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Isolation of microbe for asymmetric reduction of prochiral aromatic ketone and its reaction characters

YANG Zhonghua, WANG Yu, WANG Guanghui, ZENG Rong, YAO Shanjing

《化学科学与工程前沿（英文）》 2007年 第1卷 第4期   页码 416-420 doi: 10.1007/s11705-007-0076-7

摘要： The favorable microbes for the asymmetric reduction of prochiral aromatic ketones was isolated from soil using acetophenone as the sole carbon source, when the asymmetric reduction of acetophenone (ACP) to chiral ?-phenethyl alcohol (PEA) was chosen as the model reaction. Two microbe strains with excellent catalytic activity were obtained. They were and identified by bacteria identification. The product of the asymmetric reduction of ACP catalyzed by was mainly R-PEA and that by was mainly S-PEA. The yield and enantiomeric excesses (e.e.) could respectively reach 75% and 90% for , and 80% and 70% for , much higher than those catalyzed by baker s yeast.

关键词： excellent catalytic     prochiral aromatic     enantiomeric     -phenethyl     catalytic activity    

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USING NUTRITIONAL STRATEGIES TO MITIGATE RUMINAL METHANE EMISSIONS FROM RUMINANTS

《农业科学与工程前沿（英文）》   页码 390-402 doi: 10.15302/J-FASE-2023504

摘要：

● Microbial fermentation in the rumen is a main source of methane emissions.

关键词： nutritional strategy     mitigation     microbe     methane     ruminant    

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INTERCROPPING TEA PLANTATIONS WITH SOYBEAN AND RAPESEED ENHANCES NITROGEN FIXATION THROUGH SHIFTS IN SOIL MICROBIAL COMMUNITIES

《农业科学与工程前沿（英文）》 2022年 第9卷 第3期   页码 344-355 doi: 10.15302/J-FASE-2022451

摘要：

● Intercropping change soil bacterial communities in tea plantations.

关键词： intercropping     rapeseed     soil microbe     soybean     tea garden    

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PathogenTrack and Yeskit: tools for identifying intracellular pathogens from single-cell RNA-sequencing datasets as illustrated by application to COVID-19

《医学前沿（英文）》 2022年 第16卷 第2期   页码 251-262 doi: 10.1007/s11684-021-0915-9

摘要： Pathogenic microbes can induce cellular dysfunction, immune response, and cause infectious disease and other diseases including cancers. However, the cellular distributions of pathogens and their impact on host cells remain rarely explored due to the limited methods. Taking advantage of single-cell RNA-sequencing (scRNA-seq) analysis, we can assess the transcriptomic features at the single-cell level. Still, the tools used to interpret pathogens (such as viruses, bacteria, and fungi) at the single-cell level remain to be explored. Here, we introduced PathogenTrack, a python-based computational pipeline that uses unmapped scRNA-seq data to identify intracellular pathogens at the single-cell level. In addition, we established an R package named Yeskit to import, integrate, analyze, and interpret pathogen abundance and transcriptomic features in host cells. Robustness of these tools has been tested on various real and simulated scRNA-seq datasets. PathogenTrack is competitive to the state-of-the-art tools such as Viral-Track, and the first tools for identifying bacteria at the single-cell level. Using the raw data of bronchoalveolar lavage fluid samples (BALF) from COVID-19 patients in the SRA database, we found the SARS-CoV-2 virus exists in multiple cell types including epithelial cells and macrophages. SARS-CoV-2-positive neutrophils showed increased expression of genes related to type I interferon pathway and antigen presenting module. Additionally, we observed the Haemophilus parahaemolyticus in some macrophage and epithelial cells, indicating a co-infection of the bacterium in some severe cases of COVID-19. The PathogenTrack pipeline and the Yeskit package are publicly available at GitHub.

关键词： scRNA-seq     intracellular pathogen     microbe     COVID-19     SARS-CoV-2    

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The greater roles of indigenous microorganisms in removing nitrobenzene from sediment compared with the exogenous

Xiangqun Chi, Yingying Zhang, Daosheng Wang, Feihua Wang, Wei Liang

《环境科学与工程前沿（英文）》 2018年 第12卷 第1期 doi: 10.1007/s11783-018-1016-0

摘要： The feasibility of using -JS45 system in removing nitrobenzene from sediments was conducted. However, it was observed that nitrobenzene degraded rapidly and was removed completely within 20 days in native sediments, raising the possibility that indigenous microorganisms may play important roles in nitrobenzene degradation. Consequently, this study aimed to verify this possibility and investigate the potential nitrobenzene degraders among indigenous microorganisms in sediments. The abundance of inoculated strain JS45 and indigenous bacteria in sediments was quantified using real-time polymerase chain reaction. Furthermore, community structure of the indigenous bacteria was analyzed through high throughput sequencing based on Illumina MiSeq platform. The results showed that indigenous bacteria in native sediments were abundant, approximately 10 CFU/g dry weight, which is about six orders of magnitude higher than that in fertile soils. In addition, the levels of indigenous ( , , , and ) and ( , , , , and ) increased significantly during nitrobenzene removal. Their quantities sharply decreased after nitrobenzene was removed completely, except for and . Based on the results, it can be concluded that indigenous microorganisms including and can have great potential for removing nitrobenzene from sediments. Although . - JS45 system was set up in an attempt to eliminate nitrobenzene from sediments, and the system did not meet the expectation. The findings still provide valuable information on enhancing nitrobenzene removal by optimizing the sediment conditions for better growth of indigenous and .

