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GENOME EDITING: A GROUND BREAKING RESEARCH HAS BEEN RANKED TOP 10 ENGINEERING FRONTS FROM 2017 TO 2021

《农业科学与工程前沿（英文）》 2022年 第9卷 第2期   页码 309-311 doi: 10.15302/J-FASE-2022440

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Genome reprogramming for synthetic biology

Kylie Standage-Beier,Xiao Wang

《化学科学与工程前沿（英文）》 2017年 第11卷 第1期   页码 37-45 doi: 10.1007/s11705-017-1618-2

摘要： The ability to go from a digitized DNA sequence to a predictable biological function is central to synthetic biology. Genome engineering tools facilitate rewriting and implementation of engineered DNA sequences. Recent development of new programmable tools to reengineer genomes has spurred myriad advances in synthetic biology. Tools such as clustered regularly interspace short palindromic repeats enable RNA-guided rational redesign of organisms and implementation of synthetic gene systems. New directed evolution methods generate organisms with radically restructured genomes. These restructured organisms have useful new phenotypes for biotechnology, such as bacteriophage resistance and increased genetic stability. Advanced DNA synthesis and assembly methods have also enabled the construction of fully synthetic organisms, such as J. Craig Venter Institute (JCVI)-syn 3.0. Here we summarize the recent advances in programmable genome engineering tools.

关键词： CRISPR     genome engineering     synthetic biology     rational design    

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材料基因工程专题主编寄语

王海舟, 谢建新

《工程（英文）》 2020年 第6卷 第6期   页码 585-586 doi: 10.1016/j.eng.2020.05.007

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Exploring the cancer genome in the era of next-generation sequencing

null

《医学前沿（英文）》 2012年 第6卷 第1期   页码 48-55 doi: 10.1007/s11684-012-0182-x

摘要：

The emergence of next-generation sequencing technologies has led to dramatic advances in cancer genome studies. The increased efficiency and resolution of next-generation sequencing greatly facilitate the detection of genetic, genomic, and epigenomic alterations, such as single nucleotide mutations, small insertions and deletions, chromosomal rearrangements, copy number variations, and DNA methylation. Comprehensive analysis of cancer genomes through approaches of whole genome, exome, and transcriptome sequencing has significantly improved the understanding of cancer biology, diagnosis, and therapy. The present study briefly reviews the recent pioneering studies on cancer genome sequencing and provides an unprecedented insight into the landscape of genomic alterations in human sporadic cancers.

关键词： next-generation sequencing     cancer genome     whole genome sequencing     exome     transcriptome    

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The development and application of genome editing technology in ruminants: a review

Mengke YUAN, Yuanpeng GAO, Jing HAN, Teng WU, Jingcheng ZHANG, Yongke WEI, Yong ZHANG

《农业科学与工程前沿（英文）》 2020年 第7卷 第2期   页码 171-180 doi: 10.15302/J-FASE-2019302

摘要：

Transgenic ruminants are a valuable resource for both animal breeding and biomedical research. The development of transgenic breeding is proceeding slowly, because it suffers from low efficiency of gene transfer and possible safety problems from uncontrolled random integration. However, new breeding methods combined with genome editing and somatic cell nuclear transfer or microinjection can offer an economic and efficient way to produce gene-edited ruminants, which can serve as bioreactors or have improved disease resistance, animal welfare and product quality. Recent advances in precise genome editing technologies, especially clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 nucleases, are enabling the systematic development of gene-edited ruminant production. This review covers the development of gene-edited ruminants, the particulars of site-specific engineered nucleases and the state of the art and new insights into practical applications and social acceptance of genome editing technology in ruminants. It is concluded that the production of gene-edited ruminants is feasible and through improvements in genome editing technology it is possible to help feed the world.

