agressivo. Entre os diferentes subgrupos de AH apenas os que expressaram positividade para GH apresentaram índice de proliferação significativamente maior. A invasão nos AH = 10 mm, que apresentaram índice de proliferação igual a zero, não é dependente da atividade proliferativa. A maior expressão do p53 se correlacionou com o maior índice de proliferação (Ki 67) nesta amostra. O p53, a DMV e GAL não são marcadores de prognóstico nos AH. Os índices mais elevados da DMV em AH com ausência de expressão da GAL, podem indicar comportamento biológico mais agressivo / Abstract: Pituitary Adenomas (PA) are an easily identifiable and benign epithelial neoplasia. They are clinically detected through symptoms of an increased or decreased hormone rate and/or alterations of intra-cranial mass. They are classed in accordance with radiological / macroscopical aspects (macro versus microadenoma / invasive versus non-invasive), functional status (functional versus non-functional), cytological (acidophil, basophilic and chromophobic) and immunohistochemical / ultra-structural (somatotrophinomas, prolactinomas, corticotrophinomas, thyrotrophinomas, gonadotrophinomas and those from null cells). Amongst their various forms of disclosure, evolution, and clinical manifestation, invasive adenomas and non-invasive macroadenomas impose limits to surgical procedures, resulting in recidivist determination of endocrine and / or neurological morbidity. Aggressive and non-aggressive variants may display similar histological aspects, which require immunohistochemical, genetic and molecular-biological investigation, attempting to relate tumorigenesis mechanisms to the biological behavior of these tumors, such as invasive growth and recurrence. Objectives Classification and study of the occurrence of the sampled PA under a functional viewpoint based upon clinical symptomatology; Neuro-radiological / anatomic classification based upon tumor size and invasive rate through the Jules Hardy labeling index; Analysis and classification of the occurrence of hormonal subtypes, through the immunohistochemical method; Co-relate clinical, anatomical, and immunohistochemical data with the aggressivity of the PA, seeking prognostic factors using proliferous activity markers (Ki 67), suppressive tumorous gene alteration (p53 and menin), angiogenesis (CD 34) and neuropeptide (galanin). Materials and Methods 61 PA patients who had undergone surgical re-section were studied: clinical, anatomical / neurological, and immunohistochemical aspects were considered. The immunohistochemical technique was used to determine the different hormonal subtypes, and for the Ki 67 as a proliferation marker, the p53 and menin as a tumor suppression marker, CD34 for the assessment of the agiogenesis, and galanin to observe the presence of this neuropeptide. Results The sample contains 57 (93.4% macro-adenomas (19 invasive and 38 non-invasive) and 4 non-invasive microadenomas; the invasion rate equaled 62.3%. Twenty-five (41%) PA are clinically functional (13 somatotrophinomas, 6 prolactinomas, 6 corticotrophinomas) and 36 (59%) non-functional (32 PA silenced and 4 null cells). Invasive, non-functional macroadenomas stood out when compared to invasive, functional macroadenomas (p=0.014). 54.09% recidivists were detected. Immunohistochemistry revealed positive expression of the growth hormone (GH) in 18 PA, 10 PA expressed prolactin (PRL), 12 showed positive for corticotrophin (ACTH), 17 for gonadotrophin, and 4 PA showed negative for all hormones. Endocrine symptomatology occurred in 42.62% of the cases, and neurological symptoms were present in 88%. Male and female patients were affected indistinctly, and most PA patients were in their 40s and 50s. Ki 67 was positive in 83.69% of the total sampled, rating at an average of 4.39% (varying from 0 ¿ 36.9%); amongst hormonal subtypes, PA showing positive expression of GH (mono or plurihormonal) had a significantly increased proliferative activity when compared to other subtypes (p=0.001). Invasive, functional macroadenomas showed a higher proliferation rate than invasive, non-functional macroadenomas (p=0.0328). p53 was positive in 60.65% of the total sampled, and the average rate of dyed nuclei equaled 1.23% (varying from 0 ¿ 16%). There was no meaningful change in the expression of p53 as to the invasion, hormonal phenotype, functional and recidivist status. However, a positive co-relation between the proliferation rate and the p53 was detected (p=0.0004). Concerning the angiogenesis, CD34 showed that the microvascular density (MVD) in PA is lower when compared to the healthy adenohypophysial tissue. Galanin (GAL) was positive in 57% of the cases. The PA negative for GAL showed significantly increased MVD rates than the GAL positive (p=0.0464). Immunoreaction for menin was positive in 41 PA (67.21%) and negative in 20 PA (32.7%). The large variety of menin expression, regarding chromatic intensity and cytoplasmic or nuclear location made the interpretation of the results more difficult, which required comparative genetic studies that could guide the understanding of the data obtained. Conclusions Higher rates of non-functional PA cases may be a result of late diagnosis. Ki 67 expression could not be linked to the Hardy index. Invasive, functional macro-adenomas showed a higher proliferation rate than the rate obtained from the non-functional types ¿ which may signal increased aggressivity. Amongst the various PA subgroups, only those with GH positive expression had a significantly higher proliferation rate. The invasion of PA =10 mm, whose proliferation rate was null, is not dependent on proliferative activity. In this sample, the largest p53 expression matched the highest proliferation rate (Ki 67). p53, MVD and GAL are not PA prognostic markers. The highest MVD rates among PA combined with a null GAL expression may indicate more aggressive biological behavior / Doutorado / Ciencias Biomedicas / Mestre em Ciências Médicas

While the digital market, especially the music streaming market, has rapidly grown in recent years, however the physical music segment still remains relevant in the Thai market. The Thai music market has inimitable characteristics within the market in terms of the physical music record offers, recorded musical works, and a growth trend in physical sales. Moreover, the behaviour in physical music consumption is opposite to that in world markets. Music consumption practices in the Thai market and why physical music, and CDs in particular, remain relevant to the Thai music industry are an enigma. The music industry itself has suggested that the physical music market needs to be revamped and its physical products redeveloped. In addition, the major record companies have also refocused into developing physical markets. However, precisely how this is to be achieved has not been specified. The twin aims of this study are to more fully comprehend Thai music consumption practices in today’s market and to examine how the concepts of product development could be effective in responding to consumer needs and desires. Consumer-led product development is the main concept of this study used to create ideas to enhance music CDs. This study combined many perspectives related to consumer-led product development and then applied them to construct the conceptual framework named “The Seminal Framework for CD Development”. The framework is a roadmap to create a new set of features for a new form of music CD based on the input of the music industry’s representatives and consumers. A new form of music CD which includes a new set of features is named in this study as the “prototype CD”. Also, the framework is used to evaluate the effectiveness of the prototype CD; how the prototype CD is responsive to consumer needs as far as functional and psychological perspectives are concerned. Bearing in mind the aim of this research, the researcher considered the interpretive paradigm to be the most appropriate approach for capturing consumers’ experiences in music consumption practices and for studying the opinions, points of view and ideas derived from the consumers, and the experts in music CD development. In the data collection process, this study employed the technique of purposive sampling for selecting from the population. The purposive sampling technique allows the researcher to judge and select people or prospective participants who: 1) are available to participate I in conducting the research, 2) are knowledgeable about the industry, 3) have experience related to the context of the study, and 4) can provide the reliable and detailed information required to understand the focal themes of the study. This study conducted nine interviews with the music industry’s experts, 60 one-on-one interviews and four group interviews with consumers. For the data analysis, this study adopted the manual coding analysis. The Seminal Framework determined the coding structure, and sets of data could be organised into distinct themes, such as the new features of music CDs or future positive possibilities for music consumption. This enabled, at the end of the process, an easier and more efficient identification of the experiential values derived from prototype music CDs. In addition, in more fully understanding the needs and expectations inherent in music consumption practices, such careful coding analysis helps to re-define the typology of music consumers. The typology and the concepts also facilitated the identification of music consumption behaviour in today’s environment. This study contributes a wider concept in consumer-led product development that has been applied to the context of music consumption practices and music product (CD) development.

