Thesis advisor: Mary F. Roberts / Crystallization studies in presence of organic osmolytes were conducted to better understand the specific mechanism of compatible solute binding to the inositol monophosphatase of Archaeoglobus fulgidus. The synthesis of a-diglycerol phosphate, one of the natural osmolytes of A. fulgidus, was also completed for kinetic testing of its I-1-Pase thermoprotective properties and for crystallization trials. / Thesis (MS) — Boston College, 2011. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

Actin is a highly abundant protein in most eukaryotic cells. The assembly of actin monomers to double helical filaments is crucial for many cellular functions, including cell movement and cell division. Actin filament assembly in cells occurs in a crowded intracellular environment consisting of various molecules, including cations and organic osmolytes. Recent studies show that cation binding stiffens actin filaments, and a small organic osmolyte trimethylamine-N-oxide (TMAO) modulates filament assembly. However, how cations and TMAO combined affect actin filament mechanics is not understood. We hypothesize that depending on the concentrations of cations and osmolytes, there will be different effects on the stiffness and assembly of actin filaments. In this study, using TIRF we evaluate actin filament mechanics and assembly. Our findings indicate that when TMAO is present alone, it can increase the elongation rate and stiffness of actin filaments, however the inclusion of potassium levels alongside TMAO reduces the persistence length of actin filaments, suggesting a decrease in filament stiffness compared to the influence of TMAO alone. Furthermore, the elongation rate of actin filaments decreases when both TMAO and potassium ions are present. This study will help us better understand how cations and osmolytes together can affect actin filament mechanics in the living cells.

No description available.

Myocilin, expressed in the trabecular meshwork of the eye, has been linked to inherited primary open-angle glaucoma (POAG). The biological function of myocilin is unknown, but mutant myocilin exhibits a gain-of-function mechanism, aggregating within the endoplasmic reticulum of human trabecular meshwork cells, causing cell stress and eventually apoptosis. After apoptosis occurs, the trabecular meshwork is compromised, leading to an increase in intraocular pressure, a symptom of glaucoma. In this thesis, I have expressed and purified the wild-type olfactomedin (OLF) domain and 24 reported disease-causing variants. I developed a facile thermal stability assay using differential scanning fluorimetry, which follows the unfolding of a protein through the fluorescence of a dye sensitive to hydrophobic regions of a protein. Also in this thesis I have determined melting temperatures for the wild-type and for each of the disease-causing mutants. I have tested the stability of the mutants in the presence of seven osmolytes, with sarcosine and trimethylamine-N-oxide restoring the melting temperature closest to wild-type. Additionally, I expressed and purified three reported single nucleotide polymorphisms (SNPs) (E352Q, E396D, K398R), which are considered benign variants. Variants were also compared by circular dichroism, revealing high b-sheet content and wild-type structure. When compared to previous studies, there is a positive correlation between the melting temperature, and previously reported qualitative assays, which measure the mutant myocilin solubility in detergent, secretion from mammalian cells, and aggregation propensity. Taken together, these data give insight into the relationship between glaucoma genotypes and phenotypes.

