1
|
Yan Y, Murphy TH. Decoding state-dependent cortical-cerebellar cellular functional connectivity in the mouse brain. Cell Rep 2024; 43:114348. [PMID: 38865245 DOI: 10.1016/j.celrep.2024.114348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 04/16/2024] [Accepted: 05/26/2024] [Indexed: 06/14/2024] Open
Abstract
The cortex and cerebellum form multi-synaptic reciprocal connections. We investigate the functional connectivity between single spiking cerebellar neurons and the population activity of the mouse dorsal cortex using mesoscale imaging. Cortical representations of individual cerebellar neurons vary significantly across different brain states but are drawn from a common set of cortical networks. These cortical-cerebellar connectivity features are observed in mossy fibers and Purkinje cells as well as neurons in different cerebellar lobules, albeit with variations across cell types and regions. Complex spikes of Purkinje cells preferably associate with the sensorimotor cortex, whereas simple spikes display more diverse cortical connectivity patterns. The spontaneous functional connectivity patterns align with cerebellar neurons' functional responses to external stimuli in a modality-specific manner. The tuning properties of subsets of cerebellar neurons differ between anesthesia and awake states, mirrored by state-dependent changes in their long-range functional connectivity patterns with mesoscale cortical activity.
Collapse
Affiliation(s)
- Yuhao Yan
- Department of Psychiatry, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
| | - Timothy H Murphy
- Department of Psychiatry, Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada.
| |
Collapse
|
2
|
Choi YK, Feng L, Jeong WK, Kim J. Connecto-informatics at the mesoscale: current advances in image processing and analysis for mapping the brain connectivity. Brain Inform 2024; 11:15. [PMID: 38833195 DOI: 10.1186/s40708-024-00228-9] [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: 03/29/2024] [Accepted: 05/08/2024] [Indexed: 06/06/2024] Open
Abstract
Mapping neural connections within the brain has been a fundamental goal in neuroscience to understand better its functions and changes that follow aging and diseases. Developments in imaging technology, such as microscopy and labeling tools, have allowed researchers to visualize this connectivity through high-resolution brain-wide imaging. With this, image processing and analysis have become more crucial. However, despite the wealth of neural images generated, access to an integrated image processing and analysis pipeline to process these data is challenging due to scattered information on available tools and methods. To map the neural connections, registration to atlases and feature extraction through segmentation and signal detection are necessary. In this review, our goal is to provide an updated overview of recent advances in these image-processing methods, with a particular focus on fluorescent images of the mouse brain. Our goal is to outline a pathway toward an integrated image-processing pipeline tailored for connecto-informatics. An integrated workflow of these image processing will facilitate researchers' approach to mapping brain connectivity to better understand complex brain networks and their underlying brain functions. By highlighting the image-processing tools available for fluroscent imaging of the mouse brain, this review will contribute to a deeper grasp of connecto-informatics, paving the way for better comprehension of brain connectivity and its implications.
Collapse
Affiliation(s)
- Yoon Kyoung Choi
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, South Korea
- Department of Computer Science and Engineering, Korea University, Seoul, South Korea
| | | | - Won-Ki Jeong
- Department of Computer Science and Engineering, Korea University, Seoul, South Korea
| | - Jinhyun Kim
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, South Korea.
- Department of Computer Science and Engineering, Korea University, Seoul, South Korea.
- KIST-SKKU Brain Research Center, SKKU Institute for Convergence, Sungkyunkwan University, Suwon, South Korea.
| |
Collapse
|
3
|
Lambert T, Brunner C, Kil D, Wuyts R, D'Hondt E, Montaldo G, Urban A. A deep learning classification task for brain navigation in rodents using micro-Doppler ultrasound imaging. Heliyon 2024; 10:e27432. [PMID: 38495198 PMCID: PMC10943389 DOI: 10.1016/j.heliyon.2024.e27432] [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: 06/15/2023] [Revised: 02/28/2024] [Accepted: 02/28/2024] [Indexed: 03/19/2024] Open
Abstract
Positioning and navigation are essential components of neuroimaging as they improve the quality and reliability of data acquisition, leading to advances in diagnosis, treatment outcomes, and fundamental understanding of the brain. Functional ultrasound imaging is an emerging technology providing high-resolution images of the brain vasculature, allowing for the monitoring of brain activity. However, as the technology is relatively new, there is no standardized tool for inferring the position in the brain from the vascular images. In this study, we present a deep learning-based framework designed to address this challenge. Our approach uses an image classification task coupled with a regression on the resulting probabilities to determine the position of a single image. To evaluate its performance, we conducted experiments using a dataset of 51 rat brain scans. The training positions were extracted at intervals of 375 μm, resulting in a positioning error of 176 μm. Further GradCAM analysis revealed that the predictions were primarily driven by subcortical vascular structures. Finally, we assessed the robustness of our method in a cortical stroke where the brain vasculature is severely impaired. Remarkably, no specific increase in the number of misclassifications was observed, confirming the method's reliability in challenging conditions. Overall, our framework provides accurate and flexible positioning, not relying on a pre-registered reference but rather on conserved vascular patterns.
