41 results on '"Stephan Y. Thiberge"'
Search Results
2. An Accumulation-of-Evidence Task Using Visual Pulses for Mice Navigating in Virtual Reality
- Author
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Lucas Pinto, Sue A. Koay, Ben Engelhard, Alice M. Yoon, Ben Deverett, Stephan Y. Thiberge, Ilana B. Witten, David W. Tank, and Carlos D. Brody
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evidence accumulation ,spatial navigation ,virtual reality ,mouse ,behavior ,decision making ,Neurosciences. Biological psychiatry. Neuropsychiatry ,RC321-571 - Abstract
The gradual accumulation of sensory evidence is a crucial component of perceptual decision making, but its neural mechanisms are still poorly understood. Given the wide availability of genetic and optical tools for mice, they can be useful model organisms for the study of these phenomena; however, behavioral tools are largely lacking. Here, we describe a new evidence-accumulation task for head-fixed mice navigating in a virtual reality (VR) environment. As they navigate down the stem of a virtual T-maze, they see brief pulses of visual evidence on either side, and retrieve a reward on the arm with the highest number of pulses. The pulses occur randomly with Poisson statistics, yielding a diverse yet well-controlled stimulus set, making the data conducive to a variety of computational approaches. A large number of mice of different genotypes were able to learn and consistently perform the task, at levels similar to rats in analogous tasks. They are sensitive to side differences of a single pulse, and their memory of the cues is stable over time. Moreover, using non-parametric as well as modeling approaches, we show that the mice indeed accumulate evidence: they use multiple pulses of evidence from throughout the cue region of the maze to make their decision, albeit with a small overweighting of earlier cues, and their performance is affected by the magnitude but not the duration of evidence. Additionally, analysis of the mice's running patterns revealed that trajectories are fairly stereotyped yet modulated by the amount of sensory evidence, suggesting that the navigational component of this task may provide a continuous readout correlated to the underlying cognitive variables. Our task, which can be readily integrated with state-of-the-art techniques, is thus a valuable tool to study the circuit mechanisms and dynamics underlying perceptual decision making, particularly under more complex behavioral contexts.
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- 2018
- Full Text
- View/download PDF
3. Germ Plasm Anchoring Is a Dynamic State that Requires Persistent Trafficking
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Kristina S. Sinsimer, Jack J. Lee, Stephan Y. Thiberge, and Elizabeth R. Gavis
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Biology (General) ,QH301-705.5 - Abstract
Localized cytoplasmic determinants packaged as ribonucleoprotein (RNP) particles direct embryonic patterning and cell fate specification in a wide range of organisms. Once established, the asymmetric distributions of such RNP particles must be maintained, often over considerable developmental time. A striking example is the Drosophila germ plasm, which contains RNP particles whose localization to the posterior of the egg during oogenesis results in their asymmetric inheritance and segregation of germline from somatic fates in the embryo. Although actin-based anchoring mechanisms have been implicated, high-resolution live imaging revealed persistent trafficking of germ plasm RNP particles at the posterior cortex of the Drosophila oocyte. This motility relies on cortical microtubules, is mediated by kinesin and dynein motors, and requires coordination between the microtubule and actin cytoskeletons. Finally, we show that RNP particle motility is required for long-term germ plasm retention. We propose that anchoring is a dynamic state that renders asymmetries robust to developmental time and environmental perturbations.
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- 2013
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4. Nuclear Herpesvirus Capsid Motility Is Not Dependent on F-Actin
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Jens B. Bosse, Stina Virding, Stephan Y. Thiberge, Julian Scherer, Harald Wodrich, Zsolt Ruzsics, Ulrich H. Koszinowski, and Lynn W. Enquist
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Microbiology ,QR1-502 - Abstract
ABSTRACT A considerable part of the herpesvirus life cycle takes place in the host nucleus. While much progress has been made to understand the molecular processes required for virus replication in the nucleus, much less is known about the temporal and spatial dynamics of these events. Previous studies have suggested that nuclear capsid motility is directed and dependent on actin filaments (F-actin), possibly using a myosin-based, ATP-dependent mechanism. However, the conclusions from these studies were indirect. They either relied on the effects of F-actin depolymerizing drugs to deduce an F-actin dependency or they visualized nuclear F-actin but failed to show a direct link to capsid motility. Moreover, no direct link between nuclear capsid motility and a molecular motor has been established. In this report, we reinvestigate the involvement of F-actin in nuclear herpesvirus capsid transport. We show for representative members of all three herpesvirus subfamilies that nuclear capsid motility is not dependent on nuclear F-actin and that herpesvirus infection does not induce nuclear F-actin in primary fibroblasts. Moreover, in these cells, three F-actin-inhibiting drugs failed to effect capsid motility. Only latrunculin A treatment stalled nuclear capsids but did so by an unexpected effect: the drug induced actin rods in the nucleus. Immobile capsids accumulated around actin rods, and immunoprecipitation experiments suggested that capsid motility stopped because latrunculin-induced actin rods nonspecifically bind nuclear capsids. Interestingly, capsid motility was unaffected in cells that do not induce actin rods. Based on these data, we conclude that herpesvirus nuclear capsid motility is not dependent on F-actin. IMPORTANCE Herpesviruses are large DNA viruses whose replication is dependent on the host nucleus. However, we do not understand how key nuclear processes, including capsid assembly, genome replication, capsid packaging, and nuclear egress, are dynamically connected in space and time. Fluorescence live-cell microscopy revealed that nuclear capsids are highly mobile early in infection. Two studies suggested that this motility might be due to active myosin-based transport of capsids on nuclear F-actin. However, direct evidence for such motor-based transport is lacking. We revisited this phenomenon and found no evidence that nuclear capsid motility depended on F-actin. Our results reopen the question of how nuclear herpesvirus capsids move in the host nucleus.
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- 2014
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5. Overlapping representations of food and social stimuli in VTA dopamine neurons
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Lindsay Willmore, Adelaide R. Minerva, Ben Engelhard, Malavika Murugan, Brenna McMannon, Nirja Oak, Stephan Y. Thiberge, Catherine J. Peña, and Ilana B. Witten
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Article - Abstract
SummaryDopamine neurons of the ventral tegmental area (VTADA) respond to food and social stimuli and contribute to both forms of motivation. However, it is unclear if the same or different VTADAneurons encode these different stimuli. To address this question, we performed 2-photon calcium imaging in mice presented with food and conspecifics, and found statistically significant overlap in the populations responsive to both stimuli. Both hunger and opposite-sex social experience further increased the proportion of neurons that respond to both stimuli, implying that modifying motivation for one stimulus affects responses to both stimuli. In addition, single-nucleus RNA sequencing revealed significant co-expression of feeding- and social-hormone related genes in individual VTADAneurons. Taken together, our functional and transcriptional data suggest overlapping VTADApopulations underlie food and social motivation.
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- 2023
6. Specialized coding of sensory, motor and cognitive variables in VTA dopamine neurons
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Nathaniel D. Daw, Sharon Ornelas, Weston Fleming, Ben Engelhard, David W. Tank, Julia Cox, Ilana B. Witten, Sue Ann Koay, Hee Jae Jang, Joel Finkelstein, and Stephan Y. Thiberge
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Male ,0301 basic medicine ,Conditioning, Classical ,Decision Making ,Population ,Sensation ,Sensory system ,Motor Activity ,Biology ,Spatial memory ,Article ,Midbrain ,Mice ,03 medical and health sciences ,Cognition ,0302 clinical medicine ,Calcium imaging ,Reward ,Dopamine ,medicine ,Animals ,education ,education.field_of_study ,Multidisciplinary ,Dopaminergic Neurons ,Ventral Tegmental Area ,Virtual Reality ,Biomechanical Phenomena ,Ventral tegmental area ,030104 developmental biology ,medicine.anatomical_structure ,nervous system ,Calcium ,Female ,Cues ,Neuroscience ,030217 neurology & neurosurgery ,Spatial Navigation ,medicine.drug - Abstract
There is increased appreciation that dopamine neurons in the midbrain respond not only to reward1 and reward-predicting cues1,2, but also to other variables such as the distance to reward3, movements4-9 and behavioural choices10,11. An important question is how the responses to these diverse variables are organized across the population of dopamine neurons. Whether individual dopamine neurons multiplex several variables, or whether there are subsets of neurons that are specialized in encoding specific behavioural variables remains unclear. This fundamental question has been difficult to resolve because recordings from large populations of individual dopamine neurons have not been performed in a behavioural task with sufficient complexity to examine these diverse variables simultaneously. Here, to address this gap, we used two-photon calcium imaging through an implanted lens to record the activity of more than 300 dopamine neurons from the ventral tegmental area of the mouse midbrain during a complex decision-making task. As mice navigated in a virtual-reality environment, dopamine neurons encoded an array of sensory, motor and cognitive variables. These responses were functionally clustered, such that subpopulations of neurons transmitted information about a subset of behavioural variables, in addition to encoding reward. These functional clusters were spatially organized, with neighbouring neurons more likely to be part of the same cluster. Together with the topography between dopamine neurons and their projections, this specialization and anatomical organization may aid downstream circuits in correctly interpreting the wide range of signals transmitted by dopamine neurons.
