1
|
Banse SA, Jarrett CM, Robinson KJ, Blue BW, Shaw EL, Phillips PC. The egg-counter: a novel microfluidic platform for characterization of Caenorhabditis elegans egg-laying. LAB ON A CHIP 2024; 24:2975-2986. [PMID: 38738514 PMCID: PMC11131562 DOI: 10.1039/d3lc01073b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 04/20/2024] [Indexed: 05/14/2024]
Abstract
Reproduction is a fundamental process that shapes the demography of every living organism yet is often difficult to assess with high precision in animals that produce large numbers of offspring. Here, we present a novel microfluidic research platform for studying Caenorhabditis elegans' egg-laying. The platform provides higher throughput than traditional solid-media behavioral assays while providing a very high degree of temporal resolution. Additionally, the environmental control enabled by microfluidic animal husbandry allows for experimental perturbations difficult to achieve with solid-media assays. We demonstrate the platform's utility by characterizing C. elegans egg-laying behavior at two commonly used temperatures, 15 and 20 °C. As expected, we observed a delayed onset of egg-laying at 15 °C degrees, consistent with published temperature effects on development rate. Additionally, as seen in solid media studies, egg laying output was higher under the canonical 20 °C conditions. While we validated the Egg-Counter with a study of temperature effects in wild-type animals, the platform is highly adaptable to any nematode egg-laying research where throughput or environmental control needs to be maximized without sacrificing temporal resolution.
Collapse
Affiliation(s)
- Stephen A Banse
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA.
| | - Cody M Jarrett
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA.
| | - Kristin J Robinson
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA.
| | - Benjamin W Blue
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA.
| | - Emily L Shaw
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA.
| | - Patrick C Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA.
| |
Collapse
|
2
|
Jee Lee H, Vallier J, Lu H. Microfluidic Localized Hydrogel Polymerization Enables Simultaneous Recording of Neural Activity and Behavior in C. elegans. REACT CHEM ENG 2024; 9:666-676. [PMID: 38680986 PMCID: PMC11046317 DOI: 10.1039/d3re00516j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Monitoring an animal's brain activity during motion provides a means to interpret the brain activity in the context of movement. However, it is challenging to obtain information about the animal's movement during neural imaging in the popular model organism C. elegans due to its small size. Here, we present a microfluidic tool to immobilize only the head region of C. elegans for simultaneous recording of neuronal activity and tail movement. We combine hydrogel photopolymerization and microfluidics to realize controlled head immobilization in a semi-continuous fashion. To optimize the immobilization process, we characterize the hydrogel polymerization under different experimental conditions, including under the effect of fluid flow. We show that the Damköhler number specifically defined for our reactive transport phenomena can predict the success of such photopolymerized hydrogels used for sample immobilization. In addition to simultaneous recording of neural activity and behavior in C. elegans, we demonstrate our method's capability to temporarily reconfigure fluid flow and deliver chemical stimuli to the animal's nose to examine the animal's responses. We envision this approach to be useful for similar recordings for other small motile organisms, as well as scenarios where microfluidics and polymerization are used to control flow and rection.
Collapse
Affiliation(s)
- Hyun Jee Lee
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, USA
| | - Julia Vallier
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, USA
| | - Hang Lu
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, USA
| |
Collapse
|
3
|
Yoon S, Kilicarslan You D, Jeong U, Lee M, Kim E, Jeon TJ, Kim SM. Microfluidics in High-Throughput Drug Screening: Organ-on-a-Chip and C. elegans-Based Innovations. BIOSENSORS 2024; 14:55. [PMID: 38275308 PMCID: PMC10813408 DOI: 10.3390/bios14010055] [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: 11/24/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024]
Abstract
The development of therapeutic interventions for diseases necessitates a crucial step known as drug screening, wherein potential substances with medicinal properties are rigorously evaluated. This process has undergone a transformative evolution, driven by the imperative need for more efficient, rapid, and high-throughput screening platforms. Among these, microfluidic systems have emerged as the epitome of efficiency, enabling the screening of drug candidates with unprecedented speed and minimal sample consumption. This review paper explores the cutting-edge landscape of microfluidic-based drug screening platforms, with a specific emphasis on two pioneering approaches: organ-on-a-chip and C. elegans-based chips. Organ-on-a-chip technology harnesses human-derived cells to recreate the physiological functions of human organs, offering an invaluable tool for assessing drug efficacy and toxicity. In parallel, C. elegans-based chips, boasting up to 60% genetic homology with humans and a remarkable affinity for microfluidic systems, have proven to be robust models for drug screening. Our comprehensive review endeavors to provide readers with a profound understanding of the fundamental principles, advantages, and challenges associated with these innovative drug screening platforms. We delve into the latest breakthroughs and practical applications in this burgeoning field, illuminating the pivotal role these platforms play in expediting drug discovery and development. Furthermore, we engage in a forward-looking discussion to delineate the future directions and untapped potential inherent in these transformative technologies. Through this review, we aim to contribute to the collective knowledge base in the realm of drug screening, providing valuable insights to researchers, clinicians, and stakeholders alike. We invite readers to embark on a journey into the realm of microfluidic-based drug screening platforms, fostering a deeper appreciation for their significance and promising avenues yet to be explored.
