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We narrowed to 939 results for: genome

Showing: 141 - 160 of 939 results

  1. Screening for Successful Genome Editing with Digital PCR

    Type
    Blog Post
    ...bulk or single cell-derived genomic DNA sample as part of a precision genome editing workflow. Digital ...already) the plunge into the world of precision genome editing. When it comes time to (hopefully) validate...joining (NHEJ) (2-5), depending on your desired genome edit. Since exploitation of NHEJ to generate translational...one of the most common applications of precision genome editing, the remainder of this post will focus ...power of digital PCR screening to validate your genome edits, this paper provides detailed instructions... options can be found here. Good luck with your genome editing, and may all your NHEJ mutations be out... 1. Miyaoka, Y. et al. Isolation of single-base genome-edited human iPS cells without antibiotic selection...

  2. Five Popular Model Organisms, Part 2

    Type
    Blog Post
    ...difficult to manipulate genome and limited genetic data. To bridge this gap, the Rat Genome Sequencing Project...CRISPR interference screening enables genome-scale functional genomics study in bacteria with superior performance...cloning and metabolic engineering.  The E. coli genome has an extensive research history and characterization...biochemistry. Though limited at first, advances in axolotl genome sequencing have vastly expanded axolotl research...advances is the sequencing of the entire axolotl genome, revealing an abundance of genes related to limb...African frog. Image from Holger Krisp. The frog genome has high synteny with that of humans so they are...extensive scientific history, highly characterized genome, and widespread utilization, Arabidopsis has made...

  3. The CRISPR Software Matchmaker: A New Tool for Choosing the Best CRISPR Software for Your Needs

    Type
    Blog Post
    ...small genome”, “large genome”, and “organism biased scoring”. Trends: Many tools can handle genomes of any...lists the genomes supported by each tool. The genomes are denoted by organism name and genome assembly ...falciparum genome. To put this last point into perspective, the Plasmodium falciparum genome contains only...whereas the human genome has about 300 million. With such a sparsely targetable genome, off-targeting is...Interactions, Institut Pasteur, Paris) that changed genome editing in the malaria community for the better...edit rate of over 90% in their work editing the genome of Plasmodium falciparum (the parasite that causes...consensus on the best CRISPR software tools yet. As a genome editing tool, the CRISPR/Cas9 technology has been...

  4. CRISPR 101: Validating Your Genome Edit

    Type
    Blog Post
    ...quantitatively assess genome edits in your target sequence and other regions of the genome. The main advantage...with Cas9. Hooray! Now it’s time to make sure your genome edits went according to plan. In this blog post...insertions and deletions identified within a given genomic window, along with the estimated editing frequency...must generate a DNA molecule with homology to your genome edit to mimic what an edited sequence would look...sequencing, provided you have some idea of where in the genome you might expect off target editing to occur. Luckily...Bas van Steensel. Easy quantitative assessment of genome editing by sequence trace decomposition. (2014)...silico off-target site identification for CRISPR genome editing. (2019) Bioinformatics 36:2001–2008. https...

  5. Viral Vectors 101: An Introduction to AAV

    Type
    Blog Post
    ...the ssAAV genome has a mutation in the terminal resolution site (TRS) to form a vector genome with wild-type... non-pathogenic, do not integrate into the host genome, and can be specifically targeted to a number of... expression in a particular cell type to CRISPR genome editing, optogenetics, and chemogenetics experiments... of interest, AAVs used in research have their genomes “gutted”, meaning that all viral genes except ITRs...Remember that AAVs do not integrate into the host genome and therefore the transduced gene is episomal and...self-complementary AAV (scAAV) vector. Full-length ssAAV vector genome of both polarities are rescued from the vector ...individually packaged into the AAV capsids. As a genome conversion in the transduced cell nucleus, the ...

  6. Cre-ating New Methods for Site-specific Recombination in Drosophila

    Type
    Blog Post
    ...s004270100167. PubMed. Cryptic loxP sites in mammalian genomes: genome-wide distribution and relevance for the efficiency...system. Gerald Rubin’s lab sought to make complex genome modifications in Drosophila using multiple recombinases...recombinases. To make multiple, precise genome edits, the recombinases used must have high activity and ...recombinases. These tools should further enhance genome editing capabilities in Drosophila. References...site-specific recombinases for use in manipulating animal genomes. Nern A, Pfeiffer BD, Svoboda K, Rubin GM. Proc...

  7. Tag Your Favorite Yeast Genes with Ease

    Type
    Blog Post
    ... your experience with yeast genome modifications. In what ways have genome tagging systems enabled you...process by which nearly all domains of life repair genomic damage, specifically double strand breaks. Researchers...natural process to integrate protein tags into the genomes of S. cerevisiae and S. pombe. The protocol is ...have deposited a large collection of plasmids for genome modification in yeast developed by Dr. Pringle’...modular collection of plasmids for a wide variety of genome modifications in S. Pombe, including full and partial...