- Published
- 2019
7. Amplitude modulations of cortical sensory responses in pulsatile evidence accumulation
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Carlos D. Brody, David W. Tank, Sue Ann Koay, and Stephan Y. Thiberge
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Male ,0301 basic medicine ,Mouse ,Sensory processing ,QH301-705.5 ,medicine.medical_treatment ,media_common.quotation_subject ,Science ,evidence accumulation ,Pulsatile flow ,Posterior parietal cortex ,Sensory system ,Biology ,Choice Behavior ,General Biochemistry, Genetics and Molecular Biology ,decision making ,Mice ,03 medical and health sciences ,Discrimination, Psychological ,0302 clinical medicine ,Parietal Lobe ,Perception ,medicine ,Animals ,visual cortex ,Biology (General) ,media_common ,Cerebral Cortex ,Neurons ,Behavior, Animal ,General Immunology and Microbiology ,Pulse (signal processing) ,General Neuroscience ,Cognition ,General Medicine ,030104 developmental biology ,Visual cortex ,medicine.anatomical_structure ,Visual Perception ,Medicine ,Neuroscience ,030217 neurology & neurosurgery ,Research Article - Abstract
How does the brain internally represent a sequence of sensory information that jointly drives a decision-making behavior? Studies of perceptual decision-making have often assumed that sensory cortices provide noisy but otherwise veridical sensory inputs to downstream processes that accumulate and drive decisions. However, sensory processing in even the earliest sensory cortices can be systematically modified by various external and internal contexts. We recorded from neuronal populations across posterior cortex as mice performed a navigational decision-making task based on accumulating randomly timed pulses of visual evidence. Even in V1, only a small fraction of active neurons had sensory-like responses time-locked to each pulse. Here, we focus on how these ‘cue-locked’ neurons exhibited a variety of amplitude modulations from sensory to cognitive, notably by choice and accumulated evidence. These task-related modulations affected a large fraction of cue-locked neurons across posterior cortex, suggesting that future models of behavior should account for such influences.
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- 2020
8. Auditory activity is diverse and widespread throughout the central brain of Drosophila
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Stephan Y. Thiberge, Eftychios A. Pnevmatikakis, Mala Murthy, and Diego A. Pacheco
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0301 basic medicine ,Male ,Auditory Pathways ,Sensory processing ,medicine.medical_treatment ,media_common.quotation_subject ,Sensory system ,Motor Activity ,Article ,Courtship ,03 medical and health sciences ,Sexual Behavior, Animal ,0302 clinical medicine ,Hearing ,Postsynaptic potential ,medicine ,Connectome ,Animals ,Neural imaging ,Drosophila ,030304 developmental biology ,media_common ,0303 health sciences ,Brain Mapping ,biology ,Behavior, Animal ,General Neuroscience ,Brain ,biology.organism_classification ,Brain region ,030104 developmental biology ,Drosophila melanogaster ,Acoustic Stimulation ,Female ,Functional organization ,Vocalization, Animal ,Neuroscience ,Mechanoreceptors ,030217 neurology & neurosurgery - Abstract
Sensory pathways are typically studied by starting at receptor neurons and following postsynaptic neurons into the brain. However, this leads to a bias in analysis of sensory activity towards the earliest layers of sensory processing or to brain regions containing the majority of postsynaptic neurons. Here, we present new methods for unbiased volumetric neural imaging with precise across-brain registration, to characterize auditory activity throughout the entire central brain of Drosophila , and to make comparisons across trials, individuals, and sexes. We discover that auditory activity is widespread across nearly all central brain regions and in neurons known to carry responses to other modalities. These auditory representations are diverse in their temporal profiles, but the majority of activity, regardless of brain region, is focused on aspects of the conspecific courtship song. We find that auditory responses are stereotyped across trials and animals in early mechanosensory regions, becoming more variable at higher layers of the putative pathway. This study highlights the power of using an unbiased, brain-wide approach for mapping the functional organization of sensory activity.
- Published
- 2020
9. Chemical signatures of human odour generate a unique neural code in the brain of Aedes aegypti mosquitoes
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Jonathan Zung, Stephan Y. Thiberge, Iqbal A, Dorit Merhof, Alexis L. Kriete, Benjamin J. Matthews, Carolyn S. McBride, Martin Strauch, Meg A Younger, and Zhilei Zhao
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Glomerulus (olfaction) ,biology ,fungi ,food and beverages ,Aedes aegypti ,biology.organism_classification ,medicine.anatomical_structure ,Evolutionary biology ,parasitic diseases ,Sensory coding ,medicine ,Antennal lobe ,Neural coding ,Animal species ,Biting humans - Abstract
A globally invasive form of the mosquito Aedes aegypti specializes in biting humans, making it an efficient vector of dengue, yellow fever, Zika, and chikungunya viruses. Host-seeking females strongly prefer human odour over the odour of non-human animals, but exactly how they distinguish the two is not known. Vertebrate odours are complex blends of volatile chemicals with many shared components, making discrimination an interesting sensory coding challenge. Here we show that human and animal odour blends evoke activity in unique combinations of olfactory glomeruli within the Aedes aegypti antennal lobe. Human blends consistently activate a ‘universal’ glomerulus, which is equally responsive to diverse animal and nectar-related blends, and a more selective ‘human-sensitive’ glomerulus. This dual signal robustly distinguishes humans from animals across concentrations, individual humans, and diverse animal species. Remarkably, the human-sensitive glomerulus is narrowly tuned to the long-chain aldehydes decanal and undecanal, which we show are consistently enriched in (though not specific to) human odour and which likely originate from unique human skin lipids. We propose a model of host-odour coding wherein normalization of activity in the human-sensitive glomerulus by that in the broadly-tuned universal glomerulus generates a robust discriminatory signal of the relative concentration of long-chain aldehydes in a host odour blend. Our work demonstrates how animal brains may distil complex odour stimuli of innate biological relevance into simple neural codes and reveals novel targets for the design of next-generation mosquito-control strategies.
- Published
- 2020
10. Author response: Amplitude modulations of cortical sensory responses in pulsatile evidence accumulation
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David W. Tank, Sue Ann Koay, Stephan Y. Thiberge, and Carlos D. Brody
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Physics ,Pulsatile flow ,Response Amplitude ,Sensory system ,Neuroscience - Published
- 2020
11. Amplitude modulations of sensory responses, and deviations from Weber’s Law in pulsatile evidence accumulation
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Stephan Y. Thiberge, Sue Ann Koay, Carlos D. Brody, and David W. Tank
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Visual evidence ,Noise ,Amplitude ,Pulse (signal processing) ,Law ,Pulsatile flow ,Automatic gain control ,Posterior parietal cortex ,Sensory system ,Biology - Abstract
How do animals make behavioral decisions based on noisy sensory signals, which are moreover a tiny fraction of ongoing activity in the brain? Some theories suggest that sensory responses should be accumulated through time to reduce noise. Others suggest that feedback-based gain control of sensory responses allow small signals to be selectively amplified to drive behavior. We recorded from neuronal populations across posterior cortex as mice performed a decision-making task based on accumulating randomly timed pulses of visual evidence. Here we focus on a subset of neurons, with putative sensory responses that were time-locked to each pulse. These neurons exhibited a variety of amplitude (gain-like) modulations, notably by choice and accumulated evidence. These neural data inspired a hypothetical accumulation circuit with a multiplicative feedback-loop architecture, which parsimoniously explains deviations in perceptual discrimination from Weber-Fechner Law. Our neural observations thus led to a model that synthesizes both accumulation and feedback hypotheses.
