生物设计研究(英文)最新文献_第8页

Diverse Systems for Efficient Sequence Insertion and Replacement in Precise Plant Genome Editing. 用于精确植物基因组编辑的高效序列插入和替换的多种系统。

生物设计研究(英文) Pub Date : 2020-07-28 eCollection Date: 2020-01-01 DOI: 10.34133/2020/8659064

Yingxiao Zhang, Yiping Qi

引用次数: 0

The Role of Synthetic Biology in Atmospheric Greenhouse Gas Reduction: Prospects and Challenges. 合成生物学在减少大气温室气体中的作用：前景和挑战。

生物设计研究(英文) Pub Date : 2020-07-28 eCollection Date: 2020-01-01 DOI: 10.34133/2020/1016207

Charles DeLisi, Aristides Patrinos, Michael MacCracken, Dan Drell, George Annas, Adam Arkin, George Church, Robert Cook-Deegan, Henry Jacoby, Mary Lidstrom, Jerry Melillo, Ron Milo, Keith Paustian, John Reilly, Richard J Roberts, Daniel Segrè, Susan Solomon, Dominic Woolf, Stan D Wullschleger, Xiaohan Yang

{"title":"The Role of Synthetic Biology in Atmospheric Greenhouse Gas Reduction: Prospects and Challenges.","authors":"Charles DeLisi, Aristides Patrinos, Michael MacCracken, Dan Drell, George Annas, Adam Arkin, George Church, Robert Cook-Deegan, Henry Jacoby, Mary Lidstrom, Jerry Melillo, Ron Milo, Keith Paustian, John Reilly, Richard J Roberts, Daniel Segrè, Susan Solomon, Dominic Woolf, Stan D Wullschleger, Xiaohan Yang","doi":"10.34133/2020/1016207","DOIUrl":"10.34133/2020/1016207","url":null,"abstract":"The long atmospheric residence time of CO2 creates an urgent need to add atmospheric carbon drawdown to CO2 regulatory strategies. Synthetic and systems biology (SSB), which enables manipulation of cellular phenotypes, offers a powerful approach to amplifying and adding new possibilities to current land management practices aimed at reducing atmospheric carbon. The participants (in attendance: Christina Agapakis, George Annas, Adam Arkin, George Church, Robert Cook-Deegan, Charles DeLisi, Dan Drell, Sheldon Glashow, Steve Hamburg, Henry Jacoby, Henry Kelly, Mark Kon, Todd Kuiken, Mary Lidstrom, Mike MacCracken, June Medford, Jerry Melillo, Ron Milo, Pilar Ossorio, Ari Patrinos, Keith Paustian, Kristala Jones Prather, Kent Redford, David Resnik, John Reilly, Richard J. Roberts, Daniel Segre, Susan Solomon, Elizabeth Strychalski, Chris Voigt, Dominic Woolf, Stan Wullschleger, and Xiaohan Yang) identified a range of possibilities by which SSB might help reduce greenhouse gas concentrations and which might also contribute to environmental sustainability and adaptation. These include, among other possibilities, engineering plants to convert CO2 produced by respiration into a stable carbonate, designing plants with an increased root-to-shoot ratio, and creating plants with the ability to self-fertilize. A number of serious ecological and societal challenges must, however, be confronted and resolved before any such application can be fully assessed, realized, and deployed.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":"2020 ","pages":"1016207"},"PeriodicalIF":0.0,"publicationDate":"2020-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10521736/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41241337","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 19

Prime Editing Technology and Its Prospects for Future Applications in Plant Biology Research. Prime编辑技术及其在植物生物学研究中的应用前景。

生物设计研究(英文) Pub Date : 2020-06-26 eCollection Date: 2020-01-01 DOI: 10.34133/2020/9350905

