Relevant bibliographies by topics / Metabolic pathways analysis

Academic literature on the topic 'Metabolic pathways analysis'

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Published: 25 May 2024

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Journal articles on the topic "Metabolic pathways analysis"

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Barik, Dr Bibhuti Prasad. "In Silico Observations and Analysis of Metabolic Pathways." International Journal of Scientific Research 2, no. 11 (June 1, 2012): 44–48. http://dx.doi.org/10.15373/22778179/nov2013/14.

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Katz, J. "Mathematical analysis of metabolic pathways." American Journal of Physiology-Endocrinology and Metabolism 252, no. 4 (April 1, 1987): E571—E572. http://dx.doi.org/10.1152/ajpendo.1987.252.4.e571.

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Forst, Christian V., and Klaus Schulten. "Phylogenetic Analysis of Metabolic Pathways." Journal of Molecular Evolution 52, no. 6 (June 2001): 471–89. http://dx.doi.org/10.1007/s002390010178.

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Moreno-Sánchez, Rafael, Emma Saavedra, Sara Rodríguez-Enríquez, and Viridiana Olín-Sandoval. "Metabolic Control Analysis: A Tool for Designing Strategies to Manipulate Metabolic Pathways." Journal of Biomedicine and Biotechnology 2008 (2008): 1–30. http://dx.doi.org/10.1155/2008/597913.

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The traditional experimental approaches used for changing the flux or the concentration of a particular metabolite of a metabolic pathway have been mostly based on the inhibition or over-expression of the presumed rate-limiting step. However, the attempts to manipulate a metabolic pathway by following such approach have proved to be unsuccessful. Metabolic Control Analysis (MCA) establishes how to determine, quantitatively, the degree of control that a given enzyme exerts on flux and on the concentration of metabolites, thus substituting the intuitive, qualitative concept of rate limiting step. Moreover, MCA helps to understand (i) the underlying mechanisms by which a given enzyme exerts high or low control and (ii) why the control of the pathway is shared by several pathway enzymes and transporters. By applying MCA it is possible to identify the steps that should be modified to achieve a successful alteration of flux or metabolite concentration in pathways of biotechnological (e.g., large scale metabolite production) or clinical relevance (e.g., drug therapy). The different MCA experimental approaches developed for the determination of the flux-control distribution in several pathways are described. Full understanding of the pathway properties when working under a variety of conditions can help to attain a successful manipulation of flux and metabolite concentration.
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Mattei, Gianluca, Zhuohui Gan, Matteo Ramazzotti, Bernhard O. Palsson, and Daniel C. Zielinski. "Differential Expression Analysis Utilizing Condition-Specific Metabolic Pathways." Metabolites 13, no. 11 (November 3, 2023): 1127. http://dx.doi.org/10.3390/metabo13111127.

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Pathway analysis is ubiquitous in biological data analysis due to the ability to integrate small simultaneous changes in functionally related components. While pathways are often defined based on either manual curation or network topological properties, an attractive alternative is to generate pathways around specific functions, in which metabolism can be defined as the production and consumption of specific metabolites. In this work, we present an algorithm, termed MetPath, that calculates pathways for condition-specific production and consumption of specific metabolites. We demonstrate that these pathways have several useful properties. Pathways calculated in this manner (1) take into account the condition-specific metabolic role of a gene product, (2) are localized around defined metabolic functions, and (3) quantitatively weigh the importance of expression to a function based on the flux contribution of the gene product. We demonstrate how these pathways elucidate network interactions between genes across different growth conditions and between cell types. Furthermore, the calculated pathways compare favorably to manually curated pathways in predicting the expression correlation between genes. To facilitate the use of these pathways, we have generated a large compendium of pathways under different growth conditions for E. coli. The MetPath algorithm provides a useful tool for metabolic network-based statistical analyses of high-throughput data.
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Liao, James C. "Modelling and analysis of metabolic pathways." Current Opinion in Biotechnology 4, no. 2 (April 1993): 211–16. http://dx.doi.org/10.1016/0958-1669(93)90127-i.

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Arias-Méndez, Esteban, Diego Barquero-Morera, and Francisco J. Torres-Rojas. "Low-Cost Algorithms for Metabolic Pathway Pairwise Comparison." Biomimetics 7, no. 1 (February 21, 2022): 27. http://dx.doi.org/10.3390/biomimetics7010027.

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Metabolic pathways provide key information for achieving a better understanding of life and all its processes; this is useful information for the improvement of medicine, agronomy, pharmacy, and other similar areas. The main analysis tool used to study these pathways is based on pathway comparison, using graph data structures. Metabolic pathway comparison has been defined as a computationally complex task. In a previous work, two new algorithms were introduced to treat the problem of metabolic pathway pairwise comparison. Here we provide an extended analysis with more data and a deeper analysis of metabolic pathway comparison as listed in the discussion and results section.
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Huang, Yan, Rong Chen, Shuci Yang, Ye Chen, and Xiaoying Lü. "The Mechanism of Interaction Between Gold Nanoparticles and Human Dermal Fibroblasts Based on Integrative Analysis of Transcriptomics and Metabolomics Data." Journal of Biomedical Nanotechnology 18, no. 6 (June 1, 2022): 1562–76. http://dx.doi.org/10.1166/jbn.2022.3365.

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The aim of this paper was to combine transcriptomics and metabolomics to analyze the mechanism of gold nanoparticles (GNPs) on human dermal fibroblasts (HDFs). First, 20-nm GNPs were prepared, and the differentially expressed genes in HDFs were subsequently screened by transcriptome sequencing technology after 4, 8, and 24 h of treatment with GNPs. By comparing the metabolic pathways in which the metabolites obtained in a previous study were involved, the pathways involving both genes and metabolites were filtered, and the differentially expressed genes and metabolites with upstream and downstream relationships were screened out. The gene–metabolite–metabolic pathway network was further constructed, and the functions of metabolic pathways, genes and metabolites in the important network were analyzed and experimentally verified. The results of transcriptome sequencing experiments showed that 1904, 1216 and 489 genes were differentially expressed in HDFs after 4, 8 and 24 h of treatment with GNPs, and these genes were involved in 270, 235 and 163 biological pathways, respectively. Through the comparison and analysis of the metabolic pathways affected by the metabolites, 7, 3 and 2 metabolic pathways with genes and metabolites exhibiting upstream and downstream relationships were identified. Through analysis of the gene–metabolite–metabolic pathway network, 4 important metabolic pathways, 9 genes and 7 metabolites were identified. Combined with the results of verification experiments on oxidative stress, apoptosis, the cell cycle, the cytoskeleton and cell adhesion, it was found that GNPs regulated the synthesis of downstream metabolites through upstream genes in important metabolic pathways. GNPs inhibited oxidative stress and thus did not induce significant apoptosis, but they exerted effects on several cellular functions, including arresting the cell cycle and affecting the cytoskeleton and cell adhesion.
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Mashima, Izumi, Yu-Chieh Liao, Chieh-Hua Lin, Futoshi Nakazawa, Elaine M. Haase, Yusuke Kiyoura, and Frank A. Scannapieco. "Comparative Pan-Genome Analysis of Oral Veillonella Species." Microorganisms 9, no. 8 (August 20, 2021): 1775. http://dx.doi.org/10.3390/microorganisms9081775.