关键词： bioreactors     breeding     engineered endonucleases     genome editing     ruminants    

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Liquid metal material genome: Initiation of a new research track towards discovery of advanced energy

Lei WANG, Jing LIU

《能源前沿（英文）》 2013年 第7卷 第3期   页码 317-332 doi: 10.1007/s11708-013-0271-9

摘要： As the basis of modern industry, the roles materials play are becoming increasingly vital in this day and age. With many superior physical properties over conventional fluids, the low melting point liquid metal material, especially room-temperature liquid metal, is recently found to be uniquely useful in a wide variety of emerging areas from energy, electronics to medical sciences. However, with the coming enormous utilization of such materials, serious issues also arise which urgently need to be addressed. A biggest concern to impede the large scale application of room-temperature liquid metal technologies is that there is currently a strong shortage of the materials and species available to meet the tough requirements such as cost, melting point, electrical and thermal conductivity, etc. Inspired by the Material Genome Initiative as issued in 2011 by the United States of America, a more specific and focused project initiative was proposed in this paper—the liquid metal material genome aimed to discover advanced new functional alloys with low melting point so as to fulfill various increasing needs. The basic schemes and road map for this new research program, which is expected to have a worldwide significance, were outlined. The theoretical strategies and experimental methods in the research and development of liquid metal material genome were introduced. Particularly, the calculation of phase diagram (CALPHAD) approach as a highly effective way for material design was discussed. Further, the first-principles (FP) calculation was suggested to combine with the statistical thermodynamics to calculate the thermodynamic functions so as to enrich the CALPHAD database of liquid metals. When the experimental data are too scarce to perform a regular treatment, the combination of FP calculation, cluster variation method (CVM) or molecular dynamics (MD), and CALPHAD, referred to as the mixed FP-CVM-CALPHAD method can be a promising way to solve the problem. Except for the theoretical strategies, several parallel processing experimental methods were also analyzed, which can help improve the efficiency of finding new liquid metal materials and reducing the cost. The liquid metal material genome proposal as initiated in this paper will accelerate the process of finding and utilization of new functional materials.

关键词： liquid metal material genome     energy material     material discovery     advanced material     room-temperature liquid alloy     thermodynamics     phase diagram    

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Transforming bacterial disease surveillance and investigation using whole-genome sequence to probe the

null

《医学前沿（英文）》 2018年 第12卷 第1期   页码 23-33 doi: 10.1007/s11684-017-0607-7

摘要：

Two decades have passed since the first bacterial whole-genome sequencing, which provides new opportunity for microbial genome. Consequently, considerable genetic diversity encoded by bacterial genomes and among the strains in the same species has been revealed. In recent years, genome sequencing techniques and bioinformatics have developed rapidly, which has resulted in transformation and expedited the application of strategy and methodology for bacterial genome comparison used in dissection of infectious disease epidemics. Bacterial whole-genome sequencing and bioinformatic computing allow genotyping to satisfy the requirements of epidemiological study in disease control. In this review, we outline the significance and summarize the roles of bacterial genome sequencing in the context of bacterial disease control and prevention. We discuss the applications of bacterial genome sequencing in outbreak detection, source tracing, transmission mode discovery, and new epidemic clone identification. Wide applications of genome sequencing and data sharing in infectious disease surveillance networks will considerably promote outbreak detection and early warning to prevent the dissemination of bacterial diseases.

关键词： genome sequencing     genomic epidemiology     bacteria     surveillance     infectious diseases    

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Advancement in genetic variants conferring obesity susceptibility from genome-wide association studies

null

《医学前沿（英文）》 2015年 第9卷 第2期   页码 146-161 doi: 10.1007/s11684-014-0373-8

摘要：

Obesity prevalence has increased in recent years. Lifestyle change fuels obesity, but genetic factors cause more than 50% of average variations in obesity. The advent of genome-wide association studies (GWAS) has hastened the progress of polygenic obesity research. As of this writing, more than 73 obesity susceptibility loci have been identified in ethnic groups through GWAS. The identified loci explain only 2% to 4% of obesity heritability, thereby indicating that a large proportion of loci remain undiscovered. Thus, the next step is to identify and confirm novel loci, which may exhibit smaller effects and lower allele frequencies than established loci. However, achieving these tasks has been difficult for researchers. GWAS help researchers discover the causal loci. Moreover, numerous biological studies have been performed on the polygenic effects on obesity, such as studies on fat mass- and obesity-associated gene (FTO), but the role of these polygenic effects in the mechanism of obesity remains unclear. Thus, obesity-causing variations should be identified, and insights into the biology of polygenic effects on obesity are needed.

