Relevant bibliographies by topics / Single cell metabolic flux

Academic literature on the topic 'Single cell metabolic flux'

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Published: 10 December 2022
Last updated: 29 January 2023

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Journal articles on the topic "Single cell metabolic flux"

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Wagner, Allon, Chao Wang, David DeTomaso, Arman Koul, Aviv Regev, Vijay K. Kuchroo, and Nir Yosef. "Cell-specific metabolic models reveal novel metabolic regulators of Th17 pathogenicity: from single-cell RNA-Seq to actionable metabolic targets." Journal of Immunology 200, no. 1_Supplement (May 1, 2018): 163.21. http://dx.doi.org/10.4049/jimmunol.200.supp.163.21.

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Abstract Cellular metabolism is a powerful regulator of immune response. In order to unbiasedly search for novel metabolic regulators of Th17 development and function, we have developed COMPASS, a computational algorithm to characterize the metabolic landscape of single cells based on single-cell RNA-Seq profiles and flux balance analysis. We used COMPASS to characterize the metabolic heterogeneity in Th17 cells, whose pathogenic state triggers auto-immunity, yet whose non-pathogenic form promotes tissue homeostasis and barrier functions. COMPASS recovered known metabolic switches and predicted that the polyamine pathway should be a novel, powerful regulator of Th17 pathogenicity. We validated the pathway’s effect through an array of transcriptome, LC/MS metabolome, and functional assays. Deletion of polyamine enzymes in T cells resulted in altered metabolic space, T cell functions and, most importantly, aggravated symptoms in EAE, a murine model of multiple sclerosis. While our study is concerned with Th17 cells, COMPASS is generally applicable, and can be used to unbiasedly characterize the metabolic states of any cell population based on its single-cell transcriptome profiles. Furthermore, COMPASS predicts metabolic switches between cell states that present testable, mechanistic hypotheses.
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Land, S. C., D. M. Porterfield, R. H. Sanger, and P. J. Smith. "The self-referencing oxygen-selective microelectrode: detection of transmembrane oxygen flux from single cells." Journal of Experimental Biology 202, no. 2 (January 15, 1999): 211–18. http://dx.doi.org/10.1242/jeb.202.2.211.

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A self-referencing, polarographic, oxygen-selective microelectrode was developed for measuring oxygen fluxes from single cells. This technique is based on the translational movement of the microelectrode at a known frequency through an oxygen gradient, between known points. The differential current of the electrode was converted into a directional measurement of flux using the Fick equation. Operational characteristics of the technique were determined using artificial gradients. Calculated oxygen flux values matched theoretical values derived from static measurements. A test preparation, an isolated neuron, yielded an oxygen flux of 11.46+/−1.43 pmol cm-2 s-1 (mean +/− s.e.m.), a value in agreement with those available in the literature for single cells. Microinjection of metabolic substrates or a metabolic uncoupler increased oxygen flux, whereas microinjection of KCN decreased oxygen flux. In the filamentous alga Spirogyra greveilina, the probe could easily differentiate a 16.6% difference in oxygen flux with respect to the position of the spiral chloroplast (13.3+/−0.4 pmol cm-2 s-1 at the chloroplast and 11.4+/−0.4 pmol cm-2 s-1 between chloroplasts), despite the fact that these positions averaged only 10.6+/−1.8 microm apart (means +/− s.e.m.). A light response experiment showed real-time changes in measured oxygen flux correlated with changes in lighting. Taken together, these results show that the self-referencing oxygen microelectrode technique can be used to detect local oxygen fluxes with a high level of sensitivity and spatial resolution in real time. The oxygen fluxes detected reliably correlated with the metabolic state of the cell.
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Lee, Geonhui, Thomas Ruan, Claudia Wong, Kofi Deh, Alli Abolarin, Alexander Correa, Kayvan R. Keshari, and Sangmoo Jeong. "Micro-Slab Coil Design for Hyperpolarized Metabolic Flux Analysis in Multiple Samples." Bioengineering 10, no. 1 (December 21, 2022): 14. http://dx.doi.org/10.3390/bioengineering10010014.

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Abnormal metabolism is a hallmark of cancer cells. Accumulating evidence suggests that metabolic changes are likely to occur before other cellular responses in cancer cells upon drug treatment. Therefore, the metabolic activity or flux in cancer cells could be a potent biomarker for cancer detection and treatment monitoring. Magnetic resonance (MR)-based sensing technologies have been developed with hyperpolarized molecules for real-time flux analysis, but they still suffer from low sensitivity and throughput. To address this limitation, we have developed an innovative miniaturized MR coil, termed micro-slab MR coil, for simultaneous analysis of metabolic flux in multiple samples. Combining this approach with hyperpolarized probes, we were able to quantify the pyruvate-to-lactate flux in two different leukemic cell lines in a non-destructive manner, simultaneously. Further, we were able to rapidly assess flux changes with drug treatment in a single hyperpolarization experiment. This new multi-sample system has the potential to transform our ability to assess metabolic dynamics at scale.
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Wagner, Allon, Chao Wang, David DeTomaso, Julian Avila Pacheco, Sarah Zaghouani, Johannes Fessler, Elliot Akama-Garren, et al. "In Silico Modeling of Metabolic State in Single Th17 Cells Reveals Novel Regulators of Inflammation and Autoimmunity." Journal of Immunology 204, no. 1_Supplement (May 1, 2020): 150.22. http://dx.doi.org/10.4049/jimmunol.204.supp.150.22.