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- 2020
12. Sequential and efficient neural-population coding of complex task information
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Carlos D. Brody, Adam S. Charles, Stephan Y. Thiberge, David W. Tank, and Sue Ann Koay
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Neurons ,business.industry ,Computer science ,General Neuroscience ,SIGNAL (programming language) ,Pattern recognition ,Function (mathematics) ,Interference (wave propagation) ,Multiplexing ,Task (project management) ,Mice ,Encoding (memory) ,Biological neural network ,Animals ,Artificial intelligence ,business ,Coding (social sciences) - Abstract
Recent work has highlighted that many types of variables are represented in each neocortical area. How can these many neural representations be organized together without interference and coherently maintained/updated through time? We recorded from excitatory neural populations in posterior cortices as mice performed a complex, dynamic task involving multiple interrelated variables. The neural encoding implied that highly correlated task variables were represented by less-correlated neural population modes, while pairs of neurons exhibited a spectrum of signal correlations. This finding relates to principles of efficient coding, but notably utilizes neural population modes as the encoding unit and suggests partial whitening of task-specific information where different variables are represented with different signal-to-noise levels. Remarkably, this encoding function was multiplexed with sequential neural dynamics yet reliably followed changes in task-variable correlations throughout the trial. We suggest that neural circuits can implement time-dependent encodings in a simple way using random sequential dynamics as a temporal scaffold.
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- 2022
13. Sequential and efficient neural-population coding of complex task information
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Sue Ann Koay, Adam S. Charles, Stephan Y. Thiberge, Carlos D. Brody, and David W. Tank
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Computer science ,business.industry ,Encoding (memory) ,Posterior parietal cortex ,Pattern recognition ,Artificial intelligence ,Neural population ,business ,Subspace topology ,Coding (social sciences) - Abstract
SummaryRecent work has highlighted that many types of variables are represented in each neocortical area. How can these many neural representations be organized together without interference, and coherently maintained/updated through time? We recorded from large neural populations in posterior cortices as mice performed a complex, dynamic task involving multiple interrelated variables. The neural encoding implied that correlated task variables were represented by uncorrelated neural-population modes, while pairs of neurons exhibited a variety of signal correlations. This finding relates to principles of efficient coding for task-specific information, with neural-population modes as the encoding unit, and applied across posterior cortical regions and layers 2/3 and 5. Remarkably, this encoding function was multiplexed with sequential neural dynamics as well as reliably followed changes in task-variable correlations through time. We suggest that neural circuits can implement time-dependent encoding in a simple way by using random sequential dynamics as a temporal scaffold.
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- 2019
14. Shared Song Detector Neurons in Drosophila Male and Female Brains Drive Sex-Specific Behaviors
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David Deutsch, Jan Clemens, Stephan Y. Thiberge, Georgia Guan, and Mala Murthy
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0301 basic medicine ,Auditory perception ,Male ,animal structures ,Sensory processing ,medicine.medical_treatment ,media_common.quotation_subject ,Sensory system ,General Biochemistry, Genetics and Molecular Biology ,Article ,Courtship ,03 medical and health sciences ,Sexual Behavior, Animal ,0302 clinical medicine ,Stimulus modality ,Biological neural network ,medicine ,Animals ,Drosophila ,030304 developmental biology ,media_common ,Neurons ,0303 health sciences ,Sex Characteristics ,biology ,Brain ,biology.organism_classification ,Sex specific ,Sexual dimorphism ,030104 developmental biology ,Drosophila melanogaster ,Auditory Perception ,Female ,General Agricultural and Biological Sciences ,Neuroscience ,030217 neurology & neurosurgery ,psychological phenomena and processes - Abstract
Males and females often produce distinct responses to the same sensory stimuli. How such differences arise – at the level of sensory processing or in the circuits that generate behavior – remains largely unresolved across sensory modalities. We address this issue in the acoustic communication system of Drosophila. During courtship, males generate time-varying songs, and each sex responds with specific behaviors. We characterize male and female behavioral tuning for all aspects of song, and show that feature tuning is similar between sexes, suggesting sex-shared song detectors drive divergent behaviors. We then identify higher-order neurons in the Drosophila brain, called pC2, that are tuned for multiple temporal aspects of one mode of the male’s song, and drive sex-specific behaviors. We thus uncover neurons that are specifically tuned to an acoustic communication signal and that reside at the sensory-motor interface, flexibly linking auditory perception with sex-specific behavioral responses.
- Published
- 2019
15. Neural Correlates of Cognition in Primary Visual versus Neighboring Posterior Cortices during Visual Evidence-Accumulation-based Navigation
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Sue Ann Koay, Carlos D. Brody, Stephan Y. Thiberge, and David W. Tank
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Visual processing ,Neural correlates of consciousness ,genetic structures ,Perception ,media_common.quotation_subject ,Sensory system ,Cognition ,Context (language use) ,Psychology ,Sensory cue ,Neuroscience ,media_common ,Task (project management) - Abstract
SummaryStudies of perceptual decision-making have often assumed that the main role of sensory cortices is to provide sensory input to downstream processes that accumulate and drive behavioral decisions. We performed a systematic comparison of neural activity in primary visual (V1) to secondary visual and retrosplenial cortices, as mice performed a task where they should accumulate pulsatile visual cues through time to inform a navigational decision. Even in V1, only a small fraction of neurons had sensory-like responses to cues. Instead, in all areas neurons were sequentially active, and contained information ranging from sensory to cognitive, including cue timings, evidence, place/time, decision and reward outcome. Per-cue sensory responses were amplitude-modulated by various cognitive quantities, notably accumulated evidence. This inspired a multiplicative feedback-loop circuit hypothesis that proposes a more intricate role of sensory areas in the accumulation process, and furthermore explains a surprising observation that perceptual discrimination deviates from Weber-Fechner Law.Highlights / eTOC BlurbMice made navigational decisions based on accumulating pulsatile visual cuesThe bulk of neural activity in visual cortices was sequential and beyond-sensoryAccumulated pulse-counts modulated sensory (cue) responses, suggesting feedbackA feedback-loop neural circuit explains behavioral deviations from Weber’s LawIn a task where navigation was informed by accumulated pulsatile visual evidence, neural activity in visual cortices predominantly coded for cognitive variables across multiple timescales, including outside of a visual processing context. Even sensory responses to visual pulses were amplitude-modulated by accumulated pulse counts and other variables, inspiring a multiplicative feedback-loop circuit hypothesis that in turn explained behavioral deviations from Weber-Fechner Law.
- Published
- 2019
- Full Text
- View/download PDF
16. Task-Dependent Changes in the Large-Scale Dynamics and Necessity of Cortical Regions
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Carlos D. Brody, Brian DePasquale, David W. Tank, Stephan Y. Thiberge, Lucas Pinto, and Kanaka Rajan
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0301 basic medicine ,Male ,Computer science ,media_common.quotation_subject ,Decision Making ,Optogenetics ,Article ,03 medical and health sciences ,Mice ,0302 clinical medicine ,Perception ,Cortex (anatomy) ,medicine ,Animals ,media_common ,Cerebral Cortex ,Working memory ,General Neuroscience ,Cognition ,Mice, Inbred C57BL ,Task (computing) ,030104 developmental biology ,medicine.anatomical_structure ,Dynamics (music) ,Female ,Neural Networks, Computer ,Scale (map) ,Neuroscience ,030217 neurology & neurosurgery - Abstract
Neural activity throughout the cortex is correlated with perceptual decisions, but inactivation studies suggest that only a small number of areas are necessary for these behaviors. Here we show that the number of required cortical areas, and their dynamics, vary across related tasks with different cognitive computations. In a visually-guided virtual T-maze task, bilateral inactivation of only a few dorsal cortical regions impaired performance. In contrast, in tasks requiring evidence accumulation and/or post-stimulus memory, performance was impaired by inactivation of widespread cortical areas, with diverse patterns of behavioral deficits across areas and tasks. Widefield imaging revealed widespread ramps of Ca(2+) activity during the accumulation and visually-guided tasks. Additionally, during accumulation different regions had more diverse activity profiles, leading to reduced inter-area correlations. Using a modular recurrent neural network model trained to perform analogous tasks, we argue that differences in computational strategies alone could explain these findings.
