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Denton MR, Murphy NP, Norton-Baker B, Lua M, Steel H, Beckham GT. Integration of pH Control into Chi.Bio Reactors and Demonstration with Small-Scale Enzymatic Poly(ethylene terephthalate) Hydrolysis. Biochemistry 2024; 63:1599-1607. [PMID: 38907702 PMCID: PMC11223484 DOI: 10.1021/acs.biochem.4c00149] [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: 03/23/2024] [Revised: 06/05/2024] [Accepted: 06/05/2024] [Indexed: 06/24/2024]
Abstract
Small-scale bioreactors that are affordable and accessible would be of major benefit to the research community. In previous work, an open-source, automated bioreactor system was designed to operate up to the 30 mL scale with online optical monitoring, stirring, and temperature control, and this system, dubbed Chi.Bio, is now commercially available at a cost that is typically 1-2 orders of magnitude less than commercial bioreactors. In this work, we further expand the capabilities of the Chi.Bio system by enabling continuous pH monitoring and control through hardware and software modifications. For hardware modifications, we sourced low-cost, commercial pH circuits and made straightforward modifications to the Chi.Bio head plate to enable continuous pH monitoring. For software integration, we introduced closed-loop feedback control of the pH measured inside the Chi.Bio reactors and integrated a pH-control module into the existing Chi.Bio user interface. We demonstrated the utility of pH control through the small-scale depolymerization of the synthetic polyester, poly(ethylene terephthalate) (PET), using a benchmark cutinase enzyme, and compared this to 250 mL bioreactor hydrolysis reactions. The results in terms of PET conversion and rate, measured both by base addition and product release profiles, are statistically equivalent, with the Chi.Bio system allowing for a 20-fold reduction of purified enzyme required relative to the 250 mL bioreactor setup. Through inexpensive modifications, the ability to conduct pH control in Chi.Bio reactors widens the potential slate of biochemical reactions and biological cultivations for study in this system, and may also be adapted for use in other bioreactor platforms.
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Affiliation(s)
- Mackenzie
C. R. Denton
- Renewable
Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
- BOTTLE
Consortium, Golden, Colorado 80401, United States
| | - Natasha P. Murphy
- Renewable
Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
- BOTTLE
Consortium, Golden, Colorado 80401, United States
| | - Brenna Norton-Baker
- Renewable
Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
- BOTTLE
Consortium, Golden, Colorado 80401, United States
| | - Mauro Lua
- Catalytic
Carbon Transformation and Scale-up Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Harrison Steel
- Department
of Engineering Science, University of Oxford, Oxford OX1 3PJ, U.K.
| | - Gregg T. Beckham
- Renewable
Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
- BOTTLE
Consortium, Golden, Colorado 80401, United States
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2
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Tunens G, Einbergs E, Laganovska K, Zolotarjovs A, Vilks K, Skuja L, Smits K. Optical fiber-based open source low cost portable spectrometer system. HARDWAREX 2024; 18:e00530. [PMID: 38681502 PMCID: PMC11046214 DOI: 10.1016/j.ohx.2024.e00530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 04/09/2024] [Accepted: 04/13/2024] [Indexed: 05/01/2024]
Abstract
This article explores the development of a small, compact fiber-based spectrometer system designed to overcome the limitations of standard spectrometers, such as the high cost and restricted accessibility. Operated by a Raspberry Pi, the fiber-based spectrometer system uses the increased computing power to provide versatile modes of operation and powerful data processing, while maintaining a small size. Specifically crafted for basic chemistry and biology lab setups, where fibers allow measurements in different conditions, and customization enables fluorescence, light scattering, and absorption measurements. The system is adaptable and versatile, offering ease of modification and adaptation for a broad range of applications.
