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Current molecular biologic techniques for characterizing environmental microbial community

Dawen GAO, Yu TAO

《环境科学与工程前沿（英文）》 2012年 第6卷 第1期   页码 82-97 doi: 10.1007/s11783-011-0306-6

摘要： Microbes are vital to the earth because of their enormous numbers and instinct function maintaining the natural balance. Since the microbiology was applied in environmental science and engineering more than a century ago, researchers desire for more and more information concerning the microbial spatio-temporal variations in almost every fields from contaminated soil to wastewater treatment plant (WWTP). For the past 30 years, molecular biologic techniques explored for environmental microbial community (EMC) have spanned a broad range of approaches to facilitate the researches with the assistance of computer science: faster, more accurate and more sensitive. In this feature article, we outlined several current and emerging molecular biologic techniques applied in detection of EMC, and presented and assessed in detail the application of three promising tools.

关键词： molecular biological technique     microbial community     denaturing gradient gel electrophoresis (DGGE)     terminal restriction fragment length polymorphism (T-RFLP)     environmental applications    

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Influences and mechanisms of nanofullerene on the horizontal transfer of plasmid-encoded antibiotic resistance genes between

Qingkun Ji, Caihong Zhang, Dan Li

《环境科学与工程前沿（英文）》 2020年 第14卷 第6期 doi: 10.1007/s11783-020-1287-0

摘要： Abstract • Sub-inhibitory levels of nC60 promote conjugative transfer of ARGs. • nC60 can induce ROS generation, oxidative stress and SOS response. • nC60 can increase cell membrane permeability and alter gene expression. • Results provide evidence of nC60 promoting antibiotic resistance dissemination. The spread and development of antibiotic resistance globally have led to severe public health problems. It has been shown that some non-antibiotic substances can also promote the diffusion and spread of antibiotic resistance genes (ARGs). Nanofullerene (nC60) is a type of nanomaterial widely used around the world, and some studies have discovered both the biological toxicity and environmental toxicity of nC60. In this study, cellular and molecular biology techniques were employed to investigate the influences of nC60 at sub-minimum inhibitory concentrations (sub-MICs) on the conjugation of ARGs between the E. coli strains. Compared with the control group, nC60 significantly increased the conjugation rates of ARGs by 1.32‒10.82 folds within the concentration range of 7.03‒1800 mg/L. This study further explored the mechanism of this phenomenon, finding that sub-MICs of nC60 could induce the production of reactive oxygen species (ROS), trigger SOS-response and oxidative stress, affect the expression of outer membrane proteins (OMPs) genes, increase membrane permeability, and thus promote the occurrence of conjugation. This research enriches our understanding of the environmental toxicity of nC60, raises our risk awareness toward nC60, and may promote the more rational employment of nC60 materials.

关键词： Nanofullerene     Sub-minimum inhibitory concentrations     Antibiotic resistance genes     Conjugation     Molecular biological techniques    

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生物检测及分子诊断高端装备的研制及应用

彭年才,李 磊,李 政,苗保刚,李 明,赵 垚,蒋庄德

《中国工程科学》 2013年 第15卷 第1期   页码 57-62

摘要：

以生物检测与分子诊断技术发展为背景，总结了团队在医学诊断、疾控、食品安全、检疫检验、生物学医学科学研究等领域的分子诊断高端装备的研制情况，重点介绍了实时荧光定量聚合酶链式反应（PCR）分子诊断仪关键技术的研发及仪器工程化技术、检测性能的验证和在社会发展重点领域中的成功应用，手持式腺嘌呤核苷三磷酸（ATP）生物发光法细菌快速检测仪的研发与应用，以及后续的全自动核酸定量检测与高分辨分析设备研制。

关键词： 生物检测     分子诊断     实时荧光定量PCR     ATP荧光检测    

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Machinability of ultrasonic vibration-assisted micro-grinding in biological bone using nanolubricant

《机械工程前沿（英文）》 2023年 第18卷 第1期 doi: 10.1007/s11465-022-0717-z

摘要： Bone grinding is an essential and vital procedure in most surgical operations. Currently, the insufficient cooling capacity of dry grinding, poor visibility of drip irrigation surgery area, and large grinding force leading to high grinding temperature are the technical bottlenecks of micro-grinding. A new micro-grinding process called ultrasonic vibration-assisted nanoparticle jet mist cooling (U-NJMC) is innovatively proposed to solve the technical problem. It combines the advantages of ultrasonic vibration (UV) and nanoparticle jet mist cooling (NJMC). Notwithstanding, the combined effect of multi parameter collaborative of U-NJMC on cooling has not been investigated. The grinding force, friction coefficient, specific grinding energy, and grinding temperature under dry, drip irrigation, UV, minimum quantity lubrication (MQL), NJMC, and U-NJMC micro-grinding were compared and analyzed. Results showed that the minimum normal grinding force and tangential grinding force of U-NJMC micro-grinding were 1.39 and 0.32 N, which were 75.1% and 82.9% less than those in dry grinding, respectively. The minimum friction coefficient and specific grinding energy were achieved using U-NJMC. Compared with dry, drip, UV, MQL, and NJMC grinding, the friction coefficient of U-NJMC was decreased by 31.3%, 17.0%, 19.0%, 9.8%, and 12.5%, respectively, and the specific grinding energy was decreased by 83.0%, 72.7%, 77.8%, 52.3%, and 64.7%, respectively. Compared with UV or NJMC alone, the grinding temperature of U-NJMC was decreased by 33.5% and 10.0%, respectively. These results showed that U-NJMC provides a novel approach for clinical surgical micro-grinding of biological bone.