- Published
- 2018
17. Specialized and spatially organized coding of sensory, motor, and cognitive variables in midbrain dopamine neurons
- Author
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Ilana B. Witten, David W. Tank, Nathaniel D. Daw, Weston Fleming, Julia Cox, Sue Ann Koay, Sharon Ornelas, Ben Engelhard, Stephan Y. Thiberge, Joel Finkelstein, and Hee Jae Jang
- Subjects
0303 health sciences ,Sensory motor ,education.field_of_study ,Population ,Sensory system ,Biology ,Midbrain ,03 medical and health sciences ,0302 clinical medicine ,Calcium imaging ,Cognitive variables ,nervous system ,Dopamine ,medicine ,education ,Neuroscience ,030217 neurology & neurosurgery ,030304 developmental biology ,medicine.drug ,Coding (social sciences) - Abstract
There is increased appreciation that dopamine (DA) neurons in the midbrain respond not only to reward 1,2 and reward-predicting cues 1,3,4, but also to other variables such as distance to reward 5, movements 6–11 and behavioral choices 12–15. Based on these findings, a major open question is how the responses to these diverse variables are organized across the population of DA neurons. In other words, do individual DA neurons multiplex multiple variables, or are subsets of neurons specialized in encoding specific behavioral variables? The reason that this fundamental question has been difficult to resolve is that recordings from large populations of individual DA neurons have not been performed in a behavioral task with sufficient complexity to examine these diverse variables simultaneously. To address this gap, we used 2-photon calcium imaging through an implanted lens to record activity of >300 midbrain DA neurons in the VTA during a complex decision-making task. As mice navigated in a virtual reality (VR) environment, DA neurons encoded an array of sensory, motor, and cognitive variables. These responses were functionally clustered, such that subpopulations of neurons transmitted information about a subset of behavioral variables, in addition to encoding reward. These functional clusters were spatially organized, such that neighboring neurons were more likely to be part of the same cluster. Taken together with the topography between DA neurons and their projections, this specialization and anatomical organization may aid downstream circuits in correctly interpreting the wide range of signals transmitted by DA neurons.
- Published
- 2018
18. An accumulation-of-evidence task using visual pulses for mice navigating in virtual reality
- Author
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Lucas Pinto, Sue A. Koay, Ben Engelhard, Alice M. Yoon, Ben Deverett, Stephan Y. Thiberge, Ilana B. Witten, David W. Tank, and Carlos D. Brody
- Subjects
0301 basic medicine ,Computer science ,Cognitive Neuroscience ,evidence accumulation ,spatial navigation ,Sensory system ,Stimulus (physiology) ,Virtual reality ,Spatial memory ,decision making ,lcsh:RC321-571 ,Behavioral Neuroscience ,03 medical and health sciences ,Cognitive variables ,0302 clinical medicine ,lcsh:Neurosciences. Biological psychiatry. Neuropsychiatry ,mouse ,Original Research ,030304 developmental biology ,0303 health sciences ,behavior ,Single pulse ,Stereotypy (non-human) ,Visual evidence ,030104 developmental biology ,Neuropsychology and Physiological Psychology ,Perceptual decision ,virtual reality ,030217 neurology & neurosurgery ,Neuroscience ,Cognitive psychology - Abstract
The gradual accumulation of sensory evidence is a crucial component of perceptual decision making, but its neural mechanisms are still poorly understood. Given the wide availability of genetic and optical tools for mice, they can be useful model organisms for the study of these phenomena; however, behavioral tools are largely lacking. Here, we describe a new evidence-accumulation task for head-fixed mice navigating in a virtual reality environment. As they navigate down the stem of a virtual T-maze, they see brief pulses of visual evidence on either side, and retrieve a reward on the arm with the highest number of pulses. The pulses occur randomly with Poisson statistics, yielding a diverse yet well-controlled stimulus set, making the data conducive to a variety of computational approaches. A large number of mice of different genotypes were able to learn and consistently perform the task, at levels similar to rats in analogous tasks. They are sensitive to side differences of a single pulse, and their memory of the cues is stable over time. Moreover, using non-parametric as well as modeling approaches, we show that the mice indeed accumulate evidence: they use multiple pulses of evidence from throughout the cue region of the maze to make their decision, albeit with a small overweighting of earlier cues, and their performance is affected by the magnitude but not the duration of evidence. Additionally, analysis of the mice's running patterns revealed that trajectories are fairly stereotyped yet modulated by the amount of sensory evidence, suggesting that the navigational component of this task may provide a continuous readout correlated to the underlying cognitive variables. Our task, which can be readily integrated with state-of-the-art techniques, is thus a valuable tool to study the circuit mechanisms and dynamics underlying perceptual decision making, particularly under more complex behavioral contexts.
- Published
- 2017
19. Imaging Cortical Dynamics in GCaMP Transgenic Rats with a Head-Mounted Widefield Macroscope
- Author
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Alla Y. Karpova, Stephan Y. Thiberge, Caiying Guo, D. Gowanlock R. Tervo, David W. Tank, Benjamin B. Scott, and Carlos D. Brody
- Subjects
Male ,0301 basic medicine ,Neocortex ,Sensory system ,Biology ,Article ,03 medical and health sciences ,0302 clinical medicine ,Calcium imaging ,medicine ,Animals ,Calcium Signaling ,Calcium signaling ,Neurons ,Microscopy ,Behavior, Animal ,General Neuroscience ,Optical Imaging ,Dynamics (mechanics) ,Electrophysiology ,Luminescent Proteins ,Visual evidence ,030104 developmental biology ,medicine.anatomical_structure ,GCaMP ,Calcium ,Female ,Rats, Transgenic ,Transgenic Rats ,Neuroscience ,030217 neurology & neurosurgery - Abstract
Summary Widefield imaging of calcium dynamics is an emerging method for mapping regional neural activity but is currently limited to restrained animals. Here we describe cScope, a head-mounted widefield macroscope developed to image large-scale cortical dynamics in rats during natural behavior. cScope provides a 7.8 × 4 mm field of view and dual illumination paths for both fluorescence and hemodynamic correction and can be fabricated at low cost using readily attainable components. We also report the development of Thy-1 transgenic rat strains with widespread neuronal expression of the calcium indicator GCaMP6f. We combined these two technologies to image large-scale calcium dynamics in the dorsal neocortex during a visual evidence accumulation task. Quantitative analysis of task-related dynamics revealed multiple regions having neural signals that encode behavioral choice and sensory evidence. Our results provide a new transgenic resource for calcium imaging in rats and extend the domain of head-mounted microscopes to larger-scale cortical dynamics. Video Abstract Download : Download video (63MB)
- Published
- 2018
20. Volumetric two-photon imaging of neurons using stereoscopy (vTwINS)
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Jeffrey L. Gauthier, Alexander Song, Jonathan W. Pillow, Stephan Y. Thiberge, Sue Ann Koay, David W. Tank, and Adam S. Charles
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0301 basic medicine ,Point spread function ,Male ,Stereoscopy ,Mice, Transgenic ,Neural population ,Biology ,Biochemistry ,Hippocampus ,Article ,law.invention ,03 medical and health sciences ,Neural activity ,0302 clinical medicine ,Calcium imaging ,Imaging, Three-Dimensional ,Two-photon excitation microscopy ,law ,medicine ,Animals ,Molecular Biology ,030304 developmental biology ,Visual Cortex ,Physics ,Neurons ,0303 health sciences ,Microscopy, Confocal ,Cell Biology ,Frame rate ,Molecular Imaging ,030104 developmental biology ,Visual cortex ,medicine.anatomical_structure ,Microscopy, Fluorescence, Multiphoton ,Calcium ,Female ,030217 neurology & neurosurgery ,Algorithms ,Biotechnology ,Biomedical engineering ,Volume (compression) - Abstract
Two-photon laser scanning microscopy of calcium dynamics using fluorescent indicators is a widely used imaging method for large scale recording of neural activity in vivo. Here we introduce volumetric Two-photon Imaging of Neurons using Stereoscopy (vTwINS), a volumetric calcium imaging method that employs an elongated, V-shaped point spread function to image a 3D brain volume. Single neurons project to spatially displaced image pairs in the resulting 2D image, and the separation distance between images is proportional to depth in the volume. To demix the fluorescence time series of individual neurons, we introduce a novel orthogonal matching pursuit algorithm that also infers source locations within the 3D volume. We illustrate vTwINS by imaging neural population activity in mouse primary visual cortex and hippocampus. Our results demonstrate that vTwINS provides an effective method for volumetric two-photon calcium imaging that increases the number of neurons recorded while maintaining a high frame-rate.
