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209 Publications

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    Murphy Lab
    05/11/16 | Shared and distinct retinal input to the mouse superior colliculus and dorsal lateral geniculate nucleus.
    Ellis EM, Gauvain G, Sivyer B, Murphy GJ
    Journal of Neurophysiology. 2016 May 11;116(2):602-10. doi: 10.1152/jn.00227.2016

    The mammalian retina conveys the vast majority of information about visual stimuli to two brain regions: the dorsal lateral geniculate nucleus (dLGN) and the superior colliculus (SC). The degree to which retinal ganglion cells (RGCs) send similar or distinct information to the two areas remains unclear despite the important constraints that different patterns of RGC input place on downstream visual processing. To resolve this ambiguity we injected a glycoprotein-deficient rabies virus coding for the expression of a fluorescent protein into the dLGN or SC; rabies virus labeled a smaller fraction of RGCs than lipophilic dyes like DiI but, crucially, did not label RGC axons of passage. ~80% of the RGCs infected by rabies virus injected into the dLGN were co-labeled with DiI injected into the SC, suggesting that many dLGN-projecting RGCs also project to the SC. However, functional characterization of RGCs revealed that the SC receives input from several classes of RGCs that largely avoid the dLGN - in particular, RGCs in which (1) sustained changes in light intensity elicit transient changes in firing rate and/or (2) a small range of stimulus sizes or temporal fluctuations in light intensity elicit robust activity. Taken together, our results illustrate several unexpected asymmetries in the information that the mouse retina conveys to two major downstream targets and suggest that differences in the output of dLGN and SC neurons reflect, at least in part, differences in the functional properties of RGCs that innervate the SC but not the dLGN.

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    05/09/16 | Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome.
    Abeyrathne PD, Koh CS, Grant T, Grigorieff N, Korostelev AA
    eLife. 2016 May 9;5:. doi: 10.7554/eLife.14874

    Internal ribosome entry sites (IRESs) mediate cap-independent translation of viral mRNAs. Using electron cryo-microscopy of a single specimen, we present five ribosome structures formed with the Taura syndrome virus IRES and translocase eEF2•GTP bound with sordarin. The structures suggest a trajectory of IRES translocation, required for translation initiation, and provide an unprecedented view of eEF2 dynamics. The IRES rearranges from extended to bent to extended conformations. This inchworm-like movement is coupled with ribosomal inter-subunit rotation and 40S head swivel. eEF2, attached to the 60S subunit, slides along the rotating 40S subunit to enter the A site. Its diphthamide-bearing tip at domain IV separates the tRNA-mRNA-like pseudoknot I (PKI) of the IRES from the decoding center. This unlocks 40S domains, facilitating head swivel and biasing IRES translocation via hitherto-elusive intermediates with PKI captured between the A and P sites. The structures suggest missing links in our understanding of tRNA translocation.

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    05/05/16 | Real-time quantification of single RNA translation dynamics in living cells.
    Morisaki T, Lyon K, DeLuca KF, DeLuca JG, English BP, Zhang Z, Lavis LD, Grimm JB, Viswanathan S, Looger LL
    Science. 2016 May 05;352(6292):1425-9. doi: 10.1126/science.aaf0899

    Although mRNA translation is a fundamental biological process, it has never been imaged in real-time with single molecule precision in vivo. To achieve this, we developed Nascent Chain Tracking (NCT), a technique that uses multi-epitope tags and antibody-based fluorescent probes to quantify single mRNA protein synthesis dynamics. NCT reveals an elongation rate of ~10 amino acids per second, with initiation occurring stochastically every ~30 s. Polysomes contain ~1 ribosome every 200-900 nucleotides and are globular rather than elongated in shape. By developing multi-color probes, we show most polysomes act independently; however, a small fraction (~5%) form complexes in which two distinct mRNAs can be translated simultaneously. The sensitivity and versatility of NCT make it a powerful new tool for quantifying mRNA translation kinetics.