Abstract Sepsis is a common problem in the intensive care unit (ICU) still having a high mortality and causing high costs to health care system. Currently, there is no marker to distinguish sepsis from other causes of systemic inflammation. Leukocyte surface molecules have been proposed as markers of sepsis. The most promising markers have been neutrophil CD64 and CD11b on monocytes and neutrophils and HLA-DR on monocytes. In this thesis, leukocyte surface molecules were investigated using quantitative flow cytometry in critically ill patients with sepsis, non-septic ICU controls, and healthy volunteers. The surface molecules of interest were neutrophil CD11b and CD64, monocyte CD11b, CD14, CD40, CD64, CD80, HLA-DR, and lymphocyte CD69. First, a special emphasize was indicated in methodological aspects of the quantitative flow cytometry. Then, the surface molecule kinetics was investigated in different types of critically ill patients. Finally, the diagnostic performance of the molecules was determined and compared to that of traditionally used sepsis markers. Furthermore, an example of multiple marker analysis was introduced as a diagnostic tool. The optimal circumstances for leukocyte surface molecule analysis were +4°C temperature throughout the collection and preparation of the samples using tubes containing acid citrate dextrose (ACD) as an anticoagulant, followed by flow cytometry within 6 hours from sampling. Monocyte CD11b and CD40, neutrophil CD11b and CD64, and CD69 on CD4+ T cells and natural killer (NK) cells separated sepsis from non-septic ICU controls and healthy volunteers, neutrophil CD64, having the best area under curve. Procalcitonin (PCT) was second best marker. Monocyte CD40 and NK CD69 may predict positive blood culture detection, whereas CD11b may predict early mortality. In multiple marker analysis, combination of positive neutrophil CD64, C-reactive protein (CRP) and PCT increased post-test probability for sepsis. In conclusion, pre-analytical and analytical factors have effects on results of leukocyte surface molecule analysis. Leukocyte surface molecules may improve sepsis diagnostics in ICU setting. Neutrophil CD64 was the most promising marker. Combination of CD64, CRP and PCT increased the detection of sepsis in ICU. / Tiivistelmä Sepsis on yleinen tehohoidon ongelma, johon liittyy korkea kuolleisuus ja suuret hoidolliset kustannukset. Toistaiseksi ei ole laboratoriomerkkiainetta, joka erottaisi sepsistä sairastavat muista kriittisesti sairaista, joilla on yleistynyt tulehdusvaste. Valkosolujen pintamolekyylien käyttöä sepsiksen laboratoriomerkkiaineena on tutkittu. Lupaavimmat näistä molekyyleistä ovat olleet neutrofiilien CD64, monosyyttien ja neutrofiilien CD11b ja monosyyttien HLA-DR. Tässä väitöskirjassa tutkittiin valkosolujen pintamolekyylejä kriittisesti sairailla sepsistä sairastavilla potilailla, niillä tehohoitopotilailla, joilla ei ollut sepsistä, ja terveillä vapaaehtoisilla virtaussytometriaa käyttäen. Mielenkiinnon kohteina olivat neutrofiilien CD11b ja CD64, monosyyttien CD11b, CD14, CD40, CD64, CD80 ja HLA-DR, sekä lymfosyyttien CD69. Ensimmäiseksi tutkittiin kvantitatiivista virtaussytometriaa menetelmänä. Sen jälkeen pintamolekyylien kinetiikkaa tutkittiin eri potilasryhmillä. Lopuksi määritettiin pintamolekyylien diagnostinen tehokkuus ja sitä verrattiin perinteisempiin sepsiksen diagnostiikassa käytettyihin laboratoriomerkkiaineisiin. Lisäksi selvitettiin usean merkkiaineen mallin diagnostista osuvuutta. Parhaat olosuhteet virtaussytometrialle olivat: +4 °C:n lämpötila näytteenoton ja -käsittelyn aikana, näytteiden ottaminen putkiin, joissa on antikoagulanttina hapan sitraatti-dekstroosi (ACD) ja näytteiden analysointi kuuden tunnin kuluessa näytteenotosta. Monosyyttien CD11b ja CD40, neutrofiilien CD11b ja CD64 sekä CD4+ T-solujen ja NK-solujen CD69 erottivat sepsistä sairastavat tehohoitoverrokeista ja terveistä. Neutrofiilien CD64:llä oli paras erottelukyky. Prokalsitoniini (PCT) oli toiseksi paras merkkiaine. Monosyyttien CD40 ja NK-solujen CD69 voivat parantaa positiivisen veriviljelylöydöksen havaitsemista, kun taas CD11b voi ennustaa varhaista potilaan menehtymistä. Usean merkkiaineen mallissa neutrofiilien CD64 paransi C-reaktiivisen proteiinin (CRP) ja PCT:n tehoa sepsiksen diagnostiikassa. Loppupäätelmänä on, että valkosolujen pintamolekyylien analysointivaiheen eri muuttujilla on vaikutusta virtaussytometriatuloksiin. Valkosolujen pintamolekyylien käyttö voi parantaa sepsiksen diagnostiikkaa teho-osastolla. Neutrofiilien CD64 oli lupaavin merkkiaine. Neutrofiilien CD64:n, CRP:n ja PCT:n yhdistelmä paransi sepsiksen diagnostiikkaa teho-osastolla.

