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method for genome editing uses CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) sequences and the endonuclease Cas9 (CRISPR-associated protein 9). (wikipedia.org)
In collaboration with Stanley Qi and the laboratories of Wendell Lim , Jonathan Weissman , and Adam Arkin , we pioneered the engineering of CRISPR-Cas proteins for new purposes by converting Cas9 into a tool for targeted control of gene expression, referred to as CRISPR interference (CRISPRi). (berkeley.edu)
In this platform, catalytically inactive Cas9 serves as an RNA-guided DNA binding protein to silence gene expression in a sequence-specific manner. (berkeley.edu)
The advent of CRISPR/Cas9 gene editing, together with the plummeting cost of whole-genome sequencing, has cleared a path for the development of customised cancer cell models. (drugtargetreview.com)
CRISPR/Cas9 has enabled us to reliably and cost-effectively edit the genome of any target organism or cell line, 5-7 while whole-genome sequencing has enabled us to assemble massive sequence libraries for both healthy and tumour tissue, revealing the diverse genetic changes found in tumour cell populations. (drugtargetreview.com)
Use of CRISPR/Cas9-engineered cancer model systems to accelerate the development of targeted therapies is one example of this effect. (drugtargetreview.com)
Moreover, CRISPR/Cas9-engineered cancer models can be designed to mimic specific cancer genotypes found in clinical patient samples. (drugtargetreview.com)
CRISPR-Cas9-based genome editing has transformed the life sciences, enabling virtually unlimited genetic manipulation of genomes: The RNA-guided Cas9 endonuclease cuts DNA at a specific target sequence and the resulting double-strand breaks are mended by one of the intrinsic cellular repair pathways. (life-science-alliance.org)
These findings demonstrate the feasibility of using the system for generating recombinants and also highlight an unforeseen risk of using CRISPR-Cas9 for therapeutic intervention. (life-science-alliance.org)
CRISPR-Cas9-based genome editing has revolutionized genetic research, triggering the development of a plethora of technologies and applications that provide unprecedented control over genes in a growing list of model species ( 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 ). (life-science-alliance.org)
Genome editing is achieved by precisely targeting the nuclease activity of a modified bacterial protein (Cas9) via a user-defined guide RNA to a specific DNA sequence ( 1 ). (life-science-alliance.org)
The ability of CRISPR-Cas9 to introduce several concurrent DSBs at defined positions has enabled engineering of tumor-associated chromosomal translocations resembling those observed in cancers, and hence to establish and test novel in vitro and in vivo tumor models ( 2 , 23 , 24 , 25 ). (life-science-alliance.org)
26 ) leveraged the CRISPR-Cas9 system to produce other chromosomal rearrangements, generating targeted mitotic recombination events in yeast to enable the fine mapping of trait variants. (life-science-alliance.org)
Small RNA molecule constituting part of a 3-component naturally occurring CRISPR-Cas defense system in bacteria and serving as a link for associating the crRNA with the Cas9 protein. (corteva.com)
Thomson Reuters predicts that the developers of the CRISPR/Cas9 genome editing approach may win the Nobel Prize in Chemistry. (pharmaceuticalintelligence.com)
21.1.2 Evaluate your Cas9 gene editing vectors: CRISPR/Cas Mediated Genome Engineering - Is your CRISPR gRNA optimized for your cell lines? (pharmaceuticalintelligence.com)
Targeted genome editing using CRISPR-Cas9 has been widely adopted as a genetic engineering tool in various biological systems. (mdpi.com)
The Streptococcus pyogenes Cas9 (SpCas9) nuclease can be efficiently targeted to genomic loci by means of singleguide RNAs (sgRNAs) to enable genome editing 1 - 10 . (cdc.gov)
the CRISPR-associated nuclease Cas9 (SpCas9), a specificity-determining CRISPR RNA (crRNA), and an auxiliary trans-activating crRNA (tracrRNA) 11 . (cdc.gov)
Here, the fusion proteins MLL-AF4 (MA4) and AF4-MLL (A4M) were CRISPR/Cas9-genome edited in the AAVS1 locus of HEK293 cells as a model to study MLL fusion-mediated DNA-DSB formation/repair. (ibecbarcelona.eu)
Al-Sammarraie N, Ray S. CRISPR-Cas9 Genome Editing in GBM. (encyclopedia.pub)
CRISPR-Cas9 Genome Editing in GBM" Encyclopedia , https://encyclopedia.pub/entry/14422 (accessed December 05, 2023). (encyclopedia.pub)
The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR associated (Cas) nuclease 9 (CRISPR-Cas9) system is a cost-effective and reliable gene editing technology, which is widely used in cancer research. (encyclopedia.pub)
Here, we employ diverse CRISPR/Cas9 genome editing tools to generate a series of targeted lesions within the endogenous cis-regulatory module (CRM) required for kni expression in the L2 vein primordium. (elifesciences.org)
In 2015, researchers reported that they had used components of the CRISPR/Cas9 genome editing system to edit genes so that they could propagate in a "Super-Mendelian" fashion. (elifesciences.org)
Single xxt3 and triple xxt3xxt4xxt5 mutant Arabidopsis (Arabidopsis thaliana) plants were generated using CRISPR-Cas9 technology to determine the specific function of XXT3. (bvsalud.org)
Now, researchers at Harvard University have modified CRISPR/Cas9 technology to get around these problems, creating a new "base editor," described today (April 20) in Nature , which permanently and efficiently converts cytosine (C) to uracil (U) bases with low error in human and mouse cell lines. (pharmaceuticalintelligence.com)
To date, CRISPR/Cas9 genome-editing approaches have relied on a cellular mechanism called homology-directed repair, which is triggered by double-strand breaks in DNA. (pharmaceuticalintelligence.com)
By contrast, a normal Cas9 editing technique tested on three of those loci showed less than one percent efficiency, and more than four percent formation of indels. (pharmaceuticalintelligence.com)

