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2023 13

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DNA 2

细胞外基质 2

CO₂利用 1

DNA信息存储 1

DNA活字存储系统 1

DNA组装 1

DNA结构 1

DNA计算 1

qPCR 1

下一代测序 1

二级结构 1

人工智能 1

信使核糖核酸（mRNA）疫苗 1

凝聚物 1

分数阶离散系统；神经网络；DNA加密；彩色图像加密 1

刚性 1

创面修复 1

力学性能 1

医学图像加密；DNA；混沌吸引子；交叉；突变；电子医疗 1

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Degradation of extracellular genomic, plasmid DNA and specific antibiotic resistance genes by chlorination

Menglu Zhang, Sheng Chen, Xin Yu, Peter Vikesland, Amy Pruden

《环境科学与工程前沿（英文）》 2019年第13卷第3期 doi: 10.1007/s11783-019-1124-5

摘要：

Extracellular DNA structure damaged by chlorination was characterized.

Integrity of extracellular ARG genetic information after chlorination was determined.

Typical chlorine doses will likely effectively diminish extracellular DNA and ARGs.

Plasmid DNA/ARGs were less readily broken down than genomic DNA.

The Bioanalyzer methodology effectively documented damage incurred to DNA.

关键词： Antibiotic resistance Antibiotic resistance genes (ARGs) Extracellular DNA/ARGs Chlorination

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Decellularized extracellular matrix mediates tissue construction and regeneration

《医学前沿（英文）》 2022年第16卷第1期页码 56-82 doi: 10.1007/s11684-021-0900-3

摘要： Contributing to organ formation and tissue regeneration, extracellular matrix (ECM) constituents provide tissue with three-dimensional (3D) structural integrity and cellular-function regulation. Containing the crucial traits of the cellular microenvironment, ECM substitutes mediate cell–matrix interactions to prompt stem-cell proliferation and differentiation for 3D organoid construction in vitro or tissue regeneration in vivo. However, these ECMs are often applied generically and have yet to be extensively developed for specific cell types in 3D cultures. Cultured cells also produce rich ECM, particularly stromal cells. Cellular ECM improves 3D culture development in vitro and tissue remodeling during wound healing after implantation into the host as well. Gaining better insight into ECM derived from either tissue or cells that regulate 3D tissue reconstruction or organ regeneration helps us to select, produce, and implant the most suitable ECM and thus promote 3D organoid culture and tissue remodeling for in vivo regeneration. Overall, the decellularization methodologies and tissue/cell-derived ECM as scaffolds or cellular-growth supplements used in cell propagation and differentiation for 3D tissue culture in vitro are discussed. Moreover, current preclinical applications by which ECM components modulate the wound-healing process are reviewed.

关键词： decellularized extracellular matrix 3D culture organoids tissue repair

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Biosorption of Cu(II) to extracellular polymeric substances (EPS) from

Xiangliang PAN, Jing LIU, Wenjuan SONG, Daoyong ZHANG

《环境科学与工程前沿（英文）》 2012年第6卷第4期页码 493-497 doi: 10.1007/s11783-012-0416-9

摘要： Biosorption of extracellular polymeric substances (EPS) from sp. (cyanobacterium) with Cu(II) was investigated using fluorescence spectroscopy. Three fluorescence peaks were found in the excitation-emission matrix (EEM) fluorescence spectra of EPS. Fluorescence of peak A (Ex/Em= 275/452 nm) and peak C (Ex/Em= 350/452 nm) were originated from humic-like substances and fluorescence of peak B (Ex/Em= 275/338 nm) was attributed to protein-like substances. Fluorescence of peaks A, B, and C could be quenched by Cu(II). The effective quenching constants (lg K ) were 2.8–5.84 for peak A, 6.4–9.24 for peak B, and 3.48–6.68 for peak C, respectively. The values of lg K showed a decreasing trend with increasing temperature, indicating that the quenching processes were static in nature. The binding constants (lg K ) followed the order of peak A>peak B>peak C, implying that the humic-like substances in EPS have greater Cu(II) binding capacity than the protein-like substances. The binding site number, , in EPS-Cu(II) complexes for peaks A, B, and C was less than 1. This suggests the negative cooperativity between multiple binding sites and the presence of more than one Cu binding site.

