@article {1575, title = {Near-isotropic 3D optical nanoscopy with photon-limited chromophores.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, year = {2010}, month = {2010 Jun 1}, pages = {10068-73}, abstract = {

Imaging approaches based on single molecule localization break the diffraction barrier of conventional fluorescence microscopy, allowing for bioimaging with nanometer resolution. It remains a challenge, however, to precisely localize photon-limited single molecules in 3D. We have developed a new localization-based imaging technique achieving almost isotropic subdiffraction resolution in 3D. A tilted mirror is used to generate a side view in addition to the front view of activated single emitters, allowing their 3D localization to be precisely determined for superresolution imaging. Because both front and side views are in focus, this method is able to efficiently collect emitted photons. The technique is simple to implement on a commercial fluorescence microscope, and especially suitable for biological samples with photon-limited chromophores such as endogenously expressed photoactivatable fluorescent proteins. Moreover, this method is relatively resistant to optical aberration, as it requires only centroid determination for localization analysis. Here we demonstrate the application of this method to 3D imaging of bacterial protein distribution and neuron dendritic morphology with subdiffraction resolution.

}, keywords = {Animals, Base Sequence, Dendrites, DNA Primers, Escherichia coli K12, Escherichia coli Proteins, Fluorescence, Imaging, Luminescent Proteins, Microscopy, Nanotechnology, Optical Devices, Photons, Rats, Recombinant Fusion Proteins, Sprague-Dawley, Three-Dimensional}, issn = {1091-6490}, doi = {10.1073/pnas.1004899107}, author = {Tang, Jianyong and Akerboom, Jasper and Vaziri, Alipasha and Looger, Loren L and Shank, Charles V} } @article {3911, title = {Network mechanisms of theta related neuronal activity in hippocampal CA1 pyramidal neurons.}, journal = {Nature Neuroscience}, volume = {13}, year = {2010}, month = {2010 Aug}, pages = {967-72}, abstract = {

Although hippocampal theta oscillations represent a prime example of temporal coding in the mammalian brain, little is known about the specific biophysical mechanisms. Intracellular recordings support a particular abstract oscillatory interference model of hippocampal theta activity, the soma-dendrite interference model. To gain insight into the cellular and circuit level mechanisms of theta activity, we implemented a similar form of interference using the actual hippocampal network in mice in vitro. We found that pairing increasing levels of phasic dendritic excitation with phasic stimulation of perisomatic projecting inhibitory interneurons induced a somatic polarization and action potential timing profile that reproduced most common features. Alterations in the temporal profile of inhibition were required to fully capture all features. These data suggest that theta-related place cell activity is generated through an interaction between a phasic dendritic excitation and a phasic perisomatic shunting inhibition delivered by interneurons, a subset of which undergo activity-dependent presynaptic modulation.

}, keywords = {Animals, Gene Knock-In Techniques, Hippocampus, Inbred C57BL, Inhibitory Postsynaptic Potentials, Mice, Nerve Net, Organ Culture Techniques, Patch-Clamp Techniques, Pyramidal Cells, Theta Rhythm}, issn = {1546-1726}, doi = {10.1038/nn.2597}, author = {Losonczy, Attila and Zemelman, Boris V and Vaziri, Alipasha and Magee, Jeffrey C} } @article {5373, title = {Quantum coherence in ion channels: resonances, transport and verification.}, journal = {New Journal of Physics}, volume = {12}, year = {2010}, month = {2010}, abstract = {

Recently it was demonstrated that long-lived quantum coherence exists during excitation energy transport in photosynthesis. It is a valid question up to which length, time and mass scales quantum coherence may extend, how one may detect this coherence and what, if any, role it plays in the dynamics of the system. Here we suggest that the selectivity filter of ion channels may exhibit quantum coherence, which might be relevant for the process of ion selectivity and conduction. We show that quantum resonances could provide an alternative approach to ultrafast two-dimensional (2D) spectroscopy to probe these quantum coherences. We demonstrate that the emergence of resonances in the conduction of ion channels that are modulated periodically by time-dependent external electric fields can serve as signatures of quantum coherence in such a system. Assessments of experimental feasibility and specific paths towards the experimental realization of such experiments are presented.

}, doi = {10.1088/1367-2630/12/8/085001}, author = {Vaziri, Alipasha and Plenio, Martin B.} } @article {4284, title = {Two-photon single-cell optogenetic control of neuronal activity by sculpted light.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, year = {2010}, month = {2010 Jun 29}, pages = {11981-6}, abstract = {

Recent advances in optogenetic techniques have generated new tools for controlling neuronal activity, with a wide range of neuroscience applications. The most commonly used approach has been the optical activation of the light-gated ion channel channelrhodopsin-2 (ChR2). However, targeted single-cell-level optogenetic activation with temporal precessions comparable to the spike timing remained challenging. Here we report fast (\< or = 1 ms), selective, and targeted control of neuronal activity with single-cell resolution in hippocampal slices. Using temporally focused laser pulses (TEFO) for which the axial beam profile can be controlled independently of its lateral distribution, large numbers of channels on individual neurons can be excited simultaneously, leading to strong (up to 15 mV) and fast (\< or = 1 ms) depolarizations. Furthermore, we demonstrated selective activation of cellular compartments, such as dendrites and large presynaptic terminals, at depths up to 150 microm. The demonstrated spatiotemporal resolution and the selectivity provided by TEFO allow manipulation of neuronal activity, with a large number of applications in studies of neuronal microcircuit function in vitro and in vivo.

