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User:Prabal09/CRISPR

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Applications

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CRISPR gene editing

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CRISPR technology has been applied in the food and farming industries to engineer probiotic cultures and to immunize industrial cultures (for yogurt, for instance) against infections. It is also being used in crops to enhance yield, drought tolerance and nutritional value.[1][2]

By the end of 2014, roughly 1000 research papers had been published that mentioned CRISPR.[3][4] The technology had been used to functionally inactivate genes in human cell lines and cells, to study Candida albicans, to modify yeasts used to make biofuels and to genetically modify crop strains.[4] Hsu and his colleagues state that the ability to manipulate the genetic sequences allows for reverse engineering that can positively affect biofuel production [5] CRISPR can also be used to change mosquitos so they cannot transmit diseases such as malaria.[6] CRISPR-based approaches utilizing Cas12a have recently been utilized in the successful modification of a broad number of plant species.[7]

In July 2019, CRISPR was used to experimentally treat a patient with a genetic disorder. The patient was a 34-year-old woman with sickle cell disease.[8]

In February 2020, progress was made on HIV treatments with 60-80% of the integrated viral DNA removed in mice and some being completely free from the virus after edits involving both LASER ART, a new anti-retroviral therapy, and CRISPR.[9]

In March 2020, CRISPR-modified virus was injected into a patient's eye in an attempt to treat Leber congenital amaurosis.[10]

In the future, CRISPR gene editing could potentially be used to create new species or revive extinct species from closely related ones.[11]

CRISPR-based re-evaluations of claims for gene-disease relationships have led to the discovery of potentially important anomalies.[12]

In April 2022, an epigenetic programmable memory writer, CRISPRoff was generated to initiate DNA methylation, repression of genes and histone modification for genome-wide screening, multiplexed cell engineering, enhancer silencing, and mechanistic exploration of epigenetic inheritance.[13]

CRISPR as diagnostic tool

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CRISPR associated nucleases have shown to be useful as a tool for molecular testing due to their ability to specifically target nucleic acid sequences in a high background of non-target sequences.[14] In 2016, the Cas9 nuclease was used to deplete unwanted nucleotide sequences in next-generation sequencing libraries while requiring only 250 picograms of initial RNA input.[15] Beginning in 2017, CRISPR associated nucleases were also used for direct diagnostic testing of nucleic acids, down to single molecule sensitivity.[16][17] CRISPR diversity is used as an analysis target to discern phylogeny and diversity in bacteria, such as in xanthomonads by Martins et al., 2019.[18]: 552  Early detection of plant pathogens by molecular typing of the pathogen's CRISPRs can be used in agriculture as demonstrated by Shen et al., 2020.[18]: 553 

By coupling CRISPR-based diagnostics to additional enzymatic processes, the detection of molecules beyond nucleic acids is possible. One example of a coupled technology is SHERLOCK-based Profiling of IN vitro Transcription (SPRINT). SPRINT can be used to detect a variety of substances, such as metabolites in patient samples or contaminants in environmental samples, with high throughput or with portable point-of-care devices.[19] CRISPR/Cas platforms are also being explored for detection [20][21][22][23][24] and inactivation of SARS-CoV-2, the virus that causes COVID-19.[25]

Two different comprehensive diagnostic tests, AIOD-CRISPR and SHERLOCK test have been identified for SARS-CoV-2[26]. The SHERLOCK test is based on a fluorescently labelled press reporter RNA which has the ability to identify 10 copies per microliter[27]. The AIOD-CRISPR helps with robust and highly sensitive visual detection of the viral nucleic acid[28]

