Dissertations / Theses: 'Biochemistry'

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Suttisansanee, Uthaiwan. "Biochemistry in Bacterioferritin." Thesis, University of Waterloo, 2006. http://hdl.handle.net/10012/2983.

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Bacterioferritin, an iron storage protein having a 24-subunit quaternary structure, was used as a model for the study of host-guest interactions and guest encapsulation, making use of its spherical cage-like structure. A hexahistidine-affinity tag fused to the C-terminus of each bacterioferritin subunit was constructed. The C-terminus of each subunit points toward the inside of the cavity, while the N-terminus is exposed on the surface of the protein. The hexaHistag was able to form strong interactions with a nickel-nitrilotriacetic acid linked dye molecule (guest) and this interaction was used in attempts to develop a principle to control guest molecule encapsulation within the spherical cavity of the 24-mer bacterioferritin protein molecule. The procedure involved (1) subunit dissociation under acidic pH, (2) affinity controlled dye-Histag binding with exposed C-terminal hexahistidine residues and (3) reassociation of the subunits at neutral pH. The encapsulation conditions involving step 1 and 3 were studied preliminarily using laser light scattering to measure size (hydrodynamic radius) of the protein particle with apoferritin as a model system as it resembles the size and structure of bacterioferritin. In order to encapsulate guest molecules, the emptied shell of bacterioferritin was generated by site-directed mutagenesis resulting in ferroxidase- as well as heme-free bacterioferritin mutants (E18A/M52L/E94A), and these mutants were used to examine protein stability before conducting encapsulation experiments. However, wild-type bacterioferritin possessed highest stability in maintaining its multisubunit structure; hence, it was used for the encapsulation studies. It was found that 100% bacterioferritin with hexahistidine tag at the C-terminus, and a combination of 60% bacterioferritin with hexahistidine tag at the C-terminus and 40% bacterioferritin without hexahistidine tag at the C-terminus yielded similar amounts of encapsulated guest molecules. This suggested that all hexahistidine at the C-terminus were not equally available for dye molecule binding.

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Hoh, Hon Bing. "Biochemistry of keratoconus." Thesis, University of Bristol, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.266879.

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Chen, Xiaoren. "Biochemistry of Prox1 function /." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file, 160 p, 2007. http://proquest.umi.com/pqdweb?did=1456284231&sid=8&Fmt=2&clientId=8331&RQT=309&VName=PQD.

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Rix, Louise Katharine. "Biochemistry of heart disease." Thesis, University of Oxford, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.334889.

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Chapman, A. "Biochemistry of Trichomonas vaginalis." Thesis, Bucks New University, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.373578.

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Lawrence, Fiona Jane. "The biochemistry of keratoconus." Thesis, University of Bristol, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.268784.

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Beacham, Tracey. "Biochemistry of transgenic wheats." Thesis, Cardiff University, 2006. http://orca.cf.ac.uk/55160/.

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This investigation uses transgenic wheat lines carrying the Pisum sativum glycerol 3-phosphate acyl transferase gene and /or the Arabidopsis thaliana acyl ACP thioesterase gene to determine their role of these genes in producing the altered metabolic and physiological traits seen in wild type plants grown under enhanced greenhouse conditions. We identified and analysed lines with insertions of the lipid metabolism genes. Plant lines bombarded with the same transgenes, showed a huge diversity in genotypes and demonstrated the haphazard nature of particle bombardment. Gene stability was observed following crossing of genetically modified lines and in all instances the transgenic material was found to be active in fourth generation plants. None of the transgenic lines showed the phenotype expected (increased growth and yield), but all showed aspects. This could indicate that more than these two genes are affected by the enhanced greenhouse effect, or that neither gene is in fact involved and the phenotypes observed are merely a happy coincidence. It is also possible that the full effect of gene up-regulation was not observed since only one of the lines observed showed ubiquitous expression of the transgenes and all showed some changes in expression of the native thioesterase gene. The lipid metabolism of plants from the four genetic groups (GPAT +, thioesterase+, Dual+ and Null) was analysed and, while alterations in lipid and fatty acid metabolism were observed in all transgenic lines, the differences were highly variable between plant lines of the same group, making an overall analysis of changes difficult. It was also found that the null lines showed as much variation in lipid metabolism as the transgenic lines indicating that chromosomal damage introduced into the plant lines during the original bombardment and tissue culturing process may have had a huge impact on the phenotype of the transgenic plants.

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Huang, Po-Ssu Rees Douglas C. "Biochemistry and molecular biophysics /." Diss., Pasadena, Calif. : California Institute of Technology, 2004. http://resolver.caltech.edu/CaltechETD:etd-06012004-214823.

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Woodhouse, Jennifer Ann. "Plutonium pharmacokinetics and blood biochemistry." Thesis, University of Central Lancashire, 1997. http://clok.uclan.ac.uk/20148/.

