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OptDesign: Identifying Optimum Design Strategies in Strain Engineering for Biochemical Production [article]

Shouyong Jiang
2021 bioRxiv   pre-print
Computational tools have been widely adopted for strain optimisation in metabolic engineering, contributing to numerous success stories of producing industrially relevant biochemicals.  ...  In the second step, it computes optimal design strategies with limited manipulations (combining regulation and knockout) leading to high biochemical production.  ...  Acknowledgement This work has been supported by the Engineering and Physical Sciences Research Council (EPSRC) for funding project "Synthetic Portabolomics: Leading the way at the crossroads of the Digital  ... 
doi:10.1101/2021.12.10.472123 fatcat:jbyzuw7atrfm7li4pjjp2vrelm

Computational Identification of Metabolic Pathways of Plasmodium falciparum using the k-Shortest Path Algorithm

Jelili Oyelade, Itunuoluwa Isewon, Olufemi Aromolaran, Efosa Uwoghiren, Titilope Dokunmu, Solomon Rotimi, Oluwadurotimi Aworunse, Olawole Obembe, Ezekiel Adebiyi
2019 International Journal of Genomics  
The resulting modified iPfa GEM was a model using the k-shortest path algorithm to identify possible alternative metabolic pathways in glycolysis and pentose phosphate pathways of Plasmodium falciparum  ...  In conclusion, the application of the intelligent search technique to the metabolic network of P. falciparum predicts potential biologically relevant alternative pathways using graph theory-based approach  ...  Jelili Oyelade for the contribution from his PhD thesis.  ... 
doi:10.1155/2019/1750291 pmid:31662957 pmcid:PMC6791207 fatcat:tzblwk2ljfaffhidfbjcixlboe

NIHBA: A Network Interdiction Approach for Metabolic Engineering Design

Shouyong Jiang, Yong Wang, Marcus Kaiser, Natalio Krasnogor, Pier Luigi Martelli
2020 Bioinformatics  
To date, many computational approaches have been developed to solve the resulting bilevel optimisation problems.  ...  However, most of them are of limited use due to biased optimality principle, poor scalability with the size of metabolic networks, potential numeric issues, or low quantity of design solutions in a single  ...  This work was supported by the Engineering and Physical Sciences Research Council (EPSRC) for funding project 'Synthetic Portabolomics: Leading the way at the crossroads of the Digital and the Bio Economies  ... 
doi:10.1093/bioinformatics/btaa163 pmid:32167529 pmcid:PMC7267835 fatcat:uokyr5vb5rgjvaekp25ilptc24

Metabolic Flux Analysis in Plants: From Intelligent Design to Rational Engineering

Igor G.L. Libourel, Yair Shachar-Hill
2008 Annual Review of Plant Biology  
The application of predictive tools to high quality flux maps in particular promises to be important in the rational metabolic engineering of plants. 625  ...  In microbial systems, powerful methods have been developed for the reconstruction of metabolic networks from genomic and transcriptomic data, pathway analysis, and predictive modeling.  ...  This approach has been used to obtain information on the fluxes of glycolysis/gluconeogenesis and the oxidative pentose phosphate pathway in heterotrophic plant cells, and specifically to shed light on  ... 
doi:10.1146/annurev.arplant.58.032806.103822 pmid:18257707 fatcat:knkws3oha5enjlycwdkh6kirx4

Robustness: linking strain design to viable bioprocesses

Lisbeth Olsson, Peter Rugbjerg, Luca Torello Pianale, Cecilia Trivellin
2022 Trends in Biotechnology  
Metabolic engineering has led to the design of advanced cell factories; however, their long-term yield, titer, and productivity falter when scaled up and subjected to industrial conditions.  ...  Microbial cell factories are becoming increasingly popular for the sustainable production of various chemicals.  ...  We thank the late Professor Stefan Hohmann for fruitful discussions about robustness. Declaration of interests The authors declare no conflicts of interest.  ... 
doi:10.1016/j.tibtech.2022.01.004 pmid:35120750 fatcat:bysetjqpkzdk5mw7ab6y2z6uhy

