Works (40)

Updated: November 23rd, 2023 04:33

2023 article

An integrated chemical engineering approach to understanding microplastics

Bang, R. S., Bergman, M., Li, T., Mukherjee, F., Alshehri, A. S., Abbott, N. L., … You, F. (2023, January 26). AICHE JOURNAL, Vol. 1.

co-author countries: Saudi Arabia 🇸🇦 United States of America 🇺🇸
author keywords: artificial intelligence; biochemical engineering; interfacial processes; microplastic; hermodynamics/statisticaL
Sources: Web Of Science, ORCID
Added: February 20, 2023

2023 article

Breakdown of polyethylene therepthalate microplastics under saltwater conditions using engineered Vibrio natriegens

Li, T., Menegatti, S., & Crook, N. (2023, September 14). AICHE JOURNAL, Vol. 9.

By: T. Li n, S. Menegatti n & N. Crook n

co-author countries: United States of America 🇺🇸
author keywords: microplastics; PET biodegradation; surface display; Vibrio natriegens
Sources: ORCID, Web Of Science
Added: September 15, 2023

2023 review

Carotenoids and Their Health Benefits as Derived via Their Interactions with Gut Microbiota

[Review of ]. ADVANCES IN NUTRITION, 14(2), 238–255.

By: A. Eroglu n, I. Al'Abri n, R. Kopec*, N. Crook n & T. Bohn*

co-author countries: Luxembourg 🇱🇺 United States of America 🇺🇸
author keywords: Carotenes; xanthophylls; digestion; carotenoid metabolites; gut bacteria; microbiome; mucosal layer; inflammation; oxidative stress; bactericidal effects; Bifidobacterium spp; Akkermansia spp
MeSH headings : Humans; Carotenoids / pharmacology; Carotenoids / metabolism; Gastrointestinal Microbiome; Colon / metabolism; Prebiotics; Dietary Supplements
Sources: Web Of Science, ORCID
Added: April 11, 2023

2023 journal article

Cellulose Acetate-Stabilized Pickering Emulsions: Preparation, Rheology, and Incorporation of Agricultural Active Ingredients

ACS SUSTAINABLE CHEMISTRY & ENGINEERING, 11(42), 15178–15191.

By: M. Sohail n, T. Pirzada n, R. Guenther n, E. Barbieri n, T. Sit n, S. Menegatti n, N. Crook n, C. Opperman n, S. Khan n

co-author countries: United States of America 🇺🇸
author keywords: nonsporulating microbes; double yielding; Pseudomonas simiae; microstructure; controlledrelease
Sources: ORCID, Web Of Science
Added: October 1, 2023

2023 article

Design of 8-mer Peptides that BlockClostridioides difficileToxin A in Intestinal Cells

Sarma, S., Catella, C. M., Pedro, E. T. S., Xiao, X., Durmusoglu, D., Menegatti, S., … Hall, C. K. (2023, January 12).

co-author countries: United States of America 🇺🇸
Source: ORCID
Added: January 13, 2023

2023 journal article

Design of 8-mer peptides that block Clostridioides difficile toxin A in intestinal cells

COMMUNICATIONS BIOLOGY, 6(1).

By: S. Sarma n, C. Catella n, E. San Pedro*, X. Xiao n, D. Durmusoglu n, S. Menegatti n, N. Crook n, S. Magness*, C. Hall n

co-author countries: United States of America 🇺🇸
Sources: ORCID, Web Of Science
Added: August 27, 2023

2023 journal article

Engineering the Maize Root Microbiome: A Rapid MoClo Toolkit and Identification of Potential Bacterial Chassis for Studying Plant–Microbe Interactions

ACS Synthetic Biology.

By: J. Schaik n, Z. Li n, J. Cheadle n & N. Crook n

co-author countries: United States of America 🇺🇸
Source: ORCID
Added: September 16, 2023

2023 article

Engineering the Maize Root Microbiome: A Rapid MoClo Toolkit and Identification of Potential Bacterial Chassis for studying Plant-Microbe Interactions

Schaik, J., Li, Z., Cheadle, J., & Crook, N. (2023, June 5).

