1
|
Wu R, Ji P, Hua Y, Li H, Zhang W, Wei Y. Research progress in isolation and identification of rumen probiotics. Front Cell Infect Microbiol 2024; 14:1411482. [PMID: 38836057 PMCID: PMC11148321 DOI: 10.3389/fcimb.2024.1411482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 04/30/2024] [Indexed: 06/06/2024] Open
Abstract
With the increasing research on the exploitation of rumen microbial resources, rumen probiotics have attracted much attention for their positive contributions in promoting nutrient digestion, inhibiting pathogenic bacteria, and improving production performance. In the past two decades, macrogenomics has provided a rich source of new-generation probiotic candidates, but most of these "dark substances" have not been successfully cultured due to the restrictive growth conditions. However, fueled by high-throughput culture and sorting technologies, it is expected that the potential probiotics in the rumen can be exploited on a large scale, and their potential applications in medicine and agriculture can be explored. In this paper, we review and summarize the classical techniques for isolation and identification of rumen probiotics, introduce the development of droplet-based high-throughput cell culture and single-cell sequencing for microbial culture and identification, and finally introduce promising cultureomics techniques. The aim is to provide technical references for the development of related technologies and microbiological research to promote the further development of the field of rumen microbiology research.
Collapse
Affiliation(s)
| | - Peng Ji
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | | | | | | | - Yanming Wei
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| |
Collapse
|
2
|
Zhang D, Qiao L. Microfluidics Coupled Mass Spectrometry for Single Cell Multi-Omics. SMALL METHODS 2024; 8:e2301179. [PMID: 37840412 DOI: 10.1002/smtd.202301179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/02/2023] [Indexed: 10/17/2023]
Abstract
Population-level analysis masks significant heterogeneity between individual cells, making it difficult to accurately reflect the true intricacies of life activities. Microfluidics is a technique that can manipulate individual cells effectively and is commonly coupled with a variety of analytical methods for single-cell analysis. Single-cell omics provides abundant molecular information at the single-cell level, fundamentally revealing differences in cell types and biological states among cell individuals, leading to a deeper understanding of cellular phenotypes and life activities. Herein, this work summarizes the microfluidic chips designed for single-cell isolation, manipulation, trapping, screening, and sorting, including droplet microfluidic chips, microwell arrays, hydrodynamic microfluidic chips, and microchips with microvalves. This work further reviews the studies on single-cell proteomics, metabolomics, lipidomics, and multi-omics based on microfluidics and mass spectrometry. Finally, the challenges and future application of single-cell multi-omics are discussed.
Collapse
Affiliation(s)
- Dongxue Zhang
- Department of Chemistry, Institutes of Biomedical Sciences, and Minhang Hospital, Fudan University, Shanghai, 20000, China
| | - Liang Qiao
- Department of Chemistry, Institutes of Biomedical Sciences, and Minhang Hospital, Fudan University, Shanghai, 20000, China
| |
Collapse
|
3
|
Karnachuk OV, Beletsky AV, Rakitin AL, Ikkert OP, Avakyan MR, Zyusman VS, Napilov A, Mardanov AV, Ravin NV. Antibiotic-Resistant Desulfovibrio Produces H2S from Supplements for Animal Farming. Microorganisms 2023; 11:microorganisms11040838. [PMID: 37110261 PMCID: PMC10146906 DOI: 10.3390/microorganisms11040838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/14/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
Sulphate-reducing bacteria, primarily Desulfovibrio, are responsible for the active generation of H2S in swine production waste. The model species for sulphate reduction studies, Desulfovibrio vulgaris strain L2, was previously isolated from swine manure characterized by high rates of dissimilatory sulphate reduction. The source of electron acceptors in low-sulphate swine waste for the high rate of H2S formation remains uncertain. Here, we demonstrate the ability of the L2 strain to use common animal farming supplements including L-lysine-sulphate, gypsum and gypsum plasterboards as electron acceptors for H2S production. Genome sequencing of strain L2 revealed the presence of two megaplasmids and predicted resistance to various antimicrobials and mercury, which was confirmed in physiological experiments. Most of antibiotic resistance genes (ARG) are carried by two class 1 integrons located on the chromosome and on the plasmid pDsulf-L2-2. These ARGs, predicted to confer resistance to beta-lactams, aminoglycosides, lincosamides, sulphonamides, chloramphenicol and tetracycline, were probably laterally acquired from various Gammaproteobacteria and Firmicutes. Resistance to mercury is likely enabled by two mer operons also located on the chromosome and on pDsulf-L2-2 and acquired via horizontal gene transfer. The second megaplasmid, pDsulf-L2-1, encoded nitrogenase, catalase and type III secretion system suggesting close contact of the strain with intestinal cells in the swine gut. The location of ARGs on mobile elements allows us to consider D. vulgaris strain L2 as a possible vector transferring antimicrobials resistance determinants between the gut microbiote and microbial communities in environmental biotopes.
Collapse
|
4
|
Xie H, Ding X. The Intriguing Landscape of Single-Cell Protein Analysis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2105932. [PMID: 35199955 PMCID: PMC9036017 DOI: 10.1002/advs.202105932] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/27/2022] [Indexed: 05/15/2023]
Abstract
Profiling protein expression at single-cell resolution is essential for fundamental biological research (such as cell differentiation and tumor microenvironmental examination) and clinical precision medicine where only a limited number of primary cells are permitted. With the recent advances in engineering, chemistry, and biology, single-cell protein analysis methods are developed rapidly, which enable high-throughput and multiplexed protein measurements in thousands of individual cells. In combination with single cell RNA sequencing and mass spectrometry, single-cell multi-omics analysis can simultaneously measure multiple modalities including mRNAs, proteins, and metabolites in single cells, and obtain a more comprehensive exploration of cellular signaling processes, such as DNA modifications, chromatin accessibility, protein abundance, and gene perturbation. Here, the recent progress and applications of single-cell protein analysis technologies in the last decade are summarized. Current limitations, challenges, and possible future directions in this field are also discussed.
