Дисертації з теми "Biochemicol analysis"
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1
Delompre, Thomas. "Compréhension des mécanismes de perception sensorielle de compléments nutritionnels sous différentes formulations." Thesis, Bourgogne Franche-Comté, 2021. http://www.theses.fr/2021UBFCK038.
Анотація:
La prise de compléments nutritionnels est utile lorsque l’alimentation quotidienne ne suffit plus à couvrir les besoins de l’organisme en nutriments et en énergie. Les ingrédients actifs de ces produits sont principalement des vitamines, des minéraux, des éléments traces, des extraits de plantes. Le mode d’administration par voie orale est largement plébiscité par les consommateurs, c’est pourquoi les produits sont commercialisés sous forme de comprimés effervescents, à croquer, sous forme de poudres et comprimés à mettre en bouche ou sous formes gélifiées. Outre leur efficacité sur le plan nutritionnel, ces produits doivent satisfaire le consommateur sur le plan organoleptique. Cependant, ces compléments nutritionnels sont souvent décrits avec des défauts de goûts non identifiés qui limitent leur acceptabilité.La caractérisation sensorielle de ces « mauvais goûts », l’identification des composés impliqués et la compréhension des mécanismes à l’origine de leur détection sont un véritable challenge pour les industries concernées. Dans ce travail, une méthodologie basée sur des approches sensorielles et cellulaires a été mise en œuvre afin d’améliorer les connaissances sur la perception des « mauvais goûts » des compléments nutritionnels et mettre en évidence des pistes envisageables pour de nouvelles stratégies de masquage.Pour la caractérisation et la quantification des « mauvais goût », les profils sensoriels de différentes gammes et formes de compléments nutritionnels ont été déterminés par des panels de dégustateurs. Un protocole d’analyse sensorielle adapté à la forme galénique évalué (effervescente ou orodispersible) a permis d’identifier et de quantifier certaines perceptions négatives. Les résultats obtenus démontrent en autre la présence d’une amertume prononcée pour de nombreux compléments nutritionnels, qui pourraient contribuer de manière récurrente à leur « mauvais goût ». Une analyse sensorielle de ces mêmes compléments nutritionnels dans des conditions avec et sans blocage du flux rétronasal a révélé des interactions perceptives positives et/ou négatives entre molécules aromatiques et sapides, dont l’origine bien que discutée reste à démontrer.La corrélation entre les profils sensoriels et les compositions nutritives des compléments nutritionnels a révélé que certains composés actifs comme des vitamines pouvaient être responsable de cette amertume. L’être humain possède 25 structures moléculaires spécialisées dans la reconnaissance des molécules amères que l’on appelle des TAS2Rs. L’utilisation d’un protocole d’expérimentation fonctionnelle in vitro a montré que quatre composés vitaminiques étaient capables d’activer un ou plusieurs TAS2R(s). Parallèlement, nous avons complété cette expérimentation fonctionnelle par des mesures psychométriques de seuil de détection à l’amertume chez l’humain. La comparaison des jeux de données sensoriels et cellulaires a révélé l’impact de la physiologie orale et de l’intégration centrale de l’information sur la perception d’un stimulus gustatif. Les résultats obtenus ont démontré que la combinaison d’une approche cellulaire et sensorielle semblait être une méthode alternative efficace pour évaluer la contribution d’un ou plusieurs composés aux perceptions sensorielles négatives des compléments nutritionnelsTaking nutritional supplements is recommended when a normal diet is no sufficient to maintain a good nutritional status. The active ingredients of these products are mainly vitamins, minerals, trace elements and plant extracts. The oral method of administration is widely preferred by consumers, therefore the products are marketed as effervescent tablets, chewable, orodispersible powders and tablets or gelled forms. In addition to their nutritional effectiveness, these products must meet consumer’s expectations as “taste” or “flavor”. However, these nutritional supplements are often described with not identified taste defects, which limit their acceptability.The sensory characterization of these “off-tastes”, the involved compounds identification and the understanding of the mechanisms at the origin of their detection are a real challenge for industry concerned. In this work, a methodology based on sensory and cellular approaches has been implemented in order to improve knowledge on the perception of nutritional supplements “off-tastes” and to highlight possible options for new masking strategies.For the “off-tastes” characterization and quantification, the sensory profiles of different ranges and forms of nutritional supplements were determined by panels of tasters. A sensory analysis protocol adapted to the galenic form evaluated (effervescent or orodispersible) allows to identify and quantify some negative perceptions. The results obtained also demonstrated the presence of a slightly strong bitterness for many nutritional supplements, which could recurrently contribute to their "off-taste". A sensory analysis of these same nutritional supplements with and without retronasal flow blockage conditions revealed positive and/or negative perceptual interactions between aromatic and sapid molecules whose origin remains to be demonstrated.The correlation between sensory profiles and nutritional supplements compositions revealed that some active ingredients such as vitamins could be involved in their bitterness. In humans, bitter substances are detected in the mouth by 25 bitter taste receptors called TAS2Rs. In vitro functional experimental protocol showed that four vitamin compounds were able to activate one or more TAS2R(s). In parallel, we completed this functional experiment with psychometric measurements of the human bitter detection threshold. Comparison of sensory and cellular data revealed the importance of oral physiology and information central integration on the taste stimulus perception. The results obtained demonstrated that the combination of a cellular and sensory approach seemed to be an effective alternative method to evaluate the real contribution of one or more compounds to the negative sensory perceptions of nutritional supplements
2
Klose, Robert John. "Biochemical analysis of MeCP2." Thesis, University of Edinburgh, 2005. http://hdl.handle.net/1842/10997.
Анотація:
MeCP2 is a transcriptional repressor that recruits the Sin3a chromatin remodelling complex to methylated loci. Sin3a-associated histone deacetylases contribute to the ability of MeCP2 to repress transcription and modulate chromatin structure. The biomedical importance of normal MeCP2 function is highlighted by the discovery that inactivating mutations in MeCP2 cause the severe neurological disease Rett syndrome. By deleting the Mecp2 gene, a mouse model of Rett syndrome has been generated and used to study the molecular and physiological outcome of MeCP2 deficiency. Inefficient regulation of neuronal gene expression may have a role in the etiology of Rett syndrome. By studying the biochemical properties of MeCP2 this thesis addresses in detail three basic questions; (1) what are the native biochemical properties of MeCP2? (2) what specific DNA sequences does MeCP2 bind? and (3) what are the affects of post-translational modification on MeCP2? To address the composition of any mammalian MeCP2 complexes, native MeCP2 was purified to near homogeneity from rat brain. Native MeCP2 is an elongated monomer that does not stably associated with other cofactors including Sin3a. Analysis of MeCP2 binding sites in vivo demonstrates that MeCP2 binds unique loci when compared to other MBP’s. Using an unbiased in vitro DNA binding site evolution assay, Methyl-SELEX, MeCP2 was shown to require methyl-CpG sequences containing a flanking run of A/T rich DNA for high affinity binding. Finally, biochemical fractionation of nuclear proteins revealed activities that phosphorylate MeCP2, and the potential affects of this modification were explored.
3
Lyst, Matthew James. "Biochemical analysis of MBD1." Thesis, University of Edinburgh, 2009. http://hdl.handle.net/1842/3931.
Анотація:
Methylation of cytosines within CpG dinucleotides is a feature of vertebrate DNA. The precise role of DNA methylation is unknown to date, although it has been implicated in several processes relating to transcriptional regulation. One approach to study DNA methylation is the characterization of proteins that bind specifically to methylated DNA. One such family of proteins is the methyl-CpG binding domain (MBD) containing family and MBD1 is a member of this family. MBD1 is implicated in transcriptional repression and various mechanisms by which it might bring about gene silencing have been proposed. These are mainly based on studies reporting interactions between MBD1 and various proteins that regulate chromatin structure. Also MBD1 function can be modified by PIAS proteins, which stimulate its conjugation to SUMO (small ubiquitinlike modifier).The original aim of this work was to address two questions about MBD1: (1) Does MBD1 form part of a stable complex with other factors, and if so, what are the identities of the other components? Purification of MBD1 revealed the presence of no stably bound interacting proteins. However, some evidence indicates MBD1 may interact with itself and form dimers, a finding which impacts on many aspects of the function of MBD1. Also a proteomics screen for transient interaction partners identified candidate binding partners for MBD1 and the related protein MeCP2, which may throw light on the function of these proteins. (2) Are there any activities which regulate MBD1 function by the removal of SUMO from this protein? No activities capable of removing SUMO from native MBD1 were found but it was demonstrated that this modification leads to the destabilization of MBD1 in vitro. The relevance of this finding in vivo is yet to be determined.