By: J. Schaik n, Z. Li n, J. Cheadle n & N. Crook n

co-author countries: United States of America 🇺🇸
Source: ORCID
Added: June 6, 2023

2023 journal article

Improving therapeutic protein secretion in the probiotic yeast Saccharomyces boulardii using a multifactorial engineering approach

MICROBIAL CELL FACTORIES, 22(1).

co-author countries: Denmark 🇩🇰 United States of America 🇺🇸
MeSH headings : Saccharomyces cerevisiae / genetics; Saccharomyces cerevisiae / metabolism; Saccharomyces boulardii / genetics; Saccharomyces boulardii / metabolism; Saccharomyces / genetics; Saccharomyces / metabolism; Probiotics / metabolism; Endopeptidases / metabolism
Sources: Web Of Science, ORCID
Added: June 19, 2023

2023 article

Programming Probiotics: Diet-responsive gene expression and colonization control in engineeredS. boulardii

Durmusoglu, D., Haller, D. J., Al’Abri, I. S., Day, K., Sands, C., Clark, A., … Crook, N. C. (2023, November 17).

co-author countries: Denmark 🇩🇰 United States of America 🇺🇸
Source: ORCID
Added: November 18, 2023

2022 journal article

A Novel Method of Inducible Directed Evolution to Evolve Complex Phenotypes

BIO-PROTOCOL, 12(20).

By: I. Al'Abri*, Z. Li*, D. Haller* & N. Crook*

author keywords: Directed Evolution; Inducible Systems; Complex Phenotypes; Pathways; Gene Clusters; P1 Phage; Mutagenesis
Sources: Web Of Science, ORCID
Added: June 12, 2023

2022 review

Discovery and delivery strategies for engineered live biotherapeutic products

[Review of ]. TRENDS IN BIOTECHNOLOGY, 40(3), 354–369.

By: M. Heavey*, D. Durmusoglu n, N. Crook n & A. Anselmo*

co-author countries: United States of America 🇺🇸
MeSH headings : Administration, Oral; Genetic Engineering; Probiotics / therapeutic use
Sources: Web Of Science, ORCID
Added: March 7, 2022

2022 journal article

Engineered cell differentiation and sexual reproduction in probiotic and mating yeasts

NATURE COMMUNICATIONS, 13(1).

By: E. Jensen*, M. Deichmann*, X. Ma*, R. Vilandt*, G. Schiesaro*, M. Rojek*, B. Lengger*, L. Eliasson* ...

co-author countries: Denmark 🇩🇰 United States of America 🇺🇸
MeSH headings : Saccharomyces cerevisiae / metabolism; Reproduction / genetics; Receptors, G-Protein-Coupled / metabolism; Pheromones / metabolism; Receptors, Cell Surface / metabolism; Cell Differentiation; Cell Communication; Probiotics; Ligands
Sources: Web Of Science, ORCID
Added: October 31, 2022

2022 journal article

Functional mining of novel terpene synthases from metagenomes

BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS, 15(1).

By: S. Kwak*, N. Crook n, A. Yoneda*, N. Ahn, J. Ning*, J. Cheng*, G. Dantas*

co-author countries: United States of America 🇺🇸
author keywords: Functional metagenomics; Terpene synthase; Prenyl pyrophosphate; beta-Farnesene
Sources: Web Of Science, ORCID
Added: October 24, 2022

2022 article

Improving Therapeutic Protein Secretion in the Probiotic YeastSaccharomyces boulardiiusing a Multifactorial Engineering Approach

Durmusoglu, D., Al’Abri, I., Williams, T. I., Collins, L. B., Martínez, J. L., & Crook, N. (2022, December 31).

co-author countries: Denmark 🇩🇰 United States of America 🇺🇸
Source: ORCID
Added: January 1, 2023

2022 article

Inducible directed evolution of complex phenotypes in bacteria

Al'Abri, I. S., Haller, D. J., Li, Z., & Crook, N. (2022, February 12). NUCLEIC ACIDS RESEARCH, Vol. 2.

By: I. Al'Abri n, D. Haller n, Z. Li n & N. Crook n

co-author countries: United States of America 🇺🇸
MeSH headings : Bacteria / genetics; Bacteria / metabolism; Bacteria / virology; Bacteriophages / genetics; Directed Molecular Evolution / methods; Mutagenesis; Phenotype; Plasmids / genetics
Sources: ORCID, Web Of Science
Added: February 13, 2022

2021 journal article

A Liquid Metal Mediated Metallic Coating for Antimicrobial and Antiviral Fabrics

Advanced Materials, 33(45), 2104298.