Petri Net Based Model Validation in Systems Biology [chapter]

Monika Heiner, Ina Koch
2004 Lecture Notes in Computer Science  
Data Validation Models are widely used for biotechnological questions, e.g. for the optimization of pathways in order to maximize the yield of special products.  ...  The examples used in this paper cover signal transduction pathways as well as metabolic pathways.  ...  We would like to thank Bjoern Junker, Klaus Voss, and Jürgen Will for many fruitful discussions.  ... 
doi:10.1007/978-3-540-27793-4_13 fatcat:cekiclrstzdffbbfid7b7he3ze

NIHBA: A Network Interdiction Approach with Hybrid Benders Algorithm for Strain Design [article]

Shouyong Jiang, Yong Wang, Markus Kaiser, Natalio Krasnogor
2019 bioRxiv   pre-print
To date, many computational approaches have been developed to solve the resulting bilevel optimisation problems.  ...  However, most of them are of limited use due to biased optimality principle, poor scalability with the size of metabolic networks, potential numeric issues, or low quantity of design solutions in a single  ...  Likewise, many reactions can be excluded from consideration with a priori knowledge that, for example, they are vital for cell growth or their knockout is not likely to improve target production.  ... 
doi:10.1101/752923 fatcat:kbgst3c3cfd4jlt4bxpgeqpj54

An Overview on Target-Based Drug Design against Kinetoplastid Protozoan Infections: Human African Trypanosomiasis, Chagas Disease and Leishmaniases

Violeta Kourbeli, Eleni Chontzopoulou, Kalliopi Moschovou, Dimitrios Pavlos, Thomas Mavromoustakos, Ioannis Papanastasiou
2021 Molecules  
Target-based design expands the horizon of drug design and development and offers novel chemical entities and potential drug candidates to the therapeutic arsenal against the aforementioned neglected diseases  ...  Infections: Drug Design, Synthesis and Pharmacology".  ...  Acknowledgments: The authors would like to thank the graphic designer, Mirto Altani, for generating the Graphical Abstract and Figure 1 .  ... 
doi:10.3390/molecules26154629 pmid:34361781 pmcid:PMC8348971 fatcat:g54vkhk3bjflrkpie4mwufm46m

The Model System Saccharomyces cerevisiae Versus Emerging Non-Model Yeasts for the Production of Biofuels

Maria Priscila Lacerda, Eun Joong Oh, Carrie Eckert
2020 Life  
Recent advances in systems and synthetic biology provide new tools for metabolic engineering to design strategies and construct optimal biocatalysts for the sustainable production of desired chemicals,  ...  Modifications in microbial metabolic pathways and increased resistance to various types of stress caused by the production of these chemicals are crucial in the generation of robust and efficient production  ...  Controlling the expression of pentose phosphate pathway (PPP) genes is essential for the production of bioethanol.  ... 
doi:10.3390/life10110299 pmid:33233378 fatcat:bmdzyt5l4fgcde2zdmn75vnsde

Heurstic search for metabolic engineering: de novo synthesis of vanillin

Daniel McShan, Imran Shah
2005 Computers and Chemical Engineering  
We present the application of heuristic search to in silico metabolic pathway engineering.  ...  This paper represents a novel integration of artificial intelligence and biochemistry for computational metabolic engineering.  ...  Acknowledgments The authors acknowledge Weiming Zhang for the visualization software. This work is sponsored by the National Science Foundation (BES-9911447), the Department of En-  ... 
doi:10.1016/j.compchemeng.2004.08.038 fatcat:ef4imsd2dffz7is2gze7fzcrkq

STAble: a novel approach to de novo assembly of RNA-seq data and its application in a metabolic model network based metatranscriptomic workflow