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The genus Veillonella is a common and abundant member of the oral microbiome. It includes eight species, V. atypica, V. denticariosi, V. dispar, V. infantium, V. nakazawae, V. parvula, V. rogosae and V. tobetusensis. They possess important metabolic pathways that utilize lactate as an energy source. However, the overall metabolome of these species has not been studied. To further understand the metabolic framework of Veillonella in the human oral microbiome, we conducted a comparative pan-genome analysis of the eight species of oral Veillonella. Analysis of the oral Veillonella pan-genome revealed features based on KEGG pathway information to adapt to the oral environment. We found that the fructose metabolic pathway was conserved in all oral Veillonella species, and oral Veillonella have conserved pathways that utilize carbohydrates other than lactate as an energy source. This discovery may help to better understand the metabolic network among oral microbiomes and will provide guidance for the design of future in silico and in vitro studies.
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Leiser, Scott, Christopher Choi, Ajay Bhat, and Charles Evans. "A Metabolic Stress Response." Innovation in Aging 4, Supplement_1 (December 1, 2020): 123. http://dx.doi.org/10.1093/geroni/igaa057.404.

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Abstract An organism’s ability to respond to stress is crucial for long-term survival. These stress responses are coordinated by distinct but overlapping pathways, many of which have been found to also regulate longevity in multiple organisms across species. Despite extensive effort, our understanding of these pathways and how they affect aging remains incomplete and thus is a key area of study in Geroscience. Our previous work identified flavin-containing monooxygenase-2 (fmo-2) as a key longevity-promoting gene downstream of at least three longevity promoting pathways, including the hypoxic response, the pentose phosphate pathway, and the dietary restriction pathway. Based on the commonalities of these pathways, we hypothesized that fmo-2, a classically annotated xenobiotic enzyme, might play a key endogenous role in responding to metabolic stress. Our resulting data, using metabolic profiling and further epistatic analysis, both support this hypothesis and link fmo-2’s mechanism to modifications to one-carbon metabolism (OCM), a key intermediate pathway between the nucleotide metabolism, methylation, and transsulfuration pathways. Using mathematical modeling and a novel metabolomics approach, we were able to further identify the likely mechanism of fmo-2-mediated metabolic effects, and connect them to both OCM and downstream components. We propose a model whereby nematode fmo-2 represents a class of enzymes that are able to modify large aspects of metabolism, similar to how transcription factors modify gene expression, and that fmo-2 is a key member of a conserved metabolic stress response.
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Dissertations / Theses on the topic "Metabolic pathways analysis"

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Lisowska, Beata. "Genomic analysis and metabolic modelling of Geobacillus thermoglucosidasius NCIMB 11955." Thesis, University of Bath, 2016. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.690738.

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Geobacillus thermoglucosidasius is a Gram-positive thermophilic eubacterium (45-70‰) that has the ability to convert pre-treated lignocellulosic material LCM into ethanol. This organism has been genetically engineered such that its yield of ethanol production is in excess of 90% of the theoretical maximum [38]. There remains considerable scope to develop G.thermoglucosidasius to produce alternative fuels and chemicals of industrial importance. For such a useful bacterium the understanding of the global metabolism remains poorly characterised. To gain a better insight into the metabolic pathways and capabilities of G. thermoglucosidasius a bottom-up approach to construct a comprehensive metabolic model of the organism was applied. The model was build from manually annotated genome and incorporates data from wet lab experiments for accurate in silico analyses. The model simulations has highlighted a potential experimental design for the in silico production of succinate and butane-2,3-diol. PathwayBooster is also introduced in this study as a tool for curating metabolic pathways. The methodology is based on the assumption that the core metabolic capabilities are shared among evolutionarily closely related species [80]. This approach led to the further analysis of members of the genus Geobacillus with respect to their core metabolic capabilities, genome re-arrangements and shared unique features. Theoretical route for the biosynthesis of Vitamin B12 is presented here, which is novel to the canonical aerobic and anaerobic pathways known to date and ubiquitous amongst Geobacillus spp. The analysis of the gene assignment for this bacterium has highlighted the presence of NADP-dependent GAPDH. The theoretical function of this novel and previously uncategorised enzyme in the genus Geobacillus has been confirmed through enzymatic assays.
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Williams, H. E. "Mathematical modelling of metabolic pathways in pig muscle." Thesis, University of Nottingham, 2017. http://eprints.nottingham.ac.uk/42536/.

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Improving efficiency within the agricultural industry is vital to maintain the food demands of the increasing population, as well the current preference for a more protein rich diet. One avenue for addressing these issues is to study animal-based growth to determine if the efficiency of the production system can be improved by increasing lean muscle mass. The aim of this thesis is to provide an alternative exploration to experimental work to provide an insight into how muscle metabolism in pigs is altered by the administration of a beta-agonist which induces muscle hypertrophy. This will be incorporated into a wider body of work to determine specific pathways to target for improving feed conversion efficiency, contributing to the necessary research into global food security. We begin by compiling a selection of statistical methods to analyse muscle microarray data, which enables the identification of a selection of genes whose expressions are altered by the exposure to a beta-agonist. These differentially expressed transcripts are then grouped via a k-means algorithm, with log likelihood and the Bayesian Inference Criterion calculations providing an optimal selection of clusters. This results in selecting a group of 51 transcripts and partitioning them into 9 clusters, and identifying several pathways which appear key to the regulation of muscle metabolism in the presence of beta-agonist. We have proceeded to incorporate this information into a mathematical model for glycolysis and the TCA cycle, in an effort to analyse biological hypotheses about how the promoters work. The equations describe the concentrations of metabolites within the cytosolic and mitochondrial compartments of a cell using mass balance ODEs. An initial model is presented, which is then increased in complexity, to keep up with developments in the experimental side of the overarching project. We make use of a selection of methods to analyse the model in an attempt to determine the effects that the different parameters cause. Through steady state analysis, we determine parameter ranges which permit positive steady states. In finding these regions, we also determine the existence of time dependent solutions, which occur when critical values of certain parameters are exceeded, and result in the build up of specific metabolites. We use asymptotic analysis to generate approximate solutions when steady states do not exist. The model parameters of most interest are those which were identified through the microarray work, namely the upregulated transcripts of PCK2 and those within the serine synthesis pathway, the control mechanism for the first half of the TCA cycle, the proportion of GTP producing enzyme from the second half of the TCA cycle, and the flux into the glycolytic pathway. We find that critical values for the glycolytic flux, and the GTP production parameter exist, determining whether the model lies within the steady state regime. In a large number of cases, the parameters we choose to represent the beta-agonist case push the system into the time dependent state. The model does not exhibit any interesting behaviour when the parameter controlling the PCK2 pathway is studied, indicating that initial intuition of the key controlling reaction mechanisms were incomplete. Whilst there are shortfalls in the model, which highlight areas for investigation, the system is set up for validation and parameter fitting when appropriate experimental data become available. We have been able to determine specific metabolic pathways within the cell which may be of significance to improving feed efficiency.
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Sakakibara, Norikazu. "Metabolic analysis of the cinnamate/monolignol and lignan pathways." Kyoto University, 2005. http://hdl.handle.net/2433/145058.

