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Open Access Publications from the University of California

Scholarly Works (36 results)

  • Article
  • Peer Reviewed
UC San Francisco Previously Published Works (2010)
Intermediate conductance, calcium-activated potassium channels are gated by the binding of intracellular Ca(2+) to calmodulin, a Ca(2+)-binding protein that is constitutively associated with the C terminus of the channel. Although previous studies indicated that the pore-lining residues along the C-terminal portion of S6 contribute to the activation mechanism, little is known about whether the nonluminal face of S6 contributes to this process. Here we demonstrate that the sulfhydral reagent, parachloromercuribenze sulfonate (PCMBS), modifies an endogenous cysteine residue predicted to have a nonluminal orientation (Cys(276)) along the sixth transmembrane segment (S6). Modification of Cys(276) manipulates the steady-state and kinetic behavior of the channel by shifting the gating equilibrium toward the open state, resulting in a left shift in apparent Ca(2+) affinity and a slowing in the deactivation process. Using a six-state gating scheme, our analysis shows that PCMBS slows the transition between the open state back to the third closed state. Interpreting this result in the context of the steady-state and kinetic data suggests that PCMBS functions to shift the gating equilibrium toward the open state by disrupting channel closing. In an attempt to understand whether the nonluminal face of S6 participates in the activation mechanism, we conducted a partial tryptophan scan of this region. Substituting a tryptophan for Leu(281) recapitulated the effect on the steady-state and kinetic behavior observed with PCMBS. Considering the predicted nonluminal orientation of Cys(276) and Leu(281), a simple physical interpretation of these results is that the nonluminal face of S6 forms a critical interaction surface mediating the transition into the closed conformation, suggesting the nonluminal C-terminal portion of S6 is allosterically coupled to the activation gate.
    Cover page: Characterization of the PCMBS-dependent modification of KCa3.1 channel gating
    • Thesis
    • Peer Reviewed
    UC San Diego Electronic Theses and Dissertations (2018)

    Two-photon microscopy has had an enormous influence on animal studies of in vivo brain activity providing a tool for high-resolution imaging in live cortical tissue. Yet, the majority of 2-photon imaging studies, as of today, have focused on the top ~500 μm of the cerebral cortex due to limited penetration of light into biological tissues. Cerebral neurons, however, are wired in circuits spanning the entire cortical depth (~ 1 mm in mice), and sampling of activity throughout this depth would be required for reconstruction of circuit dynamics. Therefore, increasing the in vivo penetration depth of microscopic imaging is at the heart of brain initiative society. In this thesis, we demonstrate that the degree of freedom introduced by non-degenerate 2-photon excitation (ND-2PE), using two independently controlled pulsed laser sources of different photon energies, may provide a number of advantages over the conventional methods promising deeper penetration with higher efficiency of excitation and better signal-to-background ratio in a scattering medium. The presence of two laser beams allows:

    1) Tuning the combination of wavelengths to optimize excitation cross-section for each fluorophore;

    2) Independent control of power (and polarization) such that an increase in the IR power can be used to compensate for the loss of NIR power due to scattering and absorption;

    3) Spatial displacement of the two beams to limit the overlap to the focal volume, minimizing background excitation;

    All the advantages were validated with our experiments in this thesis. We started with investigating the cross section of widely used fluorophores under ND-2PE. The experimental results showed the enhancement to the cross-section of ND-2PE in comparison with that of D-2PE. An experiment for neuron images in mice brain also supported the signal enhancement under ND-2PE. Next, we demonstrated that ND-2PE can increase maximum excitation depth in a scattering phantom by compensating the loss of NIR beam with IR beam. Finally, we demonstrated that the out-out-focus excitation in scattering phantom can be reduced by strategically displacing two beams. The scheme of side-by-side beams was also applied to in vivo brain images.

