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Synergistic optimization framework for the process synthesis and design of biorefineries

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Frontiers of Chemical Science and Engineering 2022年第2期16卷 251-273页

作者： Nikolaus IVollmer Resul Al Krist V.Gernaey Gürkan Sin Process and Systems Engineering(PROSYS)research center Department of Chemical and Biochemical EngineeringTechnical University of Denmark2800 Kgs.LyngbyDenmark novo nordisk A/S 2880 BagsværdDenmark

The conceptual process design of novel bioprocesses in biorefinery setups is an important task,which remains yet challenging due to several *** propose a novel framework incorporating superstructure optimization and simulation-based optimization *** this context,several approaches for superstructure optimization based on different surrogate models can be *** means of a case study,the framework is introduced and validated,and the different superstructure optimization approaches are *** results indicate that even though surrogate-based optimization approaches alleviate the underlying computational issues,there remains a potential issue regarding their *** development of appropriate surrogate models,comprising the selection of surrogate type,sampling type,and size for training and cross-validation sets,are essential *** this aspect,satisfactory validation metrics do not ensure a successful outcome from its embedded use in an optimization ***,the framework’s synergistic effects by sequentially performing superstructure optimization to determine candidate process topologies and simulationbased optimization to consolidate the process design under uncertainty offer an alternative and promising *** findings invite for a critical assessment of surrogatebased optimization approaches and point out the necessity of benchmarking to ensure consistency and quality of optimized solutions.

关键词： biotechnology surrogate modelling superstructure optimization simulation-based optimization process design

Engineering of Yarrowia lipolytica for production of astaxanthin

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Synthetic and Systems Biotechnology 2017年第4期2卷 287-294页

作者： Kanchana Rueksomtawin Kildegaard Belen Adiego-Perez David Domenech Belda Jaspreet Kaur Khangura Carina Holkenbrink Irina Borodina The novo nordisk Foundation center for Biosustainability Technical University of DenmarkKemitorvet 2202800Kgs.LyngbyDenmark

Astaxanthin is a red-colored carotenoid,used as food and feed *** is mainly produced by chemical synthesis,however,the process is expensive and synthetic astaxanthin is not approved for human *** this study,we engineered the oleaginous yeast Yarrowia lipolytica for de novo production of astaxanthin by ***,we screened 12 different *** isolates for β-carotene production by introducing two genes for β-carotene biosynthesis:bi-functional phytoene synthase/lycopene cyclase(crtYB)and phytoene desaturase(crtI)from the red yeast Xanthophyllomyces *** best strain produced 31.1±0.5 mg/L β-***,we optimized the activities of 3-hydroxy-3-methylglutaryl-coenzyme A reductase(HMG1)and geranylgeranyl diphosphate synthase(GGS1/crtE)in the best producing strain and obtained 453.9±20.2 mg/L β-*** downregulation of the competing squalene synthase SQS1 increased the β-carotene titer to 797.1±57.2 mg/*** we introduced β-carotene ketolase(crtW)from Paracoccus sp.N81106 and hydroxylase(crtZ)from Pantoea ananatis to convert β-carotene into *** constructed strain accumulated 10.4±0.5 mg/L of astaxanthin but also accumulated astaxanthin biosynthesis intermediates,5.7±0.5 mg/L canthaxanthin,and 35.3±1.8 mg/L ***,we optimized the copy numbers of crtZ and crtW to obtain 3.5 mg/g DCW(54.6 mg/L)of astaxanthin in a microtiter plate *** study for the first time reports engineering of *** for the production of *** high astaxanthin content and titer obtained even in a small-scale cultivation demonstrates a strong potential for ***-based fermentation process for astaxanthin production.