关键词： micro-grinding     biological bone     ultrasonic vibration (UV)     nanoparticle jet mist cooling (NJMC)     grinding force     grinding temperature    

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Surface modification techniques of membranes to improve their antifouling characteristics: recent advancements

《化学科学与工程前沿（英文）》 2023年 第17卷 第12期   页码 1837-1865 doi: 10.1007/s11705-023-2347-3

摘要： Surface modification techniques of membranes to improve their antifouling characteristics: recent advancements and developments

关键词： Surface modification techniques    

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Microorganism-derived biological macromolecules for tissue engineering

《医学前沿（英文）》 2022年 第16卷 第3期   页码 358-377 doi: 10.1007/s11684-021-0903-0

摘要： According to literature, certain microorganism productions mediate biological effects. However, their beneficial characteristics remain unclear. Nowadays, scientists concentrate on obtaining natural materials from live creatures as new sources to produce innovative smart biomaterials for increasing tissue reconstruction in tissue engineering and regenerative medicine. The present review aims to introduce microorganism-derived biological macromolecules, such as pullulan, alginate, dextran, curdlan, and hyaluronic acid, and their available sources for tissue engineering. Growing evidence indicates that these materials can be used as biological material in scaffolds to enhance regeneration in damaged tissues and contribute to cosmetic and dermatological applications. These natural-based materials are attractive in pharmaceutical, regenerative medicine, and biomedical applications. This study provides a detailed overview of natural-based biomaterials, their chemical and physical properties, and new directions for future research and therapeutic applications.

关键词： biological macromolecules     regenerative medicine     tissue engineering     exopolysaccharide     carbohydrate    

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Low intensity ultrasound stimulates biological activity of aerobic activated sludge

LIU Hong, YAN Yixin, WANG Wenyan, YU Yongyong

《环境科学与工程前沿（英文）》 2007年 第1卷 第1期   页码 67-72 doi: 10.1007/s11783-007-0013-5

摘要： This work aims to explore a procedure to improve biological wastewater treatment efficiency using low intensity ultrasound. The aerobic activated sludge from a municipal wastewater treatment plant was used as the experimental material. Oxygen uptake rate (OUR) of the activated sludge (AS) was determined to indicate the changes of AS activity stimulated by ultrasound at 35 kHz for 0 40 min with ultrasonic intensities of 0 1.2 W/cm. The highest OUR was observed at the ultrasonic intensity of 0.3 W/cm and an irradiation period of 10 min; more than 15% increase was achieved immediately after sonication. More significantly, the AS activity stimulated by ultrasound could last 24 h after sonication, and the AS activity achieved its peak value within 8 h after sonication, or nearly 100% higher than the initial level after sonication. Therefore, to improve the wastewater treatment efficiency of bioreactors, ultrasound with an intensity of 0.3 W/cm could be employed to irradiate a part of the AS in the bioreactor for 10 min every 8 h.

关键词： sonication     irradiation     kHz     treatment efficiency     AS activity    

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Biological conversion pathways of sulfate reduction ammonium oxidation in anammox consortia