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Affiliation(s)
- Gatis Tunens
- Institute of Solid State Physics, University of Latvia, Kengaraga Str. 8, Riga LV-1063, Latvia
| | - Ernests Einbergs
- Institute of Solid State Physics, University of Latvia, Kengaraga Str. 8, Riga LV-1063, Latvia
| | - Katrina Laganovska
- Institute of Solid State Physics, University of Latvia, Kengaraga Str. 8, Riga LV-1063, Latvia
| | - Aleksejs Zolotarjovs
- Institute of Solid State Physics, University of Latvia, Kengaraga Str. 8, Riga LV-1063, Latvia
| | - Karlis Vilks
- Institute of Solid State Physics, University of Latvia, Kengaraga Str. 8, Riga LV-1063, Latvia
| | - Linards Skuja
- Institute of Solid State Physics, University of Latvia, Kengaraga Str. 8, Riga LV-1063, Latvia
| | - Krisjanis Smits
- Institute of Solid State Physics, University of Latvia, Kengaraga Str. 8, Riga LV-1063, Latvia
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3
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Le BT, Auer KM, Lopez DA, Shum JP, Suarsana B, Suh GYK, Hedde PN, Ahrar S. Orthogonal-view microscope for the biomechanics investigations of aquatic organisms. HARDWAREX 2024; 18:e00533. [PMID: 38711599 PMCID: PMC11070628 DOI: 10.1016/j.ohx.2024.e00533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 04/07/2024] [Accepted: 04/13/2024] [Indexed: 05/08/2024]
Abstract
Microscopes are essential for the biomechanical and hydrodynamical investigation of small aquatic organisms. We report a prototype of a do-it-yourself microscope that enables the visualization of organisms from two orthogonal imaging planes - top and side views. Compared to conventional imaging systems, this approach provides a comprehensive visualization strategy of organisms, which could have complex shapes and morphologies. The microscope was constructed by combining custom 3D-printed parts and off-the-shelf components. The system is designed for modularity and reconfigurability. Open-source design files and build instructions are provided in this report. Additionally, proof-of-use experiments (particularly with Hydra) and other organisms that combine the imaging with an analysis pipeline were demonstrated to highlight the system's utility. Beyond the applications demonstrated, the system can be used or modified for various imaging applications.
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Affiliation(s)
- Brian T. Le
- Department of Biomedical Engineering, California State University Long Beach, 1250 Bellflower Blvd. Long Beach, CA 90840, USA
| | - Katherine M. Auer
- Department of Biomedical Engineering, California State University Long Beach, 1250 Bellflower Blvd. Long Beach, CA 90840, USA
| | - David A. Lopez
- Department of Biomedical Engineering, California State University Long Beach, 1250 Bellflower Blvd. Long Beach, CA 90840, USA
| | - Justin P. Shum
- Department of Biomedical Engineering, California State University Long Beach, 1250 Bellflower Blvd. Long Beach, CA 90840, USA
| | - Brian Suarsana
- Department of Biomedical Engineering, California State University Long Beach, 1250 Bellflower Blvd. Long Beach, CA 90840, USA
| | - Ga-Young Kelly Suh
- Department of Biomedical Engineering, California State University Long Beach, 1250 Bellflower Blvd. Long Beach, CA 90840, USA
| | - Per Niklas Hedde
- Beckman Laser Institute and Medical Clinic, University of California Irvine, Irvine, CA 92612, USA
| | - Siavash Ahrar
- Department of Biomedical Engineering, California State University Long Beach, 1250 Bellflower Blvd. Long Beach, CA 90840, USA
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4
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Sheffield JL, Parkinson B, Bascom A, Bateman T, Magleby S, Howell LL. Expanding research impact through engaging the maker community and collaborating with digital content creators. PLoS One 2024; 19:e0302449. [PMID: 38718013 PMCID: PMC11078436 DOI: 10.1371/journal.pone.0302449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 03/29/2024] [Indexed: 05/12/2024] Open
Abstract
This paper proposes a method for increasing the impact of academic research by providing materials for public use, thus engaging the maker community, and by collaborating with internet content creators to extend the reach. We propose a framework for engagement and report a multi-year study that evaluates short, intermediate, and long-term outcomes, with a second effort to demonstrate repeatability of the short-term outcomes. In the first study, we posted forty-one 3D printable compliant mechanisms on public repositories and collaborated with physicist and content creator Derek Muller (Veritasium YouTube channel). Outputs and outcomes from this interaction were measured over 3 years. The framework was exercised again with four new 3D printable mechanisms in collaboration with engineer and STEM influencer Mark Rober. The proposed methods aim to help researchers extend the reach of their work to broader audiences, including professional engineers, hardware designers, educators, students, researchers, and hobbyists. This work demonstrates promising impacts of the framework, including (1) extending public awareness of research findings to broader audiences by engaging the maker community and collaborating with content creators, (2) accelerating the pace of innovation and further hardware-based research through public application of research findings, (3) fostering a culture of open-source design and collaboration among other researchers, engineers, educators, and makers, and (4) increasing utilization of peer-reviewed published content. These outreach practices can be valuable tools for researchers to increase impact of and excitement for their research.