4
Hairer, Gabriel. "Fluidic microsystems for biochemical analysis." Aachen Shaker, 2009. http://d-nb.info/999573519/04.
5
McEuen, Scott Jacob. "Thermal analysis of biochemical systems." Thesis, Massachusetts Institute of Technology, 2013. http://hdl.handle.net/1721.1/81702.
Анотація:
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2013.Cataloged from PDF version of thesis.
Includes bibliographical references (p. 109-112).
Scientists, both academic and industrial, develop two main types of drugs: 1) small molecule drugs, which are usually chemically synthesized and are taken orally and 2) large molecule, biotherapeutic, or protein-based drugs, which are often synthesized via ribosome transcription in bacteria cells and are injected. Historically, the majority of drug development, revenue, and products has come from small molecule drugs. However, recently biotherapeutic drugs have become more common due to their increased potency and specificity (the ability to chemically bond to the targeted protein of interest). Researchers now estimate that as much as 50% of current drug development activities (pre-market approval) are focused on these protein-based drugs. There are several well-documented steps necessary in the development of a new large molecule drug. One critical element during the end of the biotherapeutic drug discovery phase and the beginning of the manufacturing phase is known as preformulation or formulation development. During this stage scientists systematically test the effects of adding various excipients (non-protein additives added to enhance the protein stability, solubility, activity of the drug, etc.) to the potential large molecule drug. Differential scanning calorimetry (DSC) is a common technique used to perform these formulation studies. In a classic DSC experiment, a protein is heated from 20-80°C and the heat absorbed while the protein unfolds is measured. Many researchers prefer the use of a DSC instrument because of its label-free nature, meaning that no fluorescent or radio-labeled tag is necessary to perform the measurement. The heat absorbed during the unfolding event(s) is directly measured. However, current commercial DSC instruments suffer from high protein consumption (especially when compared to other labeled techniques), low sensitivity, and slow throughput. The aim of this thesis is to address two of the three areas mentioned above: high protein consumption and slow throughput. Since many formulation development studies are performed at therapeutic or high protein concentrations, one can reduce the experimental cell volume and thereby reduce the amount of protein material consumed. However, since there is less sample, less heat is produced. While in the literature there are several heat transfer models that describe how a DSC instrument literature there are several heat transfer models that describe how a DSC instrument functions, there are surprisingly few heat transfer models that detail how ambient temperature disturbances impact the thermal measurement. To better describe this behavior, a simplified state-space thermal model was created to predict the disturbance rejection of a custom DSC instrument. This model was verified experimentally using linear stochastic system identification techniques. To reduce sample throughput, the prototype calorimeter cell was made from disposable materials. Because the majority of protein systems are thermodynamically irreversible, at elevated temperatures the protein solution often aggregates and needs to be cleaned before a subsequent experiment can be run. This cleaning process constitutes a significant portion of the overall time to run an experiment. This thesis documents a fully functional DSC instrument that, while not completely disposable, has been designed, built, and tested with disposable microfluidic materials. Future work would then solve the technical hurdles of repeatably loading disposable microfluidic cells into the DSC instrument.
by Scott Jacob McEuen.
Ph.D.
6
Goel, Gautam. "Biochemical Systems Toolbox." Thesis, Georgia Institute of Technology, 2006. http://hdl.handle.net/1853/14509.
Анотація:
The field of biochemical systems modeling and analysis is faced with an unprecedented flood of data from experimental methodologies of molecular biology. While these techniques continue to leapfrog ahead in the speed, volume and finesse with which they generate data, the methods of data analysis and interpretation, however, are still playing the catch-up game. The notions of systems analysis have found a new foothold, under the banner of Systems Biology, with the promise of uncovering the rationale for the designs of biological systems from their parts lists, as they are generated by experimentation and sorted and managed by bioinformatics tools. With an aim to complement hypothesis-driven and reductionistic biological research, and not replace it, a systems biologist relies on the tools of mathematical and computational modeling to be able to contribute meaningfully to any ongoing bio-molecular systems research. These systems analysis tools, however, should not only have their roots steeped well in the theoretical foundations of biochemistry, mathematics and numerical computation, but they should be married to a framework that facilitates the required systems way of thought for all its users computational scientists, experimentalists and molecular biologists alike. Hopefully, such framework-based tools would go beyond just providing fancy GUIs, numerical packages for integrating ODEs and/or optimization libraries. The intent of this thesis is to present a framework and toolbox for biochemical systems modeling, with an application in metabolic pathway analysis and/or metabolic engineering.
The research presented here builds upon the tenets of a very well established and generic approach to biological systems modeling and analysis, called Biochemical Systems Theory (BST), which is almost forty years old. The nuances of modeling and practical hurdles to analysis are presented in the context of a real-time case study of analyzing the glucolytic pathway in the bacterium Lactococcus lactis. Alongside, the thesis presents the features of a MATLAB-based software application that has been built upon the framework of BST and is aptly named as Biochemical Systems Toolbox (BSTBox). The thesis presents novel contributions, made by the author during the course of his research, to state-of-the-art techniques in parameter estimation, and robustness and sensitivity analysis topics that, as this thesis will show, remain to be the most restrictive bottlenecks in the world of biological systems modeling and analysis.
7
Coe, Robert Ashley. "The introgression of novel biochemical traits into tomato, a biochemical analysis." Thesis, University of Sheffield, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.515444.
8
Hastings, Ian M. "Genetic and biochemical analyses of growth." Thesis, University of Edinburgh, 1989. http://hdl.handle.net/1842/10948.
9
Nabi, A. "Immobilized bioluminescent reagents in flow injection analysis." Thesis, University of Hull, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.381888.
10
Maharaj, Ramsey. "Genetic analysis of resistance to apple scab (Venturia inaequalis) in apple (Malus x domestica Borkh)." Thesis, University of the Western Cape, 2007. http://etd.uwc.ac.za/index.php?module=etd&action=viewtitle&id=gen8Srv25Nme4_4347_1258010463.
Анотація:
Amongst the many problems facing the apple industry, apple scab is one of the most challenging experienced by producers. This disease is caused by Venturia inaequalis, which causes lesions to develop on both the fruit and leaves. The fungus is usually controlled by extensive use of sprays, but molecular genetics have made more environmentally friendly techniques available. This study was aimed at constructing a genetic linkage map from apple, which would be used in marker-assisted selection (MAS).
11
Hairer, Gabriel [Verfasser]. "Fluidic Microsystems for Biochemical Analysis / Gabriel Hairer." Aachen : Shaker, 2009. http://d-nb.info/1124366237/34.
12
Pourkazemi, M. "Molecular and biochemical genetic analysis of stur." Thesis, Swansea University, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.638222.
