Phytochemical engineering: Combining chemical reaction engineering with plant science

Shanks, Jacqueline V.

doi:10.1002/aic.10418

Cited by 18 publications

(11 citation statements)

References 34 publications

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“…Furthermore, since substantial changes in flux sometimes correspond only to minor changes in metabolite levels (Fell, 2005), systemwide flux quantification is a very useful counterpart to the profiling of metabolite concentrations (through metabolomics) in the characterization of phenotype (Ratcliffe and Shachar-Hill, 2006 Flux quantification in plants is challenging compared to that in microbial and mammalian cells. This is largely because flux quantification involves performing labeling experiments and interpreting the ensuing labeling data by mathematical techniques, and such techniques grow to be quite non-trivial in case of plant metabolism due to its inherent complexity, subcellular compartmentation, and intercompartmental transport (Ratcliffe and Shachar-Hill, 2001;Shanks, 2005;Rhee et al, 2006). Consequently, flux quantification in plants through labeling experiments has received limited attention (Kruger et al, 2003;Sweetlove et al, 2003;Fernie et al, 2005), although a few elegant examples of the use of labeling experiments for pathway elucidation or discovery have been reported (e.g.…”

Section: Introductionmentioning

confidence: 98%

Flux quantification in central carbon metabolism of Catharanthus roseus hairy roots by 13C labeling and comprehensive bondomer balancing

2007

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Section: Introductionmentioning

confidence: 98%

Flux quantification in central carbon metabolism of Catharanthus roseus hairy roots by 13C labeling and comprehensive bondomer balancing

2007

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“…Understanding working of mitochondria at low temperatures can certainly help to engineer crops with better power houses -mitochondria -to cope with sub-physiological temperatures. Mitochondria are functionally "immature" in the seeds before germination and develop to fully functional organs during imbibition [84][85][86][87][88][89]. Yin et al [11] found that after imbibition at 22°C for 24 h soybean axes' cells have all the cell organelles in fully functional form, whereas in the axes imbibed at 10 and 4°C it was difficult to find endoplasmic reticulum, the intercellular space was looser and the cytoplasmic layer was irregular (also see Fig.…”

Section: Energy Metabolism In Germinating Seedsmentioning

confidence: 99%

Engineering Germination Fitness for Sub-Physiological Temperatures in Plants

Javeed¹,

Cheng²,

Song³

et al. 2012

Int J Mol Biol

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Abstract-Germination is a key event in plant life cycle and imbibition temperature is an important factor for the major reorganization processes in the germinating seeds. Sub-physiological temperature at this stage affects virtually all aspects of cellular function including protein folding, kinetic parameters of membrane fluidity, protein assembly, and general metabolic processes. In this article we will review the research which has been carried out to decipher the basic mechanisms of low temperature (LT) stress with special emphasis on germination. With the better understanding of LT tolerance in some plant species we will also discuss how these attributes can be transferred in the important food crops to attain better germination stamina at sub-physiological temperatures. At germination stage, the cellular machinery in the embryo is not at its proper place and is going through reorganisation and any environmental severity has devastating effects on the fragile plant. But LT resistant species have evolved the ability to acclimatise, with the remodelling of cell and tissue structures and the reprogramming of metabolism and gene expression. Metabolic networks are redirected towards the synthesis of cryoprotectant molecules, which in association with other proteins bring about physical and biochemical restructuring of cell membranes through changes in the lipid composition and induction of other non-enzymatic proteins that alter the freezing point of water. Genetic engineering of crops for enhanced seed germination performance will certainly help to achieve optimum agricultural yields.. Germination physiology in low temperatureAll environmental stresses disrupt the normal functioning of a living system. To re-establish metabolic homeostasis, living systems require an adjustment of metabolic pathways in a process usually referred to as acclimation. For temperate plants, low temperature (LT) is a major non-living element of the environmental that affects water and nutrient uptake, membrane fluidity and protein and nucleic acid conformation, drastically influencing cellular metabolism directly by reducing the rates of biochemical reactions [1], accompanied by changes in the transcriptome, proteome and metabolome [2]. Chilling temperatures (0 to 15°C) frequently occur in nature and affect many species of plants, especially those of tropical origin (such as rice, corn, tomato and soybean), by causing wilting, chlorosis, or necrosis, thus restricting their growth and development. Metabolic rates are lowered which create energy imbalance. Freezing (0°C and below) temperatures cause membrane injury [3], decrease the respiration rate and ATP content [4], resulting in poor germination, reduced seedling emergence, decreased seedling vigour, and ultimately severe loss in yield of the food crops of tropical and subtropical origins [5][6][7][8][9]. Embryos, excised from seed coats of soybeans, leak profusely during the first minutes of imbibition. In the embryos imbibed at 10°C or lower, disproportionately more solutes leak ...

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“…In a metabolite profiling experiment, metabolites are extracted from tissues, separated, and analyzed in a high-throughput manner (44). Metabolic fingerprinting looks at a few metabolites to help differentiate samples according to their phenotype or biological relevance (58,115). Technology has now advanced to semiautomatically quantify >1000 compounds from a single leaf extract (138).…”

Section: Metabolomics and Metabolic Fluxmentioning

confidence: 99%

Bioinformatics and Its Applications in Plant Biology

Rhee

Dickerson

2006

Annu. Rev. Plant Biol.

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Bioinformatics plays an essential role in today's plant science. As the amount of data grows exponentially, there is a parallel growth in the demand for tools and methods in data management, visualization, integration, analysis, modeling, and prediction. At the same time, many researchers in biology are unfamiliar with available bioinformatics methods, tools, and databases, which could lead to missed opportunities or misinterpretation of the information. In this review, we describe some of the key concepts, methods, software packages, and databases used in bioinformatics, with an emphasis on those relevant to plant science. We also cover some fundamental issues related to biological sequence analyses, transcriptome analyses, computational proteomics, computational metabolomics, bio-ontologies, and biological databases. Finally, we explore a few emerging research topics in bioinformatics.

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Phytochemical engineering: Combining chemical reaction engineering with plant science

Cited by 18 publications

References 34 publications

Flux quantification in central carbon metabolism of Catharanthus roseus hairy roots by 13C labeling and comprehensive bondomer balancing

Flux quantification in central carbon metabolism of Catharanthus roseus hairy roots by 13C labeling and comprehensive bondomer balancing

Engineering Germination Fitness for Sub-Physiological Temperatures in Plants

Bioinformatics and Its Applications in Plant Biology

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