Honors & Awards
United States Physics Team, International Physics Olympiad, Bad Ischl, Austria (1988)
Detur Scholar, Harvard University (1989)
John Harvard Scholarships, John Harvard Scholarships (1989-1991)
Barry Goldwater Fellowship for Excellence in Science, United States, Barry Goldwater Fellowship for Excellence in Science, United States (1990)
Junior Phi Beta Kappa for top 12 Junior men, Harvard University (1991)
Winston Churchill Fellowship, Winston Churchill Foundation of the United States (1992-1993)
Predoctoral Fellowship, NSF (1993-1996)
Predoctoral Fellowship, American Heart Association (1996-1998)
Charlotte Elizabeth Procter Honorific Fellowship, Princeton Univeristy (1997-1998)
Burroughs Wellcome Fellowship, Program in Mathematics and Molecular Biology (1998-1999)
McKnight Technological Innovations in Neuroscience Award, McKnight Foundation (2000)
Young Investigator Award (with #1 world ranking), Human Frontiers in Science Program (2002)
Cutting Edge Basic Research Award (CEBRA) Science, National Institutes of Health (2003)
Member of TR100,World's Top 100 Innovators under age 35, Technology Review Magazine (2003)
Young Investigator Award, Office of Naval Research, Cognitive & Neural Division (2004)
Klingenstein Fellowship in the Neurosciences, Klingenstein Foundation (2004)
Young Investigator Award, Beckman Foundation (2004)
Presidential Early Career Award in Science and Engineering 2004, Presented at the White House on June 13, 2005 (2004)
Alfred P. Sloan Foundation Research Fellow, Alfred P. Sloan Foundation (2005)
Fellowship in Science & Engineering, David & Lucille Packard Foundation (2005)
Beckman Interdisciplinary Translational Research Program Award, Stanford University (2005)
Terman Fellow, Stanford University (2006)
NIH Director's Pioneer Award, National Institutes of Health (2007)
The Brilliant 10, Top ten brilliant scientists under age 40, Popular Science Magazine (2007)
W.M. Keck Foundation, Medical Research Program grant, W.M. Keck Foundation (2007)
Best Techniques Paper, Co-Author, American Society of Biomechanics (2007)
HHMI Investigator, Howard Hughes Medical Institute (2008)
Michael & Kate Bárány Young Investigator Award, Biophysical Society (2010)
Allen Distinguished Investigator Award, Paul G. Allen Family Foundation (2010)
National Academy Keck Futures Initiative Award, W.M. Keck Foundation (2011)
Ellison Senior Scholar Award, Ellison Foundation (2012)
Current Research and Scholarly Interests
The long-term goal of our research is to advance experimental paradigms for understanding normal cognitive and disease processes at the level of neural circuits, with emphasis on learning and memory processes. By contrast, much current research on learning and memory concentrates on levels of organization in the nervous system that are either more macroscopic (e.g. in cognitive psychology) or more microscopic (e.g. in synaptic physiology).
Our approach combines behavioral, electrophysiological, and computational methodologies with high-resolution fluorescence optical imaging that is capable of resolving individual neurons and dendrites. By necessity, we aim to advance imaging methods so that we can examine dynamics of neuronal populations or of dendritic compartments in behaving animals. En route, we are also performing experiments on circuit properties in anesthetized animals, such as the studies that use our newly invented fluorescence endoscopes for examining hippocampal cells and dendrites in vivo.
We seek explanations that span different levels of organization, from cells to entire circuits. We work with both genetic model organisms, mice and fruit flies, and human subjects. Our research emphasizes understanding the control and learning of motor behaviors, as well as the potential application of our newly developed imaging techniques to clinical use in humans.
- Introduction to Biophysics
APPPHYS 205, BIO 126, BIO 226 (Win)
Independent Studies (17)
- Advanced Research Laboratory in Experimental Biology
BIO 199 (Aut, Win, Spr, Sum)
- Bioengineering Problems and Experimental Investigation
BIOE 191 (Aut, Win, Spr, Sum)
- Directed Investigation
BIOE 392 (Aut, Win, Spr, Sum)
- Directed Reading in Biology
BIO 198 (Aut, Win, Spr, Sum)
- Directed Reading in Biophysics
BIOPHYS 399 (Aut, Win, Spr, Sum)
- Directed Reading in Neurosciences
NEPR 299 (Aut, Win, Spr, Sum)
- Directed Studies in Applied Physics
APPPHYS 290 (Aut, Win, Spr, Sum)
- Directed Study
BIOE 391 (Aut, Win, Spr, Sum)
- Graduate Research
BIO 300 (Aut, Win, Spr, Sum)
- Graduate Research
BIOPHYS 300 (Aut, Win, Spr, Sum)
- Graduate Research
NEPR 399 (Aut, Win, Spr, Sum)
- Out-of-Department Advanced Research Laboratory in Experimental Biology
BIO 199X (Sum)
- Out-of-Department Directed Reading
BIO 198X (Aut, Win, Spr, Sum)
- Out-of-Department Graduate Research
BIO 300X (Win, Spr, Sum)
- Practical Training
APPPHYS 291 (Sum)
PHYSICS 490 (Aut, Win, Spr, Sum)
- Teaching of Biology
BIO 290 (Aut, Win, Spr)
- Advanced Research Laboratory in Experimental Biology
Prior Year Courses
- Advanced Imaging Lab in Biophysics
APPPHYS 232, BIO 132, BIO 232, BIOPHYS 232, GENE 232 (Spr)
- Introduction to Biophysics
APPPHYS 205, BIO 126, BIO 226 (Win)
- Advanced Imaging Lab in Biophysics
APPPHYS 232, BIO 132, BIO 232, BIOPHYS 232, GENE 232 (Spr)
- Introduction to Biophysics
APPPHYS 205, BIO 126, BIO 226 (Win)
- Advanced Imaging Lab in Biophysics
Postdoctoral Faculty Sponsor
Radoslaw Chrapkiewicz, Simon Haziza, Oscar Ruben Hernandez Cubero, Cheng Huang, Elizabeth Otto Hamel, Thomas Rogerson, Claudia Schmuckermair, Adam Shai, Albert Tsao, Peng Yuan, Bin Zhang
Doctoral Dissertation Reader (AC)
Doctoral Dissertation Advisor (AC)
The neural representation of taste quality at the periphery
2015; 517 (7534): 373-U511
The mammalian taste system is responsible for sensing and responding to the five basic taste qualities: sweet, sour, bitter, salty and umami. Previously, we showed that each taste is detected by dedicated taste receptor cells (TRCs) on the tongue and palate epithelium. To understand how TRCs transmit information to higher neural centres, we examined the tuning properties of large ensembles of neurons in the first neural station of the gustatory system. Here, we generated and characterized a collection of transgenic mice expressing a genetically encoded calcium indicator in central and peripheral neurons, and used a gradient refractive index microendoscope combined with high-resolution two-photon microscopy to image taste responses from ganglion neurons buried deep at the base of the brain. Our results reveal fine selectivity in the taste preference of ganglion neurons; demonstrate a strong match between TRCs in the tongue and the principal neural afferents relaying taste information to the brain; and expose the highly specific transfer of taste information between taste cells and the central nervous system.