Collapse
Affiliation(s)
- Théo Lambert
- Neuro-Electronics Research Flanders, Leuven, Belgium
- VIB, Leuven, Belgium
- Imec, Leuven, Belgium
- Department of Neuroscience, Faculty of Medicine, KU Leuven, Leuven, Belgium
| | - Clément Brunner
- Neuro-Electronics Research Flanders, Leuven, Belgium
- VIB, Leuven, Belgium
- Imec, Leuven, Belgium
- Department of Neuroscience, Faculty of Medicine, KU Leuven, Leuven, Belgium
| | - Dries Kil
- Neuro-Electronics Research Flanders, Leuven, Belgium
- VIB, Leuven, Belgium
- Imec, Leuven, Belgium
- Department of Neuroscience, Faculty of Medicine, KU Leuven, Leuven, Belgium
| | | | | | - Gabriel Montaldo
- Neuro-Electronics Research Flanders, Leuven, Belgium
- VIB, Leuven, Belgium
- Imec, Leuven, Belgium
- Department of Neuroscience, Faculty of Medicine, KU Leuven, Leuven, Belgium
| | - Alan Urban
- Neuro-Electronics Research Flanders, Leuven, Belgium
- VIB, Leuven, Belgium
- Imec, Leuven, Belgium
- Department of Neuroscience, Faculty of Medicine, KU Leuven, Leuven, Belgium
| |
Collapse
|
4
|
Bottom-Tanzer S, Corella S, Meyer J, Sommer M, Bolaños L, Murphy T, Quiñones S, Heiney S, Shtrahman M, Whalen M, Oren R, Higley MJ, Cardin JA, Noubary F, Armbruster M, Dulla C. Traumatic brain injury disrupts state-dependent functional cortical connectivity in a mouse model. Cereb Cortex 2024; 34:bhae038. [PMID: 38365273 DOI: 10.1093/cercor/bhae038] [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] [Received: 10/16/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/18/2024] Open
Abstract
Traumatic brain injury (TBI) is the leading cause of death in young people and can cause cognitive and motor dysfunction and disruptions in functional connectivity between brain regions. In human TBI patients and rodent models of TBI, functional connectivity is decreased after injury. Recovery of connectivity after TBI is associated with improved cognition and memory, suggesting an important link between connectivity and functional outcome. We examined widespread alterations in functional connectivity following TBI using simultaneous widefield mesoscale GCaMP7c calcium imaging and electrocorticography (ECoG) in mice injured using the controlled cortical impact (CCI) model of TBI. Combining CCI with widefield cortical imaging provides us with unprecedented access to characterize network connectivity changes throughout the entire injured cortex over time. Our data demonstrate that CCI profoundly disrupts functional connectivity immediately after injury, followed by partial recovery over 3 weeks. Examining discrete periods of locomotion and stillness reveals that CCI alters functional connectivity and reduces theta power only during periods of behavioral stillness. Together, these findings demonstrate that TBI causes dynamic, behavioral state-dependent changes in functional connectivity and ECoG activity across the cortex.