Igor Saggese, Elisa Bona, Max Conway, Francesco Favero, Marco Ladetto, Pietro Liò, Giovanni Manzini, Flavio Mignone
2018 BMC Bioinformatics  
STAble was also used to build a prototype workflow to analyse metatranscriptomics data in connection to a steady state metabolic modelling algorithm.  ...  This algorithm was used to produce high quality metabolic interpretations of small gene expression sets obtained from already published RNA-seq data that we assembled with STAble.  ...  Competing interests The authors declare that they have no competing interests.  ... 
doi:10.1186/s12859-018-2174-6 pmid:30066630 pmcid:PMC6069750 fatcat:zif5evrgm5cwlcwgpi7kbvvekq

Leveraging knowledge engineering and machine learning for microbial bio-manufacturing

Tolutola Oyetunde, Forrest Sheng Bao, Jiung-Wen Chen, Hector Garcia Martin, Yinjie J. Tang
2018 Biotechnology Advances  
Data driven frameworks can offer new constraints for mechanistic models to describe cellular regulations, to design pathways, to search gene targets, and to estimate fermentation titer/rate/yield under  ...  Metabolic models play important role in design-build-test-learn cycles for strain improvement, and machine learning (ML) may provide a viable complementary approach for driving strain design and deciphering  ...  This work was also part of the Joint BioEnergy Institute (http://www.jbei.org) and part of the Agile BioFoundry (http://agilebiofoundry.org) supported by the U.S.  ... 
doi:10.1016/j.biotechadv.2018.04.008 pmid:29729378 fatcat:wvoe5qasjbcr5efrshwjibdbvu

Advanced strategies for production of natural products in yeast

Ruibing Chen, Shan Yang, Lei Zhang, Yongjin J. Zhou
2020 iScience  
We then discuss advanced strategies in metabolic engineering at three different dimensions, including point, line, and plane (corresponding to the individual enzymes and cofactors, metabolic pathways,  ...  In particular, we comprehensively discuss how to engineer cofactor biosynthesis for enhancing the biosynthesis efficiency, other than the enzyme activity.  ...  ACKNOWLEDGMENTS AUTHOR CONTRIBUTIONS R.C. and S.Y. wrote and revised the manuscript. L.Z. revised and provided feedback on the manuscript. Y.J.Z. conceived this study and wrote the manuscript.  ... 
doi:10.1016/j.isci.2020.100879 pmid:32087574 pmcid:PMC7033514 fatcat:aq7vevol6fhinh6rji325pq4vy

Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism

Jie Zhang, Søren D. Petersen, Tijana Radivojevic, Andrés Ramirez, Andrés Pérez-Manríquez, Eduardo Abeliuk, Benjamín J. Sánchez, Zak Costello, Yu Chen, Michael J. Fero, Hector Garcia Martin, Jens Nielsen (+2 others)
2020 Nature Communications  
We use a genome-scale model to pinpoint engineering targets, efficient library construction of metabolic pathway designs, and high-throughput biosensor-enabled screening for training diverse machine learning  ...  tryptophan titer and productivity by up to 74 and 43%, respectively, compared to the best designs used for algorithm training.  ...  The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan).  ... 
doi:10.1038/s41467-020-17910-1 pmid:32978375 fatcat:xkk2647vp5bgddr5uguhehgsg4

A Global Metabolic Map Defines the Effects of a Si-Based Biostimulant on Tomato Plants under Normal and Saline Conditions

Kekeletso H. Chele, Paul Steenkamp, Lizelle A. Piater, Ian A. Dubery, Johan Huyser, Fidele Tugizimana
2021 Metabolites  
cycle, fatty acid and numerous amino acid biosynthesis pathways, with further reprogramming of several secondary metabolism pathways such as the phenylpropanoid pathway, flavonoid biosynthesis pathways  ...  Thus, the postulated hypothetical framework, describing biostimulant-induced metabolic events in tomato plants, provides actionable knowledge necessary for industries and farmers to, confidently and innovatively  ...  Acknowledgments: The University of Johannesburg is thanked for providing a scholarship to K.C. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/metabo11120820 pmid:34940578 pmcid:PMC8709197 fatcat:liohk7epdzdy5fhroxm4haho5m
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