Zhen Bi, Deqing Wanyan, Xiang Li, Yong Huang

《环境科学与工程前沿（英文）》 2020年 第14卷 第3期 doi: 10.1007/s11783-019-1217-1

摘要： The SRAO phenomena tended to occur only under certain conditions. High amount of biomass and non-anaerobic condition is requirement for SRAO. Anammox bacteria cannot oxidize ammonium with sulfate as electron acceptor. AOB and AnAOB are mainly responsible for ammonium conversion. Heterotrophic sulfate reduction mainly contributed to sulfate conversion. For over two decades, sulfate reduction with ammonium oxidation (SRAO) had been reported from laboratory experiments. SRAO was considered an autotrophic process mediated by anammox bacteria, in which ammonium as electron donor was oxidized by the electron acceptor sulfate. This process had been attributed to observed transformations of nitrogenous and sulfurous compounds in natural environments. Results obtained differed largely for the conversion mole ratios (ammonium/sulfate), and even the intermediate and final products of sulfate reduction. Thus, the hypothesis of biological conversion pathways of ammonium and sulfate in anammox consortia is implausible. In this study, continuous reactor experiments (with working volume of 3.8L) and batch tests were conducted under normal anaerobic (0.2≤DO<0.5 mg/L) / strict anaerobic (DO<0.2 mg/L) conditions with different biomass proportions to verify the SRAO phenomena and identify possible pathways behind substrate conversion. Key findings were that SRAO occurred only in cases of high amounts of inoculant biomass under normal anaerobic condition, while absent under strict anaerobic conditions for same anammox consortia. Mass balance and stoichiometry were checked based on experimental results and the thermodynamics proposed by previous studies were critically discussed. Thus anammox bacteria do not possess the ability to oxidize ammonium with sulfate as electron acceptor and the assumed SRAO could, in fact, be a combination of aerobic ammonium oxidation, anammox and heterotrophic sulfate reduction processes.

关键词： Anammox bacteria     Autotrophic     Biological conversion     Sulfate reducing ammonium oxidation (SRAO)    

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Special issue on “Molecular Sensors and Molecular Logic Gates”

Luling Wu , Tony D. James

《化学科学与工程前沿（英文）》 2022年 第16卷 第1期   页码 1-3 doi: 10.1007/s11705-021-2134-y

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Design of bio-oil additives via molecular signature descriptors using a multi-stage computer-aided molecular

《化学科学与工程前沿（英文）》 2022年 第16卷 第2期   页码 168-182 doi: 10.1007/s11705-021-2056-8

摘要： Direct application of bio-oil from fast pyrolysis as a fuel has remained a challenge due to its undesirable attributes such as low heating value, high viscosity, high corrosiveness and storage instability. Solvent addition is a simple method for circumventing these disadvantages to allow further processing and storage. In this work, computer-aided molecular design tools were developed to design optimal solvents to upgrade bio-oil whilst having low environmental impact. Firstly, target solvent requirements were translated into measurable physical properties. As different property prediction models consist different levels of structural information, molecular signature descriptor was used as a common platform to formulate the design problem. Because of the differences in the required structural information of different property prediction models, signatures of different heights were needed in formulating the design problem. Due to the combinatorial nature of higher-order signatures, the complexity of a computer-aided molecular design problem increases with the height of signatures. Thus, a multi-stage framework was developed by developing consistency rules that restrict the number of higher-order signatures. Finally, phase stability analysis was conducted to evaluate the stability of the solvent-oil blend. As a result, optimal solvents that improve the solvent-oil blend properties while displaying low environmental impact were identified.

关键词： computer-aided molecular design     bio-oil additives     molecular signature descriptor    

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Progress on molecular biomarkers and classification of malignant gliomas

null

《医学前沿（英文）》 2013年 第7卷 第2期   页码 150-156 doi: 10.1007/s11684-013-0267-1

摘要：

Gliomas are the most common primary intracranial tumors in adults. Anaplastic gliomas (WHO grade III) and glioblastomas (WHO grade IV) represent the major groups of malignant gliomas in the brain. Several diagnostic, predictive, and prognostic biomarkers for malignant gliomas have been reported over the last few decades, and these markers have made great contributions to the accuracy of diagnosis, therapeutic decision making, and prognosis of patients. However, heterogeneity in patient outcomes may still be observed, which highlights the insufficiency of a classification system based purely on histopathology. Great efforts have been made to incorporate new information about the molecular landscape of gliomas into novel classifications that may potentially guide treatment. In this review, we summarize three distinctive biomarkers, three most commonly altered pathways, and three classifications based on microarray data in malignant gliomas.

关键词： malignant glioma     molecular biomarker     IDH1     MGMT     molecular classification    

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Molecular classification and molecular targeted therapy of cancer

null

《医学前沿（英文）》 2013年 第7卷 第2期   页码 147-149 doi: 10.1007/s11684-013-0274-2

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Overlooked nitrogen-cycling microorganisms in biological wastewater treatment

《环境科学与工程前沿（英文）》 2021年 第15卷 第6期 doi: 10.1007/s11783-021-1426-2

摘要：

• AOA and comammox bacteria can be more abundant and active than AOB/NOB at WWTPs.

