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DNA组装效率的无偏差快速检验——基于qPCR而不依赖于转化的方法 Article

马晓焉, 梁昕鑫, 霍毅欣

《工程（英文）》 2019年第5卷第4期页码 803-810 doi: 10.1016/j.eng.2019.06.002

摘要：传统评估DNA组装效率（AE）的方法需要进行转化，整个过程耗时长达10 h，而且容易受到各种因素的干扰。随后，用此方法研究了DNA片段末端的二级结构对组装效率的影响。结果显示，所有依赖于末端序列互补的组装技术，其组装效率主要受重叠序列整体性质的影响，而发夹结构可显著降低组装效率。这种基于qPCR的测定方法将促进DNA组装技术的发展，并有助于对组装效率影响因素的评估。

关键词：组装效率 DNA组装 qPCR 二级结构转化

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Profiling influences of gene overexpression on heterologous resveratrol production in

Duo Liu,Bingzhi Li,Hong Liu,Xuejiao Guo,Yingjin Yuan

《化学科学与工程前沿（英文）》 2017年第11卷第1期页码 117-125 doi: 10.1007/s11705-016-1601-3

摘要： Metabolic engineering of heterologous resveratrol production in faces challenges as the precursor L-tyrosine is stringently regulated by a complex biosynthetic system. We overexpressed the main gene targets in the upstream pathways to investigate their influences on the downstream resveratrol production. Single-gene overexpression and DNA assembly-directed multigene overexpression affect the production of resveratrol as well as its precursor -coumaric acid. Finally, the collaboration of selected gene targets leads to an optimal resveratrol production of 66.14±3.74 mg·L , 2.27 times higher than the initial production in YPD medium (4% glucose). The newly discovered gene targets expressing phosphoribosylanthranilate isomerase, expressing 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase, and expressing 4-coumaryl-CoA ligase show notable positive impacts on resveratrol production in .

关键词： resveratrol aromatic amino acid DNA assembly metabolic engineering gene overexpression

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Assembly of biosynthetic pathways in

Lidan Ye,Xiaomei Lv,Hongwei Yu

《化学科学与工程前沿（英文）》 2017年第11卷第1期页码 126-132 doi: 10.1007/s11705-016-1597-8

摘要： A robust and versatile tool for multigene pathway assembly is a key to the biosynthesis of high-value chemicals. Here we report the rapid construction of biosynthetic pathways in using a marker recyclable integrative toolbox (pUMRI) developed in our research group, which has features of ready-to-use, convenient marker recycling, arbitrary element replacement, shuttle plasmid, auxotrophic marker independence, GAL regulation, and decentralized assembly. Functional isoprenoid biosynthesis pathways containing 4–11 genes with lengths ranging from ~10 to ~22 kb were assembled using this toolbox within 1–5 rounds of reiterative recombination. In combination with GAL-regulated metabolic engineering, high production of isoprenoids (e.g., 16.3 mg?g dcw carotenoids) was achieved. These results demonstrate the wide range of application and the efficiency of the pUMRI toolbox in multigene pathway construction of .

关键词： pathway assembly toolbox reiterative recombination S. cerevisiae biosynthesis

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A novel task-oriented framework for dual-arm robotic assembly task

《机械工程前沿（英文）》 2021年第16卷第3期页码 528-545 doi: 10.1007/s11465-021-0638-2

摘要： In industrial manufacturing, the deployment of dual-arm robots in assembly tasks has become a trend. However, making the dual-arm robots more intelligent in such applications is still an open, challenging issue. This paper proposes a novel framework that combines task-oriented motion planning with visual perception to facilitate robot deployment from perception to execution and finish assembly problems by using dual-arm robots. In this framework, visual perception is first employed to track the effects of the robot behaviors and observe states of the workpieces, where the performance of tasks can be abstracted as a high-level state for intelligent reasoning. The assembly task and manipulation sequences can be obtained by analyzing and reasoning the state transition trajectory of the environment as well as the workpieces. Next, the corresponding assembly manipulation can be generated and parameterized according to the differences between adjacent states by combining with the prebuilt knowledge of the scenarios. Experiments are set up with a dual-arm robotic system (ABB YuMi and an RGB-D camera) to validate the proposed framework. Experimental results demonstrate the effectiveness of the proposed framework and the promising value of its practical application.