- Published
- 2016
21. Volume conservation principle involved in cell lengthening and nucleus movement during tissue morphogenesis
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Matthias Kaschube, Bing He, Adam C. Martin, Stephan Y. Thiberge, Michael A. Gelbart, and Eric Wieschaus
- Subjects
Cell Nucleus ,Cytoplasm ,Embryo, Nonmammalian ,Multidisciplinary ,Movement ,Organogenesis ,Morphogenesis ,Cell Polarity ,Ventral furrow formation ,Apical constriction ,Apical cell ,Biological Sciences ,Biology ,Cell biology ,Drosophila melanogaster ,medicine.anatomical_structure ,Cell polarity ,medicine ,Animals ,Cytoskeleton ,Cell Shape ,Nucleus ,Cell Size - Abstract
Tissue morphogenesis is the process in which coordinated movements and shape changes of large numbers of cells form tissues, organs, and the internal body structure. Understanding morphogenetic movements requires precise measurements of whole-cell shape changes over time. Tissue folding and invagination are thought to be facilitated by apical constriction, but the mechanism by which changes near the apical cell surface affect changes along the entire apical–basal axis of the cell remains elusive. Here, we developed Embryo Development Geometry Explorer, an approach for quantifying rapid whole-cell shape changes over time, and we combined it with deep-tissue time-lapse imaging based on fast two-photon microscopy to study Drosophila ventral furrow formation. We found that both the cell lengthening along the apical–basal axis and the movement of the nucleus to the basal side proceeded stepwise and were correlated with apical constriction. Moreover, cell volume lost apically due to constriction largely balanced the volume gained basally by cell lengthening. The volume above the nucleus was conserved during its basal movement. Both apical volume loss and cell lengthening were absent in mutants showing deficits in the contractile cytoskeleton underlying apical constriction. We conclude that a single mechanical mechanism involving volume conservation and apical constriction-induced basal movement of cytoplasm accounts quantitatively for the cell shape changes and the nucleus movement in Drosophila ventral furrow formation. Our study provides a comprehensive quantitative analysis of the fast dynamics of whole-cell shape changes during tissue folding and points to a simplified model for Drosophila gastrulation.
- Published
- 2012
22. Metabolic cycling in single yeast cells from unsynchronized steady-state populations limited on glucose or phosphate
- Author
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Daniel Zenklusen, Daniel R. Larson, Nikolai Slavov, Robert H. Singer, Saumil J. Gandhi, Lance Parsons, Sanford J. Silverman, Allegra A. Petti, Ryan Briehof, David Botstein, and Stephan Y. Thiberge
- Subjects
Cell division ,Genes, Fungal ,Saccharomyces cerevisiae ,Chemostat ,Models, Biological ,Phosphates ,Exponential growth ,Gene Expression Regulation, Fungal ,Oscillometry ,Gene expression ,RNA, Messenger ,In Situ Hybridization, Fluorescence ,Multidisciplinary ,biology ,Gene Expression Profiling ,Metabolism ,Biological Sciences ,biology.organism_classification ,Yeast ,Cell biology ,Glucose ,Biochemistry ,Cell culture ,Energy Metabolism ,Cell Division - Abstract
Oscillations in patterns of expression of a large fraction of yeast genes are associated with the “metabolic cycle,” usually seen only in prestarved, continuous cultures of yeast. We used FISH of mRNA in individual cells to test the hypothesis that these oscillations happen in single cells drawn from unsynchronized cultures growing exponentially in chemostats. Gene-expression data from synchronized cultures were used to predict coincident appearance of mRNAs from pairs of genes in the unsynchronized cells. Quantitative analysis of the FISH results shows that individual unsynchronized cells growing slowly because of glucose limitation or phosphate limitation show the predicted oscillations. We conclude that the yeast metabolic cycle is an intrinsic property of yeast metabolism and does not depend on either synchronization or external limitation of growth by the carbon source.
- Published
- 2010
23. Remodeling nuclear architecture allows efficient transport of herpesvirus capsids by diffusion
- Author
-
Lynn W. Enquist, Beate Sodeik, Ian B. Hogue, Stephan Y. Thiberge, Jens B. Bosse, Clifford P. Brangwynne, and Marina Feric
- Subjects
Cell Nucleus ,Multidisciplinary ,Nucleoplasm ,viruses ,Motility ,Biology ,Virus Replication ,Filamentous actin ,Cell Line ,Transport protein ,Cell biology ,Diffusion ,Protein Transport ,Cell nucleus ,Capsid ,medicine.anatomical_structure ,Membrane ,PNAS Plus ,Microscopy, Fluorescence ,medicine ,Nucleus ,Herpesviridae - Abstract
The nuclear chromatin structure confines the movement of large macromolecular complexes to interchromatin corrals. Herpesvirus capsids of approximately 125 nm assemble in the nucleoplasm and must reach the nuclear membranes for egress. Previous studies concluded that nuclear herpesvirus capsid motility is active, directed, and based on nuclear filamentous actin, suggesting that large nuclear complexes need metabolic energy to escape nuclear entrapment. However, this hypothesis has recently been challenged. Commonly used microscopy techniques do not allow the imaging of rapid nuclear particle motility with sufficient spatiotemporal resolution. Here, we use a rotating, oblique light sheet, which we dubbed a ring-sheet, to image and track viral capsids with high temporal and spatial resolution. We do not find any evidence for directed transport. Instead, infection with different herpesviruses induced an enlargement of interchromatin domains and allowed particles to diffuse unrestricted over longer distances, thereby facilitating nuclear egress for a larger fraction of capsids.
- Published
- 2015
24. Cellular mechanisms of alpha herpesvirus egress: live cell fluorescence microscopy of pseudorabies virus exocytosis
- Author
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Ian B. Hogue, Jens B. Bosse, Jiun-Ruey Hu, Lynn W. Enquist, and Stephan Y. Thiberge
- Subjects
Viral Diseases ,viruses ,Nucleocapsids ,Virions ,Molecular Cell Biology ,Capsids ,Medicine and Health Sciences ,lcsh:QH301-705.5 ,Virus Release ,Vesicle ,Vector Construction ,Herpesvirus 1, Suid ,Secretory Vesicle ,3. Good health ,Cell biology ,Infectious Diseases ,Veterinary Diseases ,Viral Envelope ,Research Article ,lcsh:Immunologic diseases. Allergy ,Immunology ,Sexually Transmitted Diseases ,Viral Structure ,DNA construction ,Biology ,Microbiology ,Exocytosis ,Cell Line ,Gene Delivery ,RAB6A ,Virology ,Gene Expression and Vector Techniques ,Genetics ,Viral Components ,Humans ,Molecular Biology ,Secretory pathway ,Molecular Biology Assays and Analysis Techniques ,Biology and life sciences ,Lipid bilayer fusion ,Herpes Simplex ,Epithelial Cells ,Cell Biology ,Recombinant Gene Expression Techniques ,Veterinary Virology ,Molecular biology techniques ,Microscopy, Fluorescence ,lcsh:Biology (General) ,rab GTP-Binding Proteins ,Viral exocytosis ,Veterinary Science ,Parasitology ,Rab ,Carrier Proteins ,lcsh:RC581-607 - Abstract
Egress of newly assembled herpesvirus particles from infected cells is a highly dynamic process involving the host secretory pathway working in concert with viral components. To elucidate the location, dynamics, and molecular mechanisms of alpha herpesvirus egress, we developed a live-cell fluorescence microscopy method to visualize the final transport and exocytosis of pseudorabies virus (PRV) particles in non-polarized epithelial cells. This method is based on total internal reflection fluorescence (TIRF) microscopy to selectively image fluorescent virus particles near the plasma membrane, and takes advantage of a virus-encoded pH-sensitive probe to visualize the precise moment and location of particle exocytosis. We performed single-particle tracking and mean squared displacement analysis to characterize particle motion, and imaged a panel of cellular proteins to identify those spatially and dynamically associated with viral exocytosis. Based on our data, individual virus particles travel to the plasma membrane inside small, acidified secretory vesicles. Rab GTPases, Rab6a, Rab8a, and Rab11a, key regulators of the plasma membrane-directed secretory pathway, are present on the virus secretory vesicle. These vesicles undergo fast, directional transport directly to the site of exocytosis, which is most frequently near patches of LL5β, part of a complex that anchors microtubules to the plasma membrane. Vesicles are tightly docked at the site of exocytosis for several seconds, and membrane fusion occurs, displacing the virion a small distance across the plasma membrane. After exocytosis, particles remain tightly confined on the outer cell surface. Based on recent reports in the cell biological and alpha herpesvirus literature, combined with our spatial and dynamic data on viral egress, we propose an integrated model that links together the intracellular transport pathways and exocytosis mechanisms that mediate alpha herpesvirus egress., Author Summary Pseudorabies virus, an alpha herpesvirus, is an important veterinary pathogen, and related to human varicella-zoster virus and herpes simplex viruses. New alpha herpesvirus particles are assembled inside an infected cell, and must exit from the infected cell by taking advantage of cellular mechanisms. How these virus particles are transported inside the infected cell and secreted at the cell surface is not understood in great detail. In particular, how this process unfolds over time is not easily observed using previous methods. In this study, we developed a new method to observe this egress process. Using this method, we described how virus particles move on their way out: individual virus particles travel to the cell surface, directly to the exit site, where they pause for several seconds before crossing out of the cell. We identified several cellular proteins that are involved in this process. After exiting, virus particles remained stuck to the outer cell surface. Finally, we draw connections between our observations and other recent studies to propose an integrated model of how alpha herpesvirus particles exit from infected cells.