View details for DOI 10.1038/nature13873
View details for Web of Science ID 000347810300047
View details for PubMedID 25383521
- Visualizing mammalian brain area interactions by dual-axis two-photon calcium imaging NATURE NEUROSCIENCE 2014; 17 (12): 1825-1829
High-fidelity optical reporting of neuronal electrical activity with an ultrafast fluorescent voltage sensor
2014; 17 (6): 884-889
Accurate optical reporting of electrical activity in genetically defined neuronal populations is a long-standing goal in neuroscience. We developed Accelerated Sensor of Action Potentials 1 (ASAP1), a voltage sensor design in which a circularly permuted green fluorescent protein is inserted in an extracellular loop of a voltage-sensing domain, rendering fluorescence responsive to membrane potential. ASAP1 demonstrated on and off kinetics of ∼2 ms, reliably detected single action potentials and subthreshold potential changes, and tracked trains of action potential waveforms up to 200 Hz in single trials. With a favorable combination of brightness, dynamic range and speed, ASAP1 enables continuous monitoring of membrane potential in neurons at kilohertz frame rates using standard epifluorescence microscopy.
View details for DOI 10.1038/nn.3709
View details for Web of Science ID 000336638000025
View details for PubMedID 24755780
- Imaging neural spiking in brain tissue using FRET-opsin protein voltage sensors NATURE COMMUNICATIONS 2014; 5
Bidirectional Plasticity of Purkinje Cells Matches Temporal Features of Learning
JOURNAL OF NEUROSCIENCE
2014; 34 (5): 1731-1737
Many forms of learning require temporally ordered stimuli. In Pavlovian eyeblink conditioning, a conditioned stimulus (CS) must precede the unconditioned stimulus (US) by at least about 100 ms for learning to occur. Conditioned responses are learned and generated by the cerebellum. Recordings from the cerebellar cortex during conditioning have revealed CS-triggered pauses in the firing of Purkinje cells that likely drive the conditioned blinks. The predominant view of the learning mechanism in conditioning is that long-term depression (LTD) at parallel fiber (PF)-Purkinje cell synapses underlies the Purkinje cell pauses. This raises a serious conceptual challenge because LTD is most effectively induced at short CS-US intervals, which do not support acquisition of eyeblinks. To resolve this discrepancy, we recorded Purkinje cells during conditioning with short or long CS-US intervals. Decerebrated ferrets trained with CS-US intervals ≥150 ms reliably developed Purkinje cell pauses, but training with an interval of 50 ms unexpectedly induced increases in CS-evoked spiking. This bidirectional modulation of Purkinje cell activity offers a basis for the requirement of a minimum CS-US interval for conditioning, but we argue that it cannot be fully explained by LTD, even when previous in vitro studies of stimulus-timing-dependent LTD are taken into account.
View details for DOI 10.1523/JNEUROSCI.2883-13.2014
View details for Web of Science ID 000331455000016
View details for PubMedID 24478355
Imaging neural spiking in brain tissue using FRET-opsin protein voltage sensors.
2014; 5: 3674-?
Genetically encoded fluorescence voltage sensors offer the possibility of directly visualizing neural spiking dynamics in cells targeted by their genetic class or connectivity. Sensors of this class have generally suffered performance-limiting tradeoffs between modest brightness, sluggish kinetics and limited signalling dynamic range in response to action potentials. Here we describe sensors that use fluorescence resonance energy transfer (FRET) to combine the rapid kinetics and substantial voltage-dependence of rhodopsin family voltage-sensing domains with the brightness of genetically engineered protein fluorophores. These FRET-opsin sensors significantly improve upon the spike detection fidelity offered by the genetically encoded voltage sensor, Arclight, while offering faster kinetics and higher brightness. Using FRET-opsin sensors we imaged neural spiking and sub-threshold membrane voltage dynamics in cultured neurons and in pyramidal cells within neocortical tissue slices. In live mice, rates and optical waveforms of cerebellar Purkinje neurons' dendritic voltage transients matched expectations for these cells' dendritic spikes.
View details for DOI 10.1038/ncomms4674
View details for PubMedID 24755708
High-speed laser microsurgery of alert fruit flies for fluorescence imaging of neural activity
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
2013; 110 (46): 18374-18379
Intravital microscopy is a key means of monitoring cellular function in live organisms, but surgical preparation of a live animal for microscopy often is time-consuming, requires considerable skill, and limits experimental throughput. Here we introduce a spatially precise (<1-µm edge precision), high-speed (<1 s), largely automated, and economical protocol for microsurgical preparation of live animals for optical imaging. Using a 193-nm pulsed excimer laser and the fruit fly as a model, we created observation windows (12- to 350-µm diameters) in the exoskeleton. Through these windows we used two-photon microscopy to image odor-evoked Ca(2+) signaling in projection neuron dendrites of the antennal lobe and Kenyon cells of the mushroom body. The impact of a laser-cut window on fly health appears to be substantially less than that of conventional manual dissection, for our imaging durations of up to 18 h were ∼5-20 times longer than prior in vivo microscopy studies of hand-dissected flies. This improvement will facilitate studies of numerous questions in neuroscience, such as those regarding neuronal plasticity or learning and memory. As a control, we used phototaxis as an exemplary complex behavior in flies and found that laser microsurgery is sufficiently gentle to leave it intact. To demonstrate that our techniques are applicable to other species, we created microsurgical openings in nematodes, ants, and the mouse cranium. In conjunction with emerging robotic methods for handling and mounting flies or other small organisms, our rapid, precisely controllable, and highly repeatable microsurgical techniques should enable automated, high-throughput preparation of live animals for optical experimentation.
View details for DOI 10.1073/pnas.1216287110
View details for Web of Science ID 000326830900029
View details for PubMedID 24167298
Engineering Approaches to Illuminating Brain Structure and Dynamics
2013; 80 (3): 568-577
Historical milestones in neuroscience have come in diverse forms, ranging from the resolution of specific biological mysteries via creative experimentation to broad technological advances allowing neuroscientists to ask new kinds of questions. The continuous development of tools is driven with a special necessity by the complexity, fragility, and inaccessibility of intact nervous systems, such that inventive technique development and application drawing upon engineering and the applied sciences has long been essential to neuroscience. Here we highlight recent technological directions in neuroscience spurred by progress in optical, electrical, mechanical, chemical, and biological engineering. These research areas are poised for rapid growth and will likely be central to the practice of neuroscience well into the future.
View details for DOI 10.1016/j.neuron.2013.10.032
View details for Web of Science ID 000326609900004
View details for PubMedID 24183010
Sarcomere lengths in human extensor carpi radialis brevis measured by microendoscopy
MUSCLE & NERVE
2013; 48 (2): 286-292
Second-harmonic generation microendoscopy is a minimally invasive technique to image sarcomeres and measure their lengths in humans, but motion artifact and low signal have limited the use of this novel technique.We discovered that an excitation wavelength of 960 nm maximized image signal; this enabled an image acquisition rate of 3 frames/s, which decreased motion artifact. We then used microendoscopy to measure sarcomere lengths in the human extensor carpi radialis brevis with the wrist at 45° extension and 45° flexion in 7 subjects. We also measured the variability in sarcomere lengths within single fibers.Average sarcomere lengths in 45° extension were 2.93±0.29 μm (±SD) and increased to 3.58±0.19 μm in 45° flexion. Within single fibers the standard deviation of sarcomere lengths in series was 0.20 μm.Microendoscopy can be used to measure sarcomere lengths at different body postures. Lengths of sarcomeres in series within a fiber vary substantially. Muscle Nerve, 48: 286-292, 2013.
