Unique spatiotemporal fMRI dynamics in the awake mouse brain

Gutierrez-Barragan, Daniel; Singh, Neha Atulkumar; Alvino, Filomena Grazia; Coletta, Ludovico; Rocchi, Federico; Guzman, A. Elizabeth de; Galbusera, Alberto; Uboldi, Mauro; Panzeri, Stefano; Gozzi, Alessandro

doi:10.1016/j.cub.2021.12.015

Cited by 90 publications

(146 citation statements)

References 73 publications

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“…In contrast, CBF decreases in rats given dexmedetomidine (Ganjoo et al, 1998). The frequency of spontaneous BOLD fluctuations is increased in the mice under a combination of isoflurane and medetomidine (Grandjean et al, 2017b) which is different from 1/f infraslow spectra usually observed with light isoflurane and halothane (Gutierrez-Barragan et al, 2019) or in awake mice (Gutierrez-Barragan et al, 2022) and humans (Fox et al, 2007). Specifically, for rs-fMRI, networks are more highly localized under light isoflurane anesthesia and become less spatially specific under deep isoflurane anesthesia (e.g., 1.8% isoflurane), and much of the specificity under deep isoflurane anesthesia was recovered after global signal regression .…”

Section: Anesthesiamentioning

confidence: 58%

Section: Acquisition Parameters Conditions and Confounds In Rodents C...mentioning

confidence: 72%

“…In addition, rs-fMRI in awake rodents has been explored with a measure of reduced stress levels, despite the challenges involved, with a number of groups successfully conducting rs-fMRI studies in unanesthetized rats or mice ( Jonckers et al, 2014 ; Ma et al, 2018a , b , 2020 ; Stenroos et al, 2018 ; Liu and Huang, 2020 ). Particularly, in an awake mouse study ( Gutierrez-Barragan et al, 2022 ), though networks in the awake state were appeared to be anatomically conserved to the ones under anesthesia, evidence shows that there are network-specific regional anticorrelation pertaining to arousal-related basal forebrain areas and increased between-network crosstalk. This evidence is consistent with prior human anesthetic consciousness studies where transient anticorrelations between visual-auditory networks and the default mode network are observed by state-dependent interactions involving the basal-forebrain arousal system ( Demertzi et al, 2019 ) and stereotypic temporal transitions between networks ( Huang et al, 2020 ).…”

Section: Acquisition Parameters Conditions and Confounds In Rodents C...mentioning

confidence: 99%

“…A broadly used set of RSNs defined on human cortical regions was determined by Yeo et al (2011) , which includes the default, the somatomotor, the visual, frontoparietal, dorsal attention, salience/ventral attention, and limbic networks. In rodent studies, several functional networks have also been commonly identified from resting-state fMRI data in anesthetized mice ( Stafford et al, 2014 ; Grandjean et al, 2017a , 2020 ), anesthetized rats ( Liang et al, 2012 ), awake rats ( Liang et al, 2011 ; Ma et al, 2018a , b ), and awake mice ( Gutierrez-Barragan et al, 2022 ). Many of these brain networks are homologous to those of primates, for example, the default mode network ( Stafford et al, 2014 ; Hsu et al, 2016 ; Grandjean et al, 2017b , 2020 ), somatosensory network ( Grandjean et al, 2017b , 2020 ), and subcortical system ( Grandjean et al, 2020 ), though it is well noted that the anesthetization causes a profound impact on the RSNs being identified ( Liang et al, 2011 , 2012 ; Ma et al, 2018a , b ).…”

Section: Time-averaged Features Of Resting-state Functional Magnetic ...mentioning

confidence: 99%

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Functional Connectivity of the Brain Across Rodents and Humans

LaGrow

Anumba

et al. 2022

Front. Neurosci.

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Resting-state functional magnetic resonance imaging (rs-fMRI), which measures the spontaneous fluctuations in the blood oxygen level-dependent (BOLD) signal, is increasingly utilized for the investigation of the brain’s physiological and pathological functional activity. Rodents, as a typical animal model in neuroscience, play an important role in the studies that examine the neuronal processes that underpin the spontaneous fluctuations in the BOLD signal and the functional connectivity that results. Translating this knowledge from rodents to humans requires a basic knowledge of the similarities and differences across species in terms of both the BOLD signal fluctuations and the resulting functional connectivity. This review begins by examining similarities and differences in anatomical features, acquisition parameters, and preprocessing techniques, as factors that contribute to functional connectivity. Homologous functional networks are compared across species, and aspects of the BOLD fluctuations such as the topography of the global signal and the relationship between structural and functional connectivity are examined. Time-varying features of functional connectivity, obtained by sliding windowed approaches, quasi-periodic patterns, and coactivation patterns, are compared across species. Applications demonstrating the use of rs-fMRI as a translational tool for cross-species analysis are discussed, with an emphasis on neurological and psychiatric disorders. Finally, open questions are presented to encapsulate the future direction of the field.

