1
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Nunn LR, Juang TD, Beebe DJ, Wheeler NJ, Zamanian M. A high-throughput sensory assay for parasitic and free-living nematodes. Integr Biol (Camb) 2023; 15:zyad010. [PMID: 37555835 PMCID: PMC10752570 DOI: 10.1093/intbio/zyad010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/12/2023] [Accepted: 07/14/2023] [Indexed: 08/10/2023]
Abstract
Sensory pathways first elucidated in Caenorhabditis elegans are conserved across free-living and parasitic nematodes, even though each species responds to a diverse array of compounds. Most nematode sensory assays are performed by tallying observations of worm behavior on two-dimensional planes using agarose plates. These assays have been successful in the study of volatile sensation but are poorly suited for investigation of water-soluble gustation or parasitic nematodes without a free-living stage. In contrast, gustatory assays tend to be tedious, often limited to the manipulation of a single individual at a time. We have designed a nematode sensory assay using a microfluidics device that allows for the study of gustation in a 96-well, three-dimensional environment. This device is suited for free-living worms and parasitic worms that spend their lives in an aqueous environment, and we have used it to show that ivermectin inhibits the gustatory ability of vector-borne parasitic nematodes. Insight box Nematodes are powerful model organisms for understanding the sensory biology of multicellular eukaryotes, and many parasitic species cause disease in humans. Simple sensory assays performed on agarose plates have been the bedrock for establishing the neuronal, genetic, and developmental foundations for many sensory modalities in nematodes. However, these classical assays are poorly suited for translational movement of many parasitic nematodes and the sensation of water-soluble molecules (gustation). We have designed a device for high-throughput nematode sensory assays in a gel matrix. This 'gustatory microplate' is amenable to several species and reveals novel responses by free-living and parasitic nematodes to cues and drugs.
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Affiliation(s)
- Leonardo R. Nunn
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI USA
| | - Terry D. Juang
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI USA
| | - David J. Beebe
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI USA
| | - Nicolas J. Wheeler
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI USA
- Department of Biology, University of Wisconsin-Eau Claire, Eau Claire, WI USA
| | - Mostafa Zamanian
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI USA
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2
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Williamson C, van Zee M, Di Carlo D. PicoShells: Hollow Hydrogel Microparticles for High-Throughput Screening of Clonal Libraries. Methods Mol Biol 2023; 2689:53-64. [PMID: 37430046 DOI: 10.1007/978-1-0716-3323-6_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
Microfluidics enables the creation of monodisperse, micron-scale aqueous droplets, or other compartments. These droplets serve as picolitre-volume reaction chambers which can be utilized for various chemical assays or reactions. Here we describe the use of a microfluidic droplet generator to encapsulate single cells within hollow hydrogel microparticles called PicoShells. The PicoShell fabrication utilizes a mild pH-based crosslinking modality of an aqueous two-phase prepolymer system, avoiding the cell death and unwanted genomic modifications that accompany more typical, ultraviolet light crosslinking techniques. The cells are grown inside of these PicoShells into monoclonal colonies in any number of environments, including scaled production environments using commercially relevant incubation methods. Colonies can be phenotypically analyzed and/or sorted using standard, high-throughput laboratory techniques, namely, fluorescence-activated cell sorting (FACS). Cell viability is maintained throughout particle fabrication and analysis, and cells exhibiting a desired phenotype can be selected and released for re-culturing and downstream analysis. Large-scale cytometry runs are of particular use when measuring the protein expression of heterogeneous cells in response to environmental stimuli, notably to identify targets early in the drug discovery process. The sorted cells can also be encapsulated multiple times to direct the evolution of a cell line to a desired phenotype.
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Affiliation(s)
- Cayden Williamson
- Department of Bioengineering, University of California, Los Angeles, CA, USA
| | - Mark van Zee
- Department of Bioengineering, University of California, Los Angeles, CA, USA
| | - Dino Di Carlo
- Department of Bioengineering, University of California, Los Angeles, CA, USA.
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, CA, USA.
- California NanoSystems Institute, University of California, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA.
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3
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Jiang S, Guo C, Song P, Wang T, Wang R, Zhang T, Wu Q, Pandey R, Zheng G. High-throughput digital pathology via a handheld, multiplexed, and AI-powered ptychographic whole slide scanner. Lab Chip 2022; 22:2657-2670. [PMID: 35583207 DOI: 10.1039/d2lc00084a] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The recent advent of whole slide imaging (WSI) systems has moved digital pathology closer to diagnostic applications and clinical practices. Integrating WSI with machine learning promises the growth of this field in upcoming years. Here we report the design and implementation of a handheld, colour-multiplexed, and AI-powered ptychographic whole slide scanner for digital pathology applications. This handheld scanner is built using low-cost and off-the-shelf components, including red, green, and blue laser diodes for sample illumination, a modified stage for programmable sample positioning, and a synchronized image sensor pair for data acquisition. We smear a monolayer of goat blood cells on the main sensor for high-resolution lensless coded ptychographic imaging. The synchronized secondary sensor acts as a non-contact encoder for precisely tracking the absolute object position for ptychographic reconstruction. For WSI, we introduce a new phase-contrast-based focus metric for post-acquisition autofocusing of both stained and unstained specimens. We show that the scanner can resolve the 388-nm linewidth on the resolution target and acquire gigapixel images with a 14 mm × 11 mm area in ∼70 seconds. The imaging performance is validated with regular stained pathology slides, unstained thyroid smears, and malaria-infected blood smears. The deep neural network developed in this study further enables high-throughput cytometric analysis using the recovered complex amplitude. The reported do-it-yourself scanner offers a portable solution to transform the high-end WSI system into one that can be made widely available at a low cost. The capability of high-throughput quantitative phase imaging may also find applications in rapid on-site evaluations.
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Affiliation(s)
- Shaowei Jiang
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269, USA.
| | - Chengfei Guo
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269, USA.
| | - Pengming Song
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269, USA.
| | - Tianbo Wang
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269, USA.
| | - Ruihai Wang
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269, USA.
| | - Terrance Zhang
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269, USA.
| | - Qian Wu
- Pathology and Laboratory Medicine, University of Connecticut Health Centre, Farmington, CT, 06030, USA
| | - Rishikesh Pandey
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269, USA.
| | - Guoan Zheng
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, 06269, USA.
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4
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Liu X, Li M, Li Y, Chen Z, Zhuge C, Ouyang Y, Zhao Y, Lin Y, Xie Q, Yang C, Lai J. An ABHD17-like hydrolase screening system to identify de-S-acylation enzymes of protein substrates in plant cells. Plant Cell 2021; 33:3235-3249. [PMID: 34338800 PMCID: PMC8505870 DOI: 10.1093/plcell/koab199] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 07/29/2021] [Indexed: 05/25/2023]
Abstract
Protein S-acylation is an important post-translational modification in eukaryotes, regulating the subcellular localization, trafficking, stability, and activity of substrate proteins. The dynamic regulation of this reversible modification is mediated inversely by protein S-acyltransferases and de-S-acylation enzymes, but the de-S-acylation mechanism remains unclear in plant cells. Here, we characterized a group of putative protein de-S-acylation enzymes in Arabidopsis thaliana, including 11 members of Alpha/Beta Hydrolase Domain-containing Protein 17-like acyl protein thioesterases (ABAPTs). A robust system was then established for the screening of de-S-acylation enzymes of protein substrates in plant cells, based on the effects of substrate localization and confirmed via the protein S-acylation levels. Using this system, the ABAPTs, which specifically reduced the S-acylation levels and disrupted the plasma membrane localization of five immunity-related proteins, were identified respectively in Arabidopsis. Further results indicated that the de-S-acylation of RPM1-Interacting Protein 4, which was mediated by ABAPT8, resulted in an increase of cell death in Arabidopsis and Nicotiana benthamiana, supporting the physiological role of the ABAPTs in plants. Collectively, our current work provides a powerful and reliable system to identify the pairs of plant protein substrates and de-S-acylation enzymes for further studies on the dynamic regulation of plant protein S-acylation.
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Affiliation(s)
- Xiaoshi Liu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Min Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Yang Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Zian Chen
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Chun Zhuge
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Youwei Ouyang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Yawen Zhao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Yuxin Lin
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Qi Xie
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengwei Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Jianbin Lai
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, China
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5
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Raj K, Venayak N, Diep P, Golla SA, Yakunin AF, Mahadevan R. Automation assisted anaerobic phenotyping for metabolic engineering. Microb Cell Fact 2021; 20:184. [PMID: 34556155 PMCID: PMC8461876 DOI: 10.1186/s12934-021-01675-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 09/10/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microorganisms can be metabolically engineered to produce a wide range of commercially important chemicals. Advancements in computational strategies for strain design and synthetic biological techniques to construct the designed strains have facilitated the generation of large libraries of potential candidates for chemical production. Consequently, there is a need for high-throughput laboratory scale techniques to characterize and screen these candidates to select strains for further investigation in large scale fermentation processes. Several small-scale fermentation techniques, in conjunction with laboratory automation have enhanced the throughput of enzyme and strain phenotyping experiments. However, such high throughput experimentation typically entails large operational costs and generate massive amounts of laboratory plastic waste. RESULTS In this work, we develop an eco-friendly automation workflow that effectively calibrates and decontaminates fixed-tip liquid handling systems to reduce tip waste. We also investigate inexpensive methods to establish anaerobic conditions in microplates for high-throughput anaerobic phenotyping. To validate our phenotyping platform, we perform two case studies-an anaerobic enzyme screen, and a microbial phenotypic screen. We used our automation platform to investigate conditions under which several strains of E. coli exhibit the same phenotypes in 0.5 L bioreactors and in our scaled-down fermentation platform. We also propose the use of dimensionality reduction through t-distributed stochastic neighbours embedding (t-SNE) in conjunction with our phenotyping platform to effectively cluster similarly performing strains at the bioreactor scale. CONCLUSIONS Fixed-tip liquid handling systems can significantly reduce the amount of plastic waste generated in biological laboratories and our decontamination and calibration protocols could facilitate the widespread adoption of such systems. Further, the use of t-SNE in conjunction with our automation platform could serve as an effective scale-down model for bioreactor fermentations. Finally, by integrating an in-house data-analysis pipeline, we were able to accelerate the 'test' phase of the design-build-test-learn cycle of metabolic engineering.
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Affiliation(s)
- Kaushik Raj
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, M5S 3E5 Canada
| | - Naveen Venayak
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, M5S 3E5 Canada
| | - Patrick Diep
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, M5S 3E5 Canada
| | - Sai Akhil Golla
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, M5S 3E5 Canada
| | - Alexander F. Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, M5S 3E5 Canada
- School of Natural Sciences, Bangor University, Bangor, LL57 2DG UK
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, M5S 3E5 Canada
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, M5S 3G9 Canada
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6
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Woyke S, Ströhle M, Brugger H, Strapazzon G, Gatterer H, Mair N, Haller T. High-throughput determination of oxygen dissociation curves in a microplate reader-A novel, quantitative approach. Physiol Rep 2021; 9:e14995. [PMID: 34427400 PMCID: PMC8383715 DOI: 10.14814/phy2.14995] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 07/10/2021] [Indexed: 11/24/2022] Open
Abstract
In vitro determination of the hemoglobin oxygen dissociation curve (ODC) requires highly elaborate, specialized, and costly technical equipment. In addition, there is a lack of methods that combine reliable ODC recordings with high throughput in small blood samples for routine analysis. We here introduce a modified, commercial 96-well plate with an integrated unidirectional gas flow system specifically adapted for use in fluorescence microplate readers. Up to 92 samples of whole or hemolyzed, buffered or unbuffered blood, including appropriate controls or internal standard hemoglobin solutions, can be analyzed within ~25 min. Oxygen saturation is measured in each well with dual wavelength spectroscopy, and oxygen partial pressure using fluorescence lifetime of commercial oxygen sensors at the in- and outlet ports of the gas-flow system. Precision and accuracy of this method have been determined and were compared with those of a standard method. We further present two applications that exemplarily highlight the usefulness and impact of this novel approach for clinical diagnostics or basic research.