View details for DOI 10.1002/mus.23760
View details for Web of Science ID 000322158500019
View details for PubMedID 23813625
GABAergic Lateral Interactions Tune the Early Stages of Visual Processing in Drosophila
2013; 78 (6): 1075-1089
Early stages of visual processing must capture complex, dynamic inputs. While peripheral neurons often implement efficient encoding by exploiting natural stimulus statistics, downstream neurons are specialized to extract behaviorally relevant features. How do these specializations arise? We use two-photon imaging in Drosophila to characterize a first-order interneuron, L2, that provides input to a pathway specialized for detecting moving dark edges. GABAergic interactions, mediated in part presynaptically, create an antagonistic and anisotropic center-surround receptive field. This receptive field is spatiotemporally coupled, applying differential temporal processing to large and small dark objects, achieving significant specialization. GABAergic circuits also mediate OFF responses and balance these with responses to ON stimuli. Remarkably, the functional properties of L2 are strikingly similar to those of bipolar cells, yet emerge through different molecular and circuit mechanisms. Thus, evolution appears to have converged on a common strategy for processing visual information at the first synapse.
View details for DOI 10.1016/j.neuron.2013.04.024
View details for Web of Science ID 000321026900013
View details for PubMedID 23791198
- Enhanced Archaerhodopsin Fluorescent Protein Voltage Indicators PLOS ONE 2013; 8 (6)
Optical Strategies for Sensing Neuronal Voltage Using Quantum Dots and Other Semiconductor Nanocrystals
2013; 7 (5): 4601-4609
Biophysicists have long sought optical methods capable of reporting the electrophysiological dynamics of large-scale neural networks with millisecond-scale temporal resolution. Existing fluorescent sensors of cell membrane voltage can report action potentials in individual cultured neurons, but limitations in brightness and dynamic range of both synthetic organic and genetically encoded voltage sensors have prevented concurrent monitoring of spiking activity across large populations of individual neurons. Here we propose a novel, inorganic class of fluorescent voltage sensors: semiconductor nanoparticles, such as ultrabright quantum dots (qdots). Our calculations revealed that transmembrane electric fields characteristic of neuronal spiking (~10 mV/nm) modulate a qdot's electronic structure and can induce ~5% changes in its fluorescence intensity and ~1 nm shifts in its emission wavelength, depending on the qdot's size, composition, and dielectric environment. Moreover, tailored qdot sensors composed of two different materials can exhibit substantial (~30%) changes in fluorescence intensity during neuronal spiking. Using signal detection theory, we show that conventional qdots should be capable of reporting voltage dynamics with millisecond precision across several tens or more individual neurons over a range of optical and neurophysiological conditions. These results unveil promising avenues for imaging spiking dynamics in neural networks and merit in-depth experimental investigation.
View details for DOI 10.1021/nn401410k
View details for Web of Science ID 000319856300102
Long-term dynamics of CA1 hippocampal place codes
2013; 16 (3): 264-266
Using Ca(2+) imaging in freely behaving mice that repeatedly explored a familiar environment, we tracked thousands of CA1 pyramidal cells' place fields over weeks. Place coding was dynamic, as each day the ensemble representation of this environment involved a unique subset of cells. However, cells in the ∼15-25% overlap between any two of these subsets retained the same place fields, which sufficed to preserve an accurate spatial representation across weeks.
View details for DOI 10.1038/nn.3329
View details for Web of Science ID 000315474800006
Nanotools for Neuroscience and Brain Activity Mapping
2013; 7 (3): 1850-1866
Neuroscience is at a crossroads. Great effort is being invested into deciphering specific neural interactions and circuits. At the same time, there exist few general theories or principles that explain brain function. We attribute this disparity, in part, to limitations in current methodologies. Traditional neurophysiological approaches record the activities of one neuron or a few neurons at a time. Neurochemical approaches focus on single neurotransmitters. Yet, there is an increasing realization that neural circuits operate at emergent levels, where the interactions between hundreds or thousands of neurons, utilizing multiple chemical transmitters, generate functional states. Brains function at the nanoscale, so tools to study brains must ultimately operate at this scale, as well. Nanoscience and nanotechnology are poised to provide a rich toolkit of novel methods to explore brain function by enabling simultaneous measurement and manipulation of activity of thousands or even millions of neurons. We and others refer to this goal as the Brain Activity Mapping Project. In this Nano Focus, we discuss how recent developments in nanoscale analysis tools and in the design and synthesis of nanomaterials have generated optical, electrical, and chemical methods that can readily be adapted for use in neuroscience. These approaches represent exciting areas of technical development and research. Moreover, unique opportunities exist for nanoscientists, nanotechnologists, and other physical scientists and engineers to contribute to tackling the challenging problems involved in understanding the fundamentals of brain function.
View details for DOI 10.1021/nn4012847
View details for Web of Science ID 000316846700005
View details for PubMedID 23514423
Improving FRET Dynamic Range with Bright Green and Red Fluorescent Proteins
CELL PRESS. 2013: 683A-683A
View details for Web of Science ID 000316074306459
Photon Shot Noise Limits on Optical Detection of Neuronal Spikes and Estimation of Spike Timing
2013; 104 (1): 51-62
Optical approaches for tracking neural dynamics are of widespread interest, but a theoretical framework quantifying the physical limits of these techniques has been lacking. We formulate such a framework by using signal detection and estimation theory to obtain physical bounds on the detection of neural spikes and the estimation of their occurrence times as set by photon counting statistics (shot noise). These bounds are succinctly expressed via a discriminability index that depends on the kinetics of the optical indicator and the relative fluxes of signal and background photons. This approach facilitates quantitative evaluations of different indicators, detector technologies, and data analyses. Our treatment also provides optimal filtering techniques for optical detection of spikes. We compare various types of Ca(2+) indicators and show that background photons are a chief impediment to voltage sensing. Thus, voltage indicators that change color in response to membrane depolarization may offer a key advantage over those that change intensity. We also examine fluorescence resonance energy transfer indicators and identify the regimes in which the widely used ratiometric analysis of signals is substantially suboptimal. Overall, by showing how different optical factors interact to affect signal quality, our treatment offers a valuable guide to experimental design and provides measures of confidence to assess optically extracted traces of neural activity.
View details for DOI 10.1016/j.bpj.2012.07.058
View details for Web of Science ID 000313541200008
View details for PubMedID 23332058
Enhanced Archaerhodopsin Fluorescent Protein Voltage Indicators.
2013; 8 (6): e66959
A longstanding goal in neuroscience has been to develop techniques for imaging the voltage dynamics of genetically defined subsets of neurons. Optical sensors of transmembrane voltage would enhance studies of neural activity in contexts ranging from individual neurons cultured in vitro to neuronal populations in awake-behaving animals. Recent progress has identified Archaerhodopsin (Arch) based sensors as a promising, genetically encoded class of fluorescent voltage indicators that can report single action potentials. Wild-type Arch exhibits sub-millisecond fluorescence responses to trans-membrane voltage, but its light-activated proton pump also responds to the imaging illumination. An Arch mutant (Arch-D95N) exhibits no photocurrent, but has a slower, ~40 ms response to voltage transients. Here we present Arch-derived voltage sensors with trafficking signals that enhance their localization to the neural membrane. We also describe Arch mutant sensors (Arch-EEN and -EEQ) that exhibit faster kinetics and greater fluorescence dynamic range than Arch-D95N, and no photocurrent at the illumination intensities normally used for imaging. We benchmarked these voltage sensors regarding their spike detection fidelity by using a signal detection theoretic framework that takes into account the experimentally measured photon shot noise and optical waveforms for single action potentials. This analysis revealed that by combining the sequence mutations and enhanced trafficking sequences, the new sensors improved the fidelity of spike detection by nearly three-fold in comparison to Arch-D95N.
