Synthetic Biology Journal ›› 2023, Vol. 4 ›› Issue (5): 877-891.DOI: 10.12211/2096-8280.2023-027
• Invited Review • Previous Articles Next Articles
Hui LU1, Fangli ZHANG1, Lei HUANG1,2
Received:
2023-03-31
Revised:
2023-05-24
Online:
2023-11-15
Published:
2023-10-31
Contact:
Lei HUANG
卢挥1, 张芳丽1, 黄磊1,2
通讯作者:
黄磊
作者简介:
CLC Number:
Hui LU, Fangli ZHANG, Lei HUANG. Establishment of iBioFoundry for synthetic biology applications[J]. Synthetic Biology Journal, 2023, 4(5): 877-891.
卢挥, 张芳丽, 黄磊. 合成生物学自动化装置iBioFoundry的构建与应用[J]. 合成生物学, 2023, 4(5): 877-891.
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URL: https://synbioj.cip.com.cn/EN/10.12211/2096-8280.2023-027
编号 | 子任务名称 | 实验步骤 | 需编程的设备 | 程序名称 |
---|---|---|---|---|
1 | PCR反应 | PCR反应体系配置 | 移液工作站 | Pre_Target_PCR |
封膜 | ||||
离心 | ||||
PCR扩增 | 自动化PCR仪 | Target_PCR | ||
2 | 产物纯化 | 撕膜 | ||
磁珠纯化 | 移液工作站 | PCR_Product_Purification | ||
3 | 核酸片段分析 | 核酸片段检测体系配置 | 移液工作站 | Pre_Fragment_Analysis |
核酸片段分析 | 自动化核酸片段分析仪 | Fragment_Analysis_50 to 6000 bp | ||
4 | DNA组装 | 样品筛选及试剂分装 | 移液工作站 | Sample_Selection |
DNA组装反应体系配制 | 纳升级移液工作站 | Pre_DNA_Assembly | ||
封膜 | ||||
离心 | ||||
DNA组装反应 | 自动化PCR仪 | DNA_Assembly | ||
5 | 质粒转化 | 撕膜 | ||
质粒转化体系配置 | 移液工作站 | Pre_Plasmid_Transforming | ||
封膜 | ||||
热激 | 自动化PCR仪 | Plasmid_Transforming | ||
孵育 | ||||
6 | 菌液涂布培养 | 8孔矩形培养板涂布 | 移液工作站 | Dilution_Plating |
平板静置培养 | ||||
7 | 克隆挑选与培养 | 培养基分装 | ||
克隆挑选 | 移液工作站 | Clone_Picking | ||
封膜 | ||||
菌液振荡培养 | ||||
8 | 菌落鉴定 | 荧光定量PCR反应体系配置 | 移液工作站 | Pre_Clone_Verification |
封膜 | ||||
离心 | ||||
荧光定量PCR检测 | 荧光定量PCR仪 | Clone_Verification | ||
9 | 菌株保存 | 开盖 | ||
菌株挑选与保存 | 移液工作站 | Positive_Sample_Selection | ||
关盖 | ||||
样本存储 |
Table 1 Relevant operation and involved scripts of the experiment
编号 | 子任务名称 | 实验步骤 | 需编程的设备 | 程序名称 |
---|---|---|---|---|
1 | PCR反应 | PCR反应体系配置 | 移液工作站 | Pre_Target_PCR |
封膜 | ||||
离心 | ||||
PCR扩增 | 自动化PCR仪 | Target_PCR | ||
2 | 产物纯化 | 撕膜 | ||
磁珠纯化 | 移液工作站 | PCR_Product_Purification | ||
3 | 核酸片段分析 | 核酸片段检测体系配置 | 移液工作站 | Pre_Fragment_Analysis |
核酸片段分析 | 自动化核酸片段分析仪 | Fragment_Analysis_50 to 6000 bp | ||
4 | DNA组装 | 样品筛选及试剂分装 | 移液工作站 | Sample_Selection |
DNA组装反应体系配制 | 纳升级移液工作站 | Pre_DNA_Assembly | ||
封膜 | ||||
离心 | ||||
DNA组装反应 | 自动化PCR仪 | DNA_Assembly | ||
5 | 质粒转化 | 撕膜 | ||
质粒转化体系配置 | 移液工作站 | Pre_Plasmid_Transforming | ||
封膜 | ||||
热激 | 自动化PCR仪 | Plasmid_Transforming | ||
孵育 | ||||
6 | 菌液涂布培养 | 8孔矩形培养板涂布 | 移液工作站 | Dilution_Plating |
平板静置培养 | ||||
