Dissertations / Theses on the topic 'Amino acids – Analysis'
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Wong, Wai Cheong. "Electroanalysis of amino acids and dithocarbamates." HKBU Institutional Repository, 1994. http://repository.hkbu.edu.hk/etd_ra/40.
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Magnuson, David Stuart Keith. "Analysis of excitatory amino acid receptors in the rat spinal cord in vivo and in vitro." Thesis, University of British Columbia, 1988. http://hdl.handle.net/2429/29017.
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Several endogenous amino acids including L-glutamate and L-aspartate have potent excitatory effects in the central nervous system. They are thought to act as synaptic transmitters in many neural pathways including those in the spinal cord. Three distinct receptors have been described through which these excitatory amino acids exert their effects. These are referred to as quisqualate, kainate and N-methyl-D-aspartate (NMDA) receptors, after the exogenous excitants most specific for each. In addition, sub-types of the NMDA receptor have been proposed to account for differences observed in the actions of the endogenous excitant quinolinate (2,3-pyridine dicarboxylate) in various regions of the nervous system. The characterization of excitant amino acid receptors has been accomplished primarily using two or more potent antagonists which include D-(-)-2-amino-5-phosphonovalerate (APV), a specific NMDA antagonist, and kynurenate, a compound related to quinolinate which potently attenuates the actions of NMDA- and kainate-like excitants.
Structure-activity studies of amino acid receptors were undertaken using standard extracellular recording and iontophoretic techniques in the dorsal horn of the spinal cord in vivo, and compared with the neocortex of the rat. In addition, a spinal cord slice preparation was developed wherein dorso-ventral longitudinal slices were prepared from the lumbar enlargement of weanling rats (50 - 125 g). The slices were maintained in an "interface" tissue bath of novel design. Extracellular recording of several hours duration and up to 8 hours after slice preparation were routinely possible.
Conformationally restricted analogues of glutamate, aspartate and quinolinate were examined for agonist and antagonist actions in the rat spinal cord in vivo and in vitro. Compounds found to be excitants were compared directly with quisqualate, kainate, and NMDA for sensitivity to blockade by APV and kynurenate applied both iontophoretically and in the bathing medium; antagonist dose-response curves were constructed for the actions of APV and kynurenate against quisqualate, kainate, quinolinate and NMDA. The conformationally restricted compounds found to be antagonists were examined to determine their potency and specificity against excitations elicited by quisqualate, kainate, quinolinate and NMDA.
Although quinolinate is known to be NMDA-like in the hippocampus and cortex, when compared to quisqualate, kainate and NMDA in the spinal cord in vitro, it proved to be unique. A fourth receptor (the "QUIN" receptor) is proposed to account for its actions in the spinal cord.
Three of the isomers of 1-amino-1,3-cyclopentane dicarboxylate (ACPD), conformationally restricted analogues of glutamate, were potently blocked by APV and KYNA and were therefore classified as NMDA-like. The fourth, D-trans-ACPD. was indistinguishable from quinolinate in terms of both potency and sensitivity to antagonists. The (-) isomer of trans-1-amino-1,2-cyclopentane dicarboxylate proved to be an antagonist with greater potency against excitations elicited by quisqualate and kainate than those of NMDA. These findings are, in many ways, different from what has been observed in the hippocampal slice.
Several pyridine derivatives were examined; 2,5- and 2,6-pyridine dicarboxylate were weak excitants behaving like quisqualate in the presence of APV and kynurenate. No other pyridines were excitatory; however 2,4-pyridine dicarboxylate was observed to be a weak, non-specific antagonist similar in action to acridinate (an antagonist closely related to kynurenate). None of the pyridine derivatives, save quinolinate, are excitatory in the hippocampus.
Structural analysis of the active compounds tested, in consideration of previous studies, shows that three points of attachment (two carboxyl and one amino group) are necessary for activation of NMDA, quisqualate and quinolinate receptors in the spinal cord. The location of the distal or y-carboxyl group relative to the a ionic groups appears to be the primary factor determining the activity of a conforrnationally restricted compound. The absolute distance between the Y-carboxyl and α-carbon appears to play a secondary role in determining the action of a compound.Medicine, Faculty of
Graduate
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Liyanapatirana, Chamindu. "Microfluidic analysis of free amino acids from different fish species." Master's thesis, Mississippi State : Mississippi State University, 2008. http://library.msstate.edu/etd/show.asp?etd=etd-02032008-193849.
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Orwar, Owe. "Laser-based ultra-trace analysis in liquid chromatography determination of neuroactive amino acids and peptides /." Göteborg : Dept. of Analytical and Marine Chemistry, University of Göteborg, 1994. http://catalog.hathitrust.org/api/volumes/oclc/39775021.html.
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Law, Gim Hoong Erica. "Mutational analysis of solvent-exposed amino acids in Photinus pyralis luciferase." Thesis, University of Cambridge, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.615816.
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Pirogova, Elena 1968. "Examination of physicochemical properties of amino acids within the resonant recognition model." Monash University, Dept. of Electrical and Computer Systems Engineering, 2001. http://arrow.monash.edu.au/hdl/1959.1/8424.
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Lao, Hongbai. "A study of the synthesis and properties of some long chain fatty acid esters containing azido, amino, amido and amino acid residues and the analysis of some seed oils used in Chinese medicine /." [Hong Kong : University of Hong Kong], 1989. http://sunzi.lib.hku.hk/hkuto/record.jsp?B12437141.
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Delaere, Ian. "The chemistry of Vivia sativa L. selection." Title page, contents and abstract only, 1996. http://web4.library.adelaide.edu.au/theses/09PH/09phd332.pdf.
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Bibliography: leaves 151-166. This thesis describes the development of two novel and complementary analytical approaches for assaying cyanoalanine non-protein amino acids. These assays are used to determine the distribution of these compounds both within and between plants and to identify accessions of common vetch which contain low levels of the cyanoalanine non-protein amino acids in germplasm collections. These analytical tools are used to correlate toxicity observed in animal feeding experiments with the cyanoalanine content. This thesis covers also the first report of the use of diffuse reflectance using dispersive infrared spectrometry for the "in situ" quantification of specific organic components from plant tissue as well as the first use of micellar electrokinetic chromatography for the quantitative analysis of 9-fluorenylmethyl chloroformate (FMOC) derivatised and non-derivatised components of extracts from plant material.
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Lee, Johnny Chien-Yi Biotechnology & Biomolecular Sciences Faculty of Science UNSW. "Transcriptional and metabolic responses of yeast Saccharomyces cerevisiae to the addition of L-serine." Publisher:University of New South Wales. Biotechnology & Biomolecular Sciences, 2008. http://handle.unsw.edu.au/1959.4/41012.
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Sudden changes in nutrient resources are common in the natural environment. Cells are able to adapt and propagate under changing environmental conditions by making adjustments in their cellular processes. These cellular adaptations involve genome-wide transcriptional reprogramming that results in the induction or repression of metabolic pathways. Specific enzymes are then synthesised and activated to maximise the use of the newly available nutrient sources. L-serine is one of the twenty proteinogenic amino acids, and can be synthesised in yeast by the glycolytic and gluconeogenic pathways when growing on fermentable or non-fermentable carbon sources or taken up from the environment when available. L-serine is metabolically linked to glycine and is a predominant donor of one-carbon units in one-carbon metabolism. L-serine is also a source of pyruvate and ammonia and contributes to other cellular processes including the biosynthesis of cysteine and phospholipids. Previous work has shown that yeast cells exhibit transcriptional induction of the one-carbon pathway and the genes involved in the synthesis of purine and methionine after the addition of 10 mM glycine. Here it is shown that addition of 10 mM L-serine did not, however, elicit the same transcriptional response. This is primarily due to differences in the uptake of glycine and L-serine in yeast. High concentrations of extracellular L-serine were required for yeast to show an increase in intracellular L-serine concentration of the magnitude required to trigger a noticeable cellular response. Despite L-serine and glycine being interconvertable via the SHMT isozymes and being a one-carbon donor, the genome-wide transcriptional response exhibited by cells in response to L-serine addition was markedly different to that seen for glycine. The predominant response to an increase in intracellular L-serine was the induction of the general amino acid control system and the CHA1 gene encoding the serine (threonine) dehydratase. Unlike glycine, addition of L-serine triggered only minor induction of the one-carbon pathway. A large portion of intracellular L-serine was converted to pyruvate and ammonia in the mitochondrion as the result of induction of CHA1. The high intracellular concentration of L-serine stimulated the cell to increase the production of oxaloacetate and to increase the biosynthesis of L-aspartate. Transient increases in the intracellular L-glutamate and L-glutamine were also observed after the addition of L-serine. The work presented in this study shows that large increase in the intracellular concentration of amino acid is required to trigger a significant transcriptional response. Yeast cells exhibit different transcriptional and metabolic responses to the addition of L-serine and glycine even though these two amino acids are closely metabolically linked. Addition of L-serine provokes the GAAC response, expression of the CHA1 gene and stimulates the biosynthesis of L-aspartate in yeast whereas addition of glycine induces the one-carbon pathway which leads to the biosynthesis of the purine nucleotides.