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Affiliation(s)
- Simon Woyke
- Department of Anaesthesiology and Critical Care MedicineMedical University of InnsbruckInnsbruckAustria
- Institute of Mountain Emergency MedicineEurac ResearchBolzanoItaly
| | - Mathias Ströhle
- Department of Anaesthesiology and Critical Care MedicineMedical University of InnsbruckInnsbruckAustria
| | - Hermann Brugger
- Department of Anaesthesiology and Critical Care MedicineMedical University of InnsbruckInnsbruckAustria
- Institute of Mountain Emergency MedicineEurac ResearchBolzanoItaly
| | - Giacomo Strapazzon
- Department of Anaesthesiology and Critical Care MedicineMedical University of InnsbruckInnsbruckAustria
- Institute of Mountain Emergency MedicineEurac ResearchBolzanoItaly
| | - Hannes Gatterer
- Institute of Mountain Emergency MedicineEurac ResearchBolzanoItaly
| | - Norbert Mair
- Department of Physiology and Medical PhysicsInstitute of PhysiologyMedical University of InnsbruckInnsbruckAustria
| | - Thomas Haller
- Department of Physiology and Medical PhysicsInstitute of PhysiologyMedical University of InnsbruckInnsbruckAustria
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7
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Gard AL, Luu RJ, Miller CR, Maloney R, Cain BP, Marr EE, Burns DM, Gaibler R, Mulhern TJ, Wong CA, Alladina J, Coppeta JR, Liu P, Wang JP, Azizgolshani H, Fezzie RF, Balestrini JL, Isenberg BC, Medoff BD, Finberg RW, Borenstein JT. High-throughput human primary cell-based airway model for evaluating influenza, coronavirus, or other respiratory viruses in vitro. Sci Rep 2021; 11:14961. [PMID: 34294757 PMCID: PMC8298517 DOI: 10.1038/s41598-021-94095-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 07/01/2021] [Indexed: 12/15/2022] Open
Abstract
Influenza and other respiratory viruses present a significant threat to public health, national security, and the world economy, and can lead to the emergence of global pandemics such as from COVID-19. A barrier to the development of effective therapeutics is the absence of a robust and predictive preclinical model, with most studies relying on a combination of in vitro screening with immortalized cell lines and low-throughput animal models. Here, we integrate human primary airway epithelial cells into a custom-engineered 96-device platform (PREDICT96-ALI) in which tissues are cultured in an array of microchannel-based culture chambers at an air-liquid interface, in a configuration compatible with high resolution in-situ imaging and real-time sensing. We apply this platform to influenza A virus and coronavirus infections, evaluating viral infection kinetics and antiviral agent dosing across multiple strains and donor populations of human primary cells. Human coronaviruses HCoV-NL63 and SARS-CoV-2 enter host cells via ACE2 and utilize the protease TMPRSS2 for spike protein priming, and we confirm their expression, demonstrate infection across a range of multiplicities of infection, and evaluate the efficacy of camostat mesylate, a known inhibitor of HCoV-NL63 infection. This new capability can be used to address a major gap in the rapid assessment of therapeutic efficacy of small molecules and antiviral agents against influenza and other respiratory viruses including coronaviruses.
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Affiliation(s)
- A L Gard
- Bioengineering Division, Draper, Cambridge, MA, 02139, USA
| | - R J Luu
- Bioengineering Division, Draper, Cambridge, MA, 02139, USA
| | - C R Miller
- Bioengineering Division, Draper, Cambridge, MA, 02139, USA
| | - R Maloney
- Bioengineering Division, Draper, Cambridge, MA, 02139, USA
| | - B P Cain
- Bioengineering Division, Draper, Cambridge, MA, 02139, USA
| | - E E Marr
- Bioengineering Division, Draper, Cambridge, MA, 02139, USA
| | - D M Burns
- Bioengineering Division, Draper, Cambridge, MA, 02139, USA
| | - R Gaibler
- Bioengineering Division, Draper, Cambridge, MA, 02139, USA
| | - T J Mulhern
- Bioengineering Division, Draper, Cambridge, MA, 02139, USA
| | - C A Wong
- Bioengineering Division, Draper, Cambridge, MA, 02139, USA
| | - J Alladina
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - J R Coppeta
- Bioengineering Division, Draper, Cambridge, MA, 02139, USA
| | - P Liu
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - J P Wang
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - H Azizgolshani
- Bioengineering Division, Draper, Cambridge, MA, 02139, USA
| | | | - J L Balestrini
- Bioengineering Division, Draper, Cambridge, MA, 02139, USA
| | - B C Isenberg
- Bioengineering Division, Draper, Cambridge, MA, 02139, USA
| | - B D Medoff
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - R W Finberg
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - J T Borenstein
- Bioengineering Division, Draper, Cambridge, MA, 02139, USA.
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8
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Li C, Callahan AJ, Simon MD, Totaro KA, Mijalis AJ, Phadke KS, Zhang G, Hartrampf N, Schissel CK, Zhou M, Zong H, Hanson GJ, Loas A, Pohl NLB, Verhoeven DE, Pentelute BL. Fully automated fast-flow synthesis of antisense phosphorodiamidate morpholino oligomers. Nat Commun 2021; 12:4396. [PMID: 34285203 PMCID: PMC8292409 DOI: 10.1038/s41467-021-24598-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 06/11/2021] [Indexed: 11/11/2022] Open
Abstract
Rapid development of antisense therapies can enable on-demand responses to new viral pathogens and make personalized medicine for genetic diseases practical. Antisense phosphorodiamidate morpholino oligomers (PMOs) are promising candidates to fill such a role, but their challenging synthesis limits their widespread application. To rapidly prototype potential PMO drug candidates, we report a fully automated flow-based oligonucleotide synthesizer. Our optimized synthesis platform reduces coupling times by up to 22-fold compared to previously reported methods. We demonstrate the power of our automated technology with the synthesis of milligram quantities of three candidate therapeutic PMO sequences for an unserved class of Duchenne muscular dystrophy (DMD). To further test our platform, we synthesize a PMO that targets the genomic mRNA of SARS-CoV-2 and demonstrate its antiviral effects. This platform could find broad application not only in designing new SARS-CoV-2 and DMD antisense therapeutics, but also for rapid development of PMO candidates to treat new and emerging diseases.
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MESH Headings
- Animals
- COVID-19/virology
- Chemistry Techniques, Synthetic/instrumentation
- Chemistry, Pharmaceutical/instrumentation
- Chlorocebus aethiops
- Communicable Diseases, Emerging/drug therapy
- Communicable Diseases, Emerging/microbiology
- Disease Models, Animal
- High-Throughput Screening Assays/instrumentation
- High-Throughput Screening Assays/methods
- Humans
- Morpholinos/chemical synthesis
- Morpholinos/pharmacology
- Morpholinos/therapeutic use
- Muscular Dystrophy, Duchenne/drug therapy
- Muscular Dystrophy, Duchenne/genetics
- Oligonucleotides, Antisense/chemical synthesis
- Oligonucleotides, Antisense/pharmacology
- Oligonucleotides, Antisense/therapeutic use
- Precision Medicine/methods
- RNA, Messenger/antagonists & inhibitors
- RNA, Viral/antagonists & inhibitors
- SARS-CoV-2/genetics
- Time Factors
- Vero Cells
- COVID-19 Drug Treatment
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Affiliation(s)
- Chengxi Li
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alex J Callahan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mark D Simon
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kyle A Totaro
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alexander J Mijalis
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kruttika-Suhas Phadke
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Genwei Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nina Hartrampf
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- University of Zurich, Department of Chemistry, Zurich, Switzerland
| | - Carly K Schissel
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ming Zhou
- Sarepta Therapeutics, Cambridge, MA, USA
| | - Hong Zong
- Sarepta Therapeutics, Cambridge, MA, USA
| | | | - Andrei Loas
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicola L B Pohl
- Department of Chemistry, Indiana University, Bloomington, IN, USA
| | - David E Verhoeven
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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9
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Xia Y, Chen H, Li J, Hu H, Qian Q, He RX, Ding Z, Guo SS. Acoustic Droplet-Assisted Superhydrophilic-Superhydrophobic Microarray Platform for High-Throughput Screening of Patient-Derived Tumor Spheroids. ACS Appl Mater Interfaces 2021; 13:23489-23501. [PMID: 33983701 DOI: 10.1021/acsami.1c06655] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Cell-based high-throughput screening is a key step in the current disease-based research, drug development, and precision medicine. However, it is challenging to establish a rapid culture and screening platform for rare cells (patient-derived) due to the obvious differences between the traditional 2D cell model and the tumor microenvironment, as well as the lack of a low-consumption screening platform for low numbers of cells. Here, we developed an acoustic drop-assisted superhydrophilic-superhydrophobic microarray platform for the rapid culture and screening of a few cells. By employing hydrophilic and hydrophobic microarrays, we can automatically distribute the cell suspension into uniform droplets, and these cells can spontaneously form compact 3D cell spheroids within 36 h (similar to the microenvironment of tumors in vivo). By using the acoustic droplet ejection device, we can accurately inject a drug solution with a volume of ∼pL to ∼nL into the droplet, and the whole process can be completed within 20 ms (one print). By using three different cell lines (Caco-2, MCF-7, and HeLa) to optimize the platform, the culture and screening of five patients' colon cancer were subsequently realized. Using three conventional chemotherapeutics (5-fluorouracil, cetuximab, and panitumumab) of various concentrations, the best treatment was screened out and compared with the actual treatment effect of the patients, and the results were extremely similar. As a proof-of-concept application, we have proved that our platform can quickly cultivate patient samples and effectively screen the best treatment methods, highlighting its wide application in precision medicine, basic tumor research, and drug development.
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Affiliation(s)
- Yu Xia
- Key Laboratory of Artificial Micro/Nano-Structures, Ministry of Education School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Hui Chen
- Key Laboratory of Artificial Micro/Nano-Structures, Ministry of Education School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Juan Li
- Key Laboratory of Artificial Micro/Nano-Structures, Ministry of Education School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Hang Hu
- Department of Colorectal and Anal Surgery, Hubei Key Laboratory of Intestinal and Colorectal Diseases, Zhongnan Hospital of Wuhan University, Wuhan 430072, China
| | - Qun Qian
- Department of Colorectal and Anal Surgery, Hubei Key Laboratory of Intestinal and Colorectal Diseases, Zhongnan Hospital of Wuhan University, Wuhan 430072, China
| | - Rong-Xiang He
- Institute for Interdisciplinary Research & Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education, Jianghan University, Wuhan 430056, China
| | - Zhao Ding
- Department of Colorectal and Anal Surgery, Hubei Key Laboratory of Intestinal and Colorectal Diseases, Zhongnan Hospital of Wuhan University, Wuhan 430072, China
| | - Shi-Shang Guo
- Key Laboratory of Artificial Micro/Nano-Structures, Ministry of Education School of Physics and Technology, Wuhan University, Wuhan 430072, China
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10
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Warman C, Sullivan CM, Preece J, Buchanan ME, Vejlupkova Z, Jaiswal P, Fowler JE. A cost-effective maize ear phenotyping platform enables rapid categorization and quantification of kernels. Plant J 2021; 106:566-579. [PMID: 33476427 DOI: 10.1111/tpj.15166] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 12/30/2020] [Accepted: 01/13/2021] [Indexed: 06/12/2023]
Abstract
High-throughput phenotyping systems are powerful, dramatically changing our ability to document, measure, and detect biological phenomena. Here, we describe a cost-effective combination of a custom-built imaging platform and deep-learning-based computer vision pipeline. A minimal version of the maize (Zea mays) ear scanner was built with low-cost and readily available parts. The scanner rotates a maize ear while a digital camera captures a video of the surface of the ear, which is then digitally flattened into a two-dimensional projection. Segregating GFP and anthocyanin kernel phenotypes are clearly distinguishable in ear projections and can be manually annotated and analyzed using image analysis software. Increased throughput was attained by designing and implementing an automated kernel counting system using transfer learning and a deep learning object detection model. The computer vision model was able to rapidly assess over 390 000 kernels, identifying male-specific transmission defects across a wide range of GFP-marked mutant alleles. This includes a previously undescribed defect putatively associated with mutation of Zm00001d002824, a gene predicted to encode a vacuolar processing enzyme. Thus, by using this system, the quantification of transmission data and other ear and kernel phenotypes can be accelerated and scaled to generate large datasets for robust analyses.
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Affiliation(s)
- Cedar Warman
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Christopher M Sullivan
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USA
| | - Justin Preece
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Michaela E Buchanan
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USA
| | - Zuzana Vejlupkova
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Pankaj Jaiswal
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - John E Fowler
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, Oregon, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USA
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11
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Warman C, Sullivan CM, Preece J, Buchanan ME, Vejlupkova Z, Jaiswal P, Fowler JE. A cost-effective maize ear phenotyping platform enables rapid categorization and quantification of kernels. Plant J 2021; 106:566-579. [PMID: 33476427 DOI: 10.1101/2020.07.12.199000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 12/30/2020] [Accepted: 01/13/2021] [Indexed: 05/24/2023]
Abstract
High-throughput phenotyping systems are powerful, dramatically changing our ability to document, measure, and detect biological phenomena. Here, we describe a cost-effective combination of a custom-built imaging platform and deep-learning-based computer vision pipeline. A minimal version of the maize (Zea mays) ear scanner was built with low-cost and readily available parts. The scanner rotates a maize ear while a digital camera captures a video of the surface of the ear, which is then digitally flattened into a two-dimensional projection. Segregating GFP and anthocyanin kernel phenotypes are clearly distinguishable in ear projections and can be manually annotated and analyzed using image analysis software. Increased throughput was attained by designing and implementing an automated kernel counting system using transfer learning and a deep learning object detection model. The computer vision model was able to rapidly assess over 390 000 kernels, identifying male-specific transmission defects across a wide range of GFP-marked mutant alleles. This includes a previously undescribed defect putatively associated with mutation of Zm00001d002824, a gene predicted to encode a vacuolar processing enzyme. Thus, by using this system, the quantification of transmission data and other ear and kernel phenotypes can be accelerated and scaled to generate large datasets for robust analyses.