- Published
- 2014
25. An apparatus for imaging liquids, cells, and other wet samples in the scanning electron microscopy
- Author
-
Elisha Moses, Ory Zik, and Stephan Y. Thiberge
- Subjects
Materials science ,business.industry ,Resolution (electron density) ,Scanning confocal electron microscopy ,Dark field microscopy ,Characterization (materials science) ,law.invention ,Optics ,Optical microscope ,law ,Scanning ion-conductance microscopy ,Energy filtered transmission electron microscopy ,Near-field scanning optical microscope ,business ,Instrumentation - Abstract
We present a technique of scanning electron microscopy that is adapted to the study of wet samples. The wet environment is protected in a small chamber enclosed by a membrane, which is thin enough for energetic electrons to go through and interact with the sample studied. We detail both the technique and the general mechanisms of signal formation in the imaging of samples through a membrane. We first describe our setup and the properties required for the membrane, the main element in this method. Some simple measurements for its characterization are given, guiding the choice of material and thickness. We then go on to describe the capabilities of the technique in imaging a variety of different samples. We evaluate the accessible contrast and resolution, and the current needed to obtain them. Low contrast samples can be imaged with an improvement in resolution over optical microscopy. High contrast samples like gold markers labeling a biological cell can be imaged with a resolution of the order of 10 nm. The resolution depends on the location of the particle in the sample: the closer to the membrane, the better the resolution. We believe such a result opens up potential applications for routine experiments in biology, and expect this new technique to find numerous applications in domains where liquid samples are investigated such as soft materials science.
- Published
- 2004
26. Scanning electron microscopy of cells and tissues under fully hydrated conditions
- Author
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Elisha Moses, David Sprinzak, Vered Behar, Shulamit Michaeli, Ory Zik, Opher Gileadi, Yehuda Chowers, Amotz Nechushtan, Stephan Y. Thiberge, and Joseph Schlessinger
- Subjects
Materials science ,Scanning electron microscope ,Cytological Techniques ,Trypanosoma brucei brucei ,Analytical chemistry ,Electrons ,CHO Cells ,Electron ,law.invention ,Mice ,Biological specimen ,Optical microscope ,law ,Cricetinae ,Animals ,Humans ,Scattering, Radiation ,Multidisciplinary ,Staining and Labeling ,business.industry ,Histological Techniques ,Resolution (electron density) ,Scanning confocal electron microscopy ,Water ,Membrane ,Physical Sciences ,Microscopy, Electron, Scanning ,Optoelectronics ,Gold ,Electron microscope ,business ,HeLa Cells - Abstract
A capability for scanning electron microscopy of wet biological specimens is presented. A membrane that is transparent to electrons protects the fully hydrated sample from the vacuum. The result is a hybrid technique combining the ease of use and ability to see into cells of optical microscopy with the higher resolution of electron microscopy. The resolution of low-contrast materials is ≈100 nm, whereas in high-contrast materials the resolution can reach 10 nm. Standard immunogold techniques and heavy-metal stains can be applied and viewed in the fluid to improve the contrast. Images present a striking combination of whole-cell morphology with a wealth of internal details. A possibility for direct inspection of tissue slices transpires, imaging only the external layer of cells. Simultaneous imaging with photons excited by the electrons incorporates data on material distribution, indicating a potential for multilabeling and specific scintillating markers.
- Published
- 2004
27. New Aspect of the Voltage/Confinement Ratio Phase Diagram for a Confined Homeotropic Cholesteric
- Author
-
J. M. Gilli, D. Manaila-Maximean, and Stephan Y. Thiberge
- Subjects
Materials science ,Dopant ,Condensed matter physics ,Homeotropic alignment ,General Chemistry ,Condensed Matter Physics ,Topological defect ,Physics::Fluid Dynamics ,Condensed Matter::Soft Condensed Matter ,MBBA ,Dipole ,Crystallography ,chemistry.chemical_compound ,chemistry ,Liquid crystal ,General Materials Science ,SPHERES ,Phase diagram - Abstract
We have investigated the behavior of a cholesteric mixture, consisting of the negative dielectric anisotropy liquid crystal MBBA and a chiral dopant S811(1%b.w.). In the phase diagram a.c. applied voltage versus confinement ratio, in addition to the transition previously observed, before reaching the domain of the transition TIC(Translationnary Invariant Cholesteric)–modulated TIC, we have observed a new stability domain for the topological bubble. These bubbles are now surrounded by the TIC domains and necessarily associated to an hyperbolic − 1 defect of the in plane director component.We have also obtained experimentally topological defect chains, formed by topological dipoles similar to the ones formed in 2 compound materials: liquid crystal/solid spheres or liquid crystal/liquid droplets.
- Published
- 2004
28. Nuclear Herpesvirus Capsid Motility Is Not Dependent on F-Actin
- Author
-
Julian Scherer, Stephan Y. Thiberge, Jens B. Bosse, Harald Wodrich, Stina Virding, Zsolt Ruzsics, Lynn W. Enquist, and Ulrich H. Koszinowski
- Subjects
Immunoprecipitation ,viruses ,Motility ,macromolecular substances ,Microbiology ,Mice ,03 medical and health sciences ,Capsid ,Virology ,Myosin ,medicine ,Molecular motor ,Animals ,Cells, Cultured ,Herpesviridae ,Actin ,030304 developmental biology ,Cell Nucleus ,0303 health sciences ,Microscopy, Confocal ,Chemistry ,030302 biochemistry & molecular biology ,Biological Transport ,Fibroblasts ,Actins ,QR1-502 ,3. Good health ,Cell biology ,medicine.anatomical_structure ,Microscopy, Fluorescence ,Viral replication ,Nucleus ,Research Article - Abstract
A considerable part of the herpesvirus life cycle takes place in the host nucleus. While much progress has been made to understand the molecular processes required for virus replication in the nucleus, much less is known about the temporal and spatial dynamics of these events. Previous studies have suggested that nuclear capsid motility is directed and dependent on actin filaments (F-actin), possibly using a myosin-based, ATP-dependent mechanism. However, the conclusions from these studies were indirect. They either relied on the effects of F-actin depolymerizing drugs to deduce an F-actin dependency or they visualized nuclear F-actin but failed to show a direct link to capsid motility. Moreover, no direct link between nuclear capsid motility and a molecular motor has been established. In this report, we reinvestigate the involvement of F-actin in nuclear herpesvirus capsid transport. We show for representative members of all three herpesvirus subfamilies that nuclear capsid motility is not dependent on nuclear F-actin and that herpesvirus infection does not induce nuclear F-actin in primary fibroblasts. Moreover, in these cells, three F-actin-inhibiting drugs failed to effect capsid motility. Only latrunculin A treatment stalled nuclear capsids but did so by an unexpected effect: the drug induced actin rods in the nucleus. Immobile capsids accumulated around actin rods, and immunoprecipitation experiments suggested that capsid motility stopped because latrunculin-induced actin rods nonspecifically bind nuclear capsids. Interestingly, capsid motility was unaffected in cells that do not induce actin rods. Based on these data, we conclude that herpesvirus nuclear capsid motility is not dependent on F-actin., IMPORTANCE Herpesviruses are large DNA viruses whose replication is dependent on the host nucleus. However, we do not understand how key nuclear processes, including capsid assembly, genome replication, capsid packaging, and nuclear egress, are dynamically connected in space and time. Fluorescence live-cell microscopy revealed that nuclear capsids are highly mobile early in infection. Two studies suggested that this motility might be due to active myosin-based transport of capsids on nuclear F-actin. However, direct evidence for such motor-based transport is lacking. We revisited this phenomenon and found no evidence that nuclear capsid motility depended on F-actin. Our results reopen the question of how nuclear herpesvirus capsids move in the host nucleus.