View details for PubMedID 23840563
- Towards a Photonic Crystal Mode-Locked Laser NOVEL IN-PLANE SEMICONDUCTOR LASERS XII 2013; 8640
Two-photon optogenetic toolbox for fast inhibition, excitation and bistable modulation
2012; 9 (12): 1171-U132
Optogenetics with microbial opsin genes has enabled high-speed control of genetically specified cell populations in intact tissue. However, it remains a challenge to independently control subsets of cells within the genetically targeted population. Although spatially precise excitation of target molecules can be achieved using two-photon laser-scanning microscopy (TPLSM) hardware, the integration of two-photon excitation with optogenetics has thus far required specialized equipment or scanning and has not yet been widely adopted. Here we take a complementary approach, developing opsins with custom kinetic, expression and spectral properties uniquely suited to scan times typical of the raster approach that is ubiquitous in TPLSMlaboratories. We use a range of culture, slice and mammalian in vivo preparations to demonstrate the versatility of this toolbox, and we quantitatively map parameter space for fast excitation, inhibition and bistable control. Together these advances may help enable broad adoption of integrated optogenetic and TPLSMtechnologies across experimental fields and systems.
View details for DOI 10.1038/NMETH.2215
View details for Web of Science ID 000312093500018
View details for PubMedID 23169303
Unified Resolution Bounds for Conventional and Stochastic Localization Fluorescence Microscopy
PHYSICAL REVIEW LETTERS
2012; 109 (16)
Superresolution microscopy enables imaging in the optical far field with ~20 nm-scale resolution. However, classical concepts of resolution using point-spread and modulation-transfer functions fail to describe the physical limits of superresolution techniques based on stochastic localization of single emitters. Prior treatments of stochastic localization microscopy have defined how accurately a single emitter's position can be determined, but these bounds are restricted to sparse emitters, do not describe conventional microscopy, and fail to provide unified concepts of resolution for all optical methods. Here we introduce a measure of resolution, the information transfer function (ITF), that gives physical limits for conventional and stochastic localization techniques. The ITF bounds the accuracy of image determination as a function of spatial frequency and for conventional microscopy is proportional to the square of the modulation-transfer function. We use the ITF to describe how emitter density and photon counts affect imaging performance across the continuum from conventional to superresolution microscopy, without assuming emitters are sparse. This unified physical description of resolution facilitates experimental choices and designs of image reconstruction algorithms.
View details for DOI 10.1103/PhysRevLett.109.168102
View details for Web of Science ID 000309905400027
View details for PubMedID 23215134
Improving FRET dynamic range with bright green and red fluorescent proteins
2012; 9 (10): 1005-?
A variety of genetically encoded reporters use changes in fluorescence (or Förster) resonance energy transfer (FRET) to report on biochemical processes in living cells. The standard genetically encoded FRET pair consists of CFPs and YFPs, but many CFP-YFP reporters suffer from low FRET dynamic range, phototoxicity from the CFP excitation light and complex photokinetic events such as reversible photobleaching and photoconversion. We engineered two fluorescent proteins, Clover and mRuby2, which are the brightest green and red fluorescent proteins to date and have the highest Förster radius of any ratiometric FRET pair yet described. Replacement of CFP and YFP with these two proteins in reporters of kinase activity, small GTPase activity and transmembrane voltage significantly improves photostability, FRET dynamic range and emission ratio changes. These improvements enhance detection of transient biochemical events such as neuronal action-potential firing and RhoA activation in growth cones.
View details for DOI 10.1038/NMETH.2171
View details for Web of Science ID 000309519300023
View details for PubMedID 22961245
In vivo optical microendoscopy for imaging cells lying deep within live tissue.
Cold Spring Harbor protocols
2012; 2012 (10): 1029-1034
Although in vivo microscopy has been pivotal in enabling studies of neuronal structure and function in the intact mammalian brain, conventional intravital microscopy has generally been limited to superficial brain areas such as the olfactory bulb, the neocortex, or the cerebellar cortex. For imaging cells in deeper areas, this article discusses in vivo optical microendoscopy using gradient refractive index (GRIN) microlenses that can be inserted into tissue. Our general methodology is broadly applicable to many deep brain regions and areas of the body. Microendoscopes are available in a wide variety of optical designs, allowing imaging across a range of spatial scales and with spatial resolution that can now closely approach that offered by standard water-immersion microscope objectives. The incorporation of microendoscope probes into portable miniaturized microscopes allows imaging in freely behaving animals. When combined with the broad sets of available fluorescent markers, animal preparations, and genetically modified mice, microendoscopic methods enable sophisticated experimental designs for probing how cellular characteristics may underlie or reflect animal behavior and life experience, in healthy animals and animal models of disease.
View details for DOI 10.1101/pdb.top071464
View details for PubMedID 23028071
In vivo microendoscopy of the hippocampus.
Cold Spring Harbor protocols
2012; 2012 (10): 1092-1099
Conventional intravital microscopy has generally been limited to superficial brain areas such as the olfactory bulb, the neocortex, or the cerebellar cortex. In vivo optical microendoscopy uses gradient refractive index (GRIN) microlenses that can be inserted into tissue to image cells in deeper areas. This protocol describes in vivo microendoscopy of the mouse hippocampus. The general methodology can be applied to many deep brain regions and other areas of the body.
View details for DOI 10.1101/pdb.prot071472
View details for PubMedID 23028072
Estimation Theoretic Measure of Resolution for Stochastic Localization Microscopy
PHYSICAL REVIEW LETTERS
2012; 109 (4)
One approach to super-resolution fluorescence microscopy, termed stochastic localization microscopy, relies on the nanometer scale spatial localization of individual fluorescent emitters that stochastically label specific features of the specimen. The precision of emitter localization is an important determinant of the resulting image resolution but is insufficient to specify how well the derived images capture the structure of the specimen. We address this deficiency by considering the inference of specimen structure based on the estimated emitter locations. By using estimation theory, we develop a measure of spatial resolution that jointly depends on the density of the emitter labels, the precision of emitter localization, and prior information regarding the spatial frequency content of the labeled object. The Nyquist criterion does not set the scaling of this measure with emitter number. Given prior information and a fixed emitter labeling density, our resolution measure asymptotes to a finite value as the precision of emitter localization improves. By considering the present experimental capabilities, this asymptotic behavior implies that further resolution improvements require increases in labeling density above typical current values. Our treatment also yields algorithms to enhance reliable image features. Overall, our formalism facilitates the rigorous statistical interpretation of the data produced by stochastic localization imaging techniques.
View details for DOI 10.1103/PhysRevLett.109.048102
View details for Web of Science ID 000306690700012
View details for PubMedID 23006110
Miniaturized integration of a fluorescence microscope
2011; 8 (10): 871-U147
The light microscope is traditionally an instrument of substantial size and expense. Its miniaturized integration would enable many new applications based on mass-producible, tiny microscopes. Key prospective usages include brain imaging in behaving animals for relating cellular dynamics to animal behavior. Here we introduce a miniature (1.9 g) integrated fluorescence microscope made from mass-producible parts, including a semiconductor light source and sensor. This device enables high-speed cellular imaging across ?0.5 mm2 areas in active mice. This capability allowed concurrent tracking of Ca2+ spiking in >200 Purkinje neurons across nine cerebellar microzones. During mouse locomotion, individual microzones exhibited large-scale, synchronized Ca2+ spiking. This is a mesoscopic neural dynamic missed by prior techniques for studying the brain at other length scales. Overall, the integrated microscope is a potentially transformative technology that permits distribution to many animals and enables diverse usages, such as portable diagnostics or microscope arrays for large-scale screens.