Md Mahmudul Hassan, Guoliang Yuan, Jin-Gui Chen, Gerald A Tuskan, Xiaohan Yang

{"title":"Prime Editing Technology and Its Prospects for Future Applications in Plant Biology Research.","authors":"Md Mahmudul Hassan, Guoliang Yuan, Jin-Gui Chen, Gerald A Tuskan, Xiaohan Yang","doi":"10.34133/2020/9350905","DOIUrl":"10.34133/2020/9350905","url":null,"abstract":"Many applications in plant biology requires editing genomes accurately including correcting point mutations, incorporation of single-nucleotide polymorphisms (SNPs), and introduction of multinucleotide insertion/deletions (indels) into a predetermined position in the genome. These types of modifications are possible using existing genome-editing technologies such as the CRISPR-Cas systems, which require induction of double-stranded breaks in the target DNA site and the supply of a donor DNA molecule that contains the desired edit sequence. However, low frequency of homologous recombination in plants and difficulty of delivering the donor DNA molecules make this process extremely inefficient. Another kind of technology known as base editing can perform precise editing; however, only certain types of modifications can be obtained, e.g., C/G-to-T/A and A/T-to-G/C. Recently, a new type of genome-editing technology, referred to as \"prime editing,\" has been developed, which can achieve various types of editing such as any base-to-base conversion, including both transitions (C→T, G→A, A→G, and T→C) and transversion mutations (C→A, C→G, G→C, G→T, A→C, A→T, T→A, and T→G), as well as small indels without the requirement for inducing double-stranded break in the DNA. Because prime editing has wide flexibility to achieve different types of edits in the genome, it holds a great potential for developing superior crops for various purposes, such as increasing yield, providing resistance to various abiotic and biotic stresses, and improving quality of plant product. In this review, we describe the prime editing technology and discuss its limitations and potential applications in plant biology research.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":"2020 ","pages":"9350905"},"PeriodicalIF":0.0,"publicationDate":"2020-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10530660/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41241334","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 26

Plant Biosystems Design for a Carbon-Neutral Bioeconomy. 碳中和的生物经济的植物生物系统设计。

生物设计研究(英文) Pub Date : 2020-06-11 eCollection Date: 2020-01-01 DOI: 10.34133/2020/7914051

Udaya C Kalluri, Xiaohan Yang, Stan D Wullschleger

{"title":"Plant Biosystems Design for a Carbon-Neutral Bioeconomy.","authors":"Udaya C Kalluri, Xiaohan Yang, Stan D Wullschleger","doi":"10.34133/2020/7914051","DOIUrl":"10.34133/2020/7914051","url":null,"abstract":"Our society faces multiple daunting challenges including finding sustainable solutions towards climate change mitigation; efficient production of food, biofuels, and biomaterials; maximizing land-use efficiency; and enabling a sustainable bioeconomy. Plants can provide environmentally and economically sustainable solutions to these challenges due to their inherent capabilities for photosynthetic capture of atmospheric CO2, allocation of carbon to various organs and partitioning into various chemical forms, including contributions to total soil carbon. In order to enhance crop productivity and optimize chemistry simultaneously in the above- and belowground plant tissues, transformative biosystems design strategies are needed. Concerted research efforts will be required for accelerating the development of plant cultivars, genotypes, or varieties that are cooptimized in the contexts of biomass-derived fuels and/or materials aboveground and enhanced carbon sequestration belowground. Here, we briefly discuss significant knowledge gaps in our process understanding and the potential of synthetic biology in enabling advancements along the fundamental to applied research arc. Ultimately, a convergence of perspectives from academic, industrial, government, and consumer sectors will be needed to realize the potential merits of plant biosystems design for a carbon neutral bioeconomy.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":"2020 ","pages":"7914051"},"PeriodicalIF":0.0,"publicationDate":"2020-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10521676/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41241332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Agrobacterium tumefaciens: A Bacterium Primed for Synthetic Biology. 根癌农杆菌：一种适于合成生物学的细菌。

生物设计研究(英文) Pub Date : 2020-05-26 eCollection Date: 2020-01-01 DOI: 10.34133/2020/8189219

Mitchell G Thompson, William M Moore, Niklas F C Hummel, Allison N Pearson, Collin R Barnum, Henrik V Scheller, Patrick M Shih

