Works (42)

Updated: April 3rd, 2024 17:11

2024 article

Chips, guts, and gas: unraveling volatile microbial mysteries in real time!

Li, Z., & Crook, N. C. (2024, February). TRENDS IN BIOTECHNOLOGY, Vol. 42, pp. 144–146.

By: Z. Li n & N. Crook n

TL;DR: The role of hydrogen sulfide in the gastrointestinal role is explored by engineering Escherichia coli to titrate H2S levels in a gas-impermeable gut-on-chip device. (via Semantic Scholar)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: December 29, 2023

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.

author keywords: artificial intelligence; biochemical engineering; interfacial processes; microplastic; hermodynamics/statisticaL
UN Sustainable Development Goal Categories
14. Life Below Water (Web of Science)
Sources: Web Of Science, NC State University Libraries
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

author keywords: microplastics; PET biodegradation; surface display; Vibrio natriegens
TL;DR: This project leveraged synthetic biology to develop a whole‐cell biocatalyst capable of depolymerizing PET in seawater environments by using the fast‐growing, nonpathogenic, moderate halophile Vibrio natriegens. (via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water (Web of Science; OpenAlex)
Sources: ORCID, Web Of Science, NC State University Libraries
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*

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
UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: April 11, 2023

2023 review

Carotenoids in Health as Studied by Omics-Related Endpoints

[Review of ]. ADVANCES IN NUTRITION, 14(6), 1538–1578.

By: T. Bohn*, E. Balbuena n, H. Ulus n, M. Iddir*, G. Wang n, N. Crook n, A. Eroglu n

author keywords: health; inflammation; beta-carotene; lycopene; lutein; oxidative stress; metabolites; LC-MS-MS; exposome; transcription factors; cellular compartments; body tissues
TL;DR: This review highlights the use of omics technologies to assess health-related effects of carotenoids in mammalian organisms and models and (multi)omics–related techniques, especially transcriptomics, proteomics, lipidomics, and metabolomics, measured in a variety of biospecimens. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: September 9, 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

author keywords: nonsporulating microbes; double yielding; Pseudomonas simiae; microstructure; controlledrelease
UN Sustainable Development Goal Categories
2. Zero Hunger (OpenAlex)
Sources: ORCID, Web Of Science, NC State University Libraries
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).

TL;DR: An approach that combines a Peptide Binding Design (PepBD) algorithm, molecular-level simulations, rapid screening of candidate peptides for toxin binding, a primary human cell-based assay, and surface plasmon resonance (SPR) measurements to develop peptide inhibitors that block Toxin A in small intestinal and colon epithelial cells is described. (via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water (OpenAlex)
Source: ORCID
Added: January 13, 2023

2023 journal article

Design of 8-mer peptides that block <i>Clostridioides difficile</i> 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

TL;DR: An approach that combines a Pep tide B inding D esign (PepBD) algorithm, molecular-level simulations, a rapid screening assay, and surface plasmon resonance (SPR) measurements to develop peptide inhibitors that block Toxin A in colon epithelial cells is described. (via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water (OpenAlex)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: August 27, 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, September 15). ACS SYNTHETIC BIOLOGY, Vol. 9.

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

author keywords: modular cloning; synthetic community; maize; promoter trapping; electroporation; toolkit
Sources: ORCID, Web Of Science, NC State University Libraries
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

TL;DR: The development of the Maize Root ToolKit (MRTK) is described, a scalable platform that expands the genetic engineering toolbox while providing a standardized, high efficiency transformation method that can be implemented across a diverse group of root commensals. (via Semantic Scholar)
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).

MeSH headings : Saccharomyces cerevisiae / genetics; Saccharomyces cerevisiae / metabolism; Saccharomyces boulardii / genetics; Saccharomyces boulardii / metabolism; Saccharomyces / genetics; Saccharomyces / metabolism; Probiotics / metabolism; Endopeptidases / metabolism
TL;DR: A quadruple protease-deficient Sb strain is constructed that produces 5045 mg/L secretory NPA, an improvement of tenfold over wild-type Sb and highlights the ability of proteomics to highlight under-explored mediators of this process. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries, 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).

