Дисертації з теми "Single cell metabolic flux"
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Zupke, Craig Allen. "Metabolic flux analysis in mammalian cell culture." Thesis, Massachusetts Institute of Technology, 1993. http://hdl.handle.net/1721.1/12661.
Повний текст джерелаFollstad, Brian D. (Brian David) 1972. "Metabolic flux analysis and population heterogeneity in mammalian cell culture." Thesis, Massachusetts Institute of Technology, 2000. http://hdl.handle.net/1721.1/28218.
Повний текст джерелаIncludes bibliographical references (p. 189-206).
Metabolic flux and population heterogeneity analysis were used to develop relations between mammalian cell physiology and specific culture environments and to formulate strategies for increasing cell culture performance. Mitochondrial characteristics associated with respiration, membrane potential, and apoptosis along with physiological state multiplicity involving both metabolism and apoptotic death played a key role in this research. Research involving the accurate calculation of metabolic flux and the analysis of cellular behavior occurring in continuous cultures set the stage for subsequent research on physiological state multiplicity. This phenomena was observed in continuous cultures when at the same dilution rate, two physiologically different cultures were obtained which exhibited similar growth rates and viabilities but drastically different cell concentrations. Metabolic flux analysis conducted using metabolite and gas exchange rate measurements revealed a more efficient culture for the steady state with the higher cell concentration, as measured by the fraction of pyruvate carbon flux shuttled into the tri-carboxylic (TCA) cycle for energy generation. This metabolic adaptation was unlikely due to favorable genetic mutations and was implemented in subsequent research aimed at improving cell culture performance. A hypothesis stating that mitochondrial physiology and cellular physiology are correlated was tested and confirmed. A mammalian cell population was separated using FACS into subpopulations based on their mean mitochondrial membrane potential (MMP) as measured using the common mitochondrial stain, Rhodamine 123. The MMP sorted subpopulations were subjected to apoptosis inducers, and the apoptotic death was characterized both morphologically through the determination of apoptosis related chromatin condensation and also biochemically through the measurement of caspase-3 enzymatic activity. The results showed dramatic differences in apoptotic death kinetics with the higher MMP subpopulations demonstrating a higher resistance to apoptotic death. These results were applied in the development of novel fed-batch feeding and operating strategies. The first strategy showed that overfeeding cells later in culture leads to an increase in culture viable cell concentration, viability, and productivity. The second strategy showed that cell populations with a higher mean MMP are able to resist apoptosis during fed-batch culture. These results indicate that mammalian cell populations have considerable flexibility in their ability to redistribute metabolic flux in central carbon metabolism. Furthermore, these cell populations contain subpopulations that vary in their resistance to apoptotic death. The analysis of mitochondrial physiology and metabolic flux led to these discoveries, and these areas will play a key role in future mammalian cell culture research.
by Brian D. Follstad.
Ph.D.
Amaral, Ana Isabel Porém. "Metabolic flux analysis of neural cell metabolism in primary cultures." Doctoral thesis, Universidade Nova de Lisboa. Instituto de Tecnologia Química e Biológica, 2011. http://hdl.handle.net/10362/6849.
Повний текст джерелаBrain energy metabolism results from a complex group of pathways and trafficking mechanisms between all cellular components in the brain, and importantly provides the energy for sustaining most brain functions. In recent decades, 13C nuclear magnetic resonance (NMR) spectroscopy and metabolic modelling tools allowed quantifying the main cerebral metabolic fluxes in vitro and in vivo. These investigations contributed significantly to elucidate neuro-glial metabolic interactions, cerebral metabolic compartmentation and the individual contribution of neurons and astrocytes to brain energetics. However, many issues in this field remain unclear and/or under debate.
To the financial support provided by Fundação para a Ciência a Tecnologia (SFRH/BD/29666/2006; PTDC/BIO/69407/2006) and to the Clinigene – NoE (LSHBCT2006- 010933). I further acknowledge the Norwegian Research Council for a fellowship that allowed me to perform part of my PhD work at NTNU, Norway.
Waker, Christopher A. "Metabolic Characterization of MPNST Cell Lines." Wright State University / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=wright1433182427.
Повний текст джерелаMetsger, Maria [Verfasser]. "Single-cell transcriptome analysis of metabolic stress response in macrophages / Maria Metsger." Berlin : Freie Universität Berlin, 2017. http://d-nb.info/1149050527/34.
Повний текст джерелаKarim, Khairiah Abd. "Study of factors that affect growth and taxol production in Taxus spp. cell cultures : application of metabolic flux analysis." Thesis, University of Manchester, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.595834.
Повний текст джерелаOddsdóttir, Hildur Æsa. "Macroscopic Modeling of Metabolic Reaction Networks and Dynamic Identification of Elementary Flux Modes by Column Generation." Doctoral thesis, KTH, Optimeringslära och systemteori, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-172367.