Jahresüberblick 1996 Zentrale Rechner-Pools - aktueller Stand der Nutzung, Bereitstellung neuer Pools im Jahre 1997 Windows NT im PC-Pool ¨Dissertationen online¨ - ein Tagungsbericht (Archivierungssystem) Datennetzausbau 1997 Neue CD-ROM im Netz - das Telefonbuch von Deutschland

According to the International Diabetes Federation (IDF), there were 371 million people in the age from 20 to 79 years worldwide affected by diabetes in 2012. This means diabetes has become a global epidemic disease and, therefore, the importace of insulin research still grows. Insulin is a protein hormone that plays a key role in regulating blood glucose level which has a widespread impact on whole metabolism. Insulin acts through binding of its monomeric form to the insulin receptor. It is clear that insulin monomer has to undergo structural changes upon binding to the insulin receptor as the residues which are crucial for the interaction are burried within the native form. According to studies of highly active hormone analogs and the new information about the insulin-insulin receptor complex, there is a strong evidence that the C-terminal part of the B-chain is a dynamic element in insulin activation and receptor binding. Probably, there is also a great importance of the B-chain N- terminus and the transition between T and R conformations of insulin. However, the exact significance of the T and R states of insulin still remains unclear. In this work, several new insulin analogs AibB3-insulin, AibB5-insulin, AibB8- insulin, N-MeAlaB8-insulin and D-ProB8-insulin were prepared for the purpose of...

The increased frequencies of two novel B cell populations defined as IgM+ CD19+ CD27- CD21low CD38low CD24+ and IgM+ CD19+ CD27- CD21low CD38low CD24- in peripheral blood of patients with common variable immunodeficiency (CVID) compared to healthy donors were found. The aim was to search for such B cells in patients with rheumatoid arthritis (RA) and their further characterization. The production of immunoglobulin (Ig) mRNA in single B cells was analyzed using flow cytometry, single cell sorting and RT-PCR, IgVH-specific PCR, cycle sequencing and statistical analysis. The study was focused on analysis of variable regions of the heavy chains of Igs and significant differences in the usage of VH, DH and JH gene segments, mutational frequencies, distribution of silent and replacement mutations, length and composition of CDR3 regions, clonal relation and RAG gene expression in above mentioned B cell populations were found. Because of lack of the surface CD27 molecule being regarded as marker of B cells that have undergone antigen-driven germinal reactions, analyzed populations were considered as naive. However, the pattern and type of mutations suggested that these cells could represent a new type of differentiated memory/antigen- experienced B lymphocytes (in CVID less maturated) with the likely role in...