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Abstract Cellular metabolism is a major regulator of immune response, but it is difficult to study the metabolic status of an individual immune cell using current technologies. Here, we present Compass, an algorithm to characterize the metabolic landscape of single cells in silico based on single-cell RNA-Seq and flux balance analysis. We used Compass to study the landscape of metabolic heterogeneity in Th17 cells and search for novel metabolic regulators of their inflammatory function. In central carbon metabolism, Compass predicted a metabolic switch between glycolysis and fatty acid oxidation that mirrors the Th17 vs. Treg phenotype, which we validated through transcriptomic, metabolic and functional assays. The TCA cycle was predicted to break at two points, both of which have been independently identified by other groups in M1 macrophage polarization. Surprisingly, and contrary to common immunometabolic understanding, Compass predicted that glycolysis too was divided into functional modules, and that one of them supported an anti-inflammatory phenotype. We validate the paradoxical prediction and demonstrate that inhibition of this module promotes a pro-inflammatory transcriptional program in Th17 cells, resulting in neuroinflammation in an adoptive transfer model of autoimmune disease. In conclusion, Compass is a widely applicable algorithm to characterize metabolic states at single cell resolution. It allows associating cellular metabolic states with effector functions and detection of metabolic targets that regulate effector phenotypes. We expect it to become a widely used tool with the increasing availability of single-cell RNA-Seq data, spurred by efforts such as the human cell atlas.
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Dai, David, Nicholas Horvath, and Jeffrey Varner. "Dynamic Sequence Specific Constraint-Based Modeling of Cell-Free Protein Synthesis." Processes 6, no. 8 (August 17, 2018): 132. http://dx.doi.org/10.3390/pr6080132.

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Cell-free protein expression has emerged as an important approach in systems and synthetic biology, and a promising technology for personalized point of care medicine. Cell-free systems derived from crude whole cell extracts have shown remarkable utility as a protein synthesis technology. However, if cell-free platforms for on-demand biomanufacturing are to become a reality, the performance limits of these systems must be defined and optimized. Toward this goal, we modeled E. coli cell-free protein expression using a sequence specific dynamic constraint-based approach in which metabolite measurements were directly incorporated into the flux estimation problem. A cell-free metabolic network was constructed by removing growth associated reactions from the iAF1260 reconstruction of K-12 MG1655 E. coli. Sequence specific descriptions of transcription and translation processes were then added to this metabolic network to describe protein production. A linear programming problem was then solved over short time intervals to estimate metabolic fluxes through the augmented cell-free network, subject to material balances, time rate of change and metabolite measurement constraints. The approach captured the biphasic cell-free production of a model protein, chloramphenicol acetyltransferase. Flux variability analysis suggested that cell-free metabolism was potentially robust; for example, the rate of protein production could be met by flux through the glycolytic, pentose phosphate, or the Entner-Doudoroff pathways. Variation of the metabolite constraints revealed central carbon metabolites, specifically upper glycolysis, tricarboxylic acid (TCA) cycle, and pentose phosphate, to be the most effective at training a predictive model, while energy and amino acid measurements were less effective. Irrespective of the measurement set, the metabolic fluxes (for the most part) remained unidentifiable. These findings suggested dynamic constraint-based modeling could aid in the design of cell-free protein expression experiments for metabolite prediction, but the flux estimation problem remains challenging. Furthermore, while we modeled the cell-free production of only a single protein in this study, the sequence specific dynamic constraint-based modeling approach presented here could be extended to multi-protein synthetic circuits, RNA circuits or even small molecule production.
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Yasukawa, Tomoyuki, Andrew Glidle, Jonathan M. Cooper, and Tomokazu Matsue. "Electroanalysis of Metabolic Flux from Single Cells in Simple Picoliter-Volume Microsystems." Analytical Chemistry 74, no. 19 (October 2002): 5001–8. http://dx.doi.org/10.1021/ac025836u.

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Güell, Oriol, Francesco Alessandro Massucci, Francesc Font-Clos, Francesc Sagués, and M. Ángeles Serrano. "Mapping high-growth phenotypes in the flux space of microbial metabolism." Journal of The Royal Society Interface 12, no. 110 (September 2015): 20150543. http://dx.doi.org/10.1098/rsif.2015.0543.