TL;DR: Five ligand-responsive gene expression systems were developed and galactose metabolism was repaired in Sb, enabling inducible gene expression in this strain and opening new avenues for precise dosing of therapeutics by Sb via control over its in vivo gene expression levels and localization within the gastrointestinal tract. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
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
TL;DR: A new directed evolution method (Inducible Directed Evolution, IDE) is developed that combines the specificity and throughput of recent continuous directed evolution methods with the ease of ALE, which enables long DNA sequences to be mutated in a high throughput manner via a simple series of incubation steps. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
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*

MeSH headings : Administration, Oral; Genetic Engineering; Probiotics / therapeutic use
TL;DR: This review describes recent approaches (often demonstrated using traditional probiotic microorganisms) to discover LBP chassis and genetic parts utilizing omics-based methods and highlights LBP delivery strategies, with a focus on addressing physiological challenges that LBPs encounter after oral administration. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, NC State University Libraries
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* ...

MeSH headings : Saccharomyces cerevisiae / metabolism; Reproduction / genetics; Receptors, G-Protein-Coupled / metabolism; Pheromones / metabolism; Receptors, Cell Surface / metabolism; Cell Differentiation; Cell Communication; Probiotics; Ligands
TL;DR: This work reports transcriptome profiles following mating pathway activation in native and hGPCR-signaling yeast, and uses a model-guided approach to correlate gene expression to morphological changes, and devise a ligand-free screening strategy for hGpcR compatibility with the yeast mating pathway and enable hG PCR-Signaling in the probiotic yeast Saccharomyces boulardii. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
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*

author keywords: Functional metagenomics; Terpene synthase; Prenyl pyrophosphate; beta-Farnesene
TL;DR: This research proves the potential of functional metagenomics as a sequence-independent avenue for isolating targeted enzymes from uncultivated organisms in various environmental habitats. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
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). BioRxiv.

Contributors: D. Durmusoglu n, I. Al'Abri n, T. Williams n, L. Collins n, J. Martínez* & N. Crook n

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

MeSH headings : Bacteria / genetics; Bacteria / metabolism; Bacteria / virology; Bacteriophages / genetics; Directed Molecular Evolution / methods; Mutagenesis; Phenotype; Plasmids / genetics
Sources: ORCID, Web Of Science, NC State University Libraries
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* ...

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
TL;DR: The presence of the LMCu particles can eradicate over 99% of pathogens within 5 min, which is significantly more effective than control samples coated with only Cu, and is promising for generating robust antibacterial, antifungal, and antiviral fabrics and surfaces. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, NC State University Libraries, 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

TL;DR: Recent progress in understanding of small molecules that inhibit specific virulence mechanisms point to an emerging integrative approach to treatment of gastrointestinal diseases, comprising microbiologists, peptide chemists, and synthetic biologists. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
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

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
TL;DR: This work used a computational strategy that integrates a peptide binding design algorithm and explicit-solvent atomistic molecular dynamics simulation to determine promising toxin A-targeting peptides that can recognize and bind to the catalytic site of the TcdA glucosyltransferase domain (GTD). (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: ORCID, Web Of Science, NC State University Libraries
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

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
UN Sustainable Development Goal Categories
Sources: ORCID, Web Of Science, NC State University Libraries
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

MeSH headings : Anti-Bacterial Agents / pharmacology; Asthma; Child; Environmental Exposure; Escherichia coli; Gastrointestinal Microbiome; Humans; Infant; Life Style; Siblings
TL;DR: The causes, spread, and dynamics of ARGs and their relationship with asthma-associated microbiota in Danish children are studied and the relationship between asthma and the gut microbiota is studied. (via Semantic Scholar)
UN Sustainable Development Goal Categories
11. Sustainable Cities and Communities (OpenAlex)
Sources: Web Of Science, NC State University Libraries
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.

TL;DR: This work establishes S. boulardii as a genetically tractable commensal fungus and provides a set of strategies for engineering S.boulARDii to synthesize and deliver biomolecules during gut colonization. (via Semantic Scholar)
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

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*

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
TL;DR: GFP expression in the gut could often be predicted from expression levels in culture, but several strains exhibited gut-specific expression, and this work establishes the experimental design parameters and advantages of transcript barcoding to measure the performance of many engineered probiotic designs in mammalian hosts. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, NC State University Libraries
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* ...