By: K. Kwon n, S. Cheeseman*, A. Frias‐De‐Diego n, H. Hong*, J. Yang n, W. Jung*, H. Yin*, B. Murdoch* ...

co-author countries: Australia 🇦🇺 Korea (Republic of) 🇰🇷 United States of America 🇺🇸
author keywords: antimicrobial; antiviral; galvanic replacement; liquid metal fabric coating
MeSH headings : Alloys / chemistry; Anti-Infective Agents / chemistry; Anti-Infective Agents / pharmacology; Antiviral Agents / chemistry; Antiviral Agents / pharmacology; Bacteria / drug effects; Coated Materials, Biocompatible / chemistry; Coated Materials, Biocompatible / pharmacology; Copper / chemistry; Fungi / drug effects; Gallium / chemistry; Textiles / analysis; Viruses / drug effects
Sources: Web Of Science, ORCID, Crossref
Added: September 28, 2021

2021 journal article

Design and in situ biosynthesis of precision therapies against gastrointestinal pathogens

CURRENT OPINION IN PHYSIOLOGY, 23.

By: D. Durmusoglu n, C. Catella n, E. Purnell n, S. Menegatti n & N. Crook n

co-author countries: United States of America 🇺🇸
Sources: Web Of Science, ORCID
Added: October 26, 2021

2021 article

In Silico Identification and Experimental Validation of Peptide-Based Inhibitors Targeting Clostridium difficile Toxin A

Xiao, X., Sarma, S., Menegatti, S., Crook, N., Magness, S. T., & Hall, C. K. (2021, December 29). ACS CHEMICAL BIOLOGY, Vol. 17.

By: X. Xiao n, S. Sarma n, S. Menegatti n, N. Crook n, S. Magness* & C. Hall n

co-author countries: United States of America 🇺🇸
MeSH headings : Bacterial Toxins / antagonists & inhibitors; Bacterial Toxins / chemistry; Computer Simulation; Drug Design; Enterotoxins / antagonists & inhibitors; Enterotoxins / chemistry; Models, Molecular; Peptides / chemistry; Peptides / pharmacology; Protein Binding; Protein Conformation; Protein Domains; Reproducibility of Results
Sources: ORCID, Web Of Science
Added: December 30, 2021

2021 journal article

In Situ Biomanufacturing of Small Molecules in the Mammalian Gut by Probiotic Saccharomyces boulardii

ACS SYNTHETIC BIOLOGY, 10(5), 1039–1052.

By: D. Durmusoglu n, I. Al'Abri n, S. Collins n, J. Cheng n, A. Eroglu n, C. Beisel n, N. Crook n

co-author countries: Germany 🇩🇪 United States of America 🇺🇸
author keywords: Saccharomyces boulardii; probiotic engineering; metabolic engineering; colonization profile; in situ production; beta-carotene
MeSH headings : Animals; Antineoplastic Agents / metabolism; CRISPR-Cas Systems; Feces / chemistry; Female; Gastrointestinal Microbiome; Gastrointestinal Tract / metabolism; Gastrointestinal Tract / microbiology; Gene Editing / methods; Gene Expression; Indoles / metabolism; Male; Metabolic Engineering / methods; Mice; Mice, Inbred C57BL; Microorganisms, Genetically-Modified; Multigene Family; Plasmids / genetics; Probiotics / metabolism; Promoter Regions, Genetic; Provitamins / biosynthesis; Saccharomyces boulardii / genetics; Saccharomyces boulardii / metabolism; Saccharomyces cerevisiae / genetics; beta Carotene / biosynthesis
Sources: ORCID, Web Of Science
Added: May 6, 2021

2021 article

What E. coli knows about your 1-year-old infant: Antibiotic use, lifestyle, birth mode, and siblings

Al'Abri, I. S., Durmusoglu, D., & Crook, N. (2021, June 9). CELL HOST & MICROBE, Vol. 29, pp. 854–855.