Collapse
Affiliation(s)
- Haiyang Xie
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Xianting Ding
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| |
Collapse
|
5
|
Lee MS, Hyun H, Park I, Kim S, Jang DH, Kim S, Im JK, Kim H, Lee JH, Kwon T, Kang JH. Quantitative Fluorescence In Situ Hybridization (FISH) of Magnetically Confined Bacteria Enables Early Detection of Human Bacteremia. SMALL METHODS 2022; 6:e2101239. [PMID: 35112812 DOI: 10.1002/smtd.202101239] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/02/2022] [Indexed: 06/14/2023]
Abstract
The current diagnosis of bacteremia mainly relies on blood culture, which is inadequate for the rapid and quantitative determination of most bacteria in blood. Here, a quantitative, multiplex, microfluidic fluorescence in situ hybridization method (μFISH) is developed, which enables early and rapid (3-h) diagnosis of bacteremia without the need for prior blood culture. This novel technology employs mannose-binding lectin-coated magnetic nanoparticles, which effectively opsonize a broad range of pathogens, magnetically sequestering them in a microfluidic device. Therein, μFISH probes, based on unique 16S rRNA sequences, enable the identification and quantification of sequestered pathogens both in saline and whole blood, which is more sensitive than conventional polymerase chain reaction. Using μFISH, Escherichia coli (E. coli) is detected in whole blood collected from a porcine disease model and from E. coli-infected patients. Moreover, the proportion of E. coli, relative to other bacterial levels in the blood, is accurately and rapidly determined, which is not possible using conventional diagnostic methods. Blood from E. coli-infected patients is differentiated from healthy donors' blood using cutoff values with a 0.05 significance level. Thus, μFISH is a versatile method that can be used to rapidly identify pathogens and determine their levels relative to other culturable and nonculturable bacteria in biological samples.
Collapse
Affiliation(s)
- Min Seok Lee
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Hwi Hyun
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Inwon Park
- Department of Emergency Medicine, Seoul National University Bundang Hospital (SNUBH), Gyeonggi-do, 13620, Republic of Korea
| | - Sungho Kim
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Dong-Hyun Jang
- Department of Emergency Medicine, Seoul National University Bundang Hospital (SNUBH), Gyeonggi-do, 13620, Republic of Korea
| | - Seonghye Kim
- Department of Emergency Medicine, Seoul National University Bundang Hospital (SNUBH), Gyeonggi-do, 13620, Republic of Korea
| | - Jae-Kyeong Im
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Hajin Kim
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Jae Hyuk Lee
- Department of Emergency Medicine, Seoul National University Bundang Hospital (SNUBH), Gyeonggi-do, 13620, Republic of Korea
| | - Taejoon Kwon
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Joo H Kang
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| |
Collapse
|
6
|
Pereira AC, Tenreiro A, Cunha MV. When FLOW-FISH met FACS: Combining multiparametric, dynamic approaches for microbial single-cell research in the total environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150682. [PMID: 34600998 DOI: 10.1016/j.scitotenv.2021.150682] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/22/2021] [Accepted: 09/26/2021] [Indexed: 06/13/2023]
Abstract
In environmental microbiology, the ability to assess, in a high-throughput way, single-cells within microbial communities is key to understand their heterogeneity. Fluorescence in situ hybridization (FISH) uses fluorescently labeled oligonucleotide probes to detect, identify, and quantify single cells of specific taxonomic groups. The combination of Flow Cytometry (FLOW) with FISH (FLOW-FISH) enables high-throughput quantification of complex whole cell populations, which when associated with fluorescence-activated cell sorting (FACS) enables sorting of target microorganisms. These sorted cells may be investigated in many ways, for instance opening new avenues for cytomics at a single-cell scale. In this review, an overview of FISH and FLOW methodologies is provided, addressing conventional methods, signal amplification approaches, common fluorophores for cell physiology parameters evaluation, and model variation techniques as well. The coupling of FLOW-FISH-FACS is explored in the context of different downstream applications of sorted cells. Current and emerging applications in environmental microbiology to outline the interactions and processes of complex microbial communities within soil, water, animal microbiota, polymicrobial biofilms, and food samples, are described.
Collapse
Affiliation(s)
- André C Pereira
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Ana Tenreiro
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Mónica V Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal.
| |
Collapse
|
7
|
Leung HY, Yeung MHY, Leung WT, Wong KH, Tang WY, Cho WCS, Wong HT, Tsang HF, Wong YKE, Pei XM, Cheng HYL, Chan AKC, Wong SCC. The current and future applications of in situ hybridization technologies in anatomical pathology. Expert Rev Mol Diagn 2021; 22:5-18. [PMID: 34779317 DOI: 10.1080/14737159.2022.2007076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION In situ hybridization (ISH) plays an important role in the field of molecular diagnostics, especially in an anatomical pathology laboratory. ISH is a technique that can detect the targeted DNA or RNA sequences in tissue sections from frozen or fixed materials with labeled DNA or RNA probes. Radioactive and non-radioactive probes are the two major probes that can be used to label the targeted nucleic acids. AREAS COVERED Two decades after the Human Genome Project, ISH has not only simply been applied to identify the chromosomal location of a human gene but has also been extensively applied to gene expressions studies and utilized for clinical diagnosis, especially for the determination of biomarkers for breast and ovarian cancers - human epidermal growth factor receptor 2. Duchenne muscular dystrophy, Cri-du-chat syndrome, Angelman syndrome, PraderWilli syndrome, cystic fibrosis, and trisomy are diseases that can also be detected by ISH. In this review, the basic principles, historical development, advantages and disadvantages, enhancement in reporting molecules and probes, advancement in detection methods, in situ PCR, clinical applications and novel applications of ISH will be discussed. EXPERT OPINION With the advancement in ISH technologies and appropriate training, diagnosis can be improved in Anatomical Pathology.
Collapse
Affiliation(s)
- Hoi Yi Leung
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
| | - Martin Ho Yin Yeung
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
| | - Wai Tung Leung
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
| | - King Hin Wong
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
| | - Wai Yan Tang
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
| | - William Chi Shing Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong Special Administrative Region, China
| | - Heong Ting Wong
- Department of Pathology, Kiang Wu Hospital, Santo António, Macau Special Administrative Region, China
| | - Hin Fung Tsang
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
| | - Yin Kwan Evelyn Wong
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
| | - Xiao Meng Pei
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
| | - Hennie Yuk Lin Cheng
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
| | - Amanda Kit Ching Chan
- Department of Pathology, Queen Elizabeth Hospital, Kowloon, Hong Kong Special Administrative Region, China
| | - Sze Chuen Cesar Wong
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
| |
Collapse
|
8
|
Freen-van Heeren JJ. Flow-FISH as a Tool for Studying Bacteria, Fungi and Viruses. BIOTECH 2021; 10:21. [PMID: 35822795 PMCID: PMC9245478 DOI: 10.3390/biotech10040021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/03/2021] [Accepted: 10/08/2021] [Indexed: 12/20/2022] Open
Abstract
Many techniques are currently in use to study microbes. These can be aimed at detecting, identifying, and characterizing bacterial, fungal, and viral species. One technique that is suitable for high-throughput analysis is flow cytometry-based fluorescence in situ hybridization, or Flow-FISH. This technique employs (fluorescently labeled) probes directed against DNA or (m)RNA, for instance targeting a gene or microorganism of interest and provides information on a single-cell level. Furthermore, by combining Flow-FISH with antibody-based protein detection, proteins of interest can be measured simultaneously with genetic material. Additionally, depending on the type of Flow-FISH assay, Flow-FISH can also be multiplexed, allowing for the simultaneous measurement of multiple gene targets and/or microorganisms. Together, this allows for, e.g., single-cell gene expression analysis or identification of (sub)strains in mixed cultures. Flow-FISH has been used in mammalian cells but has also been extensively employed to study diverse microbial species. Here, the use of Flow-FISH for studying microorganisms is reviewed. Specifically, the detection of (intracellular) pathogens, studying microorganism biology and disease pathogenesis, and identification of bacterial, fungal, and viral strains in mixed cultures is discussed, with a particular focus on the viruses EBV, HIV-1, and SARS-CoV-2.