关键词： Astaxanthin β-carotene Isoprenoids Oleaginous yeast Yarrowia lipolytica Metabolic engineering

Natural products research in the modern age

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Synthetic and Systems Biotechnology 2020年第4期5卷 314-315页

作者： Yaojun Tong The novo nordisk Foundation center for Biosustainability Technical University of Denmark2800 KgsLyngbyDenmark

The sudden outbreak of COVID-19 clearly illustrates a complicated public health issue of global medicine *** should not forget that besides the shortage of antivirals and vaccines there also is a lack of incentives for developing many other drugs,for example,*** products produced by bacteria,fungi,and plants are one of the most important resources used by us for *** have been developed as medicines,food additives,industrial materials,and so *** is noteworthy that more than half of our antibiotics and anti-tumor drugs currently used in clinics are from natural products of Actinomyces,a group of gram-positive ***,after the golden age of natural products research in the 1950s–1960s,the speed and outputs of natural products research have been dramatically slowing *** advances in all aspects of biotechnology,we now are able to access natural products that were considered to be inaccessible.A gold mine is hidden in the genetic information of both culturable and unculturable microorganisms,waiting for us to exploit it.

关键词： drugs forget shortage

Sleep-time eating boosts exercise endurance

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Life Metabolism 2023年第5期2卷 6-7页

作者： Jonas T.Treebak novo nordisk Foundation center for Basic Metabolic research Faculty of Health and Medical SciencesUniversity of Copenhagen2200 CopenhagenDenmark

Strategies for effective entrainment of the circadian clock by external cues are continuously being refined to circumvent dysfunctional cellular metabolism that may cause metabolic *** efficacy of daytime-restricted feeding was recently investigated in mice and shown to dramatically improve exercise capacity through a mechanism involving Plin5.

关键词： metabolism boost refined

The secondary metabolite bioinformatics portal: Computational tools to facilitate synthetic biology of secondary metabolite production

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Synthetic and Systems Biotechnology 2016年第2期1卷 69-79页

作者： Tilmann Weber Hyun Uk Kim The novo nordisk Foundation center for Biosustainability Technical University of DenmarkKogle Alle 62970 HosholmDenmark BioInformatics research center Korea Advanced Institute of Science and Technology(KAIST)Daejeon 34141Republic of Korea

Natural products are among the most important sources of lead molecules for drug *** the development of affordable whole-genome sequencing technologies and other‘omics tools,the field of natural products research is currently undergoing a shift in ***,for decades,mainly analytical and chemical methods gave access to this group of compounds,nowadays genomics-based methods offer complementary approaches to find,identify and characterize such *** paradigm shift also resulted in a high demand for computational tools to assist researchers in their daily *** this context,this review gives a summary of tools and databases that currently are available to mine,identify and characterize natural product biosynthesis pathways and their producers based on‘omics data.A web portal called Secondary Metabolite Bioinformatics Portal(SMBP at http://***)is introduced to provide a one-stop catalog and links to these bioinformatics *** addition,an outlook is presented how the existing tools and those to be developed will influence synthetic biology approaches in the natural products field.

关键词： Antibiotics Biosynthesis Bioinformatics NRPS PKS Natural product

The future of genome-scale modeling of yeast through integration of a transcriptional regulatory network

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Frontiers of Electrical and Electronic Engineering in China 2014年第1期9卷 30-46页

作者： Guodong Liu Antonio Marras Jens Nielsen novo nordisk Foundation center for Biosustainability Department of Chemical and Biological Engineering Chalmers University of Technology Gothenburg SE41296 Sweden novo nordisk Foundation center for Biosustainability Technical University of Denmark Hфrsholm DK2970 Denmark

Metabolism is regulated at multiple levels in response to the changes of internal or external conditions. Transcriptional regulation plays an important role in regulating many metabolic reactions by altering the concentrations of metabolic enzymes. Thus, integration of the transcriptional regulatory information is necessary to improve the accuracy and predictive ability of metabolic models. Here we review the strategies for the reconstruction of a transcriptional regulatory network （TRN） for yeast and the integration of such a reconstruction into a flux balance analysis-based metabolic model. While many large-scale TRN reconstructions have been reported for yeast, these reconstructions still need to be improved regarding the functionality and dynamic property of the regulatory interactions. In addition, mathematical modeling approaches need to be further developed to efficiently integrate transcriptional regulatory interactions to genome-scale metabolic models in a quantitative manner.

