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Paveliev M, Egorchev AA, Musin F, Lipachev N, Melnikova A, Gimadutdinov RM, Kashipov AR, Molotkov D, Chickrin DE, Aganov AV. Perineuronal Net Microscopy: From Brain Pathology to Artificial Intelligence. Int J Mol Sci 2024; 25:4227. [PMID: 38673819 PMCID: PMC11049984 DOI: 10.3390/ijms25084227] [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: 02/02/2024] [Revised: 03/31/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Perineuronal nets (PNN) are a special highly structured type of extracellular matrix encapsulating synapses on large populations of CNS neurons. PNN undergo structural changes in schizophrenia, epilepsy, Alzheimer's disease, stroke, post-traumatic conditions, and some other brain disorders. The functional role of the PNN microstructure in brain pathologies has remained largely unstudied until recently. Here, we review recent research implicating PNN microstructural changes in schizophrenia and other disorders. We further concentrate on high-resolution studies of the PNN mesh units surrounding synaptic boutons to elucidate fine structural details behind the mutual functional regulation between the ECM and the synaptic terminal. We also review some updates regarding PNN as a potential pharmacological target. Artificial intelligence (AI)-based methods are now arriving as a new tool that may have the potential to grasp the brain's complexity through a wide range of organization levels-from synaptic molecular events to large scale tissue rearrangements and the whole-brain connectome function. This scope matches exactly the complex role of PNN in brain physiology and pathology processes, and the first AI-assisted PNN microscopy studies have been reported. To that end, we report here on a machine learning-assisted tool for PNN mesh contour tracing.
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Affiliation(s)
- Mikhail Paveliev
- Neuroscience Center, University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland
| | - Anton A. Egorchev
- Institute of Computational Mathematics and Information Technologies, Kazan Federal University, Kremlyovskaya 35, Kazan 420008, Tatarstan, Russia; (A.A.E.); (F.M.); (R.M.G.)
| | - Foat Musin
- Institute of Computational Mathematics and Information Technologies, Kazan Federal University, Kremlyovskaya 35, Kazan 420008, Tatarstan, Russia; (A.A.E.); (F.M.); (R.M.G.)
| | - Nikita Lipachev
- Institute of Physics, Kazan Federal University, Kremlyovskaya 16a, Kazan 420008, Tatarstan, Russia; (N.L.); (A.V.A.)
| | - Anastasiia Melnikova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Karl Marx 74, Kazan 420015, Tatarstan, Russia;
| | - Rustem M. Gimadutdinov
- Institute of Computational Mathematics and Information Technologies, Kazan Federal University, Kremlyovskaya 35, Kazan 420008, Tatarstan, Russia; (A.A.E.); (F.M.); (R.M.G.)
| | - Aidar R. Kashipov
- Institute of Artificial Intelligence, Robotics and Systems Engineering, Kazan Federal University, Kremlyovskaya 18, Kazan 420008, Tatarstan, Russia; (A.R.K.); (D.E.C.)
| | - Dmitry Molotkov
- Biomedicum Imaging Unit, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland;
| | - Dmitry E. Chickrin
- Institute of Artificial Intelligence, Robotics and Systems Engineering, Kazan Federal University, Kremlyovskaya 18, Kazan 420008, Tatarstan, Russia; (A.R.K.); (D.E.C.)
| | - Albert V. Aganov
- Institute of Physics, Kazan Federal University, Kremlyovskaya 16a, Kazan 420008, Tatarstan, Russia; (N.L.); (A.V.A.)
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Weiser SC, Mullen BR, Ascencio D, Ackman JB. Data-driven segmentation of cortical calcium dynamics. PLoS Comput Biol 2023; 19:e1011085. [PMID: 37126531 PMCID: PMC10174627 DOI: 10.1371/journal.pcbi.1011085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 05/11/2023] [Accepted: 04/09/2023] [Indexed: 05/02/2023] Open
Abstract
Demixing signals in transcranial videos of neuronal calcium flux across the cerebral hemispheres is a key step before mapping features of cortical organization. Here we demonstrate that independent component analysis can optimally recover neural signal content in widefield recordings of neuronal cortical calcium dynamics captured at a minimum sampling rate of 1.5×106 pixels per one-hundred millisecond frame for seventeen minutes with a magnification ratio of 1:1. We show that a set of spatial and temporal metrics obtained from the components can be used to build a random forest classifier, which separates neural activity and artifact components automatically at human performance. Using this data, we establish functional segmentation of the mouse cortex to provide a map of ~115 domains per hemisphere, in which extracted time courses maximally represent the underlying signal in each recording. Domain maps revealed substantial regional motifs, with higher order cortical regions presenting large, eccentric domains compared with smaller, more circular ones in primary sensory areas. This workflow of data-driven video decomposition and machine classification of signal sources can greatly enhance high quality mapping of complex cerebral dynamics.