Анотація:
The stock structure of two sturgeon species from the South Caspian Sea was investigated. Allozyme electrophoresis and PCR-based mDNA analysis (RFLP) was used for the study of population differentiation in the stellate sturgeon (Acipenser stellatus). The allozyme study revealed a high level of polymorphism both within and between populations. The overall average heterozygosity is estimated to be 0.108 ± 0.02 and the percentage of polymorphic loci to be 64.3%. No significant differences in allele frequencies were observed in comparisons between the four geographic regions studied. The mDNA ND 5/6 gene regions were amplified using PCR techniques followed by RFLP analysis. Nine different composite haplotypes were detected among 120 specimens. The average nucleotide and haplotype diversity within populations are estimated to be 0.009 ± 0.001 and 0.4322 ± 0.002 respectively. No significant differences in the distribution of haplotypes were observed either within or between populations. The population structure of the Russian sturgeon (Acipsenr güeldenstaedti) was investigated using PCR amplification of the mtDNA D-loop region. Seven composite haplotypes were detected and average nucleotide and haplotype diversity over all populations were found to be 0.05 ± 0.00 and 0.75 ± 0.00 (mean ± SE) respectively. Restriction digest of the mtDNA D-loop region detected two genotypes A and B with relative high frequencies of 0.5 and 0.36 respectively. A maximum of 10.8% nucleotide diversity was found between haplotypes AAAAB and BBBBF. These two genotypes (A and B) can be considered as potential genetic markers for different biological groups, stocks or seasonal races of Russian sturgeon. 100% heteroplasmy was found in Russian sturgeon and restriction digest of the mtDNA D-loop region also exhibited site heteroplasmy. PCR amplification, cloning and sequence analysis of the entire mtDNA D-loop region indicates that all five sturgeon species in the South Caspian Sea show heteroplasmy. In all five species length heteroplasmy is associated with the presence of an 82 bp sequence which is tandemly repeated in the mtDNA D-loop region.
13
Pahle, Jürgen. "Stochastic simulation and analysis of biochemical networks." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2008. http://dx.doi.org/10.18452/15786.
Анотація:
Stochastische Effekte können einen großen Einfluss auf die Funktionsweise von biochemischen Netzwerken haben. Vor allem Signalwege, z.B. Calciumsignaltransduktion, sind anfällig gegenüber zufälligen Schwankungen. Daher stellt sich die wichtige Frage, wie dadurch der Informationstransfer in diesen Systemen beeinträchtigt wird. Zunächst werden eine Reihe von stochastischen Simulationsmethoden diskutiert und systematisch klassifiziert. Dies dient als methodische Grundlage der ganzen Dissertation. Der Schwerpunkt liegt hier auf approximativen und hybriden Ansätzen, einschließlich der Hybridmethode des Softwaresystems Copasi, deren Implementierung Teil dieser Arbeit war. Die Dynamik biochemischer Systeme zeigt in den meisten Fällen einen Übergang von stochastischem zu deterministischem Verhalten mit steigender Partikelzahl. Dieser Übergang wird für Calciumsignaltransduktion und andere Systeme untersucht. Es zeigt sich, dass das Auftreten stochastischer Effekte stark von der Sensitivität des Systems abhängt. Ein Maß dafür ist die Divergenz. Systeme mit hoher Divergenz zeigen noch mit hohen Teilchenzahlen stochastische Effekte und umgekehrt. Schließlich wird der Einfluss von zufälligen Fluktuationen auf die Leistungsfähigkeit von Signalpfaden erforscht. Dazu werden simulierte sowie experimentell gemessene Calcium-Zeitreihen stochastisch an die Aktivierung eines Zielenzyms gekoppelt. Das Schätzen des informationstheoretischen Maßes Transferentropie unter unterschiedlichen zellulären Bedingungen dient zur Abschätzung des Informationstransfers. Dieser nimmt mit steigender Partikelzahl zu, ist jedoch sehr abhängig von der momentanen Dynamik (z.B. spikende, burstende oder irreguläre Oszillationen). Die hier entwickelten Methoden, wie der Gebrauch der Divergenz als Indikator für den stoch./det. Übergang oder die stochastische Kopplung und informationstheoretische Analyse mittels Transferentropie, sind wertvolle Werkzeuge für die Analyse von biochemischen Systemen.Stochastic effects in biochemical networks can affect the functioning of these systems significantly. Signaling pathways, such as calcium signal transduction, are particularly prone to random fluctuations. Thus, an important question is how this influences the information transfer in these pathways. First, a comprehensive overview and systematic classification of stochastic simulation methods is given as methodical basis for the thesis. Here, the focus is on approximate and hybrid approaches. Also, the hybrid solver in the software system Copasi is described whose implementation was part of this PhD work. Then, in most cases, the dynamic behavior of biochemical systems shows a transition from stochastic to deterministic behavior with increasing particle numbers. This transition is studied in calcium signaling as well as other test systems. It turns out that the onset of stochastic effects is very dependent on the sensitivity of the specific system quantified by its divergence. Systems with high divergence show stochastic effects even with high particle numbers and vice versa. Finally, the influence of noise on the performance of signaling pathways is investigated. Simulated and experimentally measured calcium time series are stochastically coupled to an intracellular target enzyme activation process. Then, the information transfer under different cellular conditions is estimated with the information-theoretic quantity transfer entropy. The amount of information that can be transferred increases with rising particle numbers. However, this increase is very dependent on the current dynamical mode of the system, such as spiking, bursting or irregular oscillations. The methods developed in this thesis, such as the use of the divergence as an indicator for the transition from stochastic to deterministic behavior or the stochastic coupling and information-theoretic analysis using transfer entropy, are valuable tools for the analysis of biochemical systems.
14
Bowman, Sharen. "Mitochondrial ATPase : biochemical and molecular genetic analysis." Thesis, University of Warwick, 1989. http://wrap.warwick.ac.uk/106595/.
Анотація:
S.cerevisiae mutants were isolated showing nuclear-coded resistance to the antibiotic venturicidin, a known F0ATPase binding antibiotic. Two types of mutant were identified, one of which had cross-resistance to a variety of antibiotics and appeared linked to the leu1 locus on chromosome VII, and one which was cross-resistant to chloramphenicol only and not linked to leu1. The level of resistance to venturicidin was not increased in isolated mitochondria, therefore resistance shown in both groups is believed to be due to a decrease in plasma membrane permeability to these antibiotics. The fluorescence properties of several organotin compounds, derivatives of the substituted flavones 3-hydroxyflavone (hof) and penta-hydroxyflavone (morin), were investigated on incubation with rat liver mitochondria. The compound Bu2SnBr(of) was found to show fluorescence enhancement when added to mitochondrial preparations, which could be lowered by addition of the non-fluorescent compound Bu3SnAc. Addition of Bu2SnBr(of) did not affect mitochondrial membrane potential, and conversely the energetic state of the mitochondrial inner membrane had no effect on Bu2SnBr(of) fluorescence. This compound was shown to be an inhibitor of mitochondrial ATPase, and is thought to have its binding site on the F0 moiety of that enzyme complex. The nuclear gene causing respiratory deficiency in the complementation group G57 was cloned and sequenced. This gene (PET57) encoded a protein of 36 Kdal which did not show significant homology with any known protein. The mutant strain was deficient in mitochondrial ATPase activity, but the major F1ATPase subunits were detected in mutant mitochondria, although in reduced amounts. Mutant F1 showed abnormal membrane binding and could not be isolated by standard methods. The protein encoded by the gene PET57 is transported into mitochondria and is thought to contribute to processing or assembly of one or more of the cytoplasmic subunits of the F1F0ATPase complex.
15
Zhang, Han. "Micro-Biosensor Devices for Biochemical Analysis Applications." DigitalCommons@USU, 2020. https://digitalcommons.usu.edu/etd/7712.
Анотація:
A biosensor is an analytical device integrating a biological element and a physicochemical transducer that convert a biological response into a measurable signal. The advantages of biosensors include low cost, small size, quick, sensitivity and selectivity greater than the conventional instruments. Biosensors have a wide range of applications ranging from clinical diagnostics through to environmental monitoring, agriculture industry, et al.
The different types of biosensors are classified based on the sensor device as well as the biological material. Biosensors can be broadly classified into (piezoelectric, etc.), electrochemical biosensors (potentiometric, amperometric, etc.), and optical types of biosensors (fiber optics, etc.).
Here, we introduce a novel microfluidics-integrated biosensor platform system that can be flexibly adapted to form individual biosensors for different applications. In this dissertation, we present five examples of different emerging areas with this biosensor system including anti-cancer drug screening, glucose monitoring, heavy metal elements measurement, obesity healthcare, and waterborne pathogen DNA detection. These micro-biosensors have great potential to be further developed to emerging portable sensing devices especially for the uses in the developing and undeveloped world. At the last chapter, Raman spectroscopy applied to assess gestational status and the potential for pregnancy complications is presented and discussed. This technique could significantly benefit animal reproduction.