Collapse
Affiliation(s)
- Sunhee Yoon
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea; (S.Y.); (D.K.Y.); (M.L.); (E.K.)
| | - Dilara Kilicarslan You
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea; (S.Y.); (D.K.Y.); (M.L.); (E.K.)
| | - Uiechan Jeong
- Department of Mechanical Engineering, Inha University, Incheon 22212, Republic of Korea
| | - Mina Lee
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea; (S.Y.); (D.K.Y.); (M.L.); (E.K.)
| | - Eunhye Kim
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea; (S.Y.); (D.K.Y.); (M.L.); (E.K.)
| | - Tae-Joon Jeon
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea; (S.Y.); (D.K.Y.); (M.L.); (E.K.)
- Department of Biological Engineering, Inha University, Incheon 22212, Republic of Korea
- Biohybrid Systems Research Center (BSRC), Inha University, Incheon 22212, Republic of Korea
| | - Sun Min Kim
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea; (S.Y.); (D.K.Y.); (M.L.); (E.K.)
- Department of Mechanical Engineering, Inha University, Incheon 22212, Republic of Korea
- Biohybrid Systems Research Center (BSRC), Inha University, Incheon 22212, Republic of Korea
| |
Collapse
|
4
|
Banse SA, Jarrett CM, Robinson KJ, Blue BW, Shaw EL, Phillips PC. The Egg-Counter: A novel microfluidic platform for characterization of Caenorhabditis elegans egg-laying. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.01.555781. [PMID: 37732270 PMCID: PMC10508723 DOI: 10.1101/2023.09.01.555781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Reproduction is a fundamental process that shapes the demography of every living organism yet is often difficult to assess with high precision in animals that produce large numbers of offspring. Here, we present a novel microfluidic research platform for studying Caenorhabditis elegans' egg-laying. The platform provides higher throughput than traditional solid-media assays while providing a very high degree of temporal resolution. Additionally, the environmental control enabled by microfluidic animal husbandry allows for experimental perturbations difficult to achieve with solid-media assays. We demonstrate the platform's utility by characterizing C. elegans egg-laying behavior at two commonly used temperatures, 15 and 20°C. As expected, we observed a delayed onset of egg-laying at 15°C degrees, consistent with published temperature effects on development rate. Additionally, as seen in solid media studies, egg laying output was higher under the canonical 20°C conditions. While we validated the Egg-Counter with a study of temperature effects in wild-type animals, the platform is highly adaptable to any nematode egg-laying research where throughput or environmental control needs to be maximized without sacrificing temporal resolution.
Collapse
Affiliation(s)
- Stephen A. Banse
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Cody M. Jarrett
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Kristin J. Robinson
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Benjamin W. Blue
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Emily L. Shaw
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Patrick C. Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| |
Collapse
|
5
|
Bhadra J, Sridhar N, Fajrial AK, Hammond N, Xue D, Ding X. Acoustic streaming enabled moderate swimming exercise reduces neurodegeneration in C. elegans. SCIENCE ADVANCES 2023; 9:eadf5056. [PMID: 36812319 PMCID: PMC9946341 DOI: 10.1126/sciadv.adf5056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Regular physical exercise has been shown to delay and alleviate neurodegenerative diseases. Yet, optimum physical exercise conditions that provide neuronal protection and exercise-related factors remain poorly understood. Here, we create an Acoustic Gym on a chip through the surface acoustic wave (SAW) microfluidic technology to precisely control the duration and intensity of swimming exercise of model organisms. We find that precisely dosed swimming exercise enabled by acoustic streaming decreases neuronal loss in two different neurodegenerative disease models of Caenorhabditis elegans, a Parkinson's disease model and a tauopathy model. These findings highlight the importance of optimum exercise conditions for effective neuronal protection, a key characteristic of healthy aging in the elderly population. This SAW device also paves avenues for screening for compounds that can enhance or replace the beneficial effects of exercise and for identifying drug targets for treating neurodegenerative diseases.
