1
|
Bowser RM, Farman GP, Gregorio CC. Philament: A filament tracking program to quickly and accurately analyze in vitro motility assays. BIOPHYSICAL REPORTS 2024; 4:100147. [PMID: 38404534 PMCID: PMC10884813 DOI: 10.1016/j.bpr.2024.100147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/25/2024] [Indexed: 02/27/2024]
Abstract
In vitro motility (IVM) assays allow for the examination of the basic interaction between cytoskeletal filaments with molecular motors and the influence many physiological factors have on this interaction. Examples of factors that can be studied include changes in ADP and pH that emulate fatigue, altered phosphorylation that can occur with disease, and mutations within myofilament proteins that cause disease. While IVM assays can be analyzed manually, the main limitation is the ability to extract accurate data rapidly from videos collected without individual bias. While programs have been created in the past to enable data extraction, many are now out of date or require the use of proprietary software. Here, we report the generation of a Python-based tracking program, Philament, which automatically extracts data on instantaneous and average velocities, and allows for fully automated analysis of IVM recordings. The data generated are presented in an easily accessible spreadsheet-based, comma-separated values file. Philament also contains a novel method of quantifying the smoothness of filament motion. By fitting curves to standard deviations of velocity and average velocities, the influence of different experimental conditions can be compared relative to one another. This comparison provides a qualitative measure of protein interactions where steeper slopes indicate more unstable interactions and shallower slopes indicate more stable interactions within the myofilament. Overall, Philament's automation of IVM analysis provides easier entry into the field of cardiovascular mechanics and enables users to create a truly high-throughput experimental data analysis.
Collapse
Affiliation(s)
- Ryan M. Bowser
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, The University of Arizona, Tucson, Arizona
| | - Gerrie P. Farman
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, The University of Arizona, Tucson, Arizona
| | - Carol C. Gregorio
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, The University of Arizona, Tucson, Arizona
- Cardiovascular Research Institute, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| |
Collapse
|
2
|
Papaspyros V, Escobedo R, Alahi A, Theraulaz G, Sire C, Mondada F. Predicting the long-term collective behaviour of fish pairs with deep learning. J R Soc Interface 2024; 21:20230630. [PMID: 38442859 PMCID: PMC10914514 DOI: 10.1098/rsif.2023.0630] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/06/2024] [Indexed: 03/07/2024] Open
Abstract
Modern computing has enhanced our understanding of how social interactions shape collective behaviour in animal societies. Although analytical models dominate in studying collective behaviour, this study introduces a deep learning model to assess social interactions in the fish species Hemigrammus rhodostomus. We compare the results of our deep learning approach with experiments and with the results of a state-of-the-art analytical model. To that end, we propose a systematic methodology to assess the faithfulness of a collective motion model, exploiting a set of stringent individual and collective spatio-temporal observables. We demonstrate that machine learning (ML) models of social interactions can directly compete with their analytical counterparts in reproducing subtle experimental observables. Moreover, this work emphasizes the need for consistent validation across different timescales, and identifies key design aspects that enable our deep learning approach to capture both short- and long-term dynamics. We also show that our approach can be extended to larger groups without any retraining, and to other fish species, while retaining the same architecture of the deep learning network. Finally, we discuss the added value of ML in the context of the study of collective motion in animal groups and its potential as a complementary approach to analytical models.
Collapse
Affiliation(s)
- Vaios Papaspyros
- Mobile Robotic Systems (Mobots) group, Institute of Electrical and Micro Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ramón Escobedo
- Centre de Recherches sur la Cognition Animale, Centre de Biologie Intégrative, CNRS, Université de Toulouse III – Paul Sabatier, 31062 Toulouse, France
| | - Alexandre Alahi
- VITA group, Civil Engineering Institute, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Guy Theraulaz
- Centre de Recherches sur la Cognition Animale, Centre de Biologie Intégrative, CNRS, Université de Toulouse III – Paul Sabatier, 31062 Toulouse, France
| | - Clément Sire
- Laboratoire de Physique Théorique, CNRS, Université de Toulouse III – Paul Sabatier, 31062 Toulouse, France
| | - Francesco Mondada
- Mobile Robotic Systems (Mobots) group, Institute of Electrical and Micro Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| |
Collapse
|
3
|
Tanaka Y, Valentini G, Pratt SC, Shimoji H, Mizumoto N. Protocol to obtain long movement trajectories of leaders and followers in ant tandem runs. STAR Protoc 2023; 4:102769. [PMID: 38060385 PMCID: PMC10783595 DOI: 10.1016/j.xpro.2023.102769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 11/07/2023] [Accepted: 11/22/2023] [Indexed: 01/14/2024] Open
Abstract
Tandem running in ants is a sophisticated form of communication. Precise measurement of movement coordination by the tandem pair can shed light on social interactions. Here, we describe an integrative approach to obtain long movement trajectories of a specific tandem pair within a crowd of ants. We describe a maze-like arena, video recording and editing, and movement tracking. We integrate two pieces of image-based tracking software that have distinct individual assignment strategies. This protocol aids comparative studies of recruitment communication across species. For complete details on the use and execution of this protocol, please refer to Mizumoto et al. (2023)1 and Valentini et al. (2020).2.