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Affiliation(s)
- Cedar Warman
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Christopher M Sullivan
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USA
| | - Justin Preece
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Michaela E Buchanan
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USA
| | - Zuzana Vejlupkova
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Pankaj Jaiswal
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - John E Fowler
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, Oregon, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USA
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12
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Ni S, Zhuo Z, Pan Y, Yu Y, Li F, Liu J, Wang L, Wu X, Li D, Wan Y, Zhang L, Yang Z, Zhang BT, Lu A, Zhang G. Recent Progress in Aptamer Discoveries and Modifications for Therapeutic Applications. ACS Appl Mater Interfaces 2021; 13:9500-9519. [PMID: 32603135 DOI: 10.1021/acsami.0c05750] [Citation(s) in RCA: 228] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Aptamers are oligonucleotide sequences with a length of about 25-80 bases which have abilities to bind to specific target molecules that rival those of monoclonal antibodies. They are attracting great attention in diverse clinical translations on account of their various advantages, including prolonged storage life, little batch-to-batch differences, very low immunogenicity, and feasibility of chemical modifications for enhancing stability, prolonging the half-life in serum, and targeted delivery. In this Review, we demonstrate the emerging aptamer discovery technologies in developing advanced techniques for producing aptamers with high performance consistently and efficiently as well as requiring less cost and resources but offering a great chance of success. Further, the diverse modifications of aptamers for therapeutic applications including therapeutic agents, aptamer-drug conjugates, and targeted delivery materials are comprehensively summarized.
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Affiliation(s)
- Shuaijian Ni
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Zhenjian Zhuo
- School of Chinese Medicine, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Yufei Pan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yuanyuan Yu
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Fangfei Li
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Jin Liu
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Luyao Wang
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Xiaoqiu Wu
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Dijie Li
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Youyang Wan
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Lihe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Bao-Ting Zhang
- School of Chinese Medicine, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Aiping Lu
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Ge Zhang
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
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13
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Niculescu AG, Chircov C, Bîrcă AC, Grumezescu AM. Fabrication and Applications of Microfluidic Devices: A Review. Int J Mol Sci 2021; 22:2011. [PMID: 33670545 PMCID: PMC7921936 DOI: 10.3390/ijms22042011] [Citation(s) in RCA: 133] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/13/2021] [Accepted: 02/15/2021] [Indexed: 12/11/2022] Open
Abstract
Microfluidics is a relatively newly emerged field based on the combined principles of physics, chemistry, biology, fluid dynamics, microelectronics, and material science. Various materials can be processed into miniaturized chips containing channels and chambers in the microscale range. A diverse repertoire of methods can be chosen to manufacture such platforms of desired size, shape, and geometry. Whether they are used alone or in combination with other devices, microfluidic chips can be employed in nanoparticle preparation, drug encapsulation, delivery, and targeting, cell analysis, diagnosis, and cell culture. This paper presents microfluidic technology in terms of the available platform materials and fabrication techniques, also focusing on the biomedical applications of these remarkable devices.
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Affiliation(s)
- Adelina-Gabriela Niculescu
- Faculty of Engineering in Foreign Languages, University Politehnica of Bucharest, 011061 Bucharest, Romania;
| | - Cristina Chircov
- Faculty of Applied Chemistry and Materials Science, University Politehnica of Bucharest, 011061 Bucharest, Romania; (C.C.); (A.C.B.)
| | - Alexandra Cătălina Bîrcă
- Faculty of Applied Chemistry and Materials Science, University Politehnica of Bucharest, 011061 Bucharest, Romania; (C.C.); (A.C.B.)
| | - Alexandru Mihai Grumezescu
- Faculty of Applied Chemistry and Materials Science, University Politehnica of Bucharest, 011061 Bucharest, Romania; (C.C.); (A.C.B.)
- Research Institute of the University of Bucharest—ICUB, University of Bucharest, 050657 Bucharest, Romania
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14
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Wang C, Sensale S, Pan Z, Senapati S, Chang HC. Slowing down DNA translocation through solid-state nanopores by edge-field leakage. Nat Commun 2021; 12:140. [PMID: 33420061 PMCID: PMC7794543 DOI: 10.1038/s41467-020-20409-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/23/2020] [Indexed: 01/26/2023] Open
Abstract
Solid-state nanopores allow high-throughput single-molecule detection but identifying and even registering all translocating small molecules remain key challenges due to their high translocation speeds. We show here the same electric field that drives the molecules into the pore can be redirected to selectively pin and delay their transport. A thin high-permittivity dielectric coating on bullet-shaped polymer nanopores permits electric field leakage at the pore tip to produce a voltage-dependent surface field on the entry side that can reversibly edge-pin molecules. This mechanism renders molecular entry an activated process with sensitive exponential dependence on the bias voltage and molecular rigidity. This sensitivity allows us to selectively prolong the translocation time of short single-stranded DNA molecules by up to 5 orders of magnitude, to as long as minutes, allowing discrimination against their double-stranded duplexes with 97% confidence.
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Affiliation(s)
- Ceming Wang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, USA
| | - Sebastian Sensale
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN, USA
| | - Zehao Pan
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, USA
| | - Satyajyoti Senapati
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, USA
| | - Hsueh-Chia Chang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, USA.
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN, USA.
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15
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Rathore AS, Bhambure R. High-Throughput Process Development: I-Process Chromatography. Methods Mol Biol 2021; 2178:11-20. [PMID: 33128739 DOI: 10.1007/978-1-0716-0775-6_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Chromatographic separation serves as "a workhorse" for downstream process development and plays a key role in the removal of product-related, host-cell-related, and process-related impurities. Complex and poorly characterized raw materials and feed material, low feed concentration, product instability, and poor mechanistic understanding of the processes are some of the critical challenges that are faced during the development of a chromatographic step. Traditional process development is performed as a trial-and-error-based evaluation and often leads to a suboptimal process. A high-throughput process development (HTPD) platform involves the integration of miniaturization, automation, and parallelization and provides a systematic approach for time- and resource-efficient chromatographic process development. Creation of such platforms requires the integration of mechanistic knowledge of the process with various statistical tools for data analysis. The relevance of such a platform is high in view of the constraints with respect to time and resources that the biopharma industry faces today.This protocol describes the steps involved in performing the HTPD of chromatography steps. It describes the operation of a commercially available device (PreDictor™ plates from GE Healthcare). This device is available in 96-well format with 2 or 6 μL well size. We also discuss the challenges that one faces when performing such experiments as well as possible solutions to alleviate them. Besides describing the operation of the device, the protocol also presents an approach for statistical analysis of the data that are gathered from such a platform. A case study involving the use of the protocol for examining ion exchange chromatography of the Granulocyte Colony Stimulating Factor (GCSF), a therapeutic product, is briefly discussed. This is intended to demonstrate the usefulness of this protocol in generating data that are representative of the data obtained at the traditional lab scale. The agreement in the data is indeed very significant (regression coefficient 0.93). We think that this protocol will be of significant value to those involved in performing the high-throughput process development of the chromatography process.
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Affiliation(s)
- Anurag S Rathore
- Department of Chemical Engineering, Indian Institute of Technology, New Delhi, India.
| | - R Bhambure
- Department of Chemical Engineering, Indian Institute of Technology, New Delhi, India
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16
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Cabanne C, Santarelli X. Media Selection in Ion Exchange Chromatography in a Single Microplate. Methods Mol Biol 2021; 2178:27-33. [PMID: 33128741 DOI: 10.1007/978-1-0716-0775-6_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
High-throughput process development is more and more used in chromatography. Limitations are the tools provided by the manufacturers. Here, we describe a method to select ion exchange chromatographic media using a 96-well filter microplate.
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17
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Plant H, Murray D, Semple H, Davies G, Sinclair I, Holdgate GA. The Use of Acoustic Mist Ionization Mass Spectrometry for High-Throughput Screening. Methods Mol Biol 2021; 2263:217-230. [PMID: 33877600 DOI: 10.1007/978-1-0716-1197-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
It is clear from the analysis of the distribution of approved drug targets that enzymes continue to be a major target class for the pharmaceutical industry. The application of high-throughput screens designed to monitor the activity of these enzyme targets, and the ability of test compounds to modulate this activity, is still the predominant hit finding approach in the industry. The widespread use of enzyme activity-based screens has led to the development of several useful guidelines for the development and validation of robust and reliable assays. Key learnings for the development, validation, and implementation of acoustic mist ionization mass spectrometry for high-throughput enzyme assays are described.
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Affiliation(s)
- Helen Plant
- Hit Discovery, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Alderley Park, UK.
| | - David Murray
- Hit Discovery, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Alderley Park, UK
| | - Hannah Semple
- Hit Discovery, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Alderley Park, UK
| | - Gareth Davies
- Hit Discovery, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Alderley Park, UK
| | - Ian Sinclair
- Hit Discovery, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Alderley Park, UK
| | - Geoffrey A Holdgate
- Hit Discovery, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Alderley Park, UK
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18
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Riester O, Borgolte M, Csuk R, Deigner HP. Challenges in Bone Tissue Regeneration: Stem Cell Therapy, Biofunctionality and Antimicrobial Properties of Novel Materials and Its Evolution. Int J Mol Sci 2020; 22:E192. [PMID: 33375478 PMCID: PMC7794985 DOI: 10.3390/ijms22010192] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 02/06/2023] Open
Abstract
An aging population leads to increasing demand for sustained quality of life with the aid of novel implants. Patients expect fast healing and few complications after surgery. Increased biofunctionality and antimicrobial behavior of implants, in combination with supportive stem cell therapy, can meet these expectations. Recent research in the field of bone implants and the implementation of autologous mesenchymal stem cells in the treatment of bone defects is outlined and evaluated in this review. The article highlights several advantages, limitations and advances for metal-, ceramic- and polymer-based implants and discusses the future need for high-throughput screening systems used in the evaluation of novel developed materials and stem cell therapies. Automated cell culture systems, microarray assays or microfluidic devices are required to efficiently analyze the increasing number of new materials and stem cell-assisted therapies. Approaches described in the literature to improve biocompatibility, biofunctionality and stem cell differentiation efficiencies of implants range from the design of drug-laden nanoparticles to chemical modification and the selection of materials that mimic the natural tissue. Combining suitable implants with mesenchymal stem cell treatment promises to shorten healing time and increase treatment success. Most research studies focus on creating antibacterial materials or modifying implants with antibacterial coatings in order to address the increasing number of complications after surgeries that are mostly caused by bacterial infections. Moreover, treatment of multiresistant pathogens will pose even bigger challenges in hospitals in the future, according to the World Health Organization (WHO). These antibacterial materials will help to reduce infections after surgery and the number of antibiotic treatments that contribute to the emergence of new multiresistant pathogens, whilst the antibacterial implants will help reduce the amount of antibiotics used in clinical treatment.
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Affiliation(s)
- Oliver Riester
- Institute of Precision Medicine, Medical and Life Sciences Faculty, Furtwangen University, Jakob-Kienzle-Strasse 17, 78054 Villingen-Schwenningen, Germany; (O.R.); (M.B.)
| | - Max Borgolte
- Institute of Precision Medicine, Medical and Life Sciences Faculty, Furtwangen University, Jakob-Kienzle-Strasse 17, 78054 Villingen-Schwenningen, Germany; (O.R.); (M.B.)
| | - René Csuk
- Institute of Organic Chemistry, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 2, 06120 Halle (Saale), Germany;
| | - Hans-Peter Deigner
- Institute of Precision Medicine, Medical and Life Sciences Faculty, Furtwangen University, Jakob-Kienzle-Strasse 17, 78054 Villingen-Schwenningen, Germany; (O.R.); (M.B.)
- EXIM Department, Fraunhofer Institute IZI, Leipzig, Schillingallee 68, 18057 Rostock, Germany
- Faculty of Science, University of Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
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19
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Boobphahom S, Nguyet Ly M, Soum V, Pyun N, Kwon OS, Rodthongkum N, Shin K. Recent Advances in Microfluidic Paper-Based Analytical Devices toward High-Throughput Screening. Molecules 2020; 25:E2970. [PMID: 32605281 PMCID: PMC7412548 DOI: 10.3390/molecules25132970] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 02/06/2023] Open
Abstract
Microfluidic paper-based analytical devices (µPADs) have become promising tools offering various analytical applications for chemical and biological assays at the point-of-care (POC). Compared to traditional microfluidic devices, µPADs offer notable advantages; they are cost-effective, easily fabricated, disposable, and portable. Because of our better understanding and advanced engineering of µPADs, multistep assays, high detection sensitivity, and rapid result readout have become possible, and recently developed µPADs have gained extensive interest in parallel analyses to detect biomarkers of interest. In this review, we focus on recent developments in order to achieve µPADs with high-throughput capability. We discuss existing fabrication techniques and designs, and we introduce and discuss current detection methods and their applications to multiplexed detection assays in relation to clinical diagnosis, drug analysis and screening, environmental monitoring, and food and beverage quality control. A summary with future perspectives for µPADs is also presented.