Collapse
Affiliation(s)
- Joyita Bhadra
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Nakul Sridhar
- Department of Mechanical Engineering, University of Colorado, 1111 Engineering Dr., Boulder, CO 80309, USA
| | - Apresio Kefin Fajrial
- Department of Mechanical Engineering, University of Colorado, 1111 Engineering Dr., Boulder, CO 80309, USA
| | - Nia Hammond
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Ding Xue
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Xiaoyun Ding
- Department of Mechanical Engineering, University of Colorado, 1111 Engineering Dr., Boulder, CO 80309, USA
- Biomedical Engineering Program, University of Colorado, Boulder, CO 80309, USA
- BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| |
Collapse
|
6
|
An optofluidic platform for interrogating chemosensory behavior and brainwide neural representation in larval zebrafish. Nat Commun 2023; 14:227. [PMID: 36641479 PMCID: PMC9840631 DOI: 10.1038/s41467-023-35836-2] [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: 02/13/2022] [Accepted: 01/03/2023] [Indexed: 01/15/2023] Open
Abstract
Studying chemosensory processing desires precise chemical cue presentation, behavioral response monitoring, and large-scale neuronal activity recording. Here we present Fish-on-Chips, a set of optofluidic tools for highly-controlled chemical delivery while simultaneously imaging behavioral outputs and whole-brain neuronal activities at cellular resolution in larval zebrafish. These include a fluidics-based swimming arena and an integrated microfluidics-light sheet fluorescence microscopy (µfluidics-LSFM) system, both of which utilize laminar fluid flows to achieve spatiotemporally precise chemical cue presentation. To demonstrate the strengths of the platform, we used the navigation arena to reveal binasal input-dependent behavioral strategies that larval zebrafish adopt to evade cadaverine, a death-associated odor. The µfluidics-LSFM system enables sequential presentation of odor stimuli to individual or both nasal cavities separated by only ~100 µm. This allowed us to uncover brainwide neural representations of cadaverine sensing and binasal input summation in the vertebrate model. Fish-on-Chips is readily generalizable and will empower the investigation of neural coding in the chemical senses.
Collapse
|
7
|
Park JE, Yoon S, Jeon J, Kim CR, Jhang S, Jeon T, Lee SG, Kim SM, Wie JJ. Multi-Modal Locomotion of Caenorhabditis elegans by Magnetic Reconfiguration of 3D Microtopography. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2203396. [PMID: 36316238 PMCID: PMC9798981 DOI: 10.1002/advs.202203396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/24/2022] [Indexed: 06/16/2023]
Abstract
Miniaturized untethered soft robots are recently exploited to imitate multi-modal curvilinear locomotion of living creatures that perceive change of surrounding environments. Herein, the use of Caenorhabditis elegans (C. elegans) is proposed as a microscale model capable of curvilinear locomotion with mechanosensing, controlled by magnetically reconfigured 3D microtopography. Static entropic microbarriers prevent C. elegans from randomly swimming with the omega turns and provide linear translational locomotion with velocity of ≈0.14 BL s-1 . This velocity varies from ≈0.09 (for circumventing movement) to ≈0.46 (for climbing) BL s-1 , depending on magnetic bending and twisting actuation coupled with assembly of microbarriers. Furthermore, different types of neuronal mutants prevent C. elegans from implementing certain locomotion modes, indicating the potential for investigating the correlation between neurons and mechanosensing functions. This strategy promotes a platform for the contactless manipulation of miniaturized biobots and initiates interdisciplinary research for investigating sensory neurons and human diseases.