<p>Cadmium (Cd) is a highly mobile and toxic heavy metal that negatively affects plants, soil biota, animals and humans, even in very low concentrations. Currently, Cd contamination of cocoa produced in Latin American countries is a significant problem, as concentrations can exceed acceptable levels set by the European Union (0.5 mg/kg), sometimes by more than 10 times allowable levels. In South America, <i>Theobroma cacao</i> is an essential component of the basic market basket. This crop contributes to the Latin-American trade balance, as these countries export cacao and chocolate-based products to major consumer countries such as the United States and Europe. Some soil amendments can alter the bioavailability and uptake of Cd into edible plant tissues, though cacao plants can accumulate Cd without displaying any visible symptoms of phytotoxicity, which makes it difficult to determine if potential remediation strategies are successful. Currently, the only effective way to quantify Cd accumulation in plant tissues is via destructive post-harvest practices that are time-consuming and expensive. New hyperspectral imaging (HSI) technologies developed for use in high-throughput plant phenotyping are powerful tools for monitoring environmental stress and predicting the nutritional status in plants. Consequently, the experiments described in this thesis were conducted to determine if HSI technologies could be adapted for monitoring plant stress caused by Cd, and estimating its concentration in vegetative plant tissues. Two leafy green crops were used in these experiments, basil (<i>Ocimum basilicum L.</i> var. Genovese) and kale (<i>Brassica oleracea L</i>. var. Lacinato), because they are fast growing, and therefore, could serve as indicator crops on cacao farms. In addition, we expected these two leafy green crops would differ in their morphological responses to Cd stress. Specifically, we predicted that stress responses would be visible in basil, but not kale, which is known to be a hyperaccumulator. The plants were subject to four levels of soil Cd (0, 5, 10 and 15 ppm), and half of the pots were amended with biochar at a rate of 3% (v/v), as this amendment has previously been demonstrated to improve plant health and reduce Cd uptake. The experiments were conducted at Purdue’s new Controlled Environment Phenotyping Center (CEPF). The plants were imaged weekly and manual measurements of plant growth and development were collected at the same times, and concentrations of Cd as well as many other elements were determined after harvest. Fourteen vegetation indices generated using HSI images collected from the side and top view of plants were evaluated for their potential to identify subtle signs of plant stress due soil Cd and the biochar amendment. In addition, three mathematical models were evaluated for their potential to estimate Cd concentrations in the plant biomass and determine if they exceed safe standards (0.28 mg/kg) set by the Food and Agriculture Organization (FAO) for leafy greens. Results of these studies confirm that like many plants, these leafy green crops can accumulate Cd levels that are well above safety thresholds for human health, but exhibit few visible symptoms of stress. The normalized difference vegetation index (NDVI) and the chlorophyll index at the red edge (CI_RE) were the best indices for detecting Cd stress in these crops, and the plant senescence and reflectance index (PSRI) and anthocyanin reflectance index (ARI) were the best at detecting subtle changes in plant physiology due to the biochar amendment. The heavy metal stress index (HMSSI), developed exclusively for detecting heavy metal stress, was only able to detect Cd stress in basil when images were taken from the top view. Results of the mathematical models indicated that principal components analysis (PCA) and partial least squares (PLS) models overfit despite efforts to transform the data, indicating that they are not capable of predicting Cd concentrations in these crops at these levels. However, the artificial neural networks (ANN) was able to predict whether leafy greens had levels of Cd that were above or below critical thresholds suggested by the FAO, indicating that HSI could be further developed to predict Cd concentrations in plant tissues. Further research conducted in the field and in the presence of other environmental stress factors are needed to confirm the utility of these tools, and determine whether they can be adapted to monitor Cd uptake in cacao plants.</p>

