keyword
https://read.qxmd.com/read/37392288/bacteriophage-genome-engineering-for-phage-therapy-to-combat-bacterial-antimicrobial-resistance-as-an-alternative-to-antibiotics
#1
REVIEW
Sani Sharif Usman, Abdullahi Ibrahim Uba, Evangeline Christina
Bacteriophages (phages) are viruses that mainly infect bacteria and are ubiquitously distributed in nature, especially to their host. Phage engineering involves nucleic acids manipulation of phage genome for antimicrobial activity directed against pathogens through the applications of molecular biology techniques such as synthetic biology methods, homologous recombination, CRISPY-BRED and CRISPY-BRIP recombineering, rebooting phage-based engineering, and targeted nucleases including CRISPR/Cas9, zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs)...
July 1, 2023: Molecular Biology Reports
https://read.qxmd.com/read/35592602/labeling-endogenous-proteins-using-crispr-mediated-insertion-of-exon-crispie
#2
JOURNAL ARTICLE
Evan A Wilson, Tianyi Mao, Haining Zhong
The CRISPR/Cas9 technology has transformed our ability to edit eukaryotic genomes. Despite this breakthrough, it remains challenging to precisely knock-in large DNA sequences, such as those encoding a fluorescent protein, for labeling or modifying a target protein in post-mitotic cells. Previous efforts focusing on sequence insertion to the protein coding sequence often suffer from insertions/deletions (INDELs) resulting from the efficient non-homologous end joining pathway (NHEJ). To overcome this limitation, we have developed CRISPR-mediated insertion of exon (CRISPIE)...
March 5, 2022: Bio-protocol
https://read.qxmd.com/read/35554374/an-application-of-mycobacteriophage-genome-engineering-using-bacteriophage-recombineering-with-electroporated-dna-bred-and-crispr-cas-9-systems
#3
JOURNAL ARTICLE
Ethan N Dionne, Kathleen Cornely
The increasing occurrence of antibiotic-resistant pathogens remains a global threat to public health, spurring research to develop alternative treatments for infectious bacteria. Phage therapy, the targeted use of bacteria-specific viral particles called bacteriophages, has emerged as a promising antibiotic alternative. Our lab studies mycobacteriophages - phages specific to bacteria of the genus Mycobacterium,which includes infamous, antibiotic-resistant pathogens such as M. tuberculosisand M. abscessus.For the use of many mycobacteriophages in phage therapy treatments, gene deletions are often necessary to ensure host lethality...
May 2022: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://read.qxmd.com/read/34100715/high-fidelity-efficient-and-reversible-labeling-of-endogenous-proteins-using-crispr-based-designer-exon-insertion
#4
JOURNAL ARTICLE
Haining Zhong, Cesar C Ceballos, Crystian I Massengill, Michael A Muniak, Lei Ma, Maozhen Qin, Stefanie Kaech Petrie, Tianyi Mao
Precise and efficient insertion of large DNA fragments into somatic cells using gene editing technologies to label or modify endogenous proteins remains challenging. Non-specific insertions/deletions (INDELs) resulting from the non-homologous end joining pathway make the process error-prone. Further, the insert is not readily removable. Here, we describe a method called CRISP R-mediated i nsertion of e xon (CRISPIE) that can precisely and reversibly label endogenous proteins using CRISPR/Cas9-based editing...
June 8, 2021: ELife
https://read.qxmd.com/read/33762639/crispy-bred-and-crispy-brip-efficient-bacteriophage-engineering
#5
JOURNAL ARTICLE
Katherine S Wetzel, Carlos A Guerrero-Bustamante, Rebekah M Dedrick, Ching-Chung Ko, Krista G Freeman, Haley G Aull, Ashley M Divens, Jeremy M Rock, Kira M Zack, Graham F Hatfull
Genome engineering of bacteriophages provides opportunities for precise genetic dissection and for numerous phage applications including therapy. However, few methods are available for facile construction of unmarked precise deletions, insertions, gene replacements and point mutations in bacteriophages for most bacterial hosts. Here we describe CRISPY-BRED and CRISPY-BRIP, methods for efficient and precise engineering of phages in Mycobacterium species, with applicability to phages of a variety of other hosts...