7 | 克隆挑选与培养 | 培养基分装 | ||
克隆挑选 | 移液工作站 | Clone_Picking | ||
封膜 | ||||
菌液振荡培养 | ||||
8 | 菌落鉴定 | 荧光定量PCR反应体系配置 | 移液工作站 | Pre_Clone_Verification |
封膜 | ||||
离心 | ||||
荧光定量PCR检测 | 荧光定量PCR仪 | Clone_Verification | ||
9 | 菌株保存 | 开盖 | ||
菌株挑选与保存 | 移液工作站 | Positive_Sample_Selection | ||
关盖 | ||||
样本存储 |
类型 | 名称 | 数量 | 起始位置 | 结束位置 |
---|---|---|---|---|
试剂 | 引物 | 2块 | 自动化低温冰箱1-[ | 6列耗材存储设备2-[ |
DNA模板 | 1块 | 自动化低温冰箱1-[ | 6列耗材存储设备2-[ | |
大肠杆菌感受态细胞 | 1块 | 自动化低温冰箱1-[ | 耗材回收桶 | |
PCR反应试剂 | 1块 | 自动化低温冰箱1-[ | 自动化低温冰箱1-[ | |
DNA组装试剂 | 1块 | 自动化低温冰箱1-[ | 自动化低温冰箱1-[ | |
qPCR检测试剂 | 1块 | 自动化低温冰箱1-[ | 自动化低温冰箱1-[ | |
耗材 | 50 μL黑色吸头 | 2盒 | 24列耗材存储设备1-[ | 耗材回收桶 |
200 μL黑色吸头 | 7盒 | 24列耗材存储设备2-[ | 耗材回收桶 | |
50 μL透明吸头 | 4盒 | 24列耗材存储设备1-[ | 耗材回收桶 | |
200 μL透明吸头 | 3盒 | 24列耗材存储设备3-[ | 耗材回收桶 | |
8孔矩形培养板 | 12块 | 10列耗材存储设备1-[ | 自动化低温冰箱2-[ | |
96孔微孔板 | 4块 | 24列耗材存储设备4-[ | 自动化低温冰箱1-[ | |
96孔深孔板 | 8块 | 10列耗材存储设备2-[ | 10列耗材存储设备2-[ | |
96位样本架 | 3块 | 6列耗材存储设备1-[ | Arktic冰箱 | |
384孔微孔板 | 4块 | 24列耗材存储设备4-[ | 6列耗材存储设备2-[ |
Table 2 Reagents and consumables used in experiment
类型 | 名称 | 数量 | 起始位置 | 结束位置 |
---|---|---|---|---|
试剂 | 引物 | 2块 | 自动化低温冰箱1-[ | 6列耗材存储设备2-[ |
DNA模板 | 1块 | 自动化低温冰箱1-[ | 6列耗材存储设备2-[ | |
大肠杆菌感受态细胞 | 1块 | 自动化低温冰箱1-[ | 耗材回收桶 | |
PCR反应试剂 | 1块 | 自动化低温冰箱1-[ | 自动化低温冰箱1-[ | |
DNA组装试剂 | 1块 | 自动化低温冰箱1-[ | 自动化低温冰箱1-[ | |
qPCR检测试剂 | 1块 | 自动化低温冰箱1-[ | 自动化低温冰箱1-[ | |
耗材 | 50 μL黑色吸头 | 2盒 | 24列耗材存储设备1-[ | 耗材回收桶 |
200 μL黑色吸头 | 7盒 | 24列耗材存储设备2-[ | 耗材回收桶 | |
50 μL透明吸头 | 4盒 | 24列耗材存储设备1-[ | 耗材回收桶 | |
200 μL透明吸头 | 3盒 | 24列耗材存储设备3-[ | 耗材回收桶 | |
8孔矩形培养板 | 12块 | 10列耗材存储设备1-[ | 自动化低温冰箱2-[ | |
96孔微孔板 | 4块 | 24列耗材存储设备4-[ | 自动化低温冰箱1-[ | |
96孔深孔板 | 8块 | 10列耗材存储设备2-[ | 10列耗材存储设备2-[ | |
96位样本架 | 3块 | 6列耗材存储设备1-[ | Arktic冰箱 | |
384孔微孔板 | 4块 | 24列耗材存储设备4-[ | 6列耗材存储设备2-[ |
存储设备 | 设备内载架类型(高度) | 列数 | 板位数/列 | 功能 |
---|---|---|---|---|
24列耗材存储设备 | 高位载架(69 mm) | 10列 | 7 plates | 可存放70盒SBS规格吸头盒 |
中位载架(50 mm) | 8列 | 10 plates | 可存放80块SBS规格深孔板 | |
低位载架(23 mm) | 6列 | 21 plates | 可存放126块SBS规格微孔板 | |
10列耗材存储设备 | 超高位载架(128 mm) | 2列 | 4 plates | 可存放8盒SBS规格吸头盒 |
中位载架(50 mm) | 5列 | 10 plates | 可存放50块SBS规格深孔板 | |
低位载架(23 mm) | 3列 | 21 plates | 可存放63块SBS规格微孔板 | |
6列耗材存储设备 | 高位载架(69 mm) | 2列 | 8 plates | 可存放16块SBS规格深孔板 |
低位载架(31 mm) | 4列 | 15 plates | 可存放60块SBS规格微孔板 |
Table 3 Automated consumable-storing devices and inner resource allocation
存储设备 | 设备内载架类型(高度) | 列数 | 板位数/列 | 功能 |
---|---|---|---|---|
24列耗材存储设备 | 高位载架(69 mm) | 10列 | 7 plates | 可存放70盒SBS规格吸头盒 |