  8. Cpf1 Update: Comparison to Cas9 and NgAgo

    Type
    Blog Post
    ...confirming that this protein is well suited for genome editing.  Find Cpf1 Plasmids at Addgene   ...simplest CRISPR systems and the easiest to adapt to genome editing, but the introduction of type V Cpf1-driven...GC-content, which might improve editing in AT-rich genomes. Additionally, whereas Cas9 generates blunt ends...AND FOLLOW UP STUDIES HAVE FAILED TO DEMONSTRATE GENOME EDITNG WITH THIS TOOL Cas9 and Cpf1 on-target and...Kim et al. and Kleinstiver et al. characterized genome-wide editing efficiency of two Cpf1 orthologs known...off-target editing rates, determined using sophisticated genome-wide analysis. At many of its computationally predicted...help us better understand where Cpf1 fits into the genome editing landscape. References 1. Kim D, Kim J...

  9. CRISPR Antimicrobials

    Type
    Blog Post
    ...CRISPR-induced double-stranded break (DSB) in the genome is lethal. If this DSB occurs on a plasmid, the...encoded by a high-copy plasmid. In the case of the genomically encoded quinolone resistance, mediated by a single...vectors carry CRISPR RNAs (crRNAs) targeting either genomic (blue) or plasmid-based sequences (red). Treating..., specifically targets bacteria with the given genomic or plasmid sequence from a mixed population without...without affecting the other bacteria. Targeting a genomic sequence results in cell death. Plasmid targeting...introduced is lysogenic, integrating into the bacterial genome, and it carries CRISPR machinery targeting 1) the...CRISPR design for next-generation antimicrobials.” Genome Biol. 15(11):516. (2014). PubMed: PMID 25417800...

  10. Visualizing Genomic Loci with CRISPR-Sirius

    Type
    Blog Post
    ...date for visualizing genomic loci in living cells. Previous iterations of genomic loci visualization tools...observing low-copy genomic loci or single copy genes. If you want to visualize genomic loci brightly, give... fluorescent protein (BFP, GFP, or RFP) to the genomic loci of interest. Pairs of identical hairpins within...requires high-copy chromosome-specific loci in the genome and the guides are relatively unstable.   ...CRISPR-Sirius? With all the tools out there to visualize genomic loci, what makes CRISPR-Sirius unique? Unlike fluorescent...PMC4364232. Ma, Hanhui et al. “Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow...CRISPR-Sirius: RNA scaffolds for signal amplification in genome imaging.” Nature Methods 15 (2018): 928-931. PubMed...

  11. Targeted Mutagenesis with EvolvR

    Type
    Blog Post
    ...diversify all nucleotides within a user-defined genomic region. EvolvR, a CRISPR-Cas9 based targeted mutagenesis...of all nucleotides within a defined region of a genome. Require stringent bacterial growth conditions...lambda red recombineering and Multiplex Automated Genome Engineering (MAGE) will always be limited by the...by using nCas9 to direct PolI3m to a particular genomic loci, EvolvR allows for targeted mutagenesis of...interactions, investigate non-coding segments of the genome, or engineer microbes to perform tasks. EvolvR ... DNA breaks by introducing a unique tag into a genomic site of choice via the mutational abilities of ...of guides allows EvolvR to target more than one genomic site for mutagenesis, a feature which they used...

  12. Some Like it Hot: Thermostable GeoCas9

    Type
    Blog Post
    ... Cas9 is the genome editing tool of choice for a number of model organisms: mammalian cells, yeast, drosophila...the field of thermophilic bacteria to CRISPR/Cas9 genome editing. How was GeoCas9 discovered? The discovery...occurring Cas9 diversity via the Integral Microbial Genomes (IMG) database, Harrington et al discovered a Cas9...Range for Optimal Activity 35 - 45 °C 50 - 70 °C Genome Editing in Mammalian Cells? Yes Yes Longevity... able to take some heat, GeoCas9 can introduce genomic edits in mammalian cells. Harrington et al tested...discovery of GeoCas9 clears the way for CRISPR/Cas9 genome editing in facultative and obligate thermophiles...longevity in human serum may allow for more efficient genome editing via RNPs in vivo. What aspect of GeoCas9...

  13. Sleeping Beauty Awakens for Genome Engineering

    Type
    Blog Post
    ... are sequences of DNA that can move around in a genome. In a laboratory setting, transposons can be used...used to both introduce genes into an organism’s genome (see figure) and to disrupt endogenous genes at...all, of these defenses. For some applications of genome engineering - such as certain forms of gene therapy...dinucleotide (there are many such sites in the human genome). The original plasmid is empty following the removal...gene-expression cassette that can translocate within the genome. The Sleeping Beauty transposase gains its name...fish. This transposase has been discovered in the genomes of many different fish species in a variety of ...valuable tool and an alternative to CRISPRs for genome engineering whose use is only likely to grow in...