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Dale, Ryan K. "Temperature and the biological response a multivariate statistical analysis of the variation in genomic organization, oligopeptide frequencies, and environmental temperature /." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file, 235 p, 2009. http://proquest.umi.com/pqdweb?did=1654488371&sid=7&Fmt=2&clientId=8331&RQT=309&VName=PQD.
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Wielemans, Kevin. "Amino acid signalling in yeast: functional analysis of the Stp transcription factors." Doctoral thesis, Universite Libre de Bruxelles, 2010. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/210040.
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The whole genome duplication (WGD) event is an intriguing mechanism from an evolutionary perspective. Such an event may be the source of new genes, functions or species. Traces of WGD event have been detected in the genome of all four eukaryotic kingdoms: plants, animals, fungi and protists. In fungi, an ancestor of Saccharomyces cerevisiae underwent an event of WGD, about 100 million years ago, after diverging from the Kluyveromyces lineage. In S. cerevisiae, only ten percent of the resulting duplicated genes survived as duplicates. In particular, some of these duplicates encodes for transcription factors in several nutrient sensing pathways. The main subject of this thesis’s work is the external amino acid sensing system in S. cerevisiae. The detection of extracellular amino acids in yeast begins with a transporter homologue devoid of any uptake activity, the Ssy1 sensor. The binding of extracellular amino acids to Ssy1 leads to the successive activation of Ptr3 and the Ssy5 endoprotease. This endoporotease catalyses the processing of two transcriptions factors: Stp1 and Stp2. The Stp factors, released from their N-terminal cytoplasmic-anchored domains, are then translocated into the nucleus, where they activate the transcription of several amino acid permease genes (e.g. AGP1 and DIP5). Starting this work, the Stp factors were considered as functionally redundant.
We first determined that the STP1 and STP2 genes derivate from the event of WGD. The conservation of these two genes in S. cerevisiae was accompanied by a functional divergence of their products at several levels: processing sensibility, transcriptional activation capacity, target genes, cellular abundance level and stability. The Stp2 factor with its high abundance in the cells and its higher Ssy5-processing sensibility is specialized towards induction of the AGP1 gene when the external amino acid signaling is weakly stimulated. Under strong stimulation conditions, the amino acids induce cleavage-triggered destabilization of Stp2 through the proteasomal pathway and the induction of AGP1 is mediated mainly by the Stp1 transcription factor. Unlike Stp2, the Stp1 factor is characterized by its high transcriptional activation capacity and weaker sensitivity towards Ssy5-processing. The Stp factors differ also by their genetic targets. Indeed, only Stp2 regulates the expression of DIP5. Finally, we determined that the processing sensibility and the transcriptional activation capacity of each Stp factors is directly linked to their N- and C-terminal domains, respectively.
The phosphorylation states and the degradation of the Stp2 factor were also examined. The event of degradation concerns only the processed forms of this factor and takes places principally in the nucleus. Some data indicate that such an event might be important to limit the activation capacity of this factor. The role of the Stp2 phosphorylation in the external amino acid signaling pathway is still unknown but this event might be important for the Stp2 degradation or its transcriptional activity.
The unique Stp factor from Kluyveromyces lactis (Kl-Stp), a pre-WGD species, was also studied. The Kl-Stp factor shares at least two characteristic with the S. cerevisiae Stp2 factor: high sensibility towards processing and high levels of degradation. This observation leads us to conclude to that the STP genes may have been conserved after WGD though a mechanism called neofunctionalization (one of the duplicate obtained after duplication retains the ancestral function while the other evolves to perform a novel function).
Finally, a new model for the external amino acid signaling pathway that brings together all the data obtained during this thesis’s work is proposed.
Doctorat en Sciences
info:eu-repo/semantics/nonPublished
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Cao, Ping. "Mass spectrometric analysis of amino acids, peptides, and proteins in complex biological mixtures /." Digital version accessible at:, 1998. http://wwwlib.umi.com/cr/utexas/main.
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Meissner, Peter Nicholas. "Enzyme studies in variegate porphyria." Thesis, University of Cape Town, 1990. http://hdl.handle.net/11427/25672.
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Price, Michelle B. "Functional Analysis of Plant Glutamate Receptors." Diss., Virginia Tech, 2013. http://hdl.handle.net/10919/51946.
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The plant glutamate receptors (GLRs) are homologs of mammalian ionotropic glutamate receptors (iGluRs) and are hypothesized to be potential amino acid sensors in plants. Since their first discovery in 1998, the members of plant GLRs have been implicated in diverse processes such as C/N ratio sensing, root formation, pollen germination and plant-pathogen interaction. However, the exact properties of these channels, such as the spectrum of ligands, ion specificities, and subunit compositions are still not well understood.
It is well established that animal iGluRs form homo- or hetero-tetramers in order to form ligand-gated cation channels. The first aspect of this research was to determine if plant GLRs likewise require different subunits to form functional channels. A modified yeast-2-hybrid system approach was initially taken and applied to 14 of the 20 AtGLRs to identify a number of candidate interactors in yeast. Forster resonance energy transfer (FRET), which measures the transfer of energy between interacting molecules, was performed in mammalian cells to confirm interaction between a few of those candidates. Interestingly, despite an abundance of overlapping co-localization between heteromeric combinations, only homomeric interactions were identified between GLRs 1.1 and 3.4 in HEK293 cells.
Further, amino acids have been implicated in signaling between plants and microbes, but the mechanisms for amino acid perception in defense responses are far from being understood. Recently it was demonstrated that calcium responses initiated by bacterial and fungal microbe-associated molecular patterns (MAMPs) were diminished in seedlings treated with known agonists and antagonists of mammalian iGluRs, suggesting potential roles of GLRs in pathogen responses. Analysis of publicly available microarray data shows altered gene expression of a sub-fraction of GLRs in response to pathogen infection and bacterial elicitors. Thus, the second goal of my PhD research was aimed at determining whether GLRs are involved in the interaction between plants and pathogens. Gene expression changes of a number of candidate GLRs as well as pathogen growth was examined in response to the plant pathogen Pseudomonas syringae pv. tomato DC3000. Interestingly, single gene and multi-gene deficient plants responded differently with regards to pathogen susceptibility, likely as a result of functional compensation between GLRs.Ph. D.
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El, Naggar Ossama. "Approaches to the syntheses of c-substituted-a-amino-c lactones." Thesis, McGill University, 1986. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=65948.
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Du, Fuying, and 杜富滢. "Microchip-capillary electrophoresis devices with dual-electrode detectors for determination of polyphenols, amino acids andmetabolites in wine and biofluids." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2012. http://hub.hku.hk/bib/B48521693.
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The electrochemical detector provides a promising detection mode for capillary electrophoresis (CE) due to its excellent sensitivity, good portability, high selectivity, easy miniaturization, low capital and running cost. To widen its scope for determining trace analytes in complex samples, three dual-electrode detectors were fabricated to enable the determination of electro-inactive analytes, to assess co-eluted peaks and to give a large enhancement of the detection sensitivity by modifying electrode surface using multi-walled carbon nanotubes (MWNTs).
To determine trace non-electroactive amino acids present in human tears, a serial dual-electrode detector was developed using an upstream on-capillary Pt film electrode to oxidize bromide to bromine at +1.0 V and a downstream Pt disk electrode to detect the residual bromine at +0.2 V after their reaction with amino acids eluted out from the separation capillary. The bromide reagent was introduced after CE separation by a newly designed coaxial post-column reactor fabricated onto the PMMA chip. Using optimized CE buffer containing 20 mM borate, 20 mM SDS at pH 9.8, L-glutamine, L-alanine and taurine were baseline separated with detection limits ranging from 0.56-0.65 μM and a working range of 2-200 μM for L-glutamine and of 2-300 μM for both L-alanine and taurine. Method reliability was established by close to 100% recoveries for spiked amino acids and good agreement between the measured and the literature reported amino acid concentrations in tears.