Повний текст джерелаI denna avhandling betraktar vi korsningen mellan optimeringsmetoder och modellering av djurcellodling.Vi presenterar optimeringsbaserade metoder för att analysera och bygga modeller av cellkulturer. Dessa modeller kan användas vid konstruktionen av den miljö som cellerna ska odlas i, dvs, medium.Eftersom både mediet och cellinjen är komplexa är det inte okomplicerat att utforma ett bra medium. Att utveckla en modell av cellernas ämnesomsättning är ett steg för att underlätta designen av mediet. För att utveckla en modell av metabolismen kommer de metoder som används i detta arbete att utnyttja ett underliggande metaboliskt reaktions\-nätverk och extracellulära mätningar. Externa substrat och produkter är sammankopplade via de relevanta elementära metaboliska vägarna (EFM).Modellering med hjälp av EFM är i allmänhet begränsad till små nätverk eftersom antalet EFM exploderar när de underliggande nätverket ökar i storlek. Målet med detta arbete är att möjliggöra modellering med mer komplexa nätverk genom att presentera metoder som dynamiskt identifierar en delmängd av EFM. I artikel A och B betraktar vi en modell som består av EFM och ett flöde över varje EFM.I artikel A presenterar vi hur en sådan modell kan bestämmas med hjälp av en optimeringsteknik som kallas kolumngenerering.I artikel A undersöker vi hur robust en sådan modell är med avseende till mätfel. Vi visar att en robust version av det underliggande optimeringsproblemet i artikel A kan konstrueras samt att kolumngenerering kan appliceras för att identifiera EFM dynamiskt. Artikel C och D behandlar en kinetisk makroskopisk modell. Vi visar i artikel C hur en sådan modell kan konstrueras från EFM.Denna makroskopiska modell är skapad genom att anta att flödet genom varje EFM beter sig enligt Michaelis-Menten-typ av kinetik. Denna modelleringsmetod har förmågan att fånga cellernas beteende i olika typer av media, men storleken på nätverket är en begränsning.I artikel D hanterar vi denna begränsing genom att utveckla en approximationsalgoritm som identifierar EFM dynamiskt för en kinetisk modell.
QC 20150827
Westermayer, Sonja [Verfasser], and Joachim [Akademischer Betreuer] Rädler. "Single-cell time course analysis of metabolic switching in inducible gene regulatory networks / Sonja Westermayer ; Betreuer: Joachim Rädler." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2016. http://d-nb.info/1114068128/34.
Повний текст джерелаWestermayer, Sonja Verfasser], and Joachim [Akademischer Betreuer] [Rädler. "Single-cell time course analysis of metabolic switching in inducible gene regulatory networks / Sonja Westermayer ; Betreuer: Joachim Rädler." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2016. http://d-nb.info/1114068128/34.
Повний текст джерелаAdeyileka-Tracz, Bernadette Ayokunumi. "The effect of single nucleotide polymorphisms and metabolic substrates on the cellular distribution of mammalian BK channels." Thesis, Robert Gordon University, 2017. http://hdl.handle.net/10059/2713.
Повний текст джерелаMohaghegh, Motlagh Seyed Amir H. "An Investigation into the Impact of Cell Metabolic Activity on Biofilm Formation and Flux Decline during Cross-flow Filtration of Cellulose Acetate Ultrafiltration Membranes." University of Toledo / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1310138074.
Повний текст джерелаDoineau, Raphaël. "Development of droplet-based microfluidic technology for high-throughput single-cell phenotypic screening of B cell repertoires." Thesis, Sorbonne Paris Cité, 2017. http://www.theses.fr/2017USPCC263/document.
Повний текст джерелаThe adaptive immune system plays a leading role in defense against infection. The humoral response, involving the production of antibodies, is an important component of the adaptive immune response. During an infection, specific B cells of the immune system proliferate and release large amounts of antibodies which bind selectively to the target protein (antigen) found on the invading pathogen, inducing destruction of the pathogen. However, the immune system does not always respond efficiently enough to destroy pathogens, and tolerance mechanisms prevent the generation of antibodies against human protein - such as cell surface markers on cancer cells or cytokines involved in inflammatory and autoimmune disease - that could be important therapeutic targets. Hence, there is great interest in research and development of specific antibodies that can be used for immunotherapy of patients. Due to their high affinity and selective binding to antigens, monoclonal antibodies (mAbs) have emerged as powerful therapeutic agents. Monoclonal antibodies derived from single B cells have a unique sequence and display binding affinity for a specific antigen. However, until now, the discovery of mAbs has been limited by the lack of high-throughput methods for the direct and large-scale screening of non-immortalized primary B cells to uncover rare B cells which produce the specific antibodies of clinical interest. This is now becoming possible with the emergence and improvement of in vitro compartmentalization methods for single-cell encapsulation and screening in picoliter droplets. In my PhD project, I describe the development of binding immunoassays and microfluidic devices for the direct phenotypic screening of single-cells from enriched B cell populations. This development has enabled detailed analysis of the humoral immune response, with single-cell resolution and is an essential component of an antibody-discovery pipeline coupling single-cell phenotypic screening to single-cell antibody sequencing. It is now possible, for the first time, to screen millions of single B cells based on the binding activity of the secreted antibodies and to recover the antibody sequences
Bakolo, Rodwell S. "Design and implementation of a RSFQ superconductive digital electronics cell library." Thesis, Stellenbosch : Stellenbosch University, 2011. http://hdl.handle.net/10019.1/17936.