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Affiliation(s)
- Jacob L. Sheffield
- Compliant Mechanisms Research Group, Department of Mechanical Engineering, Brigham Young University, Provo, UT, United States of America
| | - Bethany Parkinson
- Compliant Mechanisms Research Group, Department of Mechanical Engineering, Brigham Young University, Provo, UT, United States of America
| | - Aliya Bascom
- Compliant Mechanisms Research Group, Department of Mechanical Engineering, Brigham Young University, Provo, UT, United States of America
| | - Terri Bateman
- Compliant Mechanisms Research Group, Department of Mechanical Engineering, Brigham Young University, Provo, UT, United States of America
| | - Spencer Magleby
- Compliant Mechanisms Research Group, Department of Mechanical Engineering, Brigham Young University, Provo, UT, United States of America
| | - Larry L. Howell
- Compliant Mechanisms Research Group, Department of Mechanical Engineering, Brigham Young University, Provo, UT, United States of America
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Liu Y, Koch JC, Arregui L, Oune A, Bodenstein S, Gutierrez-Wing MT, Tiersch TR. Exploring pathways toward open-hardware ecosystems to safeguard genetic resources for biomedical research communities using aquatic model species. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024; 342:278-290. [PMID: 38185943 PMCID: PMC11099901 DOI: 10.1002/jez.b.23234] [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: 07/01/2023] [Revised: 11/03/2023] [Accepted: 12/04/2023] [Indexed: 01/09/2024]
Abstract
Development of reliable germplasm repositories is critical for preservation of genetic resources of aquatic species, which are widely utilized to support biomedical innovation by providing a foundational source for naturally occurring variation and development of new variants through genetic manipulations. A significant barrier in repository development is the lack of cryopreservation capability and reproducibility across the research community, posing great risks of losing advances developed from billions of dollars of research investment. The emergence of open scientific hardware has fueled a new movement across biomedical research communities. With the increasing accessibility of consumer-level fabrication technologies, such as three-dimensional printers, open hardware devices can be custom designed, and design files distributed to community members for enhancing rigor, reproducibility, and standardization. The overall goal of this review is to explore pathways to create open-hardware ecosystems among the communities using aquatic model resources for biomedical research. To gain feedback and insights from community members, an interactive workshop focusing on open-hardware applications in germplasm repository development was held at the 2022 Aquatic Models for Human Disease Conference, Woods Hole, Massachusetts. This work integrates conceptual strategies with practical insights derived from workshop interactions using examples of germplasm repository development. These insights can be generalized for establishment of open-hardware ecosystems for a broad biomedical research community. The specific objectives were to: (1) introduce an open-hardware ecosystem concept to support biomedical research; (2) explore pathways toward open-hardware ecosystems through four major areas, and (3) identify opportunities and future directions.