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Affiliation(s)
- Siraprapa Boobphahom
- Metallurgy and Materials Science Research Institute, Chulalongkorn University, Soi Chula 12, Phayathai Road, Pathumwan, Bangkok 10330, Thailand;
| | - Mai Nguyet Ly
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul 04107, Korea; (M.N.L.); (V.S.); (N.P.); (O.-S.K.)
| | - Veasna Soum
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul 04107, Korea; (M.N.L.); (V.S.); (N.P.); (O.-S.K.)
| | - Nayoon Pyun
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul 04107, Korea; (M.N.L.); (V.S.); (N.P.); (O.-S.K.)
| | - Oh-Sun Kwon
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul 04107, Korea; (M.N.L.); (V.S.); (N.P.); (O.-S.K.)
| | - Nadnudda Rodthongkum
- Metallurgy and Materials Science Research Institute, Chulalongkorn University, Soi Chula 12, Phayathai Road, Pathumwan, Bangkok 10330, Thailand;
| | - Kwanwoo Shin
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul 04107, Korea; (M.N.L.); (V.S.); (N.P.); (O.-S.K.)
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20
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Hanyu Y, Kato M. Screening Antibody Libraries with Colony Assay Using scFv-Alkaline Phosphatase Fusion Proteins. Molecules 2020; 25:molecules25122905. [PMID: 32599779 PMCID: PMC7356641 DOI: 10.3390/molecules25122905] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/20/2020] [Accepted: 06/21/2020] [Indexed: 01/17/2023] Open
Abstract
Screening antibody libraries is an important step in establishing recombinant monoclonal antibodies. The colony assay can identify positive clones without almost any false-positives; however, its antibody library is smaller than those used in other recombinant screening methods such as phage display. Thus, to improve the efficiency of colony assays, it is necessary to increase library size per screening. Here, we report developing a colony assay with single-chain variable fragment (scFv) fused to the N-terminus of bacterial alkaline phosphatase (scFv-PhoA). The scFv-PhoA library was constructed in an expression vector specifically designed for this study. Use of this library allowed the successful and direct detection of positive clones exhibiting PhoA activity, without the need for a secondary antibody. Colony assay screening with scFv-PhoA is simple, rapid, offers a higher success rate than previous methods based on scFv libraries, and—most importantly—it enables high-throughput procedures.
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Affiliation(s)
- Yoshiro Hanyu
- Biomaterials Research Group, Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8566, Japan
- Correspondence: ; Tel.: +81-298-61-5542
| | - Mieko Kato
- Department of Biochemistry, Bio-Peak Co., Ltd., 584-70 Shimonojo, Takasaki 370-0854, Japan;
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21
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Watterson WJ, Tanyeri M, Watson AR, Cham CM, Shan Y, Chang EB, Eren AM, Tay S. Droplet-based high-throughput cultivation for accurate screening of antibiotic resistant gut microbes. eLife 2020; 9:e56998. [PMID: 32553109 PMCID: PMC7351490 DOI: 10.7554/elife.56998] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 06/14/2020] [Indexed: 12/16/2022] Open
Abstract
Traditional cultivation approaches in microbiology are labor-intensive, low-throughput, and yield biased sampling of environmental microbes due to ecological and evolutionary factors. New strategies are needed for ample representation of rare taxa and slow-growers that are often outcompeted by fast-growers in cultivation experiments. Here we describe a microfluidic platform that anaerobically isolates and cultivates microbial cells in millions of picoliter droplets and automatically sorts them based on colony density to enhance slow-growing organisms. We applied our strategy to a fecal microbiota transplant (FMT) donor stool using multiple growth media, and found significant increase in taxonomic richness and larger representation of rare and clinically relevant taxa among droplet-grown cells compared to conventional plates. Furthermore, screening the FMT donor stool for antibiotic resistance revealed 21 populations that evaded detection in plate-based assessment of antibiotic resistance. Our method improves cultivation-based surveys of diverse microbiomes to gain deeper insights into microbial functioning and lifestyles.
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Affiliation(s)
- William J Watterson
- Pritzker School of Molecular Engineering, The University of ChicagoChicagoUnited States
- Institute for Genomics and Systems Biology, The University of ChicagoChicagoUnited States
| | - Melikhan Tanyeri
- Pritzker School of Molecular Engineering, The University of ChicagoChicagoUnited States
- Institute for Genomics and Systems Biology, The University of ChicagoChicagoUnited States
- Department of Engineering, Duquesne UniversityPittsburghUnited States
| | - Andrea R Watson
- Department of Medicine, The University of ChicagoChicagoUnited States
| | - Candace M Cham
- Department of Medicine, The University of ChicagoChicagoUnited States
| | - Yue Shan
- Department of Medicine, The University of ChicagoChicagoUnited States
| | - Eugene B Chang
- Department of Medicine, The University of ChicagoChicagoUnited States
| | - A Murat Eren
- Department of Medicine, The University of ChicagoChicagoUnited States
- Graduate Program in the Biophysical Sciences, The University of ChicagoChicagoUnited States
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological LaboratoryWoods HoleUnited States
| | - Savaş Tay
- Pritzker School of Molecular Engineering, The University of ChicagoChicagoUnited States
- Institute for Genomics and Systems Biology, The University of ChicagoChicagoUnited States
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22
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Geldert A, Huang H, Herr AE. Probe-target hybridization depends on spatial uniformity of initial concentration condition across large-format chips. Sci Rep 2020; 10:8768. [PMID: 32472029 PMCID: PMC7260366 DOI: 10.1038/s41598-020-65563-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 04/23/2020] [Indexed: 12/30/2022] Open
Abstract
Diverse assays spanning from immunohistochemistry (IHC), to microarrays (protein, DNA), to high-throughput screens rely on probe-target hybridization to detect analytes. These large-format 'chips' array numerous hybridization sites across centimeter-scale areas. However, the reactions are prone to intra-assay spatial variation in hybridization efficiency. The mechanism of spatial bias in hybridization efficiency is poorly understood, particularly in IHC and in-gel immunoassays, where immobilized targets are heterogeneously distributed throughout a tissue or hydrogel network. In these systems, antibody probe hybridization to a target protein antigen depends on the interplay of dilution, thermodynamic partitioning, diffusion, and reaction. Here, we investigate parameters governing antibody probe transport and reaction (i.e., immunoprobing) in a large-format hydrogel immunoassay. Using transport and bimolecular binding theory, we identify a regime in which immunoprobing efficiency (η) is sensitive to the local concentration of applied antibody probe solution, despite the antibody probe being in excess compared to antigen. Sandwiching antibody probe solution against the hydrogel surface yields spatially nonuniform dilution. Using photopatterned fluorescent protein targets and a single-cell immunoassay, we identify regimes in which nonuniformly distributed antibody probe solution causes intra-assay variation in background and η. Understanding the physicochemical factors affecting probe-target hybridization reduces technical variation in large-format chips, improving measurement precision.
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Affiliation(s)
- Alisha Geldert
- UC Berkeley - UCSF Graduate Program in Bioengineering, Berkeley, United States
| | - Haiyan Huang
- Department of Statistics, University of California Berkeley, Berkeley, California, 94720, United States
- Center for Computational Biology, University of California Berkeley, Berkeley, California, 94720, United States
| | - Amy E Herr
- UC Berkeley - UCSF Graduate Program in Bioengineering, Berkeley, United States.
- Department of Bioengineering, University of California Berkeley, Berkeley, California, 94720, United States.
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23
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Hao H, Huang J, Liu P, Xue Y, Wang J, Jia F, Ren K, Jin Q, Ji J. Rapid Buildup Arrays with Orthogonal Biochemistry Gradients via Light-Induced Thiol-Ene "Click" Chemistry for High-Throughput Screening of Peptide Combinations. ACS Appl Mater Interfaces 2020; 12:20243-20252. [PMID: 32281779 DOI: 10.1021/acsami.0c03199] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The concept of high-throughput screening sheds new light on fabrication and analysis of materials. Herein, a combinatorial surface-modified platform with biochemical gradients was developed through thiol-ene "click" chemistry by adjusting the intensity of ultraviolet (UV) irradiation. Contact angle, X-ray photoelectron spectroscopy, and ellipsometry measurement results demonstrated that the sulfhydryl molecules including polyethylene glycol and RGD (arginine-glycine-aspartic acid) and REDV (arginine-glutamic acid-aspartic acid-valine) peptides can be directly attached onto alkene-modified substrates, in which the graft density can be well controlled by the intensity of UV irradiation. The multistep attachment of different molecules onto substrates is archived via the multistep UV-initiated thiol-ene "click" reaction. The high-throughput arrays with the gradient density of single ligand and the orthogonal gradient density of two ligands were rapidly fabricated via the one-step UV gradient irradiation and the two-step orthogonal UV gradient-initiated thiol-ene "click" reaction. Endothelial cells (ECs) and smooth muscle cells (SMCs) were cocultured on the array with the orthogonal gradient density of RGD and REDV to screen the peptide combination with high EC selectivity, which is essential for in situ endothelialization during stent implant. From 64, 8 × 8, combinations investigated, a special combinatorial surface representing the really high competitiveness of ECs over SMCs was screened. This platform puts forward a facile, high-throughput method to study the combinatorial variation of biochemical signals to cell behavior.
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Affiliation(s)
- Hongye Hao
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Junjie Huang
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Ping Liu
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Yunfan Xue
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Jing Wang
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Fan Jia
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Kefeng Ren
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Qiao Jin
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Jian Ji
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
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Gilbert-Girard S, Savijoki K, Yli-Kauhaluoma J, Fallarero A. Optimization of a High-Throughput 384-Well Plate-Based Screening Platform with Staphylococcus aureus ATCC 25923 and Pseudomonas aeruginosa ATCC 15442 Biofilms. Int J Mol Sci 2020; 21:ijms21093034. [PMID: 32344836 PMCID: PMC7246797 DOI: 10.3390/ijms21093034] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 04/22/2020] [Indexed: 02/08/2023] Open
Abstract
In recent years, bacterial infections have become a main concern following the spread of antimicrobial resistance. In addition, bacterial biofilms are known for their high tolerance to antimicrobials and they are regarded as a main cause of recalcitrant infections in humans. Many efforts have been deployed in order to find new antibacterial therapeutic options and the high-throughput screening (HTS) of large libraries of compounds is one of the utilized strategies. However, HTS efforts for anti-biofilm discovery remain uncommon. Here, we miniaturized a 96-well plate (96WP) screening platform, into a 384-well plate (384WP) format, based on a sequential viability and biomass measurements for the assessment of anti-biofilm activity. During the assay optimization process, different parameters were evaluated while using Staphylococcus aureus and Pseudomonas aeruginosa as the bacterial models. We compared the performance of the optimized 384WP platform to our previously established 96WP-based platform by carrying out a pilot screening of 100 compounds, followed by the screening of a library of 2000 compounds to identify new repurposed anti-biofilm agents. Our results show that the optimized 384WP platform is well-suited for screening purposes, allowing for the rapid screening of a higher number of compounds in a run in a reliable manner.
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Affiliation(s)
- Shella Gilbert-Girard
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, FI-00014 Helsinki, Finland; (K.S.); (A.F.)
- Correspondence:
| | - Kirsi Savijoki
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, FI-00014 Helsinki, Finland; (K.S.); (A.F.)
| | - Jari Yli-Kauhaluoma
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, FI-00014 Helsinki, Finland;
| | - Adyary Fallarero
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, FI-00014 Helsinki, Finland; (K.S.); (A.F.)
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25
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Park HM, Winton VJ, Drader JJ, Manalili Wheeler S, Lazar GA, Kelleher NL, Liu Y, Tran JC, Compton PD. Novel Interface for High-Throughput Analysis of Biotherapeutics by Electrospray Mass Spectrometry. Anal Chem 2020; 92:2186-2193. [PMID: 31880920 PMCID: PMC7008517 DOI: 10.1021/acs.analchem.9b04826] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
With the rapid rise of therapeutic antibodies and antibody-drug conjugates, significant investments have been made in developing workflows that utilize mass spectrometry to detect these intact molecules, the large fragments generated by their selective digestion, and the peptides generated by traditional proteomics workflows. The resultant data is used to gain insight into a wide range of parameters, including primary sequence, disulfide bonding, glycosylation patterns, biotransformation, and more. However, many of the technologies utilized to couple these workflows to mass spectrometers have significant limitations that force nonoptimal modifications to upstream sample preparation steps, limit the throughput of high-volume workflows, and prevent the harmonization of diverse experiments onto a single hardware platform. Here, we describe a new analytical platform that enables direct and high-throughput coupling to electrospray ionization mass spectrometry. The SampleStream platform is compatible with both native and denaturing electrospray, operates with a throughput of up to 15 s/sample, provides extensive concentration of dilute samples, and affords similar sensitivity to comparable liquid chromatographic methods.