关键词： Community structure     Indigenous microorganisms     Nitrobenzene     Plant-microbe associated remediation     Sediment    

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Chemical additives affect sulfate reducing bacteria biofilm properties adsorbed on stainless steel 316L surface in circulating cooling water system

Yu Qi,Jin Li,Rui Liang,Sitong Ji,Jianxiang Li,Meng Liu

《环境科学与工程前沿（英文）》 2017年 第11卷 第2期 doi: 10.1007/s11783-017-0917-7

摘要： There are more polysaccharides than proteins in EPS on SS316L surface. NaClO cuts down more protein, while 1227 reduced more polysaccharides in EPS. HEDP slightly eased the corrosion, NaClO and 1227 inhibited the microbial corrosion. NaClO still performed pitting corrosion properties to some extent. 1227 changed the C:O and NaClO decreased the amidogen in SS316L surface film. This paper studied the biofilm properties and corrosion behavior of sulfate reducing bacteria (SRB) on stainless steel 316L (SS316L) surface in circulating cooling water system with and without additives including hydroxy ethyl fork phosphonic acid (HEDP), dodecyl dimethyl benzyl ammonium chlotide (1227) and NaClO. Biochemical technique, electrochemical technology, X-ray photoelectron spectroscopy (XPS) and scanning electron microscope (SEM) were used. The results show that the extracellular polymeric substance (EPS) in biofilm attached on the SS316L surface mainly contain proteins and polysaccharides, the contents are 98 ug·cm and 635ug·cm , respectively. The polysaccharides were cut by 1227 about 80%, while 55% by NaClO. The proteins were reduced by NaClO about 53%, while only 30% by 1227. The potentiodynamic polarization shows that the corrosion potential of SS316L was enhanced from −0.495 V to −0.390 V by the chemical additives, delaying the occurrence of the corrosion. And the corrosion rate was also reduced from 5.19 × 10 mm·a to 2.42 × 10 mm·a . But NaClO still caused pitting corrosion after sterilizing the bacteria, while 1227 can form a protective film on the surface of SS316L. Though HEDP contribute to the bacteria activity, it can enhance the breakdown potential. XPS results confirmed that 1227 can change the value of C:O in the biofilm attached on metal surface, and NaClO can eliminate the existence of amidogen. This study would provide some recommendations for the selection of chemical additives in the thermal power plant.

关键词： Sulfate reducing bacteria (SRB)     Chemical additives     Biofilm     Extracellular polymeric substance (EPS)     Microbe Corrosion    

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人体胃肠道–菌群相互作用的工程学研究模型

Marc Mac Giolla Eain, Joanna Baginska, Kacy Greenhalgh, Joëlle V. Fritz, Frederic Zenhausern, Paul Wilmes

《工程（英文）》 2017年 第3卷 第1期   页码 60-65 doi: 10.1016/J.ENG.2017.01.011

摘要：

研究宿主–胃肠道微生物的相互作用已经成为管理人类健康和疾病的关键组成部分。微生理系统的发展正在为研究人员提供前所未有的对于这种复杂关系的获取和理解。这些系统结合了微型工程、微流体和细胞培养的优点，来创建人类肠道中普遍存在的环境条件。在这里我们提出的HuMiX(人类微生物交联对话) 平台，是一个利用这种多学科方法提供具有代表性的人体胃肠道的体外模型系统，用于研究宿主–微生物分子的相互作用。我们总结了使用该平台获得的概念验证结果，强调其对于大大增强我们对宿主–微生物相互作用了解的潜力，且其可能对药物、食品和营养以及医疗保健行业产生的巨大影响。同时讨论了这些技术面临的一些关键问题和挑战。

关键词： 微生物     微流体     肠道芯片     HuMiX    

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标题 作者 时间 类型 操作

Isolation of microbe for asymmetric reduction of prochiral aromatic ketone and its reaction characters

YANG Zhonghua, WANG Yu, WANG Guanghui, ZENG Rong, YAO Shanjing

期刊论文

USING NUTRITIONAL STRATEGIES TO MITIGATE RUMINAL METHANE EMISSIONS FROM RUMINANTS

期刊论文

INTERCROPPING TEA PLANTATIONS WITH SOYBEAN AND RAPESEED ENHANCES NITROGEN FIXATION THROUGH SHIFTS IN SOIL MICROBIAL COMMUNITIES

期刊论文

PathogenTrack and Yeskit: tools for identifying intracellular pathogens from single-cell RNA-sequencing datasets as illustrated by application to COVID-19

期刊论文

The greater roles of indigenous microorganisms in removing nitrobenzene from sediment compared with the exogenous

Xiangqun Chi, Yingying Zhang, Daosheng Wang, Feihua Wang, Wei Liang

期刊论文

Chemical additives affect sulfate reducing bacteria biofilm properties adsorbed on stainless steel 316L surface in circulating cooling water system

Yu Qi,Jin Li,Rui Liang,Sitong Ji,Jianxiang Li,Meng Liu

期刊论文

人体胃肠道–菌群相互作用的工程学研究模型

Marc Mac Giolla Eain, Joanna Baginska, Kacy Greenhalgh, Joëlle V. Fritz, Frederic Zenhausern, Paul Wilmes

期刊论文