For the determination of polyphenols in wine, a microchip-CE device was fabricated with a dual-opposite carbon fiber microelectrode operated in a parallel mode to assess peak purity. Under optimized conditions, (+)-catechin, trans-resveratrol, quercetin, (-)-epicatechin and gallic acid were baseline separated within 16 min with detection limits ranging from 0.031- 0.21 mg/L and repeatability of 2.0-3.3 % (n=5). The use of an opposite dual-electrode enables the simultaneous determination of peaks and measurement of their current ratios at +0.8 V and +1.0 V vs Ag/AgCl. The capability of using current ratio to identify the presence of co-migrating impurities was demonstrated in a mixed standard solution with overlapping (+)-catechin and (-)-epicatechin peaks and in a commercial red wine with interfering impurities. Matching of both the migration time and the current ratio reduce false positive and validate polyphenol quantitation in red wine.
Lastly, a dual-opposite MWNTs modified carbon fiber microelectrode (CFME) was developed to determine the biomarkers (4-nitrophenol, 4-nitrophenyl-glucuronide and 4-nitrophenyl-sulfate) needed to assess exposure to methyl parathion. Use of the MWNTs modified CFME showed a much higher sensitivity than bare CFME, with a detection limit of 0.46 μM for 4-nitrophenol. Baseline separation of all three biomarkers was obtained within 31 min by a 45 cm long capillary under 12 kV in a 20 mM phosphate buffer at pH 7.0. The method developed was successfully utilized to determine low levels of biomarkers in human urine without using complex pretreatment steps and delivered recoveries ranging from 95.3 - 97.3% and RSDs within 5.8% (n=3). Using a parallel dual-electrode detector was shown to deliver reliable results with matching current ratios and comparable migration time to those obtained from biomarker standards.published_or_final_version
Chemistry
Doctoral
Doctor of Philosophy
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Fu, Katherine. "Isolation of human BCAD gene and analysis of putative BCAD deficiency." Thesis, McGill University, 1993. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=68175.
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The 2-methylbranched chain acyl-CoA dehydrogenase (BCAD) is a mitochondrial enzyme that catalyzes the third reaction in isoleucine and valine metabolism, the oxidation of 2-methylbutyryl-CoA and isobutyryl-CoA, respectively. BCAD deficiency would result in the accumulation of branched chain acyl-CoAs or their derivatives. Three patients with a putative defect in BCAD have been reported. This study consists of a molecular examination of one such patient as well as the characterization of the BCAD gene. In Northern blot analysis of human fibroblast RNA, the BCAD cDNA hybridized to two RNA species of 2.7 and 6.5 kb. The 2.7 kb band corresponds to the size of the BCAD cDNA, which consists of the entire coding region of 1.3 kb and a 3$ sp prime$ untranslated region of 1.4 kb. The coding regions of the BCAD gene span approximately 21 kb and consist of 12 exons and 11 introns. The exons range in size from 39 to 108 bp. In the analysis of the putative BCAD-deficient patient, no significant difference was observed at the level of DNA (Southern), RNA (Northern) or protein (Western) when compared to controls, suggesting that the BCAD gene in this patient did not contain any large insertions or deletions, or a frameshift mutation. The single strand conformation polymorphism (SSCP) technique and sequencing of the entire coding region did not reveal any disease-causing mutations but two polymorphisms were identified: one in exon 6 and the other in exon 10.
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Bandarupalli, Praveen Kumar. "Thermal Analysis of Decomposition Reactions of Aspartic and Glutamic Acids in Potassium Chloride Matrix." Youngstown State University / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=ysu1391391780.
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McCullagh, James Stephen Oswin. "Development of new analytical techniques for amino acid isotope analysis and their application to palaeodietary reconstruction." Thesis, University of Oxford, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.670162.
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Bakeman, Valerie R. "Pacific and Atlantic coast mollusk shells chromatographic amino acid racemization kinetics and interlaboratory comparisons /." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file 4.12 Mb., 271 p, 2006. http://catalog.hathitrust.org/api/volumes/oclc/133182881.html.
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Gurekian, Christine N. "Amniotic fluid amino acids as biological indicators of fetal growth in human and rat models." Thesis, McGill University, 2005. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=98718.
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Amniotic fluid (AF) is a protective pool and a resource of amino acids for the growing fetus. In study 1, we investigated if any of these AF amino acids at mid gestation were associated with fetal development in humans. Nineteen amino acids differed across birth weight percentiles. Arginine, 3-methyl histidine and tryptophan were positive predictors of birth weight, while ornithine was a negative predictor. In study 2, we used a diet induced model of IUGR to see if specific AF amino acids were predictive of fetal weight near term. Methionine and phenylalanine were modified by diet, and 12 amino acids were independently modified by gestational age, respectively. Cysteine, lysine, methionine and tyrosine were predictors of fetal weight. Thus, the AF amino acid pool is associated in animals and humans with fetal growth.
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Wróblewska, Liliana. "Refinement of reduced protein models with all-atom force fields." Atlanta, Ga. : Georgia Institute of Technology, 2007. http://hdl.handle.net/1853/26606.
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Thesis (Ph.D)--Biology, Georgia Institute of Technology, 2008.Committee Chair: Skolnick, Jeffrey; Committee Member: Fernandez, Facundo; Committee Member: Jordan, King; Committee Member: McDonald, John; Committee Member: Sherrill, David. Part of the SMARTech Electronic Thesis and Dissertation Collection.
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Whiton, Tara K., Kimitake Sato, Asher Flynn, Joseph Walters, Caleb D. Bazyler, Michael H. Stone, and Brad H. DeWeese. "Preliminary Analysis: Moderating the Stress Perception of Collegiate Distance Runners Using Branched-Chain Amino Acids." Digital Commons @ East Tennessee State University, 2018. https://dc.etsu.edu/etsu-works/3819.
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Exercise-induced fatigue may be caused by increases in cerebral serotonin resulting in symptoms of central fatigue (i.e. decreased mood, and increased stress and sleepiness). Branched-chain amino acid (BCAA) supplementation is one intervention that can reduce symptoms of central fatigue by competing for the tryptophan transporter reducing serotonin synthesis. Psychological monitoring tools such as The Daily Analysis of Life Demands for Athletes (DALDA) Questionnaire can be used to study symptoms of central fatigue by identifying sources of general and sport-specific stress as well as an athlete’s reaction to stressors. PURPOSE: To examine the response of BCAA on stress perception of trained collegiate distance runners using DALDA. METHODS: 8 collegiate distance runners (men n=4, women n=4) took BCAA supplement (SUP) (0.08g/kg) or placebo (PLA) daily for 6 weeks, alternating conditions week to week. Each morning athletes filled out the 34-item DALDA prior to training by selecting one of 3 answers corresponding to stress symptoms: A = “feel worse than normal”, B= “feel normal”, C= “feel better than normal”. Response ratios were generated for each of the 3 answers for each condition (SUP or PLA) by taking total number of responses for each answer over number of answers overall. Response ratios were calculated as weekly mean ± SD and MANOVA was used for analysis. The alpha criterion was set to p<0.05. RESULTS: Statistical significance was found (p<0.01), and further analyses were done to examine changes from week to week. On average, athletes reported fewer ‘A’ responses in SUP weeks than PLA weeks (SUP: 9.27% ± 2.21%; PLA: 13.46% ± 7.29%), while response percentage for ‘C’ was the same between both conditions (SUP: 11.78 ± 2.12%; PLA: 11.24% ± 2.32%). Changes from SUP weeks to PLA weeks produced noticeable changes in ‘A’ responses (e.g.: 14.36% SUP week to PLA week; -9.95% from PLA week to SUP week). CONCLUSIONS: Results from DALDA revealed a noticeable change in the stress response of the athletes from condition to condition. The athletes reported higher instances of feeling “worse than normal” during PLA weeks and fewer instances of feeling “worse than normal” during SUP weeks. These results indicate that BCAA supplementation seems to be an effective means of reducing the stress perception in these collegiate distance runners.
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Campeau, Eric. "Molecular genetics of biotin-dependent enzymes : mutation analysis, expression and biochemical studies." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape7/PQDD_0019/NQ55308.pdf.