Collapse
|
9
|
Abstract
FISH has gained an irreplaceable place in microbiology because of its ability to detect and locate a microorganism, or a group of organisms, within complex samples. However, FISH role has evolved drastically in the last few decades and its value has been boosted by several advances in signal intensity, imaging acquisitions, automation, method robustness, and, thus, versatility. This has resulted in a range of FISH variants that gave researchers the ability to access a variety of other valuable information such as complex population composition, metabolic activity, gene detection/quantification, or subcellular location of genetic elements. In this chapter, we will review the more relevant FISH variants, their intended use, and how they address particular challenges of classical FISH.
Collapse
Affiliation(s)
- Nuno M Guimarães
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal.
| | - Nuno F Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Carina Almeida
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, Lugar da Madalena, Vairão, Vila do Conde, Portugal
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
| |
Collapse
|
10
|
Rodriguez-Mateos P, Azevedo NF, Almeida C, Pamme N. FISH and chips: a review of microfluidic platforms for FISH analysis. Med Microbiol Immunol 2020; 209:373-391. [PMID: 31965296 PMCID: PMC7248050 DOI: 10.1007/s00430-019-00654-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 12/19/2019] [Indexed: 12/12/2022]
Abstract
Fluorescence in situ hybridization (FISH) allows visualization of specific nucleic acid sequences within an intact cell or a tissue section. It is based on molecular recognition between a fluorescently labeled probe that penetrates the cell membrane of a fixed but intact sample and hybridizes to a nucleic acid sequence of interest within the cell, rendering a measurable signal. FISH has been applied to, for example, gene mapping, diagnosis of chromosomal aberrations and identification of pathogens in complex samples as well as detailed studies of cellular structure and function. However, FISH protocols are complex, they comprise of many fixation, incubation and washing steps involving a range of solvents and temperatures and are, thus, generally time consuming and labor intensive. The complexity of the process, the relatively high-priced fluorescent probes and the fairly high-end microscopy needed for readout render the whole process costly and have limited wider uptake of this powerful technique. In recent years, there have been attempts to transfer FISH assay protocols onto microfluidic lab-on-a-chip platforms, which reduces the required amount of sample and reagents, shortens incubation times and, thus, time to complete the protocol, and finally has the potential for automating the process. Here, we review the wide variety of approaches for lab-on-chip-based FISH that have been demonstrated at proof-of-concept stage, ranging from FISH analysis of immobilized cell layers, and cells trapped in arrays, to FISH on tissue slices. Some researchers have aimed to develop simple devices that interface with existing equipment and workflows, whilst others have aimed to integrate the entire FISH protocol into a fully autonomous FISH on-chip system. Whilst the technical possibilities for FISH on-chip are clearly demonstrated, only a small number of approaches have so far been converted into off-the-shelf products for wider use beyond the research laboratory.
Collapse
Affiliation(s)
- Pablo Rodriguez-Mateos
- Department of Chemistry and Biochemistry, University of Hull, Cottingham Road, Hull, HU6 7RX, UK
| | - Nuno Filipe Azevedo
- LEPABE-Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering of University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465, Porto, Portugal.,Biomode SA, Av. Mestre José Veiga, 4715-330, Braga, Portugal
| | - Carina Almeida
- Biomode SA, Av. Mestre José Veiga, 4715-330, Braga, Portugal.,INIAV, I.P.-National Institute for Agricultural and Veterinary Research, Rua dos Lagidos, Lugar da Madalena, Vairão, 4485-655, Vila Do Conde, Portugal.,CEB-Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
| | - Nicole Pamme
- Department of Chemistry and Biochemistry, University of Hull, Cottingham Road, Hull, HU6 7RX, UK.
| |
Collapse
|
11
|
Fluorescence in situ hybridization (FISH): History, limitations and what to expect from micro-scale FISH? MICRO AND NANO ENGINEERING 2018. [DOI: 10.1016/j.mne.2018.10.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
12
|
Malla MA, Dubey A, Yadav S, Kumar A, Hashem A, Abd Allah EF. Understanding and Designing the Strategies for the Microbe-Mediated Remediation of Environmental Contaminants Using Omics Approaches. Front Microbiol 2018; 9:1132. [PMID: 29915565 PMCID: PMC5994547 DOI: 10.3389/fmicb.2018.01132] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 05/14/2018] [Indexed: 12/24/2022] Open
Abstract
Rapid industrialization and population explosion has resulted in the generation and dumping of various contaminants into the environment. These harmful compounds deteriorate the human health as well as the surrounding environments. Current research aims to harness and enhance the natural ability of different microbes to metabolize these toxic compounds. Microbial-mediated bioremediation offers great potential to reinstate the contaminated environments in an ecologically acceptable approach. However, the lack of the knowledge regarding the factors controlling and regulating the growth, metabolism, and dynamics of diverse microbial communities in the contaminated environments often limits its execution. In recent years the importance of advanced tools such as genomics, proteomics, transcriptomics, metabolomics, and fluxomics has increased to design the strategies to treat these contaminants in ecofriendly manner. Previously researchers has largely focused on the environmental remediation using single omics-approach, however the present review specifically addresses the integrative role of the multi-omics approaches in microbial-mediated bioremediation. Additionally, we discussed how the multi-omics approaches help to comprehend and explore the structural and functional aspects of the microbial consortia in response to the different environmental pollutants and presented some success stories by using these approaches.
