1
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Franz O, Häkkänen H, Kovanen S, Heikkilä-Huhta K, Nissinen R, Ihalainen JA. NIRis: A low-cost, versatile imaging system for near-infrared fluorescence detection of phototrophic cell colonies used in research and education. PLoS One 2024; 19:e0287088. [PMID: 38771771 PMCID: PMC11108223 DOI: 10.1371/journal.pone.0287088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 05/01/2024] [Indexed: 05/23/2024] Open
Abstract
A variety of costly research-grade imaging devices are available for the detection of spectroscopic features. Here we present an affordable, open-source and versatile device, suitable for a range of applications. We provide the files to print the imaging chamber with commonly available 3D printers and instructions to assemble it with easily available hardware. The imager is suitable for rapid sample screening in research, as well as for educational purposes. We provide details and results for an already proven set-up which suits the needs of a research group and students interested in UV-induced near-infrared fluorescence detection of microbial colonies grown on Petri dishes. The fluorescence signal confirms the presence of bacteriochlorophyll a in aerobic anoxygenic phototrophic bacteria (AAPB). The imager allows for the rapid detection and subsequent isolation of AAPB colonies on Petri dishes with diverse environmental samples. To this date, 15 devices have been build and more than 7000 Petri dishes have been analyzed for AAPB, leading to over 1000 new AAPB isolates. Parts can be modified depending on needs and budget. The latest version with automated switches and double band pass filters costs around 350€ in materials and resolves bacterial colonies with diameters of 0.5 mm and larger. The low cost and modular build allow for the integration in high school classes to educate students on light properties, fluorescence and microbiology. Computer-aided design of 3D-printed parts and programming of the employed Raspberry Pi computer could be incorporated in computer sciences classes. Students have been also inspired to do agar art with microbes. The device is currently used in seven different high schools in Finland. Additionally, a science education network of Finnish universities has incorporated it in its program for high school students. Video guides have been produced to facilitate easy operation and accessibility of the device.
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Affiliation(s)
- Ole Franz
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Heikki Häkkänen
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Salla Kovanen
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Kati Heikkilä-Huhta
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Riitta Nissinen
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Janne A. Ihalainen
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
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2
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Branning JM, Faughnan KA, Tomson AA, Bell GJ, Isbell SM, DeGroot A, Jameson L, Kilroy K, Smith M, Smith R, Mottel L, Branning EG, Worrall Z, Anderson F, Panditaradyula A, Yang W, Abdelmalek J, Brake J, Cash KJ. Multifunction fluorescence open source in vivo/in vitro imaging system (openIVIS). PLoS One 2024; 19:e0299875. [PMID: 38498588 PMCID: PMC10947658 DOI: 10.1371/journal.pone.0299875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 02/18/2024] [Indexed: 03/20/2024] Open
Abstract
The widespread availability and diversity of open-source microcontrollers paired with off-the-shelf electronics and 3D printed technology has led to the creation of a wide range of low-cost scientific instruments, including microscopes, spectrometers, sensors, data loggers, and other tools that can be used for research, education, and experimentation. These devices can be used to explore a wide range of scientific topics, from biology and chemistry to physics and engineering. In this study, we designed and built a multifunction fluorescent open source in vivo/in vitro imaging system (openIVIS) system that integrates a Raspberry Pi with commercial cameras and LEDs with 3D printed structures combined with an acrylic housing. Our openIVIS provides three excitation wavelengths of 460 nm, 520 nm, and 630 nm integrated with Python control software to enable fluorescent measurements across the full visible light spectrum. To demonstrate the potential applications of our system, we tested its performance against a diverse set of experiments including laboratory assays (measuring fluorescent dyes, using optical nanosensors, and DNA gel electrophoresis) to potentially fieldable applications (plant and mineral imaging). We also tested the potential use for a high school biology environment by imaging small animals and tracking their development over the course of ten days. Our system demonstrated its ability to measure a wide dynamic range fluorescent response from millimolar to picomolar concentrations in the same sample while measuring responses across visible wavelengths. These results demonstrate the power and flexibility of open-source hardware and software and how it can be integrated with customizable manufacturing to create low-cost scientific instruments with a wide range of applications. Our study provides a promising model for the development of low-cost instruments that can be used in both research and education.
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Affiliation(s)
- John M. Branning
- Quantitative Biosciences and Engineering, Colorado School of Mines, Golden, Colorado, United States of America
- The MITRE Corporation, Bedford, Massachusetts, United States of America
| | - Kealy A. Faughnan
- Chemical and Biological Engineering Department, Colorado School of Mines, Golden, Colorado, United States of America
| | - Austin A. Tomson
- Mechanical Engineering, Colorado School of Mines, Golden, Colorado, United States of America
| | - Grant J. Bell
- Quantitative Biosciences and Engineering, Colorado School of Mines, Golden, Colorado, United States of America
| | - Sydney M. Isbell
- Chemical and Biological Engineering Department, Colorado School of Mines, Golden, Colorado, United States of America
| | - Allen DeGroot
- Electrical Engineering, Colorado School of Mines, Golden, Colorado, United States of America
| | - Lydia Jameson
- Electrical Engineering, Colorado School of Mines, Golden, Colorado, United States of America
| | - Kramer Kilroy
- Mechanical Engineering, Colorado School of Mines, Golden, Colorado, United States of America
| | - Michael Smith
- Mechanical Engineering, Colorado School of Mines, Golden, Colorado, United States of America
| | - Robert Smith
- Electrical Engineering, Colorado School of Mines, Golden, Colorado, United States of America
| | - Landon Mottel
- Arvada West High School, Arvada, Colorado, United States of America
| | - Elizabeth G. Branning
- Colorado Early Colleges Castle Rock, Castle Rock, Colorado, United States of America
| | - Zoe Worrall
- Department of Engineering, Harvey Mudd College, Claremont, California, United States of America
| | - Frances Anderson
- Department of Engineering, Harvey Mudd College, Claremont, California, United States of America
| | - Ashrit Panditaradyula
- Department of Engineering, Harvey Mudd College, Claremont, California, United States of America
| | - William Yang
- Department of Engineering, Harvey Mudd College, Claremont, California, United States of America
| | - Joseph Abdelmalek
- Department of Engineering, Harvey Mudd College, Claremont, California, United States of America
| | - Joshua Brake
- Department of Engineering, Harvey Mudd College, Claremont, California, United States of America
| | - Kevin J. Cash
- Quantitative Biosciences and Engineering, Colorado School of Mines, Golden, Colorado, United States of America
- Chemical and Biological Engineering Department, Colorado School of Mines, Golden, Colorado, United States of America
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3
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Groffen J, Hoskin CJ. A portable Raspberry Pi-based camera set-up to record behaviours of frogs and other small animals under artificial or natural shelters in remote locations. Ecol Evol 2024; 14:e10877. [PMID: 38500857 PMCID: PMC10945077 DOI: 10.1002/ece3.10877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 12/29/2023] [Accepted: 01/09/2024] [Indexed: 03/20/2024] Open
Abstract
We describe a Raspberry Pi-based camera system that is portable, robust and weatherproof, with a close-up focus (2.5 cm). We show that this camera system can be used in remote locations with high rainfall and humidity. The camera has an Infrared LED light to film in dark places and can continuously record up to 21 days (504 h). We also describe how to make concrete artificial shelters to mount the camera in. One of the great strengths of this shelter/camera set-up is that the animals choose to take up residence and can then be filmed for extended periods with no disturbance. Furthermore, we give examples of how shelters and cameras could be used to film a range of behaviours in not only many small cryptic amphibian species but also other small vertebrates and invertebrates globally.
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Affiliation(s)
- Jordy Groffen
- College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
| | - Conrad J. Hoskin
- College of Science and EngineeringJames Cook UniversityTownsvilleQueenslandAustralia
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4
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Nguyen N, Van TV, Nguyen T. The synergy of nucleic acid amplification and miniaturized systems in enhancing liquid biopsy applications. Bioanalysis 2024. [PMID: 38380670 DOI: 10.4155/bio-2023-0238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024] Open
Affiliation(s)
- Ngoc Nguyen
- School of Biomedical Engineering, International University, Ho Chi Minh 700000, Vietnam & Vietnam National University, Ho Chi Minh City, 700000, Vietnam
| | - Toi Vo Van
- School of Biomedical Engineering, International University, Ho Chi Minh 700000, Vietnam & Vietnam National University, Ho Chi Minh City, 700000, Vietnam
| | - Trieu Nguyen
- Shared Research Facilities, West Virginia University, Morgantown, WV 26506, USA
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5
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Sarıyer RM, Gill K, Needs SH, Hodge D, Reis NM, Jones CI, Edwards AD. Time- and distance-resolved robotic imaging of fluid flow in vertical microfluidic strips: a new technique for quantitative, multiparameter measurement of global haemostasis. SENSORS & DIAGNOSTICS 2023; 2:1623-1637. [PMID: 38013763 PMCID: PMC10633108 DOI: 10.1039/d3sd00162h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 09/26/2023] [Indexed: 11/29/2023]
Abstract
Measuring the complex processes of blood coagulation, haemostasis and thrombosis that are central to cardiovascular health and disease typically requires a choice between high-resolution low-throughput laboratory assays, or simpler less quantitative tests. We propose combining mass-produced microfluidic devices with open-source robotic instrumentation to enable rapid development of affordable and portable, yet high-throughput and performance haematological testing. A time- and distance-resolved fluid flow analysis by Raspberry Pi imaging integrated with controlled sample addition and illumination, enabled simultaneous tracking of capillary rise in 120 individual capillaries (∼160, 200 or 270 μm internal diameter), in 12 parallel disposable devices. We found time-resolved tracking of capillary rise in each individual microcapillary provides quantitative information about fluid properties and most importantly enables quantitation of dynamic changes in these properties following stimulation. Fluid properties were derived from flow kinetics using a pressure balance model validated with glycerol-water mixtures and blood components. Time-resolved imaging revealed fluid properties that were harder to determine from a single endpoint image or equilibrium analysis alone. Surprisingly, instantaneous superficial fluid velocity during capillary rise was found to be largely independent of capillary diameter at initial time points. We tested if blood function could be measured dynamically by stimulating blood with thrombin to trigger activation of global haemostasis. Thrombin stimulation slowed vertical fluid velocity consistent with a dynamic increase in viscosity. The dynamics were concentration-dependent, with highest doses reducing flow velocity faster (within 10 s) than lower doses (10-30 s). This open-source imaging instrumentation expands the capability of affordable microfluidic devices for haematological testing, towards high-throughput multi-parameter blood analysis needed to understand and improve cardiovascular health.