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Affiliation(s)
- Yue Liu
- Aquatic Germplasm and Genetic Resources Center, School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Jack C Koch
- Aquatic Germplasm and Genetic Resources Center, School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Lucía Arregui
- Aquatic Germplasm and Genetic Resources Center, School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Allyssa Oune
- Aquatic Germplasm and Genetic Resources Center, School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Sarah Bodenstein
- Aquatic Germplasm and Genetic Resources Center, School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Maria T Gutierrez-Wing
- Aquatic Germplasm and Genetic Resources Center, School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Terrence R Tiersch
- Aquatic Germplasm and Genetic Resources Center, School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
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Singh G, Thamba A, Rao V, Roth D, Zaazoue MA. Comprehensive analysis of power tool injuries: implications for safety and injury prevention. Injury 2024; 55:111397. [PMID: 38331686 DOI: 10.1016/j.injury.2024.111397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/23/2024] [Accepted: 01/27/2024] [Indexed: 02/10/2024]
Abstract
BACKGROUND Power tools are essential for productivity but carry significant injury risks. Addressing power tool injuries across diverse age groups is vital, as existing research predominantly focuses on specific occupational or non-occupational groups, leaving a gap in understanding various age cohorts within the diverse American population. This study aims to comprehend power tool injury epidemiology, raising awareness about the importance of targeted safety measures for enhancing public health. METHODS Using a ten-year retrospective approach, this study analyzed National Electronic Injury Surveillance System (NEISS) data from US hospital emergency departments (2013-2022). Demographic and temporal trends were examined, and associations between injury occurrence and categorical variables, including injured body parts, gender, and race, were explored. RESULTS In 2013, power tool injuries were highest in the "51-60″ age group (23.70 %), followed by "41-50″ (17.31 %) and "61-70″ (19.38 %). Injury rates varied across age groups over the years. Notably, the "41-50″ age group showed a significant decrease in injuries over time (χ² = 17.12, p < .05), indicating a notable temporal trend. Hand injuries were predominant (39.08 %), followed by finger (19.19 %), lower arm (11.25 %), upper arm (8.79 %), and face (4.04 %). Lacerations constituted the most frequent injury type (60.89 %), alongside fractures, amputations, foreign body insertions, and contusions/abrasions. Significant associations emerged between injury occurrence and gender (χ² = 6.19, p < .001), as well as race (χ² = 7.42, p < .001). Males accounted for the majority of injuries (95.97 %), while white individuals constituted the largest proportion (91.84 %). Females and domestic settings exhibited increasing proportions of power tool injuries. CONCLUSIONS The higher incidence among middle-aged individuals in domestic settings, coupled with evolving gender dynamics, underscores the need for targeted safety measures. Our findings contribute crucial novel insights, emphasizing tailored preventive strategies to enhance safety outcomes in the multifaceted landscape of power tool use.
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Affiliation(s)
- Gurbinder Singh
- Department of Orthopaedic Surgery, University of California-San Francisco, San Francisco, CA, USA.
| | - Aish Thamba
- Department of Neurological Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Varun Rao
- Department of Neurological Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Dylan Roth
- Department of Neurological Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Mohamed A Zaazoue
- Department of Neurological Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
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Ohlsson JA, Leong JX, Elander PH, Ballhaus F, Holla S, Dauphinee AN, Johansson J, Lommel M, Hofmann G, Betnér S, Sandgren M, Schumacher K, Bozhkov PV, Minina EA. SPIRO - the automated Petri plate imaging platform designed by biologists, for biologists. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:584-600. [PMID: 38141174 DOI: 10.1111/tpj.16587] [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: 09/20/2023] [Accepted: 12/04/2023] [Indexed: 12/25/2023]
Abstract
Phenotyping of model organisms grown on Petri plates is often carried out manually, despite the procedures being time-consuming and laborious. The main reason for this is the limited availability of automated phenotyping facilities, whereas constructing a custom automated solution can be a daunting task for biologists. Here, we describe SPIRO, the Smart Plate Imaging Robot, an automated platform that acquires time-lapse photographs of up to four vertically oriented Petri plates in a single experiment, corresponding to 192 seedlings for a typical root growth assay and up to 2500 seeds for a germination assay. SPIRO is catered specifically to biologists' needs, requiring no engineering or programming expertise for assembly and operation. Its small footprint is optimized for standard incubators, the inbuilt green LED enables imaging under dark conditions, and remote control provides access to the data without interfering with sample growth. SPIRO's excellent image quality is suitable for automated image processing, which we demonstrate on the example of seed germination and root growth assays. Furthermore, the robot can be easily customized for specific uses, as all information about SPIRO is released under open-source licenses. Importantly, uninterrupted imaging allows considerably more precise assessment of seed germination parameters and root growth rates compared with manual assays. Moreover, SPIRO enables previously technically challenging assays such as phenotyping in the dark. We illustrate the benefits of SPIRO in proof-of-concept experiments which yielded a novel insight on the interplay between autophagy, nitrogen sensing, and photoblastic response.