March 24, 2021: Scientific Reports
https://read.qxmd.com/read/33604589/crispr-turbo-accelerated-knockout-crispy-tako-for-rapid-in-vivo-screening-of-gene-function
#6
JOURNAL ARTICLE
Sonja L Plasil, Amit Seth, Gregg E Homanics
The development of CRISPR/Cas9 technology has vastly sped up the process of mammalian genome editing by introducing a bacterial system that can be exploited for reverse genetics-based research. However, generating homozygous functional knockout (KO) animals using traditional CRISPR/Cas9-mediated techniques requires three generations of animals. A founder animal with a desired mutation is crossed to produce heterozygous F1 offspring which are subsequently interbred to generate homozygous F2 KO animals. This study describes an adaptation of the CRISPR/Cas9-mediated method to develop a cohort of homozygous gene-targeted KO animals in one generation...
October 2020: Frontiers in genome editing
https://read.qxmd.com/read/32596519/designing-sgrnas-for-crispr-best-base-editing-applications-with-crispy-web-2-0
#7
JOURNAL ARTICLE
Kai Blin, Simon Shaw, Yaojun Tong, Tilmann Weber
CRISPR/Cas9 systems are an established tool in genome engineering. As double strand breaks caused by the standard Cas9-based knock-out techniques can be problematic in some organisms, new systems were developed that can efficiently create knock-outs without causing double strand breaks to elegantly sidestep these issues. The recently published CRISPR-BEST base editor system for actinobacteria is built around a C to T or A to G base exchange. These base editing systems however require additional constraints to be considered for designing the sgRNAs...
June 2020: Synthetic and Systems Biotechnology
https://read.qxmd.com/read/31548381/highly-efficient-dsb-free-base-editing-for-streptomycetes-with-crispr-best
#8
JOURNAL ARTICLE
Yaojun Tong, Christopher M Whitford, Helene L Robertsen, Kai Blin, Tue S Jørgensen, Andreas K Klitgaard, Tetiana Gren, Xinglin Jiang, Tilmann Weber, Sang Yup Lee
Streptomycetes serve as major producers of various pharmacologically and industrially important natural products. Although CRISPR-Cas9 systems have been developed for more robust genetic manipulations, concerns of genome instability caused by the DNA double-strand breaks (DSBs) and the toxicity of Cas9 remain. To overcome these limitations, here we report development of the DSB-free, single-nucleotide-resolution genome editing system CRISPR-BEST (CRISPR-Base Editing SysTem), which comprises a cytidine (CRISPR-cBEST) and an adenosine (CRISPR-aBEST) deaminase-based base editor...
October 8, 2019: Proceedings of the National Academy of Sciences of the United States of America
https://read.qxmd.com/read/30737742/crispr-cas9-mediated-homology-directed-genome-editing-in-pichia-pastoris
#9
JOURNAL ARTICLE
Thomas Gassler, Lina Heistinger, Diethard Mattanovich, Brigitte Gasser, Roland Prielhofer
State-of-the-art strain engineering techniques for the methylotrophic yeast Pichia pastoris (syn. Komagataella spp.) include overexpression of endogenous and heterologous genes and deletion of host genes. For efficient gene deletion, methods such as the split-marker technique have been established. However, synthetic biology trends move toward building up large and complex reaction networks, which often require endogenous gene knockouts and simultaneous overexpression of individual genes or whole pathways...
2019: Methods in Molecular Biology
https://read.qxmd.com/read/30722791/structural-rearrangements-generate-cell-specific-gene-independent-crispr-cas9-loss-of-fitness-effects
#10
JOURNAL ARTICLE
Emanuel Gonçalves, Fiona M Behan, Sandra Louzada, Damien Arnol, Euan A Stronach, Fengtang Yang, Kosuke Yusa, Oliver Stegle, Francesco Iorio, Mathew J Garnett
BACKGROUND: CRISPR-Cas9 genome editing is widely used to study gene function, from basic biology to biomedical research. Structural rearrangements are a ubiquitous feature of cancer cells and their impact on the functional consequences of CRISPR-Cas9 gene-editing has not yet been assessed. RESULTS: Utilizing CRISPR-Cas9 knockout screens for 250 cancer cell lines, we demonstrate that targeting structurally rearranged regions, in particular tandem or interspersed amplifications, is highly detrimental to cellular fitness in a gene-independent manner...