Повний текст джерелаENGLISH ABSTRACT: Rapid Single Flux Quantum (RSFQ) cells are key in the design of complex and applicable RSFQ electronic circuits. These cells are low-level circuit elements that are used repeatedly to build larger, applicable RSFQ circuitry. Making these cells simple to layout and manufacture, but reliable for extensive use demands a careful development process for RSFQ cells. Cell functionality is verified through simulations, thereafter the cell is laid out in special software packages. Inductance of on-chip superconductor structures is extracted through careful modelling with numerical field solver software. A cell library has been developed by incorporating existing or published cells after further analysis and optimization, as well as developing new cells. Cells that have been adapted into the library include the Josephson transmission line (JTL), Splitter, Merger, D-Flip Flop (DFF), T-Flip Flop (TFF), NOT, AND, OR and XOR, DC-SFQ and SFQ-DC and PTL Driver and Receivers. New cells include NOR, NAND and XNOR. The cells were designed for the IPHT’s RSFQ1D 1kA/cmª and Hypres’ 4.5kA/cmª processes. The cells in the library have good bias current operating margins obtained through simulations (> ±26%). All cells have all the parameters listed in the thesis including extracted inductance values. In order to have a complete and verified RSFQ cell library, cells have been sent for fabrication at IPHT and Hypres facilities. These cells can now be tested on-chip, in the laboratory, to establish functionality and practical bias current margins. All test signal patterns and bias currents required for testing are defined to allow co-workers or collaborators to test the cells.
AFRIKAANSE OPSOMMING: "Rapid Single Flux Quantum" (RSFQ) selle is van sleutelbelang in die ontwerp van komplekse en toepaslike RSFQ elektroniese stroombane. Hierdie selle is laevlak stroombaanelemente wat herhaaldelik gebruik word om groter RSFQ bane mee te bou. Versigtige ontwikkeling is nodig om hierdie selle eenvoudig vir uitleg en vervaardiging te hou terwyl dit ook betroubaar is vir wye gebruik. Selfunksionaliteit word geverifieer deur middel van simulasies, waarna selle vir vervaardiging uitgelê word in spesiale sagtewarepakette. Induktansie van supergeleierstrukture op vervaardigde skyfies word deur versigtige modellering met behulp van numeriese veldoplossingsagteware onttrek. In hierdie tesis is ’n selbiblioteek ontwerp deur bestaande (gepubliseerde) selle verder te analiseer en optimeer, en deur nuwe selle te ontwerp om die biblioteek volledig te maak. Selle wat aangepas is vir hierdie biblioteek sluit die Josephson-Transmissielyn (JTL), Verdeler, Samevoeger, DWipkring (DFF), T-Wipkring (TFF), NIE, EN, OF en XOF, asook die DC-SFQ en SFQ-DC selle en Passiewe Transmissielyn (PTL) drywers en ontvangers in. Nuwe selle sluit die NOF, NEN en XNOF hekke in. Die selle is ontwerp en uitgelˆe vir beide IPHT se RSFQ1D 1kA/cmª en Hypres se4.5kA/cmª prosesse. Die selle in die biblioteek toon goeie voorspanningstroom-werksmarges, soos verkry deur simulasie (> ±26%). Parameters en berekende induktansies vir alle selle word in die tesis gelys vir naslaandoeleindes. Vir die daarstel van ’n volledige en geverifieerde RSFQ selbiblioteek is selontwerpe vir vervaardiging na IPHT en Hypres gestuur. Aangesien vervaardiging slegs een maal per jaar by IPHT gedoen word, is die skyfies egter nog nie beskikbaar nie. Na vervaardiging kan die skyfies egter getoets word om selfunksionaliteit in die laboratorium te meet. Ten einde hierdie toetsing vir enige medewerker te vergemaklik, word alle toetsparameters soos voorspanningstroom en intreeseinpatrone in die tesis gedefinieer.
Reinsborough, Calder. "Search for Novel DNA Modifications in Saccharomyces cerevisiae mtDNA using Single Molecule Real Time Sequencing and Effects of Mitochondrial Metabolic Dynamics on Gene Expression." Thesis, Icahn School of Medicine at Mount Sinai, 2014. http://pqdtopen.proquest.com/#viewpdf?dispub=1569125.
Повний текст джерелаIn the past five years, Single Molecule Real Time (SMRT) sequencing technology has been found to be a reliable indicator of certain epigenetic modifications in bacterial genomes. The genome of the model organism Saccharomyces cerevisiae has long been thought to be free of DNA level modification, but literature surrounding this subject is conflicting. Additionally, the mitochondria of S. cerevisiae control the transition between three distinct chronological life phases – exponential, postdiauxic, and stationary - as defined by their main metabolic processes. This study attempted to identify base modifications to mtDNA using PacBio sequencing while additionally establishing gene expression changes as a result of altered mitochondrial metabolic capabilities. PacBio results showed intriguing results but statistical analysis proved experimentation with improved protocols were necessary. Multiple genes with unknown or uncharacterized function were also shown to have significant differential expression between metabolic life phases.
Niklas, Jens [Verfasser], and Elmar [Akademischer Betreuer] Heinzle. "Primary metabolism and its regulation in the human cell line AGE1.HN – application of metabolic flux analysis for improved biopharmaceutical production / Jens Niklas. Betreuer: Elmar Heinzle." Saarbrücken : Saarländische Universitäts- und Landesbibliothek, 2012. http://d-nb.info/1052339573/34.
Повний текст джерелаHagrot, Erika. "Development of a culture system for modeling of pH effects in CHO cells." Thesis, KTH, Skolan för bioteknologi (BIO), 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-49069.