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Since its discovery in the early 1940s the element plutonium has been seen by mankind as both an opportunity and a threat. As a radioactive nuclide plutonium presents health hazards in its handling and if mankind is to make the most of this element's potential benefits it is essential that these hazards be understood. Both overestimation and underestimation of these hazards are damaging to its proper utilisation. Many studies have been carried out to determine the effects of plutonium exposure and a broad picture of the biological behaviour of plutonium has been built up. Radiological protection standards are based on such broad understanding and a "Central Dogma" has arisen viz, plutonium is bound avidly in liver and bone; clearance half-lives from these organs differ (by a factor of 2.5) but are very long - a minimum of 50 years for bone; this is why plutonium urinary excretion levels are very low. Despite all the research work that has been carried out there are many important areas of plutonium behaviour which are not well understood or in which the central ideas adopted for radiological protection purposes are questionable. One such questionable area is extended half-life in the body. Two rather different areas relate to the molecular binding interactions which plutonium enters into in body tissues and transfer mechanisms from blood into cellular organelles. Very little is known about these processes and the speciation that plutonium demonstrates within the body. This thesis explores understanding of plutonium behaviour by application of pharmacokinetic theory to observed human behaviour, both following occupational exposure and experimental injection. Occupational exposure data demonstrated behaviour consistent with pharmacokinetic expectations over periods of 25 years or more. Long-term half-lives were 10 to 30 years rather than 50 to 100 years or more. There was no evidence of differing half-lives between liver and bone. Very low renal clearance was seen in intravenous injection studies suggesting either very extensive plutonium binding to the protein transferrin in blood or pointing to reabsorption in the kidney tubule after glomerular filtration. This latter possibility might lead to a "Plutonium blood pressure" which effectively forces activity into tissues irrespective of the strength of binding forces. Experimental work indicated species differences in transferrin binding which may have relevance for extrapolation from animals to humans.

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Nasir-ud-Din. "Glycoconjugate biochemistry : structure-function relationship." Thesis, University of Edinburgh, 1996. http://hdl.handle.net/1842/27105.

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In this thesis studies on the following glycoconjugates are presented: bacterial, Micrococcus lysodeikticus, cell wall, simian cervical mucin, human pulmonary mucin, bovine gallbladder mucin, sperm surface glycoproteins and glycoconjugates of malarial parasite, Plasmodium falciparum. The information obtained on the structure of these complex carbohydrates utilising chemical, enzymatic, immunological and physical methods provided insight into the understanding, in particular, of structure-function relationship, degradation and biosynthesis of these macromolecules. Studies on model compounds and analytical methods, all of which are vitally important tools in the study of glycoconjugates, are also described. The carbohydrate prosthetic group of Micrococcus lysodeikticus cell wall was shown to consist of a glycan moiety linked to the protein and an antigenic polysaccharide attached to the glycan moiety of the peptidoglycan through a phosphodiester group. A variety of model compounds were synthesised to establish the structure of the carbohydrate moiety as well as to study the kinetics if the acid hydrolysis of the phosphodiester group linked to muramic acid and to the reducing terminus of glucose. The study was performed on Micrococcus lysodeikticus cell wall polymer resistant to lysozyme, elaborating the structural requirement for stability to the enzyme. Furthermore, a water soluble polymer from the Micrococcus lysodeikticus cell wall was isolated and characterised, a novel observation. The study on this polymer suggested the possible deficiencies in the biosynthesis or possible autolysis of the cell wall polymer. A large number of model compounds were chemically synthesised to identify the structural features of the cell wall peptidoglycans and those of the antigenic polysaccharide. In addition, several compounds were chemically synthesised to obtain the model compounds necessary to conduct kinetic studies to define the type of linkage, i.e. differentiate between the monophosphate or pyrophosphate, between the cell wall polysaccharide and peptidoglycan, more precisely the linkage between muramic acid 6-phosphate of the peptidoglycan and the reducing terminal residue, glucose, of the polysaccharide.

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Locklin, Rachel M. S. "Biochemistry of bone cell differentiation." Thesis, University of Oxford, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.363755.

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Davis, Jason John. "Fullerene biochemistry and surface investigations." Thesis, University of Oxford, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.244592.

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Parker, David Alan. "Metabonomic studies in nutritional biochemistry." Thesis, Imperial College London, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.500322.

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Wehrfitz, Josa-Marie. "The biochemistry of heterotrophic nitrification." Thesis, University of East Anglia, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.318038.

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Springer, Sebastian Hartmut. "The biochemistry of antigen presentation." Thesis, University of Oxford, 1996. http://ora.ox.ac.uk/objects/uuid:34d1afd2-fafc-4732-8e43-e00dcd8460d1.

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This thesis describes studies on the binding of peptides to the murine major histocompatibility complex (MHC) class I molecule H-2D^b (D^b). The expression of the recombinant soluble D^b molecule in Chinese hamster ovary cells and its subsequent purification by nickel affinity chromatography, gel filtration, and preparative native isoelectric focusing are reported. The product is the correct molecule, homogeneous, a dimer of dimers, and free of endogenous peptide. A novel binding assay based on the enhancement of natural tryptophan fluorescence by the binding of peptide is introduced. This assay is used to determine melting curves of the empty and peptide-loaded protein, and to measure association rate constants by stopped-flow fluorescence spectroscopy. Radioligand binding measurements of equilibrium as well as association and dissociation rate constants and their temperature dependence are reported. In agreement with earlier observations, the ratio of association and dissociation rate constants is much larger than the equilibrium association constant. Fluorescence anisotropy decay spectroscopy gives evidence for conformational alterations in the D^b molecule upon peptide binding. The data, possible errors and ways to avoid them, and mathematical models of binding are discussed to obtain an overall picture of the binding process.

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Vuillard, Laurent Michel Marie. "The biochemistry of connective tissue." Thesis, University of Edinburgh, 1989. http://hdl.handle.net/1842/19376.

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Yap, Ivan Kok-Seng. "Integrated metabonomic studies in liver biochemistry." Thesis, Imperial College London, 2005. http://hdl.handle.net/10044/1/8902.