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Kyoto University (京都大学)
0048
新制・課程博士
博士(農学)
甲第11658号
農博第1514号
新制||農||911(附属図書館)
学位論文||H17||N4051(農学部図書室)
23301
UT51-2005-D407
京都大学大学院農学研究科応用生命科学専攻
(主査)教授 島田 幹夫, 教授 關谷 次郎, 教授 坂田 完三
学位規則第4条第1項該当
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Jaques, Colin Mark. "Modelling of metabolic pathways for Saccharopolyspora erythraea using flux balance analysis." Thesis, University College London (University of London), 2004. http://discovery.ucl.ac.uk/1446668/.

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The objective of this thesis is to use metabolic modelling techniques to investigate primary and secondary metabolism in S. erythraea and from this to identify key factors controlling flux distribution during secondary metabolism. S. erythraea is a member of the actinomycetes a group of bacteria responsible for the production of a number of commercially important small molecules. Actinomycete physiology is considerably more complicated than that seen in "simple" bacteria such as E. coli. The conjecture investigated in this thesis is that metabolic modelling techniques that take into account this extra complexity should be more useful in designing strategies for overproduction of desired metabolites than simpler models. The thesis gives the first detailed description of the dynamic changes in biomass composition seen during the batch cultivation of S. erythraea. It further shows that incorporation of this information into a flux balance model of the organism's metabolism significantly improves the flux distributions generated especially in the stationary phase. Using this improved technique growth phase and stationary phase metabolism are investigated. Some of the unusual stationary phase behaviour is shown to be the result of glucose uptake being independent of demand. Rigid control of branch points in the metabolic network is not found suggesting that the organism's metabolism is flexible. A reverse metabolic engineering strategy is applied, two variants of the wild type organism are compared with an industrial strain. The industrial strain is found to have a considerably lower glucose uptake rate than the parental strain. The relationship between TCA cycle flux, oxidative phosphorylation and organic acid secretion is investigated using an uncoupler. This project demonstrates that applied correctly flux balance analysis is a powerful tool for investigating actinomycete physiology. The insights gained are of direct relevance to the commercial production of secondary metabolites in S. erythraea.
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Goel, Gautam. "Dynamic flux estimation a novel framework for metabolic pathway analysis /." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2009. http://hdl.handle.net/1853/31769.

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Thesis (Ph.D)--Biomedical Engineering, Georgia Institute of Technology, 2010.
Committee Chair: Voit, Eberhard O.; Committee Member: Butera, Robert; Committee Member: Chen, Rachel; Committee Member: Kemp, Melissa; Committee Member: Neves, Ana Rute. Part of the SMARTech Electronic Thesis and Dissertation Collection.
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Cunha, Oberdam de Lima. "SAMPA (System for Comparative Analysis of Metabolic PAthways) - uma comparação de vias metabólicas." Laboratório Nacional de Computação Científica, 2008. http://www.lncc.br/tdmc/tde_busca/arquivo.php?codArquivo=161.

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Com o advento das tecnologias que propiciaram os seqüenciamentos e as análises de genomas completos em tempo relativamente curto, muitos dados sobre vias metabólicas de procariotos e eucariotos puderam ser gerados. Análises comparativas de vias metabólicas de diferentes genomas podem auxiliar no entendimento das relações organizacionais dentre e fora das espécies. Com base em tais perspectivas, este trabalho tem como finalidade implementar um sistema que permita comparar, através de diferentes critérios, vias metabólicas de bactérias. O sistema SAMPA (System for comparative Analysis of Metabolic PAthways) é composto por um banco de dados, com informações sobre vias metabólicas de diversos organismos, e um conjunto de 5 ferramentas utilizadas para comparar estas vias metabólicas e agrupar os organismos que possuam vias metabólicas relacionadas. Como estudo de caso para teste da ferramenta, foi utilizada a família Mycoplasmataceae.
The advent of genome sequencing technology and complete genome analysis has provided new data on prokaryote and eukaryote metabolic pathways. The comparative analysis of metabolic pathways from different organisms can help us understand inter and intra species organizational relationships. Having this in mind, this work focused on building a system that allows for comparing the bacterial metabolic pathways, according to a set of pre-established criteria. SAMPA (System for comparative Analysis of Metabolic PAthways) comprises a database containing information on metabolic pathways in many organisms, and a set of five tools that can be used to compare these metabolic pathways and to group organisms carrying metabolic pathways that are related. As a case study to validate the tool, we the Mycoplasmataceae family of organisms was used.
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Antoniewicz, Maciek Robert. "Comprehensive analysis of metabolic pathways through the combined use of multiple isotopic tracers." Thesis, Massachusetts Institute of Technology, 2006. http://hdl.handle.net/1721.1/37457.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2006.
Includes bibliographical references (p. 287-294).
Metabolic Flux Analysis (MFA) has emerged as a tool of great significance for metabolic engineering and the analysis of human metabolic diseases. An important limitation of MFA, as carried out via stable isotope labeling and GC/MS measurements, is the large number of isotopomer equations that need to be solved. This restriction reduces the ability of MFA to fully utilize the power of multiple isotopic tracers in elucidating the physiology of complex biological networks. Here, we present a novel framework for modeling isotopic distributions that significantly reduces the number of system variables without any loss of information. The elementary metabolite units (EMU) framework is based on a highly efficient decomposition algorithm identifies the minimum amount of information needed to simulate isotopic labeling within a reaction network using knowledge of atomic transitions occurring in the network reactions. The developed computational and experimental methodologies were applied to two biological systems of major industrial and medical significance. First, we describe the analysis of metabolic fluxes in E. coli in a fed-batch fermentation for overproduction of 1,3-propanediol (PDO).
(cont.) A dynamic 13C-labeling experiment was performed and nonstationary intracellular fluxes (with confidence intervals) were determined by fitting labeling patterns of 191 cellular amino acids and 8 external fluxes to a detailed network model of E. coli. We established for the first time detailed time profiles of in vivo fluxes. Flux results confirmed the genotype of the organism and provided further insight into the physiology of PDO overproduction in E. coli. Second, we describe the analysis of metabolic fluxes in the pathway of gluconeogenesis in cultured primary hepatocytes, i.e. isolated liver cells. We applied multiple 13C and 2H-labeled tracers and measured isotopomer distributions of glucose fragments. From this overdetermined data set we estimated net and exchange fluxes in the gluconeogenesis pathway. We identified limitations in current methods to estimate gluconeogenesis in vivo, and developed a novel [U-13C,2Hs]glycerol method that allows accurate analysis of gluconeogenesis fluxes independent of the assumption of isotopic steady-state and zonation of tracers. The developed methodologies have wide implications for in vivo studies of glucose metabolism in Type II diabetes, and other metabolic diseases.
by Maciek Robert Antoniewicz.
Ph.D.
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Beltrame, L. "Indentification of disregulated metabolic pathways by transcriptomic analysis in renal cell carcinoma samples." Doctoral thesis, Università degli Studi di Milano, 2008. http://hdl.handle.net/2434/44738.