Повний текст джерелаpH är en viktig parameter i optimeringen av animalcellsprocesser och har sammankopplats med specifika konsumtions- och produktionsmönster rörande extracellulära metaboliter. Det extracellulära pH-värdets effekt på den intracellulära metabolismen är dock inte fullt klarlagd. Metabolisk flux analys är en matematisk metod som kan användas för att generera intracellulära fluxfördelningar i celler, exempelvis som en funktion av någon yttre parameter. Det övergripande målet i detta arbete var att utveckla ett odlingssystem och experimentellt protokoll för odling av CHO-celler som kan användas för att generera data för metabolisk flux analys där målet är att studera effekten av pH på den intracellulära cellmetabolismen. En IgG-producerande CHO-cellslinje odlades först i skakkolv för att välja ut ett akademiskt kemiskt definierat medium med känd sammansättning. Därefter följde försök att anpassa cellerna till det valda mediet. Det visade sig att ett kommersiellt medium behövde tillsättas för att ge godtagbar tillväxt och viabilitet. Effekten av den biologiska bufferten HEPES på cellernas tillväxt och viabilitet, samt pH-stabiliteten under odling, undersöktes också genom odling i skakkolv. HEPES-koncentrationer i det undersökta intervallet (7.5 – 45 mM) hade ingen större effekt på tillväxt och viabilitet. För de högre koncentrationerna var buffertkapaciteten något bättre precis vid inokulering. Dessa koncentrationer var dock ej tillräckliga för att ge stabilt pH under odlingen. Baserat på dessa resultat övergavs tanken på att använda skakkolvsodling för att odla celler vid olika pH-värden. Ett odlingssystem och ett protokoll baserat på en 100 mL Spinnerflaska med pH-reglering specialdesignades istället för projektet. I det färdiga systemet fanns lösningar för kontinuerlig övervakning av pH och DO, stabil temperatur vid 37 °C, justerbar omrörningshastighet, samt valmöjligheten att flöda in luft, O2 och CO2. Dessutom infördes möjligheten att koppla loss flaskenheten från reglersystemet för byte av medium och provtagning. För att demonstrera systemet genomfördes en odling med den anpassade IgG-producerande cellinjen enligt principen för pseudo-perfusion vid pH 7.0. Odlingen pågick under 24 dagar och optimerade reglerinställningar identifierades. Det visades att systemet kunde understödja cellkoncentrationer upp till 11 miljoner celler per milliliter, samt hög viabilitet (> 90 %). Under den senare delen av odlingen uppnåddes stabil tillväxt, vid specifika tillväxthastigheter omkring 0.7 per dygn. Den specifika konsumtions- och produktionshastigheten för metaboliterna glukos, glutamin, laktat och NH4+, samt 20 aminosyror analyserades. Majoriteten av hastigheterna stämde överens med typisk CHO-cellsmetabolism. Den förväntade konsumtionen av majoriteten av de essentiella aminosyrorna och huvudsakliga kolkällorna glukos och glutamin konfirmerades, såväl som den associerade produktionen av bi-produkterna laktat och NH4+. Odlingssystemet och det experimentella protokollet som utvecklades i detta arbete kan användas i framtida experiment för att generera data som beskriver metaboliska profiler som funktion av extracellulärt pH. Dessa data kan sedan användas i metabolisk flux analys för att dra slutsatser om pH-effekter i CHO-celler.
Hall-Ponselè, Andrew M. "Genetic engineering of the primary/secondary metabolic interface in tobacco BY-2 cells." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:be5a3ee3-33c7-455c-b043-409987395f98.
Повний текст джерелаGuo, Weihua. "Computational Modeling of Planktonic and Biofilm Metabolism." Diss., Virginia Tech, 2017. http://hdl.handle.net/10919/79669.
Повний текст джерелаPh. D.
Soubeyrand, Eric. "Etude de la régulation par l’azote de la biosynthèse des anthocyanes dans les cellules de vigne, par une approche intégrative." Thesis, Bordeaux 2, 2013. http://www.theses.fr/2013BOR22118/document.
Повний текст джерелаAnthocyanins are polyphenol compounds very abundant in most of the plants. In grapevine, they give color to red berries and they improve red wine quality and increase the organoleptic properties of the wine. Low nitrogen supply stimulates anthocyanin production in berry skin cells of red grape varieties through regulation mechanisms that are far from being fully understood. In this context, we worked on the molecular mechanisms involved in anthocyanin biosynthesis response to nitrogen supply. Two complementary biological materials were used: grapevine cell suspensions (GT3 line) that originate from a teinturier cultivar and produce anthocyanins under normal conditions; and red grape berries of cv. Cabernet-Sauvignon cultivated in a commercial vineyard. Increases of anthocyanins synthesis in response to low nitrogen levels were confirmed in the field-grown berries and the cells suspensions. Both comparative global (microarrays) and targeted (qPCR) transcriptomic analysis showed different regulations on the expression of the genes involved in the secondary (especially the anthocyanin) and nitrogen metabolisms. The expression of most structural genes of the anthocyanin biosynthesis pathway was induced by a low nitrogen supply. Nitrogen controls also the expression of the positive (MYB transcription factors) and negative (Lateral organ Boundary Domain family protein LBD39) regulatory genes of the flavonoid pathway in grapevine. Furthermore, some genes improved in energy production (ATP, NADPH) were affected. In parallel, an integrative approach combining enzymatic activities and primary and secondary metabolites measurements with developing a Flux Balance Analysis (FBA) modeling approach was used on cells suspensions GT3. The flux maps deciphered that low nitrogen increases metabolic fluxes in shikimate and phenylpropanoid pathways and represses the majority metabolic fluxes in different pathways of primary metabolism. The two exceptions included the pentose phosphate pathway, which the flux metabolism was maintained, and the starch synthesis pathway, which was enhanced. The results obtained showed a strong link between anthocyanin synthesis and energy status (ATP, NADPH) in the berry cell suspensions
Nguyen, Vu ngoc tung. "Analysis of biochemical reaction graph : application to heterotrophic plant cell metabolism." Thesis, Bordeaux, 2015. http://www.theses.fr/2015BORD0023/document.