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Velloza, Peter Edward. "The effect of branched-chain amino acid ingestion on physical performance during prolonged exercise." Master's thesis, University of Cape Town, 1996. http://hdl.handle.net/11427/26546.
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It has been hypothesized that an increase in the ratio of plasma tryptophan (TRP) to branched-chain amino acid (BCAA) concentrations may mediate an increase in cerebral serotonin synthesis, through an increased cerebral tryptophan uptake. It is postulated that the increased brain serotonin content may induce central fatigue during prolonged exercise. Until present, this postulate had not been subject to rigorous scientific testing during prolonged exercise. Therefore the aim of this study was to investigate whether ingesting a BCAA supplement during prolonged exercise improves physical performance and central fatigue. The use of such a supplement during prolonged exercise could then be expected to have a large effect on performance. Eight trained cyclists (VO₂ max= 61.9 ± 4.3 ml 02/kg/min) ingested, in random order, a drink containing either 10% carbohydrate (CHO), 10% CHO and 0.16% branched-chain amino acid (BCAA) or 0.16% BCAA. Every hour, for the duration of the exercise (4 hours, 55% VO₂ max) blood samples were analysed for amino acids, ammonia, free fatty acids, glycerol, glucose and insulin concentrations. Urine was analysed for urea and creatinine concentrations. Heart rate, oxygen consumption (VO₂), respiratory exchange ratio (RER) and rating of perceived exertion were also analysed. Thereafter, subject's 40km time trial performance and RPE was assessed on a Velodyne windtrainer. Central fatigue following the time trial was quantified using the Sternberg reaction-time paradigm. The serum concentration of the BCAA's declined as a result of the exercise, in the BCAA only trial. Tryptophan concentration, however, did not change during the exercise. The serum TRP:BCAA ratio increased (0.16 ± 0.06 to 0.20 ± 0.10; p≤0.05) in the CHO trial only. The BCAA trial differed from the two trials in which CHO was ingested because plasma ammonia and glucose concentrations did not increase, while free fatty acids (FF A's) and glycerol concentrations increased significantly (p≤0.05). The lower RER in the BCAA trials suggests a higher proportion of fat was oxidised in these trials, compared to the other two trials. Cycling performance, over a 40km time trial, (CHO= 68.59 ± 6.02; CHO+ BCAA = 68.00 ± 3.01; BCAA = 69.43 ± 5.35 min/sec), ratings of perceived exertion, submaximal or maximal heart rates, and mental performance were not different between trials. Data from this study appears to refute the thesis hypothesis that an increase in serum TRP:BCAA decreases physical performance and central fatigue, during prolonged exercise.
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Valenrod, Yevgeny. "Development of solid phase-dynamic kinetic resolution for syntheses of N-substituted [alpha]-amino acids." Diss., Online access via UMI:, 2005.
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Ellis, Greg. "Compound-Specific Stable Isotopic Analysis of Protein Amino Acids: Ecological Applications in Modern and Ancient Systems." Scholar Commons, 2012. http://scholarcommons.usf.edu/etd/4035.
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Stable isotopic analysis of the major biochemically important elements is an increasingly utilized tool in the study of ecology. Patterns of isotopic fractionation in carbon and nitrogen are used to determine trophic linkages, nutrient pathways, and sources of primary production in numerous contexts. Traditional techniques rely on measurements made of bulk samples such as tissue, but emerging methods using individual chemical compounds provide a means of achieving deeper understanding in a variety of inquiries.
Amino acids, as the building blocks of proteins, are the dominant nitrogen-bearing biomolecules and are a major constituent of all life. Patterns of isotopic fractionation during synthesis and transformations of these compounds record a variety of information about their environmental history. The purpose of this study was to utilize amino acid-specific isotopic analysis to address a variety of questions in paleoecology and trophic ecology, with an eye towards overcoming limitations inherent in bulk analyses applied to these fields.
Organic matter preserved in shells provides an archive of compounds that are typically lost quickly from the environment, such as proteins. It can be used as an analog of the soft body parts typically used isotope-based environmental measures and therefore provide a window on past environmental conditions, if it can be demonstrated that the two are chemically equivalent. Compositional differences between tissue and shell organic matter can obscure this relationship in bulk analyses, so a compound-specific approach is needed to accurately test this idea. Comparison of amino acid δ13C values between hinge muscle tissue and shell organic matter in Crassostrea virginica sampled along an estuarine salinity gradient in Rookery Bay, Florida, demonstrated functional equivalency between them. While minor isotopic offsets were observed between them, likely due to differences in turnover time between tissues, the ability to resolve location within the estuary was identical between them. This suggests that amino acid-specific isotopic measurements from shell organic matter can be effectively used in paleoreconstructions.
A complicating factor in using shell organic matter as a surrogate for body tissues arises from interspecies differences in organic matrix composition. This manifests itself as species-specific isotopic offsets in bulk analyses, making meaningful comparisons across species difficult. Amino acid nitrogen isotope analysis of a suite of mollusks from St Joe Bay, Florida, was used to infer trophic positions from shell organics and the results obtained were compared to equivalent tests using body tissue. Despite the inability to reconstruct trophic position from bulk isotopic compositions, shell organic extracts produced an identical description of trophic levels to that obtained using body tissues. CSIA, therefore, can be used to eliminate compositional biases in interspecies comparisons using organic matter preserved in biominerals.
Trophic level determinations derived from measurements of amino acid δ15N benefit from that fact that a subset of these compounds directly record ecosystem isotopic baseline values. It is therefore possible to parse the source of observed changes in bulk isotopic compositions into contributions from both baseline variation and trophic shifts. By correcting for the possibility of baseline changes, unambiguous assignments of trophic position can therefore be made. Application this technique to a collection of Bairdiella chrysoura spanning multiple year classes was used to demonstrate the timing of ontogenetic diet shifts in this species. Juveniles (<80 mm standard length) were found to consistently occupy a lower trophic level than adults (>80 mm) based upon ∆15N glutamic acid-glycine. Results obtained were compatible with previous estimates of ontogenetic effects on prey preferences derived from gut-content analysis.
Amino acid 15N-based trophic determinations assume near-constant trophic fractionation in each compound, regardless of an organism's health or nutritional status. The fact that this fractionation is influenced by internal nitrogen processing within the organism argues against such consistency, however. Effects of condition on the magnitude of compound-specific fractionation and resulting trophic estimates were tested by comparing dry season and wet season samples of Anchoa mitchilli subject to seasonal starvation in the latter period from the Alafia River, Florida. Despite significantly lower measures of condition (as measured by length:weight ratios) in the wet season fish, no differences in amino acid fractionation were detectable between them. This suggests that amino acid-specific fractionation factors are in fact robust to changes in organism health, although more rigorous assessment of this in culture is required.
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Canepa, Alberto. "Intracellular free amino acids and nutritional status in children with chronic renal failure on different treatments /." Stockholm : Karolinska Univ. Press, 2001. http://diss.kib.ki.se/2001/20010611cane/.
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Preeprem, Thanawadee. "Functional assessments of amino acid variation in human genomes." Diss., Georgia Institute of Technology, 2014. http://hdl.handle.net/1853/51869.
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The Human Genome Project, initiated in 1990, creates an enormous amount of excitement in human genetics—a field of study that seeks answers to the understanding of human evolution, diseases and development, gene therapy, and preventive medicine. The first completion of a human genome in 2003 and the breakthroughs of sequencing technologies in the past few years deliver the promised benefits of genome studies, especially in the roles of genomic variability and human health. However, intensive resource requirements and the associated costs make it infeasible to experimentally verify the effect of every genetic variation. At this stage of genome studies, in silico predictions play an important role in identifying putative functional variants. The most common practice for genome variant evaluation is based on the evolutionary conservation at the mutation site. Nonetheless, sequence conservation is not the absolute predictor for deleteriousness since phylogenetic diversity of aligned sequences used to construct the prediction algorithm has substantial effects on the analysis. This dissertation aims at overcoming the weaknesses of the conservation-based assumption for predicting the variant effects. The dissertation describes three different integrative computational approaches to identify a subset of high-priority amino acid mutations, derived from human genome data. The methods investigate variant-function relationships in three aspects of genome studies—personal genomics, genomics of epilepsy disorders, and genomics of variable drug responses.