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Section: Anesthesiamentioning

confidence: 58%

Section: Acquisition Parameters Conditions and Confounds In Rodents C...mentioning

confidence: 72%

Section: Acquisition Parameters Conditions and Confounds In Rodents C...mentioning

confidence: 99%

Section: Time-averaged Features Of Resting-state Functional Magnetic ...mentioning

confidence: 99%

See 2 more Smart Citations

Functional Connectivity of the Brain Across Rodents and Humans

LaGrow

Anumba

et al. 2022

Front. Neurosci.

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“…The use of brain templates is common for MRI recorded data ( Badea et al, 2019 ; Gutierrez-Barragan et al, 2022 ). However, for LSFM recorded data the same approach is complicated by the many different factors influencing tissue morphology and subsequent atlas registration ( Figures 1A–C ).…”

Section: Generating Digital Brain Mapsmentioning

confidence: 99%

Digital Brain Maps and Virtual Neuroscience: An Emerging Role for Light-Sheet Fluorescence Microscopy in Drug Development

Perens

Hecksher‐Sørensen

2022

Front. Neurosci.

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The mammalian brain is by far the most advanced organ to have evolved and the underlying biology is extremely complex. However, with aging populations and sedentary lifestyles, the prevalence of neurological disorders is increasing around the world. Consequently, there is a dire need for technologies that can help researchers to better understand the complexity of the brain and thereby accelerate therapies for diseases with origin in the central nervous system. One such technology is light-sheet fluorescence microscopy (LSFM) which in combination with whole organ immunolabelling has made it possible to visualize an intact mouse brain with single cell resolution. However, the price for this level of detail comes in form of enormous datasets that often challenges extraction of quantitative information. One approach for analyzing whole brain data is to align the scanned brains to a reference brain atlas. Having a fixed spatial reference provides each voxel of the sample brains with x-, y-, z-coordinates from which it is possible to obtain anatomical information on the observed fluorescence signal. An additional and important benefit of aligning light sheet data to a reference brain is that the aligned data provides a digital map of gene expression or cell counts which can be deposited in databases or shared with other scientists. This review focuses on the emerging field of virtual neuroscience using digital brain maps and discusses some of challenges incurred when registering LSFM recorded data to a standardized brain template.

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Neuromodulation in Small Animal fMRI

Hsu,

Shih

2024

Magnetic Resonance Imaging

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The integration of functional magnetic resonance imaging (fMRI) with advanced neuroscience technologies in experimental small animal models offers a unique path to interrogate the causal relationships between regional brain activity and brain‐wide network measures—a goal challenging to accomplish in human subjects. This review traces the historical development of the neuromodulation techniques commonly used in rodents, such as electrical deep brain stimulation, optogenetics, and chemogenetics, and focuses on their application with fMRI. We discuss their advantageousness roles in uncovering the signaling architecture within the brain and the methodological considerations necessary when conducting these experiments. By presenting several rodent‐based case studies, we aim to demonstrate the potential of the multimodal neuromodulation approach in shedding light on neurovascular coupling, the neural basis of brain network functions, and their connections to behaviors. Key findings highlight the cell‐type and circuit‐specific modulation of brain‐wide activity patterns and their behavioral correlates. We also discuss several future directions and feature the use of mediation and moderation analytical models beyond the intuitive evoked response mapping, to better leverage the rich information available in fMRI data with neuromodulation. Using fMRI alongside neuromodulation techniques provide insights into the mesoscopic (relating to the intermediate scale between single neurons and large‐scale brain networks) and macroscopic fMRI measures that correlate with specific neuronal events. This integration bridges the gap between different scales of neuroscience research, facilitating the exploration and testing of novel therapeutic strategies aimed at altering network‐mediated behaviors. In conclusion, the combination of fMRI with neuromodulation techniques provides crucial insights into mesoscopic and macroscopic brain dynamics, advancing our understanding of brain function in health and disease.Evidence Level1Technical EfficacyStage 1

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Unique spatiotemporal fMRI dynamics in the awake mouse brain

Cited by 90 publications

References 73 publications

Functional Connectivity of the Brain Across Rodents and Humans

Functional Connectivity of the Brain Across Rodents and Humans

Digital Brain Maps and Virtual Neuroscience: An Emerging Role for Light-Sheet Fluorescence Microscopy in Drug Development

Neuromodulation in Small Animal fMRI

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