Повний текст джерелаNowadays, systems biology are facing the challenges of analysing the huge amount of biological data and large-scale metabolic networks. Although several methods have been developed in recent years to solve this problem, it is existing hardness in studying these data and interpreting the obtained results comprehensively. This thesis focuses on analysis of structural properties, computation of elementary flux modes and determination of minimal cut sets of the heterotrophic plant cellmetabolic network. In our research, we have collaborated with biologists to reconstructa mid-size metabolic network of this heterotrophic plant cell. This network contains about 90 nodes and 150 edges. First step, we have done the analysis of structural properties by using graph theory measures, with the aim of finding its owned organisation. The central points orhub reactions found in this step do not explain clearly the network structure. The small-world or scale-free attributes have been investigated, but they do not give more useful information. In the second step, one of the promising analysis methods, named elementary flux modes, givesa large number of solutions, around hundreds of thousands of feasible metabolic pathways that is difficult to handle them manually. In the third step, minimal cut sets computation, a dual approach of elementary flux modes, has been used to enumerate all minimal and unique sets of reactions stopping the feasible pathways found in the previous step. The number of minimal cut sets has a decreasing trend in large-scale networks in the case of growing the network size. We have also combined elementary flux modes analysis and minimal cut sets computation to find the relationship among the two sets of results. The findings reveal the importance of minimal cut sets in use of seeking the hierarchical structure of this network through elementary flux modes. We have set up the circumstance that what will be happened if glucose entry is absent. Bi analysis of small minimal cut sets we have been able to found set of reactions which has to be present to produce the different sugars or metabolites of interest in absence of glucose entry. Minimal cut sets of size 2 have been used to identify 8 reactions which play the role of the skeleton/core of our network. In addition to these first results, by using minimal cut sets of size 3, we have pointed out five reactions as the starting point of creating a new branch in creationof feasible pathways. These 13 reactions create a hierarchical classification of elementary flux modes set. It helps us understanding more clearly the production of metabolites of interest inside the plant cell metabolism
Galera, Laporta Letícia 1985. "Dynamical aspects of the regulation of bacterial proliferation." Doctoral thesis, Universitat Pompeu Fabra, 2019. http://hdl.handle.net/10803/666296.
Повний текст джерелаLa proliferació bacteriana ha estat estudiada durant més de 100 anys, però el nostre coneixement dels mecanismes que controlen els aspectes dinàmics d’aquesta encara són molt limitats. En aquesta Tesi hem estudiat, tant en cèl.lules individuals com a nivell poblacional, diferents aspectes dels principals reguladors de la proliferació cel.lular, concretament el cicle cel.lular, la producció de biomassa i la estabilitat de la membrana. El nostre objectiu ha estat ajudar a explicar com pertorbacions en aquests reguladors afecten la dinàmica de les seves respostes en una varietat de situacions. Específicament, mostrem que el doblament periòdic de gens a través del cicle cel.lular bacterià entrena parcialment un oscil.lador genètic, però aquest acoblament només és significatiu quan l’oscil.lador retorna la resposta al cicle cel.lular. Tamée hem estudiat pertorbacions en l’habilitat de les cèl.lules de produir biomassa, per exemple a través d’antibiòtics que afecten la funció ribosomal. Els nostres resultats suggereixen que la supervivència sota l’efecte d’aquests antibiòtics ve determinada per l’habilitat de les cèl.lules d’incorporar ions de magnesi, la qual pot ser capturada a través de canvis en el potencial de membrana. Finalment, mostrem que les interaccions entre diferents espècies bacterianes amb diverses sensitivitats a antibiòtics que afecten la membrana cel.lular poden donar lloc a resultats inesperats quan es troben en co-cultiu, els quals poden ser explicats de forma senzilla a partir del compartiment de l’antibiòtic entre les dues espècies.
Thierie, Jacques. "Théorie et applications des systèmes polyphasiques dispersés aux cultures cellulaires en chémostat." Doctoral thesis, Universite Libre de Bruxelles, 2005. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/211011.
Повний текст джерелаDans l’énorme majorité des cas, lorsque les cellules (procaryotes ou eucaryotes) mises en jeu dans ces systèmes sont en suspension, le formalisme de ces modèles non structurés traite le système comme s’il était homogène. Or, en toute rigueur, il est clair que cette approche n’est qu’une approximation et que nous avons à faire à des phénomènes hétérogènes, formés de plusieurs phases (solide, liquide, gazeuse) intimement mélangées. Nous désignons ces systèmes comme « polyphasiques dispersés » (SPD). Ce sont des systèmes thermodynami-quement instables, (presque) toujours ouverts.
La démarche que nous avons entreprise consiste à examiner si le fait de considérer des systèmes dits « homogènes » comme des systèmes hétérogènes (ce qu’ils sont en réalité) apporte, malgré une complication du traitement mathématique, un complément d’information significatif et pertinent.
La démarche s’est faite en deux temps :
·\
Doctorat en sciences, Spécialisation biologie moléculaire
info:eu-repo/semantics/nonPublished
Bhatia, Sugandha. "EMT & MET: Underpinning the phenotypic plasticity and chemoresistance in breast cancer." Thesis, Queensland University of Technology, 2020. https://eprints.qut.edu.au/180913/1/Sugandha_Bhatia_Thesis.pdf.