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Experimental and empirical observations on cell metabolism cannot be understood as a whole without their integration into a consistent systematic framework. However, the characterization of metabolic flux phenotypes is typically reduced to the study of a single optimal state, such as maximum biomass yield that is by far the most common assumption. Here, we confront optimal growth solutions to the whole set of feasible flux phenotypes (FFPs), which provides a benchmark to assess the likelihood of optimal and high-growth states and their agreement with experimental results. In addition, FFP maps are able to uncover metabolic behaviours, such as aerobic fermentation accompanying exponential growth on sugars at nutrient excess conditions, that are unreachable using standard models based on optimality principles. The information content of the full FFP space provides us with a map to explore and evaluate metabolic behaviour and capabilities, and so it opens new avenues for biotechnological and biomedical applications.
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Sengupta, Debanti, Amy Mongersun, Tae Jin Kim, Kellen Mongersun, Rie von Eyben, Paul Abbyad, and Guillem Pratx. "Multiplexed Single-Cell Measurements of FDG Uptake and Lactate Release Using Droplet Microfluidics." Technology in Cancer Research & Treatment 18 (January 1, 2019): 153303381984106. http://dx.doi.org/10.1177/1533033819841066.

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Introduction: Glucose utilization and lactate release are 2 important indicators of cancer metabolism. Most tumors consume glucose and release lactate at a higher rate than normal tissues due to enhanced aerobic glycolysis. However, these 2 indicators of metabolism have not previously been studied on a single-cell level, in the same cell. Objective: To develop and characterize a novel droplet microfluidic device for multiplexed measurements of glucose uptake (via its analog 18F-fluorodeoxyglucose) and lactate release, in single live cells encapsulated in an array of water-in-oil droplets. Results: Surprisingly, 18F-fluorodeoxyglucose uptake and lactate release were only marginally correlated at the single-cell level, even when assayed in a standard cell line (MDA-MB-231). While 18F-fluorodeoxyglucose-avid cells released substantial amounts of lactate, the reverse was not true, and many cells released high amounts of lactate without taking up 18F-fluorodeoxyglucose. Discussion: These results confirm that cancer cells rely on multiple metabolic pathways in addition to aerobic glycolysis and that the use of these pathways is highly heterogeneous, even under controlled culture conditions. Clinically, the large cell-to-cell variability suggests that positron emission tomography measurements of 18F-fluorodeoxyglucose uptake represent metabolic flux only in an aggregate sense, not for individual cancer cells within the tumor.
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Chung, J., R. Clifford, G. Sriram, and C. Keefer. "68 Flux analysis of aerobic glycolysis in bovine blastocysts and CT1 cells." Reproduction, Fertility and Development 31, no. 1 (2019): 159. http://dx.doi.org/10.1071/rdv31n1ab68.

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Embryo quality and maternal recognition are crucial for successful initiation of bovine pregnancy. Previous studies have proposed that better quality embryos use aerobic glycolysis to meet a high demand for biomass components. While hexoses are the principal carbon sources that provide energy to glycolysis, little is known about partitioning of hexoses into metabolic pathways or alteration of partitioning when different hexoses are simultaneously available. Specific metabolic utilisation of 13C-labelled substrates can be quantified by gas chromatography-mass spectrometry, an excellent noninvasive approach for studying cellular metabolism. To assess hexose flux through central metabolism, bovine blastocysts and CT1 cells (a bovine trophectoderm cell line) were cultured in SOF-based media supplemented with combinations of 50% uniformly labelled (U) and 50% naturally abundant (NA) glucose (Glc) or fructose (Fru) (U−13C Glc+NA Glc, U−13C Fru+NA Fru, U−13C Glc+NA Fru, and U−13C Fru+NA Glc), such that total hexose concentration was 1.5mM. Metabolites in spent media from 24-h cultures of single or 5 blastocysts (40-μL drops; 5% CO2, 5% O2, 90% N2) and 1-, 2-, 3-, 6-, 8-, and 24-h incubations of CT1 cells (150 μL; ~3×104 cells per well; 5% CO2, 95% air) were extracted with a MeOH-CHCl3 reagent, derivatized, and analysed by gas chromatography-mass spectrometry. Measurement of mass isotopomer distributions of metabolites, chiefly pyruvate, lactate, and amino acids, followed by correction for natural abundances and metabolic modelling, revealed several insights. For instance, five Day 7 or Day 8 blastocysts (Day 0=fertilization) supplied with U−13C Glc+NA Fru displayed 13C enrichments of 80.3%±1.4% for pyruvate and 71.6%±2.8% for lactate, whereas when supplied with U−13C Fru+NA Glc, they displayed lower 13C enrichments of 5.7%±2.4% for pyruvate and 2.8%±0.4% lactate (mean±standard deviation, n=3 to 4). Metabolic modelling revealed that when Glc and Fru are simultaneously available, the blastocysts used 2.5±0.2 moles of Fru per 100 moles of Glc used. Furthermore, 13C enrichment of pyruvate was 42.0±0.6% when U−13C Glc+NA Glc was supplied and 37.8±2.7% when U−13C Fru+NA Fru was supplied. Lactate enrichments followed a similar trend. This indicates that, individually, Glc and Fru were utilised majorly through aerobic glycolysis with some involvement of the pentose phosphate pathway. Alanine was negligibly labelled in all of the experiments, suggesting either a low TCA flux or that alanine is diluted by extra- or intracellular amino or fatty acids. Single blastocysts and CT1 cells showed a similar labelling pattern when hexoses were available. Following Glc depletion at 8h in CT1 cultures, the 13C enrichments of alanine and citrate in the media increased, suggesting a sharp alteration of metabolic state. These findings demonstrate that metabolic flux can be comprehensively analysed for single bovine blastocysts and CT1 cell metabolism models that of the blastocyst. This project was supported by Agriculture and Food Research Initiative Competitive Grant no. 2015-67015-23237 from the USDA National Institute of Food and Agriculture.
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De Martino, A., D. Granata, E. Marinari, C. Martelli, and V. Van Kerrebroeck. "Optimal Fluxes, Reaction Replaceability, and Response to Enzymopathies in the Human Red Blood Cell." Journal of Biomedicine and Biotechnology 2010 (2010): 1–10. http://dx.doi.org/10.1155/2010/415148.