}, keywords = {Action Potentials, Animals, Cell Line, Dendrites, Electrophysiological Phenomena, Hippocampus, Humans, Lasers, Mice, Nerve Tissue Proteins, Neurons, Optical Phenomena, Patch-Clamp Techniques, Photic Stimulation, Photons, Presynaptic Terminals, Rats, Recombinant Fusion Proteins, Rhodopsin, Sprague-Dawley, Transgenic}, issn = {1091-6490}, doi = {10.1073/pnas.1006620107}, author = {Andrasfalvy, Bertalan K and Zemelman, Boris V and Tang, Jianyong and Vaziri, Alipasha} } @article {4297, title = {Ultrafast widefield optical sectioning microscopy by multifocal temporal focusing.}, journal = {Optics Express}, volume = {18}, year = {2010}, month = {2010 Sep 13}, pages = {19645-55}, abstract = {

The need for optical sectioning in bio-imaging has amongst others led to the development of the two-photon scanning microscopy. However, this comes with some intrinsic fundamental limitations in the temporal domain as the focused spot has to be scanned mechanically in the sample plane. Hence for a large number of biological applications where imaging speed is a limiting factor, it would be significantly advantageous to generate widefield excitations with an optical sectioning comparable to the two-photon scanning microscopy. Recently by using the technique of temporal focusing it was shown that high axial resolution widefield excitation can be generated in picosecond time scales without any mechanical moving parts. However the achievable axial resolution is still well above that of a two-photon scanning microscope. Here we demonstrate a new ultrafast widefield two-photon imaging technique termed Multifocal Temporal Focusing (MUTEF) which relies on the generation of a set of diffraction limited beams produced by an Echelle grating that scan across a second tilted diffraction grating in picosecond time scale, generating a widefield excitation area with an axial resolution comparable to a two-photon scanning microscope. Using this method we have shown widefield two-photon imaging on fixed biological samples with an axial sectioning with a FWHM of \ 0.85 μm.

}, keywords = {Equipment Design, Equipment Failure Analysis, Fluorescence, Image Enhancement, Lenses, Lighting, Microscopy, Multiphoton, Refractometry, Reproducibility of Results, Sensitivity and Specificity}, issn = {1094-4087}, doi = {10.1364/OE.18.019645}, author = {Vaziri, Alipasha and Shank, Charles V} } @article {5357, title = {Three dimensional super resolution fluorescence imaging of single bacterial cells by stereo photoactivated localization microscopy.}, journal = {Microscopy and Microanalysis}, volume = {15}, year = {2009}, month = {2009 July 26}, pages = {564-5}, doi = {10.1017/S1431927609095737}, author = {Tang, Jianyong and Vaziri, Alipasha and Akerboom, Jasper P. and Looger, Loren and Shank, Charles V} } @article {5363, title = {Three-dimensional nanoscopy of biological samples.}, journal = {2009 Conference on Lasers and Electro-Optics and Quantum Electronics and Laser Science Conference (CLEO/QELS 2009), Vols. 1-5}, volume = {1-5}, year = {2009}, month = {2009 Jun 5}, pages = {147-8}, abstract = {

We have demonstrated super-resolution imaging of protein distributions in cells at depth at multiple layers with a lateral localization precision better than 50 nm. The approach is based on combining photoactivated localization microscopy with temporal focusing.

}, author = {Vaziri, Alipasha and Tang, Jianyong and Shroff, Hari and Shank, Charles V} } @article {5225, title = {Multilayer three-dimensional super resolution imaging of thick biological samples.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, year = {2008}, month = {2008 Dec 23}, pages = {20221-6}, abstract = {

Recent advances in optical microscopy have enabled biological imaging beyond the diffraction limit at nanometer resolution. A general feature of most of the techniques based on photoactivated localization microscopy (PALM) or stochastic optical reconstruction microscopy (STORM) has been the use of thin biological samples in combination with total internal reflection, thus limiting the imaging depth to a fraction of an optical wavelength. However, to study whole cells or organelles that are typically up to 15 microm deep into the cell, the extension of these methods to a three-dimensional (3D) super resolution technique is required. Here, we report an advance in optical microscopy that enables imaging of protein distributions in cells with a lateral localization precision better than 50 nm at multiple imaging planes deep in biological samples. The approach is based on combining the lateral super resolution provided by PALM with two-photon temporal focusing that provides optical sectioning. We have generated super-resolution images over an axial range of approximately 10 microm in both mitochondrially labeled fixed cells, and in the membranes of living S2 Drosophila cells.

}, keywords = {Animals, Cell Line, Cells, Humans, Imaging, Microscopy, Mitochondria, Organelles, Three-Dimensional}, issn = {1091-6490}, doi = {10.1073/pnas.0810636105}, author = {Vaziri, Alipasha and Tang, Jianyong and Shroff, Hari and Shank, Charles V} }