CRISPR Journal最新文献_第9页

Fanzors: Mysterious TnpB-Like Bacterial Transposon-Related RNA-Guided DNA Nucleases of Eukaryotes. 神秘的tnpb样细菌转座子相关rna引导的真核生物DNA核酸酶。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2023-08-01 DOI: 10.1089/crispr.2023.29164.tka

Tautvydas Karvelis, Virginijus Siksnys

引用次数: 0

CRISPR Milestones for Sustainable Agriculture and Forestry. 可持续农业和林业的CRISPR里程碑。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2023-08-01 DOI: 10.1089/crispr.2023.29163.editorial

Rodolphe Barrangou

引用次数: 0

Multiplex Editing of the Nucleoredoxin1 Tandem Array in Poplar: From Small Indels to Translocations and Complex Inversions. 杨树核还原蛋白1串联阵列的多重编辑:从小索引到易位和复杂反转。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2023-08-01 DOI: 10.1089/crispr.2022.0096

Yen-Ho Chen, Shakuntala Sharma, William P Bewg, Liang-Jiao Xue, Cole R Gizelbach, Chung-Jui Tsai

{"title":"Multiplex Editing of the Nucleoredoxin1 Tandem Array in Poplar: From Small Indels to Translocations and Complex Inversions.","authors":"Yen-Ho Chen, Shakuntala Sharma, William P Bewg, Liang-Jiao Xue, Cole R Gizelbach, Chung-Jui Tsai","doi":"10.1089/crispr.2022.0096","DOIUrl":"https://doi.org/10.1089/crispr.2022.0096","url":null,"abstract":"The CRISPR-Cas9 system has been deployed for precision mutagenesis in an ever-growing number of species, including agricultural crops and forest trees. Its application to closely linked genes with extremely high sequence similarities has been less explored. In this study, we used CRISPR-Cas9 to mutagenize a tandem array of seven Nucleoredoxin1 (NRX1) genes spanning ∼100 kb in Populus tremula × Populus alba. We demonstrated efficient multiplex editing with one single guide RNA in 42 transgenic lines. The mutation profiles ranged from small insertions and deletions and local deletions in individual genes to large genomic dropouts and rearrangements spanning tandem genes. We also detected complex rearrangements including translocations and inversions resulting from multiple cleavage and repair events. Target capture sequencing was instrumental for unbiased assessments of repair outcomes to reconstruct unusual mutant alleles. The work highlights the power of CRISPR-Cas9 for multiplex editing of tandemly duplicated genes to generate diverse mutants with structural and copy number variations to aid future functional characterization.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":"6 4","pages":"339-349"},"PeriodicalIF":3.7,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10460964/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10100491","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Rapid and Technically Simple Detection of SARS-CoV-2 Variants Using CRISPR Cas12 and Cas13. 利用CRISPR Cas12和Cas13快速、技术简单地检测SARS-CoV-2变体

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2023-08-01 DOI: 10.1089/crispr.2023.0007

Gabriel Lamothe, Julie Carbonneau, Charles Joly Beauparlant, Thierry Vincent, Patrik Quessy, Anthony Guedon, Gary Kobinger, Jean-Francois Lemay, Guy Boivin, Arnaud Droit, Nathalie Turgeon, Jacques P Tremblay