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Affiliation(s)
- Rüya Meltem Sarıyer
- Reading School of Pharmacy, University of Reading Whiteknights Reading RG6 6UB UK +44 (0)118 378 4253
| | - Kirandeep Gill
- Reading School of Pharmacy, University of Reading Whiteknights Reading RG6 6UB UK +44 (0)118 378 4253
- Department of Chemical Engineering and Centre for Biosensors, Bioelectronics and Biodevices (CBio), University of Bath Bath BA2 7AY UK
| | - Sarah H Needs
- Reading School of Pharmacy, University of Reading Whiteknights Reading RG6 6UB UK +44 (0)118 378 4253
| | - Daniel Hodge
- Reading School of Biological Sciences, University of Reading Whiteknights Reading UK
| | - Nuno M Reis
- Department of Chemical Engineering and Centre for Biosensors, Bioelectronics and Biodevices (CBio), University of Bath Bath BA2 7AY UK
| | - Chris I Jones
- Reading School of Biological Sciences, University of Reading Whiteknights Reading UK
| | - Alexander D Edwards
- Reading School of Pharmacy, University of Reading Whiteknights Reading RG6 6UB UK +44 (0)118 378 4253
- School of Electronics and Computer Science, University of Southampton Highfield Southampton SO17 1BJ UK
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6
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Sarıyer RM, Edwards AD, Needs SH. Open Hardware for Microfluidics: Exploiting Raspberry Pi Singleboard Computer and Camera Systems for Customisable Laboratory Instrumentation. BIOSENSORS 2023; 13:948. [PMID: 37887141 PMCID: PMC10605846 DOI: 10.3390/bios13100948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 10/28/2023]
Abstract
The integration of Raspberry Pi miniature computer systems with microfluidics has revolutionised the development of low-cost and customizable analytical systems in life science laboratories. This review explores the applications of Raspberry Pi in microfluidics, with a focus on imaging, including microscopy and automated image capture. By leveraging the low cost, flexibility and accessibility of Raspberry Pi components, high-resolution imaging and analysis have been achieved in direct mammalian and bacterial cellular imaging and a plethora of image-based biochemical and molecular assays, from immunoassays, through microbial growth, to nucleic acid methods such as real-time-qPCR. The control of image capture permitted by Raspberry Pi hardware can also be combined with onboard image analysis. Open-source hardware offers an opportunity to develop complex laboratory instrumentation systems at a fraction of the cost of commercial equipment and, importantly, offers an opportunity for complete customisation to meet the users' needs. However, these benefits come with a trade-off: challenges remain for those wishing to incorporate open-source hardware equipment in their own work, including requirements for construction and operator skill, the need for good documentation and the availability of rapid prototyping such as 3D printing plus other components. These advances in open-source hardware have the potential to improve the efficiency, accessibility, and cost-effectiveness of microfluidic-based experiments and applications.
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7
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Gomez-Hinostroza ES, Gurdo N, Alvan Vargas MVG, Nikel PI, Guazzaroni ME, Guaman LP, Castillo Cornejo DJ, Platero R, Barba-Ostria C. Current landscape and future directions of synthetic biology in South America. Front Bioeng Biotechnol 2023; 11:1069628. [PMID: 36845183 PMCID: PMC9950111 DOI: 10.3389/fbioe.2023.1069628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/30/2023] [Indexed: 02/12/2023] Open
Abstract
Synthetic biology (SynBio) is a rapidly advancing multidisciplinary field in which South American countries such as Chile, Argentina, and Brazil have made notable contributions and have established leadership positions in the region. In recent years, efforts have strengthened SynBio in the rest of the countries, and although progress is significant, growth has not matched that of the aforementioned countries. Initiatives such as iGEM and TECNOx have introduced students and researchers from various countries to the foundations of SynBio. Several factors have hindered progress in the field, including scarce funding from both public and private sources for synthetic biology projects, an underdeveloped biotech industry, and a lack of policies to promote bio-innovation. However, open science initiatives such as the DIY movement and OSHW have helped to alleviate some of these challenges. Similarly, the abundance of natural resources and biodiversity make South America an attractive location to invest in and develop SynBio projects.
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Affiliation(s)
- E. Sebastian Gomez-Hinostroza
- Laboratorio de Investigación en Citogenética y Biomoléculas de Anfibios (LICBA), Centro de Investigación para la Salud en América Latina (CISeAL), Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Nicolás Gurdo
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, Denmark
| | | | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, Denmark
| | | | - Linda P. Guaman
- Centro de Investigación Biomédica (CENBIO), Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador
| | | | - Raúl Platero
- Laboratorio de Microbiología Ambiental, Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Carlos Barba-Ostria
- Escuela de Medicina, Colegio de Ciencias de la Salud Quito, Universidad San Francisco de Quito USFQ, Quito, Ecuador,Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Quito, Ecuador,*Correspondence: Carlos Barba-Ostria,
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8
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Abstract
Open hardware solutions are increasingly being chosen by researchers as a strategy to improve access to technology for cutting-edge biology research. The use of DIY technology is already widespread, particularly in countries with limited access to science funding, and is catalyzing the development of open-source technologies. Beyond financial accessibility, open hardware can be transformational for the access of laboratories to equipment by reducing dependence on import logistics and enabling direct knowledge transfer. Central drivers to the adoption of appropriate open-source technologies in biology laboratories around the world are open sharing, digital fabrication, local production, the use of standard parts, and detailed documentation. This Essay examines the global spread of open hardware and discusses which kinds of open-source technologies are the most beneficial in scientific environments with economic and infrastructural constraints.
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Affiliation(s)
- Tobias Wenzel
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Macul, Región Metropolitana, Chile
- * E-mail:
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9
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Diep TT, Needs SH, Bizley S, Edwards AD. Rapid Bacterial Motility Monitoring Using Inexpensive 3D-Printed OpenFlexure Microscopy Allows Microfluidic Antibiotic Susceptibility Testing. MICROMACHINES 2022; 13:mi13111974. [PMID: 36422401 PMCID: PMC9699482 DOI: 10.3390/mi13111974] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/10/2022] [Accepted: 11/12/2022] [Indexed: 05/30/2023]
Abstract
Antibiotic susceptibility testing is vital to tackle the emergence and spread of antimicrobial resistance. Inexpensive digital CMOS cameras can be converted into portable digital microscopes using 3D printed x-y-z stages. Microscopic examination of bacterial motility can rapidly detect the response of microbes to antibiotics to determine susceptibility. Here, we present a new simple microdevice-miniature microscope cell measurement system for multiplexed antibiotic susceptibility testing. The microdevice is made using melt-extruded plastic film strips containing ten parallel 0.2 mm diameter microcapillaries. Two different antibiotics, ceftazidime and gentamicin, were prepared in Mueller-Hinton agar (0.4%) to produce an antibiotic-loaded microdevice for simple sample addition. This combination was selected to closely match current standard methods for both antibiotic susceptibility testing and motility testing. Use of low agar concentration permits observation of motile bacteria responding to antibiotic exposure as they enter capillaries. This device fits onto the OpenFlexure 3D-printed digital microscope using a Raspberry Pi computer and v2 camera, avoiding need for expensive laboratory microscopes. This inexpensive and portable digital microscope platform had sufficient magnification to detect motile bacteria, yet wide enough field of view to monitor bacteria behavior as they entered antibiotic-loaded microcapillaries. The image quality was sufficient to detect how bacterial motility was inhibited by different concentrations of antibiotic. We conclude that a 3D-printed Raspberry Pi-based microscope combined with disposable microfluidic test strips permit rapid, easy-to-use bacterial motility detection, with potential for aiding detection of antibiotic resistance.