Collapse
Affiliation(s)
- Samantha Bottom-Tanzer
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA 02111, United States
- MD/PhD Program, Tufts University School of Medicine, Boston, MA 02111, United States
- Neuroscience Program, Tufts Graduate School of Biomedical Sciences, Boston, MA 02111, United States
| | - Sofia Corella
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, United States
- MD/PhD Program, Case Western Reserve University School of Medicine, Cleveland, OH 44106, United States
| | - Jochen Meyer
- Department of Neurology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Mary Sommer
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA 02111, United States
| | - Luis Bolaños
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Timothy Murphy
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Sadi Quiñones
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA 02111, United States
- Neuroscience Program, Tufts Graduate School of Biomedical Sciences, Boston, MA 02111, United States
| | - Shane Heiney
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA 52242, United States
| | - Matthew Shtrahman
- Department of Neurosciences, University of California San Diego, La Jolla, CA 92093, United States
| | - Michael Whalen
- Department of Pediatrics, Harvard Medical School, Massachusetts General Hospital, Boston, MA 02115, United States
| | - Rachel Oren
- Department of Neuroscience, Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, United States
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT 06510, United States
| | - Michael J Higley
- Department of Neuroscience, Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, United States
| | - Jessica A Cardin
- Department of Neuroscience, Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, United States
| | - Farzad Noubary
- Department of Health Sciences, Northeastern University, Boston, MA 02115, United States
| | - Moritz Armbruster
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA 02111, United States
| | - Chris Dulla
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA 02111, United States
| |
Collapse
|
5
|
Xiao D, Yan Y, Murphy TH. Mesotrode chronic simultaneous mesoscale cortical imaging and subcortical or peripheral nerve spiking activity recording in mice. eLife 2023; 12:RP87691. [PMID: 37962180 PMCID: PMC10645427 DOI: 10.7554/elife.87691] [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: 11/15/2023] Open
Abstract
Brain function originates from hierarchical spatial-temporal neural dynamics distributed across cortical and subcortical networks. However, techniques available to assess large-scale brain network activity with single-neuron resolution in behaving animals remain limited. Here, we present Mesotrode that integrates chronic wide-field mesoscale cortical imaging and compact multi-site cortical/subcortical cellular electrophysiology in head-fixed mice that undergo self-initiated running or orofacial movements. Specifically, we harnessed the flexibility of chronic multi-site tetrode recordings to monitor single-neuron activity in multiple subcortical structures while simultaneously imaging the mesoscale activity of the entire dorsal cortex. A mesoscale spike-triggered averaging procedure allowed the identification of cortical activity motifs preferentially associated with single-neuron spiking. Using this approach, we were able to characterize chronic single-neuron-related functional connectivity maps for up to 60 days post-implantation. Neurons recorded from distinct subcortical structures display diverse but segregated cortical maps, suggesting that neurons of different origins participate in distinct cortico-subcortical pathways. We extended the capability of Mesotrode by implanting the micro-electrode at the facial motor nerve and found that facial nerve spiking is functionally associated with the PTA, RSP, and M2 network, and optogenetic inhibition of the PTA area significantly reduced the facial movement of the mice. These findings demonstrate that Mesotrode can be used to sample different combinations of cortico-subcortical networks over prolonged periods, generating multimodal and multi-scale network activity from a single implant, offering new insights into the neural mechanisms underlying specific behaviors.
Collapse
Affiliation(s)
- Dongsheng Xiao
- University of British Columbia, Department of Psychiatry, Kinsmen Laboratory of Neurological ResearchVancouverCanada
- Djavad Mowafaghian Centre for Brain Health, University of British ColumbiaVancouverCanada
| | - Yuhao Yan
- University of British Columbia, Department of Psychiatry, Kinsmen Laboratory of Neurological ResearchVancouverCanada
- Djavad Mowafaghian Centre for Brain Health, University of British ColumbiaVancouverCanada
| | - Timothy H Murphy
- University of British Columbia, Department of Psychiatry, Kinsmen Laboratory of Neurological ResearchVancouverCanada
- Djavad Mowafaghian Centre for Brain Health, University of British ColumbiaVancouverCanada
| |
Collapse
|
6
|
Leikvoll A, Kara P. High fidelity sensory-evoked responses in neocortex after intravenous injection of genetically encoded calcium sensors. Front Neurosci 2023; 17:1181828. [PMID: 37250396 PMCID: PMC10213453 DOI: 10.3389/fnins.2023.1181828] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 04/12/2023] [Indexed: 05/31/2023] Open
Abstract
Two-photon imaging of genetically-encoded calcium indicators (GECIs) has traditionally relied on intracranial injections of adeno-associated virus (AAV) or transgenic animals to achieve expression. Intracranial injections require an invasive surgery and result in a relatively small volume of tissue labeling. Transgenic animals, although they can have brain-wide GECI expression, often express GECIs in only a small subset of neurons, may have abnormal behavioral phenotypes, and are currently limited to older generations of GECIs. Inspired by recent developments in the synthesis of AAVs that readily cross the blood brain barrier, we tested whether an alternative strategy of intravenously injecting AAV-PHP.eB is suitable for two-photon calcium imaging of neurons over many months after injection. We injected C57BL/6 J mice with AAV-PHP.eB-Synapsin-jGCaMP7s via the retro-orbital sinus. After allowing 5 to 34 weeks for expression, we performed conventional and widefield two-photon imaging of layers 2/3, 4 and 5 of the primary visual cortex. We found reproducible trial-by-trial neural responses and tuning properties consistent with known feature selectivity in the visual cortex. Thus, intravenous injection of AAV-PHP.eB does not interfere with the normal processing in neural circuits. In vivo and histological images show no nuclear expression of jGCaMP7s for at least 34 weeks post-injection.