16
Bailey, Fiona. "Biochemical analysis of human cancer-associated pseudokinases." Thesis, University of Sheffield, 2014. http://etheses.whiterose.ac.uk/6960/.
17
Robb, Allison. "Biochemical analysis of the yeast SRP receptor." Thesis, University of Edinburgh, 2002. http://hdl.handle.net/1842/14291.
Анотація:
The yeast Saccharomyces cerevisiae utilises many transport pathways for the efficient an accurate segregation of proteins to the compartments of the cell in which they function. Of these, the secretory pathway is responsible for the localisation of proteins to the endoplasmic reticulum (ER), Golgi apparatus, endocytic and vacuolar compartments and the cell surface. The first step along this pathway is the targeting of nascent polypeptides to the ER membrane. For many proteins, the signal recognition particle (SRP), a cytosolic ribonucleoprotein, and its cognate receptor (SR) on the ER membrane are responsible for this step. SRP and the SR direct proteins to the translocon, which forms an aqueous channel through which the nascent proteins are translocated or from which they are then integrated into the ER membrane. The aim of this study was to dissect incompletely understood interactions that occur at the ER membrane between SRP, SR and the translocation and to reconstitute the SRP-dependent translocation reaction with purified proteins. In particular, through 2-hybrid analysis and pull-down assays a novel interaction was identified between SR and the major translocon component Sec61p. To facilitate the study of this and other interactions, attempts were made to reconstitute the SRP-dependent targeting pathway with SR and translocon purified from yeast. It was demonstrated that SRP-dependent translocation could be reconstituted with solubilised yeast ER membrane proteins. SR was purified and shown to be functional, and the translocation reaction was shown to be stimulated by the presence of the ER-lumenal chaperone Kar2p. Preliminary experiments were also carried out that suggested that the purified translocon was active; indicating that the goal of reconstituting SRP-dependent translocation with purified components is attainable.
18
Nenchev, Vladislav. "Robustness Analysis of MAPK Signaling Cascades." Thesis, KTH, Reglerteknik, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-106223.
Анотація:
The MAPK cascade is responsible for transmitting information in the cytoplasm of the cell and regulating important fate decisions like cell division and apoptosis. Due to scarce experimental data and limited knowledge about many complex biochemical processes, existing MAPK pathway models, which exhibit bistability, have a significant structural uncertainty. Often, small perturbations of network interactions or components can reduce the bistable region significantly or make it even disappear and small fluctuations of the input can make the system switch back, which reflects its low robustness. However, real biological systems have developed significant robustness through evolution and this robustness should be reflected by the models. The main goal of the present thesis is the development of a methodology for increasing the robustness of biochemical models, which exhibit bistability. Based on modifying existing network interactions or introducing new interactions to the system, several methods for both internal and external robustification are proposed. Internal robustness is addressed through a sensitivity analysis, which deals with a linearization of the model and can be used sequentially to introduce multiple modifications to the model. The methods for external robustness improvement are based on eigenvalue placement and slope modification (drawing on the linear model) and on the identification of feedback structures (nonlinear model). Further, a way to integrate static interaction changes to the nonlinear model, so that these perturbations have only a local impact on its behavior, is proposed. The application of the methods to existing MAPK models shows that, by introducing small modifications, the internal and external robustness of models can be increased significantly and thus provides knowledge about complex dynamics and interactions that play a key role for the inherent robustness of real biological systems. Furthermore, by employing a robustness analysis, stable steady-state branches can be recovered and bistability can be induced.
19
Caicedo-Casso, Angelica G. "Period Robustness Analysis of Minimal Models for Biochemical Oscillators." University of Cincinnati / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1427980229.
20
O'Ryan, Colleen. "The biochemical analysis of southern African rhinoceros populations." Doctoral thesis, University of Cape Town, 1993. http://hdl.handle.net/11427/27118.
Анотація:
The drastic decline in the numbers of the five extant species of rhinoceroses world-wide, mainly as a result of poaching, have placed these species in imminent danger of extinction. This emphasizes the need to understand the relationships among the different species of rhinoceros. The advances in molecular biology have allowed the application of DNA-based genetic techniques to address a number of aspects of rhinoceros biology which have both academic interest and practical value to conservation management. There are four aspects to this study: Firstly, restriction endonuclease maps of mitochondrial DNA were constructed to estimate the time of divergence of Diceros bicornis (black rhinoceros) and Ceratotherium simum (white rhinoceros) from their common ancestor. Secondly, a population genetic study of the relationships among four subspecies of D. bicornis. Thirdly, the application of DNA fingerprinting to examine the intra- and inter-population relatedness in D. bicornis populations. Fourthly, a practical application of PCR to identify the origin of an unknown sample of DNA.
21
Galloon, Terry. "Biochemical and genetic properties of HPRT Cape Town." Master's thesis, University of Cape Town, 1987. http://hdl.handle.net/11427/26591.
Анотація:
An unusual partial HPRT deficient mutant, HPRT Cape Town was observed to have a low activity in erythrocyte lysates at high concentrations of the purine substrates, hypoxanthine and guanine. This substrate inhibition was not observed with the substrate PPRP. The low activity was not associated with changes in the Km or Vmax for any of the substrates (Steyn and Harley, 1984). The kinetics of the proband's enzyme was studied in lymphoblast extracts. The characteristic substrate inhibition was observed which showed that this phenomenon was not confined to erythrocytes but was a more generalized phenomenon. This result implies that the decreased HPRT activity observed in the proband is due to substrate inhibition by the purine bases. The HPRT enzyme is coded for by a gene which is located on the X chromosome (Pai et al., 1980). The proband's daughter was therefore studied in order to determine the cause of the mutation. It was not known whether the substrate inhibition was the result of a mutation in the gene coding for the enzyme, a mutation which results in altered post-translational modification or the absence or alteration of factors influencing normal HPRT kinetics. The daughter's transformed lymphoblasts exhibited growth patterns in selective media that resembled those of her father. The daughter's enzyme prepared from lymphoblast extracts exhibited the characteristic substrate inhibition. These results suggest that this cell line results from the selection of a clone or clones which have suppressed the function of the X chromosome carrying the maternal and presumably normal HPRT allele. The daughter's enzyme prepared from erythrocyte lysates exhibited intermediate enzyme activity between that of the proband and a normal control. This result suggests that the daughter is an obligate heterozygote and that the defect is due to a mutation in the HPRT gene itself. The defect was studied at the gene level. No difference was observed in the banding patterns of the proband's DNA and control DNA which were digested with various restriction enzymes and hybridized to ³²p-labelled HPRT cDNA. The size of the HPRT mRNA of the proband was the same as the control. These results imply that there is no major gene alteration; this is expected since the proband only has a partial deficiency of the enzyme. The HPRT cDNA was subcloned into a riboprobe vector, pGEM-3. The T7 promoter was used to transcribe antisense RNA strands which were then hybridized to the proband's RNA and control RNA. No difference was observed in the size of the protected fragment. This result does not exclude the possibility of a point mutation as the cause of the defect in HPRT Cape Town.
22
Zhu, Rui. "Liver-intestine cadherin (CDH17) in hepatocellular carcinoma molecular analysis and clinical implications /." Click to view the E-thesis via HKUTO, 2009. http://sunzi.lib.hku.hk/hkuto/record/B43703793.
23
Kent, Edward Lander. "Sensitivity analysis of biochemical systems using high-throughput computing." Thesis, University of Manchester, 2013. https://www.research.manchester.ac.uk/portal/en/theses/sensitivity-analysis-of-biochemical-systems-using-highthroughput-computing(80eb7aa9-d316-4a72-a6c2-731c6052ea84).html.