中位载架(50 mm) | 8列 | 10 plates | 可存放80块SBS规格深孔板 | |
低位载架(23 mm) | 6列 | 21 plates | 可存放126块SBS规格微孔板 | |
10列耗材存储设备 | 超高位载架(128 mm) | 2列 | 4 plates | 可存放8盒SBS规格吸头盒 |
中位载架(50 mm) | 5列 | 10 plates | 可存放50块SBS规格深孔板 | |
低位载架(23 mm) | 3列 | 21 plates | 可存放63块SBS规格微孔板 | |
6列耗材存储设备 | 高位载架(69 mm) | 2列 | 8 plates | 可存放16块SBS规格深孔板 |
低位载架(31 mm) | 4列 | 15 plates | 可存放60块SBS规格微孔板 |
1 | SISMOUR A M, BENNER S A. Synthetic biology[J]. Expert Opinion on Biological Therapy, 2005, 5(11): 1409-1414. |
2 | 张先恩. 中国合成生物学发展回顾与展望[J]. 中国科学:生命科学, 2019, 49(12): 1543-1572. |
ZHANG X E. Synthetic biology in China: Review and prospects[J]. Scientia Sinica (Vitae), 2019, 49(12): 1543-1572. | |
3 | 赵国屏. 合成生物学: 开启生命科学 "会聚" 研究新时代[J]. 中国科学院院刊, 2018, 33(11)1135-1149 |
ZHAO G P. Synthetic biology: unsealing the convergence era of life science research[J]. Bulletin of the Chinese Academy of Sciences, 2018, 33(11)1135-1149. | |
4 | CAMERON D E, BASHOR C J, COLLINS J J. A brief history of synthetic biology[J]. Nature Reviews Microbiology, 2014, 12(5): 381-390. |
5 | KHALIL A S, COLLINS J J. Synthetic biology: applications come of age[J]. Nature Reviews Genetics, 2010, 11(5): 367-379. |
6 | MARTIN V J J, PITERA D J, WITHERS S T, et al. Engineering a mevalonate pathway in Escherichia coli for production of terpenoids[J]. Nature Biotechnology, 2003, 21(7): 796-802. |
7 | WIN M N, SMOLKE C D. Higher-order cellular information processing with synthetic RNA devices[J]. Science, 2008, 322(5900): 456-460. |
8 | PADDON C J, WESTFALL P J, PITERA D J, et al. High-level semi-synthetic production of the potent antimalarial artemisinin[J]. Nature, 2013, 496(7446): 528-532. |
9 | CHAO R, MISHRA S, SI T, et al. Engineering biological systems using automated biofoundries[J]. Metabolic Engineering, 2017, 42: 98-108. |
10 | 唐婷, 付立豪, 郭二鹏, 等. 自动化合成生物技术与工程化设施平台[J]. 科学通报, 2021, 66(3): 300-309. |
TANG T, FU L H, GUO E P, et al. Automation in synthetic biology using biological foundries[J]. Chinese Science Bulletin, 2021, 66(3): 300-309. | |
11 | LE FEUVRE R A, SCRUTTON N S. A living foundry for Synthetic Biological Materials: a synthetic biology roadmap to new advanced materials[J]. Synthetic and Systems Biotechnology, 2018, 3(2): 105-112. |
12 | KANG D H, KO S C, HEO Y B, et al. RoboMoClo: a robotics-assisted modular cloning framework for multiple gene assembly in biofoundry[J]. ACS Synthetic Biology, 2022, 11(3): 1336-1348. |