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Characterizing the capabilities, key dependencies, and response to perturbations of genome-scale metabolic networks is a basic problem with important applications. A key question concerns the identification of the potentially most harmful reaction knockouts. The integration of combinatorial methods with sampling techniques to explore the space of viable flux states may provide crucial insights on this issue. We assess the replaceability of every metabolic conversion in the human red blood cell by enumerating the alternative paths from substrate to product, obtaining a complete map of he potential damage of single enzymopathies. Sampling the space of optimal steady state fluxes in the healthy and in the mutated cell reveals both correlations and complementarity between topologic and dynamical aspects.
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Dissertations / Theses on the topic "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.

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Follstad, 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.

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Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2000.
Includes 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.
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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.

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Dissertation presented to obtain the Ph.D degree in Biochemistry, Neuroscience
Brain 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.
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Waker, Christopher A. "Metabolic Characterization of MPNST Cell Lines." Wright State University / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=wright1433182427.

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Metsger, 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.

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Karim, 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.

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The purpose of this research was to study the factors that affecting the growth and Taxol production by Taxus species. Taxol, a complex diterpene alkaloid, is approved by the FDA for the treatment of ovarian and breast cancer. It was originally isolated from the bark of Taxus brevifolia. However, the bark contains very low concentrations of Taxol. Currently, Taxol is manufactured via a semi-synthetic method, but the production is limited and Taxol is stilI an expensive drug. Plant cell culture method has been recognized as a promising alternative for Taxol production. Nevertheless, the low or unstable productivity has become an obstacle to attain high yield of Taxol. This research focused on the experimental and computational modelling aspects of Taxol production in Taxus cell cultures. Callus and cell suspension cultures were successfully initiated from the seedlings of T. baccata. The addition of 1.5 % (w/v) insoluble polyvinylpolypyrrolidone (PVPP) and use of half strength of picloram in callus maintenance medium reduced the problem of cell darkening considerably. In suspension cultures, the non-ionic XAD-4 adsorbent was added to overcome the same problem. Fructose was the best carbon source compared to sucrose and glucose. The addition of fructose (10 gIL) on day 8 and methyl jasmonate (lOO IlM) on day 10 increased Taxol production to 17 mgIL from the suspension cultures initiated from needle explants of the seedlings. The experimental data obtained from this study were used in the development of the computer models: the kinetic model, fundamental and integrated dynamic metabolic flux analysis models. The in silico Taxus metabolism was reconstructed and computational metabolic flux balancing method was used in order to obtain fluxes of all the metabolic reactions with linear programming and optimisation in GAMS environment (General Algebraic Modeling System). The objective function of optimisation was either the maximisation of the specific growth rate or the maximisation of the specific Taxol production rate. Experimental values of nutrient uptake rates such as glucose, fructose and oxygen during the course of the batch culture were used as constraints to obtain different sets of optimised flux distributions for different periods of the batch culture. The computational results indicated that the transhydrogenase reactions were important to balance the need of NADPH for biosynthetic reactions in Taxus metabolism. The variation in biomass composition, inclusion of starch biosynthesis and degradation reactions, and Taxol precursors did not affect the growth of cells significantly. When the secondary cell wall biosynthesis was incorporated in the model, both growth and Taxol production rates were reduced. An increase in in silico Taxol production was observed when methyl jasmonate elicitation was combined with phenylalanine addition. An integrated dynamic model was constructed in order to combine the abilities of Excel- VBA and GAMS to optimise the objective function, handle mathematical kinetic expressions and visualise the outputs. As an example of its application, Taxol concentrations were automatically computed after the optimisation during the time course of the batch culture. These models can be developed further and used in future in order to define some strategies such as media formulation, precursor addition and genetic engineering targets in silico in order to manipulate the metabolism and increase the Taxol yield.
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Oddsdóttir, 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.