Collapse
Affiliation(s)
- Muneer A Malla
- Department of Zoology, Dr. Harisingh Gour University, Sagar, India
| | - Anamika Dubey
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University, Sagar, India
| | - Shweta Yadav
- Department of Zoology, Dr. Harisingh Gour University, Sagar, India
| | - Ashwani Kumar
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University, Sagar, India
| | - Abeer Hashem
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Elsayed Fathi Abd Allah
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| |
Collapse
|
13
|
Chakraborty R, Woo H, Dehal P, Walker R, Zemla M, Auer M, Goodwin LA, Kazakov A, Novichkov P, Arkin AP, Hazen TC. Complete genome sequence of Pseudomonas stutzeri strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site. Stand Genomic Sci 2017; 12:23. [PMID: 28194258 PMCID: PMC5299692 DOI: 10.1186/s40793-017-0233-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 01/08/2017] [Indexed: 01/21/2023] Open
Abstract
Hexavalent Chromium [Cr(VI)] is a widespread contaminant found in soil, sediment, and ground water in several DOE sites, including Hanford 100 H area. In order to stimulate microbially mediated reduction of Cr(VI) at this site, a poly-lactate hydrogen release compound was injected into the chromium contaminated aquifer. Targeted enrichment of dominant nitrate-reducing bacteria post injection resulted in the isolation of Pseudomonas stutzeri strain RCH2. P. stutzeri strain RCH2 was isolated using acetate as the electron donor and is a complete denitrifier. Experiments with anaerobic washed cell suspension of strain RCH2 revealed it could reduce Cr(VI) and Fe(III). The genome of strain RCH2 was sequenced using a combination of Illumina and 454 sequencing technologies and contained a circular chromosome of 4.6 Mb and three plasmids. Global genome comparisons of strain RCH2 with six other fully sequenced P. stutzeri strains revealed most genomic regions are conserved, however strain RCH2 has an additional 244 genes, some of which are involved in chemotaxis, Flp pilus biogenesis and pyruvate/2-oxogluturate complex formation.
Collapse
Affiliation(s)
| | - Hannah Woo
- University Of Tennessee, Knoxville, TN USA
| | | | - Robert Walker
- Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Marcin Zemla
- Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Manfred Auer
- Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Lynne A Goodwin
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | | | | | - Adam P Arkin
- Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Terry C Hazen
- Lawrence Berkeley National Laboratory, Berkeley, CA USA.,University Of Tennessee, Knoxville, TN USA
| |
Collapse
|
14
|
Microfluidics-assisted fluorescence in situ hybridization for advantageous human epidermal growth factor receptor 2 assessment in breast cancer. J Transl Med 2017; 97:93-103. [PMID: 27892928 DOI: 10.1038/labinvest.2016.121] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/20/2016] [Accepted: 10/20/2016] [Indexed: 11/08/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) is one of the recommended techniques for human epidermal growth factor receptor 2 (HER2) status assessment on cancer tissues. Here we develop microfluidics-assisted FISH (MA-FISH), in which hybridization of the FISH probes with their target DNA strands is obtained by applying square-wave oscillatory flows of diluted probe solutions in a thin microfluidic chamber of 5 μl volume. By optimizing the experimental parameters, MA-FISH decreases the consumption of the expensive probe solution by a factor 5 with respect to the standard technique, and reduces the hybridization time to 4 h, which is four times faster than in the standard protocol. To validate the method, we blindly conducted HER2 MA-FISH on 51 formalin-fixed paraffin-embedded tissue slides of 17 breast cancer samples, and compared the results with standard HER2 FISH testing. HER2 status classification was determined according to published guidelines, based on average number of HER2 copies per cell and average HER2/CEP17 ratio. Excellent agreement was observed between the two methods, supporting the validity of MA-FISH and further promoting its short hybridization time and reduced reagent consumption.
Collapse
|
15
|
Huber D, Autebert J, Kaigala GV. Micro fluorescence in situ hybridization (μFISH) for spatially multiplexed analysis of a cell monolayer. Biomed Microdevices 2016; 18:40. [PMID: 27138995 PMCID: PMC4853442 DOI: 10.1007/s10544-016-0064-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We here present a micrometer-scale implementation of fluorescence in situ hybridization that we term μFISH. This μFISH implementation makes use of a non-contact scanning probe technology, namely, a microfluidic probe (MFP) that hydrodynamically shapes nanoliter volumes of liquid on a surface with micrometer resolution. By confining FISH probes at the tip of this microfabricated scanning probe, we locally exposed approximately 1000 selected MCF-7 cells of a monolayer to perform incubation of probes - the rate-limiting step in conventional FISH. This method is compatible with the standard workflow of conventional FISH, allows re-budgeting of the sample for various tests, and results in a ~ 15-fold reduction in probe consumption. The continuous flow of probes and shaping liquid on these selected cells resulted in a 120-fold reduction of the hybridization time compared with the standard protocol (3 min vs. 6 h) and efficient rinsing, thereby shortening the total FISH assay time for centromeric probes. We further demonstrated spatially multiplexed μFISH, enabling the use of spectrally equivalent probes for detailed and real-time analysis of a cell monolayer, which paves the way towards rapid and automated multiplexed FISH on standard cytological supports.
Collapse
Affiliation(s)
- D Huber
- IBM Research - Zurich, Säumerstrasse 4, 8803, Rüschlikon, Switzerland
| | - J Autebert
- IBM Research - Zurich, Säumerstrasse 4, 8803, Rüschlikon, Switzerland
| | - G V Kaigala
- IBM Research - Zurich, Säumerstrasse 4, 8803, Rüschlikon, Switzerland.
| |
Collapse
|
16
|
Sato K. Microdevice in Cellular Pathology: Microfluidic Platforms for Fluorescence in situ Hybridization and Analysis of Circulating Tumor Cells. ANAL SCI 2016; 31:867-73. [PMID: 26353951 DOI: 10.2116/analsci.31.867] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Microfluidic devices enable the miniaturization, integration, automation, and parallelization of chemical and biochemical processes. This new technology also provides opportunity for expansion in the field of cellular pathology. Fluorescence in situ hybridization (FISH) is a well-known gene-based method to image genetic abnormalities. Development of a FISH microfluidic platform has offered the possibility of automation with significant time and cost reductions, which overcomes many drawbacks of the current protocols. Microfluidic devices are also powerful tools for single-cell analysis. Capturing the circulating tumor cells (CTCs) from blood samples is one of the most promising approaches to enable the early diagnosis of cancer. The microfluidic devices are also useful to isolate rare CTCs at high efficiency and purity. In this review, I outline recent FISH and CTC analyses using microfluidic devices, and describe their applications for the cellular diagnosis of cancers.
Collapse
Affiliation(s)
- Kae Sato
- Department of Chemical and Biological Sciences, Faculty of Science
| |
Collapse
|
17
|
Konry T, Sarkar S, Sabhachandani P, Cohen N. Innovative Tools and Technology for Analysis of Single Cells and Cell-Cell Interaction. Annu Rev Biomed Eng 2016; 18:259-84. [PMID: 26928209 DOI: 10.1146/annurev-bioeng-090215-112735] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Heterogeneity in single-cell responses and intercellular interactions results from complex regulation of cell-intrinsic and environmental factors. Single-cell analysis allows not only detection of individual cellular characteristics but also correlation of genetic content with phenotypic traits in the same cell. Technological advances in micro- and nanofabrication have benefited single-cell analysis by allowing precise control of the localized microenvironment, cell manipulation, and sensitive detection capabilities. Additionally, microscale techniques permit rapid, high-throughput, multiparametric screening that has become essential for -omics research. This review highlights innovative applications of microscale platforms in genetic, proteomic, and metabolic detection in single cells; cell sorting strategies; and heterotypic cell-cell interaction. We discuss key design aspects of single-cell localization and isolation in microfluidic systems, dynamic and endpoint analyses, and approaches that integrate highly multiplexed detection of various intracellular species.