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Affiliation(s)
- Hae-Min Park
- Proteomics Center of Excellence, Northwestern University, 2170 Campus Drive, Evanston, Illinois 60208, United States
| | - Valerie J. Winton
- Proteomics Center of Excellence, Northwestern University, 2170 Campus Drive, Evanston, Illinois 60208, United States
| | - Jared J. Drader
- Integrated Protein Technologies, Inc., 2170 Campus Drive, Evanston, IL 60208, United States
| | - Sheri Manalili Wheeler
- Integrated Protein Technologies, Inc., 2170 Campus Drive, Evanston, IL 60208, United States
| | - Greg A. Lazar
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Neil L. Kelleher
- Proteomics Center of Excellence, Northwestern University, 2170 Campus Drive, Evanston, Illinois 60208, United States
- Integrated Protein Technologies, Inc., 2170 Campus Drive, Evanston, IL 60208, United States
| | - Yichin Liu
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - John C. Tran
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Philip D. Compton
- Proteomics Center of Excellence, Northwestern University, 2170 Campus Drive, Evanston, Illinois 60208, United States
- Integrated Protein Technologies, Inc., 2170 Campus Drive, Evanston, IL 60208, United States
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26
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Halim AB. Do We have a Satisfactory Cell Viability Assay? Review of the Currently Commercially-Available Assays. Curr Drug Discov Technol 2020; 17:2-22. [PMID: 30251606 DOI: 10.2174/1570163815666180925095433] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 09/13/2018] [Accepted: 09/18/2018] [Indexed: 06/08/2023]
Abstract
Cell-based assays are an important part of the drug discovery process and clinical research. One of the main hurdles is to design sufficiently robust assays with adequate signal to noise parameters while maintaining the inherent physiology of the cells and not interfering with the pharmacology of target being investigated. A plethora of assays that assess cell viability (or cell heath in general) are commercially available and can be classified under different categories according to their concepts and principle of reactions. The assays are valuable tools, however, suffer from a large number of limitations. Some of these limitations can be procedural or operational, but others can be critical as those related to a poor concept or the lack of proof of concept of an assay, e.g. those relying on differential permeability of dyes in-and-out of viable versus compromised cell membranes. While the assays can differentiate between dead and live cells, most, if not all, of them can just assess the relative performance of cells rather than providing a clear distinction between healthy and dying cells. The possible impact of relatively high molecular weight dyes, used in most of the assay, on cell viability has not been addressed. More innovative assays are needed, and until better alternatives are developed, setup of current cell-based studies and data interpretation should be made with the limitations in mind. Negative and positive control should be considered whenever feasible. Also, researchers should use more than one orthogonal method for better assessment of cell health.
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Affiliation(s)
- Abdel-Baset Halim
- VP Translational Medicine, Biomarkers & Diagnostics, Celldex Therapeutics, 53 Frontage Road, Suite 220, Hampton, NJ 08827-4032, United States
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27
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Li X, Feng H, Li Z, Shi Y, Tian J, Zhao C, Yu M, Liu Z, Li H, Shi B, Wang Q, Li L, Wang D, Zhu L, Liu R, Li Z. High-Throughput Identification and Screening of Single Microbial Cells by Nanobowl Array. ACS Appl Mater Interfaces 2019; 11:44933-44940. [PMID: 31675212 DOI: 10.1021/acsami.9b08662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
High-throughput screening and fast identification of single bacterial cells are crucial for clinical diagnosis, bioengineering, and fermentation engineering. Although single-cell technologies have been developed extensively in recent years, the single-cell technologies for bacteria still need further exploration. In this study, we demonstrate an identification and screening technology for single bacterial cells based on a large-scale nanobowl array, which is well-ordered and size-adjustable for use with different kinds of bacteria. When the culture medium with monodispersed bacteria was placed on the nanobowl array, it successfully enabled loading of single bacterium into a single nanobowl. Because of the limitative size and depth of the nanobowls, mixture of different bacteria species could be screened according to their sizes. In addition, with the help of a low electrical current, the bacteria can be further screened according to their intrinsic surface charges. If combined with micromanipulation technology, high-throughput single bacterial selection can be achieved in future.
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Affiliation(s)
- Xiuyan Li
- Beijing Institute of Graphic Communication , Beijing 102600 , P. R. China
| | - Hongqing Feng
- CAS Center for Excellence in Nanoscience, Beijing Key Laboratory of Micro-nano Energy and Sensor , Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences , Beijing 100083 , P. R. China
- School of Nanoscience and Technology , University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Zhe Li
- CAS Center for Excellence in Nanoscience, Beijing Key Laboratory of Micro-nano Energy and Sensor , Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences , Beijing 100083 , P. R. China
- School of Nanoscience and Technology , University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Yue Shi
- Beijing Institute of Graphic Communication , Beijing 102600 , P. R. China
| | - Jingjing Tian
- CAS Center for Excellence in Nanoscience, Beijing Key Laboratory of Micro-nano Energy and Sensor , Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences , Beijing 100083 , P. R. China
- School of Nanoscience and Technology , University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Chaochao Zhao
- CAS Center for Excellence in Nanoscience, Beijing Key Laboratory of Micro-nano Energy and Sensor , Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences , Beijing 100083 , P. R. China
- School of Nanoscience and Technology , University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Min Yu
- School of Stomatology and Medicine , Foshan University , Foshan 528000 , P. R. China
| | - Zhuo Liu
- CAS Center for Excellence in Nanoscience, Beijing Key Laboratory of Micro-nano Energy and Sensor , Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences , Beijing 100083 , P. R. China
| | - Hu Li
- CAS Center for Excellence in Nanoscience, Beijing Key Laboratory of Micro-nano Energy and Sensor , Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences , Beijing 100083 , P. R. China
| | - Bojing Shi
- CAS Center for Excellence in Nanoscience, Beijing Key Laboratory of Micro-nano Energy and Sensor , Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences , Beijing 100083 , P. R. China
| | - Qian Wang
- Beijing Institute of Graphic Communication , Beijing 102600 , P. R. China
| | - Luhai Li
- Beijing Institute of Graphic Communication , Beijing 102600 , P. R. China
| | - Dongshu Wang
- State Key Laboratory of Pathogen and Biosecurity , Beijing Institute of Biotechnology , Beijing 100071 , P. R. China
| | - Li Zhu
- State Key Laboratory of Pathogen and Biosecurity , Beijing Institute of Biotechnology , Beijing 100071 , P. R. China
| | - Ruping Liu
- Beijing Institute of Graphic Communication , Beijing 102600 , P. R. China
| | - Zhou Li
- CAS Center for Excellence in Nanoscience, Beijing Key Laboratory of Micro-nano Energy and Sensor , Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences , Beijing 100083 , P. R. China
- School of Nanoscience and Technology , University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
- Center on Nanoenergy Research, School of Physical Science and Technology , Guangxi University , Nanning 530004 , P. R. China
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Fu Q, Liu L, Si Y, Yu J, Ding B. Shapeable, Underwater Superelastic, and Highly Phosphorylated Nanofibrous Aerogels for Large-Capacity and High-Throughput Protein Separation. ACS Appl Mater Interfaces 2019; 11:44874-44885. [PMID: 31670935 DOI: 10.1021/acsami.9b15760] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Developing nanofibrous aerogels with high porosity, robust underwater mechanical strength, and rich adsorption ligands, has been considered as one of the most promising strategies for preparing the next generation of high-efficiency and high-throughput chromatographic media; yet great challenges still remain. Herein, a novel type of highly phosphorylated nanofibrous aerogels (PNFAs) is fabricated, for the first time, by combining electrospinning, cryogenic induced phase separation regulation, and in situ phosphorylation modification. The PNFAs exhibit outstanding underwater superelasticity and excellent compression fatigue resistance (∼0% plastic deformation after 1000 compression cycles), as well as favorable shape-memory property. Besides, the PNFAs also can be bent and compressed even in the ultracold liquid nitrogen without obvious plastic deformation, further highlighting their robust structural stability. Benefiting from the superelastic, interconnected, and highly phosphorylated 3D nanofibrous frameworks, the PNFAs possess a superb protein adsorption capability of 3.3 × 103 mg g-1 and a large liquid flux of 1.5 × 104 L m-2 h-1, which are superior to the commercial and previously reported fiber-based chromatographic media. Moreover, the PNFAs also exhibit superior performance stability, easy assembly, and outstanding applicability, highlighting their potential actual application. The successful preparation of such fascinating PNFAs may not only provide a new option for the current protein adsorption and purification engineering, but also could open up some new perspectives for further design and development of next-generation nanofibrous aerogel-based chromatographic media for various bioseparation applications.
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Affiliation(s)
- Qiuxia Fu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Textiles , Donghua University , Shanghai 201620 , China
| | - Lifang Liu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Textiles , Donghua University , Shanghai 201620 , China
| | - Yang Si
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Textiles , Donghua University , Shanghai 201620 , China
- Innovation Center for Textile Science and Technology , Donghua University , Shanghai 200051 , China
| | - Jianyong Yu
- Innovation Center for Textile Science and Technology , Donghua University , Shanghai 200051 , China
| | - Bin Ding
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Textiles , Donghua University , Shanghai 201620 , China
- Innovation Center for Textile Science and Technology , Donghua University , Shanghai 200051 , China
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Mücke MM, Maasoumy B, Dietz J, Mücke VT, Simon CO, Canchola JA, Cornberg M, Marins EG, Manns MP, Zeuzem S, Wedemeyer H, Sarrazin C, Vermehren J. Utility of the new cobas HCV test for viral load monitoring during direct-acting antiviral therapy. PLoS One 2019; 14:e0224751. [PMID: 31738773 PMCID: PMC6860929 DOI: 10.1371/journal.pone.0224751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 10/21/2019] [Indexed: 11/23/2022] Open
Abstract
Background The COBAS AmpliPrep/COBAS TaqMan assay HCV (CAP/CTM) is widely used in clinical routine for HCV testing. Recently, the new cobas HCV test was established for high throughput testing with minimal operator intervention. As different assays may yield different quantitative/qualitative results that possibly impact treatment decisions, the aim of this study was to externally evaluate the cobas HCV test performance in comparison to CAP/CTM in a clinically relevant setting. Methods Serum samples were obtained from 270 patients who received direct acting antiviral therapy with different treatment regimens at two study sites (Hannover and Frankfurt) in 2016. Overall, 1545 samples (baseline, on-treatment and follow-up) were tested in parallel by both assays. Results The mean difference between cobas HCV and CAP/CTM for the quantification of HCV RNA was 0.008 log10 IU/ml HCV RNA (95% limits of agreement: -0.02–0.036) showing excellent agreement of both assays. With respect to clinical cut offs (HCV RNA detectable vs. target not detected and HCV RNA above the lower limit of quantification (LLOQ) vs. <LLOQ), discordant results were obtained in 9.5% and 4.6%, respectively; the greatest differences were observed during early stages of antiviral therapy (week 1, week 2 and week 4), but none were statistically significant. Overall percent agreement for SVR between cobas HCV and CAP/CTM at the 15 IU/ml cutoff was 99.2% (95%CI 92.7%-100%). Conclusion The performance of the new cobas HCV test was comparable to CAP/CTM in a clinical setting representing a large patient population with HCV GT 1 and 3 treated with DAAs.
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Affiliation(s)
- Marcus M. Mücke
- Department of Internal Medicine 1, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Benjamin Maasoumy
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Julia Dietz
- Department of Internal Medicine 1, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Victoria T. Mücke
- Department of Internal Medicine 1, University Hospital Frankfurt, Frankfurt am Main, Germany
| | | | | | - Marcus Cornberg
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Ed G. Marins
- Roche Molecular Systems, Pleasanton, CA, United States of America
| | - Michael P. Manns
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Stefan Zeuzem
- Department of Internal Medicine 1, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Heiner Wedemeyer
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
- Department of Gastroenterology and Hepatology, University Hospital Essen, Essen, Germany
| | - Christoph Sarrazin
- Department of Internal Medicine 1, University Hospital Frankfurt, Frankfurt am Main, Germany
- Department of Gastroenterology, St. Josefs-Hospital, Wiesbaden, Germany
| | - Johannes Vermehren
- Department of Internal Medicine 1, University Hospital Frankfurt, Frankfurt am Main, Germany
- * E-mail:
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Mauro A, Ng R, Li JY, Guan R, Wang Y, Singh KK, Wen XY. Protocol development for discovery of angiogenesis inhibitors via automated methods using zebrafish. PLoS One 2019; 14:e0221796. [PMID: 31730619 PMCID: PMC6857904 DOI: 10.1371/journal.pone.0221796] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 10/21/2019] [Indexed: 01/24/2023] Open
Abstract
Their optical clarity as larvae and embryos, small size, and high fecundity make zebrafish ideal for whole animal high throughput screening. A high-throughput drug discovery platform (HTP) has been built to perform fully automated screens of compound libraries with zebrafish embryos. A Tg(kdrl:EGFP) line, marking endothelial cell cytoplasm, was used in this work to help develop protocols and functional algorithms for the system, with the intent of screening for angiogenesis inhibitors. Indirubin 3’ Monoxime (I3M), a known angiogenesis inhibitor, was used at various concentrations to validate the protocols. Consistent with previous studies, a dose dependant inhibitory effect of I3M on angiogenesis was confirmed. The methods and protocols developed here could significantly increase the throughput of drug screens, while limiting human errors. These methods are expected to facilitate the discovery of novel anti-angiogenesis compounds and can be adapted for many other applications in which samples have a good fluorescent signal.
