Biology subjects

Wang, S. S.- H.

Publications and source records attributed to Wang, S. S.- H..

8 recordsLinked to original sources

bioRxiv2025

Precise calcium-to-spike inference using biophysical generative models

The intramolecular dynamics of fluorescent calcium indicators distort the relationship between calcium signals and action potentials ("spikes"), hampering efficient spike inference from calcium imaging. To address this problem, we characterized the calcium response kinetics of three widely used indicators, GCaMP6f, jGCaMP7f, and jGCaMP8f, using in vitro stopped-flow measurements and brain slice recordings. We identify previously unreported kinetic features, including use-dependent slowing of fluorescence decay, that introduce systematic errors in linear model-based inference methods. Using these observations, we developed a multistate model of GCaMP and used it to create biophysically-inspired Bayesian Sequential Monte Carlo and machine learning inference models trained on synthetic datasets. These methods outperform existing methods on spike timing accuracy and correlation benchmarks derived from diverse cell types. Our results show that using synthetic data derived from our biophysical model yields a decoder that outperforms even those trained on extensive experimental data. By separating indicator characterization from inference, our framework, Calcium Spike Processing using Integrated Kinetic Estimation and Simulation (C-SPIKES), provides a generalizable strategy applicable to existing and future calcium indicators.

neuroscience↗

bioRxiv2024

A protective role for the cerebellum in cognitive aging

BackgroundBrain reserve -- the brains resilience to age-related change or damage -- provides protection against cognitive decline. The cerebellum is relatively unstudied as a contributor to brain reserve. This study investigates cerebellar brain reserve in the largest cohort to date. MethodsWe used data from the Human Connectome Project (n=708, 36-100yrs), UK Biobank (n=45,013, 44-81yrs), and ADNI (n=1,423, 56-95yrs). ADNI participants were cognitively normal or had a diagnosis of mild cognitive impairment or Alzheimers disease (AD) dementia. We examined associations between cerebellar tissue volume, age, Montreal Cognitive Assessment (MoCA) scores, global PET amyloid burden, and APOE genotype. FindingsHCP-Aging data revealed heterogenous aging-associated changes in cerebellar volume, with the greatest effects in posterior hemispheric regions (crus I) (Bonferroni-corrected, p<0{middle dot}05). MoCA scores were associated with higher tissue density in the cerebellum (p<0{middle dot}0001) to the same extent as neocortex, and MoCA scores coupled most strongly with posterior cerebellar cortex. Strikingly, greater volume in MoCA visuospatial-related cerebellar cortex protected against aging-related cognitive decline (p=0{middle dot}0001). We replicated tissue aging results in the UK Biobank with the greatest aging-related effects in posterior cerebellum (p<0{middle dot}0001), and an association of greater cerebellar volumes with less cognitive decline (Trails Making-B: p<0{middle dot}00001; Digit Symbol Substitution: p=0{middle dot}034). AD patients with low amyloid-beta burden (A{beta}-) exhibited the strongest cerebellar association with MoCA (volume x group, A{beta}- AD: p=0{middle dot}0001). In A{beta}- individuals, APOE {varepsilon}4/{varepsilon}4 carriers showed the greatest effect with MoCA (volume x APOE, {varepsilon}4/{varepsilon}4: p=0{middle dot}017). InterpretationOur large-scale study demonstrates a potentially strong role for the cerebellum in mitigating cognitive decline. The persistence of this protection in APOE {varepsilon}4/{varepsilon}4 carriers reshapes our understanding of reserve and AD risk. Our findings open the cerebellum as a novel target for future clinical research on brain reserve in aging populations. FundingNational Science Foundation, National Academies of Sciences, Engineering and Medicine, National Institutes of Health. Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed and GoogleScholar between August 12, 2023, and September 25, 2024 for articles irrespective of language or date of publication, relating to measures of cortical and cerebellar aging. Search terms included "cerebellum", "cognitive aging", "cerebellar reserve", "Alzheimers disease", "covariance", "retrogenesis", and "connectivity". Prior research demonstrated that the cerebellum may play a role in cognitive function. Studies have shown that cerebellar development is spatially heterogenous, with posterior regions undergoing the most protracted change in structure and function. Brain reserve has been predominantly studied in the neocortex, with some studies suggesting the cerebellum may contribute to cognitive changes in diseases like Alzheimers disease (AD) dementia. Cerebellar volume differences between young and older adults have been noted, as well as between healthy adults and neurodegenerative conditions like Parkinsons disease. However, the cerebellums contribution to cognitive reserve, particularly in healthy aging and individuals with a clinical diagnosis of mild cognitive impairment or AD dementia, had not been explored especially in large population-based datasets. Added value of this studyTo our knowledge, this study is the largest to date looking into how cerebellar structures contribute to cognitive outcomes in both healthy older adults, and those with mild cognitive impairment or AD dementia. We leverage three large neuroimaging datasets -- HCP-Aging, UK Biobank, and ADNI -- and demonstrate that cerebellar aging is spatially heterogeneous, with posterior regions showing the greatest age-related decline. We further establish a significant link between larger cerebellar volumes and better cognitive outcomes, suggesting that the cerebellum plays a role in cognitive resilience. Additionally, we identify how cerebellar structures predict cognitive performance and interact with amyloid-beta brain pathology and APOE genotype, particularly in those with low amyloid brain burden and those at greatest risk of AD such as in homozygous APOE e4 allele carriers. Implications of all the available evidenceThe aging of the global population raises the challenge of maintaining cognitive health in older age. Our research focuses on the cerebellum as a novel mediator of preserved cognitive function in old age and clinical dementia. Our findings have profound implications, given that individuals with robust cerebellar structures may be missed during cognitive and clinical screenings. Greater cerebellum volume seems to be most advantageous in those at higher risk for Alzheimers disease based on APOE4 status and those who have yet to accumulate substantial amyloid-beta brain pathology. Our study underscores the importance of the cerebellum as a novel brain reserve mechanism in aging populations.