关键词： dual-arm assembly AI reasoning intelligent system task-oriented motion planning visual perception

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Pareto lexicographic α-robust approach and its application in robust multi objective assembly line balancing

null

《机械工程前沿（英文）》 2014年第9卷第3期页码 257-264 doi: 10.1007/s11465-014-0294-x

摘要：

Robustness in most of the literature is associated with min-max or min-max regret criteria. However, these criteria of robustness are conservative and therefore recently new criteria called, lexicographic α-robust method has been introduced in literature which defines the robust solution as a set of solutions whose quality or jth largest cost is not worse than the best possible jth largest cost in all scenarios. These criteria might be significant for robust optimization of single objective optimization problems. However, in real optimization problems, two or more than two conflicting objectives are desired to optimize concurrently and solution of multi objective optimization problems exists in the form of a set of solutions called Pareto solutions and from these solutions it might be difficult to decide which Pareto solution can satisfy min-max, min-max regret or lexicographic α-robust criteria by considering multiple objectives simultaneously. Therefore, lexicographic α-robust method which is a recently introduced method in literature is extended in the current research for Pareto solutions. The proposed method called Pareto lexicographic α-robust approach can define Pareto lexicographic α-robust solutions from different scenarios by considering multiple objectives simultaneously. A simple example and an application of the proposed method on a simple problem of multi objective optimization of simple assembly line balancing problem with task time uncertainty is presented to get their robust solutions. The presented method can be significant to implement on different multi objective robust optimization problems containing uncertainty.

关键词： Pareto lexicographic α-robust assembly line balancing

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工程化DNA材料构建DNA活字系统实现可持续的数据存储 Article

巩子祎, 宋理富, 裴广胜, 董雨菲, 李炳志, 元英进

《工程（英文）》 2023年第29卷第10期页码 130-136 doi: 10.1016/j.eng.2022.05.023

摘要：

DNA分子作为一种具有潜力的数据存储绿色材料，具有密度高和保存期长的优势。然而，目前DNA数据存储的数据写入依赖于DNA从头合成，写入成本高昂，且产生有害物，限制了其实际应用。在本研究中，我们开发了一种DNA活字存储系统，该系统可以利用由细胞工厂预生产的DNA活字片段进行数据写入。在这个系统中，这些预先生成的DNA片段，在这里称为“DNA活字”，是可重复使用的基本数据单元。通过这些DNA活字的快速组装来实现数据写入，从而避免了昂贵且对环境有害的DNA化学合成过程。通过DNA活字片段的反复使用和生物组装，该系统在降低写入成本方面的潜力非常突出，为经济和可持续的DNA数据存储技术开辟了一条新颖路线。

关键词：合成生物学 DNA信息存储 DNA活字存储系统经济性DNA数据存储

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Assembly design system based on engineering connection

Wensheng YIN

《机械工程前沿（英文）》 2016年第11卷第4期页码 423-432 doi: 10.1007/s11465-016-0382-1

摘要：

An assembly design system is an important part of computer-aided design systems, which are important tools for realizing product concept design. The traditional assembly design system does not record the connection information of production on the engineering layer; consequently, the upstream design idea cannot be fully used in the downstream design. An assembly design model based on the relationship of engineering connection is presented. In this model, all nodes are divided into two categories: The component and the connection. Moreover, the product is constructed on the basis of the connection relationship of the components. The model is an And/Or graph and has the ability to record all assembly schemes. This model records only the connection information that has engineering application value in the product design. In addition, this model can significantly reduce the number of combinations, and is very favorable for the assembly sequence planning in the downstream. The system contains a connection knowledge system that can be mapped to the connection node, and the connection knowledge obtained in practice can be returned to the knowledge system. Finally, VC++6.0 is used to develop a prototype system called Connect-based Assembly Planning (CAP). The relationship between the CAP system and the commercial assembly design system is also established.