Collapse
Affiliation(s)
| | - Prakash Kara
- Department of Neuroscience, University of Minnesota, Minneapolis, MN, United States
| |
Collapse
|
7
|
McElliott MC, Al-Suraimi A, Telang AC, Ference-Salo JT, Chowdhury M, Soofi A, Dressler GR, Beamish JA. High-throughput image analysis with deep learning captures heterogeneity and spatial relationships after kidney injury. Sci Rep 2023; 13:6361. [PMID: 37076596 PMCID: PMC10115810 DOI: 10.1038/s41598-023-33433-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 04/12/2023] [Indexed: 04/21/2023] Open
Abstract
Recovery from acute kidney injury can vary widely in patients and in animal models. Immunofluorescence staining can provide spatial information about heterogeneous injury responses, but often only a fraction of stained tissue is analyzed. Deep learning can expand analysis to larger areas and sample numbers by substituting for time-intensive manual or semi-automated quantification techniques. Here we report one approach to leverage deep learning tools to quantify heterogenous responses to kidney injury that can be deployed without specialized equipment or programming expertise. We first demonstrated that deep learning models generated from small training sets accurately identified a range of stains and structures with performance similar to that of trained human observers. We then showed this approach accurately tracks the evolution of folic acid induced kidney injury in mice and highlights spatially clustered tubules that fail to repair. We then demonstrated that this approach captures the variation in recovery across a robust sample of kidneys after ischemic injury. Finally, we showed markers of failed repair after ischemic injury were correlated both spatially within and between animals and that failed repair was inversely correlated with peritubular capillary density. Combined, we demonstrate the utility and versatility of our approach to capture spatially heterogenous responses to kidney injury.
Collapse
Affiliation(s)
- Madison C McElliott
- Division of Nephrology, Department of Internal Medicine, University of Michigan, 1500 E. Medical Center Drive, SPC 5364, Ann Arbor, MI, 48109, USA
| | - Anas Al-Suraimi
- Division of Nephrology, Department of Internal Medicine, University of Michigan, 1500 E. Medical Center Drive, SPC 5364, Ann Arbor, MI, 48109, USA
| | - Asha C Telang
- Division of Nephrology, Department of Internal Medicine, University of Michigan, 1500 E. Medical Center Drive, SPC 5364, Ann Arbor, MI, 48109, USA
| | - Jenna T Ference-Salo
- Division of Nephrology, Department of Internal Medicine, University of Michigan, 1500 E. Medical Center Drive, SPC 5364, Ann Arbor, MI, 48109, USA
| | - Mahboob Chowdhury
- Division of Nephrology, Department of Internal Medicine, University of Michigan, 1500 E. Medical Center Drive, SPC 5364, Ann Arbor, MI, 48109, USA
| | - Abdul Soofi
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | - Jeffrey A Beamish
- Division of Nephrology, Department of Internal Medicine, University of Michigan, 1500 E. Medical Center Drive, SPC 5364, Ann Arbor, MI, 48109, USA.
| |
Collapse
|
8
|
Alonso I, Scheer I, Palacio-Manzano M, Frézel-Jacob N, Philippides A, Prsa M. Peripersonal encoding of forelimb proprioception in the mouse somatosensory cortex. Nat Commun 2023; 14:1866. [PMID: 37045825 PMCID: PMC10097678 DOI: 10.1038/s41467-023-37575-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 03/23/2023] [Indexed: 04/14/2023] Open
Abstract
Conscious perception of limb movements depends on proprioceptive neural responses in the somatosensory cortex. In contrast to tactile sensations, proprioceptive cortical coding is barely studied in the mammalian brain and practically non-existent in rodent research. To understand the cortical representation of this important sensory modality we developed a passive forelimb displacement paradigm in behaving mice and also trained them to perceptually discriminate where their limb is moved in space. We delineated the rodent proprioceptive cortex with wide-field calcium imaging and optogenetic silencing experiments during behavior. Our results reveal that proprioception is represented in both sensory and motor cortical areas. In addition, behavioral measurements and responses of layer 2/3 neurons imaged with two-photon microscopy reveal that passive limb movements are both perceived and encoded in the mouse cortex as a spatial direction vector that interfaces the limb with the body's peripersonal space.
