Article
Chemistry, Multidisciplinary
Qixin Hu, Fariha Kanwal, Weiyuan Lyu, Jiajie Zhang, Xu Liu, Kai Qin, Feng Shen
Summary: Pancreatic cancer is a lethal disease with low survival rates. Researchers have developed a droplet-array SlipChip for the detection of KRAS mutations in pancreatic cancer using digital PCR. This high-density microwell array allows for accurate quantification of mutant genes and wild-type KRAS gene. The results obtained from this chip align well with those from next-generation sequencing, making it a promising tool for point-of-care applications.
Article
Chemistry, Analytical
Yan Yu, Ziqing Yu, Xufeng Pan, Lei Xu, Rui Guo, Xiaohua Qian, Feng Shen
Summary: Digital PCR is a method that can accurately and precisely quantify target nucleic acids. The use of digital melting curve analysis (digital MCA) allows for the multiplex quantification of multiple target molecules in a single digital PCR. This method uses a self-partitioning SlipChip microfluidic system, which can generate microdroplets with trackable physical positions. The unique melting temperature (T-m) of amplification products can be used as a fingerprint for further classification.
Article
Chemistry, Multidisciplinary
Weiyuan Lyu, Jingwei Yi, Qingsheng Guo, Yao Wang, Jiajie Zhang, Tong Sun, Haoji Ma, Tingting Tang, Xueling Quan, Hong Xu, Feng Shen, Hongchen Gu
Summary: The advent of digital immunoassays has greatly enhanced the sensitivity of protein analysis to ultra-low levels, but the background signal from premixing can hinder precise quantification, especially in multiplexed assays. This study introduces a bead-based SlipChip microfluidic device that allows massively parallel two-step sample loading, effectively suppressing the background signal. The device achieves improved detection limits for IL-6 and IL-10 compared to a commercial system. The bb-SlipChip offers a robust and universal approach for digital immunoassays and has potential applications in multidimensional detection and other biomedical studies involving microbeads.
Article
Chemistry, Analytical
Xiang Li, Qixin Hu, Xu Liu, Jianfang Liu, Nannan Wu, Feng Shen
Summary: The rise of antimicrobial resistance is a global health concern, and there is a need for new antimicrobial drugs and alternative therapies. Phage therapy has shown promising results as an alternative treatment for antimicrobial resistance. Researchers have developed a digital biosensing method on a microfluidic device for rapid quantification of infectious bacteriophages. This method provides a promising tool for phage quantification in clinical practice and can also be used for ultrasensitive and high-specificity bacteria detection.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Ziqing Yu, Lei Xu, Weiyuan Lyu, Feng Shen
Summary: Digital biological analysis compartmentalizes targets of interest and performs detection and investigation. This study presents a parallel multistep digital analysis SlipChip, which enables the manipulation of a large number of droplets for digital biological analysis. The SlipChip utilizes a self-partitioning droplet formation mechanism and can perform digital loop-mediated isothermal amplification and digital CRISPR detection in parallel.
Article
Chemistry, Analytical
Luca Miglietta, Ke Xu, Priya Chhaya, Louis Kreitmann, Kerri Hill-Cawthorne, Frances Bolt, Alison Holmes, Pantelis Georgiou, Jesus Rodriguez-Manzano
Summary: This study proposes a novel framework to identify and filter out nonspecific and low-efficient reactions from qdPCR data using outlier detection algorithms, aiming to improve the accuracy of machine learning methods. Additionally, an adaptive mapping filter strategy is developed to adjust the percentage of outliers removed based on the number of positive counts in qdPCR.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Gaozhe Cai, Wenshuai Wu, Shilun Feng, Yuanjie Liu
Summary: An enzyme assay based method in a microfluidic slipchip was proposed for the rapid and label-free detection of E. coli. The method allows for E. coli detection within 5 hours with a low concentration of 8 CFU per chamber, showing great potential in on-site E. coli detection. The steps involve culture, lysis, and enzymatic reaction conducted in a microfluidic slipchip, tailored for fluorescence detection using a commercial plate reader.