关键词： product design assembly design engineering connection assembly sequence planning

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Enzyme-instructed self-assembly of peptides containing phosphoserine to form supramolecular hydrogels

Jie Zhou, Xuewen Du, Jiaqing Wang, Natsuko Yamagata, Bing Xu

《化学科学与工程前沿（英文）》 2017年第11卷第4期页码 509-515 doi: 10.1007/s11705-017-1613-7

摘要： Enzyme-instructed self-assembly (EISA) offers a facile approach to explore the supramolecular assemblies of small molecules in cellular milieu for a variety of biomedical applications. One of the commonly used enzymes is phosphatase, but the study of the substrates of phosphatases mainly focuses on the phosphotyrosine containing peptides. In this work, we examine the EISA of phosphoserine containing small peptides for the first time by designing and synthesizing a series of precursors containing only phosphoserine or both phosphoserine and phosphotyrosine. Conjugating a phosphoserine to the -terminal of a well-established self-assembling peptide backbone, (naphthalene-2-ly)-acetyl-diphenylalanine (NapFF), affords a novel hydrogelation precursor for EISA. The incorporation of phosphotyrosine, another substrate of phosphatase, into the resulting precursor, provides one more enzymatic trigger on a single molecule, and meanwhile increases the precursors’ propensity to aggregate after being fully dephosphorylated. Exchanging the positions of phosphorylated serine and tyrosine in the peptide backbone provides insights on how the specific molecular structures influence self-assembling behaviors of small peptides and the subsequent cellular responses. Moreover, the utilization of D-amino acids largely enhances the biostability of the peptides, thus providing a unique soft material for potential biomedical applications.

关键词： enzyme-instructed self-assembly phosphoserine phosphatase supramolecular hydrogel

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The role of PARP1 in the DNA damage response and its application in tumor therapy

null

《医学前沿（英文）》 2012年第6卷第2期页码 156-164 doi: 10.1007/s11684-012-0197-3

摘要：

Single-strand break repair protein poly(ADP-ribose) polymerase 1 (PARP1) catalyzes the poly(ADP-ribosyl)ation of many key proteins in vivo and thus plays important roles in multiple DNA damage response pathways, rendering it a promising target in cancer therapy. The tumor-suppressor effects of PARP inhibitors have attracted significant interest for development of novel cancer therapies. However, recent evidence indicated that the underlying mechanism of PARP inhibitors in tumor therapy is more complex than previously expected. The present review will focus on recent progress on the role of PARP1 in the DNA damage response and PARP inhibitors in cancer therapy. The emerging resistance of BRCA-deficient tumors to PARP inhibitors is also briefly discussed from the perspective of DNA damage and repair. These recent research advances will inform the selection of patient populations who can benefit from the PARP inhibitor treatment and development of effective drug combination strategies.

关键词： PARP1 synthetic lethality PARP inhibitor DNA repair cancer NHEJ

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Functional role of ATM in the cellular response to DNA damage

Ming LIU, Wenxiang HU

《化学科学与工程前沿（英文）》 2011年第5卷第2期页码 179-187 doi: 10.1007/s11705-009-0268-4

摘要： Ataxia-telangiectasia mutated (ATM) plays a key role in regulating the cellular response to ionizing radiation. The tumor-suppressor gene ATM, mutations in which cause the human genetic disease ataxia telangiectasia, encodes a key protein kinase that controls the cellular response to double-stranded breaks. Activation of ATM results in phosphorylation of many downstream targets that modulate numerous damage response pathways, most notably cell cycle checkpoints. Here, we highlight some of the new developments in the field in our understanding of the mechanism of activation of ATM and its signaling pathways, explore whether DNA double-strand breaks are the sole activators of ATM and ATM-dependent signaling pathways, and address some of the prominent, unanswered questions related to ATM and its function. The scope of this article is to provide a brief overview of the recent literature on this subject and to raise questions that could be addressed in future studies.

关键词： ataxia-telangiectasia mutated (ATM) cell cycle checkpoint DNA damage signalling transduction

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Generation and repair of AID-initiated DNA lesions in B lymphocytes

null

《医学前沿（英文）》 2014年第8卷第2期页码 201-216 doi: 10.1007/s11684-014-0324-4

摘要：

Activation-induced deaminase (AID) initiates the secondary antibody diversification process in B lymphocytes. In mammalian B cells, this process includes somatic hypermutation (SHM) and class switch recombination (CSR), both of which require AID. AID induces U:G mismatch lesions in DNA that are subsequently converted into point mutations or DNA double stranded breaks during SHM/CSR. In a physiological context, AID targets immunoglobulin (Ig) loci to mediate SHM/CSR. However, recent studies reveal genome-wide access of AID to numerous non-Ig loci. Thus, AID poses a threat to the genome of B cells if AID-initiated DNA lesions cannot be properly repaired. In this review, we focus on the molecular mechanisms that regulate the specificity of AID targeting and the repair pathways responsible for processing AID-initiated DNA lesions.