View details for DOI 10.1038/NMETH.1694
View details for Web of Science ID 000295358000024
View details for PubMedID 21909102
Symmetries in stimulus statistics shape the form of visual motion estimators
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
2011; 108 (31): 12909-12914
The estimation of visual motion has long been studied as a paradigmatic neural computation, and multiple models have been advanced to explain behavioral and neural responses to motion signals. A broad class of models, originating with the Reichardt correlator model, proposes that animals estimate motion by computing a temporal cross-correlation of light intensities from two neighboring points in visual space. These models provide a good description of experimental data in specific contexts but cannot explain motion percepts in stimuli lacking pairwise correlations. Here, we develop a theoretical formalism that can accommodate diverse stimuli and behavioral goals. To achieve this, we treat motion estimation as a problem of Bayesian inference. Pairwise models emerge as one component of the generalized strategy for motion estimation. However, correlation functions beyond second order enable more accurate motion estimation. Prior expectations that are asymmetric with respect to bright and dark contrast use correlations of both even and odd orders, and we show that psychophysical experiments using visual stimuli with symmetric probability distributions for contrast cannot reveal whether the subject uses odd-order correlators for motion estimation. This result highlights a gap in previous experiments, which have largely relied on symmetric contrast distributions. Our theoretical treatment provides a natural interpretation of many visual motion percepts, indicates that motion estimation should be revisited using a broader class of stimuli, demonstrates how correlation-based motion estimation is related to stimulus statistics, and provides multiple experimentally testable predictions.
View details for DOI 10.1073/pnas.1015680108
View details for Web of Science ID 000293385700073
View details for PubMedID 21768376
- An infrared fluorescent protein for deeper imaging NATURE BIOTECHNOLOGY 2011; 29 (8): 715-716
Defining the Computational Structure of the Motion Detector in Drosophila
2011; 70 (6): 1165-1177
Many animals rely on visual motion detection for survival. Motion information is extracted from spatiotemporal intensity patterns on the retina, a paradigmatic neural computation. A phenomenological model, the Hassenstein-Reichardt correlator (HRC), relates visual inputs to neural activity and behavioral responses to motion, but the circuits that implement this computation remain unknown. By using cell-type specific genetic silencing, minimal motion stimuli, and in vivo calcium imaging, we examine two critical HRC inputs. These two pathways respond preferentially to light and dark moving edges. We demonstrate that these pathways perform overlapping but complementary subsets of the computations underlying the HRC. A numerical model implementing differential weighting of these operations displays the observed edge preferences. Intriguingly, these pathways are distinguished by their sensitivities to a stimulus correlation that corresponds to an illusory percept, "reverse phi," that affects many species. Thus, this computational architecture may be widely used to achieve edge selectivity in motion detection.
View details for DOI 10.1016/j.neuron.2011.05.023
View details for Web of Science ID 000292410700014
View details for PubMedID 21689602
Time-lapse imaging of disease progression in deep brain areas using fluorescence microendoscopy
2011; 17 (2): 223-U120
The combination of intravital microscopy and animal models of disease has propelled studies of disease mechanisms and treatments. However, many disorders afflict tissues inaccessible to light microscopy in live subjects. Here we introduce cellular-level time-lapse imaging deep within the live mammalian brain by one- and two-photon fluorescence microendoscopy over multiple weeks. Bilateral imaging sites allowed longitudinal comparisons within individual subjects, including of normal and diseased tissues. Using this approach, we tracked CA1 hippocampal pyramidal neuron dendrites in adult mice, revealing these dendrites' extreme stability and rare examples of their structural alterations. To illustrate disease studies, we tracked deep lying gliomas by observing tumor growth, visualizing three-dimensional vasculature structure and determining microcirculatory speeds. Average erythrocyte speeds in gliomas declined markedly as the disease advanced, notwithstanding significant increases in capillary diameters. Time-lapse microendoscopy will be applicable to studies of numerous disorders, including neurovascular, neurological, cancerous and trauma-induced conditions.
View details for DOI 10.1038/nm.2292
View details for Web of Science ID 000286969900032
View details for PubMedID 21240263
- Journal club. A neuroscientist learns about algorithms for motor learning. Nature 2010; 463 (7279): 273-?
Automated Analysis of Cellular Signals from Large-Scale Calcium Imaging Data
2009; 63 (6): 747-760
Recent advances in fluorescence imaging permit studies of Ca(2+) dynamics in large numbers of cells, in anesthetized and awake behaving animals. However, unlike for electrophysiological signals, standardized algorithms for assigning optically recorded signals to individual cells have not yet emerged. Here, we describe an automated sorting procedure that combines independent component analysis and image segmentation for extracting cells' locations and their dynamics with minimal human supervision. In validation studies using simulated data, automated sorting significantly improved estimation of cellular signals compared to conventional analysis based on image regions of interest. We used automated procedures to analyze data recorded by two-photon Ca(2+) imaging in the cerebellar vermis of awake behaving mice. Our analysis yielded simultaneous Ca(2+) activity traces for up to >100 Purkinje cells and Bergmann glia from single recordings. Using this approach, we found microzones of Purkinje cells that were stable across behavioral states and in which synchronous Ca(2+) spiking rose significantly during locomotion.
View details for DOI 10.1016/j.neuron.2009.08.009
View details for Web of Science ID 000270569700009
View details for PubMedID 19778505
In vivo brain imaging using a portable 2.9 g two-photon microscope based on a microelectromechanical systems scanning mirror
2009; 34 (15): 2309-2311
We present a two-photon microscope that is approximately 2.9 g in mass and 2.0 x 1.9 x 1.1 cm(3) in size and based on a microelectromechanical systems (MEMS) laser-scanning mirror. The microscope has a focusing motor and a micro-optical assembly composed of four gradient refractive index lenses and a dichroic microprism. Fluorescence is captured without the detected emissions reflecting off the MEMS mirror, by use of separate optical fibers for fluorescence collection and delivery of ultrashort excitation pulses. Using this microscope we imaged neocortical microvasculature and tracked the flow of erythrocytes in live mice.
View details for Web of Science ID 000269405900022
View details for PubMedID 19649080
In vivo fluorescence imaging with high-resolution microlenses
2009; 6 (7): 511-U61
Micro-optics are increasingly used for minimally invasive in vivo imaging, in miniaturized microscopes and in lab-on-a-chip devices. Owing to optical aberrations and lower numerical apertures, a main class of microlens, gradient refractive index lenses, has not achieved resolution comparable to conventional microscopy. Here we describe high-resolution microlenses, and illustrate two-photon imaging of dendritic spines on hippocampal neurons and dual-color nonlinear optical imaging of neuromuscular junctions in live mice.
