Matthew Nethery

Works (9)

Updated: July 31st, 2024 05:04

2024 article

Characterization of <i>Ligilactobacillus salivarius</i> CRISPR-Cas systems

Roberts, A., Spang, D., Sanozky-Dawes, R., Nethery, M. A., & Barrangou, R. (2024, July 11). (C. D. Ellermeier, Ed.). MSPHERE, Vol. 7.

By: A. Roberts n, D. Spang n, R. Sanozky-Dawes n, M. Nethery n & R. Barrangou n 

Ed(s): C. Ellermeier

author keywords: Ligilactobacillus; salivarius; CRISPR; Cas
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Sources: Web Of Science, ORCID, NC State University Libraries
Added: July 15, 2024

2022 journal article

CRISPR-based engineering of phages for in situ bacterial base editing

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 119(46).

By: M. Nethery n, C. Hidalgo-Cantabrana  n, A. Roberts n & R. Barrangou n 

author keywords: phage engineering; CRISPR; base editing; soil microbiome
MeSH headings : Gene Editing; CRISPR-Cas Systems / genetics; Bacteriophages / genetics; Ecosystem; Soil
TL;DR: Phage-assisted delivery, together with base editing, offers an important in situ editing approach for the genetic interrogation of microbial community members. (via Semantic Scholar)
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Sources: Web Of Science, ORCID, NC State University Libraries
Added: November 8, 2022

2022 journal article

Clustered Regularly Interspaced Short Palindromic Repeats Genotyping of Multidrug-Resistant Salmonella Heidelberg Strains Isolated From the Poultry Production Chain Across Brazil

FRONTIERS IN MICROBIOLOGY, 13.

By: D. Monte *, M. Nethery n, H. Berman n, S. Keelara n, N. Lincopan *, P. Fedorka-Cray  n, R. Barrangou n , M. Landgraf *

author keywords: antibiotic resistance; CRISPR; phylogeny; Salmonella Heidelberg; foodborne disease; WGS
TL;DR: The findings underscore the potential role of S. Heidelberg as a key pathogen disseminated from farm to fork in Brazil and reinforce the importance of CRISPR-based genotyping for salmonellae and emphasized the need for continuous mitigation programs to monitor the dissemination of this high-priority pathogen. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: July 11, 2022

2022 article

Functional characterization of diverse type I-F CRISPR-associated transposons

Roberts, A., Nethery, M. A., & Barrangou, R. (2022, November 17). NUCLEIC ACIDS RESEARCH, Vol. 11.

By: A. Roberts n, M. Nethery n & R. Barrangou n 

MeSH headings : CRISPR-Cas Systems; Plasmids; Endonucleases / metabolism; Escherichia coli / genetics; Escherichia coli / metabolism; DNA; RNA; CRISPR-Associated Proteins / genetics; CRISPR-Associated Proteins / metabolism
TL;DR: This work selected a diverse set of type I-F3 CRISPR-associated transposon systems derived from Gammaproteobacteria, predicted all components essential for transposition activity, and deployed them for functionality testing within Escherichia coli, demonstrating that these systems possess a significant range of integration efficiencies with regards to temperature, transposition size, and flexible PAM requirements. (via Semantic Scholar)
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Sources: Web Of Science, ORCID, NC State University Libraries
Added: October 19, 2022

2021 journal article

CRISPRclassify: Repeat-Based Classification of CRISPR Loci

CRISPR JOURNAL, 4(4), 558–574.

By: M. Nethery n, M. Korvink *, K. Makarova *, Y. Wolf *, E. V. Koonin * & R. Barrangou n 

MeSH headings : Algorithms; Area Under Curve; Base Sequence; CRISPR-Cas Systems; Clustered Regularly Interspaced Short Palindromic Repeats; Computational Biology / methods; Databases, Genetic; Gene Editing; Genetic Loci; Genome, Bacterial; Genomics / methods; Reproducibility of Results
TL;DR: Although the performance of cas-based identification will exceed that of a repeat-based approach in many cases, CRISprclassify provides an efficient approach to classification of CRISPR loci for cases in which cas gene information is unavailable, such as metagenomes and fragmented genome assemblies. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: September 7, 2021

2020 journal article

Whole-genome sequencing analysis and CRISPR genotyping of rare antibiotic-resistant Salmonella enterica serovars isolated from food and related sources

FOOD MICROBIOLOGY, 93.

