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Journal Article 7

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2023 1

2022 2

2018 1

2017 2

2007 1

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microbe 2

-phenethyl 1

Biofilm 1

COVID-19 1

Chemical additives 1

Community structure 1

Extracellular polymeric substance (EPS) 1

HuMiX 1

Indigenous microorganisms 1

Microbe Corrosion 1

Microbiome 1

Microfluidics 1

Nitrobenzene 1

Organ-on-a-chip 1

Plant-microbe associated remediation 1

SARS-CoV-2 1

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Sulfate reducing bacteria (SRB) 1

catalytic activity 1

enantiomeric 1

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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

Frontiers of Chemical Science and Engineering 2007, Volume 1, Issue 4,   Pages 416-420 doi: 10.1007/s11705-007-0076-7

Abstract: Two microbe strains with excellent catalytic activity were obtained.

Keywords： excellent catalytic     prochiral aromatic     enantiomeric     -phenethyl     catalytic activity    

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USING NUTRITIONAL STRATEGIES TO MITIGATE RUMINAL METHANE EMISSIONS FROM RUMINANTS

Frontiers of Agricultural Science and Engineering 2023, Volume 10, Issue 3,   Pages 390-402 doi: 10.15302/J-FASE-2023504

Abstract:

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

Keywords： 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

Frontiers of Agricultural Science and Engineering 2022, Volume 9, Issue 3,   Pages 344-355 doi: 10.15302/J-FASE-2022451

Abstract:

● Intercropping change soil bacterial communities in tea plantations.

Keywords： 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

Frontiers of Medicine 2022, Volume 16, Issue 2,   Pages 251-262 doi: 10.1007/s11684-021-0915-9

Abstract: 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.

Keywords： 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

Frontiers of Environmental Science & Engineering 2018, Volume 12, Issue 1, doi: 10.1007/s11783-018-1016-0

Abstract: 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 .

Keywords： 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

Frontiers of Environmental Science & Engineering 2017, Volume 11, Issue 2, doi: 10.1007/s11783-017-0917-7

Abstract: 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.

Keywords： Sulfate reducing bacteria (SRB)     Chemical additives     Biofilm     Extracellular polymeric substance (EPS)     Microbe    

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Engineering Solutions for Representative Models of the Gastrointestinal Human-Microbe Interface

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

Engineering 2017, Volume 3, Issue 1,   Pages 60-65 doi: 10.1016/J.ENG.2017.01.011

Abstract:

Host-microbe interactions at the gastrointestinal interface have emerged as a key component in theHuMiX presents a novel and robust means to study the molecular interactions at the host-microbe interfaceobtained using the platform and highlight its potential to greatly enhance our understanding of host-microbe

Keywords： Microbiome     Microfluidics     Organ-on-a-chip     HuMiX    

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Title Author Date Type Operation

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

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

Journal Article

USING NUTRITIONAL STRATEGIES TO MITIGATE RUMINAL METHANE EMISSIONS FROM RUMINANTS

Journal Article

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

Journal Article

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

Journal Article

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

Journal Article

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

Journal Article

Engineering Solutions for Representative Models of the Gastrointestinal Human-Microbe Interface

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

Journal Article