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Microarray analysis, with its ability of simultaneously assessing the expression of thousands of genes, has always attracted interest in cancer research. However, traditional microarray studies suffer from many shortcomings, which result often in poor reproducibility of the studies. Recently, a new approach called group testing, targeting deregulated groups of genes (such as pathways) rather than single entities, has been proposed. This work focuses on the use of group testing techniques towards the identification of deregulated pathways in renal cell carcinoma over three publicly available microarray data sets, compared to more estabilished methods.
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Henderson, David Allen. "Reconstruction of metabolic pathways by the exploration of gene expression data with factor analysis." Diss., Virginia Tech, 2001. http://hdl.handle.net/10919/30089.

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Microarray gene expression data for thousands of genes in many organisms is quickly becoming available. The information this data can provide the experimental biologist is powerful. This data may provide information clarifying the regulatory linkages between genes within a single metabolic pathway, or alternative pathway routes under different environmental conditions, or provide information leading to the identification of genes for selection in animal and plant genetic improvement programs or targets for drug therapy. Many analysis methods to unlock this information have been both proposed and utilized, but not evaluated under known conditions (e.g. simulations). Within this dissertation, an analysis method is proposed and evaluated for identifying independent and linked metabolic pathways and compared to a popular analysis method. Also, this same analysis method is investigated for its ability to identify regulatory linkages within a single metabolic pathway. Lastly, a variant of this same method is used to analyze time series microarray data. In Chapter 2, Factor Analysis is shown to identify and group genes according to membership within independent metabolic pathways for steady state microarray gene expression data. There were cases, however, where the allocation of all genes to a pathway was not complete. A competing analysis method, Hierarchical Clustering, was shown to perform poorly when negatively correlated genes are assumed unrelated, but performance improved when the sign of the correlation coefficient was ignored. In Chapter 3, Factor Analysis is shown to identify regulatory relationships between genes within a single metabolic pathway. These relationships can be explained using metabolic control analysis, along with external knowledge of the pathway structure and activation and inhibition of transcription regulation. In this chapter, it is also shown why factor analysis can group genes by metabolic pathway using metabolic control analysis. In Chapter 4, a Bayesian exploratory factor analysis is developed and used to analyze microarray gene expression data. This Bayesian model differs from a previous implementation in that it is purely exploratory and can be used with vague or uninformative priors. Additionally, 95% highest posterior density regions can be calculated for each factor loading to aid in interpretation of factor loadings. A correlated Bayesian exploratory factor analysis model is also developed in this chapter for application to time series microarray gene expression data. While this method is appropriate for the analysis of correlated observation vectors, it fails to group genes by metabolic pathway for simulated time series data.
Ph. D.
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Zychlinski-Kleffmann, Anne Kathrin von. "Rice etioplast proteome analysis: Novel insights into the complexity of metabolic and regulatory pathways /." Zürich : ETH, 2005. http://e-collection.ethbib.ethz.ch/show?type=diss&nr=16120.

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Books on the topic "Metabolic pathways analysis"

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service), ScienceDirect (Online, ed. RNA turnover in eukaryotes: Nucleases, pathways and analysis of mRNA decay. San Diego, Calif: Academic, 2008.

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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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Systems Biology: Constraint-Based Reconstruction and Analysis. Cambridge University Press, 2015.

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Palsson, Bernhard O. Systems Biology: Constraint-Based Reconstruction and Analysis. Cambridge University Press, 2015.

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Lamari, Foudil, and Jean-Marie Saudubray. Disorders of Complex Lipids Synthesis and Remodeling. Oxford University Press, 2016. http://dx.doi.org/10.1093/med/9780199972135.003.0066.

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Defective lipid catabolic pathways are involved in numerous inherited metabolic diseases such as lysosomal storage diseases and peroxisome biogenesis disorders. We recently described a new classification of a rapidly growing group of inherited metabolic disorders involving biosynthesis and remodeling of complex lipids including phospholipids and sphingolipids. The remarkable progress achieved over the last decade in high throughput gene sequencing and in lipid analysis technologies have enabled the description of more than 40 diseases linked to defects in enzymes involved in these pathways. Some of these defects present in infancy or childhood but most of them are diagnosed in adolescence or adulthood. In this review we focus on those with adult presentation.
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Voit, Eberhard O., and Néstor V. Torres. Pathway Analysis and Optimization in Metabolic Engineering. Cambridge University Press, 2002.

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Voit, Eberhard O., and Néstor V. Torres. Pathway Analysis and Optimization in Metabolic Engineering. Cambridge University Press, 2004.

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Pathway Analysis and Optimization in Metabolic Engineering. Cambridge University Press, 2002.

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Voit, Eberhard O., and Néstor V. Torres. Pathway Analysis and Optimization in Metabolic Engineering. Cambridge University Press, 2002.

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Voit, Eberhard O., and Néstor V. Torres. Pathway Analysis and Optimization in Metabolic Engineering. Cambridge University Press, 2002.

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Book chapters on the topic "Metabolic pathways analysis"

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Villadsen, John. "Primary Metabolic Pathways and Metabolic Flux Analysis." In Fundamental Bioengineering, 39–96. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2015. http://dx.doi.org/10.1002/9783527697441.ch04.

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Maudsley, Stuart, Wayne Chadwick, Liyun Wang, Yu Zhou, Bronwen Martin, and Sung-Soo Park. "Bioinformatic Approaches to Metabolic Pathways Analysis." In Methods in Molecular Biology, 99–130. Totowa, NJ: Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-160-4_5.

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Kopin, Irwin J. "Estimation of Magnitudes of Alternative Metabolic Pathways." In Methods of Biochemical Analysis, 247–78. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2006. http://dx.doi.org/10.1002/9780470110294.ch5.

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Trinh, Cong T., and R. Adam Thompson. "Elementary Mode Analysis: A Useful Metabolic Pathway Analysis Tool for Reprograming Microbial Metabolic Pathways." In Subcellular Biochemistry, 21–42. Dordrecht: Springer Netherlands, 2012. http://dx.doi.org/10.1007/978-94-007-5055-5_2.