Collapse
Affiliation(s)
- Jeong Eun Park
- The Research Institute of Industrial ScienceHanyang UniversitySeoul04763Republic of Korea
- Program in Environmental and Polymer EngineeringInha UniversityIncheon22212Republic of Korea
| | - Sunhee Yoon
- Department of Biological Sciences and BioengineeringInha UniversityIncheon22212Republic of Korea
| | - Jisoo Jeon
- Program in Environmental and Polymer EngineeringInha UniversityIncheon22212Republic of Korea
| | - Chae Ryean Kim
- Department of ChemistryUniversity of UlsanUlsan44610Republic of Korea
| | - Saebohm Jhang
- Program in Environmental and Polymer EngineeringInha UniversityIncheon22212Republic of Korea
| | - Tae‐Joon Jeon
- Department of Biological Sciences and BioengineeringInha UniversityIncheon22212Republic of Korea
| | - Seung Goo Lee
- Department of ChemistryUniversity of UlsanUlsan44610Republic of Korea
| | - Sun Min Kim
- Department of Biological Sciences and BioengineeringInha UniversityIncheon22212Republic of Korea
- Department of Mechanical EngineeringInha UniversityIncheon22212Republic of Korea
| | - Jeong Jae Wie
- Department of Organic and Nano EngineeringHanyang UniversitySeoul04763Republic of Korea
- Human‐Tech Convergence ProgramHanyang UniversitySeoul04763Republic of Korea
| |
Collapse
|
8
|
Yu YV, Xue W, Chen Y. Multisensory Integration in Caenorhabditis elegans in Comparison to Mammals. Brain Sci 2022; 12:brainsci12101368. [PMID: 36291302 PMCID: PMC9599712 DOI: 10.3390/brainsci12101368] [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: 08/31/2022] [Revised: 09/28/2022] [Accepted: 10/03/2022] [Indexed: 11/30/2022] Open
Abstract
Multisensory integration refers to sensory inputs from different sensory modalities being processed simultaneously to produce a unitary output. Surrounded by stimuli from multiple modalities, animals utilize multisensory integration to form a coherent and robust representation of the complex environment. Even though multisensory integration is fundamentally essential for animal life, our understanding of the underlying mechanisms, especially at the molecular, synaptic and circuit levels, remains poorly understood. The study of sensory perception in Caenorhabditis elegans has begun to fill this gap. We have gained a considerable amount of insight into the general principles of sensory neurobiology owing to C. elegans’ highly sensitive perceptions, relatively simple nervous system, ample genetic tools and completely mapped neural connectome. Many interesting paradigms of multisensory integration have been characterized in C. elegans, for which input convergence occurs at the sensory neuron or the interneuron level. In this narrative review, we describe some representative cases of multisensory integration in C. elegans, summarize the underlying mechanisms and compare them with those in mammalian systems. Despite the differences, we believe C. elegans is able to provide unique insights into how processing and integrating multisensory inputs can generate flexible and adaptive behaviors. With the emergence of whole brain imaging, the ability of C. elegans to monitor nearly the entire nervous system may be crucial for understanding the function of the brain as a whole.
Collapse
Affiliation(s)
- Yanxun V. Yu
- Department of Neurology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430070, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan 430070, China
- Correspondence: or
| | - Weikang Xue
- Department of Neurology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430070, China
| | - Yuanhua Chen
- Department of Neurology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430070, China
| |
Collapse
|
9
|
Wang Y, Zhao S, Qin Q, Gao X, Zhang X, Zhang M, Jiang Y, Ji X, Zhu H, Zhao X, Li H. CKMT1A is a novel potential prognostic biomarker in patients with endometrial cancer. PLoS One 2022; 17:e0262000. [PMID: 35077462 PMCID: PMC8789190 DOI: 10.1371/journal.pone.0262000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 12/15/2021] [Indexed: 12/01/2022] Open
Abstract
PURPOSE The International Federation of Gynecology and Obstetrics (FIGO) stage remains the standard staging system for the assessment of endometrial cancer (EC) prognosis. Thus, we aim to identify the significant genes or biomarkers associated with the stage of endometrial cancer, which may also help reveal the mechanism of EC progression and assess the prognosis of patients with EC. MATERIALS AND METHODS We compared the mRNA expression levels of EC patients with stages I and II as well as stages III and IV in the Cancer Genome Atlas (TCGA) database. The differentially expressed genes (DEGs) of EC patients at different stages were selected by volcano plot and Venn analysis. Gene Ontology (GO) and Pathways were applied to analyze the identified genes. Protein protein interaction (PPI) network was employed to identify the correlation. The survival analyses based on TCGA database were conducted for further screening. The Human Protein Atlas, quantitative PCR and immunohistochemistry were utilized to confirm the differences in expression of DEGs in endometrial cancer samples at different FIGO stages. RESULTS CKMT1A was identified as a candidate gene. Through survival analyses, we found that CKMT1A may be a poor prognostic factor in the overall survival of endometrial cancer patients. GO and Pathways revealed that CKMT1A is closely associated with the metabolic process. More importantly, Human Protein Atlas and quantitative PCR confirmed the differences in expression of CKMT1A in endometrial cancer samples at different FIGO stages. CONCLUSION In summary, this study shows that CKMT1A is a newly identified essential tumor progression regulator of endometrial cancer, which may give rise to novel therapeutic strategies in the management of endometrial cancer patients to prolong its prognosis and prevent tumor progression.