Повний текст джерелаPérez, Arroyo Carlos. "Large eddy simulations of a dual-stream jet with shockcells and noise emission analysis." Thesis, Toulouse, INPT, 2016. http://www.theses.fr/2016INPT0093/document.
Повний текст джерелаThis thesis deals with the shock-cell noise generated by under-expanded supersonic jets in single- and dualstream configurations. Shock-cell noise is generated by the interaction between the turbulent structures of the shear-layer and the shock-cell system developed in the potential core of the jet. In order to study shock-cell noise, large eddy simulations adapted to aeroacoustics are carried out using high-order compact schemes that allow for a non-dissipative nondispersive approach. The results are analyzed and compared to experimental results. In particular, an acoustic-hydrodynamic filtering is carried out in the near field in order to analyze the acoustic and hydrodynamic azimuthal modes. Moreover, a wavelet-based analysis is implemented in order to identify the relevant acoustic and hydrodynamic features of the supersonic jets
Brown, Steven Richard. "A design of experiments approach for engineering carbon metabolism in the yeast Saccharomyces cerevisiae." Thesis, University of Exeter, 2016. http://hdl.handle.net/10871/26158.
Повний текст джерела"Improved Microfabrication Technologies for Single Cell Metabolic Analysis." Master's thesis, 2014. http://hdl.handle.net/2286/R.I.25107.
Повний текст джерелаDissertation/Thesis
M.S. Electrical Engineering 2014
TSAI, CHIH-HENG, and 蔡志亨. "Reconstruction and Flux Analysis on Tissue-Specific Metabolic Model of Cancer Cell." Thesis, 2019. http://ndltd.ncl.edu.tw/handle/y6jzfp.
Повний текст джерела國立中正大學
化學工程研究所
107
Compared with normal cells, cancer cells have different metabolisms, and different cancers are clearly different from each other. Therefore, it is very important to establish a tissue-specific model to analyze the metabolism and subsequent research of cancer.In this study, we use the model optimization algorithm, Cost Optimization Reaction Dependency Assessment (CORDA) to construct the tissue-specific models. Base on model of human metabolic network ( Recon2.2 ) and the data of expression for protein from Human Protein Atlas (HPA). Use the above data, we can reconstruct genome-scale metabolic model of 19 tissues, and we use the matrix components of RPMI-1640 and DMEM as the standard for nutrient intake. Then, using Flux Variability Analysis (FVA) to calculate the maximum and minimum fluxes of the reactions in the cancer and normal cells as well as the flux of the compounds. We can discuss the similarities and differences in metabolic reprogramming in different cancers. This is quite helpful for searching for oncogenes, identifying drug targets and biomarkers.
Correia, Gonçalo dos Santos 1989. "Coupling metabolic footprinting and flux balance analysis to predict how single gene knockouts perturb microbial metabolism." Master's thesis, 2012. http://hdl.handle.net/10451/7524.
Повний текст джерелаThe model organisms Caenorhabditis elegans and E. coli form one of the simplest gut microbe host interaction models. Interventions in the microbe that increase the host longevity including inhibition of folate synthesis have been reported previously. To find novel single gene knockouts with an effect on lifespan, a screen of the Keio collection of E. coli was undertaken, and some of the genes found are directly involved in metabolism. The next step in those specific cases is to understand how these mutations perturb metabolism systematically, so that hypotheses can be generated. For that, I employed dynamic Flux Balance Analysis (dFBA), a constraint-based modeling technique capable of simulating the dynamics of metabolism in a batch culture and making predictions about changes in intracellular flux distribution. Since the specificities of the C. elegans lifespan experiments demand us to culture microbes in conditions differing from most of the published literature on E. coli physiology, novel data must be acquired to characterize and make dFBA simulations as realistic as possible. To do this exchange fluxes were measured using quantitative H NMR Time-Resolved Metabolic Footprinting. Furthermore, I also investigate the combination of TReF and dFBA as a tool in microbial metabolism studies. These approaches were tested by comparing wild type E. coli with one of the knockout strains found, ΔmetL, a knockout of the metL gene which encodes a byfunctional enzyme involved in aspartate and threonine metabolism. I found that the strain exhibits a slower growth rate than the wild type. Model simulation results revealed that reduced homoserine and methionine synthesis, as well as impaired sulfur and folate metabolism are the main effects of this knockout and the reasons for the growth deficiency. These results indicate that there are common mechanisms of the lifespan extension between ΔmetL and inhibition of folate biosynthesis and that the flux balance analysis/metabolic footprinting approach can help us understand the nature of these mechanisms.