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
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, NC State University Libraries
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

author keywords: Bacteria; Nuclease; Genome editing; CRISPR; Recombineering
MeSH headings : Bacteria / genetics; Clustered Regularly Interspaced Short Palindromic Repeats; Gene Editing; Humans
TL;DR: Existing barriers to implementing CRISPR-based editing across diverse bacterial species are analyzed and guidelines to help achieve and enhance editing in a wider range of bacterial species, including non-model strains are offered. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, NC State University Libraries
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* ...

TL;DR: The utility of EcN as a chassis for engineered function is shown by achieving the highest reported reduction in serum phenylalanine levels in a mouse model of phenylketonuria using an engineered probiotic. (via Semantic Scholar)
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*

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
TL;DR: The authors engineer the yeast retrotransposon Ty1 to enable the creation of large mutant libraries in vivo and use this system to generate improved variants of single enzymes and multigene pathways, which are found to yield higher-performing variants faster than error-prone PCR-derived libraries. (via Semantic Scholar)
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*

MeSH headings : Gene Expression Regulation, Fungal; Models, Genetic; Mutation / genetics; Nucleosomes / metabolism; Promoter Regions, Genetic; Saccharomyces cerevisiae / genetics
TL;DR: It is demonstrated that nucleosome architecture can have a role in defining yeast promoter activity and a computationally-guided approach is utilized that can enable both the redesign of endogenous promoter sequences and the de novo design of synthetic promoters. (via Semantic Scholar)
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*

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
TL;DR: The approach developed here enables rapid prototyping of knockdown strategies and thus accelerates and reduces the cost of the design-build-test cycle in yeast. (via Semantic Scholar)
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*

author keywords: Cellular biology and engineering; Mathematical modeling; Biological and biomolecular engineering; Metabolism; Molecular biology; Synthetic biology
TL;DR: This review summarizes efforts to quantitatively model cellular behavior (both endogenous and synthetic), especially as related to the design of living systems. (via Semantic Scholar)
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*

TL;DR: Almost all industrial microbiology processes require the initial isolation of cultures from nature, followed by small scale cultivations and optimization, before large scale production can become a reality, and the classical approach to strain engineering is concerned. (via Semantic Scholar)
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*

MeSH headings : Biotechnology / trends; Synthetic Biology / trends; Systems Biology / trends
TL;DR: This review seeks to highlight the activity at the intersection of the top-down systems approach and the bottom-up synthetic approach that enables the precise control of cellular state for systems studies and the discovery of novel parts, control strategies, and interactions for the design of robust synthetic function. (via Semantic Scholar)
UN Sustainable Development Goal Categories
9. Industry, Innovation and Infrastructure (OpenAlex)
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*

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
TL;DR: A novel approach to extract quantitative, causative links by modulating the expression of a dominant mutant allele to create a function-specific competitive inhibition is described and a graded dominant mutant approach is utilized in conjunction with a traditional knockout to study multifunctional proteins and generate higher-resolution data that more accurately probes protein domain function and influence. (via Semantic Scholar)
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.

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
TL;DR: It is shown that structure-guided directed evolution of the active site of the cytochrome P450-BM3 heme domain produces highly selective MRI probes with submicromolar affinities for small molecules. (via Semantic Scholar)
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
TL;DR: This work develops and applies a novel predictive model of structure-based translation inhibition to design improved MCSs for significantly higher and more consistent protein expression, and was able to minimize the inhibitory effects of M CSs with the yeast TEF, CYC and GPD promoters. (via Semantic Scholar)
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*

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
TL;DR: Fux balance analysis (FBA) is a mathematical approach that uses a genomic-scale metabolic network models to afford in silico prediction and optimization of metabolic changes. (via Semantic Scholar)
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*

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
TL;DR: Overall, the metabolic/protein engineering strategies described here can be of general value for improving the performance of NAD(P)H‐dependent whole‐cell biotransformations in E. coli. (via Semantic Scholar)
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*

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*

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
TL;DR: The goal was to engineer a P450BM3 variant with nativelike activity and coupling efficiency towards a structurally challenging, nonnative substrate (propane) and evaluate the impact of these features on performance in preparative-scale biotransformations. (via Semantic Scholar)
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

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