关键词： obesity     genetics     genome-wide association studies     body mass index     fat mass- and obesity-associated gene    

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中国材料基因工程研究特色和愿景

谢建新, 宿彦京, 张达威, 冯强

《工程（英文）》 2022年 第10卷 第3期   页码 10-12 doi: 10.1016/j.eng.2021.12.008

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高分子材料的智能制造平台——高分子材料基因工程 Perspective

高梁, 王立权, 林嘉平, 杜磊

《工程（英文）》 2023年 第27卷 第8期   页码 31-36 doi: 10.1016/j.eng.2023.01.018

摘要：

高性能高分子材料是高新科技和先进制造业的基石。高分子材料基因工程正在成为高分子材料智能制造的重要平台。然而，高分子材料基因工程的发展仍处于起步阶段，许多问题亟待解决。本文阐述了高分子材料基因工程的概念，总结了最新研究成果，并强调了该领域的重要挑战和发展前景。特别强调了高分子材料的性能预估方法，包括性能代理量预测和机器学习性能预测。最后，讨论了高分子材料基因工程在先进复合材料、通信和集成电路等领域所亟需的高性能高分子材料创制方面的潜在工程应用前景。

关键词： 高分子材料     材料基因组方法     机器学习     性能预测     理性设计    

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A brief review of genome editing technology for generating animal models

Haoyi WANG, Sen WU, Mario R. CAPECCHI, Rudolf JAENISCH

《农业科学与工程前沿（英文）》 2020年 第7卷 第2期   页码 123-128 doi: 10.15302/J-FASE-2019309

摘要：

The recent development of genome editing technologies has given researchers unprecedented power to alter DNA sequences at chosen genomic loci, thereby generating various genetically edited animal models. This mini-review briefly summarizes the development of major genome editing tools, focusing on the application of these tools to generate animal models in multiple species.

关键词： animal model     CRISPR     genome editing     TALEN     ZFN    

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Highlights of special issue “Genome Editing in Agriculture: Technology, Applications and Regulations”

Yaofeng ZHAO, Caixia GAO, Sen WU

《农业科学与工程前沿（英文）》 2020年 第7卷 第2期   页码 121-122 doi: 10.15302/J-FASE-2019317

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Construction, characterization and application of a genome-wide promoter library in

Ting Yuan,Yakun Guo,Junkai Dong,Tianyi Li,Tong Zhou,Kaiwen Sun,Mei Zhang,Qingyu Wu,Zhen Xie,Yizhi Cai,Limin Cao,Junbiao Dai

《化学科学与工程前沿（英文）》 2017年 第11卷 第1期   页码 107-116 doi: 10.1007/s11705-017-1621-7

摘要： Promoters are critical elements to control gene expression but could behave differently under various growth conditions. Here we report the construction of a genome-wide promoter library, in which each native promoter in was cloned upstream of a yellow fluorescent protein (YFP) reporter gene. Nine libraries were arbitrarily defined and assembled in bacteria. The resulting pools of promoters could be prepared and transformed into a yeast strain either as centromeric plasmids or integrated into a genomic locus upon enzymatic treatment. Using fluorescence activated cell sorting, we classified the yeast strains based on YFP fluorescence intensity and arbitrarily divided the entire library into 12 bins, representing weak to strong promoters. Several strong promoters were identified from the most active bins and their activities were assayed under different growth conditions. Finally, these promoters were applied to drive the expression of genes in xylose utilization to improve fermentation efficiency. Together, this library could provide a quick solution to identify and utilize desired promoters under user-defined growth conditions.

关键词： synthetic biology     yeast     promoter activity     metabolic engineering     xylose utilization    

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Analysis of the genomic landscape of primary central nervous system lymphoma using whole-genome sequencing

《医学前沿（英文）》   页码 889-906 doi: 10.1007/s11684-023-0994-x

摘要： Primary central nervous system lymphoma (PCNSL) is an uncommon non-Hodgkin’s lymphoma with poor prognosis. This study aimed to depict the genetic landscape of Chinese PCNSLs. Whole-genome sequencing was performed on 68 newly diagnosed Chinese PCNSL samples, whose genomic characteristics and clinicopathologic features were also analyzed. Structural variations were identified in all patients with a mean of 349, which did not significantly influence prognosis. Copy loss occurred in all samples, while gains were detected in 77.9% of the samples. The high level of copy number variations was significantly associated with poor progression-free survival (PFS) and overall survival (OS). A total of 263 genes mutated in coding regions were identified, including 6 newly discovered genes (ROBO2, KMT2C, CXCR4, MYOM2, BCLAF1, and NRXN3) detected in ≥ 10% of the cases. CD79B mutation was significantly associated with lower PFS, TMSB4X mutation and high expression of TMSB4X protein was associated with lower OS. A prognostic risk scoring system was also established for PCNSL, which included Karnofsky performance status and six mutated genes (BRD4, EBF1, BTG1, CCND3, STAG2, and TMSB4X). Collectively, this study comprehensively reveals the genomic landscape of newly diagnosed Chinese PCNSLs, thereby enriching the present understanding of the genetic mechanisms of PCNSL.