By: D. Monte  n, M. Nethery n, R. Barrangou n , M. Landgraf * & P. Fedorka-Cray  n

author keywords: Antibiotic resistance; CRISPR; Phylogeny; Salmonella serovars; Whole genome sequencing
MeSH headings : Anti-Bacterial Agents / pharmacology; Brazil; Clustered Regularly Interspaced Short Palindromic Repeats; Drug Resistance, Multiple, Bacterial / genetics; Food Microbiology; Genome, Bacterial; Genotype; Genotyping Techniques; Microbial Sensitivity Tests; Salmonella / classification; Salmonella / genetics; Salmonella / isolation & purification; Salmonella Food Poisoning; Salmonella enterica / classification; Salmonella enterica / drug effects; Salmonella enterica / genetics; Salmonella enterica / isolation & purification; Serogroup; Serotyping; Whole Genome Sequencing
TL;DR: CRISPR analysis revealed that the spacer content was strongly correlated with serovar and multi-locus sequence type for all strains, independently confirming the observed phylogenetic patterns, and highlighting the value of CRISPR-based genotyping for Salmonella. (via Semantic Scholar)
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Added: October 5, 2020

2019 journal article

Comparative genomics of eight Lactobacillus buchneri strains isolated from food spoilage

BMC GENOMICS, 20(1).

By: M. Nethery n, E. Henriksen n, K. Daughtry n, S. Johanningsmeier n & R. Barrangou n 

author keywords: Lactobacillus buchneri; Comparative genomics; Lactic acid bacteria; CRISPR-Cas systems; Fermentation; Spoilage; Food microbiology
MeSH headings : Computational Biology / methods; Evolution, Molecular; Fermentation; Food Microbiology; Genome, Bacterial; Genomics / methods; Lactobacillus / classification; Lactobacillus / genetics; Lactobacillus / isolation & purification; Molecular Sequence Annotation; Phylogeny; Whole Genome Sequencing
TL;DR: The findings from the comparison of eight newly-sequenced and assembled genomes against two publicly available closed reference genomes provide new insights into the genomics of L. buchneri, building a platform for future studies and identifying elements for potential strain manipulation or engineering. (via Semantic Scholar)
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Sources: Web Of Science, ORCID, NC State University Libraries
Added: December 16, 2019

2018 journal article

CRISPR Visualizer: rapid identification and visualization of CRISPR loci via an automated high-throughput processing pipeline

RNA BIOLOGY, 16(4), 577–584.

By: M. Nethery n & R. Barrangou n 

author keywords: CRISPR-Cas; repeat detection; software; CRISPR spacer; crRNA
MeSH headings : Bacteria / genetics; Base Sequence; CRISPR-Cas Systems / genetics; Computational Biology; Genetic Loci; High-Throughput Nucleotide Sequencing / methods; Time Factors
TL;DR: A high-throughput extraction pipeline coupled with a local web-based visualization tool is constructed which enables CRISPR spacer and repeat extraction, rapid visualization, graphical comparison, and progressive multiple sequence alignment and supports accelerated analysis of genomic data sets. (via Semantic Scholar)
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Sources: Web Of Science, ORCID, NC State University Libraries
Added: May 20, 2019

2018 article

Predicting and visualizing features of CRISPR-Cas systems

CRISPR-CAS ENZYMES, Vol. 616, pp. 1–25.

By: M. Nethery n & R. Barrangou n 

MeSH headings : Animals; Bacteria / genetics; CRISPR-Cas Systems; Clustered Regularly Interspaced Short Palindromic Repeats; Computer Simulation; Gene Editing / methods; Genomics / methods; Humans; RNA, Guide, Kinetoplastida / genetics; Software
TL;DR: In silico methods for predicting and visualizing notable features of CRISPR-Cas systems, including Cas domain determination,CRISPR array visualization, and inference of the protospacer-adjacent motif are described. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: December 30, 2019

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