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Slenter, Denise N., Martina Kutmon, and Egon L. Willighagen. "WikiPathways: Integrating Pathway Knowledge with Clinical Data." In Physician's Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases, 1457–66. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-030-67727-5_73.

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SummaryThroughout the chapters in this book, pathways are used to visualize how genetically inheritable metabolic disorders are related. These pathways provide common conceptual models which explain groups of chemical reactions within their biological context. Visual representations of the reactions in biological pathway diagrams provide intuitive ways to study the complex metabolic processes. In order to link (clinical) data to these pathways, they have to be understood by computers. Understanding how to move from a regular pathway drawing to its machine-readable counterpart is pertinent for creating proper models. This chapter outlines the various aspects of the digital counterparts of the pathway diagrams in this book, connecting them to databases and using them in data integration and analysis. This is followed by three examples of bioinformatics applications including a pathway enrichment analysis, a biological network extension, and a final example that integrates pathways with clinical biomarker data.
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Rosselló, Francesc, and Gabriel Valiente. "Analysis of Metabolic Pathways by Graph Transformation." In Lecture Notes in Computer Science, 70–82. Berlin, Heidelberg: Springer Berlin Heidelberg, 2004. http://dx.doi.org/10.1007/978-3-540-30203-2_7.

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Rohrschneider, Markus, Alexander Ullrich, Andreas Kerren, Peter F. Stadler, and Gerik Scheuermann. "Visual Network Analysis of Dynamic Metabolic Pathways." In Advances in Visual Computing, 316–27. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-17289-2_31.

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Fell, David A., and Simon Thomas. "Increasing the flux in a metabolic pathway: a metabolic control analysis perspective." In Regulation of Primary Metabolic Pathways in Plants, 257–73. Dordrecht: Springer Netherlands, 1999. http://dx.doi.org/10.1007/978-94-011-4818-4_13.

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Van Cauter, Sofie, and Marco Essig. "Toxic and Metabolic Disorders." In IDKD Springer Series, 129–36. Cham: Springer Nature Switzerland, 2024. http://dx.doi.org/10.1007/978-3-031-50675-8_9.

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AbstractMetabolic diseases are mostly congenital inborn errors leading to functional defects in metabolic pathways, whereas toxic and metabolic diseases in adults are usually acquired. MRI is the cornerstone in the assessment of these patients. The final diagnosis is often established in combination with laboratory findings and/or genetic analysis. Imaging patterns are almost invariably bilateral and often symmetric or nearly symmetric. The basal ganglia and thalami are often involved in acquired metabolic and toxic diseases. This chapter focuses on the most common inborn errors of metabolism that can present or persist into adulthood, as well as on the most common acquired metabolic and toxic disorders, relevant to daily clinical practice.
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Loraine, Ann. "Co-expression Analysis of Metabolic Pathways in Plants." In Plant Systems Biology, 247–64. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60327-563-7_12.

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Conference papers on the topic "Metabolic pathways analysis"

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Meitalovs, Jurijs, and Egils Stalidzans. "Analysis of synthetic metabolic pathways solution space." In 2013 IEEE International Conference on System Science and Engineering (ICSSE). IEEE, 2013. http://dx.doi.org/10.1109/icsse.2013.6614656.

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Jourdan, Fabien, and Guy Melancon. "Tool for metabolic and regulatory pathways visual analysis." In Electronic Imaging 2003, edited by Robert F. Erbacher, Philip C. Chen, Jonathan C. Roberts, Matti T. Groehn, and Katy Boerner. SPIE, 2003. http://dx.doi.org/10.1117/12.477524.

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Noriega, Fernando G. "Metabolic analysis of the juvenile hormone synthesis pathways in mosquitoes." In 2016 International Congress of Entomology. Entomological Society of America, 2016. http://dx.doi.org/10.1603/ice.2016.91917.

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Cakmak, Ali, Mustafa Kirac, Marc R. Reynolds, Zehra M. Ozsoyoglu, and Gultekin Ozsoyoglu. "Gene Ontology-Based Annotation Analysis and Categorization of Metabolic Pathways." In 19th International Conference on Scientific and Statistical Database Management (SSDBM 2007). IEEE, 2007. http://dx.doi.org/10.1109/ssdbm.2007.35.

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"METABOLIC MODELING OF CONVERGING METABOLIC PATHWAYS - Analysis of Non-steady State Stable Isotope-resolve Metabolism of UDP-GlcNAc and UDP-GalNAc." In International Conference on Bioinformatics Models, Methods and Algorithms. SciTePress - Science and and Technology Publications, 2011. http://dx.doi.org/10.5220/0003129401080115.

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Maniadi, Evaggelia M., and Ioannis G. Tollis. "Analysis and visualization of metabolic pathways and networks: A hypegraph approach." In 2014 IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI). IEEE, 2014. http://dx.doi.org/10.1109/bhi.2014.6864316.

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"STABILITY ANALYSIS FOR BACTERIAL LINEAR METABOLIC PATHWAYS WITH MONOTONE CONTROL SYSTEM THEORY." In 7th International Conference on Informatics in Control, Automation and Robotics. SciTePress - Science and and Technology Publications, 2010. http://dx.doi.org/10.5220/0002944900220029.

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Pedersen, Jay, Ryan Patch, Lotfollah Najjar, and Dhundy R. Bastola. "PathwayLinks: Network analysis of metabolic pathways across bacterial organisms in a community." In 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2014. http://dx.doi.org/10.1109/bibm.2014.6999276.

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Vetchinkina, E. P., V. Yu Gorshkov, N. E. Gogoleva, Yu V. Gogolev, and V. E. Nikitina. "Comparative analysis of transcriptomes of different morphological structures of the basidiomycete Lentinus edodes." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.270.

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A comparative analysis of transcriptomes at the vegetative and generative stages of the development of Lentinus edodes basidiomycetes was carried out. The nature of differential gene expression was described, and the activated/repressed metabolic pathways were visualized.
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Arrigo, Patrizio, Pasquale P. Cardo, and Carmelina Ruggiero. "Integrated Bioinformatics analysis of structural differences in metabolic pathways. An application to Mycobacterium Leprae." In 2007 2nd IEEE International Conference on Nano/Micro Engineered and Molecular Systems. IEEE, 2007. http://dx.doi.org/10.1109/nems.2007.352176.

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Reports on the topic "Metabolic pathways analysis"

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Aharoni, Asaph, Zhangjun Fei, Efraim Lewinsohn, Arthur Schaffer, and Yaakov Tadmor. System Approach to Understanding the Metabolic Diversity in Melon. United States Department of Agriculture, July 2013. http://dx.doi.org/10.32747/2013.7593400.bard.