By: I. Al'Abri n, D. Durmusoglu n & N. Crook n

co-author countries: United States of America 🇺🇸
MeSH headings : Anti-Bacterial Agents / pharmacology; Asthma; Child; Environmental Exposure; Escherichia coli; Gastrointestinal Microbiome; Humans; Infant; Life Style; Siblings
Sources: Web Of Science, ORCID
Added: June 28, 2021

2020 article

Establishing Probiotic Saccharomyces boulardii as a Model Organism for Synthesis and Delivery of Biomolecules

Durmusoglu, D., Al’Abri, I., Collins, S. P., Beisel, C., & Crook, N. (2020, January 23). (Vol. 1). Vol. 1.

co-author countries: United States of America 🇺🇸
Source: ORCID
Added: May 6, 2021

2020 article

Inducible Directed Evolution of Complex Phenotypes in Bacteria

Al’Abri, I. S., Haller, D. J., & Crook, N. (2020, October 31). (Vol. 10). Vol. 10.

By: I. Al’Abri n, D. Haller n & N. Crook n

co-author countries: United States of America 🇺🇸
Source: ORCID
Added: May 6, 2021

2020 journal article

Transcript Barcoding Illuminates the Expression Level of Synthetic Constructs in E. coli Nissle Residing in the Mammalian Gut

ACS SYNTHETIC BIOLOGY, 9(5), 1010–1021.

By: N. Crook n, A. Ferreiro*, Z. Condiotte* & G. Dantas*

co-author countries: United States of America 🇺🇸
MeSH headings : Animals; DNA Barcoding, Taxonomic / methods; Escherichia coli / genetics; Escherichia coli / metabolism; Gastrointestinal Microbiome; Green Fluorescent Proteins / genetics; Green Fluorescent Proteins / metabolism; Mice; Mice, Inbred C57BL; Probiotics; Promoter Regions, Genetic
Sources: Web Of Science, ORCID
Added: June 8, 2020

2019 journal article

Adaptive Strategies of the Candidate Probiotic E. coli Nissle in the Mammalian Gut

CELL HOST & MICROBE, 25(4), 499-+.

By: N. Crook*, A. Ferreiro*, A. Gasparrini*, M. Pesesky*, M. Gibson*, B. Wang*, X. Sun*, Z. Condiotte* ...

co-author countries: United States of America 🇺🇸
MeSH headings : Adaptation, Biological; Animals; Disease Models, Animal; Escherichia coli / growth & development; Escherichia coli / metabolism; Gastrointestinal Agents / administration & dosage; Gastrointestinal Tract / microbiology; Metabolism; Mice; Mutation; Phenylketonurias / therapy; Probiotics / administration & dosage; Selection, Genetic
Sources: Web Of Science, ORCID
Added: April 29, 2019

2019 review

Barriers to genome editing with CRISPR in bacteria

[Review of ]. JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY, 46(9-10), 1327–1341.

By: J. Vento n, N. Crook n & C. Beisel n

co-author countries: Germany 🇩🇪 United States of America 🇺🇸
author keywords: Bacteria; Nuclease; Genome editing; CRISPR; Recombineering
MeSH headings : Bacteria / genetics; Clustered Regularly Interspaced Short Palindromic Repeats; Gene Editing; Humans
Sources: Web Of Science, ORCID
Added: October 28, 2019

2018 article

Adaptive strategies of the candidate probiotic E. coli Nissle in the mammalian gut

Crook, N., Ferreiro, A., Gasparrini, A. J., Pesesky, M., Gibson, M. K., Wang, B., … Dantas, G. (2018, July 8). (Vol. 7). Vol. 7.

By: N. Crook n, A. Ferreiro*, A. Gasparrini*, M. Pesesky*, M. Gibson*, B. Wang*, X. Sun*, Z. Condiotte* ...

co-author countries: United States of America 🇺🇸
Source: ORCID
Added: May 6, 2021

2016 journal article

In vivo continuous evolution of genes and pathways in yeast

Nature Communications.

