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PathogenTrack and Yeskit: tools for identifying intracellular pathogens from single-cell RNA-sequencing

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

Abstract: PathogenTrack, a python-based computational pipeline that uses unmapped scRNA-seq data to identify intracellularIn addition, we established an R package named Yeskit to import, integrate, analyze, and interpret pathogen

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

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Systems understanding of plant–pathogen interactions through genome-wide protein–protein interaction

Hong LI,Ziding ZHANG

Frontiers of Agricultural Science and Engineering 2016, Volume 3, Issue 2,   Pages 102-112 doi: 10.15302/J-FASE-2016100

Abstract: Plants are frequently affected by pathogen infections.(e.g., genomics, proteomics and transcriptomics) has provided a great opportunity to explore plant–pathogenThen, we focus on reviewing the progress in genome-wide PPI networks related to plant–pathogen interactions, including pathogen-centric PPI networks, plant-centric PPI networks and interspecies PPI networks betweenWe anticipate genome-wide PPI network analysis will provide a clearer understanding of plant–pathogen

Keywords： plant–pathogen interactions     systems biology     omics     plant immunity     protein–protein interaction     network    

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spp., foodborne pathogens threatening neonates and infants

Qiming CHEN, Yang ZHU, Zhen QIN, Yongjun QIU, Liming ZHAO

Frontiers of Agricultural Science and Engineering 2018, Volume 5, Issue 3,   Pages 330-339 doi: 10.15302/J-FASE-2018208

Abstract:

Cronobacter spp. (formerly Enterobacter sakazakii) are special foodborne pathogens. Cronobacter infection can cause necrotizing enterocolitis, sepsis and meningitis in all age groups, especially neonates and infants, with a high fatality of up to 80%, although the infection is rare. Outbreaks of Cronobacter infection are epidemiologically proven to be associated with contaminated powdered infant formula (PIF). Cronobacter spp. can resist dry environments and survive for a long period in food with low water activity. Therefore, Cronobacter spp. have become serious pathogens of neonates and infants, as well as in the dairy industry. In this review, we present the taxonomy, pathogenesis, resistance, detection and control of Cronobacter spp.

Keywords： desiccation resistance     pathogen control     pathogen detection     powdered infant formula    

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Intracellular Strain Evaluation-Based Oocyte Enucleation and Its Application in Robotic Cloning Article

Mingzhu Sun, Yaowei Liu, Maosheng Cui, Qili Zhao, Xiangfei Zhao, Yidi Zhang, Jingjing Huang, Guizhang Lu, Xin Zhao

Engineering 2023, Volume 24, Issue 5,   Pages 73-83 doi: 10.1016/j.eng.2022.04.016

Abstract: In this study, we proposed an intracellular strain evaluation-based oocyte enucleation method to reducepotential intracellular damage in SCNT.We first calculated the intracellular strain based on the intracellular velocity field and then usedthe intracellular strain as a criterion to improve the enucleation operation.In addition to the cloning technique, the intracellular strain evaluation-based enucleation method is

Keywords： Oocyte enucleation     Robotic cloning     Intracellular strain     Intracellular damage     Optical flow    

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Resveratrol reduces intracellular reactive oxygen species levels by inducing autophagy through the AMPK-mTOR

Jun Song, Yeping Huang, Wenjian Zheng, Jing Yan, Min Cheng, Ruxing Zhao, Li Chen, Cheng Hu, Weiping Jia

Frontiers of Medicine 2018, Volume 12, Issue 6,   Pages 697-706 doi: 10.1007/s11684-018-0655-7

Abstract: Reduction of intracellular oxidative stress may attenuate these pathogenic processes.Taken together, these data suggest that resveratrol prevents PA-induced intracellular ROS by autophagy

Keywords： resveratrol     reactive oxygen species     AMPK     mTOR     autophagy    

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Intracellular trehalose improves the survival of human red blood cells by freeze-drying

HE Hui, LIU Baolin, HUA Zezhao, LI Chuan, WU Zhengzheng

Frontiers in Energy 2007, Volume 1, Issue 1,   Pages 120-124 doi: 10.1007/s11708-007-0014-x

Abstract: The aim of this study was to investigate the effects of intracellular trehalose on the survival of redThe results indicated that the intracellular trehalose concentration was increased with increasing concentrationof extracellular trehalose solution, and the maximum concentration of intracellular trehalose reachedThe viability of freeze-dried red blood cells increased with the increment of intracellular trehalose
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Locally enhanced electric field treatment (LEEFT) for water disinfection

