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Modified pretreatment method for total microbial DNA extraction from contaminated river sediment

Yun FANG,Meiying XU,Xingjuan CHEN,Guoping SUN,Jun GUO,Weimin WU,Xueduan LIU

《环境科学与工程前沿（英文）》 2015年 第9卷 第3期   页码 444-452 doi: 10.1007/s11783-014-0679-4

摘要： Extraction of high-quality microbial DNA from contaminated environmental samples is an essential step in microbial ecological study. Based on previously published methods for soil and sediment samples, a modified pretreatment method was developed for extracting microbial DNA from heavily contaminated river sediment samples via selection of optimal pretreatment parameters (i.e., reagent solution, reaction duration, and temperature). The pretreatment procedure involves washing the river sediment sample for three times with a solution containing 0.1 mol·L ethylene diamine tetraacetic acid (EDTA), 0.1 mol·L Tris (pH 8.0), 1.5 mol·L NaCl, 0.1 mol·L NaH PO , and Na HPO at 65°C with 180 r·min for 15 min to remove humic materials and heavy metals prior to the employment of standard DNA extraction procedures. We compared the results of standard procedure DNA extraction following pretreatment, without pretreatment, and with using a commercial PowerSoil DNA Isolation Kit. The results indicated that the pretreatment significantly improved the DNA quality based on DNA yield, DNA fragment length, and determination of prokaryotic diversity. Prokaryotic diversity exhibited in the DNA with the pretreatment was also considerably higher than that extracted with the PowerSoil DNA Isolation Kit only. The pretreatment method worked well even with a small amount of sediment sample (0.25 g or even lower). The method provides a novel, simple, cost-effective tool for DNA extraction for microbial community analysis in environmental monitoring and remediation processes.

关键词： river sediment     DNA extraction     contaminant     pretreatment     microbial community    

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Plant diversity reduces the effect of multiple heavy metal pollution on soil enzyme activities and microbial

Yang GAO, Chiyuan MIAO, Jun XIA, Liang MAO, Yafeng WANG, Pei ZHOU

《环境科学与工程前沿（英文）》 2012年 第6卷 第2期   页码 213-223 doi: 10.1007/s11783-011-0345-z

摘要： It is unclear whether certain plant species and plant diversity could reduce the impacts of multiple heavy metal pollution on soil microbial structure and soil enzyme activities. Random amplified polymorphic DNA (RAPD) was used to analyze the genetic diversity and microbial similarity in planted and unplanted soil under combined cadmium (Cd) and lead (Pb) pollution. A metal hyperaccumulator, , and a common plant, , were used in this research. The results showed that microorganism quantity in planted soil significantly increased, compared with that in unplanted soil with Cd and Pb pollution. The order of microbial community sensitivity in response to Cd and Pb stress was as follows: actinomycetes>bacteria>fungi. Respiration, phosphatase, urease and dehydrogenase activity were significantly inhibited due to Cd and Pb stress. Compared with unplanted soil, planted soils have frequently been reported to have higher rates of microbial activity due to the presence of additional surfaces for microbial colonization and organic compounds released by the plant roots. Two coexisting plants could increase microbe population and the activity of phosphatases, dehydrogenases and, in particular, ureases. Soil enzyme activity was higher in phytoremediated soil than in planted soil in this study. Heavy metal pollution decreased the richness of the soil microbial community, but plant diversity increased DNA sequence diversity and maintained DNA sequence diversity at high levels. The genetic polymorphism under heavy metal stress was higher in phytoremediated soil than in planted soil.