The aim of this thesis is to understand RNA-RNA interactions steering cellular functions, as in the case of this thesis the structure of mRNA(Sirt1) in complex with microRNA-34a (miR-34a). MiR-34a regulates the cancer protein p53 via Sirt1 modulation. This work will be the basis for future drug design and the understanding of misguided regulation in cancer. The miR-34a binds to the mRNA(Sirt1) 3’ untranslated region (3’-UTR) and will either inhibit the translation of the protein Sirtuin 1 by capturing its mRNA or by degrading it. p53, a key activator of miR-34a, prevents cancer development by inducing programmed cell death (apoptosis) on cells with DNA damage. In contrast, the protein Sirtuin 1 (Sirt1) has been shown to help cells with DNA damage to survive by down regulating the activity of protein p53 and will therefore increase the risk of cancer development. Studying the interaction between the mRNA(Sirt1) and miR-34a can present valuable information on the structure of the complex as well as the mode miR-34a uses to inhibit translation of mRNA(Sirt1) leading to down regulation of protein Sirtuin 1 and therefore prevent cancer development. For the elucidation of this question different biochemical and biophysical methods were applied, such as in vitro transcription, gel electrophoresis, RNA purification with gel, crush &amp; soak and Cicular Dichroism (CD) melting studies. For this thesis work, the target sequence in mRNA(Sirt1) was optimized and purified so melting studies could be carried out. For future structural characterization using Nuclear Magnetic Resonance (NMR) studies with the miR-34a also produced in the lab. The mRNA(Sirt1) target sequence was produced and purified with the final yield of 0.02%. The results show that the sequence is highly ATP dependent and suggest the ratio between the nucleotides ATP/CTP to be 1:2. Low yield of purified mRNA(Sirt1) was received and still contained some impurities, which imply that another method than crush &amp; soak should be used when purifying. The results, indicate that High-Preformance Liquid Chromatography (HPLC) might be a better solution for the pufication process. The melting profiles done on mRNA(Sirt1) show that the secondary structures decrease with an increase in temperature. Accroding to the results, the mRNA(Sirt1) sequence is folded in room temperature, though not very stable. The wavelength which provided the best resolution was at 268 nm and the melting point of mRNA(Sirt1) was determined to 44 °C. This thesis also contains an educational part, where an educational material was provided and testing was conducted for the subject Chemistry 2 for students age 18 and the material was evaluated with qualitative methods together with pedagogical methods. The study showed that the student can develope the different abilities stated in the curriculum with the material created. The results also showed that the students preferably choose cultural arguments when dicussing socio scientific question, rather than economical, democratic or utility arguments. / Syftet med studien är att förstå RNA-RNAinteraktioner som styr cellulära funktioner, i detta fall mRNA(Sirt1) i komplex med microRNA-34a (miR-34a). MiR-34a reglerar cancerproteinet p53 via modulation av Sirt1. Detta arbete kommer lägga grund för framtida läkemedelsdesign vid reglering av cancer. MiR-34a binder till den 3’ otranslerade regionen i mRNA(Sirt1) och hämmar antingen translationen av protein Sirtuin 1 (Sirt1) genom att fånga dess mRNA eller genom att försämra det. p53 förhindrar utvecklingen av cancer genom att framkalla programmerad cell död (apoptosis) av celler med skadat DNA. Det har visats att proteinet Sirtuin 1 hjälper celler med skadat DNA att överleva, genom att sänka aktiviteten av p53. På så vis ökar risken för utveckling av cancer. Genom att studera interaktionen mellan mRNA(Sirt1) och miR-34a kan värdefull information kring komplexets struktur fås. Samt hur miR-34a hämmar translationen av mRNA(Sirt1), vilket leder till minskad aktivitet av protein Sirt1. För att klarlägga denna fråga har olika biokemiska och biofysiska metoder använts, såsom in vitro transkription, gelelektrofores, RNA rening med gel och Circular Dichroism (CD). För detta arbete har målsekvensen i mRNA(Sirt1) optimerats och renats så CD smältstudier med kunde genomföras. Resultatet visar att mRNA(Sirt1) sekvensen renats med ett utbyte på 0.02 %. Sekvensen är beroende av ATP och förhållandet mellan ATP/CTP nukleotider bör vara 1:2. Resutatet visar på ett lågt utbyte som visar på att High-Performance Liquid Chromatography (HPLC) kan vara en bättre metod än Crush &amp; soak för reningen av mRNA(Sirt1). Ur de smältprofiler som gjorts visade det sig att de sekundära strukturerna av mRNA(Sirt1) minskade med ökande temperatur. I enlighet med resultaten visar det att mRNA(Sirt1) är veckat i rumstemperatur men är inte stabil. Den bästa upplösningen erhölls vid 268 nm och mRNA(Sirt1) har en smältpunkt runt 44 °C. Detta arbete innehåller även ett utbildningskapitel, där ett utbildningsmaterial har skapats och testats på 18-åriga kemi 2 studenter i åldern 18 år. Materialet har utvärderats med hjälp av kvalitativa metoder tillsammans med pedagogiska metoder. Studien visade att de flesta förmågorna för kemi 2 kan utvecklas med hjälp av denna typ samhällsfrågor i det naturvetenskapliga klassrummet (SNI-fall) förutom förmågan att planera och genomföra experiment. Det argument som eleverna helst väljer att använda då de diskuterar det skapade SNI-fallet är Kulturargument och det minst använda är Demikratiargument.

This work deals with Systems that combine automata and grammars. We investigate their properties compared with grammar systems and automaton systems. Work is focused on systems, which components are finite state automata, right linear grammars, pushdown automata or context free grammars. We also investigate usage of these systems in compilers.