关键词： primary central nervous system lymphoma     whole-genome sequencing     TMSB4X     copy number variation     gene mutation    

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Embryo-mediated genome editing for accelerated genetic improvement of livestock

Zachariah MCLEAN, Björn OBACK, Götz LAIBLE

《农业科学与工程前沿（英文）》 2020年 第7卷 第2期   页码 148-160 doi: 10.15302/J-FASE-2019305

摘要：

Selecting beneficial DNA variants is the main goal of animal breeding. However, this process is inherently inefficient because each animal only carries a fraction of all desirable variants. Genome editing technology with its ability to directly introduce beneficial sequence variants offers new opportunities to modernize animal breeding by overcoming this biological limitation and accelerating genetic gains. To realize rapid genetic gain, precise edits need to be introduced into genomically-selected embryos, which minimizes the genetic lag. However, embryo-mediated precision editing by homology-directed repair (HDR) mechanisms is currently an inefficient process that often produces mosaic embryos and greatly limits the numbers of available edited embryos. This review provides a summary of genome editing in bovine embryos and proposes an embryo-mediated accelerated breeding scheme that overcomes the present efficiency limitations of HDR editing in bovine embryos. It integrates embryo-based genomic selection with precise multi-editing and uses embryonic cloning with elite edited blastomeres or embryonic pluripotent stem cells to resolve mosaicism, enable multiplex editing and multiply rare elite genotypes. Such a breeding strategy would enable a more targeted, accelerated approach for livestock improvement that allows stacking of beneficial variants, even including novel traits from outside the breeding population, in the most recent elite genetic background, essentially within a single generation.

关键词： animal breeding     cattle     cloning     CRISPR/Cas9     cytoplasmic injection     embryo     genome editing     germline chimaeras     HDR     livestock improvement     TALENs    

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标题 作者 时间 类型 操作

GENOME EDITING: A GROUND BREAKING RESEARCH HAS BEEN RANKED TOP 10 ENGINEERING FRONTS FROM 2017 TO 2021

期刊论文

Genome reprogramming for synthetic biology

Kylie Standage-Beier,Xiao Wang

期刊论文

材料基因工程专题主编寄语

王海舟, 谢建新

期刊论文

Exploring the cancer genome in the era of next-generation sequencing

null

期刊论文

The development and application of genome editing technology in ruminants: a review

Mengke YUAN, Yuanpeng GAO, Jing HAN, Teng WU, Jingcheng ZHANG, Yongke WEI, Yong ZHANG

期刊论文

Liquid metal material genome: Initiation of a new research track towards discovery of advanced energy

Lei WANG, Jing LIU

期刊论文

Transforming bacterial disease surveillance and investigation using whole-genome sequence to probe the

null

期刊论文

Advancement in genetic variants conferring obesity susceptibility from genome-wide association studies

null

期刊论文

中国材料基因工程研究特色和愿景

谢建新, 宿彦京, 张达威, 冯强

期刊论文

高分子材料的智能制造平台——高分子材料基因工程

高梁, 王立权, 林嘉平, 杜磊

期刊论文

A brief review of genome editing technology for generating animal models

Haoyi WANG, Sen WU, Mario R. CAPECCHI, Rudolf JAENISCH

期刊论文

Highlights of special issue “Genome Editing in Agriculture: Technology, Applications and Regulations”

Yaofeng ZHAO, Caixia GAO, Sen WU

期刊论文

Construction, characterization and application of a genome-wide promoter library in

Ting Yuan,Yakun Guo,Junkai Dong,Tianyi Li,Tong Zhou,Kaiwen Sun,Mei Zhang,Qingyu Wu,Zhen Xie,Yizhi Cai,Limin Cao,Junbiao Dai

期刊论文

Analysis of the genomic landscape of primary central nervous system lymphoma using whole-genome sequencing

期刊论文

Embryo-mediated genome editing for accelerated genetic improvement of livestock

Zachariah MCLEAN, Björn OBACK, Götz LAIBLE

期刊论文