Анотація:
Mathematical modelling is playing an increasingly important role in helping us to understand biological systems. The construction of biological models typically requires the use of experimentally-measured parameter values. However, varying degrees of uncertainty surround virtually all parameters in these models. Sensitivity analysis is one of the most important tools for the analysis of models, and shows how the outputs of a model, such as concentrations and reaction fluxes, are dependent on the parameters which make up the input. Unfortunately, small changes in parameter values can lead to the results of a sensitivity analysis changing significantly. The results of such analyses must therefore be interpreted with caution, particularly if a high degree of uncertainty surrounds the parameter values. Global sensitivity analysis methods can help in such situations by allowing sensitivities to be calculated over a range of possible parameter values. However, these techniques are computationally expensive, particularly for larger, more detailed models. Software was developed to enable a number of computationally-intensive modelling tasks, including two global sensitivity analysis methods, to be run in parallel in a high-throughput computing environment. The use of high-throughput computing enabled the run time of these analyses to be drastically reduced, allowing models to be analysed to a degree that would otherwise be impractical or impossible. Global sensitivity analysis using high-throughput computing was performed on a selection of both theoretical and physiologically-based models. Varying degrees of parameter uncertainty were considered. These analyses revealed instances in which the results of a sensitivity analysis were valid, even under large degrees of parameter variation. Other cases were found for which only a slight change in parameter values could completely change the results of the analysis. Parameter uncertainties are a real problem in biological systems modelling. This work shows how, with the help of high-throughput computing, global sensitivity analysis can become a practical part of the modelling process.
24
Kurt, Hamza. "Photonic crystals analysis, design and biochemical sensing applications /." Diss., Available online, Georgia Institute of Technology, 2006, 2006. http://etd.gatech.edu/theses/available/etd-06252006-174301/.
Анотація:
Thesis (Ph. D.)--Electrical and Computer Engineering, Georgia Institute of Technology, 2007.Papapolymerou, John, Committee Member ; Adibi, Ali, Committee Member ; Citrin, David, Committee Chair ; Summers, Christopher, Committee Member ; Voss, Paul, Committee Member.
25
Wong, Johnson Man Su. "Biochemical and genetic analysis of excision DNA repair." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape7/PQDD_0002/NQ41344.pdf.
26
Hoang, Lee. "Genetic and biochemical analysis of structural ribosomal elements /." Diss., Digital Dissertations Database. Restricted to UC campuses, 2006. http://uclibs.org/PID/11984.
27
Zou, Rui Ghosh Avijit. "Automated sensitivity analysis on spatio-temporal biochemical systems /." Philadelphia, Pa. : Drexel University, 2007. http://hdl.handle.net/1860/1565.
28
Ruegg, Evonne Teresa Nicole. "Investigating the porphyrias through analysis of biochemical pathways." Thesis, University of Canterbury. Biochemistry, 2014. http://hdl.handle.net/10092/10257.
Анотація:
ABSTRACT
The porphyrias are a diverse group of metabolic disorders arising from diminished
activity of enzymes in the heme biosynthetic pathway. They can present with acute
neurovisceral symptoms, cutaneous symptoms, or both. The complexity of these
disorders is demonstrated by the fact that some acute porphyria patients with the
underlying genetic defect(s) are latent and asymptomatic while others present with
severe symptoms. This indicates that there is at least one other risk factor required in
addition to the genetic defect for symptom manifestation. A systematic review of the
heme biosynthetic pathway highlighted the involvement of a number of micronutrient
cofactors. An exhaustive review of the medical literature uncovered numerous reports
of micronutrient deficiencies in the porphyrias as well as successful case reports of
treatments with micronutrients. Many micronutrient deficiencies present with
symptoms similar to those in porphyria, in particular vitamin B6. It is hypothesized
that a vitamin B6 deficiency and related micronutrient deficiencies may play a major
role in the pathogenesis of the acute porphyrias. In order to further investigate the
porphyrias, a computational model of the heme biosynthetic pathway was developed
based on kinetic parameters derived from a careful analysis of the literature. This
model demonstrated aspects of normal heme biosynthesis and illustrated some of the
disordered biochemistry of acute intermittent porphyria (AIP). The testing of this
model highlighted the modifications necessary to develop a more comprehensive
model with the potential to investigated hypotheses of the disordered biochemistry of
the porphyrias as well as the discovery of new methods of treatment and symptom
control. It is concluded that vitamin B6 deficiency might be the risk factor necessary
in conjunction with the genetic defect to trigger porphyria symptoms.
29
Farrell, Angela Margaret. "Staphylococcus epidermidis lipase : biochemical and molecular genetic analysis." Thesis, University of Leeds, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.252636.
30
Halford, Katie Anne. "Biochemical analysis of yeast pre-replicative complex assembly." Thesis, University College London (University of London), 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.408271.
31
Burdge, Graham Charles. "Biochemical analysis of proteolytic fragments from desmosomal glycoproteins." Thesis, University of Southampton, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.290426.
32
He, Weiguo. "Biochemical analysis of polyketide synthases domains and modules." View abstract/electronic edition; access limited to Brown University users, 2008. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3318326.
33
Yee, Gaylin Mildred. "An integrated micromachined CMOS spectrometer for biochemical analysis /." May be available electronically:, 2007. http://proquest.umi.com/login?COPT=REJTPTU1MTUmSU5UPTAmVkVSPTI=&clientId=12498.
34
Fan, Chenguang. "Biochemical and mutational analysis of coenzyme B₁₂ biosynthesis." [Ames, Iowa : Iowa State University], 2009.
35
Ong, Mei-Lyn. "Analysis of robustness and stochasticity in biochemical networks." Thesis, Massachusetts Institute of Technology, 2012. http://hdl.handle.net/1721.1/70409.
Анотація:
Thesis (Ph. D.)--Massachusetts Institute of Technology, Computational and Systems Biology Program, 2012.Cataloged from PDF version of thesis.
Includes bibliographical references.
Cells are constantly faced with the challenge of functioning reliably while being subject to unpredictable changes from within and outside. Here, I present two studies in which I analyze how biochemical circuits that regulate signaling and gene expression can generate robustness or phenotypic variability between otherwise identical yeast cells. Using the osmosensing signaling pathway which consists of a phosphorelay connected to a MAPK cascade, we predict signaling robustness to changes in kinetic rate constants by employing a computational sensitivity analysis. Consistent with the model predictions, we find that the input-output relation of signaling activation is severely impacted by protein coding sequence changes in the MAPK cascade genes, but not the phosphorelay genes. By decoupling the network into two separate modules, we show that an input-output analysis of each of the modules can generate the observed disparity in their tolerance to kinetic parameter variations. Our analysis suggests that the input-output relation of catalytic signaling pathways i.e. MAPK cascade are intrinsically sensitive to kinetic rate perturbations. By contrast, signaling governed by stoichiometric biochemical reactions i.e. phosphorelay exhibit robust input-output functions. We further find that cells challenged to alter their input-output function mostly recovered by gaining mutations in the MAPK cascade genes, which further supports our model. We next explore how HAC1 RNA splicing contributes to heterogeneity in the unfolded protein response (UPR). We adapt the single molecule FISH (sm-FISH) method to count endogenous spliced and unspliced HAC1 transcripts in single cells. We use a stochastic bursting-transcription-and-splicing model to determine the kinetic rates from the single cell measurements. We find that the cell-to-cell variability in the degree of splicing is tightly regulated in the presence of a UPR-inducing chemical agent, but is compromised under heat stress. By considering models including extrinsic noise at the splicing or transcriptional level, we show that the increased variability in the degree of splicing under heat stress can be generated by increased fluctuations in the splicing rate. Lastly, we present an approach using sm-FISH and protein synthesis inhibitors to measure translation and we show preliminary results suggesting its feasibility.
by Mei-Lyn Ong.
Ph.D.
36
Fisher, Gemma Laura Maria. "Biochemical analysis of chromosome segregation in Bacillus subtilis." Thesis, University of Bristol, 2017. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.738555.
37
Sannazzaro, Carlos Adalberto de Camargo. "Contribuição para o estudo dos custos unitários de análises bioquímicas quantitativas realizadas pelo processo manual e pelo processo automático no laboratório de análises clínicas do hospital universitário da Universidade de São Paulo, em 1989." Universidade de São Paulo, 1993. http://www.teses.usp.br/teses/disponiveis/6/6131/tde-15012018-175512/.