View details for DOI 10.1038/nmeth.1339
View details for Web of Science ID 000267442900019
View details for PubMedID 19525959
Motor Behavior Activates Bergmann Glial Networks
2009; 62 (3): 400-412
Although it is firmly established that neuronal activity is a prime determinant of animal behavior, relationships between astrocytic excitation and animal behavior have remained opaque. Cerebellar Bergmann glia are radial astrocytes that are implicated in motor behavior and exhibit Ca(2+) excitation. However, Ca(2+) excitation in these cells has not previously been studied in behaving animals. Using two-photon microscopy we found that Bergmann glia exhibit three forms of Ca(2+) excitation in awake, behaving mice. Two of these are ongoing within the cerebellar vermis. During locomotor performance concerted Ca(2+) excitation arises in networks of at least hundreds of Bergmann glia extending across several hundred microns or more. Concerted Ca(2+) excitation was abolished by anesthesia or blockade of either neural activity or glutamatergic transmission. Thus, large networks of Bergmann glia can be activated by specific animal behaviors and undergo excitation of sufficient magnitude to potentially initiate macroscopic changes in brain dynamics or blood flow.
View details for DOI 10.1016/j.neuron.2009.03.019
View details for Web of Science ID 000266146100011
View details for PubMedID 19447095
Advances in Light Microscopy for Neuroscience
ANNUAL REVIEW OF NEUROSCIENCE
2009; 32: 435-506
Since the work of Golgi and Cajal, light microscopy has remained a key tool for neuroscientists to observe cellular properties. Ongoing advances have enabled new experimental capabilities using light to inspect the nervous system across multiple spatial scales, including ultrastructural scales finer than the optical diffraction limit. Other progress permits functional imaging at faster speeds, at greater depths in brain tissue, and over larger tissue volumes than previously possible. Portable, miniaturized fluorescence microscopes now allow brain imaging in freely behaving mice. Complementary progress on animal preparations has enabled imaging in head-restrained behaving animals, as well as time-lapse microscopy studies in the brains of live subjects. Mouse genetic approaches permit mosaic and inducible fluorescence-labeling strategies, whereas intrinsic contrast mechanisms allow in vivo imaging of animals and humans without use of exogenous markers. This review surveys such advances and highlights emerging capabilities of particular interest to neuroscientists.
View details for DOI 10.1146/annurev.neuro.051508.135540
View details for Web of Science ID 000268504100018
View details for PubMedID 19555292
IMAGING SARCOMERES OF EXTENSOR CARPI RADIALIS BREVIS IN HUMANS USING MINIMALLY INVASIVE MICROENDOSCOPY
PROCEEDINGS OF THE ASME SUMMER BIOENGINEERING CONFERENCE - 2009, PT A AND B
View details for Web of Science ID 000280089000505
High-speed, miniaturized fluorescence microscopy in freely moving mice
2008; 5 (11): 935-938
A central goal in biomedicine is to explain organismic behavior in terms of causal cellular processes. However, concurrent observation of mammalian behavior and underlying cellular dynamics has been a longstanding challenge. We describe a miniaturized (1.1 g mass) epifluorescence microscope for cellular-level brain imaging in freely moving mice, and its application to imaging microcirculation and neuronal Ca(2+) dynamics.
View details for DOI 10.1038/nmeth.1256
View details for Web of Science ID 000260532500010
View details for PubMedID 18836457
Lock-and-key mechanisms of cerebellar memory recall based on rebound currents
JOURNAL OF NEUROPHYSIOLOGY
2008; 100 (4): 2328-2347
A basic question for theories of learning and memory is whether neuronal plasticity suffices to guide proper memory recall. Alternatively, information processing that is additional to readout of stored memories might occur during recall. We formulate a "lock-and-key" hypothesis regarding cerebellum-dependent motor memory in which successful learning shapes neural activity to match a temporal filter that prevents expression of stored but inappropriate motor responses. Thus, neuronal plasticity by itself is necessary but not sufficient to modify motor behavior. We explored this idea through computational studies of two cerebellar behaviors and examined whether deep cerebellar and vestibular nuclei neurons can filter signals from Purkinje cells that would otherwise drive inappropriate motor responses. In eyeblink conditioning, reflex acquisition requires the conditioned stimulus (CS) to precede the unconditioned stimulus (US) by >100 ms. In our biophysical models of cerebellar nuclei neurons this requirement arises through the phenomenon of postinhibitory rebound depolarization and matches longstanding behavioral data on conditioned reflex timing and reliability. Although CS-US intervals<100 ms may induce Purkinje cell plasticity, cerebellar nuclei neurons drive conditioned responses only if the CS-US training interval was >100 ms. This bound reflects the minimum time for deinactivation of rebound currents such as T-type Ca2+. In vestibulo-ocular reflex adaptation, hyperpolarization-activated currents in vestibular nuclei neurons may underlie analogous dependence of adaptation magnitude on the timing of visual and vestibular stimuli. Thus, the proposed lock-and-key mechanisms link channel kinetics to recall performance and yield specific predictions of how perturbations to rebound depolarization affect motor expression.
View details for DOI 10.1152/jn.00344.2007
View details for Web of Science ID 000259967000055
View details for PubMedID 17671105
Minimally invasive high-speed imaging of sarcomere contractile dynamics in mice and humans
2008; 454 (7205): 784-788
Sarcomeres are the basic contractile units of striated muscle. Our knowledge about sarcomere dynamics has primarily come from in vitro studies of muscle fibres and analysis of optical diffraction patterns obtained from living muscles. Both approaches involve highly invasive procedures and neither allows examination of individual sarcomeres in live subjects. Here we report direct visualization of individual sarcomeres and their dynamical length variations using minimally invasive optical microendoscopy to observe second-harmonic frequencies of light generated in the muscle fibres of live mice and humans. Using microendoscopes as small as 350 microm in diameter, we imaged individual sarcomeres in both passive and activated muscle. Our measurements permit in vivo characterization of sarcomere length changes that occur with alterations in body posture and visualization of local variations in sarcomere length not apparent in aggregate length determinations. High-speed data acquisition enabled observation of sarcomere contractile dynamics with millisecond-scale resolution. These experiments point the way to in vivo imaging studies demonstrating how sarcomere performance varies with physical conditioning and physiological state, as well as imaging diagnostics revealing how neuromuscular diseases affect contractile dynamics.
View details for DOI 10.1038/nature07104
View details for Web of Science ID 000258228000049
View details for PubMedID 18600262
A portable two-photon fluorescence microendoscope based on a two-dimensional scanning mirror
2007 IEEE/LEOS INTERNATIONAL CONFERENCE ON OPTICAL MEMS AND NANOPHOTONICS
View details for Web of Science ID 000251224200004
Long-term cellular level imaging of deep brain areas using one- and two-photon fluorescence microendoscopy
CELL PRESS. 2007: 155A-155A
View details for Web of Science ID 000243972400718
Next-generation optical technologies for illuminating genetically targeted brain circuits
JOURNAL OF NEUROSCIENCE
2006; 26 (41): 10380-10386
Emerging technologies from optics, genetics, and bioengineering are being combined for studies of intact neural circuits. The rapid progression of such interdisciplinary "optogenetic" approaches has expanded capabilities for optical imaging and genetic targeting of specific cell types. Here we explore key recent advances that unite optical and genetic approaches, focusing on promising techniques that either allow novel studies of neural dynamics and behavior or provide fresh perspectives on classic model systems.