关键词： enzyme activity     soil DNA     microbial population     plant diversity     heavy metal    

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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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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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Hydrothermal carbonization of livestock mortality for the reduction of pathogens and microbially-derived DNA

Thomas F. Ducey, Jessica C. Collins, Kyoung S. Ro, Bryan L. Woodbury, D. Dee Griffin

《环境科学与工程前沿（英文）》 2017年 第11卷 第3期 doi: 10.1007/s11783-017-0930-x

摘要： Hydrothermal carbonization (HTC), utilizing high temperature and pressure, has the potential to treat agricultural waste via inactivating pathogens, antibiotic resistance genes (ARG), and contaminants of emerging concern (CEC) in a environmental and economical manner. Livestock mortality is one facet of agricultural waste that can pose a threat to the surrounding environment. While several methods are utilized to treat livestock mortality, there remains a paucity of data on the elimination of microbially-derived DNA in these treatment practices. This DNA, most notably ARGs, if it survives treatment can be reintroduced in agricultural environments where it could potentially be passed to pathogens, posing a risk to animal and human populations. HTC treatments have been successfully utilized for the treatment of CECs, however very little is understood on how ARGs survive HTC treatment. This study aims to fill this knowledge gap by examining the survivability of microbially-derived DNA in the HTC treatment of livestock mortality. We examined three treatment temperatures (100°C, 150°C, and 200°C) at autogenic pressures at three treatment times (30, 60, and 240 min). We examined the amplification of a plasmid-borne reporter gene carried by DH10B introduced to both beef bone and tissue. Results indicate that while all three temperatures, at all treatment times, were suitable for complete pathogen kill, only temperatures of 150°C and 200°C were sufficient for eliminating microbial DNA. These results serve as the basis for future potential HTC treatment recommendations for livestock mortality when considering the elimination of pathogens and ARGs.

关键词： High-temperature carbonization     Microbial DNA     Livestock mortality    

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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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Responses of microbial interactions to elevated salinity in activated sludge microbial community

《环境科学与工程前沿（英文）》 2023年 第17卷 第5期 doi: 10.1007/s11783-023-1660-x

摘要：

● Salinity led to the elevation of NAR over 99.72%.

关键词： Elevated salinity     Activated sludge system     Pollution removal     Microbial interactions     Competitive relationship    

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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    

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基于探针图的并行型图顶点着色DNA计算模型 Article

许进, 强小利, 张凯, 张成, 杨静

《工程（英文）》 2018年 第4卷 第1期   页码 61-77 doi: 10.1016/j.eng.2018.02.011

摘要：
目前DNA 计算机研究中遇到的最大瓶颈是解空间指数爆炸问题，即随着问题规模的增大，所需要作为信息处理“数据”的DNA分子呈指数级增大。本文提出了一种新颖的图顶点着色DNA计算模型，该模型正是围绕着如何克服解空间指数爆炸问题以及如何提高运行速度而设计的。本文以一个3-着色的61 个顶点的图为例，实验表明，99% 的非可行解在构建初始解空间时就被删除，并利用DNA 自组装和并行PCR 方法，通过识别、拼接以及组装等技术得到解。

关键词： DNA计算     图顶点着色问题     聚合酶链反应（PCR）    

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hydrophobic environment triggering reactive fluorescence probe to real-time monitor mitochondrial DNA

《化学科学与工程前沿（英文）》 2022年 第16卷 第1期   页码 92-102 doi: 10.1007/s11705-021-2063-9

摘要： Mitochondrial DNA has a special structure that is prone to damage resulting in many serious diseases, such as genetic diseases and cancers. Therefore, the rapid and specific monitoring of mitochondrial DNA damage is urgently needed for biological recognition. Herein, we constructed an in situ hydrophobic environment-triggering reactive fluorescence probe named MBI-CN. The fluorophore was 2-styrene-1H-benzo[d]imidazole, and malononitrile was introduced as a core into a molecule to initiate the hydrolysis reaction in the specific environment containing damaged mitochondrial DNA. In this design, MBI-CN conjugates to mitochondrial DNA without causing additional damages. Thus, MBI-CN can be hydrolyzed to generate MBI-CHO in an in situ hydrophobic environment with mitochondrial DNA damage. Meanwhile, MBI-CHO immediately emitted a significative fluorescence signal changes at 437 and 553 nm within 25 s for the damaged mitochondria DNA. Give that the specific and rapid response of MBI-CN does not cause additional damages to mitochondrial DNA, it is a potentially effective detection tool for the real-time monitoring of mitochondrial DNA damage during cell apoptosis and initial assessment of cell apoptosis.