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Affiliation(s)
- Tai The Diep
- Reading School of Pharmacy, University of Reading, Reading RG6 6AD, UK
| | - Sarah Helen Needs
- Reading School of Pharmacy, University of Reading, Reading RG6 6AD, UK
| | - Samuel Bizley
- Reading School of Pharmacy, University of Reading, Reading RG6 6AD, UK
| | - Alexander D. Edwards
- Reading School of Pharmacy, University of Reading, Reading RG6 6AD, UK
- Capillary Film Technology Ltd., Billingshurst RH14 9TF, UK
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10
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Low-cost modular systems for agarose gel documentation. Biotechniques 2022; 73:227-232. [DOI: 10.2144/btn-2022-0060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
While conducting recombinant DNA technology procedures, such as DNA purification, agarose gel electrophoresis is often used for identification, characterization and quantification of DNA. The collection of data for experiments involving such techniques frequently involves capturing images using systems that are expensive and/or proprietary, such that they are not user-serviceable when they malfunction or become antiquated. In response to these limitations, work was done to replace the authors' existing aging Mac OS-based modular system with open-source software and generic hardware. Several versions of a modular imaging system that can be adjusted to fit nearly all use cases are described. The systems developed can accommodate diverse uses from research laboratories to educational environments where commercial systems could be unaffordable.
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11
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Vidal G, Vitalis C, Muñoz Silva M, Castillo-Passi C, Yáñez Feliú G, Federici F, Rudge TJ. Accurate characterization of dynamic microbial gene expression and growth rate profiles. Synth Biol (Oxf) 2022; 7:ysac020. [PMID: 36267953 PMCID: PMC9569155 DOI: 10.1093/synbio/ysac020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 07/16/2022] [Accepted: 09/29/2022] [Indexed: 11/16/2022] Open
Abstract
Genetic circuits are subject to variability due to cellular and compositional contexts. Cells face changing internal states and environments, the cellular context, to which they sense and respond by changing their gene expression and growth rates. Furthermore, each gene in a genetic circuit operates in a compositional context of genes which may interact with each other and the host cell in complex ways. The context of genetic circuits can, therefore, change gene expression and growth rates, and measuring their dynamics is essential to understanding natural and synthetic regulatory networks that give rise to functional phenotypes. However, reconstruction of microbial gene expression and growth rate profiles from typical noisy measurements of cell populations is difficult due to the effects of noise at low cell densities among other factors. We present here a method for the estimation of dynamic microbial gene expression rates and growth rates from noisy measurement data. Compared to the current state-of-the-art, our method significantly reduced the mean squared error of reconstructions from simulated data of growth and gene expression rates, improving the estimation of timing and magnitude of relevant shapes of profiles. We applied our method to characterize a triple-reporter plasmid library combining multiple transcription units in different compositional and cellular contexts in Escherichia coli. Our analysis reveals cellular and compositional context effects on microbial growth and gene expression rate dynamics and suggests a method for the dynamic ratiometric characterization of constitutive promoters relative to an in vivo reference.
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Affiliation(s)
- Gonzalo Vidal
- Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Interdisciplinary Computing and Complex BioSystems (ICOS) Research Group, School of Computing, Newcastle University, Newcastle Upon Tyne, UK
| | - Carolus Vitalis
- Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Macarena Muñoz Silva
- Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carlos Castillo-Passi
- Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- School of Biomedical Engineering and Imaging Sciences, King’s College London, St Thomas’ Hospital, London, UK
- Millennium Institute for Intelligent Healthcare Engineering (iHEALTH), Santiago, Chile
| | - Guillermo Yáñez Feliú
- Interdisciplinary Computing and Complex BioSystems (ICOS) Research Group, School of Computing, Newcastle University, Newcastle Upon Tyne, UK
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Fernán Federici
- Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- ANID – Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio) & FONDAP Center for Genome Regulation, Santiago, Chile
| | - Timothy J Rudge
- Interdisciplinary Computing and Complex BioSystems (ICOS) Research Group, School of Computing, Newcastle University, Newcastle Upon Tyne, UK
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12
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Bak SK, Seong W, Rha E, Lee H, Kim SK, Kwon KK, Kim H, Lee SG. Novel High-Throughput DNA Part Characterization Technique for Synthetic Biology. J Microbiol Biotechnol 2022; 32:1026-1033. [PMID: 35879270 PMCID: PMC9628936 DOI: 10.4014/jmb.2207.07013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 07/19/2022] [Accepted: 07/19/2022] [Indexed: 12/15/2022]
Abstract
This study presents a novel DNA part characterization technique that increases throughput by combinatorial DNA part assembly, solid plate-based quantitative fluorescence assay for phenotyping, and barcode tagging-based long-read sequencing for genotyping. We confirmed that the fluorescence intensities of colonies on plates were comparable to fluorescence at the single-cell level from a high-end, flow-cytometry device and developed a high-throughput image analysis pipeline. The barcode tagging-based long-read sequencing technique enabled rapid identification of all DNA parts and their combinations with a single sequencing experiment. Using our techniques, forty-four DNA parts (21 promoters and 23 RBSs) were successfully characterized in 72 h without any automated equipment. We anticipate that this high-throughput and easy-to-use part characterization technique will contribute to increasing part diversity and be useful for building genetic circuits and metabolic pathways in synthetic biology.
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Affiliation(s)
- Seong-Kun Bak
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea,Biosystems and Bioengineering Program, University of Science and Technology, Daejeon 34141, Republic of Korea
| | - Wonjae Seong
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Eugene Rha
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Hyewon Lee
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Seong Keun Kim
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Kil Koang Kwon
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Haseong Kim
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea,Biosystems and Bioengineering Program, University of Science and Technology, Daejeon 34141, Republic of Korea,Corresponding authors H.S. Kim Phone: +82-42-860-4372 Fax: +82-42-860-4489 E-mail:
| | - Seung-Goo Lee
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea,Biosystems and Bioengineering Program, University of Science and Technology, Daejeon 34141, Republic of Korea,
S.G. Lee Phone: +82-42-860-4373 E-mail:
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13
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Dönmez Sİ, Needs SH, Osborn HMI, Reis NM, Edwards AD. Label-free 1D microfluidic dipstick counting of microbial colonies and bacteriophage plaques. LAB ON A CHIP 2022; 22:2820-2831. [PMID: 35792607 DOI: 10.1039/d2lc00280a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Counting viable bacterial cells and functional bacteriophage is fundamental to microbiology underpinning research, surveillance, biopharmaceuticals and diagnostics. Colony forming unit (CFU) and plaque forming unit (PFU) counting still requires slow and laborious solid culture on agar in Petri dishes or plates. Here, we show that dip-stick microfluidic strips can be used without growth indicator dye for rapid and simple CFU ml-1 and PFU ml-1 measurement. We demonstrate for the first time that fluoropolymer microcapillaries combined with digital imaging allow bacteriophage plaques to be counted rapidly in a dip-and-test format. The microfluidic length scales offer a linear 1-dimensional alternative to a 2D solid agar medium surface, with colonies or plaques clearly visible as "dashes" or "gaps". An inexpensive open source darkfield biosensor system using Raspberry Pi imaging permits label-free detection and counting of colonies or plaques within 4-8 hours in a linear, liquid matrix within ∼200 μm inner diameter microcapillaries. We obtained full quantitative agreement between 1D microfluidic colony counting in dipsticks versus conventional 2D solid agar Petri dish plates for S. aureus and E. coli, and for T2 phage and phage K, but up to 6 times faster. Time-lapse darkfield imaging permitted detailed kinetic analysis of colony growth in the microcapillaries, providing new insight into microfluidic microbiology and colony growth, not possible with Petri dishes. Surprisingly, whilst E. coli colonies appeared earlier, subsequent colony expansion was faster along the microcapillaries for S. aureus. This may be explained by the microenvironment offered for 1D colony growth within microcapillaries, linked to a mass balance between nutrient (glucose) diffusion and bacterial growth kinetics. Counting individual colonies in liquid medium was not possible for motile strains that spread rapidly along the capillary, however inclusion of soft agar inhibited spreading, making this new simple dip-and-test counting method applicable to both motile and non-motile bacteria. Label-free dipstick colony and plaque counting has potential for many analytical microbial tasks, and the innovation of 1D colony counting has relevance to other microfluidic microbiology.
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Affiliation(s)
| | - Sarah H Needs
- Reading School of Pharmacy, University of Reading, Whiteknights, RG6 6AD, UK.
| | - Helen M I Osborn
- Reading School of Pharmacy, University of Reading, Whiteknights, RG6 6AD, UK.
| | - Nuno M Reis
- Department of Chemical Engineering and Centre for Biosensors, Biodevices and Bioelectronics (C3Bio), University of Bath, Claverton Down, Bath BA2 7AY, UK
- Capillary Film Technology Ltd, Daux Road, Billingshurst, West Sussex RH14 9SJ, UK
| | - Alexander D Edwards
- Reading School of Pharmacy, University of Reading, Whiteknights, RG6 6AD, UK.
