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Works (12)
Updated: April 5th, 2024 08:02
2018 journal article
CRISPRdisco: An Automated Pipeline for the Discovery and Analysis of CRISPR-Cas Systems
CRISPR JOURNAL, 1(2), 171–181.
TL;DR:
An automated pipeline is developed, named CRISprdisco (CRISPR discovery), to identify CRISPR repeats and cas genes in genome assemblies, determine type and subtype, and describe system completeness, which opens new avenues to enable classification within a complex nomenclature.
(via Semantic Scholar)
open access via www.liebertpub.com (publisher PDF)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: February 25, 2019
2018 journal article
Comparative genomics and evolution of trans-activating RNAs in Class 2 CRISPR-Cas systems
RNA BIOLOGY, 16(4), 435–448.
MeSH headings : Bacteroides / genetics; Base Sequence; CRISPR-Cas Systems / genetics; Conserved Sequence / genetics; Evolution, Molecular; Genomics; Nucleic Acid Conformation; RNA, Bacterial / genetics; RNA, Guide, Kinetoplastida / genetics; Repetitive Sequences, Nucleic Acid / genetics; Streptococcus / genetics; Thermodynamics; Trans-Activators / genetics
TL;DR:
Reconstruction of tracrRNA evolution for 4 tight bacterial groups demonstrates random drift of repeat-antirepeat complementarity within a window of hybrid stability that is, apparently, maintained by selection.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: May 20, 2019
2018 journal article
Conserved Genome Organization and Core Transcriptome of the Lactobacillus acidophilus Complex
FRONTIERS IN MICROBIOLOGY, 9.
author keywords: Lactobacillus; core genome; core transcriptome; microbial genetics; chromosome organization
TL;DR:
The results reveal the core features of the L. acidophilus complex and open new avenues for the enhancement and formulation and of next generation probiotics and starter cultures.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: October 19, 2018
2018 journal article
Deletion-based escape of CRISPR-Cas9 targeting in Lactobacillus gasseri
MICROBIOLOGY-SGM, 164(9), 1098–1111.
author keywords: Lactobacillus; CRISPR; Cas; Cas9; interference; spacer
MeSH headings : CRISPR-Associated Protein 9 / metabolism; Clustered Regularly Interspaced Short Palindromic Repeats; Interspersed Repetitive Sequences; Lactobacillus gasseri / genetics; Mutation; Plasmids; Recombination, Genetic; Sequence Deletion; Transformation, Bacterial
TL;DR:
It is shown that deletions of spacers within CRISPR arrays constitute a key escape mechanism to evadeCRISPR targeting, while preserving the functionality of the CRISpr-Cas system.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: December 31, 2018
2018 journal article
The Lactobacillus Bile Salt Hydrolase Repertoire Reveals Niche-Specific Adaptation
MSPHERE, 3(3).
Ed(s): C. Ellermeier
author keywords: Lactobacillus; bile acid; bile salt hydrolase; gastrointestinal tract; niche; penicillin V acylase; probiotic; therapeutic
MeSH headings : Adaptation, Biological; Amidohydrolases / genetics; Genetic Variation; Genotype; Lactobacillus / classification; Lactobacillus / enzymology; Lactobacillus / genetics; Penicillin Amidase / genetics; Phylogeny; Sequence Homology
TL;DR:
The BSH repertoire across 170 sequenced species revealed that BSH-encoding lactobacilli primarily adopt the vertebrate-adapted lifestyle but not the environmental or plant-associated subsets, and will guide future mechanistic studies of BSH activity and contribute to the development and selection of Lactobacillus strains with therapeutic potential.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2017 journal article
Characterization and Exploitation of CRISPR Loci in Bifidobacterium longum
FRONTIERS IN MICROBIOLOGY, 8.
author keywords: CRISPR-Cas systems; genotyping; probiotics; Bifidobacterium longum
TL;DR:
It is suggested that CRISPR-Cas immune systems are instrumental in mounting diversified viral resistance in B. longum, and hypervariable loci can be used to gain insights into strain origin, evolution and phylogeny, and can provide discriminatory sequences to distinguish even clonal isolates.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2016 review
Deciphering and shaping bacterial diversity through CRISPR
[Review of ]. CURRENT OPINION IN MICROBIOLOGY, 31, 101–108.