关键词： transcriptional regulatory network metabolic model Saccharomyces cerevisiae integration

Introduction to the Special Issue “Bioinformatic tools and approaches for Synthetic Biology of natural products”

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Synthetic and Systems Biotechnology 2016年第2期1卷 67-68页

作者： Tilmann Weber The novo nordisk Foundation center for Biosustainability Technical University of DenmarkKogle Alle 62970 H鴕sholmDenmark

Microorganisms are the major source for the identification of novel bioactive natural products,which may serve as future lead molecules for drug development to treat infectious and other ***,the research efforts to find such molecules have been hampered by high re-discovery rates of known biomolecules and a lack of new innovative screening technologies resulting in reduced screening efforts by large parts of the pharmaceutical *** recent advances in whole-genome sequencing technologies,mass spectrometry,cheminformatics and Synthetic Biology,new technologies are now available that could become game-changers in the *** these technologies require strong computational efforts to analyze and mine the large datasets,and/or design and optimize new pathways for Synthetic Biology applications.

关键词： Synthetic innovative advances

Pangenome analysis of Enterobacteria reveals richness of secondary metabolite gene clusters and their associated gene sets

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Synthetic and Systems Biotechnology 2022年第3期7卷 900-910页

作者： Omkar S.Mohite Colton J.Lloyd Jonathan M.Monk Tilmann Weber Bernhard O.Palsson The novo nordisk Foundation center for Biosustainability Technical University of DenmarkKongens Lyngby2800Denmark Department of Bioengineering University of California San DiegoLa JollaCA92093USA

In silico genome mining provides easy access to secondary metabolite biosynthetic gene clusters(BGCs)encoding the biosynthesis of many bioactive compounds,which are the basis for many important drugs used in human ***,the association between BGCs and other functions encoded in the genomes of producers have remained ***,we present a systems biology workflow that integrates genome mining with a detailed pangenome analysis for detecting genes associated with a particular *** analyzed 3,889 enterobacterial genomes and found 13,266 BGCs,represented by 252 distinct BGC families and 347 additional singletons.A pangenome analysis revealed 88 genes putatively associated with a specific BGC coding for the colon cancer-related colibactin that code for diverse metabolic and regulatory *** presented workflow opens up the possibility to discover novel secondary metabolites,better understand their physiological roles,and provides a guide to identify and analyze BGC associated gene sets.

关键词： Pangenome analysis Workflow Secondary metabolites Colibactin Enterobacteria Secretion systems

From gut changes to type 2 diabetes remission after gastric bypass surgeries

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Frontiers of Medicine 2013年第2期7卷 191-200页

作者： Bing Li Xinrong Zhou Jiarui Wu Huarong Zhou Key Laboratory of Systems Biology SIBS-Novo Nordisk Translational Research Centre for PreDiabetesShanghai Institutes for Biological SciencesCASShanghai 200233China Tongji Hospital Tongji Medical CollegeHuazhong University of Science and TechnologyWuhan 430030China

Increasing evidence suggests that the gut may influence the host’s metabolism and ultimately change the outcomes of type 2 diabetes mellitus(T2DM).We review the evidence on the relationship between the gut and T2DM remission after gastric bypass surgery,and discuss the potential mechanisms underlying the above relationship:gut anatomical rearrangement,microbial composition changes,altered gut cells,and gut hormone ***,the exact changes and their relative importance in the metabolic improvements after gastric bypass surgery remain to be further *** the precise metabolic mechanisms of T2DM resolution after bypass surgery will help to reveal the molecular mechanisms of pathogenesis,and facilitate the development of novel diagnoses and preventative interventions for this common disease.

关键词： gastric bypass T2DM gut