- Capillary Film Technology Ltd, Daux Road, Billingshurst, West Sussex RH14 9SJ, UK
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14
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Thompson JE. Low-Cost Microplate Reader with 3D Printed Parts for under 500 USD. SENSORS 2022; 22:s22093242. [PMID: 35590932 PMCID: PMC9103534 DOI: 10.3390/s22093242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 02/01/2023]
Abstract
A 96-well microplate reader for absorption spectroscopy was designed, constructed, and tested at a total cost of ca. 500 USD. The reduced cost of the device represents the major technical contribution of this manuscript, as costs were reduced 7 fold from previous reports. The device was able to achieve 3σ limits of detection of ca. 0.01 absorbance units (AU) over a 60 second measurement for the mid-visible wavelength range. Component parts are either commercially available, or 3D printed from plans. Analysis wavelength can be altered throughout the visible region through use of various photographic or theatrical filters. This feature allows the well plate reader to be used for typical laboratory assays such as cell population estimation by optical density (OD) at 600 nm, or enzyme-linked immunosorbent assays (ELISA) at 450 nm. This manuscript reports on the motivation and process of constructing the device, lists required parts, presents data demonstrating device function, and provides the community of scholars with plans to reproduce the work. The device can be reproduced in laboratories lacking sufficient resources to purchase commercially available options and this outcome contributes towards empowerment of individuals and equity of scientific enquiry.
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Affiliation(s)
- Jonathan E Thompson
- School of Veterinary Medicine, Texas Tech University, 7671 Evans Dr., Amarillo, TX 79106, USA
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15
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Ushizima D, Chen Y, Alegro M, Ovando D, Eser R, Lee W, Poon K, Shankar A, Kantamneni N, Satrawada S, Junior EA, Heinsen H, Tosun D, Grinberg LT. Deep learning for Alzheimer's disease: Mapping large-scale histological tau protein for neuroimaging biomarker validation. Neuroimage 2022; 248:118790. [DOI: 10.1016/j.neuroimage.2021.118790] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 11/30/2021] [Accepted: 12/04/2021] [Indexed: 01/16/2023] Open
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16
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Abid HA, Ong JW, Lin ES, Song Z, Liew OW, Ng TW. Low-cost Imaging of Fluorescent DNA in Agarose Gel Electrophoresis using Raspberry Pi cameras. J Fluoresc 2022; 32:443-448. [PMID: 35064858 PMCID: PMC8888377 DOI: 10.1007/s10895-021-02884-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 12/27/2021] [Indexed: 01/13/2023]
Abstract
Low-cost analytical solutions built around microcomputers like the Raspberry Pi help to facilitate laboratory investigations in resource limited venues. Here, three camera modules (V1.3 with and without filter, as well as NoIR) that work with this microcomputer were assessed for their suitability in imaging fluorescent DNA following agarose gel electrophoresis. Evaluation of their utility was based on signal-to-noise (SNR) and noise variance metrics that were developed. Experiments conducted with samples were subjected to Polymerase Chain Reaction (PCR), and the amplified products were separated using gel electrophoresis and stained with Midori green. Image analysis revealed the NoIR camera performed the best with SNR and noise variance values of 21.7 and 0.222 respectively. In experiments conducted using UV LED lighting to simulate ethidium bromide (EtBr) excitation, the NoIR and V1.3 with filter removed cameras showed comparable SNR values.
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Affiliation(s)
- Hassan Ali Abid
- Laboratory for Optics, Department of Mechanical & Aerospace Engineering, Monash University, & Mechanics, AcousticsClayton, VIC, 3800, Australia
| | - Jian Wern Ong
- Laboratory for Optics, Department of Mechanical & Aerospace Engineering, Monash University, & Mechanics, AcousticsClayton, VIC, 3800, Australia
| | - Eric Shen Lin
- Laboratory for Optics, Department of Mechanical & Aerospace Engineering, Monash University, & Mechanics, AcousticsClayton, VIC, 3800, Australia
| | - Zhixiong Song
- Laboratory for Optics, Department of Mechanical & Aerospace Engineering, Monash University, & Mechanics, AcousticsClayton, VIC, 3800, Australia
| | - Oi Wah Liew
- Centre for Translational Medicine, Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, 14 Medical Drive, 117599, Singapore
| | - Tuck Wah Ng
- Laboratory for Optics, Department of Mechanical & Aerospace Engineering, Monash University, & Mechanics, AcousticsClayton, VIC, 3800, Australia.
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17
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Vernon J, Canyelles-Pericas P, Torun H, Dai X, Ng WP, Binns R, Busawon K, Fu YQ. Acousto-Pi: An Opto-Acoustofluidic System Using Surface Acoustic Waves Controlled With Open-Source Electronics for Integrated In-Field Diagnostics. IEEE TRANSACTIONS ON ULTRASONICS, FERROELECTRICS, AND FREQUENCY CONTROL 2022; 69:411-422. [PMID: 34524958 DOI: 10.1109/tuffc.2021.3113173] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Surface acoustic wave (SAW) devices are increasingly applied in life sciences, biology, and point-of-care applications due to their combined acoustofluidic sensing and actuating properties. Despite the advances in this field, there remain significant gaps in interfacing hardware and control strategies to facilitate system integration with high performance and low cost. In this work, we present a versatile and digitally controlled acoustofluidic platform by demonstrating key functions for biological assays such as droplet transportation and mixing using a closed-loop feedback control with image recognition. Moreover, we integrate optical detection by demonstrating in situ fluorescence sensing capabilities with a standard camera and digital filters, bypassing the need for expensive and complex optical setups. The Acousto-Pi setup is based on open-source Raspberry Pi hardware and 3-D printed housing, and the SAW devices are fabricated with piezoelectric thin films on a metallic substrate. The platform enables the control of droplet position and speed for sample processing (mixing and dilution of samples), as well as the control of temperature based on acousto-heating, offering embedded processing capability. It can be operated remotely while recording the measurements in cloud databases toward integrated in-field diagnostic applications such as disease outbreak control, mass healthcare screening, and food safety.
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18
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Jolles JW. Broad‐scale applications of the Raspberry Pi: A review and guide for biologists. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13652] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jolle W. Jolles
- Zukunftskolleg University of Konstanz Konstanz Germany
- Department of Collective Behaviour Max Planck Institute of Animal Behaviour Konstanz Germany
- Centre for Research on Ecology and Forestry Applications (CREAF) Barcelona Spain
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19
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Bounds AD, Bailey RD, Adams CT, Callaghan DC, Girkin JM. LightBox: A multiwell plate illumination system for photoactive molecule characterization. JOURNAL OF BIOPHOTONICS 2021; 14:e202000481. [PMID: 33576569 DOI: 10.1002/jbio.202000481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/20/2021] [Accepted: 01/28/2021] [Indexed: 06/12/2023]
Abstract
Multiwell plates (MWPs) are the workhorses of the life sciences. However, biophotonics research with MWPs is limited, in part due to the lack of equipment suitable for photo-irradiation of photoactive molecules in a MWP-suitable, high-throughput manner, either commercially or through open-source MWP systems. Here we present "LightBox", a calibrated controllable MWP illumination system with broad applications including screening of photoactive molecules and characterization of photocatalytic chemicals. LightBox is a high intensity, accurately controllable, uniform illumination system designed for MWPs with electronics and a control unit that provides a simple and intuitive interface. LightBox can reach intensities of 0.23 mW/mm2 at wavelengths of 405 nm with variance between well sites of <5%. The usefulness of LightBox is demonstrated by assessing the IC50 of a photosensitizing compound using a live/dead assay following simultaneous irradiation of the sample at a range of concentrations, eliminating uncontrolled variables between concentrations and drastically increasing assessment speed.
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Affiliation(s)
- A D Bounds
- Centre for Advanced Instrumentation, Department of Physics, Durham University, Durham, DH1 3LE, UK
| | - R D Bailey
- Centre for Advanced Instrumentation, Department of Physics, Durham University, Durham, DH1 3LE, UK
| | - C T Adams
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - D C Callaghan
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - J M Girkin
- Centre for Advanced Instrumentation, Department of Physics, Durham University, Durham, DH1 3LE, UK
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20
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Graham TG, Dugast‐Darzacq C, Dailey GM, Darzacq X, Tjian R. Simple, Inexpensive RNA Isolation and One-Step RT-qPCR Methods for SARS-CoV-2 Detection and General Use. Curr Protoc 2021; 1:e130. [PMID: 33905620 PMCID: PMC8206771 DOI: 10.1002/cpz1.130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The most common method for RNA detection involves reverse transcription followed by quantitative polymerase chain reaction (RT-qPCR) analysis. Commercial one-step master mixes-which include both a reverse transcriptase and a thermostable polymerase and thus allow performing both the RT and qPCR steps consecutively in a sealed well-are key reagents for SARS-CoV-2 diagnostic testing; yet, these are typically expensive and have been affected by supply shortages in periods of high demand. As an alternative, we describe here how to express and purify Taq polymerase and M-MLV reverse transcriptase and assemble a homemade one-step RT-qPCR master mix. This mix can be easily assembled from scratch in any laboratory equipped for protein purification. We also describe two simple alternative methods to prepare clinical swab samples for SARS-CoV-2 RNA detection by RT-qPCR: heat-inactivation for direct addition, and concentration of RNA by isopropanol precipitation. Finally, we describe how to perform RT-qPCR using the homemade master mix, how to prepare in vitro-transcribed RNA standards, and how to use a fluorescence imager for endpoint detection of RT-PCR amplification in the absence of a qPCR machine In addition to being useful for diagnostics, these versatile protocols may be adapted for nucleic acid quantification in basic research. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Preparation of a one-step RT-qPCR master mix using homemade enzymes Basic Protocol 2: Preparation of swab samples for direct RT-PCR Alternate Protocol 1: Concentration of RNA from swab samples by isopropanol precipitation Basic Protocol 3: One-step RT-qPCR of RNA samples using a real-time thermocycler Support Protocol: Preparation of RNA concentration standards by in vitro transcription Alternate Protocol 2: One-step RT-PCR using endpoint fluorescence detection.