For genetic variants found in genomes of healthy individuals, an eight-level variant classification scheme is implemented to rank variants that are important towards individualized health profiles. For candidate genetic variants of epilepsy disorders, a novel 3-dimensional structure-based assessment protocol for amino acid mutations is established to improve discrimination between neutral and causal variants at less conserved sites, and to facilitate variant prioritization for experimental validations. For genomic variants that may affect inter-individual variability in drug responses, an explicit structure-based predictor for structural disturbances is developed to efficiently evaluate unknown variants in pharmacogenes. Overall, the three integrative approaches provide an opportunity for examining the effects of genomic variants from multiple perspectives of genome studies. They also introduce an efficient way to catalog amino acid variants on a large scale genome data.
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Davis, Kellie M. "Open tubular capillary electrochromatography-laser induced fluorescence for the separation and detection of proteins and amino acids." Greensboro, N.C. : University of North Carolina at Greensboro, 2007. http://libres.uncg.edu/edocs/etd/1513Davis/umi-uncg-1513.pdf.
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Thesis (M.S.)--University of North Carolina at Greensboro, 2007.Title from PDF t.p. (viewed Mar. 11, 2008). Directed by G. Brent Dawson; submitted to the Dept. of Chemistry. Includes bibliographical references (p. 67-69).
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Seymour, Jennifer Lynn. "Mass spectrometric and computational methods for the analysis of Cu(II)-2,2'-bipyridine amino acid complexes /." Thesis, Connect to this title online; UW restricted, 2004. http://hdl.handle.net/1773/8637.
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Douglas, C. A. (Claire Anne). "Amino acid analysis in wines by liquid chromatography : UV and fluorescence detection without sample enrichment." Thesis, Stellenbosch : Stellenbosch University, 2003. http://hdl.handle.net/10019.1/53249.
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Thesis (MSc)--Stellenbosch University, 2003.ENGLISH ABSTRACT: In this study, the analysis of ammo acids usmg High Performance Liquid Chromatography (HPLC) with pre-column derivatisation was optimised. The derivatisation reagents include o-phthaldialdehyde (OPA), 9- fluorenylmethylchloroformate (FMOC) and iodoacetic acid (IDA). Detection was performed using UV and fluorescence in series. The developed method was utilised for the analysis and quantitation of amino acids in eighteen wines. The application of chemometric data evaluation was initiated.
AFRIKAANSE OPSOMMING: Hierdie ondersoek behels die optimisering van die aminosuuranalise deur gebruik te maak van Hoë Druk Vloeistof Chromatografie (HDVC) in kombinasie met pre-kolom derivatisering. Die derivativatiserings reagense sluit in o-phthaldialdehied (OPA), 9- fluorenielmetielchloroformaat (FMOC) en jodoasynsuur (IDA). Deteksie is gedoen deur gebruik gemaak van 'n ultraviolet (UV) en 'n fluorosensie detektor in serie. Die metode sodoende ontwikkel is gebruik vir die analise en kwantifisering van aminosure in agtien wyne. Die toepassing van chemometriese data evaluasie is ook geïnisieer.
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Crowell, Christopher Kenyon. "Depleted amino acids and sodium butyate [sic] alter the phenotype and genotype of cell lines expressing rHuEPO /." Connect to full text via ProQuest. Limited to UCD Anschutz Medical Campus, 2006.
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Thesis (Ph.D. in Pharmaceutical Sciences) -- University of Colorado at Denver and Health Sciences Center, 2006.Typescript. Includes bibliographical references (leaves 133-142). Free to UCDHSC affiliates. Online version available via ProQuest Digital Dissertations;
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Kritzer, Van Zant Miriam. "ANALYSIS AND DEVELOPMENT OF MIRABILIS EXPANSA (RUIZ AND PAV.) STANDL.; FOR POTENTIAL AS A NEW ROOT CROP OUTSIDE THE ANDES." OpenSIUC, 2016. https://opensiuc.lib.siu.edu/dissertations/1226.
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Six topics are presented, relevant to agricultural research on two horticultural varieties of Mirabilis expansa (Ruiz and Pav.) Standl. Chapter 1, “Review of the economic and ethno-botany of the genera of the family Nyctaginaceae," includes a summary of literature on the topics included in the title, and an original taxonomic update of plant names used correctly and incorrectly as synonyms for Mirabilis jalapa, the type name for the plant family Nyctaginaceae. M. jalapa has been substituted for medicinal jalap from Mexico. Names in the Convolvulaceae for medicinal Jalap are also updated here, as they show the origin of many names which have been incorrectly used as synonyms in the Mirabilis literature. Chapter 2, “History of Mirabilis expansa (Ruiz and Pav.) Standl.; Growth and use in the Andes,” is also a literature review, incorporating information from several documents and papers which have only recently become readily available internationally via the Internet. These documents were translated into English for this chapter. Research in Chapter 3, “Field trials of Mirabilis expansa (Ruiz and Pav.) Standl. grown in North America; Growth, yield and quality traits,” showed that M. expansa horticultural varieties 'L' and 'T' are tolerant to the intense weather conditions of southern Illinois, when grown on constructed sand plots. In Chapter 4, “Amino Acid profiles for two horticultural varieties of Mirabilis expansa (Ruiz and Pav.) Standl.: A rare indigenous Andean crop grown in southern Illinois,” M. expansa was examined for its amino acid values and those values considered in terms of differnces between the two varieties and above and below ground structures. In addition, soil amendments peat and steer manure, considered alone and together, as well as structure and variety, were examined for their effect on production of amino acids in ANOVAs and Tukey-adjusted LS-Means run in SAS 9.3. In Chapter 5, “Nutrients, Comparison of Amino Acid Profiles, and Cytotoxicity Testing for Mirabilis expansa (Ruiz and Pav.) Standl.,” the amino acid profiles for M. expansa from the previous chapter are compared to profiles for other crops, eggs and milk. M. expansa is shown relatively to contain extremely high amounts of total protein. In addition published values for other nutrients for M. expansa taken from translated material are combined into two tables. Also, a cytotoxicity assay carried out in collaboration with researchers at Ohio State University was used to see if the southern Illinois M. expansa material was active against highly sensitive HT-29 colon cancer cells. Negative results from that assay serves as preliminary data for a lack of toxicity due to micro-molecules in the crop. Chapter 6, “Inexpensive nitrogen chambers for conservation of herbarium specimens,” was an outgrowth of the need to find a chemically benign manner for storing herbarium specimens of Mirabilis, used in research which led to the work described in the previous chapters. The results show that valved oxygen barrier bags, designed for clothing storage, with a small number of oxygen absorbers, can retain conditions for sufficient periods to treat specimens for pests. This allows the bags to be used as inexpensive nitrogen chambers, to treat herbarium specimens in place of expensive nitrogen systems or freezers, and without the toxic chemicals historically used in herbaria for the same purpose.
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Gentz, Petra Monika. "Towards understanding the mechanism of dimerisation of Saccharomyces cerevisiae eukaryotic translation initiation factor 5A." Thesis, Rhodes University, 2008. http://eprints.ru.ac.za/1161/.
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Nielsen, Jens Munk. "Species interactions and energy transfer in aquatic food webs." Doctoral thesis, Stockholms universitet, Institutionen för ekologi, miljö och botanik, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-123600.
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Food webs are structured by intricate nodes of species interactions which govern the flow of organic matter in natural systems. Despite being long recognized as a key component in ecology, estimation of food web functioning is still challenging due to the difficulty in accurately measuring species interactions within a food web. Novel tracing methods that estimate species diet uptake and trophic position are therefore needed for assessing food web dynamics. The focus of this thesis is the use of compound specific nitrogen and carbon stable isotopes and molecular techniques for assessing predator-prey interactions and energy flow in natural aquatic ecosystems, with a particular focus on the species links between phytoplankton and zooplankton. The use of δ15N amino acid values to predict organism trophic position are evaluated through a meta-analysis of available literature which included measurements from 359 marine species (article I). Through a controlled feeding study isotope incorporation in aquatic organisms, across both plant-animal and animal-animal species linkages is further assessed (article II). These studies showed that δ15N amino acid values are useful tools for categorizing animal trophic position. Organism feeding ecology influenced nitrogen trophic discrimination (difference in isotope ratio between consumer and diet), with higher discrimination in herbivores compared to omnivores and carnivores (article I). Nitrogen isotope trophic discrimination also varied among feeding treatments in the laboratory study (article II). The combined findings from articles I & II suggest that researchers should consider using group specific nitrogen trophic discrimination values to improve accuracy in species trophic position predictions. Another key finding in the controlled laboratory study (article II) was consistently low carbon isotope discrimination in essential amino acids across all species linkages, confirming that these compounds are reliable dietary tracers. The δ13C ratios of essential amino acids were applied to study seasonal dynamics in zooplankton resource use in the Baltic Sea (article III). Data from this study indicated that zooplankton assimilate variable resources throughout the growing season. Molecular diet analysis (article IV) showed that marine copepod and cladoceran species ingested both autotrophic and heterotrophic resources. Evidence from both articles III & IV also revealed that zooplankton feed on a relatively broad range of diet items but not opportunistically on all available food sources. Mesozooplankton feeding patterns suggested that energy and nutritional flows were channelled through an omnivorous zooplankton food web including microzooplankton prey items. Overall the results of this thesis highlight that stable isotope ratios in specific compounds and molecular techniques are useful tracing approaches that improve our understanding of food web functioning.At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Manuscript. Paper 4: Manuscript.