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    Singer Lab
    05/05/16 | Translation dynamics of single mRNAs in live cells and neurons.
    Wu B, Eliscovich C, Yoon YJ, Singer RH
    Science (New York, N.Y.). 2016 May 05;352(6292):1430-5. doi: 10.1126/science.aaf1084

    Translation is the fundamental biological process converting mRNA information into proteins. Single molecule imaging in live cells has illuminated the dynamics of RNA transcription; however, it is not yet applicable to translation. Here we report Single molecule Imaging of NAscent PeptideS (SINAPS) to assess translation in live cells. The approach provides direct readout of initiation, elongation, and location of translation. We show that mRNAs coding for endoplasmic reticulum (ER) proteins are translated when they encounter the ER membrane. Single molecule fluorescence recovery after photobleaching provides direct measurement of elongation speed (5 AA/s). In primary neurons mRNAs are translated in proximal dendrites but repressed in distal dendrites and display “bursting” translation. This technology provides a tool to address the spatiotemporal translation mechanism of single mRNAs in living cells.

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    05/04/16 | Brain derived neurotrophic factor differentially modulates excitability of two classes of hippocampal output neurons.
    Graves AR, Moore SJ, Spruston N, Tryba AK, Kaczorowski CC
    Journal of Neurophysiology. 2016 May 4;116(2):466-71. doi: 10.1152/jn.00186.2016

    Brain-derived neurotrophic factor (BDNF) plays an important role in hippocampus-dependent learning and memory. Canonically, this has been ascribed to an enhancing effect on neuronal excitability and synaptic plasticity in the CA1 region. However, it is the pyramidal neurons in the subiculum that form the primary efferent pathways conveying hippocampal information to other areas of the brain, and yet the effect of BDNF on these neurons has remained unexplored. We present new data that BDNF regulates neuronal excitability and cellular plasticity in a much more complex manner than previously suggested. Subicular pyramidal neurons can be divided into two major classes, which have different electrophysiological and morphological properties, different requirements for the induction of plasticity and different extra-hippocampal projections. We found that BDNF increases excitability in one class of subicular pyramidal neurons, yet decreases excitability of the other class. Further, while endogenous BDNF was necessary for the induction of synaptic plasticity in both cell types, BDNF enhanced intrinsic plasticity in one class of pyramidal neurons, yet suppressed intrinsic plasticity in the other. Taken together, these data suggest a novel role for BDNF signaling, as it appears to dynamically and bidirectionally regulate the output of hippocampal information to different regions of the brain.

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    Svoboda Lab
    05/03/16 | Flow of information underlying a tactile decision in mice.
    Li N, Guo ZV, Chen T, Svoboda K
    Micro-, Meso- and Macro-Dynamics of the Brain:. doi: 10.1007/978-3-319-28802-4_3

    Motor planning allows us to conceive, plan, and initiate skilled motor behaviors. Motor planning involves activity distributed widely across the cortex. How this activity dynamically comes together to guide movement remains an unsolved problem. We study motor planning in mice performing a tactile decision behavior. Head-fixed mice discriminate object locations with their whiskers and report their choice by directional licking (“lick left”/“lick right”). A short-term memory component separates tactile “sensation” and “action” into distinct epochs. Using loss-of-function experiments, cell-type specific electrophysiology, and cellular imaging, we delineate when and how activity in specific brain areas and cell types drives motor planning in mice. Our results suggest that information flows serially from sensory to motor areas during motor planning. The motor cortex circuit maintains the motor plan during short-term memory and translates the motor plan into motor commands that drive the upcoming directional licking.

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    05/03/16 | RNA Polymerase II cluster dynamics predict mRNA output in living cells.
    Cho W, Jayanth N, English BP, Inoue T, Andrews JO, Conway W, Grimm JB, Spille J, Lavis LD, Lionnet T, Cisse II
    eLife. 2016 May 03;5:. doi: 10.7554/eLife.13617

    Protein clustering is a hallmark of genome regulation in mammalian cells. However, the dynamic molecular processes involved make it difficult to correlate clustering with functional consequences in vivo. We developed a live-cell super-resolution approach to uncover the correlation between mRNA synthesis and the dynamics of RNA Polymerase II (Pol II) clusters at a gene locus. For endogenous β-actin genes in mouse embryonic fibroblasts, we observe that short-lived (~8 s) Pol II clusters correlate with basal mRNA output. During serum stimulation, a stereotyped increase in Pol II cluster lifetime correlates with a proportionate increase in the number of mRNAs synthesized. Our findings suggest that transient clustering of Pol II may constitute a pre-transcriptional regulatory event that predictably modulates nascent mRNA output.

