CRISPR-Cas: more than ten years and still full of mysteries

Charpentier, Emmanuelle; Elsholz, Alexander K. W.; Marchfelder, Anita

doi:10.1080/15476286.2019.1591659

Cited by 5 publications

(2 citation statements)

References 33 publications

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“…From an evolutionary view, it is of importance to investigate the CRISPR distribution across strains of interest. Fortunately, computational tools such as CRISPRviz and CRISPRStudio have provided researchers with a large scale analysis to find and visualize the CRISPR arrays [ 39 ]. However, the functions of current tools are not complete enough and few tools are available for CRISPR visualization.…”

Section: Discussionmentioning

confidence: 99%

CrisprVi: a software for visualizing and analyzing CRISPR sequences of prokaryotes

et al. 2022

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Background Clustered regularly interspaced short palindromic repeats (CRISPR) and their spacers are important components of prokaryotic CRISPR-Cas systems. In order to analyze the CRISPR loci of multiple genomes more intuitively and comparatively, here we propose a visualization analysis tool named CrisprVi. Results CrisprVi is a Python package consisting of a graphic user interface (GUI) for visualization, a module for commands parsing and data transmission, local SQLite and BLAST databases for data storage and a functions layer for data processing. CrisprVi can not only visually present information of CRISPR direct repeats (DRs) and spacers, such as their orders on the genome, IDs, start and end coordinates, but also provide interactive operation for users to display, label and align the CRISPR sequences, which help researchers investigate the locations, orders and components of the CRISPR sequences in a global view. In comparison to other CRISPR visualization tools such as CRISPRviz and CRISPRStudio, CrisprVi not only improves the interactivity and effects of the visualization, but also provides basic statistics of the CRISPR sequences, and the consensus sequences of DRs/spacers across the input strains can be inspected from a clustering heatmap based on the BLAST results of the CRISPR sequences hitting against the genomes. Conclusions CrisprVi is a convenient tool for visualizing and analyzing the CRISPR sequences and it would be helpful for users to inspect novel CRISPR-Cas systems of prokaryotes.

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Section: Discussionmentioning

confidence: 99%

CrisprVi: a software for visualizing and analyzing CRISPR sequences of prokaryotes

et al. 2022

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“…Aging research has been gaining momentum as better tools are developed and systems biology approaches are adopted. CRISPR/ Cas techniques provide enhanced means of determining experimentally the functional consequence of gene disruption or mutation (Ran et al, 2013;Charpentier et al, 2019). These approaches can give insights into the networks that sense environmental signals that change cellular functions and thereby contributing to healthy aging or age related pathologies.…”

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confidence: 99%

The Promise of a Golden Era for Exploring the Frontiers of Aging, Metabolism and Redox Biology

Zhang

2020

Front. Aging

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From ancient times to the modern day extending longevity or even finding the elixir for eternal life has been a motivating quest for many civilizations. There are no shortage of Hollywood films and TV series that feature long-lived creatures: some heroes and others villains. Many of the ancient Greeks have what we would regard as a normal lifespan (Montagu, 1994;Batrinos, 2008). For example, Socrates before his untimely demise was in his 70s. Physicians had been directed to concoct potions to extend the life of emperors and the wealthy. In the Qin Dynasty, the emperor sent 500 young men and 500 young women to find the elixir of life in the legendary Penglai, the miraculous place of the immortals. Detailed descriptions of medicines for immortality were written in the book "Essential Formulas of Danjing Classics". Some of these concoctions we would regard as remarkably toxic as they contain mercury or arsenic. Interestingly, this quest for longevity continues unabated and has now become a central pillar for modern health care. However, the perils persist with the unverified claims of a broad range of supplements or the off-target effects of therapeutics which maybe toxic or otherwise decrease longevity. Clearly, then as now an understanding of the fundamental biology and chemistry of aging is an essential goal for modern scientific research.Despite the long history of the fascination of a long life, aging research as a systematic scientific effort is a recent affair. In the United States, the Aging Related Unit in the National Institutes of Health was formed in the 1940s, first in the NIH Division of chemotherapy, then moved to Baltimore City Hospital under the direction of Nathan Shock. In 1974 the National Institute of Aging (NIA) became an independent institute with a focus on aging biology and age related diseases. PubMed documents publications on aging as early as in 1925. In 1988, the first genetic locus age-1 that modulates lifespan was identified in C. elegans (Friedman and Johnson, 1988), and 8 years later cloned and found to encode a PI3 kinase (Morris et al., 1996). Now there are a total of ∼487,000 articles using the search term "Aging" in PubMed, with ∼20,000 articles since 2020.There has also been a long-standing interest associating aging with metabolism. Searching PubMed with "Aging and Metabolism" results in ∼188,685 articles, with 3,219 since 2020. Dietary restriction has been shown to affect longevity and age related illnesses in several organisms and model systems, with the effects on longevity dependent on genetic background (Mair et al., 2003;Liao et al., 2010;Cava and Fontana, 2013). At the molecular level, extended lifespan has been associated with insulin and IGF-1 receptor function, as well as age-1/PI3 kinase activity (Kenyon et al., 1993;Kimura et al., 1997). Modulation of sirtuins, which are NAD+ (Nicotinamide adenine dinucleotide) dependent enzymes, was reported to extend lifespan in yeast (Kennedy et al., 1995;Kaeberlein et al., 1999). AMPK (AMP activated protein kinase), a key sensor...

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CRISPR–Cas9/CRISPRi tools for cell factory construction in E. coli

Hashemi

2020

World J Microbiol Biotechnol

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CRISPR-Cas: more than ten years and still full of mysteries

Cited by 5 publications

References 33 publications

CrisprVi: a software for visualizing and analyzing CRISPR sequences of prokaryotes

CrisprVi: a software for visualizing and analyzing CRISPR sequences of prokaryotes

The Promise of a Golden Era for Exploring the Frontiers of Aging, Metabolism and Redox Biology

CRISPR–Cas9/CRISPRi tools for cell factory construction in E. coli

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