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Song, Jina. "Coagulation factor V : pathology and biochemistry." Thesis, University of British Columbia, 2008. http://hdl.handle.net/2429/5595.

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ROLE OF GLU96, ASP1O2 AND ASP111 IN FACTOR V Coagulation factor V activity is unmasked by thrombin-mediated excision of the central B domain resulting in a noncovalent heterodimer, factor Va. To understand the role of individual amino acids in maintaining the Ca²⁺-depenadent subunit interaction, G1u96 (E96A), Asp1O2 (D1O2A) or Asp111 (D111A) were mutated because of known effects on chelator sensitivity. The primary clotting activity of each mutant was reduced by “40%. Demonstrating at least two distinct inhibition mechanisms, only D111A was further inhibited by thrombin pre-treatment consistent with spontaneous subunit dissociation and severely inhibited Ca²⁺ binding. The parental factor V construct used here has a truncated B domain that does not require excision for activity. Therefore inhibition of D111A by thrombin-cleavage reveals a new B domain function that maintains factor V in a factor Va-like configuration independent of Ca²⁺ binding. In addition to Ca²⁺, factor V binds Cu²⁺, but with unknown function. Unexpectedly, D111A also lost detectable Cu²⁺. Finding that a single amino acid substitution simultaneously alters Ca²⁺ and Cu²⁺ suggests an interdependent metal ion binding site. Unlike D111A, the thrombin-mediated factor Va derived from E96A and D1O2A was stable, had only moderately faster subunit dissociation upon chelation and had normal metal ion binding. Thus, the current study defines the highly conserved acidic segment spanning G1u96-Asp112 in factor V as multifunctional. Of the three amino acids I evaluated, Asp111 is essential and likely functions through direct and indirect metal ion interactions. G1u96 and Asp102 individually influence factor V/Va function by more subtle effects at the metal ion-dependent subunit interface. FACTOR V-DEFICIENT PATIENT A factor V-deficient patient due to Y1702C mutation has been studied. The patient however did not suffer from severe bleeding despite of undetectable levels of plasma and platelet factor V. A close inspection of the patient’s blood coagulation cascade showed that the lack of available factor V was compensated by other factors that influence the intrinsic pathway. This finding suggests that the commonly observed phenotypic differences shown among factor V-deficient patients with the same genotypes may be due to existing hypercoagulant factors that influence the outcome of the disease.

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Nabbs, Brent Kenneth. "The chemistry and biochemistry of hydroxymethylpyrroles." Thesis, University of Canterbury. Chemistry, 1999. http://hdl.handle.net/10092/7302.

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This thesis examines the chemistry and biochemistry of hydroxyrnethylpyrroles of the type 1.9 (X = OH). Pyrrolic compounds play an important role in many areas of chemistry and biology. A large number of biomolecules which are essential for life are derived from simple pyrrole precursors, eg porphyrins and haemoglobin. In addition, pyrroles have been utilised as building blocks and key intermediates in synthesis. Chapter One gives a general introduction to the biological, chemical and medical applications of pyrroles, such as in the biosynthesis of uroporphyrinogen III 1.20, their use as intermediates in organic synthesis, and in the development of latent mechanism-based inhibitors of serine proteases. Chapter Two describes a sequence, based on a Mitsunobu displacement at the hydroxymethyl position of the chiral deuterium-labelled N-substituted hydroxymethylpyrroles 2.26a-d and 2.27a-d, as a means by which to determine the deactivating abilities of various N-substituents on the pyrrole ring. In this reaction, an SN2 mechanism was found to be favoured over reaction via an azafulvenium intermediate 2.20 by employing N-trifluoromethanesulfonyl as the deactivating group. Suppression of this azafulvenium reaction pathway was found to be less effective with other deactivating groups, and the order for deactivation was determined to be triflyl > mesyl > BOC ≈ acetyl. Chapter Three describes the development of a short, convenient and versatile synthetic route to dipyrromethanes which involves coupling of an N-magnesio pyrrole salt (derived from either an oxygen acetal or a thioacetal of pyrrole-2-carboxaldehyde) with a ring-deactivated chloromethylpyrrole. This methodology was extended to the preparation of dipyrromethanes containing a deuterium-label at the interpyrrolic methylene position. An X-ray crystal structure of the N-tosyl chloromethylpyrrole 3.29 showed that the aromaticity of the pyrrole ring was significantly reduced by the introduction of the electron withdrawing group onto the pyrrole nitrogen. Chapter Four describes a ¹H NMR investigation into the mechanism of hydrolysis of N-acylhydroxymethylpyrroles. In this study, the chiral deuterium-labelled N-(Nphthalyl- L-Ieucinyl)hydroxymethylpyrroles 4.8b and 4.8c in CD₃CN were treated with potassium hydroxide in the presence of an equivalent of S-(+)-sec-butylamine. ¹H NMR spectral analysis showed that the hydrolysis proceeds by an initial intramolecular N- to O-acyl transfer with retention of configuration at the labelled centre. Evidence for the subsequent release of an azafulvene 4.3 was gained from the observed scrambling of the deuterium-label at the exo-methylene position of 4.11 and 4.12 on trapping with an external nucleophile, either S-(+)-sec-butylamine or 4.11, respectively. Chapter Five describes the application of N-substituted hydroxymethylpyrroles as mechanism-based inhibitors of serine proteases. As a result, a number of alternate methodologies to incorporate the hydroxymethylpyrrole-moiety into an extended peptide-like sequence were attempted. From these synthetic approaches the pyrrole-based peptidomimetics 5.8a, 5.8b, 5.9a, 5.9b and 5.10b were prepared and subsequently assayed for α-chymotrypsin inhibition activity. These compounds were found to be modest inhibitors of α-chymotrypsin, with none proving to be better inhibitors than previously discussed examples. Chapter Six details the isolation and properties of some unexpected pyrrole-based molecules that were obtained from the attempted N-acylation of the 5-formylpyrrole-2- carboxamides 5.47a-c. Attempts to N-acylate 5.47a-c with hydrocinnamoyl chloride using the DMAP methodology gave the pyrrolizin-3-ones 6.1a-c. These compounds were identified on the basis of one and two dimensional NMR spectral techniques. Conformation of the structure of the pyrrolizin-3-one 6.1a was obtained by a single crystal X-ray analysis. Attempts to N-acylate 5.47a-c with an acid chloride using the sodium hydride methodology gave the azafulvene dimers 6.6a-c. Single crystal X-ray analysis of 6.6b and 6.6c revealed that each of these dimers were only a single diastereomer, and were further dimerised by non-covalent interactions. Spectroscopic evidence is discussed which indicates that the non-covalent dimeric structure was also present in solution. We suggest that the diastereoselective synthesis of 6.6b and 6.6c was controlled by this ability to form the non-covalent dimers, and so represents an example of molecular self-assembly. Chapter Seven describes a general synthesis of 5-acylpyrrole-2-carboxaldehydes which utilises a Stille coupling reaction between a stannylpyrrole and a (fatty) acid chloride. This methodology was used to prepare a series of 5-acyl-2-hydroxymethylpyrroles, including the previously reported natural product mycalazol 11 7.11. These compounds, together with a 5-carboxamido-2-hydroxymethylpyrrole, were assayed for in vitro cytotoxicity against the P388 cell line. From this assay we have found that an increased chain length leads to greater biological activity, and that an acyl side chain has greater activity relative to a carboxamido side chain.