Collapse
Affiliation(s)
- Ignacio Alonso
- Department of Neuroscience and Movement Science, University of Fribourg, Fribourg, Switzerland
| | - Irina Scheer
- Department of Neuroscience and Movement Science, University of Fribourg, Fribourg, Switzerland
| | - Mélanie Palacio-Manzano
- Department of Neuroscience and Movement Science, University of Fribourg, Fribourg, Switzerland
| | - Noémie Frézel-Jacob
- Department of Neuroscience and Movement Science, University of Fribourg, Fribourg, Switzerland
| | - Antoine Philippides
- Department of Basic Neurosciences, University of Geneva, Geneva, Switzerland
| | - Mario Prsa
- Department of Neuroscience and Movement Science, University of Fribourg, Fribourg, Switzerland.
| |
Collapse
|
9
|
Leikvoll A, Kara P. High fidelity sensory-evoked responses in neocortex after intravenous injection of genetically encoded calcium sensors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.09.531938. [PMID: 36945523 PMCID: PMC10028972 DOI: 10.1101/2023.03.09.531938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Two-photon imaging of genetically-encoded calcium indicators (GECIs) has traditionally relied on intracranial injections of adeno-associated virus (AAV) or transgenic animals to achieve expression. Intracranial injections require an invasive surgery and result in a relatively small volume of tissue labeling. Transgenic animals, although they can have brain-wide GECI expression, often express GECIs in only a small subset of neurons, may have abnormal behavioral phenotypes, and are currently limited to older generations of GECIs. Inspired by recent developments in the synthesis of AAVs that readily cross the blood brain barrier, we tested whether an alternative strategy of intravenously injecting AAV-PhP.eB is suitable for two-photon calcium imaging of neurons over many months after injection. We injected young (postnatal day 23 to 31) C57BL/6J mice with AAV-PhP.eB-Synapsin-jGCaMP7s via the retro-orbital sinus. After allowing 5 to 34 weeks for expression, we performed conventional and widefield two-photon imaging of layers 2/3, 4 and 5 of the primary visual cortex. We found reproducible trial-by-trial neural responses and tuning properties consistent with known feature selectivity in the visual cortex. Thus, intravenous injection of AAV-PhP.eB does not interfere with the normal processing in neural circuits. In vivo and histological images show no nuclear expression of jGCaMP7s for at least 34 weeks post-injection.
Collapse
|
10
|
Nietz AK, Streng ML, Popa LS, Carter RE, Flaherty EB, Aronson JD, Ebner TJ. To be and not to be: wide-field Ca2+ imaging reveals neocortical functional segmentation combines stability and flexibility. Cereb Cortex 2023:7024718. [PMID: 36734268 DOI: 10.1093/cercor/bhac523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 12/09/2022] [Accepted: 12/10/2022] [Indexed: 02/04/2023] Open
Abstract
The stability and flexibility of the functional parcellation of the cerebral cortex is fundamental to how familiar and novel information is both represented and stored. We leveraged new advances in Ca2+ sensors and microscopy to understand the dynamics of functional segmentation in the dorsal cerebral cortex. We performed wide-field Ca2+ imaging in head-fixed mice and used spatial independent component analysis (ICA) to identify independent spatial sources of Ca2+ fluorescence. The imaging data were evaluated over multiple timescales and discrete behaviors including resting, walking, and grooming. When evaluated over the entire dataset, a set of template independent components (ICs) were identified that were common across behaviors. Template ICs were present across a range of timescales, from days to 30 seconds, although with lower occurrence probability at shorter timescales, highlighting the stability of the functional segmentation. Importantly, unique ICs emerged at the shorter duration timescales that could act to transiently refine the cortical network. When data were evaluated by behavior, both common and behavior-specific ICs emerged. Each behavior is composed of unique combinations of common and behavior-specific ICs. These observations suggest that cerebral cortical functional segmentation exhibits considerable spatial stability over time and behaviors while retaining the flexibility for task-dependent reorganization.