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Affiliation(s)
- Thomas G.W. Graham
- Department of Molecular and Cell Biology, 475D Li Ka Shing CenterUniversity of CaliforniaBerkeleyCalifornia
| | - Claire Dugast‐Darzacq
- Department of Molecular and Cell Biology, 475D Li Ka Shing CenterUniversity of CaliforniaBerkeleyCalifornia
| | - Gina M. Dailey
- Department of Molecular and Cell Biology, 475D Li Ka Shing CenterUniversity of CaliforniaBerkeleyCalifornia
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, 475D Li Ka Shing CenterUniversity of CaliforniaBerkeleyCalifornia
| | - Robert Tjian
- Department of Molecular and Cell Biology, 475D Li Ka Shing CenterUniversity of CaliforniaBerkeleyCalifornia
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21
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Flores DP, Marzullo TC. The construction of high-magnification homemade lenses for a simple microscope: an easy "DIY" tool for biological and interdisciplinary education. ADVANCES IN PHYSIOLOGY EDUCATION 2021; 45:134-144. [PMID: 33661049 PMCID: PMC9186497 DOI: 10.1152/advan.00127.2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 06/12/2023]
Abstract
The rise of microscopy in the seventeenth century allowed scientists to discover a new world of microorganisms and achieve great physiological advances. One of the first microscopes of the epoch was Antonie van Leeuwenhoek's microscope, a deceptively simple device that contains a single ball lens housed in a metal plate allowing the observation of samples at up to ×250 magnification. Such magnification was much greater than that achieved by rudimentary compound microscopes of the era, allowing for the discovery of microscopic, single-celled life, an achievement that marked the study of biology up to the nineteenth century. Since Leeuwenhoek's design uses a single ball lens, it is possible to fabricate variations for educational activities in physics and biology university and high school classrooms. A fundamental problem, however, with home-built microscopes is that it is difficult to work with glass. We developed a simple protocol to make ball lenses of glass and gelatin with high magnification that can be done in a university/high school classroom, and we designed an optimized support for focusing and taking photographs with a smartphone. The protocol details a simple, easily accessible, low-cost, and effective tool for the observation of microscopic samples, possible to perform anywhere without the need for a laboratory or complex tools. Our protocol has been implemented in classrooms in Chile to a favorable reception.
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Affiliation(s)
- Daniela P Flores
- Laboratory of Ontogeny and Phylogeny, Faculty of Science, University of Chile, Santiago, Chile
- Foundation for the Interdisciplinary Development of Science, Technology and Arts, DICTA, Santiago, Chile
- MicroMundo Project, Faculty of Medicine, University of Chile, Santiago, Chile
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22
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Yáñez Feliú G, Earle Gómez B, Codoceo Berrocal V, Muñoz Silva M, Nuñez IN, Matute TF, Arce Medina A, Vidal G, Vitalis C, Dahlin J, Federici F, Rudge TJ. Flapjack: Data Management and Analysis for Genetic Circuit Characterization. ACS Synth Biol 2021; 10:183-191. [PMID: 33382586 DOI: 10.1021/acssynbio.0c00554] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Characterization is fundamental to the design, build, test, learn (DBTL) cycle for engineering synthetic genetic circuits. Components must be described in such a way as to account for their behavior in a range of contexts. Measurements and associated metadata, including part composition, constitute the test phase of the DBTL cycle. These data may consist of measurements of thousands of circuits, measured in hundreds of conditions, in multiple assays potentially performed in different laboratories and using different techniques. In order to inform the learn phase this large volume of data must be filtered, collated, and analyzed. Characterization consists of using this data to parametrize models of component function in different contexts, and combining them to predict behaviors of novel circuits. Tools to store, organize, share, and analyze large volumes of measurement and metadata are therefore essential to linking the test phase to the build and learn phases, closing the loop of the DBTL cycle. Here we present such a system, implemented as a web app with a backend data registry and analysis engine. An interactive frontend provides powerful querying, plotting, and analysis tools, and we provide a REST API and Python package for full integration with external build and learn software. All measurements are associated with circuit part composition via SBOL (Synthetic Biology Open Language). We demonstrate our tool by characterizing a range of genetic components and circuits according to composition and context.
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Affiliation(s)
- Guillermo Yáñez Feliú
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago 7820244, Chile
| | - Benjamín Earle Gómez
- Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago 7820244, Chile
| | - Verner Codoceo Berrocal
- Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago 7820244, Chile
| | - Macarena Muñoz Silva
- Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago 7820244, Chile
| | - Isaac N Nuñez
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago 7820244, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago 7820244, Chile
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Pontificia Universidad Católica de Chile, Santiago 8330005, Chile
| | - Tamara F Matute
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago 7820244, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago 7820244, Chile
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Pontificia Universidad Católica de Chile, Santiago 8330005, Chile
| | - Anibal Arce Medina
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Pontificia Universidad Católica de Chile, Santiago 8330005, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8330005, Chile
| | - Gonzalo Vidal
- Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago 7820244, Chile
| | - Carlos Vitalis
- Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago 7820244, Chile
| | - Jonathan Dahlin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Fernán Federici
- Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago 7820244, Chile
- ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Pontificia Universidad Católica de Chile, Santiago 8330005, Chile
- FONDAP, Center for Genome Regulation, Pontificia Universidad Católica de Chile, Santiago 8330005, Chile
| | - Timothy J Rudge
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago 7820244, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago 7820244, Chile
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23
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Nguyen T, Chidambara VA, Andreasen SZ, Golabi M, Huynh VN, Linh QT, Bang DD, Wolff A. Point-of-care devices for pathogen detections: The three most important factors to realise towards commercialization. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.116004] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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24
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Eggert S, Mieszczanek P, Meinert C, Hutmacher DW. OpenWorkstation: A modular open-source technology for automated in vitro workflows. HARDWAREX 2020; 8:e00152. [PMID: 35498237 PMCID: PMC9041211 DOI: 10.1016/j.ohx.2020.e00152] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 08/15/2020] [Accepted: 10/13/2020] [Indexed: 05/24/2023]
Abstract
Automation liberates scientific staff from repetitive tasks, decreases the probability of human error and consequently enhances the reproducibility of lab experiments. However, the use of laboratory automation in academic laboratories is limited due to high acquisition costs and the inability to customize off-the-shelf hardware. To address these challenges, we present an Open Source Hardware concept, referred to as OpenWorkstation, to build an assembly line-inspired platform consisting of ready-to-use and customizable modules. In contrast to current standalone solutions, the OpenWorkstation concept enables the combination of single hardware modules - each with a specific set of functionalities - to a modular workstation to provide a fully automated setup. The base setup consists of a pipetting and transport module and is designed to execute basic protocol steps for in vitro research applications, including pipetting operations for liquids and viscous substances and transportation of cell culture vessels between the modules. We demonstrate the successful application of this concept within a case study by the development of a storage module to facilitate high-throughput studies and a photo-crosslinker module to initiate photo-induced polymerization of hydrogel solutions. We present a Systems Engineering framework for customized module development, guidance for the design and assembly of the presented modules, and operational instructions on the usage of the workstation. By combining capabilities from various open source instrumentations into a modular technology platform, the OpenWorkstation concept will facilitate efficient and reliable experimentation for in vitro research. Ultimately, this concept will allow academic groups to improve replicability and reproducibility in cell culture process operations towards more economical and innovative research in the future.