关键词： Ammonia oxidizing archaea (AOA)     Complete ammonia oxidizing (comammox) bacteria     Dissimilatory nitrate reduction to ammonium (DNRA) bacteria     Nitrate/nitrite-dependent anaerobic methane oxidizing (NOx-DAMO) microorganisms     Engineering application    

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Mechanical behavior and semiempirical force model of aerospace aluminum alloy milling using nano biological

《机械工程前沿（英文）》 2023年 第18卷 第1期 doi: 10.1007/s11465-022-0720-4

摘要： Aerospace aluminum alloy is the most used structural material for rockets, aircraft, spacecraft, and space stations. The deterioration of surface integrity of dry machining and the insufficient heat transfer capacity of minimal quantity lubrication have become the bottleneck of lubrication and heat dissipation of aerospace aluminum alloy. However, the excellent thermal conductivity and tribological properties of nanofluids are expected to fill this gap. The traditional milling force models are mainly based on empirical models and finite element simulations, which are insufficient to guide industrial manufacturing. In this study, the milling force of the integral end milling cutter is deduced by force analysis of the milling cutter element and numerical simulation. The instantaneous milling force model of the integral end milling cutter is established under the condition of dry and nanofluid minimal quantity lubrication (NMQL) based on the dual mechanism of the shear effect on the rake face of the milling cutter and the plow cutting effect on the flank surface. A single factor experiment is designed to introduce NMQL and the milling feed factor into the instantaneous milling force coefficient. The average absolute errors in the prediction of milling forces for the NMQL are 13.3%, 2.3%, and 7.6% in the x-, y-, and z-direction, respectively. Compared with the milling forces obtained by dry milling, those by NMQL decrease by 21.4%, 17.7%, and 18.5% in the x-, y-, and z-direction, respectively.

关键词： milling     force     nanofluid minimum quantity lubrication     aerospace aluminum alloy     nano biological lubricant    

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ROOT EXUDATES FROM CANOLA EXHIBIT BIOLOGICAL NITRIFICATION INHIBITION AND ARE EFFECTIVE IN INHIBITING

《农业科学与工程前沿（英文）》 2022年 第9卷 第2期   页码 177-186 doi: 10.15302/J-FASE-2021421

摘要：

A range of plant species produce root exudates that inhibit ammonia-oxidizing microorganisms. This biological nitrification inhibition (BNI) capacity can decrease N loss and increase N uptake from the rhizosphere. This study sought evidence for the existence and magnitude of BNI capacity in canola ( Brassica napus). Seedlings of three canola cultivars, Brachiaria humidicola(BNI positive) and wheat ( Triticum aestivum) were grown in a hydroponic system. Root exudates were collected and their inhibition of the ammonia oxidizing bacterium, Nitrosospira multiformis, was tested. Subsequent pot experiments were used to test the inhibition of native nitrifying communities in soil. Root exudates from canola significantly reduced nitrification rates of both N. multiformis cultures and native soil microbial communities. The level of nitrification inhibition across the three cultivars was similar to the well-studied high-BNI species B. humidicola. BNI capacity of canola may have implications for the N dynamics in farming systems and the N uptake efficiency of crops in rotational farming systems. By reducing nitrification rates canola crops may decrease N losses, increase plant N uptake and encourage microbial N immobilization and subsequently increase the pool of organic N that is available for mineralization during the following cereal crops.

关键词： ammonia oxidizing microorganisms / biological nitrification inhibition / farming rotations / nitrogen cycling / nitrogen use efficiency    

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标题 作者 时间 类型 操作

Current molecular biologic techniques for characterizing environmental microbial community

Dawen GAO, Yu TAO

期刊论文

Influences and mechanisms of nanofullerene on the horizontal transfer of plasmid-encoded antibiotic resistance genes between

Qingkun Ji, Caihong Zhang, Dan Li

期刊论文

生物检测及分子诊断高端装备的研制及应用

彭年才,李 磊,李 政,苗保刚,李 明,赵 垚,蒋庄德

期刊论文

Machinability of ultrasonic vibration-assisted micro-grinding in biological bone using nanolubricant

期刊论文

Surface modification techniques of membranes to improve their antifouling characteristics: recent advancements

期刊论文

Microorganism-derived biological macromolecules for tissue engineering

期刊论文

Low intensity ultrasound stimulates biological activity of aerobic activated sludge

LIU Hong, YAN Yixin, WANG Wenyan, YU Yongyong

期刊论文

Biological conversion pathways of sulfate reduction ammonium oxidation in anammox consortia

Zhen Bi, Deqing Wanyan, Xiang Li, Yong Huang

期刊论文

Special issue on “Molecular Sensors and Molecular Logic Gates”

Luling Wu , Tony D. James

期刊论文

Design of bio-oil additives via molecular signature descriptors using a multi-stage computer-aided molecular

期刊论文

Progress on molecular biomarkers and classification of malignant gliomas

null

期刊论文

Molecular classification and molecular targeted therapy of cancer

null

期刊论文

Overlooked nitrogen-cycling microorganisms in biological wastewater treatment

期刊论文

Mechanical behavior and semiempirical force model of aerospace aluminum alloy milling using nano biological

期刊论文

ROOT EXUDATES FROM CANOLA EXHIBIT BIOLOGICAL NITRIFICATION INHIBITION AND ARE EFFECTIVE IN INHIBITING

期刊论文