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Hoe, Nancy Palme. "Analysis of Temperature Sensing in Yersinia pestis: A Dissertation." eScholarship@UMMS, 1994. https://escholarship.umassmed.edu/gsbs_diss/98.
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The lcrF gene of Yersinia pestis, the etiological agent of plague, encodes a transcription activator responsible for inducing expression of several virulence-related proteins (Yops) in response to temperature. The mechanism of this thermoregulation was investigated. Using a yopE::lacZ reporter fusion, lcrF-mediated thermal regulation was observed in Y. pestis and Escherichia coli. The lcrF gene was sequenced, the 30.8 kDa. LcrF protein identified and purified, and LcrF-dependent yopE-specific DNA binding activity was detected. A sequence similarity search revealed that LcrF exhibits 98% homology to VirF of Yersinia enterocolitica and significant homology to the carboxy termini of other members of the AraC family of transcription activators. During localization studies, a significant proportion of LcrF was found associated with the membrane fraction in E. coli. However, pulse-chase experiments indicated that this result is an artifact of fractionation. lcrF-mediated thermal induction of the yopE::lacZ reporter fusion remains intact in a Shigella flexneri virR mutant. The virR mutation is known to affect thermal induction of Shigellavirulence genes, which are also controlled by an activator in the AraC family.
As a first step toward identifying the temperature-sensitive step in the regulation of yop expression, lcrF::lacZ transcriptional fusions were constructed and analyzed in Y. pestis and E. coli. The activity of the fusions was not affected by the native pCD1 virulence plasmid, an intact lcrF gene, or temperature. Thus, induction of lcrF transcription is not essential for temperature-dependent activation of yopE transcription. To confirm these results, attempts were made to identify both the native lcrF message in Y. pestis, and a lcrF-lacZ hybrid message in Y. pestis and E. coli. These attempts were unsuccessful. Examination of LcrF protein production revealed temperature-dependent expression in Y. pestis. Surprisingly, high-level T7 polymerase-directed transcription of the lcrF gene in Escherichia coli also resulted in temperature-dependent production of the LcrF protein. Pulse-chase experiments showed that the LcrF protein was stable at both 26 and 37°C, suggesting that translation rate or message degradation is thermally controlled. Comparison of the amount of LcrF protein produced per unit of message at 26 and 37°C in E. coli indicated that the efficiency of translation of lcrF message increased with temperature. mRNA secondary structure predictions suggest that the lcrF Shine-Dalgarno sequence is sequestered in a stem-loop. A model in which decreased stability of this stem-loop with increasing temperature leads to increased efficiency of translation initiation of lcrF message is presented.
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Norlin, Elin. "Nitrogen isotope analysis of ammonium and glycine : method development for aqueous solutions and soil extracts /." Umeå : Dept. of Forest Ecology, Swedish University of Agricultural Sciences, 2005. http://epsilon.slu.se/200584.pdf.
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Cao, Haibo. "Protein Structure Recognition From Eigenvector Analysis to Structural Threading Method." Washington, D.C. : Oak Ridge, Tenn. : United States. Dept. of Energy. Office of Science ; distributed by the Office of Scientific and Technical Information, U.S. Dept. of Energy, 2003. http://www.osti.gov/servlets/purl/822060-2L2Xvm/native/.
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Thesis (Ph.D.); Submitted to Iowa State Univ., Ames, IA (US); 12 Dec 2003.Published through the Information Bridge: DOE Scientific and Technical Information. "IS-T 2028" Haibo Cao. 12/12/2003. Report is also available in paper and microfiche from NTIS.
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Hübner, Tatjana [Verfasser]. "Analysis of the regulatory function of amino acids on metabolic targets and serotonin production in Drosophila melanogaster / Tatjana Hübner." Bonn : Universitäts- und Landesbibliothek Bonn, 2016. http://d-nb.info/1113688424/34.
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Wan, Lili. "Determination of total selenium and seleno-amino acids in yeast and aquatic organisms by liquid chromatography and inductively coupled plasma mass spectrometry." Diss., Columbia, Mo. : University of Missouri-Columbia, 2007. http://hdl.handle.net/10355/4683.
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Thesis (Ph. D.)--University of Missouri-Columbia, 2007.The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from title screen of research.pdf file (viewed on March 4, 2008) Vita. Includes bibliographical references.
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Klinken, G. J. van. "Dating and dietary reconstruction by isotopic analysis of amino acids in fossil bone collagen-with special reference to the Caribbean." Amsterdam : Fondation for Scientific Research in the Caribbean Region, 1991. http://catalog.hathitrust.org/api/volumes/oclc/26955816.html.
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Garside, Daniel Mark. "A precolumn derivatization procedure for the analysis of marine amino acids with 9-fluorenylmethyl chloroformate and high performance liquid chromatography." Master's thesis, University of Cape Town, 1986. http://hdl.handle.net/11427/17624.
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Include bibliography.The separation of 20 amino acids has been achieved by gradient elution and reversed phase high performance liquid chromatography employing 9-fluorenylmethyl chloroformate as the precolumn derivatizing reagent. The application of this technique to assess the extent of marine bacterial uptake of amino acids released from kelp has also been determined. The problem of excess reagent reacting with water to form a hydrolysis product has largely been overcome. Pentane extraction of the reagent after amino acid reaction caused the loss of less polar amino acid derivatives. Other factors such as the formation of dilabelled products and the pH dependance of the derivatization reaction have been investigated. The reproducibility between-analyses had a percentage error of 2 - 6%. The stability of the derivatives is about 2 weeks at room temperature. The application to physiological samples and seawater has been demonstrated. The method was applied to the study of kelp release and bacterial uptake of marine amino acids. Other chemical profiles of ammonia, nitrate, total N, particulate C, together with bacterial activity and bacterial density (biomass) were determined to provide correlative profiles to the amino acid values. The experiment was set up with kelp fronds in buckets, some containing antibiotics to halt bacterial activity, and a control bucket with untreated seawater. Alanine is the most dominant amino acid (concentration between 5 and 100 nmol.dm⁻³). Values of glycine, aspartic acid, glutamic acid and arginine have much lower levels. Traces, of histidine, asparagine, cystine, serine and tyrosine appeared near the end of the experiment. It was found that the amino acid concentrations were low compared with the inorganic nitrogen species. The flux of these species was found to be too low to create a substantial response, as the activities are also low compared with normal in-shore regions. In order to infer more from the processes occurring in this study, we would have to increase the experimental time to the order of days.
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Rennell, Dale. "A Genetic and Structural Analysis of P22 Lysozyme: A Thesis." eScholarship@UMMS, 1988. https://escholarship.umassmed.edu/gsbs_diss/238.
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P22 lysozyme, encoded by gene 19, is an essential phage protein responsible for hydrolyzing the bacterial cell wall during lytic infection. P22 lysozyme is related to T4 lysozymein its mode of action, substrate specificities, and in its structure. Gene 19 was located on the phage genome, subcloned, and then sequenced. lysozyme was produced in large quantities and purified for biochemical characterization and for crystallograpic studies. Gene 19consists of 146 codons, and encodes a protein with a molecular weight of 16,117.