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Affiliation(s)
- Sebastian Eggert
- Centre in Regenerative Medicine, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane 4000, QLD, Australia
- School of Mechanical, Medical and Process Engineering, Science and Engineering Faculty, Queensland University of Technology, Brisbane 4000, QLD, Australia
- Chair of Medical Materials and Implants, Department of Mechanical Engineering and Munich School of BioEngineering, Technical University of Munich, Garching 85748, Germany
| | - Pawel Mieszczanek
- Centre in Regenerative Medicine, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane 4000, QLD, Australia
- School of Mechanical, Medical and Process Engineering, Science and Engineering Faculty, Queensland University of Technology, Brisbane 4000, QLD, Australia
| | - Christoph Meinert
- Centre in Regenerative Medicine, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane 4000, QLD, Australia
- School of Mechanical, Medical and Process Engineering, Science and Engineering Faculty, Queensland University of Technology, Brisbane 4000, QLD, Australia
| | - Dietmar W Hutmacher
- Centre in Regenerative Medicine, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane 4000, QLD, Australia
- School of Mechanical, Medical and Process Engineering, Science and Engineering Faculty, Queensland University of Technology, Brisbane 4000, QLD, Australia
- ARC ITTC in Additive Biomanufacturing, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane 4000, QLD, Australia
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25
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Kim J, Park JY, Park YJ, Park SY, Lee MS, Koo C. A portable and high-sensitivity optical sensing system for detecting fluorescently labeled enterohaemorrhagic Escherichia coli Shiga toxin 2B-subunit. PLoS One 2020; 15:e0236043. [PMID: 32673369 PMCID: PMC7365435 DOI: 10.1371/journal.pone.0236043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 06/28/2020] [Indexed: 11/18/2022] Open
Abstract
We developed a stand-alone, real-time optical detection device capable of reading fluorescence intensities from cell samples with high sensitivity and precision, for use as a portable fluorescent sensor for sensing fluorescently labeled enterohemorrhagic Escherichia coli (EHEC) Shiga toxins (Stxs). In general, the signal intensity from the fluorescently labeled Stxs was weak due to the small number of molecules bound to each cell. To address this technical challenge, we used a highly sensitive light detector (photomultiplier tube: PMT) to measure fluorescence, and designed a portable optical housing to align optical parts precisely; the housing itself was fabricated on a 3D printer. In addition, an electric circuit that amplified PMT output was designed and integrated into the system. The system shows the toxin concentration in the sample on a liquid crystal display (LCD), and a microcontroller circuit is used to read PMT output, process data, and display results. In contrast to other portable fluorescent detectors, the system works alone, without any peripheral computer or additional apparatus; its total size is about 17 × 13 × 9 cm3, and it weighs about 770 g. The detection limit was 0.01 ppm of Alexa Fluor 488 in PBS, which is ten thousand times lower than those of other smartphone-based systems and sufficiently sensitive for use with a portable optical detector. We used the portable real-time optical sensing system to detect Alexa Fluor 488–tagged Stx2B-subunits bound to monocytic THP-1 cells expressing the toxin receptor globotriaosylceramide (Gb3). The device did not detect a signal from Gb3-negative PD36 cells, indicating that it was capable of specifically detecting Stxs bound to cells expressing the toxin receptor. Following the development of a rapid and autonomous method for fluorescently tagging cells in food samples, the optical detection system described here could be used for direct detection of Shiga toxins in food in the field.
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Affiliation(s)
- Jeongtae Kim
- Department of Electronics and Control Engineering, Hanbat National University, Daejeon, Republic of Korea
| | - Jun-Young Park
- Environmental Diseases Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Young-Jun Park
- Environmental Diseases Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Seo-Young Park
- Environmental Diseases Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Moo-Seung Lee
- Environmental Diseases Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
- * E-mail: (MSL); (CK)
| | - Chiwan Koo
- Department of Electronics and Control Engineering, Hanbat National University, Daejeon, Republic of Korea
- * E-mail: (MSL); (CK)
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Chalich Y, Mallick A, Gupta B, Deen MJ. Development of a low-cost, user-customizable, high-speed camera. PLoS One 2020; 15:e0232788. [PMID: 32384109 PMCID: PMC7209243 DOI: 10.1371/journal.pone.0232788] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/21/2020] [Indexed: 01/13/2023] Open
Abstract
High-speed imaging equipment can be an expensive investment, especially when certain applications require custom solutions. In this paper, we present a low-cost high-speed prototype camera built on a low-end Zynq-7000 System-on-Chip (SoC) platform and off-the-shelf components with the aim of removing the entry barrier into various high-speed imaging applications. The camera is standalone (does not require a host computer) and can achieve 211 frames per second (fps) at its maximum resolution of 1280x1024, and up to 2329 fps at a 256x256 resolution. With a current cost of only several hundred dollars and resource utilization of ~5%, the open-source design's modularity and customizability allows users with sufficient hardware or programming experience to modify the camera to suit their needs, potentially driving the cost lower. This can be done by utilizing the large remaining programmable logic for custom image processing algorithms, creating user interface software on the CPU, attaching extensions through the peripheral Module connections, or creating custom carrier or daughter boards. The development and design of the camera is described and a figure-of-merit is presented to provide a value assessment of some available commercial high-speed cameras against which our camera is competitive. Finally, the camera was tested to record low frequency spatial vibration and was found to be useful in investigating phenotypes associated with aging in a leading animal model, the nematode (worm) Caenorhabditis elegans.
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Affiliation(s)
- Yamn Chalich
- Department of Electrical and Computer Engineering, McMaster University, Hamilton, ON, Canada
| | - Avijit Mallick
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Bhagwati Gupta
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - M. Jamal Deen
- Department of Electrical and Computer Engineering, McMaster University, Hamilton, ON, Canada
- School of Biomedical Engineering, McMaster University, Hamilton, ON, Canada
- * E-mail:
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Abstract
Electroporation is a basic yet powerful method for delivering small molecules (RNA, DNA, drugs) across cell membranes by application of an electrical field. It is used for many diverse applications, from genetically engineering cells to drug- and DNA-based vaccine delivery. Despite this broad utility, the high cost of electroporators can keep this approach out of reach for many budget-conscious laboratories. To address this need, we develop a simple, inexpensive, and handheld electroporator inspired by and derived from a common household piezoelectric stove lighter. The proposed "ElectroPen" device can cost as little as 23 cents (US dollars) to manufacture, is portable (weighs 13 g and requires no electricity), can be easily fabricated using 3D printing, and delivers repeatable exponentially decaying pulses of about 2,000 V in 5 ms. We provide a proof-of-concept demonstration by genetically transforming plasmids into Escherichia coli cells, showing transformation efficiency comparable to commercial devices, but at a fraction of the cost. We also demonstrate the potential for rapid dissemination of this approach, with multiple research groups across the globe validating the ease of construction and functionality of our device, supporting the potential for democratization of science through frugal tools. Thus, the simplicity, accessibility, and affordability of our device holds potential for making modern synthetic biology accessible in high school, community, and resource-poor laboratories. This Community Page article describes an ultra-low–cost (23-cent) 3D-printed electroporator, inspired by a common barbecue lighter, designed to enable broader access to synthetic biology in high-school, community, and budget-conscious laboratories.
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French S, Guo ABY, Brown ED. A comprehensive guide to dynamic analysis of microbial gene expression using the 3D-printed PFIbox and a fluorescent reporter library. Nat Protoc 2020; 15:575-603. [DOI: 10.1038/s41596-019-0257-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 10/11/2019] [Indexed: 01/25/2023]
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Li Y, Ma X, Wang W, Yan S, Liu F, Chu K, Xu G, Smith ZJ. Improving the limit of detection in portable luminescent assay readers through smart optical design. JOURNAL OF BIOPHOTONICS 2020; 13:e201900241. [PMID: 31602762 DOI: 10.1002/jbio.201900241] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 10/07/2019] [Accepted: 10/09/2019] [Indexed: 06/10/2023]
Abstract
Critical biomarkers of disease are increasingly being detected by point-of-care assays. Chemiluminescence (CL) and electrochemiluminescence (ECL) are often used in such assays due to their convenience and that they do not require light sources or other components that could complicate or add cost to the system. Reports of these assays often include readers built on a cellphone platform or constructed from low-cost components. However, the impact the optical design has on the limit of detection (LOD) in these systems remains unexamined. Here, we report a theoretical rubric to evaluate different optical designs in terms of maximizing the use of photons emitted from a CL or ECL assay to improve the LOD. We demonstrate that the majority of cellphone designs reported in the literature are not optimized, in part due to misunderstandings of the optical tradeoffs in collection systems, and in part due to limitations imposed on the designs arising from the use of a mobile phone with a very small lens aperture. Based on the theoretical rubric, we design a new portable reader built using off-the-shelf condenser optics, and demonstrate a nearly 10× performance enhancement compared to prior reports on an ECL assays running on a portable chip.