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Lone, Anna Mari. "The Biochemistry and Physiology of Peptidases." Thesis, Harvard University, 2012. http://dissertations.umi.com/gsas.harvard:10693.

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Peptidases regulate important physiological processes by controlling levels of bioactive peptides and occasionally through noncatalytic processes. This thesis presents a study of prolyl endopeptidase-like (PREPL), which is a peptidase involved in several human deletion syndromes, including hypotonia-cystinuria syndrome (HCS). Phenotypes tentatively attributed to PREPL deletion include hypotonia and decreased growth hormone (GH) levels. However, little is known about the mechanisms by which PREPL deletion causes these phenotypes. To better understand PREPL catalytic activity, we used an activity-based protein profiling fluorescence polarization screen to identify the first specific PREPL inhibitors. We proceeded to demonstrate the activity of these inhibitors in cells and discovered several classes of cell-active PREPL inhibitors. Further, one of these inhibitors, 1-isobutyl-3-oxo-3,5,6,7-tetrahydro-2H-cyclopenta[c]pyridine-4-carbonitrile, was able to enter mouse brains. To characterize PREPL substrate specificity, we performed several substrate profiling experiments, but no substrates could be identified, in line with reports from other groups who used related approaches to attempt to identify PREPL substrates. To characterize any noncatalytic functions of PREPL, we used an affinity purification-mass spectrometry approach (AP-MS) to search for any protein-protein interactions of PREPL. We identified brain-expressed X-linked 2 (BEX2) as a novel interactor of PREPL, and confirmed this interaction by immunoblot. Several other proteins identified in the AP-MS experiment, including several members of the STRIPAK complex are being further investigated for possible PREPL interaction. To determine whether HCS phenotypes are in fact due to PREPL deletion and to delineate the molecular pathways involved, we generated a conditional PREPL knockout mouse. These mice were visibly smaller than wildtypes and growth curve analysis verified that from week three of life, there was a significant difference in weight between wildtype and knockout mice. Initial surface righting task experiments also indicate that PREPL knockout pups may have a hypotonia phenotype. In summary, we have developed several new tools for studying PREPL catalytic and noncatalytic function, demonstrated that PREPL deletion causes a GH-related growth deficiency and possible hypotonia and thus moved several steps closer to understanding the molecular mechanisms underlying PREPL deletion phenotypes.
Chemistry and Chemical Biology

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Jordan, Peter A. "Physico-chemical studies of aluminium biochemistry." Thesis, University of East Anglia, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.294654.

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Bailey, A. C. "Biochemistry and pharmacology of beta-bungarotoxin." Thesis, University of Essex, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.372585.

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Foster, S. J. "Biochemistry of Bacillus megaterium spore germination." Thesis, University of Cambridge, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.384466.

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Duvold, Tore. "Chemistry and biochemistry of bacterial isoprenoids." Université Louis Pasteur (Strasbourg) (1971-2008), 1997. http://www.theses.fr/1997STR13195.