Made available in DSpace on 2014-12-17T14:05:23Z (GMT). No. of bitstreams: 1 UaskaBS_TESE.pdf: 2951660 bytes, checksum: 93152a3c6ea30c7f4eaa465f3f5d2969 (MD5) Previous issue date: 2013-04-16 / Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico / The screening for genes in metagenomic libraries from soil creates opportunities to explore the enormous genetic and metabolic diversity of microorganisms. Rivers are ecosystems with high biological diversity, but few were examined using the metagenomic approach. With this objective, a metagenomic library was constructed from DNA soil samples collected at three different points along the Jundia?-river (Rio Grande do Norte-Brazil). The points sampled are from open area, rough terrain and with the direct incidence of sunlight. This library was analyzed functionally and based in sequence. For functional analysis Luria-Bertani solid medium (LB) with NaCl concentration varied from 0.17M to 0.85M was used for functional analysis. Positives clones resistant to hypersaline medium were obtained. The recombinant DNAs were extracted and transformed into Escherichia coli strain DH10B and survival curves were obtained for quantification of abiotic stress resistance. The sequences of clones were obtained and submitted to the BLASTX tool. Some clones were found to hypothetical proteins of microorganisms from both Archaea and Bacteria division. One of the clones showed a complete ORF with high similarity to glucose-6-phosphate isomerase which participates in the synthesis of glycerol pathway and serves as a compatible solute to balance the osmotic pressure inside and outside of cells. Subsequently, in order to identify genes encoding osmolytes or enzymes related halotolerance, environmental DNA samples from the river soil, from the water column of the estuary and ocean were collected and pyrosequenced. Sequences of osmolytes and enzymes of different microorganisms were obtained from the UniProt and used as RefSeqs for homology identification (TBLASTN) in metagenomic databases. The sequences were submitted to HMMER for the functional domains identification. Some enzymes were identified: alpha-trehalose-phosphate synthase, L-ectoina synthase (EctC), transaminase L-2 ,4-diaminobutyric acid (EctB), L-2 ,4-diaminobutyric acetyltransferase (EctA), L-threonine 3 dehydrogenase (sorbitol pathway), glycerol-3-phosphate dehydrogenase, inositol 3-phosphate dehydrogenase, chaperones, L-proline, glycine betaine binding ABC transporter, myo-inositol-1-phosphate synthase protein of proline simportadora / PutP sodium-and trehalose-6-phosphate phosphatase These proteins are commonly related to saline environments, however the identification of them in river environment is justified by the high salt concentration in the soil during prolonged dry seasons this river. Regarding the richness of the microbiota the river substrate has an abundance of halobacteria similar to the sea and more than the estuary. These data confirm the existence of a specialized response against salt stress by microorganisms in the environment of the Jundia? river / A busca por genes baseada na constru??o e an?lise de bibliotecas metagen?micas a partir de solo gera oportunidades para explorar uma enorme diversidade gen?tica e metab?lica de microrganismos. Os rios s?o ecossistemas com alta diversidade biol?gica, mas ainda pouco explorados por meio de metagen?mica. Com o objetivo de explorar a diversidade microbiana, uma biblioteca metagen?mica foi constru?da a partir de DNA extra?do de substrato de rio em tr?s pontos ao longo do rio Jundia? (Rio Grande do Norte-Brasil). Os pontos de amostragem s?o derivados de ?rea aberta, terreno acidentado e com a incid?ncia direta da luz solar. Esta biblioteca foi analisada funcionalmente e tamb?m com base em sequ?ncias. Para a an?lise funcional foi utilizado meio de cultura s?lido LB com concentra??o de NaCl variando de 0,17M a 0,85M. Foram obtidos 15 clones positivos com caracter?sticas halotolerantes. Os DNAs recombinantes foram extra?dos e retransformados em cepa de Escherichia coli DH10B e curvas de sobreviv?ncia foram obtidas para confirma??o e quantifica??o da resist?ncia ao estresse abi?tico. As sequ?ncias dos clones foram obtidas e submetidas a ferramenta BLASTX e assim foi comprovado que alguns clones codificavam prote?nas hipot?ticas. Um dos clones apresentou uma ORF completa com elevada similaridade de glucose-6-fosfato-isomerase que participa na s?ntese do precursor de glicerol, sendo um soluto compat?vel para equilibrar a press?o osm?tica no interior e no exterior das c?lulas. Posteriormente, para identifica??o de genes que codificam osm?litos relacionados com halotoler?ncia e identifica??o da diversidade microbiol?gica, amostras de DNA ambiental do substrato do rio e da coluna d??gua do estu?rio e oceano foram coletadas e pirosequenciadas. As sequ?ncias de osm?litos de diferentes microrganismos foram obtidas a partir do UniProt e utilizadas como RefSeqs para a identifica??o por homologia (TBLASTN) nos bancos de dados metagen?micos. As sequ?ncias identificadas nos bancos de dados ambientais foram submetidas ao programa HMMER com o fim de identificar dom?nios funcionais. Foram identificadas as enzimas: alfa-trealose-fosfato sintase, L-ectoina sintase (ectC), transaminase do ?cido L-2,4-diaminobut?rico (EctB), ?cido L-2 ,4-diaminobut?rico acetiltransferase (EctA), L-treonina 3-desidrogenase (via de s?ntese do sorbitol), Glicerol-3-fosfato desidrogenase, inositol-3-fosfato desidrogenase, chaperonas, L-prolina glicina beta?na liga??o transportador ABC, mio-inositol-1-fosfato sintase, a prote?na simportadora de prolina/s?dio -PutP e trealose-6-fosfato fosfatase. Estas s?o enzimas que participam da s?ntese de osm?litos comumente relacionados a ambientes salinos, no entanto a identifica??o desses solutos em ambiente de rio ? justificada pela elevada concentra??o salina no solo durante prolongadas esta??es de seca neste rio. Quanto ? riqueza da microbiota foi identificado que o substrato do rio possui uma abund?ncia de halobact?rias semelhante a do mar e superior a do estu?rio. Esses dados confirmam a exist?ncia de uma resposta especializada contra o estresse salino por microrganismos no ambiente do rio Jundia?