this technique is able to establish point mutations, gene deletions, and short sequence insertions in several genomic loci with increased efficiency and time sensitivity. (wikipedia.org)
b, d HDR frequencies, measured by high-throughput DNA sequencing of unsorted HEK293T cells at eight endogenous genomic loci. (mycareerpeer.com)
100 predicted genomic off-target loci in 293T and 293FT cells. (cdc.gov)
Following crRNA and tracrRNA hybridization, SpCas9 is targeted to genomic loci matching a 20-nt guide sequence within the crRNA, immediately upstream of a required 5′-NGG protospacer adjacent motif (PAM) 11 . (cdc.gov)
This highly sensitive phenotypic readout of enhancer function in a native genomic context reveals novel features of CRM function undetected by traditional reporter gene analysis. (elifesciences.org)
MetaCherchant: analyzing genomic context of antibiotic resistance genes in gut microbiota. (cdc.gov)

Phylogenetic analysis of CRISPR-associated (Cas) proteins suggests there are at least seven distinct versions of this immune system. (berkeley.edu)
Open in a separate windows Fig. 2 Manipulation of HDR frequency by global manipulation of cellular repair proteins. (mycareerpeer.com)
Rapid characterization of anti-CRISPR proteins and optogenetically engineered variants using a versatile plasmid interference system. (optobase.org)
Anti-CRISPR (Acr) proteins are encoded by mobile genetic elements to overcome the CRISPR immunity of prokaryotes, displaying promises as controllable tools for modulating CRISPR-based applications. (optobase.org)
However, characterizing novel anti-CRISPR proteins and exploiting Acr-related technologies is a rather long and tedious process. (optobase.org)
Abbreviation for "CRISPR Associated" used to designate proteins that accompany a CRISPR locus that together comprises a CRISPR-Cas defense mechanism. (corteva.com)
It is organized into genes that specify the production of proteins. (corteva.com)
The cellular process of assembling amino acids into proteins using the nucleotide sequence of messenger RNA (mRNA, see "RNA") as a set of instructions. (corteva.com)
There are several forms of RNA, including messenger RNA (mRNA) which conveys the genetic information from genes (encoded by nucleotides) to proteins (encoded by amino acids). (corteva.com)
Crystal structures are available for archaeal and bacterial NAS-like proteins that carry out simpler aminobutanoyl transferase reactions. (bvsalud.org)
Herein, for the first time, we present a platform based on droplet microfluidics coupling with the recombinase aided amplification (RAA)-assisted one-pot clustered regularly interspaced short palindromic repeats together with CRISPR-associated proteins 13a (CRISPR/Cas13a) assay, and droplet encoding strategy for accurate and sensitive determination of nucleic acids from various foodborne pathogens. (bvsalud.org)
Three of the six up-regulated genes encode potential zinc transporter proteins (ZnuA1, ZnuB1, ZnuC1) suggesting involvement of s479 in regulation of zinc transport. (uni-stuttgart.de)
Interestingly, s479 is not only encoded next to CRISPR-cas genes but the mature s479 contains a crRNA-like 5´ handle and experiments with Cas protein deletion strains indicate maturation by Cas6 and interaction with Cas proteins. (uni-stuttgart.de)