{"title":"Agrobacterium tumefaciens: A Bacterium Primed for Synthetic Biology.","authors":"Mitchell G Thompson, William M Moore, Niklas F C Hummel, Allison N Pearson, Collin R Barnum, Henrik V Scheller, Patrick M Shih","doi":"10.34133/2020/8189219","DOIUrl":"10.34133/2020/8189219","url":null,"abstract":"Agrobacterium tumefaciens is an important tool in plant biotechnology due to its natural ability to transfer DNA into the genomes of host plants. Genetic manipulations of A. tumefaciens have yielded considerable advances in increasing transformational efficiency in a number of plant species and cultivars. Moreover, there is overwhelming evidence that modulating the expression of various mediators of A. tumefaciens virulence can lead to more successful plant transformation; thus, the application of synthetic biology to enable targeted engineering of the bacterium may enable new opportunities for advancing plant biotechnology. In this review, we highlight engineering targets in both A. tumefaciens and plant hosts that could be exploited more effectively through precision genetic control to generate high-quality transformation events in a wider range of host plants. We then further discuss the current state of A. tumefaciens and plant engineering with regard to plant transformation and describe how future work may incorporate a rigorous synthetic biology approach to tailor strains of A. tumefaciens used in plant transformation.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":"2020 ","pages":"8189219"},"PeriodicalIF":0.0,"publicationDate":"2020-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10530663/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41241327","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 10

Rebooting Synthetic Phage-Inducible Chromosomal Islands: One Method to Forge Them All. 重启合成噬菌体诱导的染色体岛：一种锻造它们的方法。

生物设计研究(英文) Pub Date : 2020-05-11 eCollection Date: 2020-01-01 DOI: 10.34133/2020/5783064

Rodrigo Ibarra-Chávez, Andreas F Haag, Pedro Dorado-Morales, Iñigo Lasa, José R Penadés

{"title":"Rebooting Synthetic Phage-Inducible Chromosomal Islands: One Method to Forge Them All.","authors":"Rodrigo Ibarra-Chávez, Andreas F Haag, Pedro Dorado-Morales, Iñigo Lasa, José R Penadés","doi":"10.34133/2020/5783064","DOIUrl":"10.34133/2020/5783064","url":null,"abstract":"Phage-inducible chromosomal islands (PICIs) are a widespread family of mobile genetic elements, which have an important role in bacterial pathogenesis. These elements mobilize among bacterial species at extremely high frequencies, representing an attractive tool for the delivery of synthetic genes. However, tools for their genetic manipulation are limited and timing consuming. Here, we have adapted a synthetic biology approach for rapidly editing of PICIs in Saccharomyces cerevisiae based on their ability to excise and integrate into the bacterial chromosome of their cognate host species. As proof of concept, we engineered several PICIs from Staphylococcus aureus and Escherichia coli and validated this methodology for the study of the biology of these elements by generating multiple and simultaneous mutations in different PICI genes. For biotechnological purposes, we also synthetically constructed PICIs as Trojan horses to deliver different CRISPR-Cas9 systems designed to either cure plasmids or eliminate cells carrying the targeted genes. Our results demonstrate that the strategy developed here can be employed universally to study PICIs and enable new approaches for diagnosis and treatment of bacterial diseases.","PeriodicalId":56832,"journal":{"name":"生物设计研究(英文)","volume":"2020 ","pages":"5783064"},"PeriodicalIF":0.0,"publicationDate":"2020-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10530653/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41241335","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

Advancing How We Learn from Biodesign to Mitigate Risks with Next-Generation Genome Engineering. 推进我们如何从生物设计中学习，以降低下一代基因组工程的风险。

生物设计研究(英文) Pub Date : 2020-04-25 eCollection Date: 2020-01-01 DOI: 10.34133/2020/9429650

Paul E Abraham, Jessy L Labbé, Amber A McBride

引用次数: 3

Biodesign Research to Advance the Principles and Applications of Biosystems Design. 推进生物系统设计原理和应用的生物设计研究。

生物设计研究(英文) Pub Date : 2019-11-24 eCollection Date: 2019-01-01 DOI: 10.34133/2019/9680853

Xiaohan Yang, Lei S Qi, Alfonso Jaramillo, Zong-Ming Max Cheng

引用次数: 5