Article
Food Science & Technology
Zhendi Yu, Zhangkai Xu, Jiang Chen, Lili Chen, Ningbo Liao, Ronghua Zhang, Dongqing Cheng
Summary: Foodborne diseases are a critical food safety issue globally, with shellfish carrying various foodborne viruses posing a risk of infection. Factors such as age, season, and type of shellfish are associated with different levels of infection risk.
Article
Microbiology
Yoshifumi Uwamino, Akio Aono, Yu Tomita, Kozo Morimoto, Masahiro Kawashima, Hirofumi Kamata, Yuka Sasaki, Hideaki Nagai, Naoki Hasegawa, Satoshi Mitarai
Summary: The Myco-Panel test accurately detects clinically common mycobacterial species that cause respiratory infections, providing useful information for patient management and rapid treatment initiation.
MICROBIOLOGY SPECTRUM
(2023)
Article
Medical Laboratory Technology
Liu Dong, Weijia Li, Qianqian Xu, Jianfei Gu, Zhihua Kang, Jian Chen, Xiao Xu, Xinju Zhang, Xiuming Zhang, Haoqin Jiang, Ming Guan
Summary: The study aimed to establish a new multiplex dPCR detection system that can distinguish exact species of malaria by one PCR reaction. The results showed that the dPCR system could rapidly diagnose and quantify malaria DNA samples, with low analytical sensitivity and good sensitivity and specificity in clinical samples.
CLINICA CHIMICA ACTA
(2023)
Article
Chemistry, Analytical
Juxin Yin, Liping Xia, Zheyu Zou, Jianjian Zhuang, Ying Mu
Summary: This study developed a digital PCR chip with multiplex capability and established a direct amplification detection method without nucleic acid extraction. The chip allows for accurate multiplex detection of ctDNA and eliminates the disadvantages of the extraction process.
Article
Food Science & Technology
Yuting Shang, Qinghua Ye, Qingping Wu, Rui Pang, Baoqing Zhou, Chufang Wang, Xinran Xiang, Fan Li, Juan Wang, Yinzhi Zhang, Jiasheng Wang, Xiulan Sun, Jumei Zhang
Summary: This study successfully identified species-specific molecular targets for different Cronobacter species using a bioinformatics approach and developed a multiplex PCR method for species identification. The PCR and mPCR assays showed excellent specificity and sensitivity for detecting Cronobacter species, suggesting their potential for use in food inspection and clinical diagnosis.
Article
Multidisciplinary Sciences
Igor Lazic, Susanne Feihl, Peter M. Prodinger, Ingo J. Banke, Andrej Trampuz, Rudiger von Eisenhart-Rothe, Christian Suren
Summary: Multiplex PCR for identification of pathogens in tissue biopsies of patients with periprosthetic joint infection showed low diagnostic accuracy compared to routine microbiological cultures, with potential for false negative results; however, it offers rapid pathogen identification, suggesting further exploration with careful specimen selection.
SCIENTIFIC REPORTS
(2021)
Review
Environmental Sciences
Hanyu Fu, Chunyun Zhang, Yuanyuan Wang, Guofu Chen
Summary: As the eutrophication of natural water bodies worsens, harmful algal blooms (HABs) caused by harmful algae are becoming more frequent. HABs have become a global ecological problem that poses a serious threat to human health and food safety. It is crucial to establish methods for rapid detection of harmful algal species to provide early warning for HABs. Molecular biology techniques have provided new ideas for the detection of harmful algae and have become a research hotspot. However, current methods can only detect single harmful algal species at a time. Establishing methods for the simultaneous detection of multiple harmful algal species has become a new trend in molecular detection technology.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2022)
Article
Biochemical Research Methods
Baobao Lin, Zhi Geng, Yanjing Chen, Wu Zeng, Bao Li, Yan Zhang, Peng Liu
Summary: Adequate intake of folic acid is crucial during pregnancy, but certain genetic polymorphisms hinder its absorption, posing a threat to the lives of pregnant women and causing birth defects in newborns. Traditional laboratory testing for genetic variants related to folic acid metabolism is time-consuming and labor-intensive. However, a microfluidics-based molecular diagnostic system offers rapid, sensitive, high-throughput, and automated detection by integrating sample pre-processing and nucleic acid amplification on-chip.