In light of efforts to map combinatorial gene dependencies at scale, choosing an efficient and robust CRISPR-associated (Cas) nuclease is of utmost importance. (nature.com)

Here, we established a versatile plasmid interference with CRISPR interference (PICI) system in Escherichia coli for rapidly characterizing Acrs and developing Acr-based technologies. (optobase.org)
CRISPR interference (CRISPRi) is a robust gene silencing technique that is ideal for targeting essential and conditionally essential (CE) genes. (bvsalud.org)

The Doudna lab employs protein engineering and screening strategies to bestow CRISPR-Cas enzymes with improved and novel functionalities. (berkeley.edu)
In collaboration with the laboratory of David Savage , we have also developed a series of high-throughput mutant library construction, screening, and sequencing pipelines to probe CRISPR-Cas protein function and to isolate engineered variants with novel properties. (berkeley.edu)
Recently, we used a similar large-scale protein engineering and screening platform to construct circularly permuted, viral protease-activated ProCas9s that orchestrate programmed cellular responses to pathogen-associated protease activity. (berkeley.edu)
The amino acid sequence of a protein is encoded by the nucleotide sequence of a corresponding gene. (corteva.com)
The active protein is a homodimer that binds to the interferon gamma receptor which triggers a cellular response to viral and microbial infections. (origene.com)
Phenotypic analysis of these ' in locus ' mutations based on both expression of Kni protein and adult wing phenotypes, reveals novel unexpected features of L2-CRM function including evidence for a chromosome pairing-dependent process that promotes transcription. (elifesciences.org)
This gene encodes a small GTP-binding protein that belongs to the largest family within the Ras superfamily. (nih.gov)
The sRNA gene is encoded between a CRISPR RNA locus and the Cas protein gene cluster, the s479 deletion strain is viable and was characterized in detail. (uni-stuttgart.de)
1000 Mb with up to 18,000 protein-coding genes [ 12 ]. (biomedcentral.com)

In this system, sequences matching foreign bacteriophage or plasmid DNA are incorporated as "spacer" sequences into the bacterial genome located between repeating CRISPR loci. (wikipedia.org)
CRISPR-harboring organisms generate immunological memory of previous infections by capturing short segments of foreign DNA for integration into CRISPR loci as spacer sequences. (berkeley.edu)
A piece of DNA comprising nucleotide sequences that are repeated and separated by sequences from invading viruses that serves as part of a naturally occurring CRISPR-Cas defense system in bacteria to fight invading viruses. (corteva.com)
Although an sgRNA design consisting of a truncated crRNA and tracrRNA had been previously shown to mediate efficient cleavage in vitro 12 , it failed to achieve detectable cleavage at several loci that were efficiently modified by crRNA-tracrRNA duplexes bearing identical guide sequences 1 . (cdc.gov)
However, individual transcript sequences of the same gene can differ through naturally occurring variations (e.g. polymorphisms), each with its own valid existence. (origene.com)
Using the technique at six loci in human cells, the team reported a targeted base correction rate of up to 37 percent, with only around 1 percent of the sequences showing indels. (pharmaceuticalintelligence.com)
These elements included a single promoter, which was mapped upstream of the 16S rRNA gene and which was similar to Escherichia coli consensus promoter sequences, an AT-rich upstream region, a GC-rich motif that may be involved in stringent control, leader and spacer antitermination sequences, sites for ribonuclease processing, and a putative factor-independent terminator sequence. (microbiologyresearch.org)