Collapse
Affiliation(s)
- Tania Konry
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts 02115; , , ,
| | - Saheli Sarkar
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts 02115; , , ,
| | - Pooja Sabhachandani
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts 02115; , , ,
| | - Noa Cohen
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts 02115; , , ,
| |
Collapse
|
18
|
Gumuscu B, Bomer JG, van den Berg A, Eijkel JCT. Photopatterning of Hydrogel Microarrays in Closed Microchips. Biomacromolecules 2015; 16:3802-10. [PMID: 26558488 DOI: 10.1021/acs.biomac.5b01104] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
To date, optical lithography has been extensively used for in situ patterning of hydrogel structures in a scale range from hundreds of microns to a few millimeters. The two main limitations which prevent smaller feature sizes of hydrogel structures are (1) the upper glass layer of a microchip maintains a large spacing (typically 525 μm) between the photomask and hydrogel precursor, leading to diffraction of UV light at the edges of mask patterns, (2) diffusion of free radicals and monomers results in irregular polymerization near the illumination interface. In this work, we present a simple approach to enable the use of optical lithography to fabricate hydrogel arrays with a minimum feature size of 4 μm inside closed microchips. To achieve this, we combined two different techniques. First, the upper glass layer of the microchip was thinned by mechanical polishing to reduce the spacing between the photomask and hydrogel precursor, and thereby the diffraction of UV light at the edges of mask patterns. The polishing process reduces the upper layer thickness from ∼525 to ∼100 μm, and the mean surface roughness from 20 to 3 nm. Second, we developed an intermittent illumination technique consisting of short illumination periods followed by relatively longer dark periods, which decrease the diffusion of monomers. Combination of these two methods allows for fabrication of 0.4 × 10(6) sub-10 μm sized hydrogel patterns over large areas (cm(2)) with high reproducibility (∼98.5% patterning success). The patterning method is tested with two different types of photopolymerizing hydrogels: polyacrylamide and polyethylene glycol diacrylate. This method enables in situ fabrication of well-defined hydrogel patterns and presents a simple approach to fabricate 3-D hydrogel matrices for biomolecule separation, biosensing, tissue engineering, and immobilized protein microarray applications.
Collapse
Affiliation(s)
- Burcu Gumuscu
- BIOS Lab-on-a-Chip Group, MESA+ Institute for Nanotechnology, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente , Enschede, The Netherlands
| | - Johan G Bomer
- BIOS Lab-on-a-Chip Group, MESA+ Institute for Nanotechnology, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente , Enschede, The Netherlands
| | - Albert van den Berg
- BIOS Lab-on-a-Chip Group, MESA+ Institute for Nanotechnology, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente , Enschede, The Netherlands
| | - Jan C T Eijkel
- BIOS Lab-on-a-Chip Group, MESA+ Institute for Nanotechnology, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente , Enschede, The Netherlands
| |
Collapse
|
19
|
Manaresi E, Bua G, Bonvicini F, Gallinella G. A flow-FISH assay for the quantitative analysis of parvovirus B19 infected cells. J Virol Methods 2015; 223:50-4. [DOI: 10.1016/j.jviromet.2015.07.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 06/26/2015] [Accepted: 07/24/2015] [Indexed: 01/27/2023]
|
20
|
Strachan BC, Sloane HS, Lee JC, Leslie DC, Landers JP. Investigation of the DNA target design parameters for effective hybridization-induced aggregation of particles for the sequence-specific detection of DNA. Analyst 2015; 140:2008-15. [PMID: 25673152 DOI: 10.1039/c4an02101k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In a recent publication, we presented a label-free method for the detection of specific DNA sequences through the hybridization-induced aggregation (HIA) of a pair of oligonucleotide-adducted magnetic particles. Here we show, through the use of modified hardware, that we are able to simultaneously analyze multiple (4) samples, and detect a 26-mer ssDNA sequence at femtomolar concentrations in minutes. As such, this work represents an improvement in throughput and a 100-fold improvement in sensitivity, compared to that reported previously. Here, we also investigate the design parameters of the target sequence, in an effort to maximize the sensitivity of HIA and to use as a guide in future applications of this work. Modifications were made to the original 26-mer oligonucleotide sequence to evaluate the effects of: (1) non-complementary flanking bases, (2) target sequence length, and (3) single base mismatches on aggregation response. The aggregation response decreased as the number of the non-complementary flanking bases increased, with only a five base addition lowering the LOD by four orders of magnitude. Low sensitivity was observed with short sequences of 6 and 10 complementary bases, which were only detectable at micromolar concentrations. Target sequences with 20, 26 or 32 complementary bases provided the greatest sensitivity and were detectable at femtomolar concentrations. Additionally, HIA could effectively differentiate sequences that were fully complementary from those containing 1, 2 or 3 single base mismatches at micromolar concentrations. The robustness of the HIA system to other buffer components was explored with nine potential assay interferents that could affect hybridization (aggregation) or falsely induce aggregation. Of these, purified BSA and lysed whole blood induced a false aggregation. None of the interferents inhibited aggregation when the hybridizing target was added. Having delineated the fundamental parameters affecting HIA-target hybridization, and demonstrating that HIA had the selectivity to detect single base mismatches, this fluor-free end-point detection has the potential to become a powerful tool for microfluidic DNA detection.
Collapse
Affiliation(s)
- Briony C Strachan
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA.
| | | | | | | | | |
Collapse
|
21
|
Xu Y, Wang X. Fluid and cell behaviors along a 3D printed alginate/gelatin/fibrin channel. Biotechnol Bioeng 2015; 112:1683-95. [PMID: 25727058 DOI: 10.1002/bit.25579] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 02/17/2015] [Indexed: 02/06/2023]
Abstract
Three-dimensional (3D) cell manipulation is available with the integration of microfluidic technology and rapid prototyping techniques. High-Fidelity (Hi-Fi) constructs hold enormous therapeutic potential for organ manufacturing and regenerative medicine. In the present paper we introduced a quasi-three-dimensional (Q3D) model with parallel biocompatible alginate/gelatin/fibrin hurdles. The behaviors of fluids and cells along the microfluidic channels with various widths were studied. Cells inside the newly designed microfluidic channels attached and grew well. Morphological changes of adipose-derived stem cells (ADSCs) in both two-dimensional (2D) and 3D milieu were found on the printed constructs. Endothelialization occurred with the co-cultures of ADSCs and hepatocytes. This study provides insights into the interactions among fluids, cells and biomaterials, the behaviors of fluids and cells along the microfluidic channels, and the applications of Q3D techniques.
