CRISPR-Cas technology a new era in genomic engineering

Parsaeimehr, Ali; Ebirim, Rosemary I.; Ozbay, Gulnihal

doi:10.1016/j.btre.2022.e00731

Cited by 8 publications

(5 citation statements)

References 140 publications

(133 reference statements)

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“…However, the bacteriophages have mechanisms that allow them to evade the action of CRISPR–Cas systems. Recent data indicate that these elements act at the DNA level or interfere with the binding of DNA to Cas proteins (Parsaeimehr et al, 2022 ) and in the presence of anti-CRISPR proteins in the genomes of A. baumannii (Yadav and Singh, 2022 ). However, more specific data detailing the characterization of A. baumannii and A. pitti , where anti-CRISPR Cas proteins have also been found, are still needed.…”

Section: Discussionmentioning

confidence: 99%

A bioinformatic approach to identify confirmed and probable CRISPR–Cas systems in the Acinetobacter calcoaceticus–Acinetobacter baumannii complex genomes

Mancilla-Rojano,

Flores,

Cevallos

et al. 2024

Front. Microbiol.

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IntroductionThe Acinetobacter calcoaceticus–Acinetobacter baumannii complex, or Acb complex, consists of six species: Acinetobacter baumannii, Acinetobacter calcoaceticus, Acinetobacter nosocomialis, Acinetobacter pittii, Acinetobacter seifertii, and Acinetobacter lactucae. A. baumannii is the most clinically significant of these species and is frequently related to healthcare-associated infections (HCAIs). Clustered regularly interspaced short palindromic repeat (CRISPR) arrays and associated genes (cas) constitute bacterial adaptive immune systems and function as variable genetic elements. This study aimed to conduct a genomic analysis of Acb complex genomes available in databases to describe and characterize CRISPR systems and cas genes.MethodsAcb complex genomes available in the NCBI and BV-BRC databases, the identification and characterization of CRISPR-Cas systems were performed using CRISPRCasFinder, CRISPRminer, and CRISPRDetect. Sequence types (STs) were determined using the Oxford scheme and ribosomal multilocus sequence typing (rMLST). Prophages were identified using PHASTER and Prophage Hunter.ResultsA total of 293 genomes representing six Acb species exhibited CRISPR-related sequences. These genomes originate from various sources, including clinical specimens, animals, medical devices, and environmental samples. Sequence typing identified 145 ribosomal multilocus sequence types (rSTs). CRISPR–Cas systems were confirmed in 26.3% of the genomes, classified as subtypes I-Fa, I-Fb and I-Fv. Probable CRISPR arrays and cas genes associated with CRISPR–Cas subtypes III-A, I-B, and III-B were also detected. Some of the CRISPR–Cas systems are associated with genomic regions related to Cap4 proteins, and toxin–antitoxin systems. Moreover, prophage sequences were prevalent in 68.9% of the genomes. Analysis revealed a connection between these prophages and CRISPR–Cas systems, indicating an ongoing arms race between the bacteria and their bacteriophages. Furthermore, proteins associated with anti-CRISPR systems, such as AcrF11 and AcrF7, were identified in the A. baumannii and A. pittii genomes.DiscussionThis study elucidates CRISPR–Cas systems and defense mechanisms within the Acb complex, highlighting their diverse distribution and interactions with prophages and other genetic elements. This study also provides valuable insights into the evolution and adaptation of these microorganisms in various environments and clinical settings.

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Section: Discussionmentioning

confidence: 99%

A bioinformatic approach to identify confirmed and probable CRISPR–Cas systems in the Acinetobacter calcoaceticus–Acinetobacter baumannii complex genomes

Mancilla-Rojano,

Flores,

Cevallos

et al. 2024

Front. Microbiol.

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“…Ongoing research aims to overcome these limitations by refining the differentiation protocols to generate more mature and region-specific cell types incorporating multicellular 3D organoid culture systems for enhanced disease-relevant human-based models [ 263 ]. Cutting-edge technologies such as CRISPR/Cas9 gene editing, single-cell RNA sequencing, and microfluidics organoids-on-a-chip culture systems have advanced iPSC-derived cell studies, allowing precise genetic modifications, in-depth assessments of the molecular and cellular heterogeneity, and generation of complex 3D models that enhance research on neuroinflammatory diseases [ 264 ]. As multidisciplinary collaborations span across several disciplines like stem cell technology, immunology, neurobiology and regenerative medicine, iPSC-based approaches are poised to reshape neuroinflammatory disease research and therapeutic development.…”

Section: The Use Of Ipsc-derived Cells In Neuroinflammatory Disease P...mentioning

confidence: 99%

Recent Research Trends in Neuroinflammatory and Neurodegenerative Disorders

Cohen,

Mathew,

Dourvetakis

et al. 2024

Cells

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Neuroinflammatory and neurodegenerative disorders including Alzheimer’s disease (AD), Parkinson’s disease (PD), traumatic brain injury (TBI) and Amyotrophic lateral sclerosis (ALS) are chronic major health disorders. The exact mechanism of the neuroimmune dysfunctions of these disease pathogeneses is currently not clearly understood. These disorders show dysregulated neuroimmune and inflammatory responses, including activation of neurons, glial cells, and neurovascular unit damage associated with excessive release of proinflammatory cytokines, chemokines, neurotoxic mediators, and infiltration of peripheral immune cells into the brain, as well as entry of inflammatory mediators through damaged neurovascular endothelial cells, blood–brain barrier and tight junction proteins. Activation of glial cells and immune cells leads to the release of many inflammatory and neurotoxic molecules that cause neuroinflammation and neurodegeneration. Gulf War Illness (GWI) and myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) are chronic disorders that are also associated with neuroimmune dysfunctions. Currently, there are no effective disease-modifying therapeutic options available for these diseases. Human induced pluripotent stem cell (iPSC)-derived neurons, astrocytes, microglia, endothelial cells and pericytes are currently used for many disease models for drug discovery. This review highlights certain recent trends in neuroinflammatory responses and iPSC-derived brain cell applications in neuroinflammatory disorders.

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“…To address this constraint, the conjunction of nucleic acid amplication technologies and HGD has been employed to achieve substantial signal amplication, elevating the detection capabilities by orders of magnitude. Various nucleic acid amplication techniques are being integrated with HGD for detection purposes, such as Polymerase Chain Reaction (PCR), [32][33][34][35][36][37] Loop-Mediated Isothermal Amplication (LAMP), [38][39][40][41][42][43][44] and Recombinase Polymerase Amplication (RPA). [45][46][47][48] These methods are able to amplify the signal to be detected.…”

Section: Amplication Of Target and Detectionmentioning

confidence: 99%

“…Another different detection strategy based on PCR is complementing the G-quadruplex sequence in the primer into dsDNA by amplifying to decrease the level of DNAzyme, resulting in a drop in the colorimetric signal. 33,34 Generally, the "turn off" strategy oen has a low sensitivity compared to the "turn on" strategy, due to its high background signal. In addition to adding the G-quadruplex sequence directly to the primer, complementary sequences of the Gquadruplex can also be added to the primer.…”

Section: Amplication Of Target and Detectionmentioning

confidence: 99%