Cas endonucleases are able to initiate double strand breaks within these foreign DNAs that are complement to the transcribed CRISPR RNAs (crRNA, or "protospacers"), thus degrading them. (wikipedia.org)

Genetic variants in the DNA methyltransferase 3 A (DNMT3A) locus have been associated with inflammatory bowel disease (IBD). (nature.com)
Recent studies indicate that CRISPR-induced DNA cuts may also result in the exchange of genetic information between homologous chromosome arms. (life-science-alliance.org)
CRISPR systems allow us to edit, engineer, or regulate genomes, hold great promise for clinical applications, and are likely to be used to treat diseases with genetic underpinnings, including cancer ( 9 , 10 ). (life-science-alliance.org)
Chromosomes carry genetic information in the form of genes. (corteva.com)
The complete set of genes or genetic material present in a cell or organism. (corteva.com)
including the two researchers involved in the 2015 work - have used a new active genetic element called a CopyCat element and more traditional genome editing to analyze the control of a gene that coordinates the formation of a simple structure in a fruit fly - a vein in the wing. (elifesciences.org)
Single-cell CRISPR screens in organoids could link genetic perturbations with parallel transcriptomic readout in single cells, providing a powerful method to delineate roles of cell fate regulators. (bvsalud.org)
A) Schematic of the generation of OPTiKD human pluripotent stem cells (hPSCs) and of the resulting genetic circuit which allows tetracycline (TET)-dependent induction of gene knockdown both in hPSCs and hPSC-derived cells. (berterolab.com)

In response to different stimuli many transcription factors (TFs) display different activation dynamics that trigger the expression of specific sets of target genes, suggesting that promoters have a way to decode dynamics. (optobase.org)
Some "Quimbyviridae" phages possess Diversity-Generating Retroelements (DGRs) that generate hypervariable target genes nested within defense-related genes, whereas the previously known targets of phage-encoded DGRs are structural genes. (biomedcentral.com)
In addition, we provide comprehensive guide RNA designs to target genes in common laboratory strains of P. aeruginosa and other Pseudomonas species. (bvsalud.org)

Thus, epigenetic mechanisms as long-term determinants of gene expression are a plausible link between genetics and environment, which may instigate the manifestation and/or progression of IBD. (nature.com)
This enables us to identify candidate genes underlying glucosinolate diversity, trichome density, and study the genetics of biochemical variation for glucosinolate and saponins. (pacb.com)

CRISPRi is especially valuable for investigating gene function in pathogens such as P. aeruginosa where essential and CE genes underlie clinically important phenotypes such as antibiotic susceptibility and virulence. (bvsalud.org)
We further optimized Mobile-CRISPRi for use in P. aeruginosa mouse models of acute lung infection by expressing the CRISPRi machinery at low levels constitutively, enabling partial knockdown of essential and CE genes without the need for an exogenous inducer. (bvsalud.org)

Boros I. , Csordés-Tôth E. , Kiss A. , Tôrôk I. , Udvardy K. , Venetianer P. Identification of two new promoters probably involved in the transcription of a ribosomal RNA gene of Escherichia coli. (microbiologyresearch.org)
Brosius J. , Dull D.J. , Sleeter D.D. , Noller H.F. Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. (microbiologyresearch.org)

21.1.4 Prediction of the Winner RNA Technology, the FRONTIER of SCIENCE on RNA Biology, Cancer and Therapeutics & The Start Up Landscape in BostonGene Editing - New Technology The Missing link for Gene Therapy? (pharmaceuticalintelligence.com)

CABGen: A Web Application for the Bioinformatic Analysis of Bacterial Genomes. (cdc.gov)
A search of human gut metagenomes for circular contigs encoding phage hallmark genes resulted in the identification of 3738 apparently complete phage genomes that represent 451 putative genera. (biomedcentral.com)
CPR bacteria have small genomes and very limited biosynthetic metabolic capabilities, which suggest that they depend on other organisms to obtain many essential cellular components (amino acids, lipids, nucleotides, etc.) [2,3]. (nature.com)