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bioRxiv2023

Structural covariation between cerebellum and cerebral cortex is atypically modulated by thalamus in autism spectrum disorder

Despite its strong interconnectivity with the cerebral cortex, the influence of the human cerebellum on neocortical structure and its role in the development of neuropsychiatric disorders is unclear. Because cerebellar damage in early postnatal life creates a high risk for autism spectrum disorder (ASD), we investigated inter-relationships in cerebello-cerebral morphology. Leveraging a large structural brain MRI dataset in neurotypical children (n=375) and those diagnosed with ASD (n=373), we examined whether volumetric variation in cerebellar structure across individuals was correlated with neocortical variation during development, modeling the thalamus as a moderating coupling factor. We found negative covariation between cerebellar cortical regions and thalamic/sensorimotor neocortical regions, and positive covariation between thalamic and sensorimotor neocortical regions. This pattern aligned with the major disynaptic path of cerebellar inhibition to thalamocortical excitation. Examining the dependence of this structural covariation on ASD diagnosis, we found that neurotypical and ASD children displayed inverted hemispheric biases. In ASD, the thalamus moderated structural associations between the left cerebellum and right sensorimotor cortex. For neurotypical children, right cerebellum and left sensorimotor cortex were coupled. Notably, structural coupling between cerebellum, thalamus, and neocortex was strongest in younger childhood and waned by early adolescence, a time during which behavioral differences were smallest between typically developing and autistic children. In addition to the sensorimotor cortex, cerebellar dentate nuclei in ASD displayed greater coupling to broad neocortical regions, and these nuclei related to cognitive function differently such that greater dentate nuclear volume was associated with greater behavioral impairment in ASD but not in controls. Graph analyses demonstrated that the cerebello-thalamocortical network was more densely and less prolifically interconnected in ASD than in typical development. Taken as a whole, our study reveals a developmental interplay between the cerebellum, thalamus, and neocortex which differs in ASD from neurotypical children. This pattern is consistent with a model of ASD in which early developmental influences of cerebellar output on brain maturation are specifically moderated by cerebello-thalamocortical pathways.