Collapse
Affiliation(s)
- Yasunari Tanaka
- United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
| | | | - Stephen C Pratt
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Hiroyuki Shimoji
- Department of Subtropical Agro-Environmental Sciences, Faculty of Agriculture, University of the Ryukyus, Nishihara-cho, Okinawa 903-0213, Japan.
| | - Nobuaki Mizumoto
- Evolutionary Genomics Unit, Okinawa Institute of Science & Technology Graduate University, Onna-son, Okinawa 904-0495, Japan; Computational Neuroethology Unit, Okinawa Institute of Science & Technology Graduate University, Onna-son, Okinawa 904-0495, Japan.
| |
Collapse
|
4
|
Bai Y, Henry J, Cheng E, Perry S, Mawdsley D, Wong BBM, Kaslin J, Wlodkowic D. Toward Real-Time Animal Tracking with Integrated Stimulus Control for Automated Conditioning in Aquatic Eco-Neurotoxicology. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:19453-19462. [PMID: 37956114 DOI: 10.1021/acs.est.3c07013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Aquatic eco-neurotoxicology is an emerging field that requires new analytical systems to study the effects of pollutants on animal behaviors. This is especially true if we are to gain insights into one of the least studied aspects: the potential perturbations that neurotoxicants can have on cognitive behaviors. The paucity of experimental data is partly caused by a lack of low-cost technologies for the analysis of higher-level neurological functions (e.g., associative learning) in small aquatic organisms. Here, we present a proof-of-concept prototype that utilizes a new real-time animal tracking software for on-the-fly video analysis and closed-loop, external hardware communications to deliver stimuli based on specific behaviors in aquatic organisms, spanning three animal phyla: chordates (fish, frog), platyhelminthes (flatworm), and arthropods (crustacean). The system's open-source software features an intuitive graphical user interface and advanced adaptive threshold-based image segmentation for precise animal detection. We demonstrate the precision of animal tracking across multiple aquatic species with varying modes of locomotion. The presented technology interfaces easily with low-cost and open-source hardware such as the Arduino microcontroller family for closed-loop stimuli control. The new system has potential future applications in eco-neurotoxicology, where it could enable new opportunities for cognitive research in diverse small aquatic model organisms.
Collapse
Affiliation(s)
- Yutao Bai
- The Neurotoxicology Laboratory, School of Science, RMIT University, Melbourne, VIC 3083, Australia
| | - Jason Henry
- The Neurotoxicology Laboratory, School of Science, RMIT University, Melbourne, VIC 3083, Australia
| | - Eva Cheng
- Faculty of Engineering and IT, School of Electrical and Data Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Stuart Perry
- Faculty of Engineering and IT, School of Electrical and Data Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - David Mawdsley
- Defence Science and Technology Group, Melbourne, VIC 3207, Australia
| | - Bob B M Wong
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - Jan Kaslin
- Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Donald Wlodkowic
- The Neurotoxicology Laboratory, School of Science, RMIT University, Melbourne, VIC 3083, Australia
| |
Collapse
|
5
|
Xue T, Li X, Lin G, Escobedo R, Han Z, Chen X, Sire C, Theraulaz G. Tuning social interactions' strength drives collective response to light intensity in schooling fish. PLoS Comput Biol 2023; 19:e1011636. [PMID: 37976299 PMCID: PMC10691717 DOI: 10.1371/journal.pcbi.1011636] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 12/01/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023] Open
Abstract
Schooling fish heavily rely on visual cues to interact with neighbors and avoid obstacles. The availability of sensory information is influenced by environmental conditions and changes in the physical environment that can alter the sensory environment of the fish, which in turn affects individual and group movements. In this study, we combine experiments and data-driven modeling to investigate the impact of varying levels of light intensity on social interactions and collective behavior in rummy-nose tetra fish. The trajectories of single fish and groups of fish swimming in a tank under different lighting conditions were analyzed to quantify their movements and spatial distribution. Interaction functions between two individuals and the fish interaction with the tank wall were reconstructed and modeled for each light condition. Our results demonstrate that light intensity strongly modulates social interactions between fish and their reactions to obstacles, which then impact collective motion patterns that emerge at the group level.