<p>This thesis contains two parts.</p><p>In the first part, general and versatile palladium-mediated ¹¹C-C bond forming reactions for use in the production of radiotracers for Positron Emission Tomography (PET) were explored. Two complimentarty approaches were investigated: the coupling of [¹¹C]methyl iodide with a vinyl stannane and the reaction of a [¹¹C]methylated stannane with various organohalides. The former approach resulted in an improved, fully automated method for the synthesis of the potential cell proliferation tracer 1-(2’-deoxy-2’-fluoro-β-D-arabinofuranosyl)-[<i>methyl</i>-¹¹C]- thymine. The tracer was obtained in an isolated decay-corrected radiochemical yield of 28% at 25 min after end of radionuclide production. </p><p>In the latter approach, a [¹¹C]methylated tricyclic stannane (5-[¹¹C]methyl-1-aza- 5-stannabicyclo[3.3.3]undecane) was synthesised in 47% decay-corrected radiochemical yield, starting from [¹¹C]methyl iodide. This stannane was successfully employed in palladium-mediated coupling reactions with aryl, heteroaryl and vinyl halides.</p><p>In the second part, effects of the osmolytes glycine betaine, trimethylamine <i>N</i>-oxide (TMAO) and urea on Ribonuclease A (RNase A) were investigated using Nuclear Magnetic Resonance (NMR) spectroscopy. Changes in the enzymatic activity in the presence of these osmolytes at concentrations of ≤1 M were observed by monitoring the RNase A-catalysed degradation of polyuridylic acid using ³¹P NMR spectroscopy. The decrease in activity caused by urea was counteracted by both glycine betaine and TMAO at a molar ratio of 1:1.4 and 1:1, respectively.</p><p>To investigate if the observed activity changes were accompanied by any detectable alteration in the gross conformation of RNase A, diffusion coefficients for the enzyme in the various osmolyte solutions were measured using pulsed-field gradient NMR. A pulse sequence suitable for diffusion measurements in highly concentrated aqueous osmolyte solutions was developed and assessed. The diffusion of RNase A was measured relative to a new internal standard, 2,2,5,5,-tetramethyl-1,4-dioxane. No clear, detectable change in the relative diffusion of RNase A was observed in these media.</p>

This thesis contains two parts. In the first part, general and versatile palladium-mediated 11C-C bond forming reactions for use in the production of radiotracers for Positron Emission Tomography (PET) were explored. Two complimentarty approaches were investigated: the coupling of [11C]methyl iodide with a vinyl stannane and the reaction of a [11C]methylated stannane with various organohalides. The former approach resulted in an improved, fully automated method for the synthesis of the potential cell proliferation tracer 1-(2’-deoxy-2’-fluoro-β-D-arabinofuranosyl)-[methyl-11C]- thymine. The tracer was obtained in an isolated decay-corrected radiochemical yield of 28% at 25 min after end of radionuclide production. In the latter approach, a [11C]methylated tricyclic stannane (5-[11C]methyl-1-aza- 5-stannabicyclo[3.3.3]undecane) was synthesised in 47% decay-corrected radiochemical yield, starting from [11C]methyl iodide. This stannane was successfully employed in palladium-mediated coupling reactions with aryl, heteroaryl and vinyl halides. In the second part, effects of the osmolytes glycine betaine, trimethylamine N-oxide (TMAO) and urea on Ribonuclease A (RNase A) were investigated using Nuclear Magnetic Resonance (NMR) spectroscopy. Changes in the enzymatic activity in the presence of these osmolytes at concentrations of ≤1 M were observed by monitoring the RNase A-catalysed degradation of polyuridylic acid using 31P NMR spectroscopy. The decrease in activity caused by urea was counteracted by both glycine betaine and TMAO at a molar ratio of 1:1.4 and 1:1, respectively. To investigate if the observed activity changes were accompanied by any detectable alteration in the gross conformation of RNase A, diffusion coefficients for the enzyme in the various osmolyte solutions were measured using pulsed-field gradient NMR. A pulse sequence suitable for diffusion measurements in highly concentrated aqueous osmolyte solutions was developed and assessed. The diffusion of RNase A was measured relative to a new internal standard, 2,2,5,5,-tetramethyl-1,4-dioxane. No clear, detectable change in the relative diffusion of RNase A was observed in these media.