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Affiliation(s)
- Sydney C. Weiser
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Brian R. Mullen
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Desiderio Ascencio
- Department of Psychology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - James B. Ackman
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
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Exposure to Antibiotics and Neurodevelopmental Disorders: Could Probiotics Modulate the Gut-Brain Axis? Antibiotics (Basel) 2022; 11:antibiotics11121767. [PMID: 36551423 PMCID: PMC9774196 DOI: 10.3390/antibiotics11121767] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/30/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022] Open
Abstract
In order to develop properly, the brain requires the intricate interconnection of genetic factors and pre-and postnatal environmental events. The gut-brain axis has recently raised considerable interest for its involvement in regulating the development and functioning of the brain. Consequently, alterations in the gut microbiota composition, due to antibiotic administration, could favor the onset of neurodevelopmental disorders. Literature data suggest that the modulation of gut microbiota is often altered in individuals affected by neurodevelopmental disorders. It has been shown in animal studies that metabolites released by an imbalanced gut-brain axis, leads to alterations in brain function and deficits in social behavior. Here, we report the potential effects of antibiotic administration, before and after birth, in relation to the risk of developing neurodevelopmental disorders. We also review the potential role of probiotics in treating gastrointestinal disorders associated with gut dysbiosis after antibiotic administration, and their possible effect in ameliorating neurodevelopmental disorder symptoms.
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Harshaw C, Kojima S, Wellman CL, Demas GE, Morrow AL, Taft DH, Kenkel WM, Leffel JK, Alberts JR. Maternal antibiotics disrupt microbiome, behavior, and temperature regulation in unexposed infant mice. Dev Psychobiol 2022; 64:e22289. [PMID: 35748626 PMCID: PMC9236156 DOI: 10.1002/dev.22289] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/21/2022] [Accepted: 05/12/2022] [Indexed: 12/31/2022]
Abstract
Maternal antibiotic (ABx) exposure can significantly perturb the transfer of microbiota from mother to offspring, resulting in dysbiosis of potential relevance to neurodevelopmental disorders such as autism spectrum disorder (ASD). Studies in rodent models have found long-term neurobehavioral effects in offspring of ABx-treated dams, but ASD-relevant behavior during the early preweaning period has thus far been neglected. Here, we exposed C57BL/6J mouse dams to ABx (5 mg/ml neomycin, 1.25 μg/ml pimaricin, .075% v/v acetic acid) dissolved in drinking water from gestational day 12 through offspring postnatal day 14. A number of ASD-relevant behaviors were assayed in offspring, including ultrasonic vocalization (USV) production during maternal separation, group huddling in response to cold challenge, and olfactory-guided home orientation. In addition, we obtained measures of thermoregulatory competence in pups during and following behavioral testing. We found a number of behavioral differences in offspring of ABx-treated dams (e.g., modulation of USVs by pup weight, activity while huddling) and provide evidence that some of these behavioral effects can be related to thermoregulatory deficiencies, particularly at younger ages. Our results suggest not only that ABx can disrupt microbiomes, thermoregulation, and behavior, but that metabolic effects may confound the interpretation of behavioral differences observed after early-life ABx exposure.
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Affiliation(s)
| | - Sayuri Kojima
- Department of Psychological & Brain Sciences, Indiana University, Bloomington, IN
| | - Cara L. Wellman
- Department of Psychological & Brain Sciences, Indiana University, Bloomington, IN
| | | | - Ardythe L. Morrow
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Diana Hazard Taft
- Department of Food Science and Technology, University of California, Davis, Davis, CA
| | - William M. Kenkel
- Department of Psychological and Brain Sciences, University of Delaware, Newark, DE
| | - Joseph K. Leffel
- Department of Psychological & Brain Sciences, Indiana University, Bloomington, IN
| | - Jeffrey R. Alberts
- Department of Psychological & Brain Sciences, Indiana University, Bloomington, IN
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