Collapse
Affiliation(s)
- Tingting Xue
- School of Systems Science, Beijing Normal University, Beijing, China
- Centre de Recherches sur la Cognition Animale, Centre de Biologie Intégrative (CBI), CNRS & Université de Toulouse III - Paul Sabatier, Toulouse, France
| | - Xu Li
- School of Systems Science, Beijing Normal University, Beijing, China
- Centre de Recherches sur la Cognition Animale, Centre de Biologie Intégrative (CBI), CNRS & Université de Toulouse III - Paul Sabatier, Toulouse, France
| | - GuoZheng Lin
- School of Systems Science, Beijing Normal University, Beijing, China
- Centre de Recherches sur la Cognition Animale, Centre de Biologie Intégrative (CBI), CNRS & Université de Toulouse III - Paul Sabatier, Toulouse, France
| | - Ramón Escobedo
- Centre de Recherches sur la Cognition Animale, Centre de Biologie Intégrative (CBI), CNRS & Université de Toulouse III - Paul Sabatier, Toulouse, France
| | - Zhangang Han
- School of Systems Science, Beijing Normal University, Beijing, China
| | - Xiaosong Chen
- School of Systems Science, Beijing Normal University, Beijing, China
| | - Clément Sire
- Laboratoire de Physique Théorique, CNRS & Université de Toulouse III - Paul Sabatier, Toulouse, France
| | - Guy Theraulaz
- Centre de Recherches sur la Cognition Animale, Centre de Biologie Intégrative (CBI), CNRS & Université de Toulouse III - Paul Sabatier, Toulouse, France
| |
Collapse
|
6
|
Rathore A, Sharma A, Shah S, Sharma N, Torney C, Guttal V. Multi-Object Tracking in Heterogeneous environments (MOTHe) for animal video recordings. PeerJ 2023; 11:e15573. [PMID: 37397020 PMCID: PMC10309051 DOI: 10.7717/peerj.15573] [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: 09/26/2022] [Accepted: 05/25/2023] [Indexed: 07/04/2023] Open
Abstract
Aerial imagery and video recordings of animals are used for many areas of research such as animal behaviour, behavioural neuroscience and field biology. Many automated methods are being developed to extract data from such high-resolution videos. Most of the available tools are developed for videos taken under idealised laboratory conditions. Therefore, the task of animal detection and tracking for videos taken in natural settings remains challenging due to heterogeneous environments. Methods that are useful for field conditions are often difficult to implement and thus remain inaccessible to empirical researchers. To address this gap, we present an open-source package called Multi-Object Tracking in Heterogeneous environments (MOTHe), a Python-based application that uses a basic convolutional neural network for object detection. MOTHe offers a graphical interface to automate the various steps related to animal tracking such as training data generation, animal detection in complex backgrounds and visually tracking animals in the videos. Users can also generate training data and train a new model which can be used for object detection tasks for a completely new dataset. MOTHe doesn't require any sophisticated infrastructure and can be run on basic desktop computing units. We demonstrate MOTHe on six video clips in varying background conditions. These videos are from two species in their natural habitat-wasp colonies on their nests (up to 12 individuals per colony) and antelope herds in four different habitats (up to 156 individuals in a herd). Using MOTHe, we are able to detect and track individuals in all these videos. MOTHe is available as an open-source GitHub repository with a detailed user guide and demonstrations at: https://github.com/tee-lab/MOTHe-GUI.
Collapse
Affiliation(s)
- Akanksha Rathore
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, India
| | - Ananth Sharma
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, India
| | - Shaan Shah
- Department of Electrical Engineering, Indian Institute of Technology, Bombay, Mumbai, India
| | - Nitika Sharma
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, India
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, United States of America
| | - Colin Torney
- School of Mathematics and Statistics, University of Glasgow, Glasgow, United Kingdom
| | - Vishwesha Guttal
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, India
| |
Collapse
|
7
|
Beiza-Canelo N, Moulle H, Pujol T, Panier T, Migault G, Le Goc G, Tapie P, Desprat N, Straka H, Debrégeas G, Bormuth V. Magnetic actuation of otoliths allows behavioral and brain-wide neuronal exploration of vestibulo-motor processing in larval zebrafish. Curr Biol 2023:S0960-9822(23)00621-8. [PMID: 37285844 DOI: 10.1016/j.cub.2023.05.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 11/23/2022] [Accepted: 05/11/2023] [Indexed: 06/09/2023]
Abstract
The vestibular system in the inner ear plays a central role in sensorimotor control by informing the brain about the orientation and acceleration of the head. However, most experiments in neurophysiology are performed using head-fixed configurations, depriving animals of vestibular inputs. To overcome this limitation, we decorated the utricular otolith of the vestibular system in larval zebrafish with paramagnetic nanoparticles. This procedure effectively endowed the animal with magneto-sensitive capacities: applied magnetic field gradients induced forces on the otoliths, resulting in robust behavioral responses comparable to those evoked by rotating the animal by up to 25°. We recorded the whole-brain neuronal response to this fictive motion stimulation using light-sheet functional imaging. Experiments performed in unilaterally injected fish revealed the activation of a commissural inhibition between the brain hemispheres. This magnetic-based stimulation technique for larval zebrafish opens new perspectives to functionally dissect the neural circuits underlying vestibular processing and to develop multisensory virtual environments, including vestibular feedback.