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In this work an intersection between optimization methods and animal cell culture modeling is considered. We present optimization based methods for analyzing and building models of cell culture; models that could be used when designing the environment cells are cultivated in, i.e., medium. Since both the medium and cell line considered are complex, designing a good medium is not straightforward. Developing a model of cell metabolism is a step in facilitating medium design. In order to develop a model of the metabolism the methods presented in this work make use of an underlying metabolic reaction network and extracellular measurements. External substrates and products are connected via the relevant elementary flux modes (EFMs). Modeling from EFMs is generally limited to small networks, because the number of EFMs explodes when the underlying network size increases. The aim of this work is to enable modeling with more complex networks by presenting methods that dynamically identify a subset of the EFMs. In papers A and B we consider a model consisting of the EFMs along with the flux over each mode. In paper A we present how such a model can be decided by an optimization technique named column generation. In paper B the robustness of such a model with respect to measurement errors is considered. We show that a robust version of the underlying optimization problem in paper A can be formed and column generation applied to identify EFMs dynamically. In papers C and D a kinetic macroscopic model is considered. In paper C we show how a kinetic macroscopic model can be constructed from the EFMs. This macroscopic model is created by assuming that the flux along each EFM behaves according to Michaelis-Menten type kinetics. This modeling method has the ability to capture cell behavior in varied types of media, however the size of the underlying network is a limitation. In paper D this limitation is countered by developing an approximation algorithm, that can dynamically identify EFMs for a kinetic model.
I 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

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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.

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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.

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Adeyileka-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.

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Humans are approximately 99% similar with inter-individual differences caused in part by single-nucleotide polymorphisms (SNPs), which poses a challenge for the effective treatment of disease. Bioinformatics resources can help to store and analyse gene and protein information to address this challenge, however these resources have limitations, so the collation and biocuration of gene and protein information is required. Using the large conductance calcium- and voltage-activated potassium channel, also known as the Big Potassium (BK) channel as an example, due to its ubiquitous expression and widespread varied role in human physiology, this study aimed to prioritise SNPs with the potential to affect the function of the channel. Using a BK channel resource created with bioinformatics tools and published literature, mSlo SNPs H55Q and G57A, located in the S0-S1 linker, were prioritised and selected for lab-based verification. These SNPs flank three cysteine residues proven to modulate channel cellular distribution via palmitoylation, a reversible process shown to increase protein association with the cell membrane. The SNPs alter the predicted palmitoylation status of C56, one of the cysteine residues located in the S0-S1 linker. The cellular distribution of BK channels incorporating the SNPs was assessed using confocal microscopy and revealed that the direction and magnitude of SNP mimetic cell membrane expression was closely related to the C56 predicted palmitoylation score; a 'C56 palmitoylation pattern' was observed. It was shown that exposure to metabolic substrates glucose, palmitate and oleate modulated SNP-mimetic cellular distribution and could invert the 'C56 palmitoylation pattern', indicating that there is interplay between the metabolic status of the cell and the amino-acid composition of the channel via palmitoylation. The creation of a novel BK channel resource in this thesis highlighted the limitations, and inter-dependency of bioinformatics and lab based experimentation, whilst SNP verification experiments solidified the link between S0-S1 cysteine residues and BK cellular distribution. BK channel function is linked with a number of physiological processes; thus, the potential clinical consequences of the SNPs prioritised in this thesis require further research.
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Books on the topic "Single cell metabolic flux"

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Metabolic flux analysis: Methods and protocols. New York: Humana Press, 2014.

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Shimizu, K. Bacterial Cellular Metabolic Systems: Metabolic Regulation of a Cell System with 13C-Metabolic Flux Analysis. Elsevier Science & Technology, 2013.

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Kromer, Jens O., Lars Nielsen, and Lars M. Blank. Metabolic Flux Analysis: Methods and Protocols. Springer New York, 2016.

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Bacterial Cellular Metabolic Systems Metabolic Regulation Of A Cell System With 13cmetabolic Flux Analysis. Woodhead Publishing, 2012.

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Money, Nicholas P. 1. Microbial diversity. Oxford University Press, 2014. http://dx.doi.org/10.1093/actrade/9780199681686.003.0001.

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‘Microbial diversity’ considers the vast array of microorganisms—the smallest forms of life—which exist everywhere. The three primary groups of microorganisms are bacteria, archaea, and eukaryotes. Bacteria and archaea are prokaryotes with their genetic material held in a single chromosome. In eukaryotes, most of the genome is held in multiple chromosomes. Over 11,000 species of bacteria have been identified using microscopic identification of cell shape and metabolic activity, Gram-staining techniques, and genetic identification of RNA and DNA sequences. There are 500 named species of archaea, divided into two phyla: the euryarchaeota and the crenarchaeota. There are eight supergroupings of eukaryotes, all of them include single-celled organisms, and five are entirely microbial.
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Wordsworth, B. P. Skeletal dysplasias. Oxford University Press, 2013. http://dx.doi.org/10.1093/med/9780199642489.003.0150.