- Published
- 2014
29. Critical radius of loop defects in homeotropic nematic liquid crystals
- Author
-
Ágnes Buka, Stephan Y. Thiberge, Corinne Chevallard, and J.M. Gilli
- Subjects
Materials science ,Condensed matter physics ,Biaxial nematic ,business.industry ,Tension (physics) ,Homeotropic alignment ,General Chemistry ,Disclination ,Condensed Matter Physics ,Condensed Matter::Soft Condensed Matter ,Optics ,Liquid crystal ,General Materials Science ,Boundary value problem ,Critical radius ,business ,Line (formation) - Abstract
We describe an experimental situation with a looped line defect in nematic liquid crystals observed by polarizing optical microscopy. We measured the critical size of the loop below which it spontaneously shrinks and transforms into a point defect. The experiment was done with 5CB which gives rise to twist disclinations as do most of the usual nematics. For this kind of disclination an in-plane force due to the boundary conditions acts on the line and influences the critical radius. W e have constructed a model which is in good agreement with experimental measurements and deduced the line tension of the disclination.
- Published
- 1999
30. Inversion walls in homeotropic nematic and cholesteric layers
- Author
-
A. Vierheilig, F. Fried, Stephan Y. Thiberge, and J. M. Gilli
- Subjects
Birefringence ,Materials science ,Condensed matter physics ,business.industry ,Homeotropic alignment ,General Chemistry ,Disclination ,Condensed Matter Physics ,Optics ,Liquid crystal ,Electric field ,Metastability ,Perpendicular ,General Materials Science ,business ,Directional solidification - Abstract
We describe the experimental properties of metastable domains associated with the presence of an Inversion Wall (IW) and observed with homeotropically anchored nematic and cholesteric liquid crystals sandwiched between parallel glass plates. Such a distorted situation, stabilized by the application of an electric field parallel to the plates as described in reference [1], can also be obtained transiently either when filling a sample cell by capillarity or in some studies of directional solidification at the N-I interface [2]. The application of an electric field perpendicular to the plates with Delta epsilon 0 materials allows control of the reversal region thickness in the bulk of the sample and its associated birefringence. This IW can be stabilized in the particular case of low lateral extension globules in which the line tension of the looped disclination separating the pi wall regions from the homeotropic regions counterbalances the unfavourable bulk free energy. Particular attention is devoted to th...
- Published
- 1997
31. In vivo imaging of alphaherpesvirus infection reveals synchronized activity dependent on axonal sorting of viral proteins
- Author
-
Lynn W. Enquist, Stephan Y. Thiberge, Andrea E. Granstedt, and Jens B. Bosse
- Subjects
Male ,Lipoproteins ,viruses ,Submandibular Gland ,Action Potentials ,Pseudorabies ,Virus ,Mice ,Viral Proteins ,Viral Envelope Proteins ,In vivo ,Calcium flux ,medicine ,Animals ,Humans ,Calcium Signaling ,Peripheral Nerves ,Neurons ,chemistry.chemical_classification ,Multidisciplinary ,Virulence ,biology ,Pruritus ,Intracellular Signaling Peptides and Proteins ,virus diseases ,Peripheral Nervous System Diseases ,Lipid bilayer fusion ,Viral membrane ,Phosphoproteins ,biology.organism_classification ,Herpesvirus 1, Suid ,Virology ,Axons ,Recombinant Proteins ,Luminescent Proteins ,medicine.anatomical_structure ,PNAS Plus ,nervous system ,chemistry ,Peripheral nervous system ,Glycoprotein - Abstract
A clinical hallmark of human alphaherpesvirus infections is peripheral pain or itching. Pseudorabies virus (PRV), a broad host range alphaherpesvirus, causes violent pruritus in many different animals, but the mechanism is unknown. Previous in vitro studies have shown that infected, cultured peripheral nervous system (PNS) neurons exhibited aberrant electrical activity after PRV infection due to the action of viral membrane fusion proteins, yet it is unclear if such activity occurs in infected PNS ganglia in living animals and if it correlates with disease symptoms. Using two-photon microscopy, we imaged autonomic ganglia in living mice infected with PRV strains expressing GCaMP3, a genetically encoded calcium indicator, and used the changes in calcium flux to monitor the activity of many neurons simultaneously with single-cell resolution. Infection with virulent PRV caused these PNS neurons to fire synchronously and cyclically in highly correlated patterns among infected neurons. This activity persisted even when we severed the presynaptic axons, showing that infection-induced firing is independent of input from presynaptic brainstem neurons. This activity was not observed after infections with an attenuated PRV recombinant used for circuit tracing or with PRV mutants lacking either viral glycoprotein B, required for membrane fusion, or viral membrane protein Us9, required for sorting virions and viral glycoproteins into axons. We propose that the viral fusion proteins produced by virulent PRV infection induce electrical coupling in unmyelinated axons in vivo. This action would then give rise to the synchronous and cyclical activity in the ganglia and contribute to the characteristic peripheral neuropathy.
- Published
- 2013
32. Correction for Silverman et al., Metabolic cycling in single yeast cells from unsynchronized steady-state populations limited on glucose or phosphate
- Author
-
Nikolai Slavov, Saumil J. Gandhi, David Botstein, Lance Parsons, Ryan Briehof, Allegra A. Petti, Daniel R. Larson, Robert H. Singer, Sanford J. Silverman, Daniel Zenklusen, and Stephan Y. Thiberge
- Subjects
chemistry.chemical_compound ,Multidisciplinary ,Biochemistry ,chemistry ,Steady state (chemistry) ,Biology ,Cycling ,Phosphate ,Corrections ,Yeast - Published
- 2011
33. Imaging cilia in zebrafish
- Author
-
Kimberly M, Jaffe, Stephan Y, Thiberge, Margaret E, Bisher, and Rebecca D, Burdine
- Subjects
Microscopy ,Embryo, Nonmammalian ,Movement ,Animals ,Humans ,Cilia ,Models, Biological ,Cryoultramicrotomy ,Zebrafish - Abstract
Research focused on cilia as extremely important cellular organelles has flourished in recent years. A thorough understanding of cilia regulation and function is critical, as disruptions of cilia structure and/or function have been linked to numerous human diseases and disorders. The tropical freshwater zebrafish is an excellent model organism in which to study cilia structure and function. We can readily image cilia and their motility in embryonic structures including Kupffer's vesicle during somite stages and the pronephros from 1 day postfertilization onward. Here, we describe how to image cilia by whole-mount immunofluorescence, transverse cryosection/immunohistochemistry, and transmission electron microscopy. We also describe how to obtain videos of cilia motility in living embryos.
- Published
- 2010
34. Imaging Cilia in Zebrafish
- Author
-
M. E. Bisher, Rebecca D. Burdine, Stephan Y. Thiberge, and Kimberly M. Jaffe
- Subjects
ved/biology ,Cilium ,ved/biology.organism_classification_rank.species ,Motility ,respiratory system ,Biology ,biology.organism_classification ,Cell biology ,Pronephros ,Somite ,medicine.anatomical_structure ,Embryonic Structure ,Organelle ,medicine ,Model organism ,Zebrafish - Abstract
Research focused on cilia as extremely important cellular organelles has flourished in recent years. A thorough understanding of cilia regulation and function is critical, as disruptions of cilia structure and/or function have been linked to numerous human diseases and disorders. The tropical freshwater zebrafish is an excellent model organism in which to study cilia structure and function. We can readily image cilia and their motility in embryonic structures including Kupffer's vesicle during somite stages and the pronephros from 1 day postfertilization onward. Here, we describe how to image cilia by whole-mount immunofluorescence, transverse cryosection/immunohistochemistry, and transmission electron microscopy. We also describe how to obtain videos of cilia motility in living embryos.
- Published
- 2010
35. Noise Propagation in Transcriptional Cascades
- Author
-
R. Weis, Stephan Y. Thiberge, and Sara Hooshangi
- Subjects
Network complexity ,Steady state (electronics) ,Computer science ,Stochastic modelling ,Function (mathematics) ,Sensitivity (control systems) ,Biological system ,Noise (electronics) ,Simulation ,Biological network ,Noise propagation - Abstract
The flow of information through a biological network can greatly influence the operation and behavior of the system. The synthetic transcriptional cascades of various lengths and study of their dynamic and steady state behavior both experimentally and through a stochastic model are presented. These systems are used to analyze sensitivity and noise propagation as a function of synthetic network complexity. The steady state switching behavior that becomes sharper with longer cascades is demonstrated experimentally. The experimental results demonstrating the network properties correlate well with the simulated model.