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Il etait unanimement accepte que la biosynthese des isoprenoides passait par le mevalonate. Des etudes recentes ont revele l'existence d'une voie alternative independante du mevalonate passante par le glyceraldehyde 3-phosphate (gap) et la pyruvate via une condensation et un rearrangement. Nous avons etudie le role du 2-c-methyleerythritol comme precurseur dans cette voie. En effet, des incorporations de glucose marque au #1#3c ont montre que chez corynebacterium ammoniagenes les squelettes du methylerythritol et des unites isopreniques etait formes de la meme facon. L'incorporation de #2h-2-c-methyl-d-erythritol dans les isoprenoides d'escherichia coli a confirme le role de ce polyol ramifie comme precurseur de l'ipp. La bacterie zymomonas mobilis produit des hopanoides complexes. La conservation des deux atomes de deuterium sur le carbone c-31 apres incorporation du 6,6-#2h#2glucose indique qu'une reaction de substitution permet l'insertion de la chaine laterale en c#5. Les marquages de la squelette hopane a confirme l'intervention de la voie gap/pyruvate. Nous avons developpe une hemisynthese du ribosylhopane qui donne acces a des hopanoides qui pourrait etre des precurseurs des bacteriohopanepolyols ou des hopanoides avec des activites biologiques interessantes. Nous avons synthetise un analogue du bacteriohopanetetrol en serie sterane avec une chaine laterale c#5 polyhydroxylee lie au carbone c-3 en utilisant une strategie synthetique similaire a celle utilisee pour l'obtention du ribosylhopane. Cet analogue a ete propose comme precurseur biologique des 3-alkylsteranes et des 3-carboxyalkylsteranes, abondants dans les sediments et serait a rechercher dans des microorganismes.

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Pearce, Nicholas David. "An investigation of biochemistry higher education as a process of socialisation into the culture of the biochemistry community." Thesis, King's College London (University of London), 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.396269.

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Engström, Gunnar. "Temperamental diagnostics and biochemistry in suicide attempters." Lund : Dept. of Clinical Neuroscience, Division of Psychiatry, University Hospital, 1997. http://books.google.com/books?id=y9lrAAAAMAAJ.

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Messier, Marc D. "The chemistry and biochemistry of aromatase inhibitors." Thesis, University of Ottawa (Canada), 1993. http://hdl.handle.net/10393/6735.

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Aromatase is the last enzyme in estrogenesis, and as such is of central importance in estrogen metabolic and reproductive processes. Four central postulates of aromatase active site topology were elaborated: 1. The C-19 cavity postulate predicted that a cavity exists in aromatase. Steroids synthesized to investigate this postulate have confirmed that a 6A deep pocket exists to accommodate C-19 androgen derivatives. 2. The C-3 chelation postulate suggested that chelating groups at the C-3 position might constitute a new generation of aromatase inhibitors and cause aromatase inactivation. Steroidal derivatives with C-3 ethylenedioxy and C-3 thioketal groups have shown this approach to be invalid. 3. The C-5 nucleophile postulate led to investigate the mechanism of action of known C-4, C-5 and C-6 pharmacophores via C-4,5 and C-5,6 androgen epoxides. No inactivation of the enzyme was reported in the presence of these epoxy-steroids, thus weakening contemporary aromatase mechanistic theory involving mechanisms relying on an incoming C-4 nucleophile. Topological analysis and computer simulations of known pharmacophoric patterns led to the biochemical investigations of over 80 steroidal test compounds, many exhibiting potent competitive and some inactivating kinetic profiles. The synthesis of hitherto unreported androgen derivatives was described. 4. Bioorganic simulations of the aromatase mechanism have led to a novel approach to the aromatase mechanism of action. These approaches are based on altered A-ring reactivity via thioketal or hemi-thioketal enzyme intermediates. The chemistry of postulated active site generated analogues was investigated and the resulting rearrangement products lend credence to mechanisms requiring altered reactivities during aromatase oxidations.

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Abebe, Adal T. "Biochemistry of 1,2-dehydro-n-acetyldopamine derivatives." Thesis, University of Massachusetts Boston, 2013. http://pqdtopen.proquest.com/#viewpdf?dispub=3564657.

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Dehydrodopa/dopamine derivatives form an important group of biomolecules participating in sclerotization of all arthropod cuticles, gluing and cementing mussels and related organisms to solid surfaces, and defense reactions of countless marine and invertebrate organisms. Yet very little information is available on the biochemistry of these highly reactive and unstable molecules. To understand their physiological role, I conducted a thorough biochemical study on three representative compounds that cover the entire plethora of dehydrodopa/dopamine derivatives. Employing diode array UV-visible spectroscopy, HPLC, liquid chromatography-mass spectrometry, and electrospray ionization tandem mass spectrometry, I investigated the oxidation chemistry of 1,2-dehydro-N-acetyldopamine (dehydro NADA), 1,2-dehydro-N-acetyldopa and 1,2-dehydro-N-acetyldopa methyl ester. Tyrosinase converted dehydro NADA to a reactive quinone methide that formed oligomeric products with the parent compound. The sister enzyme laccase, produced semiquinone radicals that exhibited a novel coupling reaction producing just dimers. Nonenzymatic oxidation of dehydro NADA also produced semiquinone radicals that formed oligomeric products. Moreover, nonenzymatic oxidation resulted in the production of superoxide anions that could function in defense reactions. The nonenzymatic oxidation studies on dehydro NADA at mild alkaline conditions revealed the mechanisms of defense reactions and tunic formation in a vast array of tunicates. Oxidative transformations of 1,2-dehydro-N-acetyldopa indicated a new route for the biosynthesis of a vast array of bioactive marine molecules possessing dihydroxycoumarin skeleton. In addition, it revealed new transformations of coumarins to oligomeric products via highly reactive quinone methide intermediates. Biochemical studies on 1,2-dehydro-N-acetyldopa methyl ester revealed a new Diels Alder type condensation of its quinone with the parent compound. This reaction shed light on the mode of gluing of mussels and other bivalves to solid surfaces as well as the hardening reactions occurring in their periostracum. I also examined the oxidation chemistry of dehydro NADA with a model nucleophile, N-acetylcysteine and discovered yet another new addition reaction of dehydro NADA that has tremendous biological significance. Finally, I investigated the mechanism of dehydro NADA binding to insect cuticle using labeled compounds and established that they could uniquely produce ketocatecholic compound, arterenone upon hydrolysis. The biochemical significances of all these new reactions are discussed in the dissertation.