MeSH headings : Bacteria / genetics; Bacteria / virology; Bacteriophages / genetics; CRISPR-Cas Systems / genetics; Clustered Regularly Interspaced Short Palindromic Repeats / genetics; Genome, Bacterial / genetics; Host-Pathogen Interactions / genetics
TL;DR:
Although the ability to target and cleave DNA in a sequence-specific manner is a powerful mechanism utilized by bacteria to fend off phage, plasmids, and potentially harmful nucleic acids, it is also a promising technology for programmable targeting of undesirable bacteria in microbiome consortia.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2016 journal article
Identifying and Visualizing Functional PAM Diversity across CRISPR-Cas Systems
MOLECULAR CELL, 62(1), 137–147.
MeSH headings : Bacillus / chemistry; Bacillus / metabolism; CRISPR-Associated Proteins / chemistry; CRISPR-Associated Proteins / genetics; CRISPR-Cas Systems; Escherichia coli / chemistry; Escherichia coli / metabolism; Francisella / chemistry; Francisella / metabolism; High-Throughput Screening Assays / methods; Protein Structure, Tertiary; Streptococcus thermophilus / chemistry; Streptococcus thermophilus / metabolism
TL;DR:
An in vivo, positive, and tunable screen termed PAM-SCANR (PAM screen achieved by NOT-gate repression) to elucidate functional PAMs as well as an interactive visualization scheme termed the PAM wheel to convey individual PAM sequences and their activities to accelerate ability to understand and exploit the multitude of CRISPR-Cas systems in nature.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2015 journal article
Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera
NATURE COMMUNICATIONS, 6.
MeSH headings : Biotechnology; Genome, Bacterial; Lactobacillus / enzymology; Lactobacillus / genetics; Leuconostoc / genetics; Pediococcus / genetics; Phylogeny; Sequence Analysis, DNA
TL;DR:
The genome sequences of 213 different Lactobacilli strains and associated genera are reported, and new insight is provided into phylogenomic organization and adaptive immunity elements in this bacteria family, presenting a robust phylogenomic framework of existing species and for classifying new species.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2015 journal article
Occurrence and Diversity of CRISPR-Cas Systems in the Genus Bifidobacterium
PLOS ONE, 10(7).
Ed(s): C. Riedel
MeSH headings : Bifidobacterium / genetics; CRISPR-Cas Systems / genetics; Chromosomes, Bacterial / genetics; Clustered Regularly Interspaced Short Palindromic Repeats / genetics; DNA / genetics; Evolution, Molecular; Genetic Variation / genetics; Genome, Bacterial / genetics; Prophages / genetics
TL;DR:
It is found that many Bifidobacterium species have unusually large and diverse CRISPR-Cas systems that contain spacer sequences showing homology to foreign genetic elements like prophages, which may shed light on evolutionary processes and strain divergence.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2014 journal article
Guide RNA Functional Modules Direct Cas9 Activity and Orthogonality
MOLECULAR CELL, 56(2), 333–339.
MeSH headings : Bacterial Proteins / chemistry; CRISPR-Associated Protein 9; CRISPR-Associated Proteins / chemistry; CRISPR-Cas Systems; Clustered Regularly Interspaced Short Palindromic Repeats; DNA / chemistry; DNA Cleavage; Endonucleases / chemistry; Genetic Engineering / methods; HEK293 Cells; Humans; Nucleic Acid Conformation; RNA, Guide, Kinetoplastida / chemistry; RNA, Guide, Kinetoplastida / genetics; RNA, Guide, Kinetoplastida / ultrastructure
TL;DR:
Six conserved modules within native crRNA:tracrRNA duplexes and single guide RNAs that direct Cas9 endonuclease activity are identified and characterized and it is shown the bulge and nexus are necessary for DNA cleavage and the nexus and hairpins are instrumental in defining orthogonality between systems.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2013 journal article
Lactobacillus buchneri Genotyping on the Basis of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Locus Diversity
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 80(3), 994–1001.
MeSH headings : Clustered Regularly Interspaced Short Palindromic Repeats; DNA, Bacterial / chemistry; DNA, Bacterial / genetics; Food Microbiology; Genetic Variation; Genotype; Lactobacillus / classification; Lactobacillus / genetics; Lactobacillus / isolation & purification; Molecular Sequence Data; Molecular Typing / methods; Sequence Analysis, DNA
TL;DR:
Findings suggest that type II-A CRISPR-Cas systems are valuable for genotyping of L. buchneri, a species relevant for commercial silage, bioethanol, and vegetable fermentations.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
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