>Magister Scientiae - MSc / Abiotic stress, mainly in the form of extreme temperatures, drought and salinity has caused major crop losses worldwide, putting a severe strain on agriculture. Salinity severely limits plant growth and productivity and affects all aspects of the plant’s development including the most crucial stage; germination. This study investigated the effect of salt (NaCl) stress on Sorghum bicolor seedlings and the role of exogenously applied calcium (Ca2+) to ameliorate the effects of salt stress during germination. Sorghum seeds were germinated in the presence and absence of various NaCl (100, 200 and 300 mM) and Ca2+ (5, 15 and 35 mM) concentrations. Several assays including physiological (germination and growth assays), biochemical (osmolytes and oxidative stress markers), anatomical (epidermal and xylem layers) and expression profiles of key genes [antioxidant (SbSOD, SbAPX2 and SbCAT3), Salt Overly Sensitive (SbSOS1, 2 and 3) pathway enzymes and the vacuolar Na+/H+ exchanger antiporter2 (SbNHX2)] were investigated. Salt stress delayed germination and negatively affected growth as observed by the reduced root and shoot length and decreased fresh and dry weight. There was an increase in proline content and oxidative stress markers (H2O2 and MDA) under salt stress. Oxidative stress resulted in damage to the epidermal and xylem layers as observed on Scanning Electron Microscopy (SEM) images. Quantitative real-time polymerase chain reaction revealed that salt stress induced the expression of SbAPX2, SbCAT3 and SbSOS1 genes, whereas SbSOD4A, SbSOS2, SbSOS3 and SbNHX2 genes were not affected by salt. Exogenous application of Ca2+ counteracted the harmful effects of salt stress by improving germination efficiency, promoting seedling growth, reducing oxidative damage and the Na+/K+ ratio, indicating the protective effect. Ca2+ also effectively protected the epidermis and xylem layers from the severe damage caused by salt stress. In the presence of Ca2+ the expression of SbAPX2 and SbCAT3 was reduced except for the SbNHX2 gene, which increased by 65-fold compared to the control. The results obtained suggests that sorghum is able to respond to salt stress by inducing osmolytes, the antioxidant defence system as well as the SOS pathway. Furthermore, 5 mM Ca2+ was determined as the optimum Ca2+ concentration required to enhance sorghum’s tolerance to salt stress.