Collapse
Affiliation(s)
- Natalia Beiza-Canelo
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 75005 Paris, France
| | - Hippolyte Moulle
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 75005 Paris, France
| | - Thomas Pujol
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 75005 Paris, France; IBENS, Département de Biologie, École Normale Supérieure, CNRS, Inserm, PSL Research University, 75005 Paris, France
| | - Thomas Panier
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 75005 Paris, France; Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Plateforme d'Imagerie, 75005 Paris, France
| | - Geoffrey Migault
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 75005 Paris, France
| | - Guillaume Le Goc
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 75005 Paris, France
| | - Pierre Tapie
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 75005 Paris, France
| | - Nicolas Desprat
- Laboratoire de Physique de l'École Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université Paris Cité, 75005 Paris, France; Université Paris Diderot, 10 Rue Alice Domon et Leonie Duquet, 75013 Paris, France
| | - Hans Straka
- Faculty of Biology, Ludwig-Maximilians-University Munich, Grosshadernerstr. 2, 82152 Planegg, Germany
| | - Georges Debrégeas
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 75005 Paris, France
| | - Volker Bormuth
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 75005 Paris, France.
| |
Collapse
|
8
|
Lafoux B, Moscatelli J, Godoy-Diana R, Thiria B. Illuminance-tuned collective motion in fish. Commun Biol 2023; 6:585. [PMID: 37258699 DOI: 10.1038/s42003-023-04861-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 04/21/2023] [Indexed: 06/02/2023] Open
Abstract
We experimentally investigate the role of illumination on the collective dynamics of a large school (ca. 50 individuals) of Hemigrammus rhodostomus. The structure of the group, defined using two order parameters, is quantified while progressively altering the visual range of the fish through controlled cycles of ambient light intensity. We show that, at low light levels, the individuals within the group are unable to form a cohesive group, while at higher illuminance the degree of alignment of the school correlates with the light intensity. When increasing the illuminance, the school structure is successively characterized by a polarized state followed by a highly regular and stable rotational configuration (milling). Our study shows that vision is necessary to achieve cohesive collective motion for free swimming fish schools, while the short-range lateral line sensing is insufficient in this situation. The present experiment therefore provides new insights into the interaction mechanisms that govern the emergence and intensity of collective motion in biological systems.
Collapse
Affiliation(s)
- Baptiste Lafoux
- Laboratoire de Physique et Mécanique des Milieux Hétérogènes (PMMH), CNRS UMR 7636, ESPCI Paris-PSL Research University, Sorbonne Université-Université Paris Cité, 10 rue Vauquelin, 75005, Paris, France.
| | - Jeanne Moscatelli
- Laboratoire de Physique et Mécanique des Milieux Hétérogènes (PMMH), CNRS UMR 7636, ESPCI Paris-PSL Research University, Sorbonne Université-Université Paris Cité, 10 rue Vauquelin, 75005, Paris, France
| | - Ramiro Godoy-Diana
- Laboratoire de Physique et Mécanique des Milieux Hétérogènes (PMMH), CNRS UMR 7636, ESPCI Paris-PSL Research University, Sorbonne Université-Université Paris Cité, 10 rue Vauquelin, 75005, Paris, France.
| | - Benjamin Thiria
- Laboratoire de Physique et Mécanique des Milieux Hétérogènes (PMMH), CNRS UMR 7636, ESPCI Paris-PSL Research University, Sorbonne Université-Université Paris Cité, 10 rue Vauquelin, 75005, Paris, France.
| |
Collapse
|
9
|
Malik H, Idris AS, Toha SF, Mohd Idris I, Daud MF, Azmi NL. A review of open-source image analysis tools for mammalian cell culture: algorithms, features and implementations. PeerJ Comput Sci 2023; 9:e1364. [PMID: 37346656 PMCID: PMC10280419 DOI: 10.7717/peerj-cs.1364] [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: 11/11/2022] [Accepted: 04/04/2023] [Indexed: 06/23/2023]
Abstract
Cell culture is undeniably important for multiple scientific applications, including pharmaceuticals, transplants, and cosmetics. However, cell culture involves multiple manual steps, such as regularly analyzing cell images for their health and morphology. Computer scientists have developed algorithms to automate cell imaging analysis, but they are not widely adopted by biologists, especially those lacking an interactive platform. To address the issue, we compile and review existing open-source cell image processing tools that provide interactive interfaces for management and prediction tasks. We highlight the prediction tools that can detect, segment, and track different mammalian cell morphologies across various image modalities and present a comparison of algorithms and unique features of these tools, whether they work locally or in the cloud. This would guide non-experts to determine which is best suited for their purposes and, developers to acknowledge what is worth further expansion. In addition, we provide a general discussion on potential implementations of the tools for a more extensive scope, which guides the reader to not restrict them to prediction tasks only. Finally, we conclude the article by stating new considerations for the development of interactive cell imaging tools and suggesting new directions for future research.