  1. ^ "What is CRISPR and How does it work?". Livescience.Tech. 30 April 2018. Retrieved 2019-12-14.
  2. ^ Verma AK, Mandal S, Tiwari A, Monachesi C, Catassi GN, Srivastava A, Gatti S, Lionetti E, Catassi C (2 October 2021). "Current Status and Perspectives on the Application of CRISPR/Cas9 Gene-Editing System to Develop a Low-Gluten, Non-Transgenic Wheat Variety". Foods. 10 (2351): 2351. doi:10.3390/foods10102351. PMC 8534962. PMID 34681400.
  3. ^ Doudna JA, Charpentier E (November 2014). "Genome editing. The new frontier of genome engineering with CRISPR-Cas9". Science. 346 (6213): 1258096. doi:10.1126/science.1258096. PMID 25430774. S2CID 6299381.
  4. ^ a b Ledford H (June 2015). "CRISPR, the disruptor". Nature. 522 (7554): 20–24. Bibcode:2015Natur.522...20L. doi:10.1038/522020a. PMID 26040877.
  5. ^ Hsu PD, Lander ES, Zhang F (June 2014). "Development and applications of CRISPR-Cas9 for genome engineering". Cell. 157 (6): 1262–1278. doi:10.1016/j.cell.2014.05.010. PMC 4343198. PMID 24906146.
  6. ^ Alphey L (February 2016). "Can CRISPR-Cas9 gene drives curb malaria?". Nature Biotechnology. 34 (2): 149–150. doi:10.1038/nbt.3473. PMID 26849518. S2CID 10014014.
  7. ^ Bernabé-Orts JM, Casas-Rodrigo I, Minguet EG, Landolfi V, Garcia-Carpintero V, Gianoglio S, et al. (October 2019). "Assessment of Cas12a-mediated gene editing efficiency in plants". Plant Biotechnology Journal. 17 (10): 1971–1984. doi:10.1111/pbi.13113. PMC 6737022. PMID 30950179.
  8. ^ "In A 1st, Doctors In U.S. Use CRISPR Tool To Treat Patient With Genetic Disorder". NPR.org. Retrieved 2019-07-31.
  9. ^ National Institute on Drug Abuse (2020-02-14). "Antiretroviral Therapy Combined With CRISPR Gene Editing Can Eliminate HIV Infection in Mice". National Institute on Drug Abuse. Retrieved 2020-11-15.
  10. ^ "In A 1st, Scientists Use Revolutionary Gene-Editing Tool To Edit Inside A Patient". NPR.org.
  11. ^ The-Crispr (2019-07-15). "Listen Radiolab CRISPR podcast". The Crispr. Archived from the original on 2019-07-15. Retrieved 2019-07-15.
  12. ^ Ledford H (2017). "CRISPR studies muddy results of older gene research". Nature. doi:10.1038/nature.2017.21763. S2CID 90757972.
  13. ^ Nuñez, James K.; Chen, Jin; Pommier, Greg C.; Cogan, J. Zachery; Replogle, Joseph M.; Adriaens, Carmen; Ramadoss, Gokul N.; Shi, Quanming; Hung, King L.; Samelson, Avi J.; Pogson, Angela N.; Kim, James Y. S.; Chung, Amanda; Leonetti, Manuel D.; Chang, Howard Y. (2021-04-29). "Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing". Cell. 184 (9): 2503–2519.e17. doi:10.1016/j.cell.2021.03.025. ISSN 0092-8674. PMC 8376083. PMID 33838111.{{cite journal}}: CS1 maint: PMC format (link)
  14. ^ Reis AC, Halper SM, Vezeau GE, Cetnar DP, Hossain A, Clauer PR, Salis HM (November 2019). "Simultaneous repression of multiple bacterial genes using nonrepetitive extra-long sgRNA arrays". Nature Biotechnology. 37 (11): 1294–1301. doi:10.1038/s41587-019-0286-9. OSTI 1569832. PMID 31591552. S2CID 203852115.
  15. ^ Gu W, Crawford ED, O'Donovan BD, Wilson MR, Chow ED, Retallack H, DeRisi JL (March 2016). "Depletion of Abundant Sequences by Hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications". Genome Biology. 17 (1): 41. doi:10.1186/s13059-016-0904-5. PMC 4778327. PMID 26944702.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  16. ^ Gootenberg JS, Abudayyeh OO, Lee JW, Essletzbichler P, Dy AJ, Joung J, et al. (April 2017). "Nucleic acid detection with CRISPR-Cas13a/C2c2". Science. 356 (6336): 438–442. Bibcode:2017Sci...356..438G. doi:10.1126/science.aam9321. PMC 5526198. PMID 28408723.