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Affiliation(s)
- Jonas A Ohlsson
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-750 07, Sweden
| | - Jia Xuan Leong
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, Heidelberg, 69120, Germany
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen, D-72076, Germany
| | - Pernilla H Elander
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-750 07, Sweden
| | - Florentine Ballhaus
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-750 07, Sweden
| | - Sanjana Holla
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-750 07, Sweden
| | - Adrian N Dauphinee
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-750 07, Sweden
| | | | - Mark Lommel
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, Heidelberg, 69120, Germany
- Department of Microbiology, Saarland University, Campus A1.5, Saarbrücken, 66123, Germany
| | - Gero Hofmann
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, Heidelberg, 69120, Germany
| | - Staffan Betnér
- Northern Registry Centre, Department of Public Health and Clinical Medicine, Umeå University, Umeå, 90187, Sweden
| | - Mats Sandgren
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-750 07, Sweden
| | - Karin Schumacher
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, Heidelberg, 69120, Germany
| | - Peter V Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-750 07, Sweden
| | - Elena A Minina
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-750 07, Sweden
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, Heidelberg, 69120, Germany
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Zehrer AC, Martin-Villalba A, Diederich B, Ewers H. An open-source, high-resolution, automated fluorescence microscope. eLife 2024; 12:RP89826. [PMID: 38436658 PMCID: PMC10942636 DOI: 10.7554/elife.89826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2024] Open
Abstract
Fluorescence microscopy is a fundamental tool in the life sciences, but the availability of sophisticated equipment required to yield high-quality, quantitative data is a major bottleneck in data production in many laboratories worldwide. This problem has long been recognized and the abundancy of low-cost electronics and the simplification of fabrication through 3D-printing have led to the emergence of open-source scientific hardware as a research field. Cost effective fluorescence microscopes can be assembled from cheaply mass-produced components, but lag behind commercial solutions in image quality. On the other hand, blueprints of sophisticated microscopes such as light-sheet or super-resolution systems, custom-assembled from high quality parts, are available, but require a high level of expertise from the user. Here, we combine the UC2 microscopy toolbox with high-quality components and integrated electronics and software to assemble an automated high-resolution fluorescence microscope. Using this microscope, we demonstrate high resolution fluorescence imaging for fixed and live samples. When operated inside an incubator, long-term live-cell imaging over several days was possible. Our microscope reaches single molecule sensitivity, and we performed single particle tracking and SMLM super-resolution microscopy experiments in cells. Our setup costs a fraction of its commercially available counterparts but still provides a maximum of capabilities and image quality. We thus provide a proof of concept that high quality scientific data can be generated by lay users with a low-budget system and open-source software. Our system can be used for routine imaging in laboratories that do not have the means to acquire commercial systems and through its affordability can serve as teaching material to students.
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Affiliation(s)
| | - Ana Martin-Villalba
- Department of Molecular Neurobiology, German Cancer Research CenteHeidelbergGermany
| | | | - Helge Ewers
- Institut für Chemie und Biochemie, Freie Universität BerlinBerlinGermany
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Gleason SM, Stewart JJ, Allen B, Polutchko SK, McMahon J, Spitzer D, Barnard DM. Development and application of an inexpensive open-source dendrometer for detecting xylem water potential and radial stem growth at high spatial and temporal resolution. AOB PLANTS 2024; 16:plae009. [PMID: 38510929 PMCID: PMC10953470 DOI: 10.1093/aobpla/plae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 02/26/2024] [Indexed: 03/22/2024]
Abstract
There is currently a need for inexpensive, continuous, non-destructive water potential measurements at high temporal resolution (<1 min). We describe here the development and testing of an entirely open-source dendrometer that, when combined with periodic Scholander pressure chamber measurements, provides sub-minute resolution estimates of water potential when placed on tissues exhibiting little or no secondary growth (petioles, monocotyledon stems). The dendrometer can also be used to measure radial growth of stems and branches when placed on dicotyledon and gymnosperm species. The dendrometer can be interfaced directly with a computer in real time in the lab or greenhouse, or connected to a datalogger for long periods of use in the field on batteries. We tested this device on a herbaceous dicotyledon (Helianthus annuus) (petioles and stems) and a monocotyledon (Zea mays) species (stems) for 1 week during dehydration and re-watering treatments under laboratory conditions. We also demonstrated the ability of the device to record branch and trunk diameter variation of a woody dicotyledon (Rhus typhina) in the field. Under laboratory conditions, we compared our device (hereafter 'contact' dendrometer) with modified versions of another open-source dendrometer (the 'optical' dendrometer). Overall, contact and optical dendrometers were well aligned with one another, with Pearson correlation coefficients ranging from 0.77 to 0.97. Both dendrometer devices were well aligned with direct measurements of xylem water potential, with calibration curves exhibiting significant non-linearity, especially at water potentials near the point of incipient plasmolysis, with pseudo R2 values (Efron) ranging from 0.89 to 0.99. Overall, both dendrometers were comparable and provided sufficient resolution to detect subtle differences in stem water potential (ca. 50 kPa) resulting from light-induced changes in transpiration, vapour pressure deficit and drying/wetting soils. All hardware designs, alternative configurations, software and build instructions for the contact dendrometers are provided.