      Cover page: Non-degenerated two photon excitation for fluorescence microscopy in the scattering media
      • Article
      • Peer Reviewed
      UC San Diego Previously Published Works (2011)
      Multielectrode array recordings of extracellular electrical field potentials along the depth axis of the cerebral cortex are gaining popularity as an approach for investigating the activity of cortical neuronal circuits. The low-frequency band of extracellular potential, i.e., the local field potential (LFP), is assumed to reflect synaptic activity and can be used to extract the laminar current source density (CSD) profile. However, physiological interpretation of the CSD profile is uncertain because it does not disambiguate synaptic inputs from passive return currents and does not identify population-specific contributions to the signal. These limitations prevent interpretation of the CSD in terms of synaptic functional connectivity in the columnar microcircuit. Here we present a novel anatomically informed model for decomposing the LFP signal into population-specific contributions and for estimating the corresponding activated synaptic projections. This involves a linear forward model, which predicts the population-specific laminar LFP in response to synaptic inputs applied at different positions along each population and a linear inverse model, which reconstructs laminar profiles of synaptic inputs from laminar LFP data based on the forward model. Assuming spatially smooth synaptic inputs within individual populations, the model decomposes the columnar LFP into population-specific contributions and estimates the corresponding laminar profiles of synaptic input as a function of time. It should be noted that constant synaptic currents at all positions along a neuronal population cannot be reconstructed, as this does not result in a change in extracellular potential. However, constraining the solution using a priori knowledge of the spatial distribution of synaptic connectivity provides the further advantage of estimating the strength of active synaptic projections from the columnar LFP profile thus fully specifying synaptic inputs.
        Cover page: On the Estimation of Population-Specific Synaptic Currents from Laminar Multielectrode Recordings
        • Article
        • Peer Reviewed
        UC San Diego Previously Published Works (2014)
        We present a database client software-Neurovascular Network Explorer 1.0 (NNE 1.0)-that uses MATLAB(®) based Graphical User Interface (GUI) for interaction with a database of 2-photon single-vessel diameter measurements from our previous publication (Tian et al., 2010). These data are of particular interest for modeling the hemodynamic response. NNE 1.0 is downloaded by the user and then runs either as a MATLAB script or as a standalone program on a Windows platform. The GUI allows browsing the database according to parameters specified by the user, simple manipulation and visualization of the retrieved records (such as averaging and peak-normalization), and export of the results. Further, we provide NNE 1.0 source code. With this source code, the user can database their own experimental results, given the appropriate data structure and naming conventions, and thus share their data in a user-friendly format with other investigators. NNE 1.0 provides an example of seamless and low-cost solution for sharing of experimental data by a regular size neuroscience laboratory and may serve as a general template, facilitating dissemination of biological results and accelerating data-driven modeling approaches.
          Cover page: Neurovascular Network Explorer 1.0: a database of 2-photon single-vessel diameter measurements with MATLAB® graphical user interface
          • Article
          • Peer Reviewed
          UC San Diego Previously Published Works (2016)
          Laminar population analysis (LPA) is a method for analysis of electrical data recorded by linear multielectrodes passing through all lamina of cortex. Like principal components analysis (PCA) and independent components analysis (ICA), LPA offers a way to decompose the data into contributions from separate cortical populations. However, instead of using purely mathematical assumptions in the decomposition, LPA is based on physiological constraints, i.e., that the observed LFP (low-frequency part of signal) is driven by action-potential firing as observed in the MUA (multi-unit activity; high-frequency part of the signal). In the presently developed generalized laminar population analysis (gLPA) the set of basis functions accounting for the LFP data is extended compared to the original LPA, thus allowing for a better fit of the model to experimental data. This enhances the risk for overfitting, however, and we therefore tested various versions of gLPA on virtual LFP data in which we knew the ground truth. These synthetic data were generated by biophysical forward-modeling of electrical signals from network activity in the comprehensive, and well-known, thalamocortical network model developed by Traub and coworkers. The results for the Traub model imply that while the laminar components extracted by the original LPA method overall are in fair agreement with the ground-truth laminar components, the results may be improved by use of gLPA method with two (gLPA-2) or even three (gLPA-3) postsynaptic LFP kernels per laminar population.
            Cover page: Generalized Laminar Population Analysis (gLPA) for Interpretation of Multielectrode Data from Cortex
            • Article
            • Peer Reviewed
            UC San Diego Previously Published Works (2017)
              Cover page: Neurovascular Network Explorer 2.0: A Database of 2-Photon Single-Vessel Diameter Measurements from Mouse SI Cortex in Response To Optogenetic Stimulation
              • Article
              • Peer Reviewed
              UC San Diego Previously Published Works (2009)
              A new method is presented for extraction of population firing-rate models for both thalamocortical and intracortical signal transfer based on stimulus-evoked data from simultaneous thalamic single-electrode and cortical recordings using linear (laminar) multielectrodes in the rat barrel system. Time-dependent population firing rates for granular (layer 4), supragranular (layer 2/3), and infragranular (layer 5) populations in a barrel column and the thalamic population in the homologous barreloid are extracted from the high-frequency portion (multi-unit activity; MUA) of the recorded extracellular signals. These extracted firing rates are in turn used to identify population firing-rate models formulated as integral equations with exponentially decaying coupling kernels, allowing for straightforward transformation to the more common firing-rate formulation in terms of differential equations. Optimal model structures and model parameters are identified by minimizing the deviation between model firing rates and the experimentally extracted population firing rates. For the thalamocortical transfer, the experimental data favor a model with fast feedforward excitation from thalamus to the layer-4 laminar population combined with a slower inhibitory process due to feedforward and/or recurrent connections and mixed linear-parabolic activation functions. The extracted firing rates of the various cortical laminar populations are found to exhibit strong temporal correlations for the present experimental paradigm, and simple feedforward population firing-rate models combined with linear or mixed linear-parabolic activation function are found to provide excellent fits to the data. The identified thalamocortical and intracortical network models are thus found to be qualitatively very different. While the thalamocortical circuit is optimally stimulated by rapid changes in the thalamic firing rate, the intracortical circuits are low-pass and respond most strongly to slowly varying inputs from the cortical layer-4 population.
                Cover page: Estimation of Thalamocortical and Intracortical Network Models from Joint Thalamic Single-Electrode and Cortical Laminar-Electrode Recordings in the Rat Barrel System
                • Article
                • Peer Reviewed
                UC San Diego Previously Published Works (2016)
                The cerebral metabolic rate of oxygen ([Formula: see text]) is an essential parameter for evaluating brain function and pathophysiology. However, the currently available approaches for quantifying [Formula: see text] rely on complex multimodal imaging and mathematical modeling. Here, we introduce a method that allows estimation of [Formula: see text] based on a single measurement modality-two-photon imaging of the partial pressure of oxygen ([Formula: see text]) in cortical tissue. We employed two-photon phosphorescence lifetime microscopy (2PLM) and the oxygen-sensitive nanoprobe PtP-C343 to map the tissue [Formula: see text] distribution around cortical penetrating arterioles. [Formula: see text] is subsequently estimated by fitting the changes of tissue [Formula: see text] around arterioles with the Krogh cylinder model of oxygen diffusion. We measured the baseline [Formula: see text] in anesthetized rats and modulated tissue [Formula: see text] levels by manipulating the depth of anesthesia. This method provides [Formula: see text] measurements localized within [Formula: see text] and it may provide oxygen consumption measurements in individual cortical layers or within confined cortical regions, such as in ischemic penumbra and the foci of functional activation.
                  Cover page: Two-photon microscopy measurement of cerebral metabolic rate of oxygen using periarteriolar oxygen concentration gradients
                  • Article
                  • Peer Reviewed
                  UC San Diego Previously Published Works (2018)