Анотація:
Com o objetivo geral de elaborar e testar uma metodologia para comparar custos diretos unitários totais de análises bioquímicas quantitativas em processo manual e em processo automático no Laboratório de Análises Clínicas do Hospital Universitário da USP-LAC/HU e com os objetivos específicos de (a) aplicar a metodologia no LAC/HU, (b) avaliar se o auto-analisador era adequado à rotina, (c) qual o tempo teórico despendido por cada um dos processos - manual e automático - para realizar o total de análises requisitadas em 1989 e (d) proceder simulações do modelo de análises para situações hipotéticas a fim de verificar sua sensibilidade, foram estudados 7 tipos de análise - glicose, creatinina, uréia, sódio & potássio, ácido úrico, proteínas totais e cálcio. Adequou-se uma metodologia para avaliar o custo unitário direto total de cada um e conhecer qual processo apresentava os menores valores; os 7 tipos estudados foram submetidos a ambos no decorrer da pesquisa em 1989. Procurou-se, também, constatar se o equipamento utilizado no processo automático era adequado à rotina do HU e determinar o tempo teórico despendido por ambos os processos na execução de cada tipo de análise. O número estudado de análises foi determinado estatisticamente, o tempo de mão-de- obra gasto na execução das análises foi cronometrado, os dados referentes ao material de consumo, manutenção e depreciação foram obtidos nos respectivos processos de licitação e/ou aquisição. Para determinar os diversos custos unitários diretos totais foram selecionados os custos relevantes dos dois processos de execução e os resultados obtidos foram comparados. Verificou-se que os custos unitários diretos totais do processo manual foram menores que os do processo automático, exceto aqueles referentes à análise de sódio & potássio. Foi constatado, igualmente, pela comparação do tempo teórico despendido, se as análises dos 7 tipos fossem realizadas por ambos os processos, que o processo automático teria gasto um tempo menor que o processo manual na realização das duas etapas. Como os resultados encontrados divergiram dos esperados, pois a maioria dos custos unitários diretos totais do processo manual foi menor que os do processo automático, a pesquisa foi ampliada para serem acrescentadas 5 situações hipotéticas nas quais se admitiu, primeiramente, que dos 7 tipos de análises mencionados foram realizadas (a) 28.509 análises (número total das glicemias, o tipo mais requisitado) e (b) 47.894 análises (capacidade operacional do autoanalisador); a seguir admitiu-se que outros 4 tipos de análises-colesterol, bilirrubina, ferro e triglicérides, programados no auto-analisador e cujas análises não foram realizadas, o teriam sido nas seguintes quantidades: (a) o número real de análises executadas em 1989 das 11 análises e, também, os dois números das duas primeiras hipóteses, isto é, (b) 28.509 análises (número total das glicemias, o tipo mais requisitado) e (c) 47.894 análises (capacidade operacional do autoanalisador). Realizada a comparação do custo unitário direto total de cada um dos processos verificou-se que o processo automático, mesmo utilizando o auto-analisador em suas capacidades quantitativa e qualitativa totais, teria para a maioria das análises um custo unitário direto total maior que o do processo manual.Seven types of biochemical analyses were studied (glucose, creatinine, urea, sodium & potassium, uric acid, total proteins and calcium), in orden to design and test a methodology aiming the comparison of total unitary direct cost of quantitative biochemical analyses between a manual process and an automatic one in the Clinical Analysis Laboratory (LAC) of Hospital Universitário from the University of São Paulo (HU). The specific objectives were a) to aply the methodology in the LAC, b) to determine wether the autoanalyzer was adequate for routine work, c) to measure the theorical time spent for each one of the processes - manual and automatic - to satisfy the demand of all the analyses accomplished during 1989, and d) to simulate a model of analyses for hypothetical situations in order to test its sensitivity. A specific methodoly was designed in order to evaluate the total unitary direct cost of each of the biochemical tests and to find out which of them had the lowest values. A side observation dealt with the adequacy to HU routine of the equipment used for the automatic process. All studies were done in 1989. The sample was determined with statistical tools, the time of manual labor was chronometered and the data related to supplies, maintenance and depreciation were gathered from their bidding and/or acquisition processes. To obtain the different total unitary direct costs, a comparison among relevant costs from the processes was established. The total unitary direct costs from the manual processes were lower than the automatic ones, except for sodium & potassium. If all 7 types were done by both processes, the automatic process would have taken less time than the manual one. These findings were different from what was expected, since costs for manual processes were lower than those for automatic ones. Therefore, the research was redesigned, to add 5 new hypothetic situations: a) the 7 types equaled 28509 analyses (total of glukemia tests, the one with the largest demand); b) the 5 types equaled 47894 analyses (operational capacity of the autoanalyzer) and c) under the false assumption that cholesterol, bilirubina, iron and triglycerides were done using autoanalyzer, three situations were simulated: (a) the actual number of analyses done in 1989; (b) 28509 analyses (see a above) and (c) 47894 (see b above). Comparing the total unitary direct cost of each of the processes, it was observed that for the automatic process, even using the autoanalyzer in full capacity (quantitative and qualitative), it would be greater than for the the manual process, for most cases.
38
Angeles, Martinez Liliana. "Detailed biochemical modelling and analysis methodologies for industrial biotechnology." Thesis, University of Manchester, 2015. https://www.research.manchester.ac.uk/portal/en/theses/detailed-biochemical-modelling-and-analysis-methodologies-for-industrial-biotechnology(2cb31353-0e30-41fe-a648-49f098d07e2c).html.
Анотація:
Many industrial processes use biological agents as catalysts. In this context, the study of the cellular metabolism becomes relevant for planning the best strategies (environmental and/or genetic modifications) to manipulate the cell in order to maximise the production of a metabolite of interest and minimise the by-products one. This increases the yield of the fermentation and reduces the cost of product recovery; thereby the profitability of the process is improved. The intracellular reactions are carried out in a complex, crowded and heterogeneous medium composed by solid components (macromolecules, ions, enzymes, small solutes, etc.) in a fluid phase called cytoplasm, all of them enclosed within the cellular membrane. The interactions among the intracellular components (as well as with the extracellular environment) determine the behaviour of the organism. The modelling and simulations of these interactions help the understanding of the metabolism. The aim of this thesis is to provide generic tools for the analysis and simulation of metabolic systems under the intracellular environmental conditions. In particular, this research focuses on the estimation of metabolic fluxes and the simulation of the diffusion process. The stoichiometric models have been widely used for the calculation of unmeasured fluxes in a metabolic network, assuming the system is at steady state. The addition of thermodynamic constraints allows only the prediction of fluxes that go in the direction of the Gibbs free energy drop. The Gibbs free energy change ( ) depends on the (intracellular) environmental conditions and determine the direction, feasibility and reversibility of the reactions involved in the pathways. The thermodynamically constrained stoichiometric model proposed here allows the estimation of the range of fluxes of a metabolic network, where the information about the presence of the enzymes that catalyse the reactions can be incorporated (if available). The effect of considering a zero flux reaction as blocked or at equilibrium on the flux predictions was investigated, as well as the environmental conditions ionic strength, temperature and pH. Additionally, since the solid components within the cell occupy about 40% of its total volume, these crowding conditions could alter the thermodynamic feasibility of the pathways. For this reason, the thermodynamically constrained stoichiometric model is extended to incorporate the crowding effect. The case study used in this work is the central carbon metabolic network of Actinobacillus succinogenes for the production of succinic acid from glycerol, a by-product in the biodiesel manufacture. Moreover, the crowding conditions also affect the diffusion of the molecules. The prokaryotic cells have been widely used in fermentation processes for the production of metabolites of interest. In this type of cells the diffusion is the primary mean of the particles’ motion, so that the diffusion reduction due to the crowding conditions could affect the possibility of encounter among the reactants, decreasing the reactions’ rate and therefore the yield of the process. A methodology based on the Lattice Boltzmann Method (LBM) and the Scaled Particle Theory (SPT) is presented in this thesis for fast simulations of the diffusion of hard-disk molecules in 2D crowded systems, which also allows evaluating the effect of the molecules’ size on their diffusion.