Jianfeng Zhou, Ting Wang, Cecilia Yu, Xing Xie

Frontiers of Environmental Science & Engineering 2020, Volume 14, Issue 5, doi: 10.1007/s11783-020-1253-x

Abstract: • Nanowire-assisted LEEFT is applied for water disinfection with low voltages. • LEEFT inactivates bacteria by disrupting cell membrane through electroporation. • Multiple electrodes and device configurations have been developed for LEEFT. • The LEEFT is low-cost, highly efficient, and produces no DBPs. • The LEEFT can potentially be applicable for water disinfection at all scales. Water disinfection is a critical step in water and wastewater treatment. The most widely used chlorination suffers from the formation of carcinogenic disinfection by-products (DBPs) while alternative methods (e.g., UV, O3, and membrane filtration) are limited by microbial regrowth, no residual disinfectant, and high operation cost. Here, a nanowire-enabled disinfection method, locally enhanced electric field treatment (LEEFT), is introduced with advantages of no chemical addition, no DBP formation, low energy consumption, and efficient microbial inactivation. Attributed to the lightning rod effect, the electric field near the tip area of the nanowires on the electrode is significantly enhanced to inactivate microbes, even though a small external voltage (usually<5 V) is applied. In this review, after emphasizing the significance of water disinfection, the theory of the LEEFT is explained. Subsequently, the recent development of the LEEFT technology on electrode materials and device configurations are summarized. The disinfection performance is analyzed, with respect to the operating parameters, universality against different microorganisms, electrode durability, and energy consumption. The studies on the inactivation mechanisms during the LEEFT are also reviewed. Lastly, the challenges and future research of LEEFT disinfection are discussed.

Keywords： Water treatment     Nanotechnology     Pathogen inactivation     Electroporation     Nanowire     Chemical-free    

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Clinical manifestations and pathogen characteristics in children admitted for suspected COVID-19

Xiaofang Cai, Hanlan Jiang, Simin Zhang, Shengying Xia, Wenhui Du, Yaoling Ma, Tao Yu, Wenbin Li

Frontiers of Medicine 2020, Volume 14, Issue 6,   Pages 776-785 doi: 10.1007/s11684-020-0820-7

Abstract: Notably, no pathogen was detected in 43 (44.3%) patients.The most frequently detected pathogen was (29, 29.9%). One patient with confirmed COVID 19 died.

Keywords： coronavirus disease 2019     pediatrics     emergency     retrospective investigation     severe acute respiratory syndrome coronavirus 2    

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Intracellular and extracellular TGF-β signaling in cancer: some recent topics

Kohei Miyazono, Yoko Katsuno, Daizo Koinuma, Shogo Ehata, Masato Morikawa

Frontiers of Medicine 2018, Volume 12, Issue 4,   Pages 387-411 doi: 10.1007/s11684-018-0646-8

Abstract:

Transforming growth factor (TGF)-β regulates a wide variety of cellular responses, including cell growth arrest, apoptosis, cell differentiation, motility, invasion, extracellular matrix production, tissue fibrosis, angiogenesis, and immune function. Although tumor-suppressive roles of TGF-β have been extensively studied and well-characterized in many cancers, especially at early stages, accumulating evidence has revealed the critical roles of TGF-β as a pro-tumorigenic factor in various types of cancer. This review will focus on recent findings regarding epithelial-mesenchymal transition (EMT) induced by TGF-β, in relation to crosstalk with some other signaling pathways, and the roles of TGF-β in lung and pancreatic cancers, in which TGF-β has been shown to be involved in cancer progression. Recent findings also strongly suggested that targeting TGF-β signaling using specific inhibitors may be useful for the treatment of some cancers. TGF-β plays a pivotal role in the differentiation and function of regulatory T cells (Tregs). TGF-β is produced as latent high molecular weight complexes, and the latent TGF-β complex expressed on the surface of Tregs contains glycoprotein A repetitions predominant (GARP, also known as leucine-rich repeat containing 32 or LRRC32). Inhibition of the TGF-β activities through regulation of the latent TGF-β complex activation will be discussed.