February 5, 2019: Genome Biology
https://read.qxmd.com/read/29867139/targeting-repair-pathways-with-small-molecules-increases-precise-genome-editing-in-pluripotent-stem-cells
#11
JOURNAL ARTICLE
Stephan Riesenberg, Tomislav Maricic
A now frequently used method to edit mammalian genomes uses the nucleases CRISPR/Cas9 and CRISPR/Cpf1 or the nickase CRISPR/Cas9n to introduce double-strand breaks which are then repaired by homology-directed repair using DNA donor molecules carrying desired mutations. Using a mixture of small molecules, the "CRISPY" mix, we achieve a 2.8- to 7.2-fold increase in precise genome editing with Cas9n, resulting in the introduction of the intended nucleotide substitutions in almost 50% of chromosomes or of gene encoding a blue fluorescent protein in 27% of cells, to our knowledge the highest editing efficiency in human induced pluripotent stem cells described to date...
June 4, 2018: Nature Communications
https://read.qxmd.com/read/29625203/crispys-optimal-sgrna-design-for-editing-multiple-members-of-a-gene-family-using-the-crispr-system
#12
JOURNAL ARTICLE
Gal Hyams, Shiran Abadi, Shlomtzion Lahav, Adi Avni, Eran Halperin, Eilon Shani, Itay Mayrose
The development of the CRISPR-Cas9 system in recent years has made eukaryotic genome editing, and specifically gene knockout for reverse genetics, a simple and effective task. The system is directed to a genomic target site by a programmed single-guide RNA (sgRNA) that base-pairs with it, subsequently leading to site-specific modifications. However, many gene families in eukaryotic genomes exhibit partially overlapping functions, and thus, the knockout of one gene might be concealed by the function of the other...
July 20, 2018: Journal of Molecular Biology
https://read.qxmd.com/read/29062934/crispy-web-an-online-resource-to-design-sgrnas-for-crispr-applications
#13
JOURNAL ARTICLE
Kai Blin, Lasse Ebdrup Pedersen, Tilmann Weber, Sang Yup Lee
CRISPR/Cas9-based genome editing has been one of the major achievements of molecular biology, allowing the targeted engineering of a wide range of genomes. The system originally evolved in prokaryotes as an adaptive immune system against bacteriophage infections. It now sees widespread application in genome engineering workflows, especially using the Streptococcus pyogenes endonuclease Cas9. To utilize Cas9, so-called single guide RNAs (sgRNAs) need to be designed for each target gene. While there are many tools available to design sgRNAs for the popular model organisms, only few tools that allow designing sgRNAs for non-model organisms exist...
June 2016: Synthetic and Systems Biotechnology
https://read.qxmd.com/read/24827782/accelerating-genome-editing-in-cho-cells-using-crispr-cas9-and-crispy-a-web-based-target-finding-tool
#14
JOURNAL ARTICLE
Carlotta Ronda, Lasse Ebdrup Pedersen, Henning Gram Hansen, Thomas Beuchert Kallehauge, Michael J Betenbaugh, Alex Toftgaard Nielsen, Helene Faustrup Kildegaard
Chinese hamster ovary (CHO) cells are widely used in the biopharmaceutical industry as a host for the production of complex pharmaceutical proteins. Thus genome engineering of CHO cells for improved product quality and yield is of great interest. Here, we demonstrate for the first time the efficacy of the CRISPR Cas9 technology in CHO cells by generating site-specific gene disruptions in COSMC and FUT8, both of which encode proteins involved in glycosylation. The tested single guide RNAs (sgRNAs) created an indel frequency up to 47...
August 2014: Biotechnology and Bioengineering
1
Fetch more papers »
Fetching more papers... Fetching...
Remove bar
Read by QxMD icon Read
×

Save your favorite articles in one place with a free QxMD account.

×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"

We want to hear from doctors like you!

Take a second to answer a survey question.