  14. Using CRISPR/Cas9 to Edit Disease Out of the Genome

    Type
    Blog Post
    ...Cas9 technology has been a breakthrough for the genome-editing field. It has the possibility to treat ...Institute in The Netherlands used the CRISPR/Cas9 genome editing system to correct the cystic fibrosis transmembrane...difference with CRISPR/Cas9 in comparison to other genome editing techniques is its ease of use.  “I was ...They are the first direct demonstration of use of genome editing to correct point mutations in two diseases...adult stem cells has huge potential, because the genomes of adult stem cells in organoid cultures are stable.../jcp.30064 2. Barman et al. 2020. “A glance at genome editing with CRISPR-Cas9 technology.” Current genetics...s00294-019-01040-3 3. Khatibi et al. 2021.  “CRISPR Genome Editing Technology and its Application in Genetic...

  15. Plasmids 101: Mammalian Vectors

    Type
    Blog Post
    ...part of the genome. Because the foreign DNA becomes a permanent addition to the host genome, the cells ...incorporate the genetic material directly into the genome to form a stable transfection. Unlike bacterial...transfection process is not integrated into the nuclear genome, in the absence of plasmid replication, the foreign...incorporated foreign genetic material into their genomes. Unlike plasmids used for expression in yeast and...force cells to incorporate the plasmid DNA into the genome. For the purposes of this post, we will define ...gets targeted to a specific location within the genome. Positive selection in mammalian cells works similarly...

  16. Delivery Methods for Generating iPSCs

    Type
    Blog Post
    ...Retrovirus Integrating High Low Efficient and Stable Genome integration Insertional mutagenesis, transgene ...Lentivirus Integrating High Low Efficient and Stable Genome integration Insertional mutagenesis, residual expression...Generates transgene-free and vector-free cells Genome integration Need to sequence cells to verify excision...Generates transgene-free and vector-free cells No genomic integration Inefficient Sendai Virus Non-integrating...Generates transgene-free and vector-free cells No genomic integration Can be difficult to fully remove virus...Generates transgene-free and vector-free cells Limited genomic integration Multiple transfections required Need... Need to sequence to verify there’s no genomic integration Replicating EBNA1 episome Non-integrating...

  17. PiggyBac-ing Through the Genome Editing Field

    Type
    Blog Post
    ...randomly dispersed in the genome. The predicted frequency of ‘TTAA’ in the genome is 1 in every 256 base-...sites throughout the genome. When using piggyBac™, the cargo is inserted into the genome fully intact, while...up on Genome Engineering with FLEx Vectors  Learn how Homology Directed Repair Is Used for Genome Editing... many TTAA sequences distributed throughout the genome. We encourage you to deposit your piggyBac™ transposon...incorporation of your specific edit into the host genome. Through the use of an excision-only piggyBac™ ... behind only those cells with a Footprint-Free™ genome edit.   Figure 2: Editing DNA using the...be effective, a loxP site is left behind in the genome following donor removal, which alters the endogenous...

  18. Pathways Over Time Plasmids Engage Students in Functional Genomics Research

    Type
    Blog Post
    ...ago. Over time, the two genomes have become very different due to a whole genome duplication and extensive...projects. In the O'Connor lab, we recognized that genome sequencing projects were generating huge amounts...basis for student projects in introductory labs. Genome projects use computational methods to identify ...characterization of the Saccharomyces cerevisiae genome by gene deletion and parallel analysis. Science...PMID: 10436161. 7. Dujon, B. Yeast evolutionary genomics. Nat Rev Genet 11, 512-524. (2010). PubMed PMID... O'Connor, C.M. Pathways over time: Functional genomics research in an introductory laboratory course.... functional genomics...

  19. Targeting HIV-1 with CRISPR: Shock and Kill or Cut it Out?

    Type
    Blog Post
    ...HIV-1 out of the genome with CRISPR/Cas9 Before the introduction of CRISPR, HIV-1 genome editing with ZFNs... other using wild-type Cas9 to remove the HIV-1 genome from infected cells. Read on to learn how CRISPR...second strategy is the simple removal of the HIV-1 genome from infected cells, an idea that became much more... increase transcription of the integrated HIV-1 genome. For a targeted approach, Zhang et al. turned to... the 5’ long terminal repeat (LTR) of the HIV-1 genome, which acts as a promoter, and found that SAM targeting...also interested in precisely excising the HIV-1 genome from infected cells. ZFNs were used for proof-of-concept..., CRISPR/Cas9 would need to 1. excise the HIV-1 genome from every infected cell and 2. prevent reinfection...

  20. CRISPR-based Genome Editing Systems For Editing in E. coli

    Type
    Blog Post
    ...mechanism of genome editing in microorganisms which could be applied to optimization of genome editing tools...pTargetF system has been one of the most popular genomic editing systems in E. coli. However, some users.... This system works well for engineering single genome edits but the double strand breaks it introduces...difficult to perform two or more integrations on the genome. Most recently, we’ve developed a new system “Multicopy...replicon, pTargetF contains the sgRNA targeting the genomic site of interest. The donor template is supplied...and will be replaced by the sgRNA targeting the genomic site of interest. We compared the pCas/pTargetF...require only single chromosomal integration (ex: genome editing), our MUCICAT system which is based on ...
Showing: 141 - 160 of 939 results