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Bone is metabolically active throughout life and metabolic disturbances may have wide-ranging consequences that are not restricted to altering its mechanics. The study of some genetic bone diseases has already provided remarkable insights into the normal regulation of bone metabolism. Skeletal dysplasias are developmental disorders of the chondro-osseous tissues commonly resulting in short stature, which is often disproportionate. The underlying mutations are often in the structural genes encoding components of the matrix but may also involve growth factors or cell signalling. In contrast, the dysostoses tend to affect single bones or groups of bones, reflecting the transient nature of the many different signalling factors to which they are responsive during development. Abnormalities of bone density (high or low) may be due to primary deficiency of bone matrix synthesis (e.g. osteogenesis imperfecta and hypophosphatasia) but may also reflect an imbalance between bone formation and resorption. This may be caused by abnormalities of bone formation (e.g. hyperostosis/sclerosteosis and osteoporosis pseudoglioma syndrome) or bone resorption (e.g. classic osteopetrosis and fibrous dysplasia).
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Reber, Arthur S. The First Minds. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780190854157.001.0001.

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The book presents a novel theory of the origins of mind and consciousness dubbed the Cellular Basis of Consciousness (CBC). It argues that sentience emerged with life itself. The most primitive unicellular species of bacteria are conscious, though it is a sentience of a primitive kind. They have minds, though they are tiny and limited in scope. There is nothing even close to this thesis in the current literature on consciousness. Hints that cells might be conscious can be found in the writings of a few cell biologists, but a fully developed theory has never been put forward before. Other approaches to the origins of consciousness are examined and shown to be seriously or fatally flawed, specifically ones based on: (a) the assumption that minds are computational and can be captured by an artificial intelligence (AI), (b) efforts to discover the neurocorrelates of mental experiences, the so-called Hard Problem, and (c) looking for consciousness in less complex species by identifying those that possess precursors of those neurocorrelates. Each of these approaches is shown to be either essentially impossible (the AI models) or so burdened by philosophical and empirical difficulties that they are effectively unworkable. The CBC approach is developed using standard models of evolutionary biology. The remarkable repertoire of single-celled species that micro- and cell-biologists have discovered is reviewed. Bacteria, for example, have sophisticated sensory and perceptual systems, learn, form memories, make decisions based on information about their environment relative to internal metabolic states, communicate with one another, and even show a primitive form of altruism. All such functions are indicators of sentience. Conversations with a caterpillar function as a literary vehicle Finally, the implications of the CBC model are discussed along with a number of related issues in evolutionary biology, philosophy of mind, the possibility of sentient plants, the ethical repercussions of universal animal sentience, and the long-range impact of adopting the CBC stance.
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Book chapters on the topic "Single cell metabolic flux"

1

Martens, D. E. "Metabolic Flux Analysis of Mammalian Cells." In Cell Engineering, 275–99. Dordrecht: Springer Netherlands, 2007. http://dx.doi.org/10.1007/1-4020-5252-9_9.

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Goudar, Chetan T., Richard Biener, James M. Piret, and Konstantin B. Konstantinov. "Metabolic Flux Estimation in Mammalian Cell Cultures." In Animal Cell Biotechnology, 301–17. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-399-8_14.

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Goudar, Chetan T., Richard K. Biener, James M. Piret, and Konstantin B. Konstantinov. "Metabolic Flux Estimation in Mammalian Cell Cultures." In Animal Cell Biotechnology, 193–209. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-733-4_13.

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van Gulik, Walter M., Wouter A. van Winden, and Joseph J. Heijnen. "Metabolic Flux Analysis, Modeling, and Engineering Solutions." In Handbook of Industrial Cell Culture, 349–92. Totowa, NJ: Humana Press, 2003. http://dx.doi.org/10.1007/978-1-59259-346-0_15.

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Sá, João V., Tiago M. Duarte, Manuel J. T. Carrondo, Paula M. Alves, and Ana P. Teixeira. "Metabolic Flux Analysis: A Powerful Tool in Animal Cell Culture." In Cell Engineering, 521–39. Cham: Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-10320-4_16.

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Krylov, Gleb, and Eby G. Friedman. "Sense Amplifier for Spin-Based Cryogenic Memory Cell." In Single Flux Quantum Integrated Circuit Design, 133–39. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-76885-0_10.

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Wu, Duojiao. "System Immunology in Metabolic Research of Dendritic Cells." In Single Cell Sequencing and Systems Immunology, 65–72. Dordrecht: Springer Netherlands, 2015. http://dx.doi.org/10.1007/978-94-017-9753-5_5.

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Niklas, Jens, and Elmar Heinzle. "Metabolic Flux Analysis in Systems Biology of Mammalian Cells." In Genomics and Systems Biology of Mammalian Cell Culture, 109–32. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/10_2011_99.

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Vasdekis, A. E., and G. Stephanopoulos. "Single-Cell Phenotypic Screening in Inverse Metabolic Engineering." In Microfluidic Methods for Molecular Biology, 189–204. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-30019-1_9.

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Goudar, Chetan, Richard Biener, Chun Zhang, James Michaels, James Piret, and Konstantin Konstantinov. "Towards Industrial Application of Quasi Real-Time Metabolic Flux Analysis for Mammalian Cell Culture." In Cell Culture Engineering, 99–118. Berlin, Heidelberg: Springer Berlin Heidelberg, 2006. http://dx.doi.org/10.1007/10_020.