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Affiliation(s)
- Antonio Mauro
- Zebrafish Centre for Advanced Drug Discovery, Keenan Research Center, Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Unity Health Toronto, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
- Cardiovascular Sciences Collaborative Program, University of Toronto, Toronto, Ontario, Canada
- * E-mail: (AM); (XYW)
| | - Robin Ng
- Zebrafish Centre for Advanced Drug Discovery, Keenan Research Center, Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Jamie Yuanjun Li
- Zebrafish Centre for Advanced Drug Discovery, Keenan Research Center, Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Rui Guan
- Zebrafish Centre for Advanced Drug Discovery, Keenan Research Center, Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Youdong Wang
- Zebrafish Centre for Advanced Drug Discovery, Keenan Research Center, Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | - Krishna Kumar Singh
- Zebrafish Centre for Advanced Drug Discovery, Keenan Research Center, Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Unity Health Toronto, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
- Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Department of Medical Biophysics, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Xiao-Yan Wen
- Zebrafish Centre for Advanced Drug Discovery, Keenan Research Center, Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Unity Health Toronto, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
- Cardiovascular Sciences Collaborative Program, University of Toronto, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- * E-mail: (AM); (XYW)
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31
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Wei Z, Xie Z, Kuvelkar R, Shah V, Bateman K, McLaren DG, Cooks RG. High-Throughput Bioassays using "Dip-and-Go" Multiplexed Electrospray Mass Spectrometry. Angew Chem Int Ed Engl 2019; 58:17594-17598. [PMID: 31589796 DOI: 10.1002/anie.201909047] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Indexed: 12/16/2022]
Abstract
A multiplexed system based on inductive nanoelectrospray mass spectrometry (nESI-MS) has been developed for high-throughput screening (HTS) bioassays. This system combines inductive nESI and field amplification micro-electrophoresis to achieve a "dip-and-go" sample loading and purification strategy that enables nESI-MS based HTS assays in 96-well microtiter plates. The combination of inductive nESI and micro-electrophoresis makes it possible to perform efficient in situ separations and clean-up of biological samples. The sensitivity of the system is such that quantitative analysis of peptides from 1-10 000 nm can be performed in a biological matrix. A prototype of the automation system has been developed to handle 12 samples (one row of a microtiter plate) at a time. The sample loading and electrophoretic clean-up of biosamples can be done in parallel within 20 s followed by MS analysis at a rate of 1.3 to 3.5 s per sample. The system was used successfully for the quantitative analysis of BACE1-catalyzed peptide hydrolysis, a prototypical HTS assay of relevance to drug discovery. IC50 values for this system were in agreement with LC-MS but recorded in times more than an order of magnitude shorter.
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Affiliation(s)
- Zhenwei Wei
- Aston Labs, Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47906-1393, USA
| | - Zhuoer Xie
- Aston Labs, Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47906-1393, USA
| | - Reshma Kuvelkar
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | - Vinit Shah
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | - Kevin Bateman
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | - David G McLaren
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | - R Graham Cooks
- Aston Labs, Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47906-1393, USA
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32
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Simonneau C, Yang J, Kong X, Kilker R, Edelstein L, Fortina P, Londin E, Horowitz A. Validation of a Miniaturized Permeability Assay Compatible with CRISPR-Mediated Genome-Wide Screen. Sci Rep 2019; 9:14238. [PMID: 31578372 PMCID: PMC6775082 DOI: 10.1038/s41598-019-50588-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 09/11/2019] [Indexed: 12/28/2022] Open
Abstract
The impermeability of the luminal endothelial cell monolayer is crucial for the normal performance of the vascular and lymphatic systems. A key to this function is the integrity of the monolayer's intercellular junctions. The known repertoire of junction-regulating genes is incomplete. Current permeability assays are incompatible with high-throughput genome-wide screens that could identify these genes. To overcome these limitations, we designed a new permeability assay that consists of cell monolayers grown on ~150 μm microcarriers (MCs). Each MC functions as a miniature individual assay of permeability (MAP). We demonstrate that false-positive results can be minimized, and that MAP sensitivity to thrombin-induced increase in monolayer permeability is similar to the sensitivity of impedance measurement. We validated the assay by showing that the expression of single guide RNAs (sgRNAs) that target genes encoding known thrombin signaling proteins blocks effectively thrombin-induced junction disassembly, and that MAPs carrying such cells can be separated effectively by fluorescence-assisted sorting from those that carry cells expressing non-targeting sgRNAs. These results indicate that MAPs are suitable for high-throughput experimentation and for genome-wide screens for genes that mediate the disruptive effect of thrombin on endothelial cell junctions.
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Affiliation(s)
- Claire Simonneau
- Cardeza Center for Hematology Research, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
- Roche Innovation Center Basel, Zürich, Switzerland
| | - Junning Yang
- Cardeza Center for Hematology Research, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Xianguo Kong
- Cardeza Center for Hematology Research, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Robert Kilker
- Cardeza Center for Hematology Research, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Leonard Edelstein
- Cardeza Center for Hematology Research, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Paolo Fortina
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
- Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Eric Londin
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
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33
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Walters N, Nguyen LTH, Zhang J, Shankaran A, Reátegui E. Extracellular vesicles as mediators of in vitro neutrophil swarming on a large-scale microparticle array. Lab Chip 2019; 19:2874-2884. [PMID: 31343025 DOI: 10.1039/c9lc00483a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Neutrophils combat infections and promote healing of damaged tissues while protecting the surrounding healthy tissue through a process called swarming. Swarming neutrophils release soluble factors that recruit additional neutrophils and shape the inflammation response. Additionally, neutrophils release extracellular vesicles (EVs), which are gaining attention as important intercellular mediators. We developed a large-scale array of bioparticles on a glass substrate that triggers neutrophil swarming in vitro in a spatially and temporally controlled manner that facilitates the analysis of neutrophil migration. Our platform can generate 30 000 neutrophil swarms on a glass slide in a highly reproducible manner (98% patterning efficiency), which produces an EV-rich supernatant that enables quantitative characterization of inflammation-specific EVs. Healthy neutrophils were able to form uniform swarms across the bioparticle array, which demonstrates a high degree of intercellular coordination. However, neutrophils swarming on the bioparticle array tended to have a lower radial velocity than neutrophils swarming toward a single target. After collecting and isolating EVs released by swarming and non-swarming neutrophils, we found that neutrophils constitutively release exosomes and microvesicles. Furthermore, EVs released by swarming neutrophils cause neutrophil activation and contain the proinflammatory mediator galectin-3, suggesting that EVs have an active role during neutrophil swarming. Ultimately, understanding EVs' role in intercellular communication during swarming will improve understanding of the complex signaling pathways involved in the regulation of inflammation.
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Affiliation(s)
- Nicole Walters
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA.
| | - Luong T H Nguyen
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA.
| | - Jingjing Zhang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA.
| | - Ajay Shankaran
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA.
| | - Eduardo Reátegui
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA. and Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
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Vandergrift GW, Gill CG. Paper spray mass spectrometry: A new drug checking tool for harm reduction in the opioid overdose crisis. J Mass Spectrom 2019; 54:729-737. [PMID: 31432563 DOI: 10.1002/jms.4431] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 08/14/2019] [Accepted: 08/15/2019] [Indexed: 06/10/2023]
Abstract
Fentanyl and related psychoactive substances are at the forefront of the opioid overdose crisis, for which a complete solution is not immediately obvious. Drug testing for harm reduction may be an effective approach to both reduce overdoses and importantly, engage people who use drugs (PWUD) with the medical system. Paper spray mass spectrometry (PS-MS) is an ambient ionization strategy that is uniquely suited to address this complicated analytical task. This perspectives article presents the merits of PS-MS, with a focus upon the current state of its use as a candidate drug checking strategy for harm reduction. PS-MS is inherently sensitive and selective, with detection limits in the picogram range. It requires small drug samples (~1 mg) for quantitative drug testing, critical to encourage pre-consumption measurements by PWUD in the context of a harm reduction strategy. Calibrations obtained in surrogate drug matrices containing highly concentrated primary drugs demonstrate comparable sensitivities, a wide calibration range, and minimal matrix effects. PS-MS can be interfaced with high-resolution MS for non-targeted analysis, allowing the identification of novel psychoactive substances as they appear in street drugs. Individual quantitative PS-MS measurements for drug testing can be done in 1 minute or less, resulting in high sample throughput. Significant advancement in mass spectrometer miniaturization and mobilization has concomitant benefits for direct, on-site drug checking, such as reduced cost, simplified maintenance and ease of use by less skilled operators. While PS-MS technology continues to rapidly advance, it is our opinion that PS-MS can be utilized as an effective tool for harm reduction in the opioid overdose crisis.
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Affiliation(s)
- Gregory W Vandergrift
- Applied Environmental Research Laboratories (AERL), Chemistry Department, Vancouver Island University, Nanaimo, BC, Canada
- Chemistry Department, University of Victoria, Victoria, BC, Canada
| | - Chris G Gill
- Applied Environmental Research Laboratories (AERL), Chemistry Department, Vancouver Island University, Nanaimo, BC, Canada
- Chemistry Department, University of Victoria, Victoria, BC, Canada
- Chemistry Department, Simon Fraser University, Burnaby, BC, Canada
- Environmental and Occupational Health Sciences Department, University of Washington, Seattle, Washington
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35
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Pandarakalam GC, Speake M, McElroy S, Alturkistani A, Philippe L, Pettitt J, Müller B, Connolly B. A high-throughput screen for the identification of compounds that inhibit nematode gene expression by targeting spliced leader trans-splicing. Int J Parasitol Drugs Drug Resist 2019; 10:28-37. [PMID: 31015150 PMCID: PMC6479105 DOI: 10.1016/j.ijpddr.2019.04.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 03/28/2019] [Accepted: 04/01/2019] [Indexed: 02/05/2023]
Abstract
Infections with parasitic nematodes are among the most significant of the neglected tropical diseases affecting about a billion people living mainly in tropical regions with low economic activity. The most effective current strategy to control nematode infections involves large scale treatment programs with anthelmintic drugs. This strategy is at risk from the emergence of drug resistant parasites. Parasitic nematodes also affect livestock, which are treated with the same limited group of anthelmintic drugs. Livestock parasites resistant to single drugs, and even multi-drug resistant parasites, are appearing in many areas. There is therefore a pressing need for new anthelmintic drugs. Here we use the nematode Caenorhabditis elegans as a model for parasitic nematodes and demonstrate that sinefungin, a competitive inhibitor of methyltransferases, causes a delay in development and reduced fecundity, and inhibits spliced leader trans-splicing. Spliced leader trans-splicing is an essential step in gene expression that does not occur in the hosts of parasitic nematodes, and is therefore a potential target for new anthelmintic drugs. We have exploited the ability of sinefungin to inhibit spliced leader trans-splicing to adapt a green fluorescent protein based reporter gene assay that monitors spliced leader trans-splicing for high-throughput screening for new anthelmintic compounds. We have established a protocol for robust high-throughput screening, combining mechanical dispensing of living C. elegans into 384- or 1536- well plates with addition of compounds using an acoustic liquid dispenser, and the detection of the inhibition of SL trans-splicing using a microplate reader. We have tested this protocol in a first pilot screen and envisage that this assay will be a valuable tool in the search for new anthelmintic drugs.