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Affiliation(s)
- Yaning Li
- University of Science and Technology of China, Department of Precision Machinery and Precision Instrumentation, Hefei, Anhui, China
- Key Laboratory of Precision Scientific Instrumentation of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, Anhui, China
| | - Xiangui Ma
- A State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, China
- University of Science and Technology of China, School of Applied Chemistry and Engineering, Hefei, Anhui, China
| | - Wenhe Wang
- A State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, China
- University of Science and Technology of China, School of Applied Chemistry and Engineering, Hefei, Anhui, China
| | - Shaojie Yan
- University of Science and Technology of China, Department of Precision Machinery and Precision Instrumentation, Hefei, Anhui, China
- Key Laboratory of Precision Scientific Instrumentation of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, Anhui, China
| | - Fangshuo Liu
- A State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, China
- University of Science and Technology of China, School of Applied Chemistry and Engineering, Hefei, Anhui, China
| | - Kaiqin Chu
- University of Science and Technology of China, Department of Precision Machinery and Precision Instrumentation, Hefei, Anhui, China
- Key Laboratory of Precision Scientific Instrumentation of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, Anhui, China
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, China
| | - Guobao Xu
- A State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, China
- University of Science and Technology of China, School of Applied Chemistry and Engineering, Hefei, Anhui, China
| | - Zachary J Smith
- University of Science and Technology of China, Department of Precision Machinery and Precision Instrumentation, Hefei, Anhui, China
- Key Laboratory of Precision Scientific Instrumentation of Anhui Higher Education Institutes, University of Science and Technology of China, Hefei, Anhui, China
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Needs SH, Diep TT, Bull SP, Lindley-Decaire A, Ray P, Edwards AD. Exploiting open source 3D printer architecture for laboratory robotics to automate high-throughput time-lapse imaging for analytical microbiology. PLoS One 2019; 14:e0224878. [PMID: 31743346 PMCID: PMC6863568 DOI: 10.1371/journal.pone.0224878] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/23/2019] [Indexed: 12/21/2022] Open
Abstract
Growth in open-source hardware designs combined with the low-cost of high performance optoelectronic and robotics components has supported a resurgence of in-house custom lab equipment development. We describe a low cost (below $700), open-source, fully customizable high-throughput imaging system for analytical microbiology applications. The system comprises a Raspberry Pi camera mounted on an aluminium extrusion frame with 3D-printed joints controlled by an Arduino microcontroller running open-source Repetier Host Firmware. The camera position is controlled by simple G-code scripts supplied from a Raspberry Pi singleboard computer and allow customized time-lapse imaging of microdevices over a large imaging area. Open-source OctoPrint software allows remote access and control. This simple yet effective design allows high-throughput microbiology testing in multiple formats including formats for bacterial motility, colony growth, microtitre plates and microfluidic devices termed ‘lab-on-a-comb’ to screen the effects of different culture media components and antibiotics on bacterial growth. The open-source robot design allows customization of the size of the imaging area; the current design has an imaging area of ~420 × 300mm, which allows 29 ‘lab-on-a-comb’ devices to be imaged which is equivalent 3480 individual 1μl samples. The system can also be modified for fluorescence detection using LED and emission filters embedded on the PiCam for more sensitive detection of bacterial growth using fluorescent dyes.
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Affiliation(s)
- Sarah H. Needs
- Reading School of Pharmacy, University of Reading, Whiteknights, Reading, United Kingdom
- * E-mail:
| | - Tai The Diep
- Reading School of Pharmacy, University of Reading, Whiteknights, Reading, United Kingdom
| | - Stephanie P. Bull
- Reading School of Pharmacy, University of Reading, Whiteknights, Reading, United Kingdom
| | | | - Partha Ray
- Department of Animal Sciences, School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
| | - Alexander D. Edwards
- Reading School of Pharmacy, University of Reading, Whiteknights, Reading, United Kingdom
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Tristan-Landin SB, Gonzalez-Suarez AM, Jimenez-Valdes RJ, Garcia-Cordero JL. Facile assembly of an affordable miniature multicolor fluorescence microscope made of 3D-printed parts enables detection of single cells. PLoS One 2019; 14:e0215114. [PMID: 31600202 PMCID: PMC6786622 DOI: 10.1371/journal.pone.0215114] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 09/20/2019] [Indexed: 11/18/2022] Open
Abstract
Fluorescence microscopy is one of the workhorses of biomedical research and laboratory diagnosis; however, their cost, size, maintenance, and fragility has prevented their adoption in developing countries or low-resource settings. Although significant advances have decreased their size, cost and accessibility, their designs and assembly remain rather complex. Here, inspired on the simple mechanism from a nut and a bolt, we report the construction of a portable fluorescence microscope that operates in bright-field mode and in three fluorescence channels: UV, green, and red. It is assembled in under 10 min from only six 3D printed parts, basic electronic components, a microcomputer (Raspberry Pi) and a camera, all of which can be readily purchased in most locations or online for US $122. The microcomputer was programmed in Python language to capture time-lapse images and videos. Resolution and illumination conditions of the microscope were characterized, and its performance was compared with a high-end fluorescence microscope in bright-field and fluorescence mode. We demonstrate that our miniature microscope can resolve and track single cells in both modes. The instructions on how to assemble the microscope are shown in a video, and the software to control it and the design files of the 3D-printed parts are freely available online. Our portable microscope is ideal in applications where space is at a premium, such as lab-on-a-chips or space missions, and can find applications in basic and clinical research, diagnostics, telemedicine and in educational settings.
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Affiliation(s)
- Samuel B. Tristan-Landin
- Unidad Monterrey, Centro de Investigación y de Estudios Avanzados del IPN, Parque PIIT, Apodaca, Nuevo León, Mexico
| | - Alan M. Gonzalez-Suarez
- Unidad Monterrey, Centro de Investigación y de Estudios Avanzados del IPN, Parque PIIT, Apodaca, Nuevo León, Mexico
| | - Rocio J. Jimenez-Valdes
- Unidad Monterrey, Centro de Investigación y de Estudios Avanzados del IPN, Parque PIIT, Apodaca, Nuevo León, Mexico
| | - Jose L. Garcia-Cordero
- Unidad Monterrey, Centro de Investigación y de Estudios Avanzados del IPN, Parque PIIT, Apodaca, Nuevo León, Mexico
- * E-mail:
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Sun Q, Zheng W, Lin C, Shen D. A Low-Cost Micro-Volume Nephelometric System for Quantitative Immunoagglutination Assays. SENSORS 2019; 19:s19204359. [PMID: 31600932 PMCID: PMC6832725 DOI: 10.3390/s19204359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 09/29/2019] [Accepted: 10/02/2019] [Indexed: 12/11/2022]
Abstract
Immunoassays have been widely used in scientific research and clinical diagnosis due to their versatile detection capability and high specificity. Immunoagglutination assays are kinds of immunoassay, which can simply and rapidly measure the concentration of analytes. In this work, we developed a low-cost micro-volume nephelometric system for quantitative immunoagglutination assays. We used off-the-shelf components to build the system, and the total cost of key components is only about 20 US dollars. The total detection volume in our system was as low as 3 µL, which could significantly reduce the reagent cost and required sample volume. We further evaluated the system performance via the immunoagglutination assay to measure the concentration of C-reactive protein, a plasma protein with levels rising in response to inflammation. The results demonstrated that our system could measure the concentration of analytes with relatively high sensitivity and precision within four minutes, and has high potential to be applied for clinical diagnostic tests.
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Affiliation(s)
- Qiqi Sun
- Research Laboratory for Biomedical Optics and Molecular Imaging, Shenzhen Key Laboratory for Molecular Imaging, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
- Edan Instruments, Inc., Shenzhen 518067, China.
| | - Wei Zheng
- Research Laboratory for Biomedical Optics and Molecular Imaging, Shenzhen Key Laboratory for Molecular Imaging, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
| | - Chao Lin
- Edan Instruments, Inc., Shenzhen 518067, China.
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Booeshaghi AS, Beltrame EDV, Bannon D, Gehring J, Pachter L. Principles of open source bioinstrumentation applied to the poseidon syringe pump system. Sci Rep 2019; 9:12385. [PMID: 31455877 PMCID: PMC6711986 DOI: 10.1038/s41598-019-48815-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 08/08/2019] [Indexed: 12/18/2022] Open
Abstract
The poseidon syringe pump and microscope system is an open source alternative to commercial systems. It costs less than $400 and can be assembled in under an hour using the instructions and source files available at https://pachterlab.github.io/poseidon . We describe the poseidon system and use it to illustrate design principles that can facilitate the adoption and development of open source bioinstruments. The principles are functionality, robustness, safety, simplicity, modularity, benchmarking, and documentation.
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Affiliation(s)
- A Sina Booeshaghi
- Department of Mechanical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Eduardo da Veiga Beltrame
- Department of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Dylan Bannon
- Department of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Jase Gehring
- Department of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.
| | - Lior Pachter
- Department of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.
- Department of Computing & Mathematical Sciences, California Institute of Technology, Pasadena, CA, 91125, USA.
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A Low-Cost and Portable Smart Instrumentation for Detecting Colorectal Cancer Cells. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9173510] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Fluorescence imaging is a well-known method for monitoring fluorescence emitted from the subject of interest and provides important insights about cell dynamics and molecules in mammalian cells. Currently, many solutions exist for measuring fluorescence, but the application methods are complex and the costs are high. This paper describes the design and development of a low-cost, smart and portable fluorimeter for the detection of colorectal cancer cell expressing IRFP702. A flashlight is used as a light source, which emits light in the visible range and acts as an excitation source, while a photodiode is used as a detector. It also uses a longpass filter to only allow the wavelength of interest to pass from the cultured cell. It eliminates the need of both the dichroic mirror and excitation filter, which makes the developed device low cost, compact and portable as well as lightweight. The custom-built sample chamber is black in color to minimize interference and is printed with a 3D printer to accommodate the detector circuitry. An established colorectal cancer cell line (human colorectal carcinoma (HCT116)) was cultured in the laboratory environment. A near-infrared fluorescent protein IRFP702 was expressed in the colorectal cancer cells that were used to test the proof-of-concept. The fluorescent cancer cells were first tested with a commercial imaging system (Odyssey® CLx) and then with the developed prototype to validate the result in a preclinical setting. The developed fluorimeter is versatile as it can also be used to detect multiple types of cancer cells by simply replacing the filters based on the fluorophore.