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Fruit quality is determined by numerous genetic factors that affect taste, aroma, ‎color, texture, nutritional value and shelf life. To unravel the genetic components ‎involved in the metabolic pathways behind these traits, the major goal of the project was to identify novel genes that are involved in, or that regulate, these pathways using correlation analysis between genotype, metabolite and gene expression data. The original and specific research objectives were: (1) Collection of replicated fruit from a population of 96 RI lines derived from parents distinguished by great diversity in fruit development and quality phenotypes, (2) Phenotypic and metabolic profiling of mature fruit from all 96 RI lines and their parents, (3) 454 pyrosequencing of cDNA representing mRNA of mature fruit from each line to facilitate gene expression analysis based on relative EST abundance, (4) Development of a database modeled after an existing database developed for tomato introgression lines (ILs) to facilitate online data analysis by members of this project and by researchers around the world. The main functions of the database will be to store and present metabolite and gene expression data so that correlations can be drawn between variation in target traits or metabolites across the RI population members and variation in gene expression to identify candidate genes which may impact phenotypic and chemical traits of interest, (5) Selection of RI lines for segregation and/or hybridization (crosses) analysis to ascertain whether or not genes associated with traits through gene expression/metabolite correlation analysis are indeed contributors to said traits. The overall research strategy was to utilize an available recombinant inbred population of melon (Cucumis melo L.) derived from phenotypically diverse parents and for which over 800 molecular markers have been mapped for the association of metabolic trait and gene expression QTLs. Transcriptomic data were obtained by high throughput sequencing using the Illumina platform instead of the originally planned 454 platform. The change was due to the fast advancement and proven advantages of the Illumina platform, as explained in the first annual scientific report. Metabolic data were collected using both targeted (sugars, organic acids, carotenoids) and non-targeted metabolomics analysis methodologies. Genes whose expression patterns were associated with variation of particular metabolites or fruit quality traits represent candidates for the molecular mechanisms that underlie them. Candidate genes that may encode enzymes catalyzingbiosynthetic steps in the production of volatile compounds of interest, downstream catabolic processes of aromatic amino acids and regulatory genes were selected and are in the process of functional analyses. Several of these are genes represent unanticipated effectors of compound accumulation that could not be identified using traditional approaches. According to the original plan, the Cucurbit Genomics Network (http://www.icugi.org/), developed through an earlier BARD project (IS-3333-02), was expanded to serve as a public portal for the extensive metabolomics and transcriptomic data resulting from the current project. Importantly, this database was also expanded to include genomic and metabolomic resources of all the cucurbit crops, including genomes of cucumber and watermelon, EST collections, genetic maps, metabolite data and additional information. In addition, the database provides tools enabling researchers to identify genes, the expression patterns of which correlate with traits of interest. The project has significantly expanded the existing EST resource for melon and provides new molecular tools for marker-assisted selection. This information will be opened to the public by the end of 2013, upon the first publication describing the transcriptomic and metabolomics resources developed through the project. In addition, well-characterized RI lines are available to enable targeted breeding for genes of interest. Segregation of the RI lines for specific metabolites of interest has been shown, demonstrating the utility in these lines and our new molecular and metabolic data as a basis for selection targeting specific flavor, quality, nutritional and/or defensive compounds. To summarize, all the specific goals of the project have been achieved and in many cases exceeded. Large scale trascriptomic and metabolomic resources have been developed for melon and will soon become available to the community. The usefulness of these has been validated. A number of novel genes involved in fruit ripening have been selected and are currently being functionally analyzed. We thus fully addressed our obligations to the project. In our view, however, the potential value of the project outcomes as ultimately manifested may be far greater than originally anticipated. The resources developed and expanded under this project, and the tools created for using them will enable us, and others, to continue to employ resulting data and discoveries in future studies with benefits both in basic and applied agricultural - scientific research.
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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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Fait, Aaron, Grant Cramer, and Avichai Perl. Towards improved grape nutrition and defense: The regulation of stilbene metabolism under drought. United States Department of Agriculture, May 2014. http://dx.doi.org/10.32747/2014.7594398.bard.

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The goals of the present research proposal were to elucidate the physiological and molecular basis of the regulation of stilbene metabolism in grape, against the background of (i) grape metabolic network behavior in response to drought and of (ii) varietal diversity. The specific objectives included the study of the physiology of the response of different grape cultivars to continuous WD; the characterization of the differences and commonalities of gene network topology associated with WD in berry skin across varieties; the study of the metabolic response of developing berries to continuous WD with specific attention to the stilbene compounds; the integration analysis of the omics data generated; the study of isolated drought-associated stress factors on the regulation of stilbene biosynthesis in plantaand in vitro. Background to the topic Grape quality has a complex relationship with water input. Regulated water deficit (WD) is known to improve wine grapes by reducing the vine growth (without affecting fruit yield) and boosting sugar content (Keller et al. 2008). On the other hand, irregular rainfall during the summer can lead to drought-associated damage of fruit developmental process and alter fruit metabolism (Downey et al., 2006; Tarara et al., 2008; Chalmers et al., 792). In areas undergoing desertification, WD is associated with high temperatures. This WD/high temperature synergism can limit the areas of grape cultivation and can damage yields and fruit quality. Grapes and wine are the major source of stilbenes in human nutrition, and multiple stilbene-derived compounds, including isomers, polymers and glycosylated forms, have also been characterized in grapes (Jeandet et al., 2002; Halls and Yu, 2008). Heterologous expression of stilbenesynthase (STS) in a variety of plants has led to an enhanced resistance to pathogens, but in others the association has not been proven (Kobayashi et al., 2000; Soleas et al., 1995). Tomato transgenic plants harboring a grape STS had increased levels of resveratrol, ascorbate, and glutathione at the expense of the anthocyanin pathways (Giovinazzo et al. 2005), further emphasizing the intermingled relation among secondary metabolic pathways. Stilbenes are are induced in green and fleshy parts of the berries by biotic and abiotic elicitors (Chong et al., 2009). As is the case for other classes of secondary metabolites, the biosynthesis of stilbenes is not very well understood, but it is known to be under tight spatial and temporal control, which limits the availability of these compounds from plant sources. Only very few studies have attempted to analyze the effects of different environmental components on stilbene accumulation (Jeandet et al., 1995; Martinez-Ortega et al., 2000). Targeted analyses have generally shown higher levels of resveratrol in the grape skin (induced), in seeded varieties, in varieties of wine grapes, and in dark-skinned varieties (Gatto et al., 2008; summarized by Bavaresco et al., 2009). Yet, the effect of the grape variety and the rootstock on stilbene metabolism has not yet been thoroughly investigated (Bavaresco et al., 2009). The study identified a link between vine hydraulic behavior and physiology of stress with the leaf metabolism, which the PIs believe can eventually lead to the modifications identified in the developing berries that interested the polyphenol metabolism and its regulation during development and under stress. Implications are discussed below.
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Droby, S., J. L. Norelli, M. E. Wisniewski, S. Freilich, A. Faigenboim, and C. Dardick. Microbial networks on harvested apples and the design of antagonistic consortia to control postharvest pathogens. Israel: United States-Israel Binational Agricultural Research and Development Fund, 2020. http://dx.doi.org/10.32747/2020.8134164.bard.