39
López, i. Losada Raül. "Analysing toxicity for biochemical-producing organisms." Thesis, KTH, Hållbarhet och miljöteknik, 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-235713.
Анотація:
Using macroalgae as bio-feedstock for the bio-based plastic industry is a developing process that possesses inherent comparative advantages with regard to its environmental impacts compared to using other bio-feedstock sources. Thus, research effort is considered necessary to improve its competitiveness and resolve the technical challenges that it is currently facing. Within this context, this thesis aims at improving existing knowledge on ecotoxicity impacts from metals found in macroalgae tissue to microbes used within bio-reactors for their fermentation. The basis for a novel impact pathway within LCA methodologies is provided according to a fate- exposure-effect approach. Namely: microbial biota within a bio-reactor is exposed to metal that is bioaccumulated by macroalgae tissue from background sea water, which derives into potential ecotoxicity effects. This pathway can be further studied to incorporate microbial ecotoxicity in bio- reactors within current LCA practices. Under this approach, two data sets have been analysed to evaluate levels of pollution of metals in macroalgae feedstocks against their potential ecotoxicological effects in biochemicals producing microbes: one concerning metal uptake by macroalgae, including measurements on algae tissue and background sea water; and a second one including metal ecotoxicity measurements on relevant microbial species used in biochemicals production processes. As a result of this analysis, it is concluded that there is basis for including microbial ecotoxicity from macroalgae feedstock as a relevant criterion within decision-making in the bio-based plastic industry. Moreover, input for the industry is obtained as direct recommendations and score tables that can be used under case-specific scenarios for macroalgae and microbial species selection. The conducted project should be regarded as a first iteration to the problem. Further work is required in order to refine the outcome of research and maximise input recommendations for the bio-based plastic industry.
40
Serra, Marco. "Une approche innovante pour la manipulation de supports solides magnétiques en microfluidique des gouttes." Thesis, Paris Sciences et Lettres (ComUE), 2018. http://www.theses.fr/2018PSLET003.
Анотація:
La microfluidique de gouttes est un domaine en pleine essor et ce grâce à ses caractéristiques particulières (faible consommation d’échantillon et de réactifs, diminution des temps d’analyse) qui en font un candidat de choix pour les applications bioanalytiques. Cet engouement est également lié aux différentes fonctionnalités disponibles en microfluidique de gouttes, telles que la génération de gouttes, leur fusion, leur brisure, leur tri ou l’encapsulation d’objet en leur sein. Ces différentes fonctionnalités ont notamment permis de réaliser de nombreuses réactions en phase liquide.Récemment, des stratégies innovantes ont été proposées afin d’introduire une phase solide dans les gouttes et ce via la manipulation de particules magnétiques. Différentes approches ont ainsi été reportées dans la littérature, mais à ce jour aucune approche microfluidique n’a été développée qui permettrait d’extraire et de préconcentrer un analyte d’intérêt présent dans une matrice complexe le tout avec des performance comparables au format conventionnel mais avec un temps d’analyse plus court et dans un format intégré.Dans ce contexte, nous avons conçu, microfabriqué et caractérisé un nouvelle approche de microfluidique de gouttes basée sur l’intégration de structures magnétiques adjacentes au microcanal principal qui permettent de générer une force magnétique importante localement lorsque ce structures sont activées par un aimant extérieur. Notre nouvelle approche permet notamment de combiner des étapes de capture/relargage mais aussi de clean-up et ce à haut débit. Nous avons ainsi montré que cette nouvelle approche permet l’intégration de processus multi-étapes complexes. Nous l’avons illustré en mettant en œuvre cette approche pour la préparation de librairies pour le séquençage nouvelle générationDroplet microfluidics systems are experiencing a growing relevance in the bioanalytical-related fields, especially due to lower sample/reagents consumption, increased sensitivity and faster reaction time of its derived bioassays. This is due to the wide set of functionalities currently available in the droplet microfluidic toolbox (i.e., droplet generation, merging, splitting, sorting, cell encapsulation,…), fostering the implementation of homogeneous (liquid/liquid) processes. Recently, innovative strategies for the development of heterogeneous (typically solid/liquid) reactions have been proposed, based on the manipulation of functionalized magnetic solid-state supports to target specific entities. Different microfluidic principles have been presented for the manipulation of such supports; however, a robust device allowing the possibility to enrich or extract an analyte of interest from a complex matrix with performances comparable with those of lab-scale methods but guaranteeing faster processing times is still highly desired.To answer these needs, in this work we present the conception, fabrication and characterization of a novel droplet microfluidic approach based on the integration of a pair of soft magnetic components, placed adjacently to a microchannel and able to generate a strong and local magnetic force along the path of the droplet. Our concept combines both the capture/release and the clean/up functionality with the high throughput processing, including thus all the skills required for the implementation of multi-steps protocol. In particular, the size selection of nucleic acid libraries in next generation sequencing (NGS) application will be presented as a first proof of concept of our device
41
Baldwin, Samantha, and n/a. "Models for genetic analysis of polyploid plant species." University of Otago. Department of Biochemistry, 2008. http://adt.otago.ac.nz./public/adt-NZDU20090826.092431.
Анотація:
A number of major crop species, such as allohexaploid wheat and autotetraploid potato are polyploid. Potato is the fourth most important crop in terms of production and has become an important food source in many countries. Therefore, the molecular analysis was directed towards investigating ways to develop markers to assist the potato breeding process; for example breeding for powdery scab disease resistance, and tolerance to cold induced sweetening. Polyploids have more possible genotypes per population, allele dosage effects and increased marker complexity compared to diploids. Potato is also outcrossing and therefore highly heterozygous.
Various methods for detecting marker-trait associations including, linkage, quantitative trait locus (QTL) and association mapping were studied and protocols developed. A mapping population was produced and a number of traits were measured including powdery scab resistance. Powdery scab disease assays were carried out over six seasons and markers associated with disease resistance were identified. Markers associated with resistance to powdery scab were identified on chromosomes I, IV, V, VI, VIII and IX using analysis of variance (ANOVA). Linkage maps were produced for each parent of the population and QTL associated with resistance and susceptibility to disease were identified using interval mapping, which revealed QTL on chromosomes II, V, VII , VIII, IX and an unanchored linkage group. QTL were detected across years on regions of chromosomes VIII and IX. These QTL results had some overlap with the marker-trait associations that were identified using ANOVA analysis. Another marker identification technique was tested, known as association or linkage disequilibrium mapping. Alleles of candidate genes were tested for association with cold-induced sweetening using a germplasm collection. The alleles identified as important were of the apoplastic invertase and UGPase genes and a unique interaction between alleles of the apoplastic invertase and apoplastic invertase inhibitor was also detected.
This thesis describes the first study into the genetics of powdery scab resistance and the markers identified as associated with resistance will be validated for use in a marker-assisted selection (MAS) programme. The tools and resources developed as part of this thesis are vital to the potato breeding programme that requires the identification of associated molecular markers.
42
Moffatt, James. "The development and application of chemometrics to process analysis in an industrial environment." Thesis, University of Hull, 1999. http://hydra.hull.ac.uk/resources/hull:3963.