Article
Microbiology
Xiaowei Zheng, Wang Liu, Xin Dai, Yaxin Zhu, Jinfeng Wang, Yongqiang Zhu, Huajun Zheng, Ying Huang, Zhiyang Dong, Wenbin Du, Fangqing Zhao, Li Huang
Summary: Research on viral diversity in deep-sea sediments of Southwest Indian Ocean revealed a large number of unclassified viral groups, with most contigs belonging to dsDNA viruses in the order Caudovirales that primarily infect Proteobacteria. Auxiliary metabolic genes on viral contigs play a crucial role in modulating host responses to environmental changes and nutrient metabolism.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Chemistry, Analytical
Yan Yu, Ziqing Yu, Xufeng Pan, Lei Xu, Rui Guo, Xiaohua Qian, Feng Shen
Summary: Digital PCR is a method that can accurately and precisely quantify target nucleic acids. The use of digital melting curve analysis (digital MCA) allows for the multiplex quantification of multiple target molecules in a single digital PCR. This method uses a self-partitioning SlipChip microfluidic system, which can generate microdroplets with trackable physical positions. The unique melting temperature (T-m) of amplification products can be used as a fingerprint for further classification.
Article
Chemistry, Analytical
Shun Ye, Caiming Li, Xu Zheng, Weihang Huang, Yi Tao, Yanghuan Yu, Limin Yang, Ying Lan, Liang Ma, Shengtai Bian, Wenbin Du
Summary: This paper describes a versatile chip-free droplet generator, OsciDrop, which can produce size-tunable droplets on demand by oscillating its distal end. The study reveals a previously underexplored regime that leverages inertial force to generate droplets. The method has been successfully applied in nucleic acid amplification tests and shows great potential in digital molecular diagnostics.
ANALYTICAL CHEMISTRY
(2022)
Article
Engineering, Environmental
Yuxin Qiao, Ran Hu, Dongwei Chen, Li Wang, Zhiyi Wang, Haiyan Yu, Ye Fu, Chunli Li, Zhiyang Dong, Yun-Xuan Weng, Wenbin Du
Summary: A high-throughput screening pipeline was developed to identify PET-degrading microorganisms or enzymes, successfully isolating species capable of degrading PET from environmental samples and genetically deriving and validating two putative PETases. The FADS pipeline shows promise for discovering new plastic-degrading microorganisms and enzymes, potentially aiding in the directed evolution of degrading enzymes through synthetic biology.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Multidisciplinary Sciences
Haichao Feng, Yu Lv, Tino Krell, Ruixin Fu, Yunpeng Liu, Zhihui Xu, Wenbin Du, Qirong Shen, Nan Zhang, Ruifu Zhang
Summary: Bacteria have evolved multiple signal transduction systems to adapt to changing environmental conditions. The chemoreceptor McpA of Bacillus velezensis SQR9 has been found to directly bind to 13 chemoattractants. Structural biology studies and mutagenesis experiments have identified key amino acid residues that play roles in recognizing multiple ligands. This discovery reveals a mechanism in which a single chemoreceptor can integrate diverse signals through two modules.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Multidisciplinary
Xu Liu, Xiang Li, Nannan Wu, Yang Luo, Jiajie Zhang, Ziqing Yu, Feng Shen
Summary: The study presents a novel microfluidic device that enables instrument-free gradient droplet formation and parallel manipulation for screening tests. The device demonstrates good performance in antimicrobial susceptibility testing and shows consistent results with clinical culture-based tests.
Article
Immunology
Jing-Lin Zhang, Juanli Yun, Lin Yue, Wenbin Du, Yu-Hong Liang
Summary: Post-treatment apical periodontitis (PoAP) is characterized by bacterial invasion and infection in root canal treatment. This study investigated the bacterial composition and changes in PoAP samples compared to healthy oral and primary apical periodontitis samples. The results showed that PoAP samples had distinct microbial compositions with decreased microbial diversity. Opportunistic pathogens such as Clostridia and Synergistia might play a significant role in PoAP. The microbial communities in PoAP also exhibited more active metabolic capacity.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Bingliang Xie, Jian Wang, Yong Nie, Jing Tian, Zerui Wang, Dongwei Chen, Beiyu Hu, Xiao-Lei Wu, Wenbin Du
Summary: Recent studies have identified a novel microbial community called TM7, which is an obligate symbiont that binds to its host through twitching-like motility mediated by type IV pili (T4P). This research provides insights into the lifestyle of TM7 and the diversity of CPR bacteria.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Multidisciplinary
Qixin Hu, Fariha Kanwal, Weiyuan Lyu, Jiajie Zhang, Xu Liu, Kai Qin, Feng Shen
Summary: Pancreatic cancer is a lethal disease with low survival rates. Researchers have developed a droplet-array SlipChip for the detection of KRAS mutations in pancreatic cancer using digital PCR. This high-density microwell array allows for accurate quantification of mutant genes and wild-type KRAS gene. The results obtained from this chip align well with those from next-generation sequencing, making it a promising tool for point-of-care applications.