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Affiliation(s)
- George Cherian Pandarakalam
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Michael Speake
- European Screening Centre, University of Dundee, Biocity Scotland, Bo'ness Road, Newhouse, ML1 5UH, Scotland, UK
| | - Stuart McElroy
- European Screening Centre, University of Dundee, Biocity Scotland, Bo'ness Road, Newhouse, ML1 5UH, Scotland, UK
| | - Ammar Alturkistani
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Lucas Philippe
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Jonathan Pettitt
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Berndt Müller
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, AB25 2ZD, UK.
| | - Bernadette Connolly
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, AB25 2ZD, UK
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36
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Zhao ZY, Qin L, Dong M, Zhang YY, Huang XH, Du M, Zhou DY, Zhu BW. High-Throughput, Rapid Quantification of Phthalic Acid Esters and Alkylphenols in Fish Using a Coated Direct Inlet Probe Coupled with Atmospheric Pressure Chemical Ionization. J Agric Food Chem 2019; 67:7174-7182. [PMID: 31240931 DOI: 10.1021/acs.jafc.9b01335] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Intake of endocrine-disrupting chemicals (EDCs) by humans could disturb the metabolism of hormones, induce cancer, and damage the liver and other organs. Phthalate acid esters (PAEs) and alkylphenols (APs) are important EDCs and environmental contaminants. With the increasing use of plastics and nonionic surfactants worldwide, PAEs and APs have entered environmental water and accumulated in edible fish, which are finally consumed by humans. In this study, a coated direct inlet probe (CDIP) based on an atmospheric solid analysis probe, which can rapidly and simultaneously extract both PAEs and APs in fish, was developed. Twelve PAEs and APs were quantified by using a stable-isotope-labeled internal standard. Standard curves of the PAEs and APs having correlation coefficients of R2 ≥ 0.9837 were obtained. The limit of detection of the PAEs and APs was distributed from 0.01 to 40 ng g-1. The relative recovery of the method was 78-120% between low, medium, and high spiked levels. Combined with principal component analysis, PAE- and AP-contaminated Carassius auratus from different habitats could be identified. Multiple sample analysis mode allowed the extraction of up to 12 samples at once, and the total analysis time (including sample pretreatment, extraction, and analysis time) was less than 10 min per sample, which indicates that CDIP is useful for rapid quantitative analysis.
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Affiliation(s)
- Zi-Yuan Zhao
- National Engineering Research Center of Seafood, School of Food Science and Technology , Dalian Polytechnic University , Dalian 116034 , China
| | - Lei Qin
- National Engineering Research Center of Seafood, School of Food Science and Technology , Dalian Polytechnic University , Dalian 116034 , China
| | - Meng Dong
- National Engineering Research Center of Seafood, School of Food Science and Technology , Dalian Polytechnic University , Dalian 116034 , China
| | - Yu-Ying Zhang
- National Engineering Research Center of Seafood, School of Food Science and Technology , Dalian Polytechnic University , Dalian 116034 , China
| | - Xu-Hui Huang
- National Engineering Research Center of Seafood, School of Food Science and Technology , Dalian Polytechnic University , Dalian 116034 , China
| | - Ming Du
- National Engineering Research Center of Seafood, School of Food Science and Technology , Dalian Polytechnic University , Dalian 116034 , China
| | - Da-Yong Zhou
- National Engineering Research Center of Seafood, School of Food Science and Technology , Dalian Polytechnic University , Dalian 116034 , China
| | - Bei-Wei Zhu
- National Engineering Research Center of Seafood, School of Food Science and Technology , Dalian Polytechnic University , Dalian 116034 , China
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37
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Jian N, Zhao M, Liang S, Cao J, Wang C, Xu Q, Li J. High-Throughput and High-Efficient Micro-solid Phase Extraction Based on Sulfonated-Polyaniline/Polyacrylonitrile Nanofiber Mats for Determination of Fluoroquinolones in Animal-Origin Foods. J Agric Food Chem 2019; 67:6892-6901. [PMID: 31125221 DOI: 10.1021/acs.jafc.9b01312] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We herein describe a high-throughput 96-well plate micro-solid phase extraction sample preparation technique based on novel sulfonated-polyaniline/polyacrylonitrile nanofiber mats (sulfonated-PANI/PAN NFMs) for multiresidue detection of fluoroquinolones (FQs) in various animal-origin food samples. Through the double-modification of polyaniline and sulfonic acid, the resulting functionalized sulfonated-PANI/PAN NFMs present high extraction efficiency for FQs. Compared with the existing methods, this approach demonstrates its advantages of being suitable for more sample matrices (milk, animal muscle, liver, kidney, and egg), lower sample amount (0.5 g), lower sorbent requirement (5.0 mg), lower volume of organic solvent (0.7 mL), shorter time (0.2 min per sample), and high sensitivity (0.012-0.06 μg·kg-1). In addition, sulfonated-PANI/PAN NFMs possess excellent reusability which could be reused 10 times without an obvious decrease in extraction efficiency. Combined with ultra performance liquid chromatography-tandem mass spectrometry, the novel sample preparation technique can be expected as an efficient method for routine trace FQ residue monitoring in animal-origin food samples.
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Affiliation(s)
- Ningge Jian
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health , Southeast University , Nanjing 210009 , China
| | - Meng Zhao
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health , Southeast University , Nanjing 210009 , China
| | - Sihui Liang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health , Southeast University , Nanjing 210009 , China
| | - Jiankun Cao
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health , Southeast University , Nanjing 210009 , China
| | - Chunmin Wang
- Suzhou Municipal Center for Disease Prevention and Control, Suzhou 215004 , China
| | - Qian Xu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health , Southeast University , Nanjing 210009 , China
| | - Jian Li
- Suzhou Municipal Center for Disease Prevention and Control, Suzhou 215004 , China
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Rathahao-Paris E, Alves S, Boussaid N, Picard-Hagen N, Gayrard V, Toutain PL, Tabet JC, Rutledge DN, Paris A. Evaluation and validation of an analytical approach for high-throughput metabolomic fingerprinting using direct introduction-high-resolution mass spectrometry: Applicability to classification of urine of scrapie-infected ewes. Eur J Mass Spectrom (Chichester) 2019; 25:251-258. [PMID: 30335517 DOI: 10.1177/1469066718806450] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Direct injection-mass spectrometry can be used to perform high-throughput metabolomic fingerprinting. This work aims to evaluate a global analytical workflow in terms of sample preparation (urine sample dilution), high-resolution detection (quality of generated data based on criteria such as mass measurement accuracy and detection sensitivity) and data analysis using dedicated bioinformatics tools. Investigation was performed on a large number of biological samples collected from sheep infected or not with scrapie. Direct injection-mass spectrometry approach is usually affected by matrix effects, eventually hampering detection of some relevant biomarkers. Reference compounds were spiked in biological samples to help evaluate the quality of direct injection-mass spectrometry data produced by Fourier Transform mass spectrometry. Despite the potential of high-resolution detection, some drawbacks still remain. The most critical is the presence of matrix effects, which could be minimized by optimizing the sample dilution factor. The data quality in terms of mass measurement accuracy and reproducible intensity was evaluated. Good repeatability was obtained for the chosen dilution factor (i.e., 2000). More than 150 analyses were performed in less than 16 hours using the optimized direct injection-mass spectrometry approach. Discrimination of different status of sheeps in relation to scrapie infection (i.e., scrapie-affected, preclinical scrapie or healthy) was obtained from the application of Shrinkage Discriminant Analysis to the direct injection-mass spectrometry data. The most relevant variables related to this discrimination were selected and annotated. This study demonstrated that the choice of appropriated dilution faction is indispensable for producing quality and informative direct injection-mass spectrometry data. Successful application of direct injection-mass spectrometry approach for high throughput analysis of a large number of biological samples constitutes the proof of the concept.
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Affiliation(s)
- Estelle Rathahao-Paris
- 1 UMR Ingénierie Procédés Aliments, AgroParisTech, Inra, Université Paris-Saclay, Massy, France
- 2 Sorbonne Université, Faculté des Sciences et de l'Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), Paris, France
| | - Sandra Alves
- 2 Sorbonne Université, Faculté des Sciences et de l'Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), Paris, France
| | - Nawel Boussaid
- 1 UMR Ingénierie Procédés Aliments, AgroParisTech, Inra, Université Paris-Saclay, Massy, France
| | - Nicole Picard-Hagen
- 3 Toxalim, Université de Toulouse, INRA (Institut National de la Recherche Agronomique), INP (Institut National Polytechnique de Toulouse)-ENVT (Ecole Nationale Vétérinaire de Toulouse), Toulouse, France
| | - Véronique Gayrard
- 3 Toxalim, Université de Toulouse, INRA (Institut National de la Recherche Agronomique), INP (Institut National Polytechnique de Toulouse)-ENVT (Ecole Nationale Vétérinaire de Toulouse), Toulouse, France
| | | | - Jean-Claude Tabet
- 2 Sorbonne Université, Faculté des Sciences et de l'Ingénierie, Institut Parisien de Chimie Moléculaire (IPCM), Paris, France
- 5 CEA-INRA, Service de Pharmacologie et d'Immunoanalyse, Laboratoire d'Etude du Métabolisme des Médicaments, MetaboHUB, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Douglas N Rutledge
- 1 UMR Ingénierie Procédés Aliments, AgroParisTech, Inra, Université Paris-Saclay, Massy, France
| | - Alain Paris
- 6 Unité Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle, CNRS, CP54, Paris, France
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39
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Zhu H, Huang G. High-throughput paper spray mass spectrometry via induced voltage. Rapid Commun Mass Spectrom 2019; 33:392-398. [PMID: 30394606 DOI: 10.1002/rcm.8336] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/23/2018] [Accepted: 10/26/2018] [Indexed: 06/08/2023]
Abstract
RATIONALE Paper spray (PS) has been developed as a method of choice for point-of-care analysis in many real cases, where its applications can be further expanded with delicate high-throughput design. To achieve this goal, we developed a new PS regime, with the assembly of an induced high voltage into the ion source. Compared with regular DC high voltage, the newly developed setup is capable of high-throughput, simple configuration and rapid switching between individual papers without complicated electric/mechanic design. METHODS A device of high-throughput induced PS (IPS) was designed by using a two-dimensional (2D) rotating platform equipped with a circular glass plate. The paper substrate was placed on the circular glass plate and separated from the electrode. The method avoids physical contact between the electrode and the sample. Charged droplets were generated at the paper tip once an induced high voltage was applied to a wet paper. RESULTS A relatively rapid analytical speed of 2.6 s per sample was achieved via IPS-MS. Rapid quantification of amitriptyline (AMT) in complicated matrices was obtained within 1 min using an isotope internal standard method. Limits of detection for AMt in urine, FBS and blood were calculated to be 1.04, 0.84 and 1.33 ng/mL, respectively. In addition, high-throughput IPS-MS can be used for chemical reaction monitoring. CONCLUSIONS We have demonstrated the versatility of high-throughput IPS-MS in ambient ionization, which successfully simplified the experimental installation and facilitated the experimental operation. Therefore, we believe that high-throughput IPS-MS analysis will be widely used for discovering drugs and screening reactions, and the present design has the potential for applications in paper chip-MS analysis.
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Affiliation(s)
- Haijing Zhu
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China (USTC), Hefei, 230026, China
| | - Guangming Huang
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China (USTC), Hefei, 230026, China
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40
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Abstract
Biomimetic systems such as model lipid membranes are vital to many research fields including synthetic biology, drug discovery and membrane biophysics. One of the most commonly used are giant unilamellar vesicles (GUVs) due to their size similarity with biological cells and their ease of production. Typical methods for handling such delicate objects are low-throughput and do not allow solution exchange or long-term observations, all of which limits the experimental options. Herein, we present a new device designed to confine large assemblies of GUVs in microfluidic traps but is still able to perform precise and fast solution exchanges. An optimised design allows efficient filling with as many as 114 GUVs per trap and over 23 000 GUVs per device. This allows high-throughput dataset acquisitions which we demonstrate with two proof-of-concept experiments: (i) end-point measurements of vesicle interior pH and (ii) membrane transport kinetics. Moreover, we show that the design is able to selectively trap sub-populations of specific vesicle sizes and assemble them in different layers. The device can easily be applied to other high-throughput membrane studies and will pave the way for future applications using vesicle assemblies to model cellular tissues or even prototissues.
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Affiliation(s)
- Naresh Yandrapalli
- Department of Theory & Bio-Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.
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41
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Manglani M, Rua R, Hendricksen A, Braunschweig D, Gao Q, Tan W, Houser B, McGavern DB, Oh K. Method to quantify cytokines and chemokines in mouse brain tissue using Bio-Plex multiplex immunoassays. Methods 2019; 158:22-26. [PMID: 30742997 DOI: 10.1016/j.ymeth.2019.02.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 01/31/2019] [Accepted: 02/06/2019] [Indexed: 01/03/2023] Open
Abstract
This protocol describes how to prepare mouse brain tissue for quantification of multiple inflammatory mediators using a multiplex bead-based immunoassay. It is important to have methods that allow quantification of multiple analytes from small amounts of tissue. Bio-Plex is a Luminex xMAP-based multiplex bead-based immunoassay technology that permits simultaneous analysis of up to 100 analytes from a single tissue sample. This assay has been used extensively to investigate analytes in plasma and serum samples as well as cultured and primary cells. Here, we describe a method for simultaneous analysis of 33 different inflammatory cytokines and chemokines from mouse brain tissue using the Bio-Plex Pro Mouse Chemokine Panel 33-Plex.