Os organismos modelo Caenorhabditis elegans e E. coli formam um dos modelos mais simples de interacções entre micróbio do tracto digestivo e hospedeiro. Intervenções no micróbio capazes de aumentar a longevidade do hospedeiro, incluindo inibição de síntese de folatos, foram reportadas previamente. Para encontrar novas delecções génicas do micróbio capazes de aumentar a longevidade do hospedeiro, a colecção Keio de deleções génicas de E. coli foi rastreada. Alguns dos genes encontrados participam em processos metabólicos, e nesses casos, o próximpo passo é perceber como as deleções perturbam o metabolismo sistémicamente, para gerar hipóteses. Para isso, utilizo dynamic Flux Balance Analysis (dFBA), uma técnica de modelação metabólica capaz de fazer previsões sobre alterações na distribuição intracelular de fluxos. As especificidades das experiências de tempo de vida em C.elegans obrigam-nos a trabalhar em condições diferentes das usadas na maioria da literatura publicada em fisiologia de E. coli, e para dar o máximo realismo às simulações de dFBA novos dados foram adquiridos, utilizando H NMR Time-Resolved Metabolic Footprinting para medir fluxos de troca de metabolitos entre microorganismo e meio de cultura. A combinação de TReF e dFBA como ferramenta de estudo do metabolism microbiano é também investigada. Estas abordagens foram testadas ao comparar E. coli wild-type com uma das estirpes encontradas no rastreio, ΔmetL, knockout do gene metL, que codifica um enzima bifunctional participante no metabolismo de aspartato e treonina, e que exibe uma taxa de crescimento reduzida comparativamente ao wild-type. Os resultados das simulações revelaram que os principais efeitos da deleção deste gene, e as razões para a menor taxa de crescimento observada, são a produção reduzida de homoserina e metionina e os efeitos que provoca no metabolismo de folatos e enxofre. Estes resultados indicam que há mecanismos comuns na extensão da longevidade causada por esta deleção e inibição de síntese de folatos, e que a combinação metabolic footprinting/flux balance analysis pode ajudar-nos a compreender a natureza desses mecanismos.
"Development of Microfabrication Technologies on Oil-based Sealing Devices for Single Cell Metabolic Analysis." Doctoral diss., 2017. http://hdl.handle.net/2286/R.I.44196.
Повний текст джерелаDissertation/Thesis
Doctoral Dissertation Electrical Engineering 2017
Dorka, Penny. "Modelling Batch and Fed-batch Mammalian Cell Cultures for Optimizing MAb Productivity." Thesis, 2007. http://hdl.handle.net/10012/3166.
Повний текст джерелаVelagapudi, Vidya R. [Verfasser]. "Physiological and metabolic flux screening of Saccharomyces cerevisiae single knockout mutants on different carbon sources / von Vidya R. Velagapudi." 2009. http://d-nb.info/997745398/34.
Повний текст джерела"Transcriptome and Metabolic Profiling of Premalignant Progression in Barrett's Esophagus." Doctoral diss., 2014. http://hdl.handle.net/2286/R.I.25152.
Повний текст джерелаDissertation/Thesis
Ph.D. Biological Design 2014
Koshkin, Alexey. "Application of metabolic systems biology to the production of cell- and virus-based therapeutics." Master's thesis, 2015. http://hdl.handle.net/10362/16496.
Повний текст джерела"Improved Understanding of Apoptosis and Metabolism in Chinese Hamster Ovary Cell Culture." Thesis, 2011. http://hdl.handle.net/1911/70459.
Повний текст джерелаSantos, Inês Vasconcelos Miranda. "Analysis of metabolic heterogeneity over cell division cycle in non-synchronized yeast a 13c based experimental-computational approach." Doctoral thesis, 2019. http://hdl.handle.net/10316/88784.
Повний текст джерелаHá cada vez mais evidências sobre alterações metabólicas significativas ao longo do ciclo de divisão celular (CDC) em células eucarióticas. No entanto, devido a limitações técnicas, não há informação quantitativa sobre a distribuição dos fluxos metabólicos (DFM) nas fases distintas do CDC. Nomeadamente, os métodos de sincronização do CDC perturbam o metabolismo sendo propensos a artefactos e os métodos de separação de células têm baixa eficiência e uma capacidade limitada para separar adequadamente as células de acordo com o CDC. Procurando ultrapassar estas limitações, idealizámos uma metodologia para marcar e seguir o perfil de distribuição de fluxos metabólico (DFM) de células eucarióticas numa fase específica do CDC, contornando a necessidade de sincronização ou de separação de células. A metodologia idealizada assenta no uso de marcadores isotópicos para seguir o metabolismo intermediário partindo da abundância dos isótopos de monómeros constituintes dos biopolímeros que são polimerizados apenas durante as fases-alvo do CDC. Como estudo preliminar para validar o conceito, analisámos a abundância de isótopos de desoxinucleósidos e nucleósidos a partir de DNA nuclear e RNA citoplasmático, respectivamente, de Saccharomyces cerevisiae cultivada com glicose marcada com 13C afim de determinar o metabolismo na fase S e fora da fase S, respectivamente, do CDC. Neste sentido, primeiro implementámos uma abordagem baseada em GC-MS para elucidar isotopómeros posicionais dos desoxinucleósidos e nucleósidos de DNA e RNA, inspeccionando os espectros de fragmentação de seus derivados de trimetilsilil. Identificámos a porção do ião molecular que constitui os respectivos fragmentos, focando particularmente nos átomos de carbono do esqueleto molecular. Os nucleósidos fragmentados ao nível da ligação N-glicosídica geram nucleobases e / ou iões de fragmentos de ribose ou desoxirribose e seus fragmentos. Também se observaram fragmentos de nucleósidos compostos pela nucleobase e alguns carbonos do anel de ribose. No total, atribuímos inequivocamente 31 fragmentos. A fim de avaliar a viabilidade da determinação da DFM em estudo a partir de informações obtidas a partir do método GC-MS anteriormente descrito e optimizar as condições experimentais, desenvolvemos