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Affiliation(s)
- Sean M Gleason
- Water Management and Systems Research Unit, USDA-ARS, Fort Collins, CO 80526, USA
- Department of Forest and Rangeland Stewardship, Colorado State University, Fort Collins, CO 80523, USA
| | - Jared J Stewart
- Water Management and Systems Research Unit, USDA-ARS, Fort Collins, CO 80526, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
| | - Brendan Allen
- Water Management and Systems Research Unit, USDA-ARS, Fort Collins, CO 80526, USA
- Department of Forest and Rangeland Stewardship, Colorado State University, Fort Collins, CO 80523, USA
| | - Stephanie K Polutchko
- Water Management and Systems Research Unit, USDA-ARS, Fort Collins, CO 80526, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
| | - Jordan McMahon
- Water Management and Systems Research Unit, USDA-ARS, Fort Collins, CO 80526, USA
- College of Engineering, Science, Technology, and Agriculture, Central State University, Wilberforce, OH 45384, USA
| | - Daniel Spitzer
- Department of Forest and Rangeland Stewardship, Colorado State University, Fort Collins, CO 80523, USA
| | - David M Barnard
- Water Management and Systems Research Unit, USDA-ARS, Fort Collins, CO 80526, USA
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10
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Howell LL, Bateman T. Extending research impact by sharing maker information. Nat Commun 2023; 14:6170. [PMID: 37794043 PMCID: PMC10550907 DOI: 10.1038/s41467-023-41886-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/22/2023] [Indexed: 10/06/2023] Open
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11
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Liu D, Kulkarni A, Jaqua VF, Cole CA, Pearce JM. Distributed manufacturing of an open-source tourniquet testing system. HARDWAREX 2023; 15:e00442. [PMID: 37457304 PMCID: PMC10338363 DOI: 10.1016/j.ohx.2023.e00442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/16/2023] [Accepted: 06/11/2023] [Indexed: 07/18/2023]
Abstract
Tourniquets are effective for casualty-prevention in emergency situations. The use of centrally-manufactured commercial tourniquets, however, is not always possible due to supply chain disruptions. The open-source hardware model has been applied to overcome these disruptions in humanitarian crises and several low-cost digitally manufacturable open-source tourniquets have been developed. With the low reliability of improvised tourniquets, it is important to ensure that distributed manufacturing of tourniquets is effective and safe. Tourniquets can be tested, but existing tourniquet testers are expensive, bulky, and complex to operate, which limits their accessibility to an even greater extent than tourniquets in extreme settings. This article fulfills a need by providing a small, transportable, open-source additive-manufactured tourniquet tester that enables inexpensive and accurate testing of tourniquets against known clinical parameters. The <$100 tourniquet tester is validated and tested for operating force of tourniquets in the field or in distributed manufacturing facilities. The tourniquet tester has a significant economic and operational advantage compared to proprietary counterparts available on the market. Once calibrated with a blood pressure monitor, the built-in LCD displays the measuring range of the tester as 0 to 200 N, which is enough to test the validation of all tourniquets.
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Affiliation(s)
- Dawei Liu
- Department of Electrical and Computer Engineering, Western University, London, Canada
| | - Apoorv Kulkarni
- Department of Electrical and Computer Engineering, Western University, London, Canada
| | | | | | - Joshua M. Pearce
- Department of Electrical and Computer Engineering, Western University, London, Canada
- Ivey Business School, Western University, London, Canada
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Hohlbein J. Open hardware in microscopy. HARDWAREX 2023; 15:e00473. [PMID: 37700785 PMCID: PMC10493255 DOI: 10.1016/j.ohx.2023.e00473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
The field of microscopy has been empowering humankind for many centuries by enabling the observation of objects that are otherwise too small to detect for the naked human eye. Microscopy techniques can be loosely divided into three main branches, namely photon-based optical microscopy, electron microscopy, and scanning probe microscopy with optical microscopy being the most prominent one. On the high-end level, optical microscopy nowadays enables nanometer resolution covering many scientific disciplines ranging from material sciences over the natural sciences and life sciences to the food sciences. On the lower-end level, simplified hardware and openly available description and blueprints have helped to make powerful microscopes widely available to interested scientists and researchers. For this special issue, we invited contributions from the community to share their latest ideas, designs, and research results on open-source hardware in microscopy. With this collection of articles, we hope to inspire the community to further increase the accessibility, interoperability, and reproducibility of microscopy. We further touch on the standardization of methodologies and devices including the use of computerized control of data acquisition and data analysis to achieve high quality and efficiency in research and development.