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Affiliation(s)
- Monica Manglani
- Viral Immunology and Intravital Imaging Section, National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Rejane Rua
- Viral Immunology and Intravital Imaging Section, National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | | | | | - Qian Gao
- Bio-Rad Laboratories, Hercules, CA 94547, USA
| | - Woei Tan
- Bio-Rad Laboratories, Hercules, CA 94547, USA
| | | | - Dorian B McGavern
- Viral Immunology and Intravital Imaging Section, National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Kenneth Oh
- Bio-Rad Laboratories, Hercules, CA 94547, USA
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42
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Coppock MB, Stratis-Cullum DN. A universal method for the functionalization of dyed magnetic microspheres with peptides. Methods 2019; 158:12-16. [PMID: 30707950 DOI: 10.1016/j.ymeth.2019.01.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 12/20/2018] [Accepted: 01/23/2019] [Indexed: 11/19/2022] Open
Abstract
The need for the functionalization of magnetic, water-soluble dyed microspheres with peptides is apparent with the ever-growing biointeraction capabilities and the increased use of dyed microspheres in multiplex, microsphere-based detection assays. This method describes the attachment of any peptide to dyed magnetic microspheres regardless of peptide length, size, or sequence. The method exploits 'click' chemistry with short reaction times in a mixed organic/water system for simultaneous selective surface functionalization and reduction of microsphere dye leaching. All optimization studies were performed using a Luminex 200 assay platform, but the functionalized microspheres are capable of use in any similar multiplex format.
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Affiliation(s)
- Matthew B Coppock
- Sensors and Electron Devices Directorate, U.S. Army Research Laboratory, 2800 Powder Mill Rd, Adelphi, MD, United States.
| | - Dimitra N Stratis-Cullum
- Sensors and Electron Devices Directorate, U.S. Army Research Laboratory, 2800 Powder Mill Rd, Adelphi, MD, United States
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43
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Abstract
Multiple studies focused on tumor heterogeneity and cellular hierarchies have demonstrated the role of cancer stem cells (CSC) in tumor initiation and recurrence. Colorectal cancer is one of the leading causes of cancer-related death and is hierarchically organized, with the majority of tumor cells descending from a small population of colon cancer stem cells (CCSCs). Such a rare self-renewing population is marked by the acquisition of distinct chromatin regulation and transcriptional programs. Fundamental molecular deviations between CCSCs and bulk tumor cells as well as normal tissues represent a unique therapeutic access to develop novel, selective anticancer therapies.In this chapter, we describe a methodological pipeline to identify novel molecules to selectively target human CCSC. We present a point-by-point description of a typical phenotypic molecular screening experiment, aiming to identify selective modulators of human CCSCs vs. normal intestinal progenitor cells.
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Affiliation(s)
- Yannick D Benoit
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.
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44
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Chen Z, He S, Zilberberg J, Lee W. Pumpless platform for high-throughput dynamic multicellular culture and chemosensitivity evaluation. Lab Chip 2019; 19:254-261. [PMID: 30547180 PMCID: PMC6333476 DOI: 10.1039/c8lc00872h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We report here a novel pumpless, 96-well plate-based platform for high-throughput dynamic multicellular culture and chemosensitivity evaluation. A gravity-driven flow strategy was developed to generate and sustain the flow rate of culture medium within 10% in the platform's 20 culture chambers. The ability of the platform to generate and sustain the medium flow was demonstrated by computational simulation, flow visualization, and ascertaining the previously known effect of flow-induced shear stress on the stimulated osteogenic differentiation of osteoblasts. The high-throughput utility of the platform was demonstrated by in situ cell staining and high content screening of chemosensitivity assays of multiple myeloma and osteoblast co-cultures. Endpoint characterization and data analyses for all 20 culture chambers required less than 1 hour.
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Affiliation(s)
- Zhehuan Chen
- Department of Chemical Engineering and Materials Science, Stevens Institute of Technology, 1 Castle Point on Hudson, Hoboken, New Jersey 07030, USA.
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45
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Gill NK, Ly C, Nyberg KD, Lee L, Qi D, Tofig B, Reis-Sobreiro M, Dorigo O, Rao J, Wiedemeyer R, Karlan B, Lawrenson K, Freeman MR, Damoiseaux R, Rowat AC. A scalable filtration method for high throughput screening based on cell deformability. Lab Chip 2019; 19:343-357. [PMID: 30566156 DOI: 10.1039/c8lc00922h] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Cell deformability is a label-free biomarker of cell state in physiological and disease contexts ranging from stem cell differentiation to cancer progression. Harnessing deformability as a phenotype for screening applications requires a method that can simultaneously measure the deformability of hundreds of cell samples and can interface with existing high throughput facilities. Here we present a scalable cell filtration device, which relies on the pressure-driven deformation of cells through a series of pillars that are separated by micron-scale gaps on the timescale of seconds: less deformable cells occlude the gaps more readily than more deformable cells, resulting in decreased filtrate volume which is measured using a plate reader. The key innovation in this method is that we design customized arrays of individual filtration devices in a standard 96-well format using soft lithography, which enables multiwell input samples and filtrate outputs to be processed with higher throughput using automated pipette arrays and plate readers. To validate high throughput filtration to detect changes in cell deformability, we show the differential filtration of human ovarian cancer cells that have acquired cisplatin-resistance, which is corroborated with cell stiffness measurements using quantitative deformability cytometry. We also demonstrate differences in the filtration of human cancer cell lines, including ovarian cancer cells that overexpress transcription factors (Snail, Slug), which are implicated in epithelial-to-mesenchymal transition; breast cancer cells (malignant versus benign); and prostate cancer cells (highly versus weekly metastatic). We additionally show how the filtration of ovarian cancer cells is affected by treatment with drugs known to perturb the cytoskeleton and the nucleus. Our results across multiple cancer cell types with both genetic and pharmacologic manipulations demonstrate the potential of this scalable filtration device to screen cells based on their deformability.
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Affiliation(s)
- Navjot Kaur Gill
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, California, USA.
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46
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Dafni E, Weiner I, Shahar N, Tuller T, Yacoby I. Image-Processing Software for High-Throughput Quantification of Colony Luminescence. mSphere 2019; 4:e00676-18. [PMID: 30602526 PMCID: PMC6315083 DOI: 10.1128/msphere.00676-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 12/07/2018] [Indexed: 11/20/2022] Open
Abstract
Many microbiological assays include colonies that produce a luminescent or fluorescent (here generalized as "luminescent") signal, often in the form of luminescent halos around the colonies. These signals are used as reporters for a trait of interest; therefore, exact measurements of the luminescence are often desired. However, there is currently a lack of high-throughput methods for analyzing these assays, as common automatic image analysis tools are unsuitable for identifying these halos in the presence of the inherent biological noise. In this work, we have developed CFQuant-automatic, high-throughput software for the analysis of images from colony luminescence assays. CFQuant overcomes the problems of automatic identification by relying on the luminescence halo's expected shape and provides measurements of several features of the colonies and halos. We examined the performance of CFQuant using one such colony luminescence assay, where we achieved a high correlation (R = 0.85) between the measurements of CFQuant and known protein expression levels. This demonstrates CFQuant's potential as a fast and reliable tool for analysis of colony luminescence assays.IMPORTANCE Luminescent markers are widely used as reporters for various biologically interesting traits. In colony luminescence assays, the levels of luminescence around each colony can be used to compare the levels of traits of interest for different strains, treatments, etc., using quantitative measurements of the luminescence. However, automatic methods of obtaining this data are underdeveloped, making this a laborious manual process, especially in analyzing large numbers of colonies. The significance of this work is in developing an automatic, high-throughput tool for quantitative analysis of colony luminescence assays, which will allow fast collection of qualitative data from these assays and thus increase their overall usability.
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Affiliation(s)
- Eyal Dafni
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Iddo Weiner
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Noam Shahar
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel
- The Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Iftach Yacoby
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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47
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Najdekr L, Blanco GR, Dunn WB. Collection of Untargeted Metabolomic Data for Mammalian Urine Applying HILIC and Reversed Phase Ultra Performance Liquid Chromatography Methods Coupled to a Q Exactive Mass Spectrometer. Methods Mol Biol 2019; 1996:1-15. [PMID: 31127542 DOI: 10.1007/978-1-4939-9488-5_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Ultra performance liquid chromatography-mass spectrometry (UPLC-MS) is the most frequently applied analytical platform in the untargeted metabolomic study of mammalian urine. Here we describe two complementary UPLC-MS methods for metabolomic analysis or urine, a reversed phase C18 method and a hydrophilic interaction liquid chromatography (HILIC) method. We discuss the inclusion of pooled quality control (QC) samples and a recommended analysis list construction. Up to 96 injections can be performed every 24 h, and up to 2000 metabolites can be routinely detected.
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Affiliation(s)
- Lukáš Najdekr
- School of Biosciences, University of Birmingham, Birmingham, UK.
- Phenome Centre Birmingham, University of Birmingham, Birmingham, UK.
| | | | - Warwick B Dunn
- School of Biosciences, University of Birmingham, Birmingham, UK
- Phenome Centre Birmingham, University of Birmingham, Birmingham, UK
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
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48
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Abstract
Autophagy is an evolutionarily conserved degradative pathway, and the core autophagy machinery acts in a highly regulated, hierarchical manner to engulf cytoplasmic material in a double-membrane-bound organelle and deliver it to the lysosome. High-throughput screening approaches lead to the identification of novel autophagy regulators, and we describe an autophagy pathway mapping strategy to determine the stage of the autophagy pathway at which these novel candidate proteins function.
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Affiliation(s)
- Martina Wirth
- Molecular Cell Biology of Autophagy Laboratory, The Francis Crick Institute, London, UK
| | - Sharon A Tooze
- Molecular Cell Biology of Autophagy Laboratory, The Francis Crick Institute, London, UK.
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49
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Shinn P, Chen L, Ferrer M, Itkin Z, Klumpp-Thomas C, McKnight C, Michael S, Mierzwa T, Thomas C, Wilson K, Guha R. High-Throughput Screening for Drug Combinations. Methods Mol Biol 2019; 1939:11-35. [PMID: 30848454 DOI: 10.1007/978-1-4939-9089-4_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The identification of drug combinations as alternatives to single-agent therapeutics has traditionally been a slow, largely manual process. In the last 10 years, high-throughput screening platforms have been developed that enable routine screening of thousands of drug pairs in an in vitro setting. In this chapter, we describe the workflow involved in screening a single agent versus a library of mechanistically annotated, investigation, and approved drugs using a full dose-response matrix scheme using viability as the readout. We provide details of the automation required to run the screen and the informatics required to process data from screening robot and subsequent analysis and visualization of the datasets.
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Affiliation(s)
- Paul Shinn
- National Center for Advancing Translational Science, Rockville, MD, USA
| | - Lu Chen
- National Center for Advancing Translational Science, Rockville, MD, USA
| | - Marc Ferrer
- National Center for Advancing Translational Science, Rockville, MD, USA
| | - Zina Itkin
- National Center for Advancing Translational Science, Rockville, MD, USA
| | | | - Crystal McKnight
- National Center for Advancing Translational Science, Rockville, MD, USA
| | - Sam Michael
- National Center for Advancing Translational Science, Rockville, MD, USA
| | - Tim Mierzwa
- National Center for Advancing Translational Science, Rockville, MD, USA
| | - Craig Thomas
- National Center for Advancing Translational Science, Rockville, MD, USA
| | - Kelli Wilson
- National Center for Advancing Translational Science, Rockville, MD, USA
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50
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Abstract
Biosensing of cancer biomarkers enabling early diagnosis of cancer constitutes an essential tool for clinical intervention and application of novel therapies against cancer disease. Optical biosensor instruments as point-of-care (POC) devices and operating under label-free scheme have demonstrated to provide fast, simple, and high-sensitivity assays even at home care environment. Nanoplasmonic biosensors are thought to be a powerful tool for detection of complex analytes of relevant clinical applications. Using high-throughput fabrication techniques, large surface patterned with gold nanodisk structures is obtained showing surface sensitivities with limit of detection (LOD) in the order of picomolar concentration range. Here, we describe two major assay methodologies used for detection of lung and colorectal cancer, respectively. Particularly, we have selected a complementary hybridization DNA/RNA assay for the assessment of two miRNAs (miRNA-210 and miRNA-205) for detection of lung cancer. However, for colorectal cancer we present the detection of four tumor-associated antigen (TAA) biomarkers (MAPKAPK3, PIM-1, STK4, and GTF2B) as possible TAA targets for autoantibody production. Strategies for detecting these biomarkers in real samples such as serum are also presented, demonstrating the capabilities of these assays to be transferred to real clinical settings.
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Affiliation(s)
- Alejandro Portela
- Nanobiosensors and Bioanalytical Applications Group (NanoB2A), Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Barcelona, Spain.
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain.
| | - Enelia C Peláez
- Nanobiosensors and Bioanalytical Applications Group (NanoB2A), Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Barcelona, Spain
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain
| | - Olalla Calvo-Lozano
- Nanobiosensors and Bioanalytical Applications Group (NanoB2A), Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Barcelona, Spain
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain
| | - Mari C Estévez
- Nanobiosensors and Bioanalytical Applications Group (NanoB2A), Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Barcelona, Spain
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain
| | - Laura M Lechuga
- Nanobiosensors and Bioanalytical Applications Group (NanoB2A), Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Barcelona, Spain
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain
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