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Partington, Joanna Clair. "Biochemistry and molecular biology of potato bruising." Thesis, Royal Holloway, University of London, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.265182.

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Baverstock, Jenny. "Biochemistry of visual transduction in squid photoreceptors." Thesis, University of Oxford, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.302983.

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Langmack, Keith Antony. "Structure and biochemistry of squid photoreceptor microvilli." Thesis, University of Oxford, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.253282.

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Channell, Guy Andrew. "Oxidative flavour chemistry and biochemistry in parsley." Thesis, University of Nottingham, 1996. http://eprints.nottingham.ac.uk/13970/.

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Deterioration of flavour quality during processing and storage is often brought about by oxidative processes. These typically involve oxygen or an active form of oxygen in effecting transformation of a wide range of volatile and non-volatile compounds, including key quality chemicals, flavour precursors and antioxidants. To investigate the nature of the chemical and biochemical change within vegetables and herbs, unblanched frozen parsley was selected as a suitable tissue. The chemical status of parsley during technological processing was determined using novel analytical protocols (SNCV A/SNCNV A) implemented as part of a unified strategy for the quantitative analysis of volatile and non-volatile species. The analysis utilized a single stabilized solution produced from plant tissue, under a regime which minimized isolation stress and artifact formation. On frozen storage (-10OC) the principal volatiles of parsley, myrcene, beta-phellandrene and menthatriene were extensively degraded to non-volatile products at differential rates. p-Cymenene and the tentatively assigned menthatriene diepoxide were formed as minor volatile oxidation products. Myristicin remained largely unchanged. Under similar frozen storage, chlorophyll 'a' displayed significant degradation with only minor amounts of chlorophyllide 'a', pheophytin 'a' and 13[superscript]2 hydroxychlorophyll 'a' formed. Ascorbic acid was extensively degraded in timescales preceding monoterpene and chlorophyll loss. Thermal blanching of parsley extensively prevented the degradation of the monoterpenes, suggesting that endogenous enzymes were responsible for the changes. Elimination of oxygen, in the absence of blanching, prevented volatile loss, confirming the requirement for oxygen. The hypothesis that peroxidase can operate in a co oxidative couple with the flavonoid, apigenin-7-glucoside and hydrogen peroxide, as proposed by Yamauchi (1985), was investigated to establish its potential role in the degradation of terpenoids and chlorophyll. In model experiments, using horseradish peroxidase, menthatriene and chlorophyll showed extensive degradation only when all components of the couple were present. In addition the requirement for oxygen was also established. Naringenin and umbelliferone have been shown to behave similarly to apigenin, as co-substrates for peroxidase. Lycopene, with some structural similarity to menthatriene, was also susceptible to co-oxidation. Polyphenol oxidase, proposed to operate in a similar fashion to peroxidase with mono- and di-phenols as substrates (Montedoro et al. 1995), in model experiments did not cause the degradation of chlorophyll. The co-oxidative role of lipoxygenase in parsley is believed to be of minor significance, however, it is likely to be responsible for the production of low levels of hexanal observed during thawing of frozen parsley. From this thesis it is concluded that the aroma and colour quality loss in frozen unblanched parsley probably results from the oxidative degradation of the unsaturated monoterpenes and chlorophyll 'a' respectively via an oxidative cascade initiated by the action of peroxidase.

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33

Bhatia, Jeetendra. "Biochemistry of visual transduction in cuttlefish receptors." Thesis, Birkbeck (University of London), 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.271670.

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34

Brown, Andrew M. G. "Biochemistry, tissue culture and pharmacology of Tanacetum." Thesis, University of Nottingham, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.363563.

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35

Buckberry, Lorraine Dawn. "The biochemistry of mammalian C-S lyases." Thesis, University of Nottingham, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.276184.

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36

Shams, Saleema Bashir. "Some new micro analytical techniques in biochemistry." Thesis, University of Salford, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.245056.

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37

Law, Samantha P. "The microbial biochemistry of slow sand filters." Thesis, Robert Gordon University, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.270109.

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Partridge, Robert James. "The biochemistry of the bovine preimplantation embryo." Thesis, University of York, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.245866.

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39

Taylor, Stephen Murray. "Rheology and biochemistry of whey protein gels." Thesis, University of Cambridge, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.308255.

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40

Rastall, Robert A. "The cell surface biochemistry of Erwinia amylovora." Thesis, University of Greenwich, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.258366.

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41

McGeary, Sean E. (Sean Edward). "Understanding microRNA targeting with high-throughput biochemistry." Thesis, Massachusetts Institute of Technology, 2021. https://hdl.handle.net/1721.1/130661.