Pyrosequencing is a new DNA sequencing method relying on thesequencing-by-synthesis principle and bioluminometric detectionof nucleotide incorporation events. The objective of thisthesis was improvement of the Pyrosequencing method byincreasing the thermal stability of firefly luciferase, and byintroducing an alternative DNA polymerase and a new nucleotideanalog. Furthermore, the development of a new bioluminescentassay is described for the detection of inorganicpyrophosphatase activity. The wild-type North American firefly(Photinus pyralis)luciferase is a heat-sensitiveenzyme, the catalytic activity of which is rapidly lost attemperatures over 30°C. Two strategies for increasing thethermostability of the enzyme are presented and discussed. Inthe first strategy, the solution thermodynamics of the systemis affected by osmolytes in such a way that heat-mediatedinactivation of the enzyme is prevented. In the secondstrategy, the enzyme is thermostabilized by mutagenesis. Bothstabilizing strategies can be utilized to allow bioluminometricassays to be performed at higher temperatures. For instance,both DNA polymerase and ATP sulfurylase activity could beanalyzed at 37°C. The osmolyte strategy was successfully employed forincreasing the reaction temperature for the Pyrosequencingmethod. By increasing the reaction temperature to 37°Cunspecific signals from primer-dimers and 3’-end loopswere reduced. Furthermore, sequencing of a challenging templateat 37°C, which previously yielded poor, non-interpretablesequence signals at lower temperatures was now possible. Introduction of a new adenosine nucleotide analog,7-deaza-2’-deoxyadenosine-5’-triphosphate (c7dATP) reduced the inhibitory effect on apyraseobserved with the currently used analog,2’-deoxyadenosine-5’-O-(1-thiotriphosphate)(dATPαS). Sequencing of homopolymeric T-regions has previously beendifficult with the exonuclease-deficient form of the DNApolymerase I large (Klenow) fragment. By using the DNApolymerase from bacteriophage T7, known as Sequenase, templateswith homopolymeric T-regions were successfully sequenced.Furthermore, it was found that the strand displacement activityfor both polymerases was strongly assisted if the displacedstrand had a 5’-overhang. In contrast, the stranddisplacement activity for both polymerases was inhibitedwithout an overhang, resulting in reduced sequencingperformance in double stranded regions. A firefly bioluminescent assay for the real-time detectionof inorganic pyrophosphatase in the hydrolytic direction wasalso developed. The assay is versatile and has a linearresponse in the range between 8 and 500 mU. Key words:bioluminescence, osmolytes, glycine betaine,thermostability, firefly luciferase, inorganic pyrophosphatase,inorganic pyrophosphate, Pyrosequencing technology, secondaryDNA-structures, Sequenase, Klenow-polymerase, reaction rates,temperature, c7dATP, dATPαS. / <p>QCR 20161027</p>

Einleitung: Mit der vorliegenden Studie wurden zum ersten Mal beim Menschen die Auswirkungen von Dehydration (Dehy) und anschließender Rehydratation (Rehy) auf cerebrale volumenregulatorische Metabolite (myo-Inosit (mI), N-Azetylaspartat+N-Azetylaspartylglutamat (tNAA), Kreatin (Cr), Glyzerophosphocholin+Phosphocholin (Cho) und Glutamat+Glutamin (Glx)) sowie auf Flüssigkeitsverschiebungen untersucht. Methoden: 14 Radsportler (26.6 (22.7/29.8) Jahre, Median und 25./75. Perzentile) wurden mittels 1H-Spektroskopie (1H-MRS) in der okzipitoparietalen grauen Substanz (GM) und parietalen weißen Substanz rechts (WMR) und links (WML) untersucht (GE Signa Horizon 3T94; PRESS: TE 30ms, TR 6000ms, VOI 8ml). Die Messungen erfolgten vor, direkt nach Dehy und nach Rehy (180min, Zufuhr von 150\% der verlorenen Körpermasse (KM)). Zusätzlich wurde durch T2-Relaxationsmessungen der Atrophieindex alpha (Verhältnis cerebrales Gewebewasser (HW) zu Liquor (CSF)) bestimmt. Resultate: Die KM der Probanden reduzierte sich durch Dehy um 3.7 (3.4/4.1)% und stieg durch Rehy wieder um 4.5 (3.7/5.3)% an (Wilcoxon: p / Introduction: In the present study the influence of Dehy on cerebral volume regulatory metabolites (myo-Inositol (mI), N-Acetyl-aspartata+N-Acetyl-aspartyl-glutamate (tNAA), Creatine (Cr), Glycerophosphocholine+Phosphocholine (Cho) and Glutamate+Glutamine (Glx)) and fluid shifts has been investigated for the first time in humans. Methods: 14 cyclists (26.6 (22.7/29.8) y, median and 25./75. percentile) have been examined with proton NMR spectroscopy in the occipito-parietal gray matter (GM) and the right (WMR) and left (WML) parietal with matter (GE Signa Horizon 3T94; PRESS: TE 30ms, TR 6000ms, VOI 8ml). Spectra were acquired before, immediately after Dehy and after rehydration (Rehy). Rehy took place during 180min and 150% of lost body weight (BW) was substituted. Additionally the atrophy index alpha (ratio between cerebral water and liquor) was assessed (T2 signal decay as a function of echo time). Results: BW of volunteers has been decreased 3.7 (3.4/4.1)% after Dehy and increased 4.5 (3.7/5.3)% after Rehy (Wilcoxon: p