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Alam MW, Wahid KA, Goel RK, Lukong KE. Development of a low-cost and portable smart fluorometer for detecting breast cancer cells. BIOMEDICAL OPTICS EXPRESS 2019; 10:399-410. [PMID: 30800488 PMCID: PMC6377908 DOI: 10.1364/boe.10.000399] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 12/09/2018] [Accepted: 12/11/2018] [Indexed: 06/09/2023]
Abstract
Instruments that allow the detection of fluorescence signal are invaluable tools for biomedical and clinical researchers. The technique is widely used in cell biology to microscopically detect target proteins of interest in mammalian cells. Importantly, fluorescence microscopy finds major applications in cancer biology where cancer cells are chemically labelled for detection. However, conventional fluorescence detection instruments such as fluorescence imaging microscopes are expensive, not portable and entail potentially high maintenance costs. Here we describe the design, development and applicability of a low-cost and portable fluorometer for the detection of fluorescence signal emitted from a model breast cancer cell line, engineered to stably express the green fluorescent protein (GFP). This device utilizes a flashlight which works in the visible range as an excitation source and a photodiode as the detector. It also utilizes an emission filter to mainly allow the fluorescence signal to reach the detector while eliminating the use of an excitation filter and dichroic mirror, hence, making the device compact, low-cost, portable and lightweight. The custom-built sample chamber is fabricated with a 3D printer to house the detector circuitry. We demonstrate that the developed fluorometer is able to distinguish between the cancer cell expressing GFP and the control cell. The fluorometer we developed exhibits immense potential for future applicability in the selective detection of fluorescently-labelled breast cancer cells.
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Affiliation(s)
- Mohammad Wajih Alam
- Department of Electrical and Computer Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9, Saskatchewan, Canada
| | - Khan A. Wahid
- Department of Electrical and Computer Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9, Saskatchewan, Canada
| | - Raghuveera Kumar Goel
- Department of Biochemistry, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Saskatchewan, Canada
| | - Kiven Erique Lukong
- Department of Biochemistry, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Saskatchewan, Canada
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Lien MR, Barker RJ, Ye Z, Westphall MH, Gao R, Singh A, Gilroy S, Townsend PA. A low-cost and open-source platform for automated imaging. PLANT METHODS 2019; 15:6. [PMID: 30705688 PMCID: PMC6348682 DOI: 10.1186/s13007-019-0392-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/21/2019] [Indexed: 05/18/2023]
Abstract
BACKGROUND Remote monitoring of plants using hyperspectral imaging has become an important tool for the study of plant growth, development, and physiology. Many applications are oriented towards use in field environments to enable non-destructive analysis of crop responses due to factors such as drought, nutrient deficiency, and disease, e.g., using tram, drone, or airplane mounted instruments. The field setting introduces a wide range of uncontrolled environmental variables that make validation and interpretation of spectral responses challenging, and as such lab- and greenhouse-deployed systems for plant studies and phenotyping are of increasing interest. In this study, we have designed and developed an open-source, hyperspectral reflectance-based imaging system for lab-based plant experiments: the HyperScanner. The reliability and accuracy of HyperScanner were validated using drought and salt stress experiments with Arabidopsis thaliana. RESULTS A robust, scalable, and reliable system was created. The system was built using open-sourced parts, and all custom parts, operational methods, and data have been made publicly available in order to maintain the open-source aim of HyperScanner. The gathered reflectance images showed changes in narrowband red and infrared reflectance spectra for each of the stress tests that was evident prior to other visual physiological responses and exhibited congruence with measurements using full-range contact spectrometers. CONCLUSIONS HyperScanner offers the potential for reliable and inexpensive laboratory hyperspectral imaging systems. HyperScanner was able to quickly collect accurate reflectance curves on a variety of plant stress experiments. The resulting images showed spectral differences in plants shortly after application of a treatment but before visual manifestation. HyperScanner increases the capacity for spectroscopic and imaging-based analytical tools by providing more access to hyperspectral analyses in the laboratory setting.
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Affiliation(s)
- Max R. Lien
- Russell Labs, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706 USA
| | - Richard J. Barker
- Birge Hall, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706 USA
| | - Zhiwei Ye
- Russell Labs, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706 USA
| | - Matthew H. Westphall
- Russell Labs, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706 USA
| | - Ruohan Gao
- Russell Labs, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706 USA
| | - Aditya Singh
- Frazier Rogers Hall, 1741 Museum Road, Gainesville, FL 32611 USA
| | - Simon Gilroy
- Birge Hall, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI 53706 USA
| | - Philip A. Townsend
- Russell Labs, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706 USA
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Szymula KP, Magaraci MS, Patterson M, Clark A, Mannickarottu SG, Chow BY. An Open-Source Plate Reader. Biochemistry 2018; 58:468-473. [PMID: 30511843 DOI: 10.1021/acs.biochem.8b00952] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Microplate readers are foundational instruments in experimental biology and bioengineering that enable multiplexed spectrophotometric measurements. To enhance their accessibility, we here report the design, construction, validation, and benchmarking of an open-source microplate reader. The system features full-spectrum absorbance and fluorescence emission detection, in situ optogenetic stimulation, and stand-alone touch screen programming of automated assay protocols. The total system costs less than $3500, a fraction of the cost of commercial plate readers, and can detect the fluorescence of common dyes at concentrations as low as ∼10 nM. Functional capabilities were demonstrated in the context of synthetic biology, optogenetics, and photosensory biology: by steady-state measurements of ligand-induced reporter gene expression in a model of bacterial quorum sensing and by flavin photocycling kinetic measurements of a LOV (light-oxygen-voltage) domain photoreceptor used for optogenetic transcriptional activation. Fully detailed guides for assembling the device and automating it using the custom Python-based API (Application Program Interface) are provided. This work contributes a key technology to the growing community-wide infrastructure of open-source biology-focused hardware, whose creation is facilitated by rapid prototyping capabilities and low-cost electronics, optoelectronics, and microcomputers.
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Affiliation(s)
- Karol P Szymula
- Department of Bioengineering , University of Pennsylvania , 210 South 33rd Street , Philadelphia , Pennsylvania 19104 , United States
| | - Michael S Magaraci
- Department of Bioengineering , University of Pennsylvania , 210 South 33rd Street , Philadelphia , Pennsylvania 19104 , United States
| | - Michael Patterson
- Department of Bioengineering , University of Pennsylvania , 210 South 33rd Street , Philadelphia , Pennsylvania 19104 , United States
| | - Andrew Clark
- Department of Bioengineering , University of Pennsylvania , 210 South 33rd Street , Philadelphia , Pennsylvania 19104 , United States
| | - Sevile G Mannickarottu
- Department of Bioengineering , University of Pennsylvania , 210 South 33rd Street , Philadelphia , Pennsylvania 19104 , United States
| | - Brian Y Chow
- Department of Bioengineering , University of Pennsylvania , 210 South 33rd Street , Philadelphia , Pennsylvania 19104 , United States
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Maia Chagas A. Haves and have nots must find a better way: The case for open scientific hardware. PLoS Biol 2018; 16:e3000014. [PMID: 30260950 PMCID: PMC6177193 DOI: 10.1371/journal.pbio.3000014] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 10/09/2018] [Indexed: 12/02/2022] Open
Abstract
Many efforts are making science more open and accessible; they are mostly concentrated on issues that appear before and after experiments are performed: open access journals, open databases, and many other tools to increase reproducibility of science and access to information. However, these initiatives do not promote access to scientific equipment necessary for experiments. Mostly due to monetary constraints, equipment availability has always been uneven around the globe, affecting predominantly low-income countries and institutions. Here, a case is made for the use of free open source hardware in research and education, including countries and institutions where funds were never the biggest problem.
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Affiliation(s)
- André Maia Chagas
- Werner Reichardt Centre for Integrative Neurosciences, University of Tübingen, Tübingen, Germany
- Graduate School for Neural and Behavioural Sciences, University of Tübingen, Tübingen, Germany
- TReND in Africa gUG, Bonn, Germany
- Institute of Ophthalmic Research, University of Tübingen, Tübingen, Germany
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
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French S, Coutts BE, Brown ED. Open-Source High-Throughput Phenomics of Bacterial Promoter-Reporter Strains. Cell Syst 2018; 7:339-346.e3. [PMID: 30172841 DOI: 10.1016/j.cels.2018.07.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 05/25/2018] [Accepted: 07/10/2018] [Indexed: 11/17/2022]
Abstract
Open-source electronics are becoming more prevalent in biological sciences, enabling novel and unique means of data acquisition. Here, we present 3D-printed, open-source tools to acquire fluorescence phenotypes with high temporal resolution. Printed fluorescence imaging boxes (PFIboxes) cost approximately 200 US dollars to assemble, can be placed in incubators or hypoxic chambers, and accurately read high-density colony arrays of microorganisms. We demonstrate the utility of PFIboxes using a time course gene expression approach, examining global Escherichia coli promoter activity using a fluorescent reporter library across a diverse panel of 15 antibiotics, each at several concentrations. Many secondary and indirect effects were observed when E. coli was challenged with various drugs, including increased gene expression in carbon metabolism processes. Further, kinetic data acquisition enabled non-destructive time course gene expression, clustering of which revealed patterns of co-expression. In all, PFIboxes provide an open solution to gene expression, for about 2 US dollars per treatment condition, including technical replicates.
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Affiliation(s)
- Shawn French
- Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Brittney E Coutts
- Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
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