Анотація:
This thesis describes two main sections of work, an examination of a commercial product, Intrasite Gel, and the development of an algorithm for variable selection using projected latent structures.Following on from the successful development of a variable selection procedure for multivariate linear regression this work looks at transferring this idea for use with projected latent structures. The first part of this thesis will show how the variable selection algorithm was developed and used with three different data sets. The algorithm will be shown to be superior to standard projected latent structures, for linear multi-component data. Although the final algorithm developed requires considerable computing resources to carry out this is compensated for by significantly improved model predictions and robustness. The final algorithm developed is written to run using MATLAB on any computer platform that supports this application, though the principles of operation could be transferred to another method of execution, for example custom code written in C or Pascal. The approach used in the development of this method is that the ability of the model to predict unknownsamples is of far greater importance than the internal performance of the model. All the assessments of the procedures developed are based on the ability of the model to predict accurately and precisely samples that were not presented to the model during the training stage.The second section of this thesis is concerned with the study of Intrasite Gel, produced by Smith & Nephew Ltd. Hull. The material in question is a medical device intended to assist in the treatment and healing of wounds that are necrotic, sloughy or granulating. The product is characterised by its ability to maintain moisture equilibrium in a wound environment and to provide a suitable medium to encourage the growth of new cell tissue. Medical devices require registration, and as part of that registration a number of tests are made on samples to ensure that the material meets the required specifications. There was some concern at Smith & Nephew that the tests they were required to carry out as part of the device registration were not providing appropriate information about the product. Of particular interest was the fluid absorption property as it was suspected that the test has a large amount of random error associated with it and an investigation was required to examine this test and to provide an alternative procedure should the fluid absorption test prove inadequate. Also of interest to Smith & Nephew was the issue of sampling frequency, as it was felt that this should also be examined to determine whether the correct rate of sampling to ensure product quality was being carried out. The work reported here shows that the fluid absorption test as it stands is insufficient to the task of monitoring this property of Intrasite gel and that an alternative test should be considered. This work also showed that current sampling rate was too high and that the high sampling rate may in fact cause misleading assumptions as to the stability and quality of the product.
43
Mole, Simon. "Tannins : a biochemical re-analysis of their importance as anti-feedants." Thesis, University of Strathclyde, 1986. http://oleg.lib.strath.ac.uk:80/R/?func=dbin-jump-full&object_id=21472.
Анотація:
Tannins have long been thought of as antifeedants owing to their presumed digestibility-reducing properties. In this thesis information, at the molecular level, is presented in a reassessment of this assumption and the apparency theory of plant chemical defence which is dependent upon it. An introductory review provides chemical and opperational descriptions of tannins and a general outline of their ecological impact. Detailed attention is given to (i) tannin-protein complex formation and (ii), an assesment of in vivo evidence concerning the effects of tannins on herbivores. It is concluded that the evidence does not support the hypothesis that tannins uniformly reduce digestion, even though they do generally act as antifeedants. A series of crude tannin-containing plant extracts were prepared and characterised by chemical analyses and by their ability to precipitate protein and inhibit pepsin/cellulase digestion of celulose. Results indicated between-tannin variation but not that the chemical properties of crude tannins might be used to predict their interaction with the other components of a herbivore's diet. Experiments under conditions where soluble tannin-protein complexes formed and which modelled some digestive systems, showed that tannins could under varying circumstances, inhibit or promote the digestion of protein. Soluble tannin-protein complexes were also formed in the presence of bile salts when they would otherwise have occured as precipitates. In these conditions clear relief from digestibility reduction was found. In the light of these results a new model describing the effects of tannins on digestion, consistent with results obtained in vivo, is proposed.
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Guo, Xiangxue. "Biochemical and Bioinformatics Analysis of CVAB C-Terminal Domain." Digital Archive @ GSU, 2006. http://digitalarchive.gsu.edu/biology_diss/3.
Анотація:
Cytoplasmic membrane proteins CvaB and CvaA and the outer membrane protein TolC form the bacteriocin colicin V (ColV) secretion system in Escherichia coli. CvaB functions as an ATP-binding cassette transporter with nucleotide-binding motifs in the C-terminal domain (CTD). To study the role of CvaB-CTD in the ColV secretion, a truncated construct of this domain was made and over-expressed. Different forms of CvaB-CTD were obtained during purification, and were identified as monomer, dimer, and oligomer on gel filtration. Nucleotide binding was shown critical for the CvaB-CTD dimerization: oligomers could be converted into dimers by nucleotide bindings; the removal of nucleotide from dimers resulted in transient monomers followed by CTD oligomerization and aggregation; no dimer form could be cross-linked from the nucleotide-binding deficient mutant D654H. The spatial proximity of the Walker A site and ABC signature motif in CTD dimer was identified through disulfide cross-linking of mixed CvaB-CTD with mutants A530C and L630C, while mutations did not dimerize individually. Those results indicated that the CvaB-CTD formed a nucleotide-dependent head-to-tail dimer. Molecular basis of differential nucleotide bindings was also studied through bioinformatics prediction and biochemical verification. Through sequence alignment and homology modeling with bound ATP or GTP, it was found that the Ser503 and Gln504 on aromatic stacking region (Y501DSQ-loop) of CvaB-CTD provided two additional hydrogen-bonds to GTP, but not to ATP. Site-directed mutations of the S503A and/or Q504L were designed based on the model. While site-directed mutagenesis studies of Walker A&B sites or the ABC signature motif affected little on the GTP-binding preference, the double mutation (S503A/Q504L) on the Y501DSQ-loop increased both ATP-binding and ATPase activity at low temperatures. The double mutant showed slight decrease of GTP-binding and about 10-fold increase of the ATP/GTP-binding ratio. Similar temperature sensitivity in nucleotide-binding and activity assays were identified in the double mutant at the same time. Mutations on the Y501DSQ-loop did not affect the ColV secretion level in vivo. Together, the Y501DSQ-loop is structurally involved in the differential binding of GTP over ATP.
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Wu, Jialiang. "Hybrid modeling and analysis of multiscale biochemical reaction networks." Diss., Georgia Institute of Technology, 2011. http://hdl.handle.net/1853/47723.
Анотація:
This dissertation addresses the development of integrative modeling strategies capable of combining deterministic and stochastic, discrete and continuous, as well as multi-scale features. The first set of studies combines the purely deterministic modeling methodology of Biochemical Systems Theory (BST) with a hybrid approach, using Functional Petri Nets, which permits the account of discrete features or events, stochasticity, and different types of delays. The efficiency and significance of this combination is demonstrated with several examples, including generic biochemical networks with feedback controls, gene regulatory modules, and dopamine based neuronal signal transduction.
A study expanding the use of stochasticity toward systems with small numbers of molecules proposes a rather general strategy for converting a deterministic process model into a corresponding stochastic model. The strategy characterizes the mathematical connection between a stochastic framework and the deterministic analog. The deterministic framework is assumed to be a generalized mass action system and the stochastic analogue is in the format of the chemical master equation. The analysis identifies situations where internal noise affecting the system needs to be taken into account for a valid conversion from a deterministic to a stochastic model. The conversion procedure is illustrated with several representative examples, including elemental reactions, Michaelis-Menten enzyme kinetics, a genetic regulatory motif, and stochastic focusing.
The last study establishes two novel, particle-based methods to simulate biochemical diffusion-reaction systems within crowded environments. These simulation methods effectively simulate and quantify crowding effects, including reduced reaction volumes, reduced diffusion rates, and reduced accessibility between potentially reacting particles. The proposed methods account for fractal-like kinetics, where the reaction rate depends on the local concentrations of the molecules undergoing the reaction. Rooted in an agent based modeling framework, this aspect of the methods offers the capacity to address sophisticated intracellular spatial effects, such as macromolecular crowding, active transport along cytoskeleton structures, and reactions on heterogeneous surfaces, as well as in porous media.
Taken together, the work in this dissertation successfully developed theories and simulation methods which extend the deterministic, continuous framework of Biochemical Systems Theory to allow the account of delays, stochasticity, discrete features or events, and spatial effects for the modeling of biological systems, which are hybrid and multiscale by nature.
46
Hyde, Stephen Charles. "Biochemical and genetic analysis of ATP-dependent transport systems." Thesis, University of Oxford, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.302926.
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Ling-Hon, Chu Matthew. "Biochemical and structural analysis of the human kinase MPS1." Thesis, University of Manchester, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.502855.
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Schell, Ursula. "Biochemical analysis of phosphorylation signalling through the Legionella pneumophila." Diss., Ludwig-Maximilians-Universität München, 2015. http://nbn-resolving.de/urn:nbn:de:bvb:19-183854.
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Jarvis, Lisa Marie. "A biochemical analysis of the antigens of Trichinella spiralis." Thesis, University of Nottingham, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.334833.
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Duarte, Julio Antonio Bargao. "Genetic and biochemical analysis of translational fidelity in yeast." Thesis, University of Kent, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.256999.