Collapse
Affiliation(s)
- Hafizi Malik
- Healthcare Engineering and Rehabilitation Research, Department of Mechatronics Engineering, International Islamic University Malaysia, Gombak, Selangor, Malaysia
| | - Ahmad Syahrin Idris
- Department of Electrical and Electronic Engineering, University of Southampton Malaysia, Iskandar Puteri, Johor, Malaysia
| | - Siti Fauziah Toha
- Healthcare Engineering and Rehabilitation Research, Department of Mechatronics Engineering, International Islamic University Malaysia, Gombak, Selangor, Malaysia
| | - Izyan Mohd Idris
- Institute for Medical Research (IMR), National Institutes of Health (NIH), Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia
| | - Muhammad Fauzi Daud
- Institute of Medical Science Technology, Universiti Kuala Lumpur, Kajang, Selangor, Malaysia
| | - Nur Liyana Azmi
- Healthcare Engineering and Rehabilitation Research, Department of Mechatronics Engineering, International Islamic University Malaysia, Gombak, Selangor, Malaysia
| |
Collapse
|
10
|
Escoubet N, Brette R, Pontani LL, Prevost AM. Interaction of the mechanosensitive microswimmer Paramecium with obstacles. ROYAL SOCIETY OPEN SCIENCE 2023; 10:221645. [PMID: 37234495 PMCID: PMC10206458 DOI: 10.1098/rsos.221645] [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: 01/12/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023]
Abstract
In this work, we report investigations of the swimming behaviour of Paramecium tetraurelia, a unicellular microorganism, in micro-engineered pools that are decorated with thousands of cylindrical pillars. Two types of contact interactions are measured, either passive scattering of Paramecium along the obstacle or avoiding reactions (ARs), characterized by an initial backward swimming upon contact, followed by a reorientation before resuming forward motion. We find that ARs are only mechanically triggered approximately 10% of the time. In addition, we observe that only a third of all ARs triggered by contact are instantaneous while two-thirds are delayed by approximately 150 ms. These measurements are consistent with a simple electrophysiological model of mechanotransduction composed of a strong transient current followed by a persistent one upon prolonged contact. This is in apparent contrast with previous electrophysiological measurements where immobilized cells were stimulated with thin probes, which showed instantaneous behavioural responses and no persistent current. Our findings highlight the importance of ecologically relevant approaches to unravel the motility of mechanosensitive microorganisms in complex environments.
Collapse
Affiliation(s)
- Nicolas Escoubet
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Jean Perrin, 4 place Jussieu, Paris 75005, France
| | - Romain Brette
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, Paris 75012, France
| | - Lea-Laetitia Pontani
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Jean Perrin, 4 place Jussieu, Paris 75005, France
| | - Alexis Michel Prevost
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Jean Perrin, 4 place Jussieu, Paris 75005, France
| |
Collapse
|
11
|
Elices I, Kulkarni A, Escoubet N, Pontani LL, Prevost AM, Brette R. An electrophysiological and kinematic model of Paramecium, the "swimming neuron". PLoS Comput Biol 2023; 19:e1010899. [PMID: 36758112 PMCID: PMC9946239 DOI: 10.1371/journal.pcbi.1010899] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 02/22/2023] [Accepted: 01/26/2023] [Indexed: 02/11/2023] Open
Abstract
Paramecium is a large unicellular organism that swims in fresh water using cilia. When stimulated by various means (mechanically, chemically, optically, thermally), it often swims backward then turns and swims forward again in a new direction: this is called the avoiding reaction. This reaction is triggered by a calcium-based action potential. For this reason, several authors have called Paramecium the "swimming neuron". Here we present an empirically constrained model of its action potential based on electrophysiology experiments on live immobilized paramecia, together with simultaneous measurement of ciliary beating using particle image velocimetry. Using these measurements and additional behavioral measurements of free swimming, we extend the electrophysiological model by coupling calcium concentration to kinematic parameters, turning it into a swimming model. In this way, we obtain a model of autonomously behaving Paramecium. Finally, we demonstrate how the modeled organism interacts with an environment, can follow gradients and display collective behavior. This work provides a modeling basis for investigating the physiological basis of autonomous behavior of Paramecium in ecological environments.
Collapse
Affiliation(s)
- Irene Elices
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Anirudh Kulkarni
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
- Department of Bioengineering and Centre for Neurotechnology, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Nicolas Escoubet
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), Paris
| | - Léa-Laetitia Pontani
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), Paris
| | - Alexis Michel Prevost
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), Paris
| | - Romain Brette
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| |
Collapse
|
12
|
Larbi MC, Messa G, Jalal H, Koutsikou S. An early midbrain sensorimotor pathway is involved in the timely initiation and direction of swimming in the hatchling Xenopus laevis tadpole. Front Neural Circuits 2022; 16:1027831. [PMID: 36619662 PMCID: PMC9810627 DOI: 10.3389/fncir.2022.1027831] [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: 08/25/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022] Open
Abstract
Vertebrate locomotion is heavily dependent on descending control originating in the midbrain and subsequently influencing central pattern generators in the spinal cord. However, the midbrain neuronal circuitry and its connections with other brainstem and spinal motor circuits has not been fully elucidated. Vertebrates with very simple nervous system, like the hatchling Xenopus laevis tadpole, have been instrumental in unravelling fundamental principles of locomotion and its suspraspinal control. Here, we use behavioral and electrophysiological approaches in combination with lesions of the midbrain to investigate its contribution to the initiation and control of the tadpole swimming in response to trunk skin stimulation. None of the midbrain lesions studied here blocked the tadpole's sustained swim behavior following trunk skin stimulation. However, we identified that distinct midbrain lesions led to significant changes in the latency and trajectory of swimming. These changes could partly be explained by the increase in synchronous muscle contractions on the opposite sides of the tadpole's body and permanent deflection of the tail from its normal position, respectively. We conclude that the tadpole's embryonic trunk skin sensorimotor pathway involves the midbrain, which harbors essential neuronal circuitry to significantly contribute to the appropriate, timely and coordinated selection and execution of locomotion, imperative to the animal's survival.