Article
Chemistry, Analytical
Xiang Li, Qixin Hu, Xu Liu, Jianfang Liu, Nannan Wu, Feng Shen
Summary: The rise of antimicrobial resistance is a global health concern, and there is a need for new antimicrobial drugs and alternative therapies. Phage therapy has shown promising results as an alternative treatment for antimicrobial resistance. Researchers have developed a digital biosensing method on a microfluidic device for rapid quantification of infectious bacteriophages. This method provides a promising tool for phage quantification in clinical practice and can also be used for ultrasensitive and high-specificity bacteria detection.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Yan Yu, Sheng Wang, Yang Luo, Chang Gu, Xin Shi, Feng Shen
Summary: Methylation is an essential epigenetic modification involved in regulating gene expression and maintaining genome stability. Current methods of methylation analysis face limitations of high cost, time-consuming workflows, and difficulty in accurate heterogeneity analysis and precise quantification. A droplet array SlipChip-based digital melting curve analysis (MCA) method was developed for accurate quantification of both methylation level and density. This method has been demonstrated to distinguish healthy individuals from patients with atrial fibrillation and holds potential for broader application in various research and clinical settings requiring methylation analysis.
Article
Mycology
Jiarui Yang, Juanli Yun, Xingzhong Liu, Wenbin Du, Meichun Xiang
Summary: In this study, the occurrence of early diverging fungi (EDF) in rhizosphere and bulk soils from different ecosystems in Beijing-Hebei area was investigated. More than 500 new operational taxonomic units (OTUs) of EDF were identified based on 18S rRNA genes. The dominant groups were Microsporida and Aphelida, while Rozellosporida was rare. The occurrence of EDF was influenced by soil chemical characteristics, vegetation, and other eukaryotic microorganisms, and the assembly of EDF community was primarily driven by stochastic processes.
MYCOLOGY-AN INTERNATIONAL JOURNAL ON FUNGAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Xiang Li, Xu Liu, Ziqing Yu, Yang Luo, Qixin Hu, Zhenye Xu, Jia Dai, Nannan Wu, Feng Shen
Summary: Bacterial antimicrobial resistance is a global threat, and a rapid high-throughput phenotypic antimicrobial susceptibility testing (AST) method is needed. The cs-SlipChip, containing 192 nanoliter-sized compartments, allows for high-throughput AST by monitoring bacterial growth and analyzing changes in bright-field imaging. The chip can measure the minimum inhibitory concentration (MIC) of Escherichia coli against four antibiotics within 3 hours and has been validated against a VITEK 2 automated system. This technology provides a practical and rapid method for AST and screening antibiotic combinations for treating multiple antibiotic-resistant bacteria.
Article
Biochemical Research Methods
Ziqing Yu, Lei Xu, Weiyuan Lyu, Feng Shen
Summary: Digital biological analysis compartmentalizes targets of interest and performs detection and investigation. This study presents a parallel multistep digital analysis SlipChip, which enables the manipulation of a large number of droplets for digital biological analysis. The SlipChip utilizes a self-partitioning droplet formation mechanism and can perform digital loop-mediated isothermal amplification and digital CRISPR detection in parallel.
Article
Materials Science, Multidisciplinary
Jin Li, Chang He, Haijun Qu, Feng Shen, Jian Ye
Summary: The study introduces the design of O-GERTs for creating PUF security labels, achieving a large encoding capacity and high information density. Digitized from signals of embedded alkyne Raman reporters, the PUF labels exhibit robustness against interference and demonstrate high reliability.
JOURNAL OF MATERIALS CHEMISTRY C
(2022)