Collapse
Affiliation(s)
- Yaping Wang
- Gynecologic Oncology, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Shujun Zhao
- Gynecologic Oncology, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Key Laboratory of gynecological oncology, Zhengzhou, Henan, China
| | - Qiaohong Qin
- Gynecologic Oncology, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Key Laboratory of gynecological oncology, Zhengzhou, Henan, China
| | - Xiang Gao
- Gynecologic Oncology, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xinlu Zhang
- Gynecologic Oncology, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Min Zhang
- Gynecologic Oncology, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yi Jiang
- Gynecologic Oncology, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xiaorong Ji
- Gynecologic Oncology, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Hai Zhu
- Gynecologic Oncology, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xin Zhao
- The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Hongyu Li
- Gynecologic Oncology, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Key Laboratory of gynecological oncology, Zhengzhou, Henan, China
| |
Collapse
|
10
|
Zhang X, Sun J, Yuan X, Lu X, Sun X. Advances in C. elegans behavior research with microfluidic devices and its future prospects in the evaluation of exogenous pollutants. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116195] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
11
|
Chaudhary S, Lee SA, Li Y, Patel DS, Lu H. Graphical-model framework for automated annotation of cell identities in dense cellular images. eLife 2021; 10:e60321. [PMID: 33625357 PMCID: PMC8032398 DOI: 10.7554/elife.60321] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 02/23/2021] [Indexed: 12/11/2022] Open
Abstract
Although identifying cell names in dense image stacks is critical in analyzing functional whole-brain data enabling comparison across experiments, unbiased identification is very difficult, and relies heavily on researchers' experiences. Here, we present a probabilistic-graphical-model framework, CRF_ID, based on Conditional Random Fields, for unbiased and automated cell identification. CRF_ID focuses on maximizing intrinsic similarity between shapes. Compared to existing methods, CRF_ID achieves higher accuracy on simulated and ground-truth experimental datasets, and better robustness against challenging noise conditions common in experimental data. CRF_ID can further boost accuracy by building atlases from annotated data in highly computationally efficient manner, and by easily adding new features (e.g. from new strains). We demonstrate cell annotation in Caenorhabditis elegans images across strains, animal orientations, and tasks including gene-expression localization, multi-cellular and whole-brain functional imaging experiments. Together, these successes demonstrate that unbiased cell annotation can facilitate biological discovery, and this approach may be valuable to annotation tasks for other systems.
Collapse
Affiliation(s)
- Shivesh Chaudhary
- School of Chemical & Biomolecular Engineering, Georgia Institute of TechnologyAtlantaUnited States
| | - Sol Ah Lee
- School of Chemical & Biomolecular Engineering, Georgia Institute of TechnologyAtlantaUnited States
| | - Yueyi Li
- School of Chemical & Biomolecular Engineering, Georgia Institute of TechnologyAtlantaUnited States
| | - Dhaval S Patel
- School of Chemical & Biomolecular Engineering, Georgia Institute of TechnologyAtlantaUnited States
| | - Hang Lu
- School of Chemical & Biomolecular Engineering, Georgia Institute of TechnologyAtlantaUnited States
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of TechnologyAtlantaUnited States
| |
Collapse
|
12
|
Berlanda SF, Breitfeld M, Dietsche CL, Dittrich PS. Recent Advances in Microfluidic Technology for Bioanalysis and Diagnostics. Anal Chem 2020; 93:311-331. [DOI: 10.1021/acs.analchem.0c04366] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Simon F. Berlanda
- Department of Biosystems Science and Engineering, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Maximilian Breitfeld
- Department of Biosystems Science and Engineering, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Claudius L. Dietsche
- Department of Biosystems Science and Engineering, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Petra S. Dittrich
- Department of Biosystems Science and Engineering, ETH Zurich, CH-8093 Zurich, Switzerland
| |
Collapse
|