View details for DOI 10.1523/JNEUROSCI.3863-06.2006
View details for Web of Science ID 000241192800010
View details for PubMedID 17035522
Fast-scanning two-photon fluorescence imaging based on a microelectromechanical systems two-dimensional scanning mirror
2006; 31 (13): 2018-2020
Towards overcoming the size limitations of conventional two-photon fluorescence microscopy, we introduce two-photon imaging based on microelectromechanical systems (MEMS) scanners. Single crystalline silicon scanning mirrors that are 0.75 mm x 0.75 mm in size and driven in two dimensions by microfabricated vertical comb electrostatic actuators can provide optical deflection angles through a range of approximately16 degrees . Using such scanners we demonstrated two-photon microscopy and microendoscopy with fast-axis acquisition rates up to 3.52 kHz.
View details for Web of Science ID 000238494600026
View details for PubMedID 16770418
In vivo Imaging of mammalian cochlear blood flow using fluorescence microendoscopy
OTOLOGY & NEUROTOLOGY
2006; 27 (2): 144-152
We sought to develop techniques for visualizing cochlear blood flow in live mammalian subjects using fluorescence microendoscopy.Inner ear microcirculation appears to be intimately involved in cochlear function. Blood velocity measurements suggest that intense sounds can alter cochlear blood flow. Disruption of cochlear blood flow may be a significant cause of hearing impairment, including sudden sensorineural hearing loss. However, inability to image cochlear blood flow in a nondestructive manner has limited investigation of the role of inner ear microcirculation in hearing function. Present techniques for imaging cochlear microcirculation using intravital light microscopy involve extensive perturbations to cochlear structure, precluding application in human patients. The few previous endoscopy studies of the cochlea have suffered from optical resolution insufficient for visualizing cochlear microvasculature. Fluorescence microendoscopy is an emerging minimally invasive imaging modality that provides micron-scale resolution in tissues inaccessible to light microscopy. In this article, we describe the use of fluorescence microendoscopy in live guinea pigs to image capillary blood flow and movements of individual red blood cells within the basal turn of the cochlea.We anesthetized eight adult guinea pigs and accessed the inner ear through the mastoid bulla. After intravenous injection of fluorescein dye, we made a limited cochleostomy and introduced a compound doublet gradient refractive index endoscope probe 1 mm in diameter into the inner ear. We then imaged cochlear blood flow within individual vessels in an epifluorescence configuration using one-photon fluorescence microendoscopy.We observed single red blood cells passing through individual capillaries in several cochlear structures, including the round window membrane, spiral ligament, osseous spiral lamina, and basilar membrane. Blood flow velocities within inner ear capillaries varied widely, with observed speeds reaching up to approximately 500 microm/s.Fluorescence microendoscopy permits visualization of cochlear microcirculation with micron-scale optical resolution and determination of blood flow velocities through analysis of video sequences.
View details for Web of Science ID 000235346400003
View details for PubMedID 16436982
Fiber-optic fluorescence imaging
2005; 2 (12): 941-950
Optical fibers guide light between separate locations and enable new types of fluorescence imaging. Fiber-optic fluorescence imaging systems include portable handheld microscopes, flexible endoscopes well suited for imaging within hollow tissue cavities and microendoscopes that allow minimally invasive high-resolution imaging deep within tissue. A challenge in the creation of such devices is the design and integration of miniaturized optical and mechanical components. Until recently, fiber-based fluorescence imaging was mainly limited to epifluorescence and scanning confocal modalities. Two new classes of photonic crystal fiber facilitate ultrashort pulse delivery for fiber-optic two-photon fluorescence imaging. An upcoming generation of fluorescence imaging devices will be based on microfabricated device components.
View details for DOI 10.1038/NMETH820
View details for Web of Science ID 000233767700016
View details for PubMedID 16299479
Statistical kinetics of macromolecular dynamics
2005; 89 (4): 2277-2285
Fluctuations in biochemical processes can provide insights into the underlying kinetics beyond what can be gleaned from studies of average rates alone. Historically, analysis of fluctuating transmembrane currents supplied information about ion channel conductance states and lifetimes before single-channel recording techniques emerged. More recently, fluctuation analysis has helped to define mechanochemical pathways and coupling ratios for the motor protein kinesin as well as to probe the contributions of static and dynamic disorder to the kinetics of single enzymes. As growing numbers of assays are developed for enzymatic or folding behaviors of single macromolecules, the range of applications for fluctuation analysis increases. To evaluate specific biochemical models against experimental data, one needs to predict analytically the distribution of times required for completion of each reaction pathway. Unfortunately, using traditional methods, such calculations can be challenging for pathways of even modest complexity. Here, we derive an exact expression for the distribution of completion times for an arbitrary pathway with a finite number of states, using a recursive method to solve algebraically for the appropriate moment-generating function. To facilitate comparisons with experiments on processive motor proteins, we develop a theoretical formalism for the randomness parameter, a dimensionless measure of the variance in motor output. We derive the randomness for motors that take steps of variable sizes or that move on heterogeneous substrates, and then discuss possible applications to enzymes such as RNA polymerase, which transcribes varying DNA sequences, and to myosin V and cytoplasmic dynein, which may advance by variable increments.
View details for DOI 10.1529/biophysj.105.064295
View details for Web of Science ID 000232147600011
View details for PubMedID 16040752
In vivo brain imaging using a portable 3.9 gram two-photon fluorescence microendoscope
2005; 30 (17): 2272-2274
We introduce a compact two-photon fluorescence microendoscope based on a compound gradient refractive index endoscope probe, a DC micromotor for remote adjustment of the image plane, and a flexible photonic bandgap fiber for near distortion-free delivery of ultrashort excitation pulses. The imaging head has a mass of only 3.9 g and provides micrometer-scale resolution. We used portable two-photon microendoscopy to visualize hippocampal blood vessels in the brains of live mice.
View details for Web of Science ID 000231436900028
View details for PubMedID 16190441
Retinal coding of visual scenes - Repetitive and redundant too?
2005; 46 (3): 357-359
Visual information reaches the brain by way of a fine cable, the optic nerve. The million or so axons in the optic nerve represent an information bottleneck in the visual pathway-where the fewest number of neurons convey the visual scene. It has long been thought that to make the most of the optic nerve's limited capacity the retina may encode visual information in an optimally efficient manner. In this issue of Neuron, Puchalla et al. report a test of this hypothesis using multielectrode recordings from retinal ganglion cells stimulated with movies of natural scenes. The authors find substantial redundancy in the retinal code and estimate that there is an approximately 10-fold overrepresentation of visual information.
View details for DOI 10.1016/j.neuron.2005.04.018
View details for Web of Science ID 000229011400002
View details for PubMedID 15882630
Fiber optic two-photon fluorescence microendoscopy: Towards brain imaging in freely moving mice
2005 CONFERENCE ON LASERS & ELECTRO-OPTICS (CLEO), VOLS 1-3
View details for Web of Science ID 000234819902231
In vivo mammalian brain Imaging using one- and two-photon fluorescence microendoscopy
JOURNAL OF NEUROPHYSIOLOGY
2004; 92 (5): 3121-3133
One of the major limitations in the current set of techniques available to neuroscientists is a dearth of methods for imaging individual cells deep within the brains of live animals. To overcome this limitation, we developed two forms of minimally invasive fluorescence microendoscopy and tested their abilities to image cells in vivo. Both one- and two-photon fluorescence microendoscopy are based on compound gradient refractive index (GRIN) lenses that are 350-1,000 microm in diameter and provide micron-scale resolution. One-photon microendoscopy allows full-frame images to be viewed by eye or with a camera, and is well suited to fast frame-rate imaging. Two-photon microendoscopy is a laser-scanning modality that provides optical sectioning deep within tissue. Using in vivo microendoscopy we acquired video-rate movies of thalamic and CA1 hippocampal red blood cell dynamics and still-frame images of CA1 neurons and dendrites in anesthetized rats and mice. Microendoscopy will help meet the growing demand for in vivo cellular imaging created by the rapid emergence of new synthetic and genetically encoded fluorophores that can be used to label specific brain areas or cell classes.
