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Development of pretreatment protocol for DNA extraction from biofilm attached to biologic activated carbon

Shuting ZHANG, Bo WEI, Xin YU, Bing LIU, Zhuoying WU, Li GU

《环境科学与工程前沿（英文）》 2010年 第4卷 第4期   页码 459-465 doi: 10.1007/s11783-010-0249-3

摘要： The biologic activated carbon (BAC) process is widely used in drinking water treatments. A comprehensive molecular analysis of the microbial community structure provides very helpful data to improve the reactor performance. However, the bottleneck of deoxyribonucleic acid (DNA) extraction from BAC attached biofilm has to be solved since the conventional procedure was unsuccessful due to firm biomass attachment and adsorption capacity of the BAC granules. In this study, five pretreatments were compared, and adding skim milk followed by ultrasonic vibration was proven to be the optimal choice. This protocol was further tested using the vertical BAC samples from the full-scale biofilter of Pinghu Water Plant. The results showed the DNA yielded a range of 40 μg·g BAC (dry weight) to over 100 μg·g BAC (dry weight), which were consistent with the biomass distribution. All results suggested that the final protocol could produce qualified genomic DNA as a template from the BAC filter for downstream molecular biology researches.

关键词： bacterial DNA extraction     biological activated carbon (BAC)     biofilm     water treatment     pretreatment protocol    

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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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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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结合基于滤纸的DNA提取技术和RPA-LFD检测技术对有毒植物钩吻进行快速鉴别

郑夏生, 安文丽, 姚晖, 徐江, 陈士林

《工程（英文）》 2021年 第7卷 第1期   页码 14-16 doi: 10.1016/j.eng.2020.02.012

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Entity and relation extraction with rule-guided dictionary as domain knowledge

《工程管理前沿（英文）》   页码 610-622 doi: 10.1007/s42524-022-0226-0

摘要： Entity and relation extraction is an indispensable part of domain knowledge graph construction, which can serve relevant knowledge needs in a specific domain, such as providing support for product research, sales, risk control, and domain hotspot analysis. The existing entity and relation extraction methods that depend on pretrained models have shown promising performance on open datasets. However, the performance of these methods degrades when they face domain-specific datasets. Entity extraction models treat characters as basic semantic units while ignoring known character dependency in specific domains. Relation extraction is based on the hypothesis that the relations hidden in sentences are unified, thereby neglecting that relations may be diverse in different entity tuples. To address the problems above, this paper first introduced prior knowledge composed of domain dictionaries to enhance characters’ dependence. Second, domain rules were built to eliminate noise in entity relations and promote potential entity relation extraction. Finally, experiments were designed to verify the effectiveness of our proposed methods. Experimental results on two domains, including laser industry and unmanned ship, showed the superiority of our methods. The F1 value on laser industry entity, unmanned ship entity, laser industry relation, and unmanned ship relation datasets is improved by +1%, +6%, +2%, and +1%, respectively. In addition, the extraction accuracy of entity relation triplet reaches 83% and 76% on laser industry entity pair and unmanned ship entity pair datasets, respectively.

关键词： entity extraction     relation extraction     prior knowledge     domain rule    

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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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Antibiotic resistome mostly relates to bacterial taxonomy along a suburban transmission chain

《环境科学与工程前沿（英文）》 2022年 第16卷 第3期 doi: 10.1007/s11783-021-1466-7

摘要：

• The α-diversities of resistome were lower in manure and compost than in soils.

关键词： Antibiotic resistance genes     Resistome     Bacterial taxonomy     Transmission chain    

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Characterization of bacterial communities during persistent fog and haze events in the Qingdao coastal

《环境科学与工程前沿（英文）》 2021年 第15卷 第3期 doi: 10.1007/s11783-020-1334-x

摘要：

• Light haze had little effect on bacterial communities.

关键词： Bacterial community     Persistent fog and haze     Particle size    

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Materials and surface engineering to control bacterial adhesion and biofilm formation: A review of recent

Huan GU, Dacheng REN

《化学科学与工程前沿（英文）》 2014年 第8卷 第1期   页码 20-33 doi: 10.1007/s11705-014-1412-3

摘要： Bacterial adhesion to surfaces and subsequent biofilm formation are a leading cause of chronic infections and biofouling. These processes are highly sensitive to environmental factors and present a challenge to research using traditional approaches with uncontrolled surfaces. Recent advances in materials research and surface engineering have brought exciting opportunities to pattern bacterial cell clusters and to obtain synthetic biofilms with well-controlled cell density and morphology of cell clusters. In this article, we will review the recent achievements in this field and comment on the future directions.

关键词： surface engineering     materials     bacterial adhesion     biofilm     control     review    

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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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标题 作者 时间 类型 操作

Development of pretreatment protocol for DNA extraction from biofilm attached to biologic activated carbon

Shuting ZHANG, Bo WEI, Xin YU, Bing LIU, Zhuoying WU, Li GU

期刊论文

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

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

Chao Yang, Wenjun Sun, Xiuwei Ao

期刊论文

结合基于滤纸的DNA提取技术和RPA-LFD检测技术对有毒植物钩吻进行快速鉴别

郑夏生, 安文丽, 姚晖, 徐江, 陈士林

期刊论文

Entity and relation extraction with rule-guided dictionary as domain knowledge

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

Antibiotic resistome mostly relates to bacterial taxonomy along a suburban transmission chain

期刊论文

Characterization of bacterial communities during persistent fog and haze events in the Qingdao coastal

期刊论文

Materials and surface engineering to control bacterial adhesion and biofilm formation: A review of recent

Huan GU, Dacheng REN

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

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

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

Shen YIN,Junyu MA,Wei SHEN

期刊论文