Collapse
|
13
|
Gallois B, Pontani LL, Debrégeas G, Candelier R. A scalable assay for chemical preference of small freshwater fish. Front Behav Neurosci 2022; 16:990792. [PMID: 36212190 PMCID: PMC9541871 DOI: 10.3389/fnbeh.2022.990792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 09/01/2022] [Indexed: 11/13/2022] Open
Abstract
Sensing the chemical world is of primary importance for aquatic organisms, and small freshwater fish are increasingly used in toxicology, ethology, and neuroscience by virtue of their ease of manipulation, tissue imaging amenability, and genetic tractability. However, precise behavioral analyses are generally challenging to perform due to the lack of knowledge of what chemical the fish are exposed to at any given moment. Here we developed a behavioral assay and a specific infrared dye to probe the preference of young zebrafish for virtually any compound. We found that the innate aversion of zebrafish to citric acid is not mediated by modulation of the swim but rather by immediate avoidance reactions when the product is sensed and that the preference of juvenile zebrafish for ATP changes from repulsion to attraction during successive exposures. We propose an information-based behavioral model for which an exploration index emerges as a relevant behavioral descriptor, complementary to the standard preference index. Our setup features a high versatility in protocols and is automatic and scalable, which paves the way for high-throughput preference compound screening at different ages.
Collapse
|
14
|
Kappel JM, Förster D, Slangewal K, Shainer I, Svara F, Donovan JC, Sherman S, Januszewski M, Baier H, Larsch J. Visual recognition of social signals by a tectothalamic neural circuit. Nature 2022; 608:146-152. [PMID: 35831500 PMCID: PMC9352588 DOI: 10.1038/s41586-022-04925-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 06/02/2022] [Indexed: 12/23/2022]
Abstract
Social affiliation emerges from individual-level behavioural rules that are driven by conspecific signals1-5. Long-distance attraction and short-distance repulsion, for example, are rules that jointly set a preferred interanimal distance in swarms6-8. However, little is known about their perceptual mechanisms and executive neural circuits3. Here we trace the neuronal response to self-like biological motion9,10, a visual trigger for affiliation in developing zebrafish2,11. Unbiased activity mapping and targeted volumetric two-photon calcium imaging revealed 21 activity hotspots distributed throughout the brain as well as clustered biological-motion-tuned neurons in a multimodal, socially activated nucleus of the dorsal thalamus. Individual dorsal thalamus neurons encode local acceleration of visual stimuli mimicking typical fish kinetics but are insensitive to global or continuous motion. Electron microscopic reconstruction of dorsal thalamus neurons revealed synaptic input from the optic tectum and projections into hypothalamic areas with conserved social function12-14. Ablation of the optic tectum or dorsal thalamus selectively disrupted social attraction without affecting short-distance repulsion. This tectothalamic pathway thus serves visual recognition of conspecifics, and dissociates neuronal control of attraction from repulsion during social affiliation, revealing a circuit underpinning collective behaviour.
Collapse
Affiliation(s)
- Johannes M Kappel
- Max Planck Institute for Biological Intelligence (formerly Max Planck Institute of Neurobiology), Planegg, Germany
| | - Dominique Förster
- Max Planck Institute for Biological Intelligence (formerly Max Planck Institute of Neurobiology), Planegg, Germany
| | - Katja Slangewal
- Max Planck Institute for Biological Intelligence (formerly Max Planck Institute of Neurobiology), Planegg, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany
| | - Inbal Shainer
- Max Planck Institute for Biological Intelligence (formerly Max Planck Institute of Neurobiology), Planegg, Germany
| | - Fabian Svara
- Max Planck Institute for Biological Intelligence (formerly Max Planck Institute of Neurobiology), Planegg, Germany
- Max Planck Institute for Neurobiology of Behavior - caesar, Bonn, Germany
| | - Joseph C Donovan
- Max Planck Institute for Biological Intelligence (formerly Max Planck Institute of Neurobiology), Planegg, Germany
| | - Shachar Sherman
- Max Planck Institute for Biological Intelligence (formerly Max Planck Institute of Neurobiology), Planegg, Germany
| | | | - Herwig Baier
- Max Planck Institute for Biological Intelligence (formerly Max Planck Institute of Neurobiology), Planegg, Germany.
| | - Johannes Larsch
- Max Planck Institute for Biological Intelligence (formerly Max Planck Institute of Neurobiology), Planegg, Germany.