Collapse
Affiliation(s)
- Angela K Nietz
- Department of Neuroscience, University of Minnesota, 2001 Sixth Street S.E., Minneapolis 55455, MN, United States
| | - Martha L Streng
- Department of Neuroscience, University of Minnesota, 2001 Sixth Street S.E., Minneapolis 55455, MN, United States
| | - Laurentiu S Popa
- Department of Neuroscience, University of Minnesota, 2001 Sixth Street S.E., Minneapolis 55455, MN, United States
| | - Russell E Carter
- Department of Neuroscience, University of Minnesota, 2001 Sixth Street S.E., Minneapolis 55455, MN, United States
| | - Evelyn B Flaherty
- Department of Neuroscience, University of Minnesota, 2001 Sixth Street S.E., Minneapolis 55455, MN, United States
| | - Justin D Aronson
- Department of Neuroscience, University of Minnesota, 2001 Sixth Street S.E., Minneapolis 55455, MN, United States
| | - Timothy J Ebner
- Department of Neuroscience, University of Minnesota, 2001 Sixth Street S.E., Minneapolis 55455, MN, United States
| |
Collapse
|
11
|
Bauer J, Devinsky O, Rothermel M, Koch H. Autonomic dysfunction in epilepsy mouse models with implications for SUDEP research. Front Neurol 2023; 13:1040648. [PMID: 36686527 PMCID: PMC9853197 DOI: 10.3389/fneur.2022.1040648] [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: 09/09/2022] [Accepted: 12/12/2022] [Indexed: 01/09/2023] Open
Abstract
Epilepsy has a high prevalence and can severely impair quality of life and increase the risk of premature death. Sudden unexpected death in epilepsy (SUDEP) is the leading cause of death in drug-resistant epilepsy and most often results from respiratory and cardiac impairments due to brainstem dysfunction. Epileptic activity can spread widely, influencing neuronal activity in regions outside the epileptic network. The brainstem controls cardiorespiratory activity and arousal and reciprocally connects to cortical, diencephalic, and spinal cord areas. Epileptic activity can propagate trans-synaptically or via spreading depression (SD) to alter brainstem functions and cause cardiorespiratory dysfunction. The mechanisms by which seizures propagate to or otherwise impair brainstem function and trigger the cascading effects that cause SUDEP are poorly understood. We review insights from mouse models combined with new techniques to understand the pathophysiology of epilepsy and SUDEP. These techniques include in vivo, ex vivo, invasive and non-invasive methods in anesthetized and awake mice. Optogenetics combined with electrophysiological and optical manipulation and recording methods offer unique opportunities to study neuronal mechanisms under normal conditions, during and after non-fatal seizures, and in SUDEP. These combined approaches can advance our understanding of brainstem pathophysiology associated with seizures and SUDEP and may suggest strategies to prevent SUDEP.
Collapse
Affiliation(s)
- Jennifer Bauer
- Department of Epileptology and Neurology, RWTH Aachen University, Aachen, Germany,Institute for Physiology and Cell Biology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Orrin Devinsky
- Departments of Neurology, Neurosurgery and Psychiatry, NYU Langone School of Medicine, New York, NY, United States
| | - Markus Rothermel
- Institute for Physiology and Cell Biology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Henner Koch
- Department of Epileptology and Neurology, RWTH Aachen University, Aachen, Germany,*Correspondence: Henner Koch ✉
| |
Collapse
|
12
|
Ramandi D, Michelson NJ, Raymond LA, Murphy TH. Chronic multiscale resolution of mouse brain networks using combined mesoscale cortical imaging and subcortical fiber photometry. NEUROPHOTONICS 2023; 10:015001. [PMID: 36694618 PMCID: PMC9867602 DOI: 10.1117/1.nph.10.1.015001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
SIGNIFICANCE Genetically encoded optical probes to image calcium levels in neurons in vivo are used widely as a real-time measure of neuronal activity in the brain. Mesoscale calcium imaging through a cranial window provides a method of studying the interaction of circuit activity between cortical areas but lacks access to subcortical regions. AIM We have developed an optical and surgical preparation that preserves wide-field imaging of the cortical surface while also permitting access to specific subcortical networks. APPROACH This was achieved using an optical fiber implanted in the striatum, along with a bilateral widefield cranial window, enabling simultaneous mesoscale cortical imaging and subcortical fiber photometry recording of calcium signals in a transgenic animal expressing GCaMP. Subcortical signals were collected from the dorsal regions of the striatum. We combined this approach with multiple sensory-motor tasks, including specific auditory and visual stimulation, and video monitoring of animal movements and pupillometry during head-fixed behaviors. RESULTS We found high correlations between cortical and striatal activity in response to sensory stimulation or movement. Furthermore, spontaneous activity recordings revealed that specific motifs of cortical activity are correlated with presynaptic activity recorded in the striatum, enabling us to select for corticostriatal activity motifs. CONCLUSION We believe that this method can be utilized to reveal not only global patterns but also cell-specific connectivity that provides insight into corticobasal ganglia circuit organization.