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bioRxiv2021

Enhanced learning and sensory salience in a cerebellar mouse autism model

Perturbation to the cerebellum can lead to deficits in motor function, cognition, and behavioral flexibility. Here we report that a cerebellum-specific transgenic mouse autism model with disrupted Purkinje cell function shows unexpectedly accelerated learning on a sensory evidence-accumulation task, as well as enhanced sensory reactivity to touch and auditory cues. Computational latent-state analysis of behavior revealed that accelerated learning was associated with enhanced focus on current over past trials. In on-task states, a subset of Purkinje cells in crus I produced more complex spikes to sensory stimuli. Learning was accelerated by providing cue-locked optogenetic stimulation of Purkinje cells, but unaffected by continuous optogenetic interference with Purkinje cell activity. Complex spikes fired in response to both correct and incorrect choices, but less so when mice were on-task. Both transgenic mice and mice receiving cue-locked optogenetic stimulation showed prolonged sensory responses in Purkinje-cell complex spikes and anterior cingulate cortex. We suggest that cerebellar activity may shape evidence-accumulation learning by enhancing task focus and neocortical processing of current experience. HighlightsO_LIFaster learning and enhanced sensory salience with cerebellar manipulations in mice C_LIO_LIAccelerated learning arises from prolonged occupancy in an on-task behavioral state C_LIO_LICerebellar manipulations can influence neocortex via altered complex spike activity C_LIO_LICerebellum findings consistent with a weak global coherence account of autism C_LI eTOC blurbIn a cerebellum-based mouse autism model, perturbed function leads to faster learning of a working-memory task, mediated by higher focus on current trials. The effects are emulated by optogenetic perturbation of Purkinje cells, and both perturbations drive enhanced neocortical activity. Results are consistent with a weak coherence model for autism.

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bioRxiv2021

Cerebellar contributions to a brainwide network for flexible behavior

The cerebellum regulates nonmotor behavior, but the routes by which it exerts its influence are not well characterized. Here we report a necessary role for the posterior cerebellum in guiding a reversal learning task, acting through a network of diencephalic and neocortical structures. After chemogenetic inhibition of Purkinje cells in lobule VI or crus I, mice could learn a water Y-maze task but were impaired in their ability to reverse their initial choice. To map targets of perturbation, we imaged c-Fos activation in cleared whole brains using light-sheet microscopy. Reversal learning activated diencephalic regions and associative neocortical regions. Distinctive subsets of structures were altered by perturbation of lobule VI (including thalamus and habenula) and crus I (including hypothalamus and prelimbic/orbital cortex), and both perturbations influenced anterior cingulate and infralimbic cortex. To identify functional networks, we used correlated variation in c-Fos activation within each test group. Lobule VI inactivation weakened within-thalamus correlations, while crus I inactivation divided neocortical activity into well-separated sensorimotor and associative subnetworks. In both groups, high-throughput automated analysis of complex whole-body movement revealed deficiencies in across-day adaptation to an open field environment. Neither perturbation affected gait, within-day open-field adaptation, or location preference. Taken together, these experiments reveal brainwide systems for cerebellar influence that can affect multiple flexible responses. Significance statementThe cerebellum, a part of all vertebrate brains, provides feedback to the rest of the brain on a split-second basis in response to unexpected events. The consequent changes can range from minute adjustments in movement to broad changes in behavior. In mice, we investigated cerebellar regions that help guide flexible behavior. Inactivation of these regions prevented mice from responding flexibly to a changing Y-shaped maze. We used light-sheet microscopy of c-fos protein expression to map brainwide effects of different stages of learning and cerebellar inactivation. Inactivation caused changes in thalamocortical activity that were similar in pattern, but opposite in sign, from normal learning. Lobule VI inactivation weakened thalamic functional networks, while crus I inactivation divided sensorimotor from associative neocortical networks. The same inactivation also impaired multiday adaptation to an open arena, as tracked using machine vision. Our work shows how the cerebellums influence over flexible response can be mediated by a widespread brain network.