- Published
- 2006
36. Ultrasensitivity and noise propagation in a synthetic transcriptional cascade
- Author
-
Sara Hooshangi, Ron Weiss, and Stephan Y. Thiberge
- Subjects
Genetics ,education.field_of_study ,Network complexity ,Stochastic Processes ,Multidisciplinary ,Transcription, Genetic ,Stochastic process ,Population ,Noise attenuation ,Gene Expression Regulation, Bacterial ,Biology ,Biological Sciences ,Luminescent Proteins ,Bacterial Proteins ,Cascade ,Ultrasensitivity ,Biological system ,education ,Biological network ,Noise propagation - Abstract
The precise nature of information flow through a biological network, which is governed by factors such as response sensitivities and noise propagation, greatly affects the operation of biological systems. Quantitative analysis of these properties is often difficult in naturally occurring systems but can be greatly facilitated by studying simple synthetic networks. Here, we report the construction of synthetic transcriptional cascades comprising one, two, and three repression stages. These model systems enable us to analyze sensitivity and noise propagation as a function of network complexity. We demonstrate experimentally steady-state switching behavior that becomes sharper with longer cascades. The regulatory mechanisms that confer this ultrasensitive response both attenuate and amplify phenotypical variations depending on the system's input conditions. Although noise attenuation allows the cascade to act as a low-pass filter by rejecting short-lived perturbations in input conditions, noise amplification results in loss of synchrony among a cell population. The experimental results demonstrating the above network properties correlate well with simulations of a simple mathematical model of the system.
- Published
- 2005
37. Spatiotemporal control of gene expression with pulse-generating networks
- Author
-
Stephan Y. Thiberge, Rishabh Mehreja, Ming Tang Chen, Subhayu Basu, and Ron Weiss
- Subjects
Regulation of gene expression ,Multidisciplinary ,Pulse generator ,Feed forward ,Biology ,Biological Sciences ,Green fluorescent protein ,Cell biology ,Synthetic biology ,Biochemistry ,Gene Expression Regulation ,Gene expression ,Inducer ,Cell-cell signaling - Abstract
One of the important challenges in the emerging field of synthetic biology is designing artificial networks that achieve coordinated behavior in cell communities. Here we present a synthetic multicellular bacterial system where receiver cells exhibit transient gene expression in response to a long-lasting signal from neighboring sender cells. The engineered sender cells synthesize an inducer, an acyl-homoserine lactone (AHL), which freely diffuses to spatially proximate receiver cells. The receiver cells contain a pulse-generator circuit that incorporates a feed-forward regulatory motif. The circuit responds to a long-lasting increase in the level of AHL by transiently activating, and then repressing, the expression of a GFP. Based on simulation models, we engineered variants of the pulse-generator circuit that exhibit different quantitative responses such as increased duration and intensity of the pulse. As shown by our models and experiments, the maximum amplitude and timing of the pulse depend not only on the final inducer concentration, but also on its rate of increase. The ability to differentiate between various rates of increase in inducer concentrations affords the system a unique spatiotemporal behavior for cells grown on solid media. Specifically, receiver cells can respond to communication from nearby sender cells while completely ignoring communication from senders cells further away, despite the fact that AHL concentrations eventually reach high levels everywhere. Because of the resemblance to naturally occurring feed-forward motifs, the pulse generator can serve as a model to improve our understanding of such systems.
- Published
- 2004
38. New methods in femtosecond multiphoton microscopy
- Author
-
Yaron Silberberg, Dan Oron, Nirit Dudovich, Dvir Yelin, and Stephan Y. Thiberge
- Subjects
symbols.namesake ,Optics ,Multiphoton fluorescence microscope ,Materials science ,business.industry ,Femtosecond ,Microscopy ,symbols ,Nanotechnology ,business ,Raman spectroscopy - Abstract
The field of multiphoton microscopy has undergone significant advances since its beginning just over a decade ago. One of these was the development of coherent multiphoton techniques, which typically image intrinsic properties of the sample, without resorting to staining or labeling. Here we describe some recent technological developments in the two leading coherent multiphoton techniques: third-harmonic generation and coherent anti-Stokes Raman spectroscopy. These techniques are applied for visualization of a variety of biological and other samples.
- Published
- 2003
39. Is the Electromechanical Coupling the Driving Force for the Perpendicular Drift of First Class Cholesteric Finger?
- Author
-
Stephan Y. Thiberge and L. Gil
- Subjects
Physics ,Physics and Astronomy (miscellaneous) ,business.industry ,General Engineering ,02 engineering and technology ,021001 nanoscience & nanotechnology ,01 natural sciences ,Atomic and Molecular Physics, and Optics ,Condensed Matter::Soft Condensed Matter ,Optics ,[PHYS.HIST]Physics [physics]/Physics archives ,0103 physical sciences ,Perpendicular ,Electromechanical coupling ,Atomic physics ,010306 general physics ,0210 nano-technology ,business - Abstract
Dans un cristal liquide cholesterique pris en sandwich entre deux lames de verres conductrices avec des conditions d'ancrage homeotrope, l'apparition de structures spatiales isolees, appelees doigts cholesteriques de premiere espece, est maintenant bien comprise. Quand on soumet le cristal liquide a un champ electrique vertical, on observe alors que ces doigts cholesteriques se mettent a bouger perpendiculairement a son grand axe avec une vitesse V⊥. Dans ce papier, on montre analytiquement que cette vitesse pourrait etre reliee a l'effet Lehmann, et que sa mesure permettrait alors d'estimer la valeur du coefficient de couplage electromecanique.
- Published
- 1997
40. Multiphoton plasmon-resonance microscopy
- Author
-
Yaron Silberberg, Elisha Moses, Dan Oron, Stephan Y. Thiberge, and Dvir Yelin
- Subjects
Materials science ,Laser scanning ,business.industry ,technology, industry, and agriculture ,Physics::Optics ,Resonance ,Atomic and Molecular Physics, and Optics ,Interference microscopy ,Autofluorescence ,Optics ,Live cell imaging ,Microscopy ,Surface plasmon resonance ,business ,Plasmon - Abstract
A novel method for detection of noble-metal nanoparticles by their nonlinear optical properties is presented and applied for specific labeling of cellular organelles. When illuminated by laser light in resonance with their plasmon frequency these nanoparticles generate an enhanced multiphoton signal. This enhanced signal is measured to obtain a depth-resolved image in a laser scanning microscope setup. Plasmon-resonance images of both live and fixed cells, showing specific labeling of cellular organelles and membranes, either by two-photon autofluorescence or by third-harmonic generation, are presented.
- Published
- 2003
41. Zebrafish mutations affecting cilia motility share similar cystic phenotypes and suggest a mechanism of cyst formation that differs from pkd2 morphants
- Author
-
Noriko Okabe, Jodi Schottenfeld, Stephan Y. Thiberge, Christine L. Hostetter, Jessica Sullivan-Brown, Fabrizio C. Serluca, and Rebecca D. Burdine
- Subjects
switch hitter ,medicine.medical_specialty ,Embryo, Nonmammalian ,lrrc50 ,Kidney Glomerulus ,Motility ,Kidney ,Article ,Pronephros ,oda7 ,pkd2 ,Internal medicine ,Nephron ,Polycystic kidney disease ,medicine ,Animals ,Cyst ,Cilia ,Cloning, Molecular ,Molecular Biology ,Zebrafish ,Cystic kidney ,Microscopy, Video ,biology ,kurly ,Cilium ,locke ,Nephrons ,Cell Biology ,Zebrafish Proteins ,medicine.disease ,biology.organism_classification ,Cell biology ,Kidney Tubules ,Phenotype ,Endocrinology ,LRRC50 ,Mutagenesis ,Mutation ,Developmental Biology - Abstract
Zebrafish are an attractive model for studying the earliest cellular defects occurring during renal cyst formation because its kidney (the pronephros) is simple and genes that cause cystic kidney diseases (CKD) in humans, cause pronephric dilations in zebrafish. By comparing phenotypes in three different mutants, locke, swt and kurly, we find that dilations occur prior to 48 hpf in the medial tubules, a location similar to where cysts form in some mammalian diseases. We demonstrate that the first observable phenotypes associated with dilation include cilia motility and luminal remodeling defects. Importantly, we show that some phenotypes common to human CKD, such as an increased number of cells, are secondary consequences of dilation. Despite having differences in cilia motility, locke, swt and kurly share similar cystic phenotypes, suggesting that they function in a common pathway. To begin to understand the molecular mechanisms involved in cyst formation, we have cloned the swt mutation and find that it encodes a novel leucine rich repeat containing protein (LRRC50), which is thought to function in correct dynein assembly in cilia. Finally, we show that knock-down of polycystic kidney disease 2 (pkd2) specifically causes glomerular cysts and does not affect cilia motility, suggesting multiple mechanisms exist for cyst formation.
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