Collapse
Affiliation(s)
- Daniel Ramandi
- University of British Columbia, Djavad Mowafaghian Centre for Brain Health, Department of Psychiatry, Vancouver, British Columbia, Canada
| | - Nicholas J. Michelson
- University of British Columbia, Djavad Mowafaghian Centre for Brain Health, Department of Psychiatry, Vancouver, British Columbia, Canada
| | - Lynn A. Raymond
- University of British Columbia, Djavad Mowafaghian Centre for Brain Health, Department of Psychiatry, Vancouver, British Columbia, Canada
| | - Timothy H. Murphy
- University of British Columbia, Djavad Mowafaghian Centre for Brain Health, Department of Psychiatry, Vancouver, British Columbia, Canada
| |
Collapse
|
13
|
Water-Reaching Platform for Longitudinal Assessment of Cortical Activity and Fine Motor Coordination Defects in a Huntington Disease Mouse Model. eNeuro 2023; 10:ENEURO.0452-22.2022. [PMID: 36596592 PMCID: PMC9833054 DOI: 10.1523/eneuro.0452-22.2022] [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: 11/06/2022] [Accepted: 12/20/2022] [Indexed: 01/05/2023] Open
Abstract
Huntington disease (HD), caused by dominantly inherited expansions of a CAG repeat results in characteristic motor dysfunction. Although gross motor defects have been extensively characterized in multiple HD mouse models using tasks such as rotarod and beam walking, less is known about forelimb deficits. We develop a high-throughput alternating reward/nonreward water-reaching task and training protocol conducted daily over approximately two months to simultaneously monitor forelimb impairment and mesoscale cortical changes in GCaMP activity, comparing female zQ175 (HD) and wild-type (WT) littermate mice, starting at ∼5.5 months. Behavioral analysis of the water-reaching task reveals that HD mice, despite learning the water-reaching task as proficiently as wild-type mice, take longer to learn the alternating event sequence as evident by impulsive (noncued) reaches and initially display reduced cortical activity associated with successful reaches. At this age gross motor defects determined by tapered beam assessment were not apparent. Although wild-type mice displayed no significant changes in cortical activity and reaching trajectory throughout the testing period, HD mice exhibited an increase in cortical activity, especially in the secondary motor and retrosplenial cortices, over time, as well as longer and more variable reaching trajectories by approximately seven months. HD mice also experienced a progressive reduction in successful performance. Tapered beam and rotarod tests as well as reduced DARPP-32 expression (striatal medium spiny neuron marker) after water-reaching assessment confirmed HD pathology. The water-reaching task can be used to inform on a daily basis, HD and other movement disorder onset and manifestation, therapeutic intervention windows, and test drug efficacy.
Collapse
|
14
|
O'Connor D, Mandino F, Shen X, Horien C, Ge X, Herman P, Hyder F, Crair M, Papademetris X, Lake E, Constable RT. Functional network properties derived from wide-field calcium imaging differ with wakefulness and across cell type. Neuroimage 2022; 264:119735. [PMID: 36347441 PMCID: PMC9808917 DOI: 10.1016/j.neuroimage.2022.119735] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/21/2022] [Accepted: 11/04/2022] [Indexed: 11/08/2022] Open
Abstract
To improve 'bench-to-bedside' translation, it is integral that knowledge flows bidirectionally-from animal models to humans, and vice versa. This requires common analytical frameworks, as well as open software and data sharing practices. We share a new pipeline (and test dataset) for the preprocessing of wide-field optical fluorescence imaging data-an emerging mode applicable in animal models-as well as results from a functional connectivity and graph theory analysis inspired by recent work in the human neuroimaging field. The approach is demonstrated using a dataset comprised of two test-cases: (1) data from animals imaged during awake and anesthetized conditions with excitatory neurons labeled, and (2) data from awake animals with different genetically encoded fluorescent labels that target either excitatory neurons or inhibitory interneuron subtypes. Both seed-based connectivity and graph theory measures (global efficiency, transitivity, modularity, and characteristic path-length) are shown to be useful in quantifying differences between wakefulness states and cell populations. Wakefulness state and cell type show widespread effects on canonical network connectivity with variable frequency band dependence. Differences between excitatory neurons and inhibitory interneurons are observed, with somatostatin expressing inhibitory interneurons emerging as notably dissimilar from parvalbumin and vasoactive polypeptide expressing cells. In sum, we demonstrate that our pipeline can be used to examine brain state and cell-type differences in mesoscale imaging data, aiding translational neuroscience efforts. In line with open science practices, we freely release the pipeline and data to encourage other efforts in the community.