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    05/02/16 | Distinct subpopulations of FOXD1 stroma-derived cells regulate renal erythropoietin.
    Kobayashi H, Liu Q, Binns TC, Urrutia AA, Davidoff O, Kapitsinou PP, Pfaff AS, Olauson H, Wernerson A, Fogo AB, Fong G, Gross KW, Haase VH
    The Journal of Clinical Investigation. 2016 May 02;126(5):1926-38. doi: 10.1172/JCI83551

    Renal peritubular interstitial fibroblast-like cells are critical for adult erythropoiesis, as they are the main source of erythropoietin (EPO). Hypoxia-inducible factor 2 (HIF-2) controls EPO synthesis in the kidney and liver and is regulated by prolyl-4-hydroxylase domain (PHD) dioxygenases PHD1, PHD2, and PHD3, which function as cellular oxygen sensors. Renal interstitial cells with EPO-producing capacity are poorly characterized, and the role of the PHD/HIF-2 axis in renal EPO-producing cell (REPC) plasticity is unclear. Here we targeted the PHD/HIF-2/EPO axis in FOXD1 stroma-derived renal interstitial cells and examined the role of individual PHDs in REPC pool size regulation and renal EPO output. Renal interstitial cells with EPO-producing capacity were entirely derived from FOXD1-expressing stroma, and Phd2 inactivation alone induced renal Epo in a limited number of renal interstitial cells. EPO induction was submaximal, as hypoxia or pharmacologic PHD inhibition further increased the REPC fraction among Phd2-/- renal interstitial cells. Moreover, Phd1 and Phd3 were differentially expressed in renal interstitium, and heterozygous deficiency for Phd1 and Phd3 increased REPC numbers in Phd2-/- mice. We propose that FOXD1 lineage renal interstitial cells consist of distinct subpopulations that differ in their responsiveness to Phd2 inactivation and thus regulation of HIF-2 activity and EPO production under hypoxia or conditions of pharmacologic or genetic PHD inactivation.

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    05/02/16 | Opponent and bidirectional control of movement velocity in the basal ganglia.
    Yttri EA, Dudman JT
    Nature. 2016 May 2:. doi: 10.1038/nature17639

    For goal-directed behaviour it is critical that we can both select the appropriate action and learn to modify the underlying movements (for example, the pitch of a note or velocity of a reach) to improve outcomes. The basal ganglia are a critical nexus where circuits necessary for the production of behaviour, such as the neocortex and thalamus, are integrated with reward signalling to reinforce successful, purposive actions. The dorsal striatum, a major input structure of basal ganglia, is composed of two opponent pathways, direct and indirect, thought to select actions that elicit positive outcomes and suppress actions that do not, respectively. Activity-dependent plasticity modulated by reward is thought to be sufficient for selecting actions in the striatum. Although perturbations of basal ganglia function produce profound changes in movement, it remains unknown whether activity-dependent plasticity is sufficient to produce learned changes in movement kinematics, such as velocity. Here we use cell-type-specific stimulation in mice delivered in closed loop during movement to demonstrate that activity in either the direct or indirect pathway is sufficient to produce specific and sustained increases or decreases in velocity, without affecting action selection or motivation. These behavioural changes were a form of learning that accumulated over trials, persisted after the cessation of stimulation, and were abolished in the presence of dopamine antagonists. Our results reveal that the direct and indirect pathways can each bidirectionally control movement velocity, demonstrating unprecedented specificity and flexibility in the control of volition by the basal ganglia.

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    05/02/16 | Robust estimation of self-exciting point process models with application to neuronal modeling.
    Abbas Kazemipour , Min Wu , Behtash Babadi

    We consider the problem of estimating discrete selfexciting point process models from limited binary observations, where the history of the process serves as the covariate. We analyze the performance of two classes of estimators, namely the `1-regularized maximum likelihood and greedy estimators, for a canonical self-exciting point process and characterize the sampling tradeoffs required for stable recovery in the non-asymptotic regime. Our results extend those of compressed sensing for linear and generalized linear models with i.i.d. covariates to point processes with highly inter-dependent covariates. We further provide simulation studies as well as application to real spiking data from mouse’s lateral geniculate nucleus and ferret’s retinal ganglion cells which agree with our theoretical predictions.

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