  17. ^ Chen JS, Ma E, Harrington LB, Da Costa M, Tian X, Palefsky JM, Doudna JA (April 2018). "CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity". Science. 360 (6387): 436–439. Bibcode:2018Sci...360..436C. doi:10.1126/science.aar6245. PMC 6628903. PMID 29449511.
  18. ^ a b Shami A, Mostafa M, Abd-Elsalam KA (2021). "CRISPR Applications in Plant Bacteriology: today and future perspectives". In Abd-Elsalam KA, Lim KT (eds.). CRISPR and RNAi Systems: Nanobiotechnology Approaches to Plant Breeding and Protection. Amsterdam: Elsevier. pp. xxxvi+804. ISBN 978-0-12-821911-9. OCLC 1240283203.
  19. ^ Iwasaki RS, Batey RT (September 2020). "SPRINT: a Cas13a-based platform for detection of small molecules". Nucleic Acids Research. 48 (17): e101. doi:10.1093/nar/gkaa673. PMC 7515716. PMID 32797156.
  20. ^ Broughton JP, Deng X, Yu G, Fasching CL, Servellita V, Singh J, et al. (July 2020). "CRISPR-Cas12-based detection of SARS-CoV-2". Nature Biotechnology. 38 (7): 870–874. doi:10.1038/s41587-020-0513-4. PMC 9107629. PMID 32300245.
  21. ^ Joung J, Ladha A, Saito M, Kim NG, Woolley AE, Segel M, et al. (October 2020). "Detection of SARS-CoV-2 with SHERLOCK One-Pot Testing". The New England Journal of Medicine. 383 (15): 1492–1494. doi:10.1056/NEJMc2026172. PMC 7510942. PMID 32937062.
  22. ^ Dhamad AE, Abdal Rhida MA (October 2020). "COVID-19: molecular and serological detection methods". PeerJ. 8: e10180. doi:10.7717/peerj.10180. PMC 7547594. PMID 33083156.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  23. ^ Patchsung M, Jantarug K, Pattama A, Aphicho K, Suraritdechachai S, Meesawat P, et al. (December 2020). "Clinical validation of a Cas13-based assay for the detection of SARS-CoV-2 RNA". Nature Biomedical Engineering. 4 (12): 1140–1149. doi:10.1038/s41551-020-00603-x. PMID 32848209.
  24. ^ Nguyen LT, Smith BM, Jain PK (September 2020). "Enhancement of trans-cleavage activity of Cas12a with engineered crRNA enables amplified nucleic acid detection". Nature Communications. 11 (1): 4906. Bibcode:2020NatCo..11.4906N. doi:10.1038/s41467-020-18615-1. PMC 7528031. PMID 32999292.
  25. ^ Konwarh R (September 2020). "Can CRISPR/Cas Technology Be a Felicitous Stratagem Against the COVID-19 Fiasco? Prospects and Hitches". Frontiers in Molecular Biosciences. 7: 557377. doi:10.3389/fmolb.2020.557377. PMC 7511716. PMID 33134311.
  26. ^ Shademan, Behrouz; Nourazarian, Alireza; Hajazimian, Saba; Isazadeh, Alireza; Biray Avci, Cigir; Oskouee, Mahin Ahangar (2022-01-11). "CRISPR Technology in Gene-Editing-Based Detection and Treatment of SARS-CoV-2". Frontiers in Molecular Biosciences. 8: 772788. doi:10.3389/fmolb.2021.772788. ISSN 2296-889X. PMC 8787289. PMID 35087864.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  27. ^ Kellner, Max J.; Koob, Jeremy G.; Gootenberg, Jonathan S.; Abudayyeh, Omar O.; Zhang, Feng (2019-10). "SHERLOCK: nucleic acid detection with CRISPR nucleases". Nature Protocols. 14 (10): 2986–3012. doi:10.1038/s41596-019-0210-2. ISSN 1754-2189. PMC 6956564. PMID 31548639. {{cite journal}}: Check date values in: |date= (help)CS1 maint: PMC format (link)
  28. ^ Ding, Xiong; Yin, Kun; Li, Ziyue; Liu, Changchun (2020-03-21). "All-in-One Dual CRISPR-Cas12a (AIOD-CRISPR) Assay: A Case for Rapid, Ultrasensitive and Visual Detection of Novel Coronavirus SARS-CoV-2 and HIV virus". doi:10.1101/2020.03.19.998724. PMC 7239053. PMID 32511323. {{cite journal}}: Cite journal requires |journal= (help)CS1 maint: PMC format (link)
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