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Conference papers on the topic "Single cell metabolic flux"

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Song, Ganquan, Rishabh M. Shetty, Haixin Zhu, Shashanka Ashili, Liqiang Zhang, Grace Kim, Andrew Shabilla, et al. "Multiple sensor arrays for single cell metabolic analysis." In 2013 IEEE Sensors. IEEE, 2013. http://dx.doi.org/10.1109/icsens.2013.6688453.

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Xue, Min, Wei Wei, Yapeng Su, Young Shik Shin, Jungwoo Kim, and James R. Heath. "Abstract 1995: Developing integrated single-cell metabolic/proteomic assays." In Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1538-7445.am2015-1995.

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Suzuki, Masayasu, Hiroyuki Tanaka, and Yasunori Iribe. "Detection and collection system of target single cell based on respiration and metabolic activity." In 2009 International Symposium on Micro-NanoMechatronics and Human Science (MHS). IEEE, 2009. http://dx.doi.org/10.1109/mhs.2009.5351919.

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Gogolewski, Krzysztof, and Anna Gambin. "PCA-like Methods for the Integration of Single Cell RNA-seq Data with Metabolic Networks." In 2018 IEEE 8th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS). IEEE, 2018. http://dx.doi.org/10.1109/iccabs.2018.8542112.

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Ashili, Shashanka P., Laimonas Kelbauskas, Jeff Houkal, Dean Smith, Yanqing Tian, Cody Youngbull, Haixin Zhu, et al. "Automated platform for multiparameter stimulus response studies of metabolic activity at the single-cell level." In SPIE MOEMS-MEMS, edited by Holger Becker and Bonnie L. Gray. SPIE, 2011. http://dx.doi.org/10.1117/12.875438.

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Wu, D., D. Harrison, T. Szasz, C. F. Yeh, A. Y. Meliton, R. T. Huang, T. P. Shentu, et al. "Single-Cell Metabolic Imaging Reveals a Slc2a3/RhoA-Dependent Glycolytic Burst in Motile Endothelial Cells." In American Thoracic Society 2022 International Conference, May 13-18, 2022 - San Francisco, CA. American Thoracic Society, 2022. http://dx.doi.org/10.1164/ajrccm-conference.2022.205.1_meetingabstracts.a5748.

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Achreja, Abhinav, Hongyun Zhao, Ziwen Zhu, Jonathan Gerszberg, Marina Y. Konopleva, Michael Andreeff, and Deepak Nagrath. "Abstract 439: Metabolic flux analysis reveals targets to sensitize chemoresistance in acute myeloid leukemia induced by mesenchymal stromal cell-derived exosomes." In Proceedings: AACR Annual Meeting 2017; April 1-5, 2017; Washington, DC. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7445.am2017-439.

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Wang, Fangzhou, and Sandeep Gupta. "Multi-cell characterization: Developing robust cells and abstraction for Rapid Single Flux Quantum (RSFQ) Logic." In 2019 IEEE International Test Conference (ITC). IEEE, 2019. http://dx.doi.org/10.1109/itc44170.2019.9000132.

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Sawada, Kazunao, Tomoki Watanabe, Hiroshi Shimada, and Yoshinao Mizugaki. "Design and Operation of ROM-Dedicated Single-Flux-Quantum Cell Comprising Splitters and Confluence Buffers." In 2015 15th International Superconductive Electronics Conference (ISEC). IEEE, 2015. http://dx.doi.org/10.1109/isec.2015.7383443.

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Dong, Guang, and Yulan Song. "Topology Optimization for the Single Phase Flow Using Two Point Flux Approximation Model." In ASME 2013 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/imece2013-65475.

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The topology optimization method is extended to solve a single phase flow in porous media optimization problem based on the Two Point Flux Approximation model. In particular, this paper discusses both strong form and matrix form equations for the flow in porous media. The design variables and design objective are well defined for this topology optimization problem, which is based on the Solid Isotropic Material with Penalization approach. The optimization problem is solved by the Generalized Sequential Approximate Optimization algorithm iteratively. To show the effectiveness of the topology optimization in solving the single phase flow in porous media, the examples of two-dimensional grid cell TPFA model with impermeable regions as constrains are presented in the numerical example section.
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Reports on the topic "Single cell metabolic flux"

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Dale, Taraka T. High Throughput Whole Cell Screening for Optimized Metabolic Flux. Office of Scientific and Technical Information (OSTI), November 2018. http://dx.doi.org/10.2172/1481959.

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Pell, Eva J., Sarah M. Assmann, Amnon Schwartz, and Hava Steinberger. Ozone Altered Stomatal/Guard Cell Function: Whole Plant and Single Cell Analysis. United States Department of Agriculture, December 2000. http://dx.doi.org/10.32747/2000.7573082.bard.