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Affiliation(s)
- Johannes Hohlbein
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, the Netherlands
- Microspectroscopy Research Facility, Wageningen University & Research, Wageningen, the Netherlands
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Le BT, Auer KM, Lopez DA, Shum JP, Suarsana B, Suh GYK, Hedde PN, Ahrar S. Orthogonal-view Microscope for the Biomechanics Investigations of Aquatic Organisms. ARXIV 2023:arXiv:2307.13079v1. [PMID: 37547659 PMCID: PMC10402206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Microscopes are essential for the biomechanical and hydrodynamical investigation of small aquatic organisms. We report a do-it-yourself microscope (GLUBscope) that enables the visualization of organisms from two orthogonal imaging planes - top and side views. Compared to conventional imaging systems, this approach provides a comprehensive visualization strategy of organisms, which could have complex shapes and morphologies. The microscope was constructed by combining custom 3D-printed parts and off-the-shelf components. The system is designed for modularity and reconfigurability. Open-source design files and build instructions are provided in this report. Additionally, proof-of-use experiments (particularly with Hydra) and other organisms that combine the GLUBscope with an analysis pipeline were demonstrated to highlight the system's utility. Beyond the applications demonstrated, the system can be used or modified for various imaging applications.
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Affiliation(s)
- Brian T. Le
- Department of Biomedical Engineering, California State University Long Beach 1250 Bellflower Blvd. Long Beach, CA 90840, USA
| | - Katherine M. Auer
- Department of Biomedical Engineering, California State University Long Beach 1250 Bellflower Blvd. Long Beach, CA 90840, USA
| | - David A. Lopez
- Department of Biomedical Engineering, California State University Long Beach 1250 Bellflower Blvd. Long Beach, CA 90840, USA
| | - Justin P. Shum
- Department of Biomedical Engineering, California State University Long Beach 1250 Bellflower Blvd. Long Beach, CA 90840, USA
| | - Brian Suarsana
- Department of Biomedical Engineering, California State University Long Beach 1250 Bellflower Blvd. Long Beach, CA 90840, USA
| | - Ga-Young Kelly Suh
- Department of Biomedical Engineering, California State University Long Beach 1250 Bellflower Blvd. Long Beach, CA 90840, USA
| | - Per Niklas Hedde
- Beckman Laser Institute and Medical Clinic, University of California Irvine Irvine, CA 92612, USA
| | - Siavash Ahrar
- Department of Biomedical Engineering, California State University Long Beach 1250 Bellflower Blvd. Long Beach, CA 90840, USA
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Keller O, Appelhoff S, Paffhausen B, Wenzel T. Development and Sharing of Open Science Hardware: Lessons Learned from Wikimedia Fellowships. RESEARCH IDEAS AND OUTCOMES 2023. [DOI: 10.3897/rio.9.e95174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The promise of open hardware as a branch of open science is a sustainable change of research instrumentation towards more openly documented and licensed designs. Methods, code, and data are already valued by journal editors and peer-reviews to judge if a study's result can be replicated with the information provided in a manuscript. The open hardware movement seeks to include laboratory tools and research instrumentation into the same category. Availability of and access to open hardware equipment are set to democratize professional lab work and field studies as well as enhance the transferability of methods to civic science settings. Here, we report four case studies from the first five years of the Wikimedia Program "Free Knowledge", an open science fellowship funded by Wikimedia Germany and partners. The project developers discuss and evaluate the impact related to key aspects typically attributed with open hardware: costs, availability, adaptability, community and educational value. The open hardware projects covered in this review span from natural sciences to life sciences to education.
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