By: N. Crook*, J. Abatemarco*, J. Sun*, J. Wagner*, A. Schmitz* & H. Alper*

co-author countries: United States of America 🇺🇸
MeSH headings : Directed Molecular Evolution / methods; Gene Expression Regulation, Fungal; Gene Library; Genes, Fungal / genetics; Kluyveromyces / genetics; Metabolic Networks and Pathways / genetics; Models, Genetic; Mutagenesis, Insertional; Mutation; Retroelements / genetics; Saccharomyces cerevisiae / genetics; Yeasts / classification; Yeasts / genetics; Yeasts / metabolism
Source: ORCID
Added: May 6, 2021

2014 journal article

Design of synthetic yeast promoters via tuning of nucleosome architecture

Nat Comms, 5.

By: K. Curran*, N. Crook*, A. Karim*, A. Gupta*, A. Wagman* & H. Alper*

co-author countries: United States of America 🇺🇸
MeSH headings : Gene Expression Regulation, Fungal; Models, Genetic; Mutation / genetics; Nucleosomes / metabolism; Promoter Regions, Genetic; Saccharomyces cerevisiae / genetics
Source: ORCID
Added: May 6, 2021

2014 journal article

Optimization of a Yeast RNA Interference System for Controlling Gene Expression and Enabling Rapid Metabolic Engineering

ACS Synth. Biol., 3(5), 307–313.

By: N. Crook*, A. Schmitz* & H. Alper*

co-author countries: United States of America 🇺🇸
author keywords: yeast; RNA interference; metabolic engineering; itaconic acid; gene knockdown
MeSH headings : Escherichia coli; Gene Expression / genetics; Gene Knockdown Techniques; Metabolic Engineering / methods; Nucleic Acid Conformation; RNA Interference; RNA, Small Interfering / chemistry; RNA, Small Interfering / genetics; RNA, Small Interfering / metabolism; Saccharomyces cerevisiae / genetics; Saccharomyces cerevisiae / metabolism; Succinates / analysis; Succinates / metabolism; Synthetic Biology
Source: ORCID
Added: May 6, 2021

2013 journal article

Model-based design of synthetic, biological systems

Chemical Engineering Science, 103, 2–11.

By: N. Crook* & H. Alper*

co-author countries: United States of America 🇺🇸
author keywords: Cellular biology and engineering; Mathematical modeling; Biological and biomolecular engineering; Metabolism; Molecular biology; Synthetic biology
Source: ORCID
Added: May 6, 2021

2012 article

Classical Strain Improvement

Crook, N., & Alper, H. S. (2012, October). Engineering Complex Phenotypes in Industrial Strains, pp. 1–33.

By: N. Crook* & H. Alper*

co-author countries: United States of America 🇺🇸
Source: ORCID
Added: May 6, 2021

2012 journal article

Innovation at the intersection of synthetic and systems biology

Current Opinion in Biotechnology, 23(5), 712–717.

By: A. Lanza*, N. Crook* & H. Alper*

co-author countries: United States of America 🇺🇸
MeSH headings : Biotechnology / trends; Synthetic Biology / trends; Systems Biology / trends
Source: ORCID
Added: May 6, 2021

2012 journal article

Linking Yeast Gcn5p Catalytic Function and Gene Regulation Using a Quantitative, Graded Dominant Mutant Approach

PLoS ONE, 7(4), e36193.

By: A. Lanza*, J. Blazeck*, N. Crook* & H. Alper*

co-author countries: United States of America 🇺🇸

Ed(s): C. Chan

MeSH headings : Acetylation; Biocatalysis; Gene Expression Regulation, Fungal / genetics; Histone Acetyltransferases / metabolism; Histones / metabolism; Mutation; Phenotype; Saccharomyces cerevisiae / cytology; Saccharomyces cerevisiae / genetics; Saccharomyces cerevisiae / metabolism; Saccharomyces cerevisiae Proteins / metabolism; Systems Biology; Transcriptome / genetics
Source: ORCID
Added: May 6, 2021

2012 journal article

Structure-Guided Directed Evolution of Highly Selective P450-Based Magnetic Resonance Imaging Sensors for Dopamine and Serotonin

Journal of Molecular Biology, 422(2), 245–262.

co-author countries: Canada 🇨🇦 United States of America 🇺🇸
author keywords: directed evolution; cytochrome P450; MRI contrast agents; neurotransmitter; biosensors
MeSH headings : Animals; Catalytic Domain; Cells, Cultured; Cytochrome P-450 Enzyme System / chemistry; Cytochrome P-450 Enzyme System / metabolism; Dopamine / chemistry; Dopamine / metabolism; Evolution, Molecular; Heme / chemistry; Heme / metabolism; Magnetic Resonance Spectroscopy; Oxidation-Reduction; Rats; Serotonin / chemistry; Serotonin / metabolism
Source: ORCID
Added: May 6, 2021

2011 journal article

Re-engineering multicloning sites for function and convenience

Nucleic Acids Research, 39(14), e92–e92.