{"title":"Rapid and Technically Simple Detection of SARS-CoV-2 Variants Using CRISPR Cas12 and Cas13.","authors":"Gabriel Lamothe, Julie Carbonneau, Charles Joly Beauparlant, Thierry Vincent, Patrik Quessy, Anthony Guedon, Gary Kobinger, Jean-Francois Lemay, Guy Boivin, Arnaud Droit, Nathalie Turgeon, Jacques P Tremblay","doi":"10.1089/crispr.2023.0007","DOIUrl":"https://doi.org/10.1089/crispr.2023.0007","url":null,"abstract":"The worldwide proliferation of the SARS-CoV-2 virus in the past 3 years has allowed the virus to accumulate numerous mutations. Dangerous lineages have emerged one after another, each leading to a new wave of the pandemic. In this study, we have developed the THRASOS pipeline to rapidly discover lineage-specific mutation signatures and thus advise the development of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based diagnostic tests. We also optimized a strategy to modify loop-mediated isothermal amplification amplicons for downstream use with Cas12 and Cas13 for future multiplexing. The close ancestry of the BA.1 and BA.2 variants of SARS-CoV-2 (Omicron) made these excellent candidates for the development of a first test using this workflow. With a quick turnaround time and low requirements for laboratory equipment, the test we have created is ideally suited for settings such as mobile clinics lacking equipment such as Next-Generation Sequencers or Sanger Sequencers and the personnel to run these devices.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":"6 4","pages":"369-385"},"PeriodicalIF":3.7,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10027205","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

CRISPR-Cas-Based Biomonitoring for Marine Environments: Toward CRISPR RNA Design Optimization Via Deep Learning. 基于CRISPR- cas的海洋环境生物监测:通过深度学习实现CRISPR RNA设计优化。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2023-08-01 DOI: 10.1089/crispr.2023.0019

Benjamín Durán-Vinet, Karla Araya-Castro, Anastasija Zaiko, Xavier Pochon, Susanna A Wood, Jo-Ann L Stanton, Gert-Jan Jeunen, Michelle Scriver, Anya Kardailsky, Tzu-Chiao Chao, Deependra K Ban, Maryam Moarefian, Kiana Aran, Neil J Gemmell

{"title":"CRISPR-Cas-Based Biomonitoring for Marine Environments: Toward CRISPR RNA Design Optimization Via Deep Learning.","authors":"Benjamín Durán-Vinet, Karla Araya-Castro, Anastasija Zaiko, Xavier Pochon, Susanna A Wood, Jo-Ann L Stanton, Gert-Jan Jeunen, Michelle Scriver, Anya Kardailsky, Tzu-Chiao Chao, Deependra K Ban, Maryam Moarefian, Kiana Aran, Neil J Gemmell","doi":"10.1089/crispr.2023.0019","DOIUrl":"https://doi.org/10.1089/crispr.2023.0019","url":null,"abstract":"Almost all of Earth's oceans are now impacted by multiple anthropogenic stressors, including the spread of nonindigenous species, harmful algal blooms, and pathogens. Early detection is critical to manage these stressors effectively and to protect marine systems and the ecosystem services they provide. Molecular tools have emerged as a promising solution for marine biomonitoring. One of the latest advancements involves utilizing CRISPR-Cas technology to build programmable, rapid, ultrasensitive, and specific diagnostics. CRISPR-based diagnostics (CRISPR-Dx) has the potential to allow robust, reliable, and cost-effective biomonitoring in near real time. However, several challenges must be overcome before CRISPR-Dx can be established as a mainstream tool for marine biomonitoring. A critical unmet challenge is the need to design, optimize, and experimentally validate CRISPR-Dx assays. Artificial intelligence has recently been presented as a potential approach to tackle this challenge. This perspective synthesizes recent advances in CRISPR-Dx and machine learning modeling approaches, showcasing CRISPR-Dx potential to progress as a rising molecular tool candidate for marine biomonitoring applications.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":"6 4","pages":"316-324"},"PeriodicalIF":3.7,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10494903/pdf/crispr.2023.0019.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10220671","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

CRISPR and the Plant Pathologists' Holy Grail. CRISPR和植物病理学家的圣杯。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2023-08-01 DOI: 10.1089/crispr.2023.29165.mwi

Matthew R Willmann

引用次数: 0

CRISPR Comparison Toolkit: Rapid Identification, Visualization, and Analysis of CRISPR Array Diversity. CRISPR比较工具箱:快速鉴定，可视化和分析CRISPR阵列多样性。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2023-08-01 DOI: 10.1089/crispr.2022.0080