Keywords： TGF-β     EMT     lung cancer     pancreatic cancer     latent form     immune function     GARP    

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Composition, dispersion, and health risks of bioaerosols in wastewater treatment plants: A review

Yunping Han, Lin Li, Ying Wang, Jiawei Ma, Pengyu Li, Chao Han, Junxin Liu

Frontiers of Environmental Science & Engineering 2021, Volume 15, Issue 3, doi: 10.1007/s11783-020-1330-1

Abstract: Abstract • Bioaerosols are produced in the process of wastewater biological treatment. • The concentration of bioaerosol indoor is higher than outdoor. • Bioaerosols contain large amounts of potentially pathogenic biomass and chemicals. • Inhalation is the main route of exposure of bioaerosol. • Both the workers and the surrounding residents will be affected by the bioaerosol. Bioaerosols are defined as airborne particles (0.05–100 mm in size) of biological origin. They are considered potentially harmful to human health as they can contain pathogens such as bacteria, fungi, and viruses. This review summarizes the most recent research on the health risks of bioaerosols emitted from wastewater treatment plants (WWTPs) in order to improve the control of such bioaerosols. The concentration and size distribution of WWTP bioaerosols; their major emission sources, composition, and health risks; and considerations for future research are discussed. The major themes and findings in the literature are as follows: the major emission sources of WWTP bioaerosols include screen rooms, sludge-dewatering rooms, and aeration tanks; the bioaerosol concentrations in screen and sludge-dewatering rooms are higher than those outdoors. WWTP bioaerosols contain a variety of potentially pathogenic bacteria, fungi, antibiotic resistance genes, viruses, endotoxins, and toxic metal(loid)s. These potentially pathogenic substances spread with the bioaerosols, thereby posing health risks to workers and residents in and around the WWTP. Inhalation has been identified as the main exposure route, and children are at a higher risk of this than adults. Future studies should identify emerging contaminants, establish health risk assessments, and develop prevention and control systems.

Keywords： Wastewater treatment plant     Bioaerosols     Pathogen     Dispersion     Risk assessment    

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Effect of the ultraviolet/chlorine process on microbial community structure, typical pathogens, and antibiotic resistance genes in reclaimed water

Frontiers of Environmental Science & Engineering 2022, Volume 16, Issue 8, doi: 10.1007/s11783-022-1521-z

Abstract:

• UV/chlorine can effectively remove VBNC pathogens, ARGs and MGEs in reclaimed water.

Keywords： UV/chlorine process     Pathogen     Antibiotic resistance genes     High-throughput qPCR     Reclaimed water    

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Progress on the Detection Technology of Bacterial Pathogens in Marine Aquaculture

Xiao Jingfan,Wang Yue,Zhang Yuanxing,Lei Jilin

Strategic Study of CAE 2014, Volume 16, Issue 9,   Pages 10-15

Abstract:

With the rapid developments in marine aquaculture, the bacterial pathogen

Keywords： Marine aquaculture     bacterial pathogen     detection technology    

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The preparation and application of inactivated vaccine and its antiserum from eight common pathogens of Flatfish.

Gan Lingling,Wang Weifang,Gao Chunren,Lei Jilin

Strategic Study of CAE 2014, Volume 16, Issue 9,   Pages 21-25

Abstract:

In this study, formal dehyde was used to inactivate Edwardsiella tarda, Vibrio anguillarum, Vibrio harveyi, Vibrio vulnificus, Vibrio alginolyticus, Aeromonas caviae, Edwardsiella ictaluri, Aeromonas hydrophila, in order to preparethe inactivated vaccine. Then vaccine was used to immune turbot by intramuscular injection. In this way ,we got the antiserum of all bacterium above. Enzyme-linked immunosorbent assay was used to determine the content of antibody in serum. The antibody can be detect after four week in the immune, and the level of antibody is research highest in the tenth week which is inoculated inactivated vaccine of Edwardsiella tarda, and the highest titer of other vaccines are 1:102400, 1:6400, 1:6400, 1:12800, 1:12800, 1:6400, 1:6400, 1:12800. The results of cross reaction of the bacteria and their anti-serum shows that the effect is most intense when the bacteria react with its own antiserum, and it is very weak when the bacteria react with other antiserum.