Collapse
Affiliation(s)
- D O'Connor
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
| | - F Mandino
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
| | - X Shen
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
| | - C Horien
- Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT, USA
| | - X Ge
- Department of Physiology, School of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - P Herman
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
| | - F Hyder
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA; Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
| | - M Crair
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA; Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA; Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, CT, USA
| | - X Papademetris
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA; Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
| | - Emr Lake
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA
| | - R T Constable
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT, USA; Interdepartmental Neuroscience Program, Yale School of Medicine, New Haven, CT, USA; Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| |
Collapse
|
15
|
Wang Y, LeDue JM, Murphy TH. Multiscale imaging informs translational mouse modeling of neurological disease. Neuron 2022; 110:3688-3710. [PMID: 36198319 DOI: 10.1016/j.neuron.2022.09.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/26/2022] [Accepted: 09/06/2022] [Indexed: 11/05/2022]
Abstract
Multiscale neurophysiology reveals that simple motor actions are associated with changes in neuronal firing in virtually every brain region studied. Accordingly, the assessment of focal pathology such as stroke or progressive neurodegenerative diseases must also extend widely across brain areas. To derive mechanistic information through imaging, multiple resolution scales and multimodal factors must be included, such as the structure and function of specific neurons and glial cells and the dynamics of specific neurotransmitters. Emerging multiscale methods in preclinical animal studies that span micro- to macroscale examinations fill this gap, allowing a circuit-based understanding of pathophysiological mechanisms. Combined with high-performance computation and open-source data repositories, these emerging multiscale and large field-of-view techniques include live functional ultrasound, multi- and single-photon wide-scale light microscopy, video-based miniscopes, and tissue-penetrating fiber photometry, as well as variants of post-mortem expansion microscopy. We present these technologies and outline use cases and data pipelines to uncover new knowledge within animal models of stroke, Alzheimer's disease, and movement disorders.
Collapse
Affiliation(s)
- Yundi Wang
- University of British Columbia, Department of Psychiatry, Kinsmen Laboratory of Neurological Research, Detwiller Pavilion, 2255 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada; Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2215 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| | - Jeffrey M LeDue
- University of British Columbia, Department of Psychiatry, Kinsmen Laboratory of Neurological Research, Detwiller Pavilion, 2255 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada; Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2215 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| | - Timothy H Murphy
- University of British Columbia, Department of Psychiatry, Kinsmen Laboratory of Neurological Research, Detwiller Pavilion, 2255 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada; Djavad Mowafaghian Centre for Brain Health, University of British Columbia, 2215 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada.
| |
Collapse
|
16
|
MacDowell CJ, Tafazoli S, Buschman TJ. A Goldilocks theory of cognitive control: Balancing precision and efficiency with low-dimensional control states. Curr Opin Neurobiol 2022; 76:102606. [PMID: 35870301 PMCID: PMC9653176 DOI: 10.1016/j.conb.2022.102606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/11/2022] [Accepted: 06/16/2022] [Indexed: 12/11/2022]
Abstract
Cognitive control orchestrates interactions between brain regions, guiding the transformation of information to support contextually appropriate and goal-directed behaviors. In this review, we propose a hierarchical model of cognitive control where low-dimensional control states direct the flow of high-dimensional representations between regions. This allows cognitive control to flexibly adapt to new environments and maintain the representational capacity to capture the richness of the world.
Collapse
Affiliation(s)
- Camden J MacDowell
- Princeton Neuroscience Institute, Princeton University, Washington Rd, Princeton, NJ, USA; Rutgers Robert Wood Johnson Medical School, 125 Paterson St, New Brunswick, NJ, USA. https://twitter.com/CamdenMacdowell
| | - Sina Tafazoli
- Princeton Neuroscience Institute, Princeton University, Washington Rd, Princeton, NJ, USA. https://twitter.com/tafazolisina
| | - Timothy J Buschman
- Princeton Neuroscience Institute, Princeton University, Washington Rd, Princeton, NJ, USA; Department of Psychology, Princeton University, Washington Rd, Princeton, NJ, USA.
| |
Collapse
|