Transcriptome data modeling for targeted plant metabolic engineering

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Highlights► Network analysis is essential for data mining of omics-based large-scale data sets. ► Gene coexpression analysis is useful for prediction of gene function. ► Comparative network analysis can reveal common and unique plant metabolic pathways. ► Novel genome editing tools facilitate rational metabolic engineering.     

Comparative genomics: a revolutionary tool for wine yeast strain development

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Highlights► Phylogeny of Saccharomyces cerevisiae reveals industry-relevant groupings. ► Comparative genomics reveals genomic variation across industrial yeast strains. ► Next-gen sequencing in next-gen wine yeast strain development. ► Precise mapping of QTLs for marker-assisted breeding of industrial yeast. ► Discovery of putative mobile gene cluster that uses novel type of transposition.     

Network,nodes and nexus: systems approach to multitarget therapeutics

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Highlights► Complex diseases are an outcome of multiple triggers that precipitate into similar phenotypes. ► Systems level understanding can reveal dynamic aspects of disease progression profile. ► Correlation of metabolic remodeling to phenotypic alteration can delineate critical nodes of interventions. ► Multitargeting of key nodes of metabolic networks can be an effective therapeutic strategy. ► Robust and high-throughput data integration in conjunction with simulation would make the drug discovery process more efficient.     

Profiling metabolic networks to study cancer metabolism

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Highlights► Metabolic dependencies that arise in tumors may present new opportunities for therapy. ► Advanced methods in metabolic systems biology can help identify these dependencies. ► Application of isotope tracers to cancer models can facilitates quantitation of fluxes. ► Tumors with compromised TCA metabolism exhibit unique metabolic profiles.     

Stable isotope-assisted metabolomics to detect metabolic flux changes in mammalian cell cultures

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Highlights► Stable isotope-assisted metabolomics is powerful to determine metabolic fluxes. ► Stable isotope-assisted metabolomics is more complex for mammalian cell cultures. ► Biotechnological processes can be improved by assessing metabolic flux changes. ► Metabolic flux analysis is an attractive tool for toxicity studies. ► There is a huge potential for future applications on mammalian systems.     

Recent progress in the metabolic engineering of alkaloids in plant systems

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Highlights► Recent metabolic engineering efforts for plant alkaloids. ► Characterizing, reconfiguring and fine-tuning metabolic ‘parts’ improves titers. ► Additional strategies are necessary to produce ‘unnatural’ natural products.     

Enzyme and metabolic engineering for the production of novel biopolymers: crossover of biological and chemical processes

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Highlights► Poly(ω-hydroxy fatty acids) are polyethylene-like biobased polyester. ► Medium-chain-length polyhydroxyalkanoate homopolymers are processed to stretchy film. ► Microbial lactate-based polyesters exhibit transparent and flexible properties. ► Enzyme and metabolic engineering facilitates the expanding of bio-based polymers.     

Metabolic network flux analysis for engineering plant systems

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Highlights► A powerful range of tools has been developed for metabolic network flux analysis. ► These tools yield insights that are used to aid microbial metabolic engineering. ► Plants present great opportunities and special challenges to applying these tools. ► Tool selection and knowledge of plant systems is key to practical success.     

Metabolomics platforms for genome wide association studies—linking the genome to the metabolome

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Highlights► Genome-wide association studies with metabolomics constitute mGWAS. ► mGWAS provide insights into genetic and environmental impact on metabolic processes. ► We review essential strategies for mGWAS. ► Examples of mGWAS in large cohort studies are discussed.     

The challenges of cellular compartmentalization in plant metabolic engineering

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Highlights► Targeting enzymes to organelles with highest precursor pool affects product yield. ► Targeting of nonendogenous enzymes to organelles is a useful tool for engineering. ► Identification of transporters is central for effective metabolic engineering. ► Advances in metabolomics of isolated organelles will impact engineering strategies. ► Future plant metabolic engineering will include introduction of entire pathways.     

Gut metabotypes govern health effects of dietary polyphenols

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Highlights► Health effects of dietary polyphenols often depend on multiple metabolic processes. ► Gut metabotypes with specific polyphenol metabolism patterns can be differentiated. ► Physiologically achievable concentrations of relevant metabolites should be tested. ► Novel products and applications can exploit polyphenol–microbiota interactions.     

Towards metagenome-scale models for industrial applications — the case of Lactic Acid Bacteria

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Highlights► Genome-scale metabolic modelling is being increasingly applied in LAB research. ► Novel techniques that broaden applicability of models remain to be applied to LAB. ► Additional constraints allow better predictions of genome-scale metabolic models. ► Novel approaches to move from modelling monocultures to mixed cultures are being developed. ► The feasibility of metagenome-based modelling approaches is being appreciated.     

From measurement to implementation of metabolic fluxes

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Highlights► In vivo flux distributions can be determined with increasing accuracy and breadth. ► Enzyme activity can partly be identified from codon usage and other DNA features. ► Stoichiometric constraints of metabolism set a frame that can be exploited to design efficient metabolic networks. ► Insights into DNA-sequence–function relationships lead to first examples of rational DNA writing. ► Increasing DNA synthesis speed moves metabolic engineering from tinkering to green field design.     

Plant genome-scale metabolic reconstruction and modelling

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Highlights► Recent advances have been made on plant genome-scale metabolic reconstruction. ► Cellular compartmentation makes plant genome-scale reconstruction challenging. ► Current reconstructions capture important features of plant metabolism. ► The models have been used to study isolated tissues and tissue interaction. ► We review the challenges and potential of plant reconstruction and modelling.     

Magnetic nanoparticles-based diagnostics and theranostics

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Highlights► Magnetic nanoparticles (MNPs) can be in engineered and functionalized. ► MNPs can be used as magnetic resonance imaging contrast agents and targeted MNPs can be used in theranostic applications. ► MNPs are useful for in vivo drug and gene delivery. ► MNPs are useful for photodynamic, phototherapy and hyperthermia. ► MNPs can be used for controlled released and manipulation of cell in vivo.     

Clawing back: broadening the notion of metal chelators in medicine

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Highlights► Not all chelators are the same: more than metal sequestration and elimination. ► Metal chelates can redistribute metals across biological membranes. ► Metal-chelating fragments provide leads for metalloenzyme inhibition. ► Metal chelation can enhance metal reactivity and thus cytotoxicity. ► Prochelators provide site-activated metal chelation and passivation.     

Engineering plant metabolism into microbes: from systems biology to synthetic biology

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Highlights► Microbial production of pharmaceutical and fuel molecules. ► Systems biology tools advanced our understanding about synthetic pathway design. ► Synthetic biology led us to cell factories tailor-made for chemical production. ► Combinatorial gene assembly for synthetic pathway diversification. ► Engineering static, dynamic and spatial control for better production phenotype.