We are interested in understanding and harnessing RNA-mediated control of the genome, including CRISPR-Cas bacterial adaptive immunity and related systems. (berkeley.edu)

Our results uncover the structural basis for foreign DNA capture and the mechanism by which Cas1-Cas2 functions as a molecular ruler to dictate the sequence architecture of CRISPR loci. (berkeley.edu)
The molecular sequence of this clone aligns with the gene accession number as a point of reference only. (origene.com)
Sequence and primer extension analysis revealed the presence of putative genes encoding tRNA lle and tRNA Ala within the 16S-23S spacer region, as well as a number of potential regulatory features. (microbiologyresearch.org)

We get around 10% of our energy from metabolites produced by gut microorganisms, and polysaccharide utilization loci are major determinants of these chemical transformations. (wisc.edu)

In contrast, some bacterial pathogens (including Listeria monocytogenes and Shigella flexneri ) have mechanisms to escape from the phagosome and proliferate in the cytosol ( 13 ). (frontiersin.org)
Targeting of bacterial pathogens by the autophagy machinery is often mediated by ubiquitination, a posttranslational modification ( 16 , 17 ). (frontiersin.org)
Kirsten Bos is a specialist in ancient DNA research, with a focus on bacterial pathogens. (agbt.org)
However, the application of new techniques, such as CRISPR, to the study of trematodes and nematodes has opened new avenues for genome editing-powered functional genomics for these pathogens. (biomedcentral.com)

Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing. (cdc.gov)
Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling. (cdc.gov)
These loci (rrnA, rrnB and rrnC) were isolated on recombinant lambda clones, and comprised 16S, 23S and 5S rRNA genes closely linked in that order. (microbiologyresearch.org)
Potential open reading frames (ORFs) were identified within the regions flanking the rrn loci, with identical copies of the 3′ terminal ORF present downstream of each rRNA operon. (microbiologyresearch.org)
Baylis H.A. , Bibb M.J. Transcriptional analysis of the 16S rRNA gene of the rrnD gene set of Streptomjces A3(2). (microbiologyresearch.org)

We employ traditional biochemistry, combined with sequencing, live-cell imaging, and structural biology approaches, to uncover the fundamental mechanisms driving the CRISPR effectors now being developed as genome editing and diagnostic tools. (berkeley.edu)
Adaptation of the bacterial CRISPR-Cas system for genome editing purposes by combining crRNA and tracrRNA into a single guide RNA molecule. (corteva.com)
used genome editing to make mutations in a stretch of DNA that regulates the gene involved in wing vein formation. (elifesciences.org)

This gene encodes a soluble cytokine that is a member of the type II interferon class. (origene.com)
The knirps ( kni ) locus encodes transcription factors required for induction of the L2 wing vein in Drosophila . (elifesciences.org)

Imprecise double-strand repair will introduce random mutations such as indels or point mutations, whereas precise editing will restore or specifically edit the locus as mandated by an endogenous or exogenously provided template. (life-science-alliance.org)
To avoid the use of hybrid gRNAs for orthogonal applications, we engineered the multiplex SpCas9-enAsCas12a approach (multiSPAS) that avoids RNA processing for efficient orthogonal gene editing. (nature.com)

The above mentioned experiments utilized donor layouts which contain PAM-blocking mutations at five from the eight loci examined (sgRNA 1, sgRNA 2, HEK site 2, HEK site 3, and HEK site 4), and donor layouts that lacked PAM-blocking mutations because of unavailability of the silent PAM-blocking mutation as well as the focus on stage mutation at the rest of the three sites (LDLR, HBB, and SERPA1). (mycareerpeer.com)
Furthermore, both sgRNA designs efficiently modified PVALB loci that were previously not targetable using crRNA-tracrRNA duplexes 1 ( Fig. 1b and Supplementary Fig. 1b ). (cdc.gov)