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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, February, 2021
Cataloged from the official PDF of thesis. Vita.
Includes bibliographical references.
MicroRNAs (miRNAs) are short RNAs that, in complex with Argonaute (AGO) proteins, guide repression of mRNA targets. miRNAs negatively regulate most mammalian mRNAs, and disruption of this regulation often results in severe defects at the cellular and organismal level. miRNA repression occurs primarily through base-pairing between the miRNA seed region (nucleotides 2-8) and mRNA 3'-UTR sites, leading to transient recruitment of mRNA-destabilizing factors. However, only a small fraction of the gene-expression changes caused by a miRNA can currently be predicted, which precludes a deeper understanding of how miRNA regulation impacts the animal transcriptome. miRNA targeting efficacy should in principle be a function of the affinity between AGO-miRNA complexes and their targets. However, only a few such measurements had been reported, with measured values differing from those predicted for RNA-RNA pairing in solution.
We therefore adapted a high-throughput biochemical platform utilizing random-sequence RNA libraries to obtain the vast quantity of affinity values required to predict miRNA targeting efficacy. Through a novel analytical approach, we assigned relative dissociation (K[subscript D]) constants to all binding sites We found unique 3'-pairing preferences for each miRNA, and evidence for two distinct binding modes. The miRNA-specific differences and two binding modes depended on G nucleotides in the miRNA 3' region, thus providing a heuristic by which to extend these findings to target prediction in vivo. This work establishes high-throughput biochemistry combined with mathematical modeling and deep learning as a powerful paradigm for building quantitative models of gene regulation, which might aid in eventually building a complete model of the cell.
by Sean E. McGeary.
Ph. D.
Ph.D. Massachusetts Institute of Technology, Department of Biology

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42

Darkwa, Alfred Anthony. "Growth and biochemistry of hardy European orchids." Thesis, University of Sussex, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.495011.

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43

Oikonomou, Eftychia. "Molecular biology and biochemistry of brain tumours." Thesis, Aston University, 2004. http://publications.aston.ac.uk/11021/.

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Elucidating some molecular mechanisms and biochemistry of brain tumours is an important step towards the development of adjuvant medical therapies. The present study concentrates on cholecystokinin (CCK), a gut-brain peptide that has been described to be able to induce mitosis of rat gliomas as well as hormone secretion by the anterior pituitary, via the CCK-B receptor. The significance of a polymorphism in the growth hormone releasing hormone (GHRH) receptor (GHRH-R) gene was also determined. Finally, defects in the b-catenin gene, an important component of the developmental pathway, in a sub-set of craniopharyngiomas were investigated. Reverse transcription-polymerase chain reaction (RT-PCR), restriction digestion analysis and direct sequencing demonstrated expression of CCK peptide itself and its A and B receptors by human gliomas, meningiomas and pituitary tumours. CCK peptides stimulated growth of cultured gliomas and meningiomas as well as in vitro hormone secretion [growth hormone (GH), luteinizing hormone (LH) and follicle stimulating hormone (FSH)] by human pituitary tumours. These biological effects were reduced or abolished by CCK antagonists. In addition, an antibody to CCK reduced mitosis by gliomas and meningiomas, and the same antibody inhibited hormone secretion by cultured human pituitary tumours. CCK peptides stimulated phosphatidylinositol (PI) hydrolysis, indicating coupling of the CCK receptors to phopsholipase C. Cyclic AMP was unaffected. In addition, caspase-3 activity was significantly and markedly increased, whilst proteasome activity was decreased. Taken together, these results may indicate an autocrine/paracrine role of CCK in the control of growth and/or functioning of gliomas, meningiomas and pituitary tumours. Further findings of this study, using PCR and direct sequencing, were the demonstration of an association between b-catenin gene alterations and craniopharyngiomas of the adamantinomatous type.

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44

Churchill, Thomas Allen Carleton University Dissertation Biology. "Metabolic biochemistry of freeze tolerance in vertebrates." Ottawa, 1992.

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45

Bunn, Tristan. "Prion protein biochemistry in Creutzfeldt-Jakob disease." Thesis, University of Edinburgh, 2003. http://hdl.handle.net/1842/23281.

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46

Jones, Colleen P. "Biochemistry of Selenium in Pariette Wetlands, Utah." DigitalCommons@USU, 2014. https://digitalcommons.usu.edu/etd/3303.

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The Pariette Wetlands was constructed to provide wildlife habitat in an arid environment. Elevated levels of selenium (Se) have been detected in water, soil, and biota. Selenium concentrations have ranged from below detection limit to four times the water quality criterium limit. Here we report on three interrelated research topics: 1) selenium mass balance and flux in water, 2) selenium accumulation, concentration and volatilization of water and plant tissues; and 3) selenium sorption by upland and wetlands soils. 1) Mass balance and mass water flux of selenium for the Pariette Wetlands were studied. A comparison of inlet and outlet Se fluxes was used to determine the mass of Se stored. Selenium concentrations were higher at the inlet (2.1-16.3 μg L-1) than at the outlet (2.0-14.0 μg L-1). The average amount of Se retention and/or loss was 75%. 2) Elevated levels of selenium (Se) in water, soil, and biota of the Pariette Wetlands, Utah. Twelve sample sites were selected to determine the spatial and temporal variation of Se accumulation, concentration and volatilization. At the inlet, concentrations of waterborne Se during low-flow period (winter) were significantly higher than concentrations during high-flow irrigation season (summer). Se concentrations in water at the outlet were lower during the high-flow period ranging from. In contrast, plant tissue Se concentration was lower at the inlet and higher at the outlet. Selenium volatilization results indicated that there were spatial and temporal differences among samples sites. 3) The physical and chemical properties were compared for two soils in the Pariette Draw of Utah. It appears that Se mobility is associated with the distribution of soluble salts. We surmise that soluble Se is regulated by the solubility of a sodium selenate sulfate coprecipitate.. Knowledge gained about the mass balance, storage of Se, and the associated biogeochemical processes in water, plants, and soils that contribute to the accumulation or loss of Se in the wetlands will be beneficial to future land management decisions to minimize the impact of Se exposure to wildlife.