13 | SI T, CHAO R, MIN Y H, et al. Automated multiplex genome-scale engineering in yeast[J]. Nature Communications, 2017, 8: 15187. |
14 | CHAO R, LIANG J, TASAN I, et al. Fully automated one-step synthesis of single-transcript TALEN pairs using a biological foundry[J]. ACS Synthetic Biology, 2017, 6(4): 678-685. |
15 | STORCH M, HAINES M C, BALDWIN G S. DNA-BOT: a low-cost, automated DNA assembly platform for synthetic biology[J]. Synthetic Biology, 2020, 5(1): ysaa010. |
16 | 崔金明, 张炳照, 马迎飞, 等. 合成生物学研究的工程化平台[J]. 中国科学院院刊, 2018, 33(11): 1249-1257. |
CUI J M, ZHANG B Z, MA Y F, et al. Engineering platforms for synthetic biology research[J]. Bulletin of the Chinese Academy of Sciences, 2018, 33(11): 1249-1257. | |
17 | HILLSON N, CADDICK M, CAI Y Z, et al. Building a global alliance of biofoundries[J]. Nature Communications, 2019, 10: 2040. |
18 | 晁然, 原永波, 赵惠民. 构建合成生物学制造厂[J]. 中国科学:生命科学, 2015, 45(10): 976-984. |
CHAO R, YUAN Y B, ZHAO H M. Building biological foundries for next generation synthetic biology[J]. Scientia Sinica (Vitae), 2015, 45(10): 976-984. | |
19 | 张亭, 冷梦甜, 金帆, 等. 合成生物研究重大科技基础设施概述[J]. 合成生物学, 2022(1): 184-194. |
ZHANG T, LENG M T, JIN F, et al. Overview on platform for synthetic biology research at Shenzhen[J]. Synthetic Biology Journal, 2022(1): 184-194. | |
20 | ZHANG J Z, CHEN Y C, FU L H, et al. Accelerating strain engineering in biofuel research via build and test automation of synthetic biology[J]. Current Opinion in Biotechnology, 2021, 67: 88-98. |
21 | WU F, JIN S T, JIANG Y H, et al. Pre-training of equivariant graph matching networks with conformation flexibility for drug binding[J]. Advanced Science, 2022, 9(33): 2203796. |
22 | WANG J, ZHANG X Q, CHENG L X, et al. An overview and metanalysis of machine and deep learning-based CRISPR gRNA design tools[J]. RNA Biology, 2020, 17(1): 13-22. |
23 | CARBONELL P, RADIVOJEVIC T, GARCÍA MARTÍN H. Opportunities at the intersection of synthetic biology, machine learning, and automation[J]. ACS Synthetic Biology, 2019, 8(7): 1474-1477. |
24 | ZHANG J, HANSEN L G, GUDICH O, et al. A microbial supply chain for production of the anti-cancer drug vinblastine[J]. Nature, 2022, 609(7926): 341-347. |
25 | CAI T, SUN H B, QIAO J, et al. Cell-free chemoenzymatic starch synthesis from carbon dioxide[J]. Science, 2021, 373(6562): 1523-1527. |
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