The λ-red recombineering system was published in 1998 and allows for insertion, deletion, or mutations to E. coli genes. (wikipedia.org)
Many bacteria use a system known as CRISPR-Cas to defend themselves against infection by viruses called phages. (elifesciences.org)
This system protects the bacterial cell by taking a short length of DNA from the phage and inserting this 'spacer' into its own genome. (elifesciences.org)
A Small RNA molecule encoded by the CRISPR locus constituting part of a 3-component naturally occurring CRISPR-Cas defense system in bacteria. (corteva.com)
Overall, in view of superiorities in high sensitivity, outstanding selectivity, and large-scale multiplexing, the one-pot CRISPR/Cas13a-based droplet microfluidic system could be expanded and universalized for identifying other bacteria. (bvsalud.org)
Together this might suggest that the CRISPR-Cas system is involved in s479 function. (uni-stuttgart.de)

Now, in eLife, Nora Pyenson and Luciano Marraffini from the Rockefeller University report that the number of spacers each bacterial cell acquires depends on its local environment ( Pyenson and Marraffini, 2020 ). (elifesciences.org)

In this work, we present a side-by-side and systematic comparison of combinatorial and orthogonal CRISPR screening approaches and identified optimized metrics for combinatorial genotype-to-phenotype associations. (nature.com)

We generated a set of sgRNAs targeting multiple sites within the human EMX1 and PVALB loci with different tracrRNA 3′ truncations ( Fig. 1a ). (cdc.gov)

Immunological recognition of commensal microbes, such as bacterial species resident in the gut or lung as well as dormant viral species, i.e., cytomegalovirus (CMV) or Epstein-Barr virus (EBV), in combination with a balanced immune regulation, is central to achieve immune-protection. (frontiersin.org)
Mutations in this gene are associated with an increased susceptibility to viral, bacterial and parasitic infections and to several autoimmune diseases. (origene.com)
NFkB is a nuclear transcription factor activated by various extra and intracellular stimuli such as cytokines, UV radiation, stress, in injury, and by bacterial and viral products. (thermofisher.com)

Using the knowledge acquired, we build a synthetic circuit that allows obtaining two gene expression programs depending solely on TF dynamics. (optobase.org)
These results help elucidate how gene expression is regulated in mammalian cells and open up the possibility to build complex synthetic circuits steered by TF dynamics. (optobase.org)
RNA is essential in various biological roles in coding, decoding, regulation, and expression of genes. (corteva.com)
We found that the tricarboxylic acid cycle-associated enzyme α-ketoglutarate (α-KG) dehydrogenase (KGDH) entered the nucleus, where it interacted with various JMJs to regulate α-KG-dependent histone demethylations by JMJs, and thus controlled genome-wide gene expression in plants. (bvsalud.org)
Through temporal profiling of chromatin accessibility and gene expression in vivo, we identify dynamic changes in the epigenome that occur as osteosarcoma tumors form and grow within the lung microenvironment. (bvsalud.org)
The NFkB complex is expressed in most cell types, and is primarily found in the cytoplasm in an inactive state in association with I-kappa-B. Phosphorylation of I-kappa-B releases the complex, allowing translocation to the nucleus and modification of gene expression. (thermofisher.com)
PULs also may influence global gene expression patterns in the gut. (wisc.edu)
Anderson B.J. , Bills M.M. , Egerton J.R. , Mattick J.S. Cloning and expression in E coli of the gene encoding the structural subunit of Bacteroides nodosus fimbriae. (microbiologyresearch.org)

Their comprehensive study on the fitness of Bacteroides uniformis provides a deeper understanding of how diverse PULs contribute to glycan utilization, microbial interactions, and bacterial colonization of the mammalian gut. (wisc.edu)
By introducing different PULs deletion mutants (PULs that are missing metabolic pathways) into a microbial community created in the lab, the researchers found that PULs can benefit or harm bacterial colonization depending on specific conditions in the microbial community. (wisc.edu)
Previously, people thought that polysaccharide utilization loci always promoted bacterial colonization. (wisc.edu)