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Original objectives (revisions from original proposal are highlighted) 1. Elucidate the direct effects O3 and H2O2 on guard cell function, utilizing assays of stomatal response in isolated epidermal peels and whole cell gas exchange. 2. Determine the mechanistic basis of O3 and H2O2 effects on the plasma membrane through application of the electrophysiological technique of patch clamping to isolated guard cells. 3. Determine the relative sensitivity of Israeli cultivars of economically important crops to O3 and determine whether differential leaf conductance responses to O3 can explain relative sensitivity to the air pollutant: transfer of technological expertise to Israel. Background to the topic For a long time O3 has been known to reduce gas exchange in plants; it has however been unclear if O3 can affect the stomatal complex directly. Ion channels are essential in stomatal regulation, but O3 has never before been shown to affect these directly. Major conclusions, solution, achievements 1. Ozone inhibits light-induced stomatal opening in epidermal peels isolated from Vicia faba, Arabidopsis thaliana and Nicotiana tabacum in V. faba plants this leads to reduced assimilation without a direct effect on the photosynthetic apparatus. Stomatal opening is more sensitive to O3 than stomatal closure. 2. Ozone causes inhibition of inward K+ channels (involved in stomatal opening) while no detectable effect is observed o the outward K+ channels (stomatal closure). 3. Hydrogen peroxide inhibits stomatal opening and induces stomatal closure in epidermal peels isolated from Vicia faba. 4. Hydrogen peroxide enhances stomatal closure by increasing K+ efflux from guard cells via outward rectifying K+ channels. 5. Based on epidermal peel experiments we have indirectly shown that Ca2+ may play a role in the guard cell response to O3. However, direct measurement of the guard cell [Ca2+]cyt did not show a response to O3. 6. Three Israeli cultivars of zucchini, Clarita, Yarden and Bareqet, were shown to be relatively sensitive to O3 (0.12 ml1-1 ). 7. Two environmentally important Israeli pine species are adversely affected by O3, even at 0.050 ml1-1 , a level frequently exceeded under local tropospheric conditions. P. brutia may be better equipped than P. halepensis to tolerate O3 stress. 8. Ozone directly affects pigment biosynthesis in pine seedlings, as well as the metabolism of O5 precursors, thus affecting the allocation of resources among various metabolic pathways. 9. Ozone induces activity of antioxidant enzymes, and of ascorbate content i the mesophyll and epidermis cells of Commelina communis L. Implications, both scientific and agricultural We have improved the understanding of how O3 and H2O2 do affect guard cell and stomatal function. We have shown that economical important Israeli species like zucchini and pine are relatively sensitive to O3.
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Sharon, Amir, and Maor Bar-Peled. Identification of new glycan metabolic pathways in the fungal pathogen Botrytis cinerea and their role in fungus-plant interactions. United States Department of Agriculture, 2012. http://dx.doi.org/10.32747/2012.7597916.bard.

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The involvement of glycans in microbial adherence, recognition and signaling is often a critical determinant of pathogenesis. Although the major glycan components of fungal cell walls have been identified there is limited information available on its ‘minor sugar components’ and how these change during different stages of fungal development. Our aim was to define the role of Rhacontaining-glycans in the gray mold disease caused by the necrotrophic fungus B. cinerea. The research was built on the discovery of two genes, Bcdhand bcer, that are involved in formation of UDP-KDG and UDP-Rha, two UDP- sugars that may serve as donors for the synthesis of cell surface glycans. Objectives of the proposed research included: 1) To determine the function of B. cinereaBcDh and BcEr in glycan biosynthesis and in pathogenesis, 2) To determine the expression pattern of BcDH and BcERand cellular localization of their encoded proteins, 3) Characterize the structure and distribution of Rha- containing glycans, 4) Characterization of the UDP-sugar enzymes and potential of GTs involved in glycanrhamnosylation. To address these objectives we generated a series of B. cinereamutants with modifications in the bchdhand bcergenes and the phenotype and sugar metabolism in the resulting strains were characterized. Analysis of sugar metabolites showed that changes in the genes caused changes in primary and secondary sugars, including abolishment of rhamnose, however abolishment of rhamnose synthesis did not cause changes in the fungal phenotype. In contrast, we found that deletion of the second gene, bcer, leads to accumulation of the intermediate sugar – UDP- KDG, and that such mutants suffer from a range of defects including reduced virulence. Further analyses confirmed that UDP-KDG is toxic to the fungus. Studies on mode of action suggested that UDP-KDG might affect integrity of the fungal cell wall, possibly by inhibiting UDP-sugars metabolic enzymes. Our results confirm that bcdhand bcerrepresent a single pathway of rhamnose synthesis in B. cinerea, that rhamnose does not affect in vitro development or virulence of the fungus. We also concluded that UDP-KDG is toxic to B. cinereaand hence UDP-KDG or compounds that inhibit Er enzymes and lead to accumulation of UDP-KDG might have antifungal activity. This toxicity is likely the case with other fungi, this became apparent in a collaborative work with Prof. Bart Thomma of Wageningen University, NETHERLANDS . We have shown the deletion of ER mutant in Verticillium dahlia gave plants resistance to the fungal infection.
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