Amber mutations were created in gene 19 by in vitro primer-directed mutagenesis. The mutations were crossed by homologous recombination onto the phage genome. The phages bearing the amber mutations in gene 19 were screened for the ability to grow on six different amber suppressor strains. Amino acid substitutions that resulted in nonfunctional or less functional lysozyme were determined. Of 60 possible amino acid substitutions at 11 different sites in P22 lysozyme, 20 are deleterious. The phage bearing amber mutations in gene 19that failed to grow on given suppressor strains were reverted and second site intragenic revertants were obtained. The mutations were sequenced.
A substitution of serine for glutamine at residue 82 is compensated for by changing residue 46 from serine to leucine. This single change enables the phage to form a plaque at 300C but not at 400C. When the triple change asn42->lys; ser46->leu; and ser43->pro is present the lysozyme produced is no longer temperature sensitive. The crystal structure of P22 lysozyme is not yet solved. Assuming that the structures of T4 lysozyme and P22 lysozyme are similar, one can examine the positions of equivalent residues in the T4 lysozyme structure. The spatial arrangement of the residues changed by the secondary site mutations and the original substitution can then be visualized. The mutations discussed above all map far from the original mutation on the T4 three dimensional model.
A substitution of leucine for tyrosine at position 22 is compensated for by the double mutation of arg18->ser and ser23->lys. When the equivalent residues are mapped on the T4 three dimensional model the changes map in close proximity to the original mutation.
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Alhedabi, Taleb Flieh Hassen. "Design of a suitable material at the nano to micrometer scale as support for electrolysis. : Study of the electropolymerization of concentrated L-amino acids in aqueous solutions." Thesis, Besançon, 2015. http://www.theses.fr/2015BESA2052.
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L'oxyde d'aluminium anodique poreux (AAO) est formé par anodisationde l'aluminium dans une solution électrolytique acide, sous une tensionconstante et de la température de l'électrolyte. Des techniques spectroscopiquespareilles que la spectroscopie infrarouge FT (ATR-FTIR), diffraction des rayonsX (XRD), spectroscopie Raman, la microscopie à force atomique (AFM) etmicroscopie électronique à balayage (MEB) utilisés pour caractériser la matrice.L'oxydation anodique d'acides L-aminés et des mélanges de monomèrescomprenant 0,1 M aniline et des acides L-aminés dans le milieu aqueux acide deplatine et électrode lisses électrodes Pt modifié (Pt / AAO) est étudié.L'oxydation des acides L-aminés et les électropolymérisation de l'aniline 0,1 Mavec des acides L-aminés tels que la L-alanine, la L-sérine, la L-méthionine,acide L-aspartique, la L-lysine, et phénylalanine en acide le milieu a étéeffectuée par voltammetric cyclique électrochimique couplée à microbalance àcristal de quartz (EQCM). La concentration des acides aminés, le pH del'électrolyte et les effets de balayage de numéros de voltamétrie cyclique ont étéexaminées. L'analyse spectroscopique comme réflectance totale atténuée FTspectroscopie infrarouge (ATR-FTIR), UV-visible, la spectroscopiephotoélectronique à rayons X (XPS), la spectroscopie Raman, et la diffractiondes rayons X (XRD) sont utilisés pour caractériser les couches minces obtenues.Microscopie électronique à balayage (MEB) utilisé pour étudier la morphologiede surface mince de films. La solubilité pour les polymères sont étudiées. Laprésence de liaisons peptidiques est clairement mise en évidence. DFTmodélisation de poly-L-acides aminés volet sur Pt (001) couplée à des mesuresspectroscopiques sont en faveur de L-amino-acides électropolymérisation enacides poly-L-aminés d'une manière irréversible.Les électrosynthèses de poly-L-amino acides, la polyaniline et depolymères ont été utilisées en tant que récepteur de protons à l'état solide pHcapteur solideAnodic aluminum oxide porous (AAO) is formed by the anodization ofaluminum in acidic electrolytic solution under at constant voltage and electrolytetemperature. Spectroscopic techniques such as FT infrared spectroscopy (ATRFTIR),X-ray diffraction (XRD), Raman spectroscopy, atomic force microscopy(AFM) and scanning electron microscopy (SEM) used to characterize thetemplate.The anodic oxidation of L-amino acids and monomer mixtures comprising0.1 M aniline and some L-amino acids in acidic aqueous medium on platinumsmooth electrodes and modified Pt electrode (Pt/AAO) is studied. The oxidationof L-amino acids and in presence of aniline 0.1 M with L-amino acids such as Lalanine,L-serine, L-methionine, L-aspartic acid, L-lysine, and L- phenylalaninein acidic media was carried out by cyclic voltammetry coupled withelectrochemical quartz crystal microbalance (EQCM). The Amino acidconcentration, pH of the electrolyte and the scan number effects on cyclicvoltammetry were examined. Spectroscopic analysis such as attenuated totalreflectance FT infrared spectroscopy (ATR-FTIR), UV-Visible, X-rayphotoelectron spectroscopy (XPS), Raman spectroscopy, and X-ray diffraction(XRD) are used to characterize the resulting thin film coatings. Scanningelectron microscopy (SEM) used to study the morphology of thin films surfaceas well as the solubility are studied. The presence of peptide bonds is clearlyhighlighted. DFT modelization of poly-L-amino acids strand on Pt(001) coupledto spectroscopic measurements are in favor of L-amino acidselectropolymerization into poly-L-amino acids in an irreversible way.The electrosynthesis of poly-L-amino acids, polyaniline and polymerswere used as proton receptor for solid state pH solid sensor
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Blinder, Dmitry B. "Genetic Analysis of the Saccharomyces Cerevisiae Pheromone Response Pathway: a Thesis." eScholarship@UMMS, 1990. https://escholarship.umassmed.edu/gsbs_diss/127.
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The cell division of Saccharomyces cerevisiae is controlled by the action of pheromones at the G1 phase of the cell cycle. A general method was developed for the isolation of constitutive mutants in the pheromone response pathway. Recessive alleles of the SCG1 gene (encoding the α subunit of a G protein) were isolated as well as a dominant mutation in the STE4 gene (encoding the β subunit of a G protein). Analysis of double mutants suggested that the STE4 gene product functions after the SCG1 product but before the STE5 gene product. Double mutants carrying either scg1 or STE4Hp1 constitutive alleles together with the temperature-sensitive unresponsive mutation, ste5-3ts, showed arrest and recovery when shifted from 34° C to 22° C. Recovery from the constitutive signal was independent of the receptor. The STE4Hp1 sst2 ste5ts triple mutant was not able to recover from arrest, suggesting that an SST2-dependent mechanism is involved in recovery of the STE4Hp1 mutant from constitutive arrest. In contrast, the scg1-7 sst2 ste5ts triple mutant recovered only partially suggesting that even though SST2 gene product is probably involved in recovery of the scg1-7 mutant, this mutant can recover by an SST2-independent mechanism. This implies existence of another, SST2-independent postreceptor recovery mechanism. The scg1-null mutant do not recover from constitutive arrest (J. Hirschman, personal communication). Both recovery mechanisms probably operate at the G protein step. Isolation of a constitutive allele of STE5 allowed the definition of its site of action as being after the STE4-controlled step. In addition, constitutive activation of the pheromone pathway by STE5Hp1 mutation was found to be partially dependent on the STE4 and STE18 gene products, the β and γ subunits of a G protein. A comprehensive genetic model is presented to explain the mechanisms of signal transduction and recovery.
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Bukusoglu, Gul H. "Genetic and Biochemical Analysis of the Activation Mechanism of the Saccharomyces Cerevisiae Pheromone Receptor." eScholarship@UMMS, 1998. https://escholarship.umassmed.edu/gsbs_diss/152.
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Activation mechanism of the α-factor pheromone receptor of Saccharomyces cerevisiae was analyzed using biochemical and genetic techniques. An in vitro partial proteolysis assay was developed to determine the conformational change of the receptor that occurs upon binding of agonist. The activation specific cleavages were established by comparing cleavage products with antagonist versus agonist occupied receptor. Of the changes in peptide pattern that were revealed by trypsinization, the fragment resulting from the exposure of the third loop to the protease was found to be agonist specific and to be G-protein independent. A low-affinity binding receptor mutant was isolated which failed to undergo this agonist induced conformational change. Four intra-allelic suppressors of this receptor mutant were isolated and all were mapped to the ends of transmembrane helices 4, 5, 6 and 7; all were found to be replacements of non-polar residues by polar ones. The role of the suppressor mutations in conformational change was analyzed.