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47

Carlsson, Jens. "Challenges in Computational Biochemistry: Solvation and Ligand Binding." Doctoral thesis, Uppsala University, Department of Cell and Molecular Biology, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8738.

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Accurate calculations of free energies for molecular association and solvation are important for the understanding of biochemical processes, and are useful in many pharmaceutical applications. In this thesis, molecular dynamics (MD) simulations are used to calculate thermodynamic properties for solvation and ligand binding.

The thermodynamic integration technique is used to calculate pK_a values for three aspartic acid residues in two different proteins. MD simulations are carried out in explicit and Generalized-Born continuum solvent. The calculated pK_a values are in qualitative agreement with experiment in both cases. A combination of MD simulations and a continuum electrostatics method is applied to examine pK_a shifts in wild-type and mutant epoxide hydrolase. The calculated pK_a values support a model that can explain some of the pH dependent properties of this enzyme.

Development of the linear interaction energy (LIE) method for calculating solvation and binding free energies is presented. A new model for estimating the electrostatic term in the LIE method is derived and is shown to reproduce experimental free energies of hydration. An LIE method based on a continuum solvent representation is also developed and it is shown to reproduce binding free energies for inhibitors of a malaria enzyme. The possibility of using a combination of docking, MD and the LIE method to predict binding affinities for large datasets of ligands is also investigated. Good agreement with experiment is found for a set of non-nucleoside inhibitors of HIV-1 reverse transcriptase.

Approaches for decomposing solvation and binding free energies into enthalpic and entropic components are also examined. Methods for calculating the translational and rotational binding entropies for a ligand are presented. The possibility to calculate ion hydration free energies and entropies for alkali metal ions by using rigorous free energy techniques is also investigated and the results agree well with experimental data.

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48

Thong, Kam-Wah. "Biochemistry of sulphur-containing amino acids in trichomonads." Thesis, University of Glasgow, 1986. http://theses.gla.ac.uk/1635/.

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49

Miller, S. Shea. "Oat beta-glucan: Biochemistry, structure and genetic variation." Thesis, University of Ottawa (Canada), 1992. http://hdl.handle.net/10393/7507.

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An enzymatic assay designed for measurement of $\beta$-glucan in barley was modified to allow measurement of total $\beta$-glucan content in oats by manipulating the grinding and incubation protocol. Using the modified enzymatic assay, the range of genetic and environmental variation of $\beta$-glucan content in Canadian domestic and breeder's lines of oats was assessed using several cultivars grown in 5 locations in eastern Canada in 3 growing seasons. Analysis of variance indicated that the predominant source of variation was genetic. A second assay using Flow Injection Analysis (FIA) to measure $\beta$-glucan was also evaluated. Although a high correlation was observed for the results of the two methods (r = 0.90), the results obtained using FIA tended to be somewhat lower than those obtained using the modified enzymatic assay: the enzymatic assay was judged to be more accurate for estimation of total $\beta$-glucan in oats. Nevertheless, because of its greater speed and simplicity, FIA would be a valuable screening tool for routine-applications. Using the enzymatic assay, $\beta$-glucan content was also measured in 18 primitive species of Avena to evaluate possible sources of germplasm for expanding the range of $\beta$-glucan content currently available in domestic cultivars. A comparison of $\beta$-glucan content with protein content, oil content and thousand kernel weight in domestic oats showed that these quality parameters are independent of $\beta$-glucan concentration in oats. Scanning microspectrofluorometry was used to map $\beta$-glucan distribution in single kernels of oats: differences were observed within single kernels, and also among kernels from different cultivars of oats. Microscopic examination suggests that the different distribution patterns are due to differences in cell wall thickness adjacent to the germ and around the periphery of the kernel, and also to differences in cell size and shape in the central endosperm. A high $\beta$-glucan (Marion) and a low $\beta$-glucan oat cultivar (OA516-2) were selected for isolation and preliminary characterization of the endosperm cell walls, which are the major source of $\beta$-glucan in the oat kernel. It was concluded that the differences in $\beta$-glucan content that were observed in whole groats were not due to differences in the composition of isolated endosperm cell walls, but to variation in cell size and cell wall thickness in different areas of the groats. (Abstract shortened by UMI.)

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50

Kelly, Ronan. "Biophysics and biochemistry of the pancreatic β-cell." Thesis, University of Oxford, 1989. https://ora.ox.ac.uk/objects/uuid:e815cdec-ad16-4271-84e8-4ec8aaac842e.

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The β-cells of the pancreatic islets of Langerhans are the endocrine cells which secrete the hypoglycaemic hormone insulin. The primary stimulus for insulin secretion is an increase in the plasma glucose concentration, although secretion can be modulated by a variety of hormones and neurotransmitters. The immediate signal for insulin release is calcium entry through the β-cell plasma membrane. Primary secretagogues are glucose and those other secretagogues capable of initiating insulin secretion (e.g. glyceraldehyde, leucine, 2- ketoisokaproate); secondary secretagogues are those which potentiate the effect of glucose but which cannot initiate insulin secretion in the absence of glucose (glucagon, ACh, Forskolin, phorbol esters). Both glucose and the various agents which modulate insulin secretion do so by altering the pattern of B-cell electrical activity, and hence Ca²⁺ influx. This thesis examines the ionic basis of B-cell electrical activity and the mechanism of its initiation by glucose.

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Dissertations / Theses on the topic 'Biochemistry'

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