By: N. Crook*, E. Freeman & H. Alper

MeSH headings : 5' Untranslated Regions; Cloning, Molecular / methods; Codon; Genetic Vectors / chemistry; Promoter Regions, Genetic; Protein Biosynthesis; Saccharomyces cerevisiae / genetics
Source: ORCID
Added: May 6, 2021

2011 article

Using Flux Balance Analysis to Guide Microbial Metabolic Engineering

Curran, K. A., Crook, N. C., & Alper, H. S. (2011, November). Microbial Metabolic Engineering, pp. 197–216.

By: K. Curran*, N. Crook* & H. Alper*

co-author countries: United States of America 🇺🇸
author keywords: Flux balance analysis; MOMA; Genomic-scale metabolic model; Metabolic engineering; Strain engineering
MeSH headings : Algorithms; Computational Biology / methods; Internet; Metabolic Engineering / methods; Metabolic Networks and Pathways / genetics; Models, Biological; Reproducibility of Results; Software
Source: ORCID
Added: May 6, 2021

2010 journal article

Improved product-per-glucose yields in P450-dependent propane biotransformations using engineered Escherichia coli

Biotechnol. Bioeng., 108(3), 500–510.

By: R. Fasan*, N. Crook*, M. Peters*, P. Meinhold*, T. Buelter*, M. Landwehr*, P. Cirino*, F. Arnold*

co-author countries: United States of America 🇺🇸
author keywords: cytochrome P450 monooxygenase; alkane oxidation; BM-3; whole-cell biotransformations; protein engineering; Escherichia coli
MeSH headings : Biotransformation; Cytochrome P-450 Enzyme System / metabolism; Escherichia coli / genetics; Escherichia coli / metabolism; Genetic Engineering; Glucose / metabolism; Metabolic Networks and Pathways / genetics; NADP / metabolism; Organisms, Genetically Modified; Oxidation-Reduction; Propane / metabolism; Recombinant Proteins / genetics
Source: ORCID
Added: May 6, 2021

2007 journal article

Engineered Alkane-Hydroxylating Cytochrome P450BM3 Exhibiting Nativelike Catalytic Properties

Angew. Chem., 119(44), 8566–8570.

By: R. Fasan*, M. Chen*, N. Crook* & F. Arnold*

co-author countries: United States of America 🇺🇸
Source: ORCID
Added: May 6, 2021

2007 journal article

Engineered Alkane-Hydroxylating Cytochrome P450BM3 Exhibiting Nativelike Catalytic Properties

Angew. Chem. Int. Ed., 46(44), 8414–8418.

By: R. Fasan*, M. Chen*, N. Crook* & F. Arnold*

co-author countries: United States of America 🇺🇸
author keywords: alkane oxidation; biotransformations; cytochrome P450; directed evolution; protein engineering
MeSH headings : Bacterial Proteins / chemistry; Binding Sites; Catalysis; Catalytic Domain; Cytochrome P-450 Enzyme System / chemistry; Escherichia coli / metabolism; Heme / chemistry; Mixed Function Oxygenases / chemistry; Models, Molecular; Molecular Conformation; Mutagenesis, Site-Directed; NADPH-Ferrihemoprotein Reductase; Oxygen / metabolism; Protein Conformation; Protein Engineering / methods; Protein Structure, Tertiary; Proteins / chemistry; Substrate Specificity
Source: ORCID
Added: May 6, 2021

Employment

Updated: December 30th, 2022 21:48

2014 - 2017

Washington University in St Louis Saint Louis, MO, US
Postdoctoral Research Associate Pathology

Education

Updated: September 17th, 2014 15:12

2009 - 2014

University of Texas at Austin Austin, TX, US
Doctor of Philosophy Chemical Engineering

2005 - 2009

California Institute of Technology Pasadena, CA, US
Bachelor of Science Chemical Engineering