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Kalsoom, Umme. "Analysis of plant analytes using capillary electrophoresis and high performance liquid chromatography." Thesis, Edith Cowan University, Research Online, Perth, Western Australia, 2015. https://ro.ecu.edu.au/theses/1690.
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Plants contain an enormous array of organic and inorganic components, the analysis for which may involve a wide range of methods. The focus of this study was to develop high performance liquid chromatography and capillary electrophoresis methods for the analysis of three classes of analytes: osmoregulants, minerals and amino acids.
Firstly, this study explored the potential of capillary electrophoresis for the analysis of three very common osmoregulants (proline, glycine betaine and mannitol). A diverse array of methods has been reported for determining each of these analytes, however, the literature on osmoregulants and their analysis is quite disjointed and traverses both biological and chemistry fields. Therefore, a comprehensive review of this literature has been completed (Chapter 2). Considerably fewer methods are available for the simultaneous determination of these osmoregulants, compared to individual analysis. In chapter 3, a method is described for the simultaneous analysis of proline and betaine by capillary electrophoresis at low pH and specifically various cationic probes for the indirect detection of proline and betaine were explored. Sulfanilamide was identified as a suitable probe and was employed to quantify proline and betaine in spinach and beetroot. However, this method could not detect mannitol as it is not charged at low pH.
In Chapter 4, a high performance liquid chromatography method for the simultaneous determination of all three osmoregulants is described. For separation, a NH2 column with formic acid and acetonitrile as the mobile phase were used. The high performance liquid chromatography evaporative light scattering detection method was applied to determine osmoregulants in Stylosanthes guianensis, Atriplex cinerea and Rhagodia baccata plant extracts. A complementary method, using a C18 column with heptafluorobutyric acid added to acetonitrile was used for verification of the analytes.
Secondly, the potential for using capillary electrophoresis was investigated to simplify and shorten the complex sample preparation procedure. Chapter 5 describes a capillary electrophoresis method that allows direct injection from plant tissues. The experiments highlighted that uncontrolled hydrodynamic injection of sample on piercing of food sample resulted in non-reproducibility. The addition of hydroxypropylmethlycellulose to the background reduced the uncontrolled hydrodynamic injection up to 95% for all of the analytes. The sample was injected electrokinetically and an imidazole buffer consisting of hydroxypropylmethlycellulose was used for separation. The issue of reducing the reliance on prior separation is also relevant to minerals, thus the developed capillary zone electrophoresis-UV method was applied for the direct injection of inorganic cations from apple, mushroom, zucchini, green bean and strawberries. The applicability of the method across fruit varieties was determined by analysing four apple varieties including red delicious, fuji, pink lady and royal gala.
Thirdly, the potential of the direct injection method was explored for the analysis of amino acids in zucchini. As amino acids are present at low concentrations and lack a chromophore, a more sensitive detector, capacitively coupled contactless conductivity, and pre-concentration of amino acids using isotachophoresis (leading electrolyte = HCl, terminating electrolyte = hydroxyproline) was performed. The separation of amino acids was carried using acetic acid. For minimising uncontrolled hydrodynamic injection poly(ethylene oxide) was used. Using this method sensitive detection of amino acids was possible (Chapter 6). In short, the developed methods allow for quick, inexpensive, sensitive and efficient analysis of plant components.
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Simmons, Robert. "Thermodynamic and structural analysis of the interactions between Epstein-Barr virus transcription factors and the host targeting factor RBP-Jkappa." Thesis, University of Sussex, 2018. http://sro.sussex.ac.uk/id/eprint/77332/.
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Loh, Tamalette. "Mutational Analysis of the MutH from Escherichia Coli: a Dissertation." eScholarship@UMMS, 2000. https://escholarship.umassmed.edu/gsbs_diss/79.
Full textAbstract:
DNA mismatch repair is one process in the preservation of genomic integrity. It has been found in Archeae, bacteria, plants, yeast and mammals. The mismatch repair system is highly conserved among species and allows the strand-specific elimination of base-base mispairs, chemical base modifications, as well as short insertion/deletion loops following DNA replication. The repair system also has important effects on homeologous recombination, contributing to the frequency of reciprocal exchanges. In humans, defects in the repair system have been found to be associated with tumorigenesis.
In Escherichia coli, this pathway was originally called long patch repair before being renamed the methyl-directed mismatch repair system. It is unique in that it utilizes a DNA methylation pattern to discriminate between the parental DNA strand and the newly synthesized daughter DNA strand. The current model for the initiation of methyl-directed mismatch repair is that the mispaired bases are recognized and bound by the MutS protein with MutL as a helper protein for binding. MutL also assists the MutH protein to bind, thereby forming the completed initiation complex of MutS, MutL and MutH. In the presence of ATP, there is evidence for translocation ofthe complex along the DNA forming alpha loops. At a d(GATC) site the MutH protein binds and nicks the unmethylated daughter DNA strand 5' to the d(G) (by recognizing the N6-d(A) methylation of the parental DNA strand which it is unable to cut). This completes the initiation of the repair system and allows the hydrolysis and resynthesis of the daughter DNA strand.
MutH is a monomer of 25.5 kD in solution and contains a latent Mg2+-dependent endonuclease activity. Unmethylated DNA is nicked without any discrimination on one of the two strands and fully methylated DNA is resistant to cleavage by MutH even though the protein is able to bind the d(GATC) site. The structure of MutH was recently solved and compared to a group of restriction endonucleases that share a structural common core domain with similarly placed catalytic residues. The MutH protein is comprised of two major domains that are able to pivot and rotate with respect to one another. The cleft between the two domains is large enough for double-strand DNA to bind.
This research started with the determination of the MutH structure before it was known. After crystallizing the protein and collecting several heavy atom data sets, it was found that the electron density maps were too discontinuous to trace the structure of the protein. Following that work, site-directed mutagenesis was performed on several areas of MutH based on the similarity of MutH and PvuII structural models. The aims were to identify DNA binding residues (in two flexible loop regions), to determine if MutH has the same mechanism for DNA binding and catalysis as PvuII (MutH histidines 112 and 115), and to localize the residues responsible for MutH stimulation by MutL (MutH C-terminal tail region). An in-vivoscreen based on the mutator phenotype was used to select for functionally defective MutH mutants. These bacteria accumulate mutations at a greater frequency than wild-type and this was monitored by selection on plates with rifampicin. Three MutH mutants were identified from this screen (K48A, G49A, and Δ214). They were purified and assayed for total activity and binding ability. Four other mutants with wild-type phenotypic screen results were also chosen to confirm they were not involved in any MutH function (D47A, H112A, H115A, and Δ224).
No DNA binding residues (such as D47A) were identified in the two flexible loop regions of MutH, although similar loops in PvuII are involved in DNA binding. The purified D47A MutH protein showed wild-type biochemical activity. Instead, the lysine residue (K48) in the first flexible loop was found to function in catalysis together with the three presumed catalytic amino acids (Asp70, Glu77, and Lys79). This purified MutH protein (K48A) had wild-type binding ability but no endonuclease activity without MutL. In the presence of MutL, the K48A protein had only a three-fold reduction in endonuclease activity. This research has shown that MutL stimulates the wild-type MutH activity by 1000-fold. The wild-type MutH stimulation by MutL for binding was only shown to be 16-fold. The G49A MutH mutant interferes with the proper functioning of the protein but is not informative about the mechanism of action. The binding ability of this mutant was the same as wild-type and the endonuclease activity was down 30-fold with a 10-fold stimulation by MutL. The extra methyl group of the alanine may cause slight structural changes in the lysine 48 side chain that slows catalysis.
The two histidines (H112 and H115) in MutH that are in a similar position as the two histidines (H84 and H85) in PvuII (that signal for DNA binding and catalysis) were changed to alanines, but had wild-type activity both in-vivo and in-vitro. These results indicate that the MutH signal for DNA binding and catalysis remains unknown.
The two deletion mutations (MutHΔ224 and MutHΔ214) in the C-terminal end of the protein, localized the MutL stimulation region to five amino acids (Ala220, Leu221, Leu222, Ala223, and Arg224). Mutant MutHΔ224 had wild-type MutL stimulation activity, while MutHΔ214 showed no MutL stimulation. Another deletion mutant, MutHΔ119, from another laboratory was shown to have wild-type MutL stimulation also. This leaves one (or more) of the remaining five residues as important for MutL stimulation.