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Showing 1 to 12 of 56 entries
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Transduction and segregation in Escherichia coli K12.

Virology

CAMPBELL A.
PMID: 13496552
Virology. 1957 Oct;4(2):366-84. doi: 10.1016/0042-6822(57)90070-3.

No abstract available.

Systems biology meets synthetic biology: a case study of the metabolic effects of synthetic rewiring.

Molecular bioSystems

Noirel J, Ow SY, Sanguinetti G, Wright PC.
PMID: 19756311
Mol Biosyst. 2009 Oct;5(10):1214-23. doi: 10.1039/b904729h. Epub 2009 Jul 07.

We present a systems biology approach to study the global metabolic effects of the insertion of synthetic circuits in a cellular chassis. Our approach combines high-throughput proteomics with the MMG probabilistic tool, which integrates the data with the metabolic...

Construction and completion of flux balance models from pathway databases.

Bioinformatics (Oxford, England)

Latendresse M, Krummenacker M, Trupp M, Karp PD.
PMID: 22262672
Bioinformatics. 2012 Feb 01;28(3):388-96. doi: 10.1093/bioinformatics/btr681. Epub 2012 Jan 18.

MOTIVATION: Flux balance analysis (FBA) is a well-known technique for genome-scale modeling of metabolic flux. Typically, an FBA formulation requires the accurate specification of four sets: biochemical reactions, biomass metabolites, nutrients and secreted metabolites. The development of FBA models...

Dynamic Changes of Intracellular Monomer Levels Regulate Block Sequence of Polyhydroxyalkanoates in Engineered Escherichia coli.

Biomacromolecules

Matsumoto K, Hori C, Fujii R, Takaya M, Ooba T, Ooi T, Isono T, Satoh T, Taguchi S.
PMID: 29323923
Biomacromolecules. 2018 Feb 12;19(2):662-671. doi: 10.1021/acs.biomac.7b01768. Epub 2018 Jan 22.

Biological polymer synthetic systems, which utilize no template molecules, normally synthesize random copolymers. We report an exception, a synthesis of block polyhydroxyalkanoates (PHAs) in an engineered Escherichia coli. Using an engineered PHA synthase, block copolymers poly[(R)-2-hydroxybutyrate(2HB)-b-(R)-3-hydroxybutyrate(3HB)] were produced in...

CRISPR EnAbled Trackable genome Engineering for isopropanol production in Escherichia coli.

Metabolic engineering

Liang L, Liu R, Garst AD, Lee T, Nogué VSI, Beckham GT, Gill RT.
PMID: 28216108
Metab Eng. 2017 May;41:1-10. doi: 10.1016/j.ymben.2017.02.009. Epub 2017 Feb 16.

Isopropanol is an important target molecule for sustainable production of fuels and chemicals. Increases in DNA synthesis and synthetic biology capabilities have resulted in the development of a range of new strategies for the more rapid design, construction, and...

Metabolic Engineering of .

Journal of agricultural and food chemistry

Hou Y, Liu X, Li S, Zhang X, Yu S, Zhao GR.
PMID: 32627549
J Agric Food Chem. 2020 Aug 05;68(31):8370-8380. doi: 10.1021/acs.jafc.0c02949. Epub 2020 Jul 21.

Betalains are emerging natural pigments with high tinctorial strength and stability, physiological activities, and fluorescent properties for potential application in food, cosmetic, and pharmaceutical industries. Betalains including yellow betaxanthins and red betacyanins are mainly restricted in the Caryophyllales plants....

LK-DFBA: a linear programming-based modeling strategy for capturing dynamics and metabolite-dependent regulation in metabolism.

BMC bioinformatics

Dromms RA, Lee JY, Styczynski MP.
PMID: 32122331
BMC Bioinformatics. 2020 Mar 02;21(1):93. doi: 10.1186/s12859-020-3422-0.

BACKGROUND: The systems-scale analysis of cellular metabolites, "metabolomics," provides data ideal for applications in metabolic engineering. However, many of the computational tools for strain design are built around Flux Balance Analysis (FBA), which makes assumptions that preclude direct integration...

CRISPR-Cas9/CRISPRi tools for cell factory construction in E. coli.

World journal of microbiology & biotechnology

Hashemi A.
PMID: 32583135
World J Microbiol Biotechnol. 2020 Jun 25;36(7):96. doi: 10.1007/s11274-020-02872-9.

The innovative CRISPR-Cas based genome editing technology provides some functionality and advantages such as the high efficiency and specificity as well as ease of handling. Both aspects of the CRISPR-Cas9 system including genetic engineering and gene regulation are advantageously...

Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations.

Metabolic engineering

Hameri T, Fengos G, Ataman M, Miskovic L, Hatzimanikatis V.
PMID: 30455161
Metab Eng. 2019 Mar;52:29-41. doi: 10.1016/j.ymben.2018.10.005. Epub 2018 Oct 26.

Large-scale kinetic models are used for designing, predicting, and understanding the metabolic responses of living cells. Kinetic models are particularly attractive for the biosynthesis of target molecules in cells as they are typically better than other types of models...

VFFVA: dynamic load balancing enables large-scale flux variability analysis.

BMC bioinformatics

Guebila MB.
PMID: 32993482
BMC Bioinformatics. 2020 Sep 29;21(1):424. doi: 10.1186/s12859-020-03711-2.

BACKGROUND: Genome-scale metabolic models are increasingly employed to predict the phenotype of various biological systems pertaining to healthcare and bioengineering. To characterize the full metabolic spectrum of such systems, Fast Flux Variability Analysis (FFVA) is commonly used in parallel...

Improving flux predictions by integrating data from multiple strains.

Bioinformatics (Oxford, England)

Long MR, Reed JL.
PMID: 27998937
Bioinformatics. 2017 Mar 15;33(6):893-900. doi: 10.1093/bioinformatics/btw706.

MOTIVATION: Incorporating experimental data into constraint-based models can improve the quality and accuracy of their metabolic flux predictions. Unfortunately, routinely and easily measured experimental data such as growth rates, extracellular fluxes, transcriptomics and even proteomics are not always sufficient...

Network motifs modulate druggability of cellular targets.

Scientific reports

Wu F, Ma C, Tan C.
PMID: 27824147
Sci Rep. 2016 Nov 08;6:36626. doi: 10.1038/srep36626.

Druggability refers to the capacity of a cellular target to be modulated by a small-molecule drug. To date, druggability is mainly studied by focusing on direct binding interactions between a drug and its target. However, druggability is impacted by...

Showing 1 to 12 of 56 entries