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bioRxiv2021

Deep behavioral phenotyping of mouse autism models using open-field behavior

AO_SCPLOWBSTRACTC_SCPLOWAutism is noted for both its genotypic and phenotypic diversity. Repetitive action, resistance to environmental change, and motor disruptions vary from individual to individual. In animal models, conventional behavioral phenotyping captures such fine-scale variations incompletely. Here we use advances in computer vision and deep learning to develop a framework for characterizing mouse behavior on multiple time scales using a single popular behavioral assay, the open field test. We observed male and female C57BL/6J mice to develop a dynamic baseline of adaptive behavior over multiple days. We then examined two rodent models of autism, a cerebellum-specific model, L7-Tsc1, and a whole-brain knockout model, Cntnap2. Both Cntnap2 knockout and L7-Tsc1 mutants showed forelimb lag during gait. L7-Tsc1 mutants showed complex defects in multi-day adaptation, lacking the tendency of wild-type mice to spend progressively more time in corners of the arena. In L7-Tsc1 mutant mice, failure-to-adapt took the form of maintained ambling, turning, and locomotion, and an overall decrease in grooming. Adaptation in Cntnap2 knockout mice more broadly resembled that of wild-type. L7-Tsc1 mutant and Cntnap2 knockout mouse models showed different patterns of behavioral state occupancy. Our automated pipeline for deep phenotyping successfully captures model-specific deviations in adaptation and movement as well as differences in the detailed structure of behavioral dynamics.

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bioRxiv2020

Parallel organization of cerebellar pathways to sensorimotor, associative, and modulatory forebrain

Cerebellar outputs take polysynaptic routes to reach the rest of the brain, impeding conventional tracing. Here we quantify pathways between cerebellum and forebrain using transsynaptic tracing viruses and a whole-brain quantitative analysis pipeline. Retrograde tracing found a majority of descending paths originating from somatomotor cortex. Anterograde tracing of ascending paths encompassed most thalamic nuclei, especially ventral posteromedial, lateral posterior, mediodorsal, and reticular nuclei; in neocortex, sensorimotor regions contained the most labeled neurons, but higher densities were found in associative areas, including orbital, anterior cingulate, prelimbic, and infralimbic cortex. Patterns of ascending expression correlated with c-Fos expression after optogenetic inhibition of Purkinje cells. Our results reveal homologous networks linking single areas of cerebellar cortex to diverse forebrain targets. We conclude that shared areas of cerebellum are positioned to provide sensory-motor information to regions implicated in both movement and nonmotor function. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/979153v3_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@1bead0corg.highwire.dtl.DTLVardef@1531de2org.highwire.dtl.DTLVardef@1cf02f6org.highwire.dtl.DTLVardef@1cb6774_HPS_FORMAT_FIGEXP M_FIG C_FIG

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bioRxiv2018

A cerebellar role in evidence-guided decision-making

To make successful evidence-based decisions, the brain must rapidly and accurately transform sensory inputs into specific goal-directed behaviors. Most experimental work on this subject has focused on forebrain mechanisms. Here we show that during perceptual decision-making over a period of seconds, decision-, sensory-, and error-related information converge on the lateral posterior cerebellum in crus I, a structure that communicates bidirectionally with numerous forebrain regions. We trained mice on a novel evidence-accumulation task and demonstrated that cerebellar inactivation reduces behavioral accuracy without impairing motor parameters of action. Using two-photon calcium imaging, we found that Purkinje cell somatic activity encoded choice- and evidence-related variables. Decision errors were represented by dendritic calcium spikes, which are known to drive plasticity. We propose that cerebellar circuitry may contribute to the set of distributed computations in the brain that support accurate perceptual decision-making.

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