关键词： hydrolysis reaction     mitochondrial DNA damage     in situ hydrophobic environment trigger     fluorescence probe     apoptosis    

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Bacterial inactivation, DNA damage, and faster ATP degradation induced by ultraviolet disinfection

Chao Yang, Wenjun Sun, Xiuwei Ao

《环境科学与工程前沿（英文）》 2020年 第14卷 第1期 doi: 10.1007/s11783-019-1192-6

摘要： • Long amplicon is more effective to test DNA damage induced by UV. • ATP in bacteria does not degrade instantly but does eventually after UV exposure. • After medium pressure UV exposure, ATP degraded faster. The efficacy of ultraviolet (UV) disinfection has been validated in numerous studies by using culture-based methods. However, the discovery of viable but non-culturable bacteria has necessitated the investigation of UV disinfection based on bacterial viability parameters. We used quantitative polymerase chain reaction (qPCR) to investigate DNA damage and evaluated adenosine triphosphate (ATP) to indicate bacterial viability. The results of qPCR effectively showed the DNA damage induced by UV when using longer gene amplicons, in that sufficiently long amplicons of both 16S and gadA indicated that the UV induced DNA damages. The copy concentrations of the long amplicons of 16S and gadA decreased by 2.38 log/mL and 1.88 log/mL, respectively, after exposure to 40 mJ/cm2 low-pressure UV. After UV exposure, the ATP level in the bacteria did not decrease instantly. Instead it decreased gradually at a rate that was positively related to the UV fluence. For low-pressure UV, this rate of decrease was slow, but for medium pressure UV, this rate of decrease was relatively high when the UV fluence reached 40 mJ/cm2. At the same UV fluence, the ATP level in the bacteria decreased at a faster rate after exposure to medium-pressure UV.

关键词： UV disinfection     DNA damage     qPCR     ATP    

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标题 作者 时间 类型 操作

Modified pretreatment method for total microbial DNA extraction from contaminated river sediment

Yun FANG,Meiying XU,Xingjuan CHEN,Guoping SUN,Jun GUO,Weimin WU,Xueduan LIU

期刊论文

Plant diversity reduces the effect of multiple heavy metal pollution on soil enzyme activities and microbial

Yang GAO, Chiyuan MIAO, Jun XIA, Liang MAO, Yafeng WANG, Pei ZHOU

期刊论文

工程化DNA材料构建DNA活字系统实现可持续的数据存储

巩子祎, 宋理富, 裴广胜, 董雨菲, 李炳志, 元英进

期刊论文

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

null

期刊论文

Functional role of ATM in the cellular response to DNA damage

Ming LIU, Wenxiang HU

期刊论文

Hydrothermal carbonization of livestock mortality for the reduction of pathogens and microbially-derived DNA

Thomas F. Ducey, Jessica C. Collins, Kyoung S. Ro, Bryan L. Woodbury, D. Dee Griffin

期刊论文

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

null

期刊论文

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

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

期刊论文

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

null

期刊论文

Responses of microbial interactions to elevated salinity in activated sludge microbial community

期刊论文

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

Shen YIN,Junyu MA,Wei SHEN

期刊论文

表征不同DNA高阶结构的单分子分析方法

刘泳麟, 边天元, 刘岩, 李治民, 裴羽丰, 宋杰

期刊论文

基于探针图的并行型图顶点着色DNA计算模型

许进, 强小利, 张凯, 张成, 杨静

期刊论文

hydrophobic environment triggering reactive fluorescence probe to real-time monitor mitochondrial DNA

期刊论文

Bacterial inactivation, DNA damage, and faster ATP degradation induced by ultraviolet disinfection

Chao Yang, Wenjun Sun, Xiuwei Ao

期刊论文