View details for DOI 10.1152/jn.00234.2004
View details for Web of Science ID 000224475000044
View details for PubMedID 15128753
Fiber optic in vivo imaging in the mammalian nervous system
CURRENT OPINION IN NEUROBIOLOGY
2004; 14 (5): 617-628
The compact size, mechanical flexibility, and growing functionality of optical fiber and fiber optic devices are enabling several new modalities for imaging the mammalian nervous system in vivo. Fluorescence microendoscopy is a minimally invasive fiber modality that provides cellular resolution in deep brain areas. Diffuse optical tomography is a non-invasive modality that uses assemblies of fiber optic emitters and detectors on the cranium for volumetric imaging of brain activation. Optical coherence tomography is a sensitive interferometric imaging technique that can be implemented in a variety of fiber based formats and that might allow intrinsic optical detection of brain activity at a high resolution. Miniaturized fiber optic microscopy permits cellular level imaging in the brains of behaving animals. Together, these modalities will enable new uses of imaging in the intact nervous system for both research and clinical applications.
View details for DOI 10.1016/j.conb.2004.08.017
View details for Web of Science ID 000224721200014
View details for PubMedID 15464896
2003; 28 (11): 902-904
Despite widespread use of multiphoton fluorescence microscopy, development of endoscopes for nonlinear optical imaging has been stymied by the degradation of ultrashort excitation pulses that occurs within optical fiber as a result of the combined effects of group-velocity dispersion and self-phase modulation. We introduce microendoscopes (350-1000 microm in diameter) based on gradient-index microlenses that effectively eliminate self-phase modulation within the endoscope. Laser-scanning multiphoton fluorescence endoscopy exhibits micrometer-scale resolution. We used multiphoton endoscopes to image fluorescently labeled neurons and dendrites.
View details for Web of Science ID 000182927700012
View details for PubMedID 12816240
Multineuronal firing patterns in the signal from eye to brain
2003; 37 (3): 499-511
Population codes in the brain have generally been characterized by recording responses from one neuron at a time. This approach will miss codes that rely on concerted patterns of action potentials from many cells. Here we analyze visual signaling in populations of ganglion cells recorded from the isolated salamander retina. These neurons tend to fire synchronously far more frequently than expected by chance. We present an efficient algorithm to identify what groups of cells cooperate in this way. Such groups can include up to seven or more neurons and may account for more than 50% of all the spikes recorded from the retina. These firing patterns represent specific messages about the visual stimulus that differ significantly from what one would derive by single-cell analysis.
View details for Web of Science ID 000181081600014
View details for PubMedID 12575956
- Biological computation: Amazing algorithms NATURE 2002; 416 (6882): 683-683
- Molecular motors - Doing a rotary two-step NATURE 2001; 410 (6831): 878-?
Force production by single kinesin motors
NATURE CELL BIOLOGY
2000; 2 (10): 718-723
Motor proteins such as kinesin, myosin and polymerase convert chemical energy into work through a cycle that involves nucleotide hydrolysis. Kinetic rates in the cycle that depend upon load identify transitions at which structural changes, such as power strokes or diffusive motions, are likely to occur. Here we show, by modelling data obtained with a molecular force clamp, that kinesin mechanochemistry can be characterized by a mechanism in which a load-dependent isomerization follows ATP binding. This model quantitatively accounts for velocity data over a wide range of loads and ATP levels, and indicates that movement may be accomplished through two sequential 4-nm substeps. Similar considerations account for kinesin processivity, which is found to obey a load-dependent Michaelis-Menten relationship.
View details for Web of Science ID 000089697000017
View details for PubMedID 11025662
Single kinesin molecules studied with a molecular force clamp
1999; 400 (6740): 184-189
Kinesin is a two-headed, ATP-driven motor protein that moves processively along microtubules in discrete steps of 8 nm, probably by advancing each of its heads alternately in sequence. Molecular details of how the chemical energy stored in ATP is coupled to mechanical displacement remain obscure. To shed light on this question, a force clamp was constructed, based on a feedback-driven optical trap capable of maintaining constant loads on single kinesin motors. The instrument provides unprecedented resolution of molecular motion and permits mechanochemical studies under controlled external loads. Analysis of records of kinesin motion under variable ATP concentrations and loads revealed several new features. First, kinesin stepping appears to be tightly coupled to ATP hydrolysis over a wide range of forces, with a single hydrolysis per 8-nm mechanical advance. Second, the kinesin stall force depends on the ATP concentration. Third, increased loads reduce the maximum velocity as expected, but also raise the apparent Michaelis-Menten constant. The kinesin cycle therefore contains at least one load-dependent transition affecting the rate at which ATP molecules bind and subsequently commit to hydrolysis. It is likely that at least one other load-dependent rate exists, affecting turnover number. Together, these findings will necessitate revisions to our understanding of how kinesin motors function.
View details for Web of Science ID 000081324900059
View details for PubMedID 10408448
Force and velocity measured for single molecules of RNA polymerase
1998; 282 (5390): 902-907
RNA polymerase (RNAP) moves along DNA while carrying out transcription, acting as a molecular motor. Transcriptional velocities for single molecules of Escherichia coli RNAP were measured as progressively larger forces were applied by a feedback-controlled optical trap. The shapes of RNAP force-velocity curves are distinct from those of the motor enzymes myosin or kinesin, and indicate that biochemical steps limiting transcription rates at low loads do not generate movement. Modeling the data suggests that high loads may halt RNAP by promoting a structural change which moves all or part of the enzyme backwards through a comparatively large distance, corresponding to 5 to 10 base pairs. This contrasts with previous models that assumed force acts directly upon a single-base translocation step.
View details for Web of Science ID 000076727300038
View details for PubMedID 9794753
Kinesin hydrolyses one ATP per 8-nm step
1997; 388 (6640): 386-390
Kinesin is a two-headed, ATP-dependent motor protein that moves along microtubules in discrete steps of 8 nm. In vitro, single molecules produce processive movement; motors typically take approximately 100 steps before releasing from a microtubule. A central question relates to mechanochemical coupling in this enzyme: how many molecules of ATP are consumed per step? For the actomyosin system, experimental approaches to this issue have generated considerable controversy. Here we take advantage of the processivity of kinesin to determine the coupling ratio without recourse to direct measurements of ATPase activity, which are subject to large experimental uncertainties. Beads carrying single molecules of kinesin moving on microtubules were tracked with high spatial and temporal resolution by interferometry. Statistical analysis of the intervals between steps at limiting ATP, and studies of fluctuations in motor speed as a function of ATP concentration, allow the coupling ratio to be determined. At near-zero load, kinesin molecules hydrolyse a single ATP molecule per 8-nm advance. This finding excludes various one-to-many and many-to-one coupling schemes, analogous to those advanced for myosin, and places severe constraints on models for movement.
View details for Web of Science ID A1997XM52800053
View details for PubMedID 9237757
- Statistical kinetics of processive enzymes COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT. 1995: 793-802
Theory of continuum random walks and application to chemotaxis.
Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics
1993; 48 (4): 2553-2568
View details for PubMedID 9960890