Collapse
Affiliation(s)
- Yufan Xu
- Department of Mechanical Engineering, Key Laboratory for Advanced Materials Processing Technology, Ministry of Education & Center of Organ Manufacturing, Tsinghua University, Beijing, 100084, P.R. China
| | - Xiaohong Wang
- Department of Mechanical Engineering, Key Laboratory for Advanced Materials Processing Technology, Ministry of Education & Center of Organ Manufacturing, Tsinghua University, Beijing, 100084, P.R. China. .,State Key Laboratory of Materials Processing and Die & Mould Technology, Huazhong University of Science and Technology, Wuhan, 430074, P.R. China.
| |
Collapse
|
22
|
Abstract
Flow-cytometric (FC) detection of proteins in single cells is a rapid, quantitative method for single-cell protein analysis. Recent advancements in microfluidic technologies have leveraged miniaturization and automation to adapt flow cytometry for analyzing single cell protein profiles both for cell surface and intracellular proteins. Here, we describe the method for microfluidic FC, along with instructions to build a microfluidic platform capable of automated cell culture, cell surface receptor immunostaining, intracellular phosphoprotein and intracellular cytokine immunostaining, and analysis using micro-flow cytometry. As a demonstration of our platform and protocol, we detail the profiling of TLR4 receptor activation, ERK1/2 phosphorylation, and TNFα production in LPS stimulated macrophages using the microfluidic platform.
Collapse
Affiliation(s)
- Meiye Wu
- Biotechnology and Bioengineering, Sandia National Laboratories, Livermore, CA, USA
| | - Anup K Singh
- Biological Science and Technology, Sandia National Laboratories, 969, MS 9292, 7011 East Avenue, Livermore, CA, 94551-0969, USA.
- Joint BioEnergy Institute, Emeryville, CA, USA.
| |
Collapse
|
23
|
Ma L, Datta SS, Karymov MA, Pan Q, Begolo S, Ismagilov RF. Individually addressable arrays of replica microbial cultures enabled by splitting SlipChips. Integr Biol (Camb) 2014; 6:796-805. [PMID: 24953827 PMCID: PMC4131746 DOI: 10.1039/c4ib00109e] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Isolating microbes carrying genes of interest from environmental samples is important for applications in biology and medicine. However, this involves the use of genetic assays that often require lysis of microbial cells, which is not compatible with the goal of obtaining live cells for isolation and culture. This paper describes the design, fabrication, biological validation, and underlying physics of a microfluidic SlipChip device that addresses this challenge. The device is composed of two conjoined plates containing 1000 microcompartments, each comprising two juxtaposed wells, one on each opposing plate. Single microbial cells are stochastically confined and subsequently cultured within the microcompartments. Then, we split each microcompartment into two replica droplets, both containing microbial culture, and then controllably separate the two plates while retaining each droplet within each well. We experimentally describe the droplet retention as a function of capillary pressure, viscous pressure, and viscosity of the aqueous phase. Within each pair of replicas, one can be used for genetic analysis, and the other preserves live cells for growth. This microfluidic approach provides a facile way to cultivate anaerobes from complex communities. We validate this method by targeting, isolating, and culturing Bacteroides vulgatus, a core gut anaerobe, from a clinical sample. To date, this methodology has enabled isolation of a novel microbial taxon, representing a new genus. This approach could also be extended to the study of other microorganisms and even mammalian systems, and may enable targeted retrieval of solutions in applications including digital PCR, sequencing, single cell analysis, and protein crystallization.
Collapse
Affiliation(s)
- Liang Ma
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, USA.
| | | | | | | | | | | |
Collapse
|
24
|
He S, Yu X, Wang X, Tan J, Yan S, Wang P, Huang BH, Zhang ZL, Li L. Fast magnetic isolation of simple sequence repeat markers in microfluidic channels. LAB ON A CHIP 2014; 14:1410-1414. [PMID: 24615343 DOI: 10.1039/c3lc51371h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Simple sequence repeat (SSR) markers are widely used for genome mapping, genetic diversity characterization and medical diagnosis. The fast isolation by AFLP of sequence containing repeats (FIASCO) is a powerful method for SSR marker isolation, but it is laborious, costly, and time consuming and requires multiple rounds of washing. Here, we report a superparamagnetic bead (SPMB)-based FIASCO method in a magnetic field controllable microfluidic chip (MFCM-Chip). This method dramatically reduces the assay time by 4.25-fold and reduces the quantity of magnetic beads and probes by 10-fold through the magnetic capture of (AG)n-containing fragments from Herba Leonuri, followed by washing and eluting on a microchip. The feasibility of this method was further evaluated by PCR and sequencing, and the results showed that the proportion of fragments containing SSRs was 89%, confirming that this platform is a fast and efficient method for SSR marker isolation. This cost-effective platform will make the powerful FIASCO technique more accessible for routine use with a wide variety of materials.
Collapse
Affiliation(s)
- Shibin He
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, and State Key Laboratory of Virology, Wuhan University, Wuhan 430072, PR China.
| | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Wu M, Piccini ME, Singh AK. MiRNA detection at single-cell resolution using microfluidic LNA flow-FISH. Methods Mol Biol 2014; 1211:245-260. [PMID: 25218391 DOI: 10.1007/978-1-4939-1459-3_20] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Flow cytometry in combination with fluorescent in situ hybridization (flow-FISH) is a powerful technique that can be utilized to rapidly detect nucleic acids at single-cell resolution without the need for homogenization or nucleic acid extraction. Here, we describe a microfluidic-based method which enables the detection of microRNAs or miRNAs in single intact cells by flow-FISH using locked nucleic acid (LNA)-containing probes. Our method can be applied to all RNA species including mRNA and small noncoding RNA and is suitable for multiplexing with protein immunostaining in the same cell. For demonstration of our method, this chapter details the detection of miR155 and CD69 protein in PMA and ionomycin-stimulated Jurkat cells. We also include instructions on how to set up a microfluidic chip sample preparation station to prepare cells for imaging and analysis on a commercial flow cytometer or a custom-built micro-flow cytometer.
Collapse
Affiliation(s)
- Meiye Wu
- Biological Science and Technology, Sandia National Laboratories, MS 9292, 969, Livermore, CA, 94551-0969, USA
| | | | | |
Collapse
|
26
|
Kirleis MA, Mathews SA, Verbarg J, Erickson JS, Piqué A. Reconfigurable acquisition system with integrated optics for a portable flow cytometer. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2013; 84:115109. [PMID: 24289439 DOI: 10.1063/1.4831835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Portable and inexpensive scientific instruments that are capable of performing point of care diagnostics are needed for applications such as disease detection and diagnosis in resource-poor settings, for water quality and food supply monitoring, and for biosurveillance activities in autonomous vehicles. In this paper, we describe the development of a compact flow cytometer built from three separate, customizable, and interchangeable modules. The instrument as configured in this work is being developed specifically for the detection of selected Centers for Disease Control (CDC) category B biothreat agents through a bead-based assay: E. coli O157:H7, Salmonella, Listeria, and Shigella. It has two-color excitation, three-color fluorescence and light scattering detection, embedded electronics, and capillary based flow. However, these attributes can be easily modified for other applications such as cluster of differentiation 4 (CD4) counting. Proof of concept is demonstrated through a 6-plex bead assay with the results compared to a commercially available benchtop-sized instrument.