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We have demonstrated, at a global level, the existence of spatial variation in the fungal and bacterial composition of different fruit tissues. The composition, diversity and abundance varied in fruit harvested in different geographical locations and suggests a potential link between location and the type and rate of postharvest diseases that develop in each country. The global core microbiome of apple fruit was determined and found to be represented by several beneficial microbial taxa and accounted for a large fraction of the fruit microbial community. To further characterize apple fruit the microbiome after harvest, a detailed study was performed to evaluate effects of postharvest practices on the composition of the fruit peel. Microbiota. Results of this work conformed our findings that tissue-type is the main factor driving fungal and bacterial diversity and community composition on apple fruit. Both postharvest treatments and low temperature storage had a great impact on the fungal and bacterial diversity and community composition of these tissue types. Distinct spatial and temporal changes in the composition and diversity of the microbiota were observed in response to various postharvest management practices. Our results clearly indicated that apple fruit has a unique core microbiome that is universal. Analysis of the microbiome across Malus species indicates that the microbiome of domesticated apple has a higher diversity and abundance and is an admixture of the microbiome present in its wild progenitors, with clear evidence for introgression. These findings support the existence of co-evolution between Malus species and their microbiome during domestication. A network analysis of the metagenomics data was used to further elucidate functional differences between the microbiome of organic vs. conventional fruit. Our analysis predicted a link between Capnodiales and the degradation of aromatic compounds. Alternaria, a genus in the Capnodiales genus, is one of the main pathogens of stored apple fruit and was also abundant in our samples. The potential role of Alternaria in the degradation of aromatic compounds is in agreement with previous studies indicating a link between Alternaria and the metabolism of the aromatic compound, alphafarnesene38, a key volatile secreted by the fruit during maturation. A greater number of metabolic pathways related to plant defense substances (e.g. terpenoids and alkaloids) were identified in the microbiome of organic fruit samples, while more antibiotic-related metabolic pathways for compounds such as Erythromycin, Avermectin, Ansamycin, and Penicillin were present in the microbiome of apple fruit samples grown using conventional management practices.
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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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Or, Etti, David Galbraith, and Anne Fennell. Exploring mechanisms involved in grape bud dormancy: Large-scale analysis of expression reprogramming following controlled dormancy induction and dormancy release. United States Department of Agriculture, December 2002. http://dx.doi.org/10.32747/2002.7587232.bard.

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The timing of dormancy induction and release is very important to the economic production of table grape. Advances in manipulation of dormancy induction and dormancy release are dependent on the establishment of a comprehensive understanding of biological mechanisms involved in bud dormancy. To gain insight into these mechanisms we initiated the research that had two main objectives: A. Analyzing the expression profiles of large subsets of genes, following controlled dormancy induction and dormancy release, and assessing the role of known metabolic pathways, known regulatory genes and novel sequences involved in these processes B. Comparing expression profiles following the perception of various artificial as well as natural signals known to induce dormancy release, and searching for gene showing similar expression patterns, as candidates for further study of pathways having potential to play a central role in dormancy release. We first created targeted EST collections from V. vinifera and V. riparia mature buds. Clones were randomly selected from cDNA libraries prepared following controlled dormancy release and controlled dormancy induction and from respective controls. The entire collection (7920 vinifera and 1194 riparia clones) was sequenced and subjected to bioinformatics analysis, including clustering, annotations and GO classifications. PCR products from the entire collection were used for printing of cDNA microarrays. Bud tissue in general, and the dormant bud in particular, are under-represented within the grape EST database. Accordingly, 59% of the our vinifera EST collection, composed of 5516 unigenes, are not included within the current Vitis TIGR collection and about 22% of these transcripts bear no resemblance to any known plant transcript, corroborating the current need for our targeted EST collection and the bud specific cDNA array. Analysis of the V. riparia sequences yielded 814 unigenes, of which 140 are unique (keilin et al., manuscript, Appendix B). Results from computational expression profiling of the vinifera collection suggest that oxidative stress, calcium signaling, intracellular vesicle trafficking and anaerobic mode of carbohydrate metabolism play a role in the regulation and execution of grape-bud dormancy release. A comprehensive analysis confirmed the induction of transcription from several calcium–signaling related genes following HC treatment, and detected an inhibiting effect of calcium channel blocker and calcium chelator on HC-induced and chilling-induced bud break. It also detected the existence of HC-induced and calcium dependent protein phosphorylation activity. These data suggest, for the first time, that calcium signaling is involved in the mechanism of dormancy release (Pang et al., in preparation). We compared the effects of heat shock (HS) to those detected in buds following HC application and found that HS lead to earlier and higher bud break. We also demonstrated similar temporary reduction in catalase expression and temporary induction of ascorbate peroxidase, glutathione reductase, thioredoxin and glutathione S transferase expression following both treatments. These findings further support the assumption that temporary oxidative stress is part of the mechanism leading to bud break. The temporary induction of sucrose syntase, pyruvate decarboxylase and alcohol dehydrogenase indicate that temporary respiratory stress is developed and suggest that mitochondrial function may be of central importance for that mechanism. These finding, suggesting triggering of identical mechanisms by HS and HC, justified the comparison of expression profiles of HC and HS treated buds, as a tool for the identification of pathways with a central role in dormancy release (Halaly et al., in preparation). RNA samples from buds treated with HS, HC and water were hybridized with the cDNA arrays in an interconnected loop design. Differentially expressed genes from the were selected using R-language package from Bioconductor project called LIMMA and clones showing a significant change following both HS and HC treatments, compared to control, were selected for further analysis. A total of 1541 clones show significant induction, of which 37% have no hit or unknown function and the rest represent 661 genes with identified function. Similarly, out of 1452 clones showing significant reduction, only 53% of the clones have identified function and they represent 573 genes. The 661 induced genes are involved in 445 different molecular functions. About 90% of those functions were classified to 20 categories based on careful survey of the literature. Among other things, it appears that carbohydrate metabolism and mitochondrial function may be of central importance in the mechanism of dormancy release and studies in this direction are ongoing. Analysis of the reduced function is ongoing (Appendix A). A second set of hybridizations was carried out with RNA samples from buds exposed to short photoperiod, leading to induction of bud dormancy, and long photoperiod treatment, as control. Analysis indicated that 42 genes were significant difference between LD and SD and 11 of these were unique.
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Blumwald, Eduardo, and Avi Sadka. Citric acid metabolism and mobilization in citrus fruit. United States Department of Agriculture, October 2007. http://dx.doi.org/10.32747/2007.7587732.bard.