关键词： biosorption conditional binding constant extracellular polymeric substances (EPS) fluorescence quenching

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ARGs-OAP v3.0——抗生素耐药基因数据库的筛选和分析流程优化 Article

Xiaole Yin, Xiawan Zheng, Liguan Li, An-Ni Zhang, Xiao-Tao Jiang, Tong Zhang

《工程（英文）》 2023年第27卷第8期页码 234-241 doi: 10.1016/j.eng.2022.10.011

摘要：

Antibiotic resistance, which is encoded by antibiotic-resistance genes (ARGs), has proliferated to become a growing threat to public health around the world. With technical advances, especially in the popularization of metagenomic sequencing, scientists have gained the ability to decipher the profiles of ARGs in diverse samples with high accuracy at an accelerated speed. To analyze thousands of ARGs in a highthroughput way, standardized and integrated pipelines are needed. The new version (v3.0) of the widely used ARGs online analysis pipeline (ARGs-OAP) has made significant improvements to both the reference database—the structured ARGs (SARG) database—and the integrated analysis pipeline. SARG has been enhanced with sequence curation to improve annotation reliability, incorporate emerging resistance genotypes, and determine rigorous mechanism classification. The database has been further organized and visualized online in the format of a tree-like structure with a dictionary. It has also been divided into sub-databases for different application scenarios. In addition, the ARGs-OAP has been improved with adjusted quantification methods, simplified tool implementation, and multiple functions with userdefined reference databases. Moreover, the online platform now provides a diverse biostatistical analysis workflow with visualization packages for the efficient interpretation of ARG profiles. The ARGs-OAP v3.0 with an improved database and analysis pipeline will benefit academia, governmental management, and consultation regarding risk assessment of the environmental prevalence of ARGs.

关键词： SARG database ARGs-OAP Antibiotic-resistance genes Environmental metagenome Quantification

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Enhancement of extracellular Cr(VI) reduction for anammox recovery using hydrazine: performance, pathways

《环境科学与工程前沿（英文）》 2023年第17卷第9期 doi: 10.1007/s11783-023-1715-z

摘要：

● N₂H₄ addition enhanced and recovered anammox performance under Cr(VI) stress.

关键词： Extracellular Cr(VI) reduction Electron transfer Anammox Hydrazine Cr(VI) inhibition

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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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Contributions of adsorption, bioreduction and desorption to uranium immobilization by extracellular polymeric

《环境科学与工程前沿（英文）》 2023年第17卷第9期 doi: 10.1007/s11783-023-1707-z

摘要：

● EPS immobilizes U(VI) via adsorption, bioreduction and desorption.

关键词： Adsorption Bioreduction Desorption Kinetics Isotherm Uranium

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Mechanisms behind the accelerated extracellular electron transfer in

Feng ZHANG,Shengsong YU,Jie LI,Wenwei LI,Hanqing YU

《环境科学与工程前沿（英文）》 2016年第10卷第3期页码 531-538 doi: 10.1007/s11783-015-0793-y

摘要： Modification of electrode surface with carboxylic acid terminated alkanethiol self-assembled monolayers (SAMs) has been found to be an effective approach to improve the extracellular electron transfer (EET) of electrochemically active bacteria (EAB) on electrode surface, but the underlying mechanism behind such enhanced EET remains unclear. In this work, the gold electrodes modified by mercapto-acetic acid and mercapto-ethylamine (Au-COOH, Au-NH ) were used as anodes in microbial electrolysis cells (MECs) inoculated with DL-1, and their electrochemical performance and the bacteria-electrode interactions were investigated. Results showed that the redox reaction occurred on the Au-NH with a higher rate and a lower resistance than that on the Au or the Au-COOH. Both the MECs with the Au-COOH and Au-NH anodes exhibited a higher current density than that with a bare Au anode. The biofilm formed on the Au-COOH was denser than that on bare Au, while the biofilm on the Au-NH had a greater thickness, suggesting a critical role of direct EET in this system. This work suggests that functional groups such as –COOH and-NH could promote electrode performance by accelerating the direct EET of EAB on electrode surface.

关键词： biofilm extracellular electron transfer (EET) Geobacter sulfurreducens DL-1 gold self-assembled monolayers

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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