RNA-targeting CRISPR-Cas systems - We use biochemical activity assays in conjunction with structural techniques and sequencing to investigate RNA-targeting CRISPR systems, such as the Type VI effector, Cas13a. (berkeley.edu)
The workflow takes full advantage of CRISPR/Cas13a signal amplification and droplet confinement effects, which enhances the detection sensitivity and enables end-point quantitation. (bvsalud.org)

Further experiments showed that compared to bacteria grown in liquid culture, bacterial cells in the resistant colonies had often acquired multiple spacers and were able to fight off phages with other mutations ( Figure 1 , right). (elifesciences.org)
The effects of these mutations unexpectedly suggested that pairs of chromosomes might be interacting to control the activity of this gene. (elifesciences.org)
Researchers develop a CRISPR-based technique that efficiently corrects point mutations without cleaving DNA. (pharmaceuticalintelligence.com)

Here, we systematically compared combinatorial SpCas9, AsCas12a, and CHyMErA in hTERT-immortalized retinal pigment epithelial cells and extracted performance-critical parameters for combinatorial and orthogonal CRISPR screens. (nature.com)

A plasmid expressing flippase (FLP) can be transformed into the recombined cells, which can specifically cleave FLP recognition target sites (FRTs) flanking the antibiotic resistance gene. (wikipedia.org)

Following λ-red operon activity induction, a linear, double-stranded cassette encoding a selectable marker, such as antibiotic resistance, is transformed into the cells in place of the target gene and incorporated into the DNA behind a specific inducible promoter. (wikipedia.org)

In the figure, each bacterial cell has one of four different spacers (shown in blue, green, orange and pink). (elifesciences.org)
In order to stay protected, some bacterial cells within the colony acquire multiple spacers (multi-colored bacterial cells) and can fight off various mutant phages. (elifesciences.org)
Analysis of CRISPR spacers indicates that phages of all three putative families infect bacteria of the phylum Bacteroidetes. (biomedcentral.com)

If the bacterial cell becomes re-infected, the spacer allows the cell to recognize the phage and stop it from replicating by cutting and destroying its DNA. (elifesciences.org)
When growing in a liquid environment (left), individual bacterial cells usually acquire a single spacer that targets just one region of the wild-type (WT) phage (shown in grey). (elifesciences.org)

These include providing new ways to explore how genes control the formation and activity of different organisms. (elifesciences.org)

NFkB is involved in regulation of various cellular events including cell growth, differentiation, proliferation, apoptosis and inflammation. (thermofisher.com)
Transcriptome studies of wild type Haloferax cells and the deletion mutant revealed up-regulation of six genes in the deletion strain, showing that the sRNA has a clearly defined function. (uni-stuttgart.de)

Upregulation of these genes in the deletion strain was confirmed by northern blot and proteome analyses. (uni-stuttgart.de)

A multilevel framework for taxonomic classification of viruses was recently adopted, facilitating the classification of phages into evolutionary informative taxonomic units based on hallmark genes. (biomedcentral.com)
Hundreds of phages in these three and other families are shown to encode catalases and iron-sequestering enzymes that can be predicted to enhance cellular tolerance to reactive oxygen species. (biomedcentral.com)

RecA is certainly a bacterial homolog of hRad51 that catalyzes strand invasion between homologous strands of DNA. (mycareerpeer.com)

Leishmania braziliensis causing human disease in Northeast Brazil presents loci with genotypes in long-term equilibrium. (cdc.gov)
The most frequent rearrangement of the human MLL gene fuses MLL to AF4 resulting in high-risk infant B-cell acute lymphoblastic leukemia (B-ALL). (ibecbarcelona.eu)
The Venturelli Lab has now overturned prior knowledge about how polysaccharide utilization loci (PULs) mediate the fitness and community-level interactions of Bacteroides uniformis , one of the most abundant species of bacteria in the human gut. (wisc.edu)

Currently, two types of combinatorial CRISPR screens are established: single and orthogonal. (nature.com)
While combinatorial CRISPR screens are powerful, they suffer from scalability issues related to large numbers of to-be-investigated query genes 20 . (nature.com)
Furthermore, we show through paired in vivo and in vitro CRISPR drop-out screens and pharmacological validation that the upstream transcription factors represent a class of metastasis-specific dependency genes. (bvsalud.org)

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