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Accumulation of citric acid is a major determinant of maturity and fruit quality in citrus. Many citrus varieties accumulate citric acid in concentrations that exceed market desires, reducing grower income and consumer satisfaction. Citrate is accumulated in the vacuole of the juice sac cell, a process that requires both metabolic changes and transport across cellular membranes, in particular, the mitochondrial and the vacuolar (tonoplast) membranes. Although the accumulation of citrate in the vacuoles of juice cells has been clearly demonstrated, the mechanisms for vacuolar citrate homeostasis and the components controlling citrate metabolism and transport are still unknown. Previous results in the PIs’ laboratories have indicated that the expression of a large number of a large number of proteins is enhanced during fruit development, and that the regulation of sugar and acid content in fruits is correlated with the differential expression of a large number of proteins that could play significant roles in fruit acid accumulation and/or regulation of acid content. The objectives of this proposal are: i) the characterization of transporters that mediate the transport of citrate and determine their role in uptake/retrieval in juice sac cells; ii) the study of citric acid metabolism, in particular the effect of arsenical compounds affecting citric acid levels and mobilization; and iii) the development of a citrus fruit proteomics platform to identify and characterize key processes associated with fruit development in general and sugar and acid accumulation in particular. The understanding of the cellular processes that determine the citrate content in citrus fruits will contribute to the development of tools aimed at the enhancement of citrus fruit quality. Our efforts resulted in the identification, cloning and characterization of CsCit1 (Citrus sinensis citrate transporter 1) from Navel oranges (Citrus sinesins cv Washington). Higher levels of CsCit1 transcripts were detected at later stages of fruit development that coincided with the decrease in the juice cell citrate concentrations (Shimada et al., 2006). Our functional analysis revealed that CsCit1 mediates the vacuolar efflux of citrate and that the CsCit1 operates as an electroneutral 1CitrateH2-/2H+ symporter. Our results supported the notion that it is the low permeable citrateH2 - the anion that establishes the buffer capacity of the fruit and determines its overall acidity. On the other hand, it is the more permeable form, CitrateH2-, which is being exported into the cytosol during maturation and controls the citrate catabolism in the juice cells. Our Mass-Spectrometry-based proteomics efforts (using MALDI-TOF-TOF and LC2- MS-MS) identified a large number of fruit juice sac cell proteins and established comparisons of protein synthesis patterns during fruit development. So far, we have identified over 1,500 fruit specific proteins that play roles in sugar metabolism, citric acid cycle, signaling, transport, processing, etc., and organized these proteins into 84 known biosynthetic pathways (Katz et al. 2007). This data is now being integrated in a public database and will serve as a valuable tool for the scientific community in general and fruit scientists in particular. Using molecular, biochemical and physiological approaches we have identified factors affecting the activity of aconitase, which catalyze the first step of citrate catabolism (Shlizerman et al., 2007). Iron limitation specifically reduced the activity of the cytosolic, but not the mitochondrial, aconitase, increasing the acid level in the fruit. Citramalate (a natural compound in the juice) also inhibits the activity of aconitase, and it plays a major role in acid accumulation during the first half of fruit development. On the other hand, arsenite induced increased levels of aconitase, decreasing fruit acidity. We have initiated studies aimed at the identification of the citramalate biosynthetic pathway and the role(s) of isopropylmalate synthase in this pathway. These studies, especially those involved aconitase inhibition by citramalate, are aimed at the development of tools to control fruit acidity, particularly in those cases where acid level declines below the desired threshold. Our work has significant implications both scientifically and practically and is directly aimed at the improvement of fruit quality through the improvement of existing pre- and post-harvest fruit treatments.
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Zhou, Min, Qinghua Wang, Xinyi Lu, Ping Zhang, Rui Yang, Yu Chen, Jiazeng Xia, and Daozhen Chen. Exhaled breath and urinary volatile organic compounds (VOCs) for cancer diagnoses, and microbial-related VOC metabolic pathway analysis. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, August 2023. http://dx.doi.org/10.37766/inplasy2023.8.0061.

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yu, luyou, jinping yang, xi meng, and yanhua lin. Effectiveness of the gut microbiota-bile acid pathway (BAS) in the treatment of Type 2 diabetes: A protocol for systematic review and meta analysis. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, July 2022. http://dx.doi.org/10.37766/inplasy2022.7.0117.

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Review question / Objective: To systematically evaluate the efficacy of the intestinal microbiome - bile acid pathway (BAS) in the treatment of T2DM. Condition being studied: Bile acids (BAs), an important component of bile, are also metabolites derived from cholesterol and promote intestinal absorption and transportation of dietary lipids . Studies have shown that bile acid receptor agonists can promote glP-1 secretion and improve glucose metabolism in preclinical mouse models of obesity and insulin resistance , which may become a new therapeutic target for Type 2 diabetes. However, no systematic review and meta-analysis has been found on the treatment of type 2 diabetes by intestinal microbiome - bile acid pathway. Therefore, we conducted a systematic review and meta-analysis to evaluate the safety and effectiveness of intestinal microbiome-bile acid pathway in the treatment of type 2 diabetes.
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Galili, Gad, Harry J. Klee, and Asaph Aharoni. Elucidating the impact of enhanced conversion of primary to secondary metabolism on phenylpropanoids secondary metabolites associated with flavor, aroma and health in tomato fruits. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7597920.bard.

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• Targeted manipulating Phenylalanine (Phe) synthesis is one of the most powerful strategies to boost the biologically and economically important secondary metabolites, including phenylpropaniods, aromatic volatiles and specialized secondary metabolites. • Over-expression of the petunia MYB transcript factor, ODORANT1 (ODO1), results in significant alterations of the levels of specific phenylpropanoid compounds in plants. • Our previous studies indicated that ectopic expression of the feedback-insensitive AroG could break the bottleneck between primary and secondary metabolisms in tomato, thereby aiding in producing new tomato composition and identifying the unknown roles of multiple key regulators in specialized metabolism. Therefore, combining the AroG and ODO1 is of particular interest for elucidating the combined regulatory role of both of these genes in the Phe metabolic pathway, as well as generating tomato fruits that contain higher levels of secondary metabolites. • Here, we performed the LC-MS and GC-MS analyses on fruits of four tomato genotypes, namely, wild type tomato fruits as well as tomato fruits expressing the AroG, ODO1 and the combination of AroG plus ODO1 (AO) genotypes. Our results elaborated that the levels of many of the Phe-derived metabolites were predominately altered in fruits of the AO genotype, compared to tomato fruits expressing either AroG or ODO1 individually. The levels of most of these metabolites were significantly stimulated, such as Tyrosine (Tyr), coumaric acid and ferulic acid derived metabolites, but the levels of some important secondary metabolites were reduced in the AO transgenic genotypes as compared to either AroG or ODO1 lines. Nevertheless, our results also revealed that the levels of aromatic volatiles were obviously down regulated in the AO, compared to that in AroG transgenic fruits, but were boosted while compared to the wild type and ODO1 transgenic fruits. • Our results suggest that ODO1 expression may also have a negative effect on the production of some of the aromatic volatiles in tomato fruits, indicating that ODO1 acts as an important regulator of the shikimate pathway, which leads to the production of the aromatic amino acids and secondary metabolites derived from them. Key words: AroG, ODO1, tomato, metabolism, shikimate pathway
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