| |
Collapse
|
15
|
Bertram MG, Martin JM, McCallum ES, Alton LA, Brand JA, Brooks BW, Cerveny D, Fick J, Ford AT, Hellström G, Michelangeli M, Nakagawa S, Polverino G, Saaristo M, Sih A, Tan H, Tyler CR, Wong BB, Brodin T. Frontiers in quantifying wildlife behavioural responses to chemical pollution. Biol Rev Camb Philos Soc 2022; 97:1346-1364. [PMID: 35233915 PMCID: PMC9543409 DOI: 10.1111/brv.12844] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/13/2022] [Accepted: 02/16/2022] [Indexed: 12/26/2022]
Abstract
Animal behaviour is remarkably sensitive to disruption by chemical pollution, with widespread implications for ecological and evolutionary processes in contaminated wildlife populations. However, conventional approaches applied to study the impacts of chemical pollutants on wildlife behaviour seldom address the complexity of natural environments in which contamination occurs. The aim of this review is to guide the rapidly developing field of behavioural ecotoxicology towards increased environmental realism, ecological complexity, and mechanistic understanding. We identify research areas in ecology that to date have been largely overlooked within behavioural ecotoxicology but which promise to yield valuable insights, including within- and among-individual variation, social networks and collective behaviour, and multi-stressor interactions. Further, we feature methodological and technological innovations that enable the collection of data on pollutant-induced behavioural changes at an unprecedented resolution and scale in the laboratory and the field. In an era of rapid environmental change, there is an urgent need to advance our understanding of the real-world impacts of chemical pollution on wildlife behaviour. This review therefore provides a roadmap of the major outstanding questions in behavioural ecotoxicology and highlights the need for increased cross-talk with other disciplines in order to find the answers.
Collapse
Affiliation(s)
- Michael G. Bertram
- Department of Wildlife, Fish, and Environmental StudiesSwedish University of Agricultural SciencesSkogsmarksgränd 17UmeåVästerbottenSE‐907 36Sweden
| | - Jake M. Martin
- School of Biological SciencesMonash University25 Rainforest WalkMelbourneVictoria3800Australia
| | - Erin S. McCallum
- Department of Wildlife, Fish, and Environmental StudiesSwedish University of Agricultural SciencesSkogsmarksgränd 17UmeåVästerbottenSE‐907 36Sweden
| | - Lesley A. Alton
- School of Biological SciencesMonash University25 Rainforest WalkMelbourneVictoria3800Australia
| | - Jack A. Brand
- School of Biological SciencesMonash University25 Rainforest WalkMelbourneVictoria3800Australia
| | - Bryan W. Brooks
- Department of Environmental ScienceBaylor UniversityOne Bear PlaceWacoTexas76798‐7266U.S.A.
| | - Daniel Cerveny
- Department of Wildlife, Fish, and Environmental StudiesSwedish University of Agricultural SciencesSkogsmarksgränd 17UmeåVästerbottenSE‐907 36Sweden
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of HydrocenosesUniversity of South Bohemia in Ceske BudejoviceZátiší 728/IIVodnany389 25Czech Republic
| | - Jerker Fick
- Department of ChemistryUmeå UniversityLinnaeus väg 10UmeåVästerbottenSE‐907 36Sweden
| | - Alex T. Ford
- Institute of Marine SciencesUniversity of PortsmouthWinston Churchill Avenue, PortsmouthHampshirePO1 2UPU.K.
| | - Gustav Hellström
- Department of Wildlife, Fish, and Environmental StudiesSwedish University of Agricultural SciencesSkogsmarksgränd 17UmeåVästerbottenSE‐907 36Sweden
| | - Marcus Michelangeli
- Department of Wildlife, Fish, and Environmental StudiesSwedish University of Agricultural SciencesSkogsmarksgränd 17UmeåVästerbottenSE‐907 36Sweden
- Department of Environmental Science and PolicyUniversity of California350 E Quad, DavisCaliforniaCA95616U.S.A.
| | - Shinichi Nakagawa
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental SciencesUniversity of New South Wales, Biological Sciences West (D26)SydneyNSW2052Australia
| | - Giovanni Polverino
- School of Biological SciencesMonash University25 Rainforest WalkMelbourneVictoria3800Australia
- Centre for Evolutionary Biology, School of Biological SciencesUniversity of Western Australia35 Stirling HighwayPerthWA6009Australia
- Department of Ecological and Biological SciencesTuscia UniversityVia S.M. in Gradi n.4ViterboLazio01100Italy
| | - Minna Saaristo
- Environment Protection Authority VictoriaEPA Science2 Terrace WayMacleodVictoria3085Australia
| | - Andrew Sih
- Department of Environmental Science and PolicyUniversity of California350 E Quad, DavisCaliforniaCA95616U.S.A.
| | - Hung Tan
- School of Biological SciencesMonash University25 Rainforest WalkMelbourneVictoria3800Australia
| | - Charles R. Tyler
- Biosciences, College of Life and Environmental SciencesUniversity of ExeterStocker RoadExeterDevonEX4 4QDU.K.