Alan J Collins, Rachel J Whitaker

引用次数: 4

CRISPR Empowers Tree Bioengineering for a Sustainable Future. CRISPR助力树木生物工程实现可持续未来

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2023-08-01 Epub Date: 2023-07-31 DOI: 10.1089/crispr.2023.29161.gli

Gen Li, Yiping Qi

引用次数: 1

Novel and Engineered Type II CRISPR Systems from Uncultivated Microbes with Broad Genome Editing Capability. 来自具有广泛基因组编辑能力的未培养微生物的新型和工程化II型CRISPR系统。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2023-06-01 DOI: 10.1089/crispr.2022.0090

Lisa M Alexander, Daniela S Aliaga Goltsman, Jason Liu, Jyun-Liang Lin, Morayma M Temoche-Diaz, Sarah M Laperriere, Andreas Neerincx, Christien Bednarski, Philipp Knyphausen, Andre Cohnen, Justine Albers, Liliana Gonzalez-Osorio, Rodrigo Fregoso Ocampo, Jennifer Oki, Audra E Devoto, Cindy J Castelle, Rebecca C Lamothe, Gregory J Cost, Cristina N Butterfield, Brian C Thomas, Christopher T Brown

{"title":"Novel and Engineered Type II CRISPR Systems from Uncultivated Microbes with Broad Genome Editing Capability.","authors":"Lisa M Alexander, Daniela S Aliaga Goltsman, Jason Liu, Jyun-Liang Lin, Morayma M Temoche-Diaz, Sarah M Laperriere, Andreas Neerincx, Christien Bednarski, Philipp Knyphausen, Andre Cohnen, Justine Albers, Liliana Gonzalez-Osorio, Rodrigo Fregoso Ocampo, Jennifer Oki, Audra E Devoto, Cindy J Castelle, Rebecca C Lamothe, Gregory J Cost, Cristina N Butterfield, Brian C Thomas, Christopher T Brown","doi":"10.1089/crispr.2022.0090","DOIUrl":"https://doi.org/10.1089/crispr.2022.0090","url":null,"abstract":"Type II Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 nucleases have been extensively used in biotechnology and therapeutics. However, many applications are not possible owing to the size, targetability, and potential off-target effects associated with currently known systems. In this study, we identified thousands of CRISPR type II effectors by mining an extensive, genome-resolved metagenomics database encompassing hundreds of thousands of microbial genomes. We developed a high-throughput pipeline that enabled us to predict tracrRNA sequences, to design single guide RNAs, and to demonstrate nuclease activity in vitro for 41 newly described subgroups. Active systems represent an extensive diversity of protein sequences and guide RNA structures and require diverse protospacer adjacent motifs (PAMs) that collectively expand the known targeting capability of current systems. Several nucleases showed activity levels comparable to or significantly higher than SpCas9, despite being smaller in size. In addition, top systems exhibited low levels of off-target editing in mammalian cells, and PAM-interacting domain engineered chimeras further expanded their targetability. These newly discovered nucleases are attractive enzymes for translation into many applications, including therapeutics.","PeriodicalId":54232,"journal":{"name":"CRISPR Journal","volume":"6 3","pages":"261-277"},"PeriodicalIF":3.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10278012/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9678223","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

The Promises and Pitfalls of CRISPR-Mediated Base Editing in Stem Cells. 干细胞中crispr介导的碱基编辑的希望和缺陷。

IF 3.7 4区生物学

CRISPR Journal Pub Date : 2023-06-01 DOI: 10.1089/crispr.2023.0013

Poh Kuan Wong, Nurul Nadia Mohamad Zamberi, Saiful Effendi Syafruddin, Fook Choe Cheah, Norazrina Azmi, Jia Xian Law, Eng Wee Chua

引用次数: 1