                  Background

                  Recent progress in electrophysiological and optical methods for neuronal recordings provides vast amounts of high-resolution data. In parallel, the development of computer technology has allowed simulation of ever-larger neuronal circuits. A challenge in taking advantage of these developments is the construction of single-cell and network models in a way that faithfully reproduces neuronal biophysics with subcellular level of details while keeping the simulation costs at an acceptable level.

                  New method

                  In this work, we develop and apply an automated, stepwise method for fitting a neuron model to data with fine spatial resolution, such as that achievable with voltage sensitive dyes (VSDs) and Ca2+ imaging.

                  Result

                  We apply our method to simulated data from layer 5 pyramidal cells (L5PCs) and construct a model with reduced neuronal morphology. We connect the reduced-morphology neurons into a network and validate against simulated data from a high-resolution L5PC network model.

                  Comparison with existing methods

                  Our approach combines features from several previously applied model-fitting strategies. The reduced-morphology neuron model obtained using our approach reliably reproduces the membrane-potential dynamics across the dendrites as predicted by the full-morphology model.

                  Conclusions

                  The network models produced using our method are cost-efficient and predict that interconnected L5PCs are able to amplify delta-range oscillatory inputs across a large range of network sizes and topologies, largely due to the medium after hyperpolarization mediated by the Ca2+-activated SK current.
                    Cover page: A stepwise neuron model fitting procedure designed for recordings with high spatial resolution: Application to layer 5 pyramidal cells
                    • Article
                    • Peer Reviewed
                    UC San Diego Previously Published Works (2018)
                    The importance of sharing experimental data in neuroscience grows with the amount and complexity of data acquired and various techniques used to obtain and process these data. However, the majority of experimental data, especially from individual studies of regular-sized laboratories never reach wider research community. A graphical user interface (GUI) engine called Neurovascular Network Explorer 2.0 (NNE 2.0) has been created as a tool for simple and low-cost sharing and exploring of vascular imaging data. NNE 2.0 interacts with a database containing optogenetically-evoked dilation/constriction time-courses of individual vessels measured in mice somatosensory cortex in vivo by 2-photon microscopy. NNE 2.0 enables selection and display of the time-courses based on different criteria (subject, branching order, cortical depth, vessel diameter, arteriolar tree) as well as simple mathematical manipulation (e.g. averaging, peak-normalization) and data export. It supports visualization of the vascular network in 3D and enables localization of the individual functional vessel diameter measurements within vascular trees. NNE 2.0, its source code, and the corresponding database are freely downloadable from UCSD Neurovascular Imaging Laboratory website1. The source code can be utilized by the users to explore the associated database or as a template for databasing and sharing their own experimental results provided the appropriate format.
                      Cover page: Neurovascular Network Explorer 2.0: A Simple Tool for Exploring and Sharing a Database of Optogenetically-evoked Vasomotion in Mouse Cortex In Vivo.
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