| | - Bob B.M. Wong
- School of Biological SciencesMonash University25 Rainforest WalkMelbourneVictoria3800Australia
| | - Tomas Brodin
- Department of Wildlife, Fish, and Environmental StudiesSwedish University of Agricultural SciencesSkogsmarksgränd 17UmeåVästerbottenSE‐907 36Sweden
| |
Collapse
|
16
|
Ray S, Stopfer MA. Argos: A toolkit for tracking multiple animals in complex visual environments. Methods Ecol Evol 2022; 13:585-595. [PMID: 37920569 PMCID: PMC10621779 DOI: 10.1111/2041-210x.13776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 10/25/2021] [Indexed: 11/29/2022]
Abstract
Automatically tracking the positions of multiple animals is often necessary for studying behaviours. This task involves multiple object tracking, a challenging problem in computer vision. Recent advances in machine learning applied to video analysis have been helpful for animal tracking. However, existing tools work well only in homogeneous environments with uniform illumination, features rarely found in natural settings. Moreover, available algorithms cannot effectively process discontinuities in animal motion such as sudden jumps, thus requiring laborious manual review.Here we present Argos, a software toolkit for tracking multiple animals in inhomogeneous environments. Argos includes tools for compressing videos based on animal movement, for generating training sets for a convolutional neural network (CNN) to detect animals, for tracking multiple animals in a video and for facilitating review and correction of the tracks manually, with simple graphical user interfaces.We demonstrate that Argos can help reduce the amount of video data to be stored and analysed, speed up analysis and allow analysing difficult and ambiguous conditions in a scene.Thus, Argos supports multiple approaches to animal tracking suited for varying recording conditions and available computational resources. Together, these tools allow the recording and tracking of movements of multiple markerless animals in inhomogeneous environments over many hours.
Collapse
Affiliation(s)
- Subhasis Ray
- Section on Sensory Coding and Neural Ensembles, NICHD, NIH, Bethesda, MD, USA
| | - Mark A Stopfer
- Section on Sensory Coding and Neural Ensembles, NICHD, NIH, Bethesda, MD, USA
| |
Collapse
|
17
|
Kamkar S, Moghaddam HA, Lashgari R, Erlhagen W. Brain-inspired multiple-target tracking using Dynamic Neural Fields. Neural Netw 2022; 151:121-131. [DOI: 10.1016/j.neunet.2022.03.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 02/01/2022] [Accepted: 03/22/2022] [Indexed: 10/18/2022]
|
18
|
Goc GL, Lafaye J, Karpenko S, Bormuth V, Candelier R, Debrégeas G. Thermal modulation of Zebrafish exploratory statistics reveals constraints on individual behavioral variability. BMC Biol 2021; 19:208. [PMID: 34548084 PMCID: PMC8456632 DOI: 10.1186/s12915-021-01126-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/18/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Variability is a hallmark of animal behavior. It contributes to survival by endowing individuals and populations with the capacity to adapt to ever-changing environmental conditions. Intra-individual variability is thought to reflect both endogenous and exogenous modulations of the neural dynamics of the central nervous system. However, how variability is internally regulated and modulated by external cues remains elusive. Here, we address this question by analyzing the statistics of spontaneous exploration of freely swimming zebrafish larvae and by probing how these locomotor patterns are impacted when changing the water temperatures within an ethologically relevant range. RESULTS We show that, for this simple animal model, five short-term kinematic parameters - interbout interval, turn amplitude, travelled distance, turn probability, and orientational flipping rate - together control the long-term exploratory dynamics. We establish that the bath temperature consistently impacts the means of these parameters, but leave their pairwise covariance unchanged. These results indicate that the temperature merely controls the sampling statistics within a well-defined kinematic space delineated by this robust statistical structure. At a given temperature, individual animals explore the behavioral space over a timescale of tens of minutes, suggestive of a slow internal state modulation that could be externally biased through the bath temperature. By combining these various observations into a minimal stochastic model of navigation, we show that this thermal modulation of locomotor kinematics results in a thermophobic behavior, complementing direct gradient-sensing mechanisms. CONCLUSIONS This study establishes the existence of a well-defined locomotor space accessible to zebrafish larvae during spontaneous exploration, and quantifies self-generated modulation of locomotor patterns. Intra-individual variability reflects a slow diffusive-like probing of this space by the animal. The bath temperature in turn restricts the sampling statistics to sub-regions, endowing the animal with basic thermophobicity. This study suggests that in zebrafish, as well as in other ectothermic animals, ambient temperature could be used to efficiently manipulate internal states in a simple and ethological way.
Collapse
Affiliation(s)
- Guillaume Le Goc
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), Paris, France
| | - Julie Lafaye
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), Paris, France
| | - Sophia Karpenko
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), Paris, France.,Université Paris Sciences et Lettres, Paris, France.,Present address : Department of Collective Behavior, Max Planck Institute of Animal Behavior, Konstanz, Germany
| | - Volker Bormuth
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), Paris, France
| | - Raphaël Candelier
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), Paris, France
| | - Georges Debrégeas
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), Paris, France.
| |
Collapse
|