关键词： class switch recombination somatic hypermutation activation-induced deaminase DNA repair genomic instability

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Molecular simulation of the interaction mechanism between CodY protein and DNA in

Linchen Yuan, Hao Wu, Yue Zhao, Xiaoyu Qin, Yanni Li

《化学科学与工程前沿（英文）》 2019年第13卷第1期页码 133-139 doi: 10.1007/s11705-018-1737-4

摘要： In , the global transcriptional regulatory factor CodY can interact with the promoter DNA to regulate the growth, metabolism, environmental adaptation and other biological activities of the strains. In order to study the mechanism of interaction between CodY and its target DNA, molecular docking and molecular dynamics simulations were used to explore the binding process at molecular level. Through the calculations of the free energy of binding, hydrogen bonding and energy decomposition, nine key residues of CodY were identified, corresponding to SER184, SER186, SER208, THR217, ARG218, SER219, ASN223, LYS242 and GLY243, among which SER186, ARG218 and LYS242 play a vital role in DNA binding. Our research results provide important theoretical guidance for using wet-lab methods to study and optimize the metabolic network regulated by CodY.

关键词： CodY DNA molecular docking molecular dynamics

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Environmental pollution and DNA methylation: carcinogenesis, clinical significance, and practical applications

null

《医学前沿（英文）》 2015年第9卷第3期页码 261-274 doi: 10.1007/s11684-015-0406-y

摘要：

Environmental pollution is one of the main causes of human cancer. Exposures to environmental carcinogens result in genetic and epigenetic alterations which induce cell transformation. Epigenetic changes caused by environmental pollution play important roles in the development and progression of environmental pollution-related cancers. Studies on DNA methylation are among the earliest and most conducted epigenetic research linked to cancer. In this review, the roles of DNA methylation in carcinogenesis and their significance in clinical medicine were summarized, and the effects of environmental pollutants, particularly air pollutants, on DNA methylation were introduced. Furthermore, prospective applications of DNA methylation to environmental pollution detection and cancer prevention were discussed.

关键词： environmental pollution DNA methylation cancer biomarker diagnosis therapy prevention

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Effects of DNA damage on oocyte meiotic maturation and early embryonic development

Shen YIN,Junyu MA,Wei SHEN

《农业科学与工程前沿（英文）》 2014年第1卷第3期页码 185-190 doi: 10.15302/J-FASE-2014035

摘要： DNA damage is one of the most common threats to meiotic cells. It has the potential to induce infertility and genetic abnormalities that may be passed to the embryo. Here, we reviewed exogenous factors which could induce DNA damage. Specially, we addressed the different effects of DNA damage on mouse oocytes and embryonic development. Complex DNA damage, double-strand breaks, represents a more difficult repair process and involves various repair pathways. Understanding the mechanisms involved in DNA damage responses may improve therapeutic strategies for ovarian cancer and fertility preservation.

关键词： DNA damage double-strand breaks (DSBs) oocyte embryo

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表征不同DNA高阶结构的单分子分析方法 Review

刘泳麟, 边天元, 刘岩, 李治民, 裴羽丰, 宋杰

《工程（英文）》 2023年第24卷第5期页码 277-292 doi: 10.1016/j.eng.2022.10.009

摘要：

DNA不仅是生命遗传信息的载体，而且是一种高度可编程和自组装的纳米材料。不同的DNA结构与其生物学和化学功能有关。因此，了解各种DNA结构的物理和化学性质在生物学和纳米化学中具有重要意义。然而，群体分子实验忽略了溶液中DNA结构的异质性。单分子分析方法是观察单个分子的行为和探测自由能态的高异质性的有力工具。本文介绍了单分子检测和操纵等单分子分析方法，并讨论了这些方法如何用于测量单/双链DNA（ss/dsDNA）、DNA高阶结构和DNA纳米结构的分子性质。最后，将DNA纳米技术和单分子分析方法进行结合以了解DNA和其他生物物质、软物质的生物物理特性。

关键词：单分子分析方法 DNA结构力学性能构象转变