Collapse
Affiliation(s)
- Matthew A Kirleis
- Naval Research Laboratory, 4555 Overlook Ave. SW, Washington, DC 20375, USA
| | | | | | | | | |
Collapse
|
27
|
Liu Y, Barua D, Liu P, Wilson BS, Oliver JM, Hlavacek WS, Singh AK. Single-cell measurements of IgE-mediated FcεRI signaling using an integrated microfluidic platform. PLoS One 2013; 8:e60159. [PMID: 23544131 PMCID: PMC3609784 DOI: 10.1371/journal.pone.0060159] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 02/21/2013] [Indexed: 11/18/2022] Open
Abstract
Heterogeneity in responses of cells to a stimulus, such as a pathogen or allergen, can potentially play an important role in deciding the fate of the responding cell population and the overall systemic response. Measuring heterogeneous responses requires tools capable of interrogating individual cells. Cell signaling studies commonly do not have single-cell resolution because of the limitations of techniques used such as Westerns, ELISAs, mass spectrometry, and DNA microarrays. Microfluidics devices are increasingly being used to overcome these limitations. Here, we report on a microfluidic platform for cell signaling analysis that combines two orthogonal single-cell measurement technologies: on-chip flow cytometry and optical imaging. The device seamlessly integrates cell culture, stimulation, and preparation with downstream measurements permitting hands-free, automated analysis to minimize experimental variability. The platform was used to interrogate IgE receptor (FcεRI) signaling, which is responsible for triggering allergic reactions, in RBL-2H3 cells. Following on-chip crosslinking of IgE-FcεRI complexes by multivalent antigen, we monitored signaling events including protein phosphorylation, calcium mobilization and the release of inflammatory mediators. The results demonstrate the ability of our platform to produce quantitative measurements on a cell-by-cell basis from just a few hundred cells. Model-based analysis of the Syk phosphorylation data suggests that heterogeneity in Syk phosphorylation can be attributed to protein copy number variations, with the level of Syk phosphorylation being particularly sensitive to the copy number of Lyn.
Collapse
Affiliation(s)
- Yanli Liu
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, California, United States of America
| | - Dipak Barua
- Theoretical Biology and Biophysics Group, Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Peng Liu
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, California, United States of America
| | - Bridget S. Wilson
- Department of Pathology and Cancer Center, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Janet M. Oliver
- Department of Pathology and Cancer Center, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - William S. Hlavacek
- Theoretical Biology and Biophysics Group, Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Anup K. Singh
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, California, United States of America
- * E-mail:
| |
Collapse
|
28
|
Hazen TC. The SuperChip for microbial community structure, and function from all environments. Microb Biotechnol 2013; 6:450-2. [PMID: 23464831 PMCID: PMC3918150 DOI: 10.1111/1751-7915.12045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 01/27/2013] [Indexed: 12/01/2022] Open
Abstract
Summary We have the technology and capability to develop an all-in-one microarray that can provide complete information on a microbial community, including algae, protozoa, bacteria, archaea, fungi, viruses, antimicrobial resistance, biotoxins and functional activity. With lab-on-a-chip, nanotechnology integrating a variety of the latest methods for a large number of sample types (water, sediment, waste water, food, blood, etc.) it is possible to make a desktop instrument that would have universal applications. There are two major thrusts to this grand challenge that will allow us to take advantage of the latest biotechnological breakthroughs in real time. The first is a bioengineering thrust that will take advantage of the large multidisciplinary laboratories in developing key technologies. Miniaturization will reduce reagent costs and increase sensitivity and reaction kinetics for rapid turnaround time. New and evolving technologies will allow us to port the designs for state-of-the-art microarrays today to completely new nanotechnology inspired platforms as they mature. The second thrust is in bioinformatics to use our existing expertise to take advantage of the rapidly evolving landscape of bioinformatics data. This increasing capacity of the data set will allow us to resolve microbial species to greatly improved levels and identify functional genes beyond the hypothetical protein level. A cheap and portable assay would impact countless areas, including clean water technologies, emerging diseases, bioenergy, infectious disease diagnosis, climate change, food safety, environmental clean-up and bioterrorism. In my opinion it is possible but it will require a very large group of multidiscplenary scientists from multiple institutions crossing many international boundaries and funding over a 5-year period of more than $100 million. Given the impact that this SuperChip could have it is well worth the price!!!
Collapse
Affiliation(s)
- Terry C Hazen
- Departments of Civil & Environmental Engineering, Earth & Planetary Sciences, Microbiology, University of Tennessee, Knoxville, TN 37996, USA.
| |
Collapse
|
29
|
|
30
|
Wu M, Piccini M, Koh CY, Lam KS, Singh AK. Single cell microRNA analysis using microfluidic flow cytometry. PLoS One 2013; 8:e55044. [PMID: 23383050 PMCID: PMC3559333 DOI: 10.1371/journal.pone.0055044] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2012] [Accepted: 12/18/2012] [Indexed: 11/29/2022] Open
Abstract
MicroRNAs (miRNAs) are non-coding small RNAs that have cell type and cell context-dependent expression and function. To study miRNAs at single-cell resolution, we have developed a novel microfluidic approach, where flow fluorescent in situ hybridization (flow-FISH) using locked-nucleic acid probes is combined with rolling circle amplification to detect the presence and localization of miRNA. Furthermore, our flow cytometry approach allows analysis of gene-products potentially targeted by miRNA together with the miRNA in the same cells. We demonstrate simultaneous measurement of miR155 and CD69 in 12-O-tetradecanoylphorbol 13-acetate (PMA) and Ionomycin stimulated Jurkat cells. The flow-FISH method can be completed in ∼10 h, utilizes only 170 nL of reagent per experimental condition, and is the first to directly detect miRNA in single cells using flow cytometry.