um modelo computacional do metabolismo intermediário de S. cerevisiae; é um modelo desenvolvido a partir de levantamento genómico e adequado à investigação da DFM ao longo do CDC. Conceptualizámos duas subpopulações de células – células em fase S e fora da fase S do CDC. O modelo é viável e está terminado, pronto para ser usado para uma análise de sensibilidade meticulosa tendo como fim o desenho de experiências e a respectiva análise dos fluxos metabólicos por marcação com 13C (13C-MFA). S. cerevisae foi cultivada em cultura contínua em meio enriquecido com [1,2-13C] glicose. Os desoxinucleósidos e nucleósidos de DNA e RNA, respectivamente, foram isolados separadamente e a distribuição dos isótopos de massa (DIM) dos seus fragmentos foi medida por GC-MS. Uma análise qualitativa dessa DIM mostrou que: i) a porção de ribose dos nucleosídeos pirimidínicos foi biossintetizada via ramo oxidativo da via das pentoses juntamente com vai-e-vem no ramo não oxidativo; ii) desoxirribose de desoxinucleósidos pirimidínicos foram biossintetizados via glicólise e ramo não oxidativo da via das pentoses; iii) as nucleobases das desoxipirinas foram biossintetizadas via através de um fluxo concertado de vai-e-vem entre a glicólise e o ramo não oxidativo da via das pentoses seguindo-se fluxo pelo ramo oxidativo da via da pentoses; iv) o DIM da nucleobases da citidina, desoxicitidina e timidina revelam atividade do ramo oxidativo da via das pentoses, carboxilase do piruvate e ciclo dos ácidos tricarboxílicos. Esta evidência de multiplicidade de vias metabólicas contribuintes para a biosíntese de nucleobases da citidina, desoxicitidina e timidina pode ser resultante de um tempo de meia vida mais longo dos reservatórios de aspartato. A atividade combinada da carboxilase do piruvato e do ciclo dos ácidos tricarboxílicos pode dever-se à necessidade de satisfazer o recrutamento simultâneo de biossíntese de aminoácidos e ácidos gordos a partir dos intermediários do ciclo dos ácidos tricarboxílicos, exigindo, assim, um ciclo dos ácidos tricarboxílicos activo e o reabastecimento dos seus respectivo reservatórios. Os isotopómeros 13C dos monómeros do DNA diferem dos do RNA, indicando que uma DFM heterogénea ao longo do CDC.
There is increasing evidence of extensive metabolic changes over the division cycle of eukaryotic cells. However, quantitative information about how flux redistributes in distinct phases of this cycle is lacking, due to technical difficulties. Namely, cell division cycle (CDC) synchronization methods disrupt metabolism, and are thus artifact-prone, and cell sorting methods have low throughput and a limited ability to adequately separate cells by CDC. Seeking to bypass these shortcomings, we devised a methodology to profile the metabolic flux distribution (MFD) of eukaryotic cells in a specific phase of CDC without requiring CDC synchronization or cell sorting. The general principle consists in using isotopic tracers to back trace intermediary metabolism from the isotopomer abundances of building-blocks of biopolymers that are polymerized only during the target phases of the CDC. As a proof of principle, we analyzed the isotopomer abundances of building-blocks from nuclear DNA and cytoplasmic RNA of Saccharomyces cerevisiae grown on 13Clabeled glucose to profile the metabolism in S phase and non-S-phase (respectively) of the CDC. Towards this goal, we first implemented a Gas Chromatography – Mass Spectrometry (GC-MS) based approach to elucidate positional isotopomers of nucleosides from RNA and DNA by screening the fragmentation spectra of their trimethylsilyl derivatives. We identified the molecular ion moieties retained in the respective fragment ions, focusing particularly on the carbon backbone. Nucleosides fragmented at the N-glycosidic bond provide nucleobase and/or ribose or deoxyribose fragment ions and fragments thereof. Nucleoside fragments composed of the nucleobase plus some carbons of the ribose ring were also observed. In total, we unequivocally assigned 31 fragments. In order to assess the viability of determining the sought MFD from information obtainable from the previous GC-MS method and to optimize the experimental conditions, we developed a customized genome-wide computational model of intermediary metabolism of S. cerevisiae. Its design accounts for two sub-populations of cells – in and out of S-phase of the CDC. The model is feasible, ready to be used for a meticulous sensitivity analysis, to design further experiments and to perform 13C-metabolic flux analysis (13C-MFA). A continuous culture of S. cerevisae was fed with [1,2-13C]glucose. deoxynucleosides and nucleosides from DNA and RNA, respectively, were isolated separately and the mass isotopomer distribution (MID) of their fragments was measured in GC-MS. A qualitative analysis of these MID showed that: i) the ribose moiety of pyrimidinic nucleosides was biosynthesized via the oxidative branch of pentose phosphate pathway (PPP) followed by shunting back and forward in the non-oxidative branch of PPP; ii) deoxyribose of pyrimidinic deoxynucleosides was biosynthesized via glycolysis followed by the non-oxidative branch of PPP; iii) nucleobases of deoxypurines were biosynthesized via a concerted flux of shunting back and forward between glycolysis and non-oxidative PPP followed by the oxidative branch of PPP; iv) the MID of nucleobases of cytidine, deoxycytidine and thymidine reveal activity of the oxidative branch of PPP, PC and TCA cycle. This would come from the longer turnover of TCA cycle related pools. The concerted activity of PC and TCA cycle may satisfy the joint demand for amino acids and fatty acids biosynthesis from the intermediaries of TCA cycle, thus requiring an active TCA cycle and the respective replenishing of its pools. The 13C-isotopomers of DNA building blocks differ from those of RNA, indicating that the MFD is heterogeneous over CDC.