Keywords： Flatfish     Vaccine     Antiserum     pathogen    

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New insights in the battle between wheat and

Chunlei TANG,Xiaojie WANG,Yulin CHENG,Minjie LIU,Mengxin ZHAO,Jinping WEI,Zhensheng KANG

Frontiers of Agricultural Science and Engineering 2015, Volume 2, Issue 2,   Pages 101-114 doi: 10.15302/J-FASE-2015068

Abstract: Wheat stripe rust caused by f. sp. ( ) poses a great threat to wheat production worldwide. The rapid change in virulence of leads to a loss of resistance in currently resistant wheat cultivars, which results in frequent disease epidemics. Therefore, a major focus is currently placed on investigating the molecular mechanisms underlying this rapid variation of pathogenicity and coevolving wheat resistance. Limited by the lack of a system for stable transformation of and the difficulties in wheat transformation, it is not easy to generate deeper insights into the wheat- interaction using established genetic methods. Nevertheless, considerable effort has been made to unravel the wheat- interaction and significant progress is being made. Histology and cytology have revealed basic details of infection strategies and defense responses during wheat- interactions, identified cellular components involved in wheat- interactions, and have helped to elucidate their role in the infection process or in plant defense responses. Transcriptome and genome sequencing has revealed the molecular features and dynamics of the wheat- pathosystem. Extensive molecular analyses have led to the identification of major components in the wheat resistance response and in virulence. Studies of wheat- interactions have now entered a new phase in which cellular and molecular approaches are being used. This review focuses on the cellular biology of wheat- interactions and integrates the emerging data from molecular analyses with the histocytological observations.

Keywords： tritici     host defense     pathogen virulence     biotrophic fungus    

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Title Author Date Type Operation

PathogenTrack and Yeskit: tools for identifying intracellular pathogens from single-cell RNA-sequencing

Journal Article

Systems understanding of plant–pathogen interactions through genome-wide protein–protein interaction

Hong LI,Ziding ZHANG

Journal Article

spp., foodborne pathogens threatening neonates and infants

Qiming CHEN, Yang ZHU, Zhen QIN, Yongjun QIU, Liming ZHAO

Journal Article

Intracellular Strain Evaluation-Based Oocyte Enucleation and Its Application in Robotic Cloning

Mingzhu Sun, Yaowei Liu, Maosheng Cui, Qili Zhao, Xiangfei Zhao, Yidi Zhang, Jingjing Huang, Guizhang Lu, Xin Zhao

Journal Article

Resveratrol reduces intracellular reactive oxygen species levels by inducing autophagy through the AMPK-mTOR

Jun Song, Yeping Huang, Wenjian Zheng, Jing Yan, Min Cheng, Ruxing Zhao, Li Chen, Cheng Hu, Weiping Jia

Journal Article

Intracellular trehalose improves the survival of human red blood cells by freeze-drying

HE Hui, LIU Baolin, HUA Zezhao, LI Chuan, WU Zhengzheng

Journal Article

Locally enhanced electric field treatment (LEEFT) for water disinfection

Jianfeng Zhou, Ting Wang, Cecilia Yu, Xing Xie

Journal Article

Clinical manifestations and pathogen characteristics in children admitted for suspected COVID-19

Xiaofang Cai, Hanlan Jiang, Simin Zhang, Shengying Xia, Wenhui Du, Yaoling Ma, Tao Yu, Wenbin Li

Journal Article

Intracellular and extracellular TGF-β signaling in cancer: some recent topics

Kohei Miyazono, Yoko Katsuno, Daizo Koinuma, Shogo Ehata, Masato Morikawa

Journal Article

Composition, dispersion, and health risks of bioaerosols in wastewater treatment plants: A review

Yunping Han, Lin Li, Ying Wang, Jiawei Ma, Pengyu Li, Chao Han, Junxin Liu

Journal Article

Sun Yu: Robotic Intracellular Management and Measurement (2019-8-25)

孙钰(院士)

20 Jan 2021

Conference Videos

Effect of the ultraviolet/chlorine process on microbial community structure, typical pathogens, and antibiotic resistance genes in reclaimed water

Journal Article

Progress on the Detection Technology of Bacterial Pathogens in Marine Aquaculture

Xiao Jingfan,Wang Yue,Zhang Yuanxing,Lei Jilin

Journal Article

The preparation and application of inactivated vaccine and its antiserum from eight common pathogens of Flatfish.

Gan Lingling,Wang Weifang,Gao Chunren,Lei Jilin

Journal Article

New insights in the battle between wheat and

Chunlei TANG,Xiaojie WANG,Yulin CHENG,Minjie LIU,Mengxin ZHAO,Jinping WEI,Zhensheng KANG

Journal Article