Collapse
Affiliation(s)
- Meiye Wu
- Department of Biotechnology and Bioengineering, Sandia National Laboratory, Livermore, CA, USA
| | | | | | | | | |
Collapse
|
31
|
Kovarik ML, Ornoff DM, Melvin AT, Dobes NC, Wang Y, Dickinson AJ, Gach PC, Shah PK, Allbritton NL. Micro total analysis systems: fundamental advances and applications in the laboratory, clinic, and field. Anal Chem 2013; 85:451-72. [PMID: 23140554 PMCID: PMC3546124 DOI: 10.1021/ac3031543] [Citation(s) in RCA: 170] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Michelle L. Kovarik
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Douglas M. Ornoff
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Adam T. Melvin
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Nicholas C. Dobes
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Yuli Wang
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Alexandra J. Dickinson
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Philip C. Gach
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Pavak K. Shah
- Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC 27599 and North Carolina State University, Raleigh, NC 27695
| | - Nancy L. Allbritton
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599
- Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC 27599 and North Carolina State University, Raleigh, NC 27695
| |
Collapse
|
32
|
Watts BR, Zhang Z, Xu CQ, Cao X, Lin M. A photonic-microfluidic integrated device for reliable fluorescence detection and counting. Electrophoresis 2012; 33:3236-44. [DOI: 10.1002/elps.201200311] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 06/08/2012] [Accepted: 07/01/2012] [Indexed: 11/08/2022]
Affiliation(s)
- Benjamin R. Watts
- Department of Engineering Physics; McMaster University; Hamilton; Ontario; Canada
| | - Zhiyi Zhang
- Institute for Microstructural Sciences; National Research Council of Canada; Ottawa; Ontario; Canada
| | - Chang Qing Xu
- Department of Engineering Physics; McMaster University; Hamilton; Ontario; Canada
| | - Xudong Cao
- Department of Chemical and Biological Engineering; University of Ottawa; Ottawa; Ontario; Canada
| | - Min Lin
- Canadian Food Inspection Agency; Ottawa; Ontario; Canada
| |
Collapse
|
33
|
Wu M, Perroud TD, Srivastava N, Branda CS, Sale KL, Carson BD, Patel KD, Branda SS, Singh AK. Microfluidically-unified cell culture, sample preparation, imaging and flow cytometry for measurement of cell signaling pathways with single cell resolution. LAB ON A CHIP 2012; 12:2823-2831. [PMID: 22777012 DOI: 10.1039/c2lc40344g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We have developed a microfluidic platform that enables, in one experiment, monitoring of signaling events spanning multiple time-scales and cellular locations through seamless integration of cell culture, stimulation and preparation with downstream analysis. A combination of two single-cell resolution techniques-on-chip multi-color flow cytometry and fluorescence imaging provides multiplexed and orthogonal data on cellular events. Automated, microfluidic operation allows quantitatively- and temporally-precise dosing leading to fine time-resolution and improved reproducibility of measurements. The platform was used to profile the toll-like receptor (TLR4) pathway in macrophages challenged with lipopolysaccharide (LPS)-beginning with TLR4 receptor activation by LPS, through intracellular MAPK signaling, RelA/p65 translocation in real time, to TNF-α cytokine production, all in one small macrophage population (< 5000 cells) while using minute reagent volume (540 nL/condition). The platform is easily adaptable to many cell types including primary cells and provides a generic platform for profiling signaling pathways.
Collapse
Affiliation(s)
- Meiye Wu
- Biotechnology and Bioengineering Department, Sandia National Laboratory, P.O. Box 969, Livermore, CA 94551, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Kamke J, Bayer K, Woyke T, Hentschel U. Exploring symbioses by single-cell genomics. THE BIOLOGICAL BULLETIN 2012; 223:30-43. [PMID: 22983031 DOI: 10.1086/bblv223n1p30] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Single-cell genomics has advanced the field of microbiology from the analysis of microbial metagenomes where information is "drowning in a sea of sequences," to recognizing each microbial cell as a separate and unique entity. Single-cell genomics employs Phi29 polymerase-mediated whole-genome amplification to yield microgram-range genomic DNA from single microbial cells. This method has now been applied to a handful of symbiotic systems, including bacterial symbionts of marine sponges, insects (grasshoppers, termites), and vertebrates (mouse, human). In each case, novel insights were obtained into the functional genomic repertoire of the bacterial partner, which, in turn, led to an improved understanding of the corresponding host. Single-cell genomics is particularly valuable when dealing with uncultivated microorganisms, as is still the case for many bacterial symbionts. In this review, we explore the power of single-cell genomics for symbiosis research and highlight recent insights into the symbiotic systems that were obtained by this approach.
Collapse
Affiliation(s)
- Janine Kamke
- Julius-von-Sachs Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs Platz 3, 97082 Würzburg, Germany
| | | | | | | |
Collapse
|
35
|
Systems biology approach to bioremediation. Curr Opin Biotechnol 2012; 23:483-90. [DOI: 10.1016/j.copbio.2012.01.015] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 01/20/2012] [Accepted: 01/28/2012] [Indexed: 11/21/2022]
|
36
|
Meagher RJ, Thaitrong N. Microchip electrophoresis of DNA following preconcentration at photopatterned gel membranes. Electrophoresis 2012; 33:1236-46. [DOI: 10.1002/elps.201100675] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
37
|
Kovarik ML, Gach PC, Ornoff DM, Wang Y, Balowski J, Farrag L, Allbritton NL. Micro total analysis systems for cell biology and biochemical assays. Anal Chem 2012; 84:516-40. [PMID: 21967743 PMCID: PMC3264799 DOI: 10.1021/ac202611x] [Citation(s) in RCA: 180] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Michelle L. Kovarik
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Phillip C. Gach
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Douglas M. Ornoff
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Yuli Wang
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Joseph Balowski
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Lila Farrag
- School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Nancy L. Allbritton
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599
- Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC 27599 and North Carolina State University, Raleigh, NC 27695
| |
Collapse
|
38
|
Sueyoshi K. Recent Progress of On-line Combination of Preconcentration Device with Microchip Electrophoresis. CHROMATOGRAPHY 2012. [DOI: 10.15583/jpchrom.2012.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Kenji Sueyoshi
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University
| |
Collapse
|
39
|
Yilmaz S, Singh AK. Single cell genome sequencing. Curr Opin Biotechnol 2011; 23:437-43. [PMID: 22154471 DOI: 10.1016/j.copbio.2011.11.018] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 11/11/2011] [Indexed: 11/29/2022]
Abstract
Whole genome amplification and next-generation sequencing of single cells have become a powerful approach for studying uncultivated microorganisms that represent 90-99% of all environmental microbes. Single cell sequencing enables not only the identification of microbes but also linking of functions to species, a feat not achievable by metagenomic techniques. Moreover, it allows the analysis of low abundance species that may be missed in community-based analyses. It has also proved very useful in complementing metagenomics in the assembly and binning of single genomes. With the advent of drastically cheaper and higher throughput sequencing technologies, it is expected that single cell sequencing will become a standard tool in studying the genome and transcriptome of microbial communities.
Collapse
Affiliation(s)
- Suzan Yilmaz
- Department of Bioengineering and Biotechnology, Sandia National Laboratory, Livermore, CA 94551, United States
| | | |
Collapse
|