Timothy Murphy

Professor

Research Classification

Neuronal Systems

Research Interests

brain imaging
stroke
depression
Autism

Relevant Degree Programs

 

Research Methodology

in vivo imaging and optogenetics
automated data acquisition
homecage imaging in mice

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Doctoral students
Postdoctoral Fellows
2019
I support public scholarship, e.g. through the Public Scholars Initiative, and am available to supervise students and Postdocs interested in collaborating with external partners as part of their research.
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Postdoctoral Fellows

Great Supervisor Week Mentions

Each year graduate students are encouraged to give kudos to their supervisors through social media and our website as part of #GreatSupervisorWeek. Below are students who mentioned this supervisor since the initiative was started in 2017.

 

He is an inspirational leader who has vision years ahead of others in the same discipline. And he leaves you focused on what you are best.

David Cheng (2019)

 

Graduate Student Supervision

Doctoral Student Supervision (Jan 2008 - May 2019)
Characterizing single neuron activity patterns and dynamics using multi-scale spontaneous neuronal activity recordings of cat and mouse cortex (2018)

Throughout most of the 20th century the brain has been studied as a reflexive system with ever improving recording methods being applied within a variety of sensory and behavioural paradigms.Yet the brains of most animals (and all mammals) are spontaneously active with incoming sensory stimuli modulating rather than driving neural activity.The aim of this thesis is to characterize spontaneous neural activity across multiple temporal and spatial scales relying on biophysical simulations, experiments and analysis of recordings from the visual cortex of cats and dorsal cortex and thalamus of mouse.Biophysically detailed simulations yielded novel datasets for testing spike sorting algorithms which are critical for isolating single neuron activity. Sorting algorithms tested provided low error rates with operator skill being as important as sorting suite. Simulated datasets have similar characteristics to in vivo acquired data and ongoing larger-scope efforts are proposed for developing the next generation of spike sorting algorithms and extracellular probes.Single neuron spontaneous activity was correlated to dorsal cortex neural activity in mice. Spike-triggered-maps revealed that spontaneously firing cortical neurons were co-activated with homotopic and mono-synaptically connected cortical areas, whereas thalamic neurons co-activatedwith more diversely connected areas. Both bursting and tonic firing modes yielded similar maps and the time courses of spike-triggered-maps revealed distinct patterns suggesting such dynamics may constitute intrinsic single neuron properties. The mapping technique extends previous work tofurther link spontaneous neural activity across temporal and spatial scales and suggests additional avenues of investigation.Synchronized state cat visual and mouse sensory cortex electrophysiological recordings revealed that spontaneously occurring activity UP-state transitions fall into stereotyped classes of events that can be grouped. Single visual cortex neurons active during UP-state transitions fire in a partially preserved order extending previous findings on high firing rate neurons in rat somatosensory and auditory cortex. The firing order for many neurons changes over periods longer than 30-minutes suggesting a complex non-stationary temporal neural code may underlie spontaneous and stimulusevoked neural activity.This thesis shows that ongoing spontaneous brain activity contains substantial structure that can be used to further our understanding of brain function.

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Optogenetic investigation of neuronal excitability and sensory-motor function following a transient global ischemia in mice (2016)

Global ischemia occurs during cardiac arrest and has been implicated as a complication that can occur during cardiac surgery. It induces delayed neuronal death in human and animal models, particularly in the hippocampus, while it also can affect the cortex. Other than morphology and measures of cell death, relatively few studies have examined neuronal networks and motor-sensory function following reversible global ischemia in vivo. Optogenetics allows the combination of genetics and optics to control or monitor cells in living tissues. Here, I adapted optogenetics to examine neuronal excitability and motor function in the mouse cortex following a transient global ischemia. Following optogenetic stimulation, I recorded electrical signals from direct stimulation to targeted neuronal populations before and after a 5 min transient global ischemia. I found that both excitatory and inhibitory neuronal network in the somatosensory cortex exhibited prolonged suppression of synaptic transmission despite reperfusion, while the excitability and morphology of neurons recovered rapidly and more completely. Next, I adapted optogenetic motor mapping to investigate the changes of motor processing, and compared to the changes of sensory processing following the transient global ischemia. I found that both sensory and motor processing showed prolonged impairments despite of the recovery of neuronal excitability following reperfusion, presumably due to the unrestored synaptic transmission. Interestingly, motor processing recovered faster and more completely than sensory processing. My results suggest a uniform suppression of synaptic transmission, both in excitatory and inhibitory network, despite the rapid recovery of neuronal excitability and morphology, following a global ischemia and reperfusion. This prolonged suppression of synaptic transmission might impede the recovery of sensory and motor processing with differential severity. Besides, I extended tools for mesoscopic imaging using novel optogenetic sensors, including genetically encoded Ca2+ indicators - GCaMPs, and extracellular glutamate sensor - iGluSnFR. I found that iGluSnFR has fastest kinetics for reporting both sensory and spontaneous activity in the cortex, which can resolve temporal features of sensory processing that were not readily observed with GECIs. I suggest that iGluSnFR tools have potential utility in normal physiology, and neurologic pathologies in which abnormalities in glutamatergic signaling are implicated, such as stroke.

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Development and application of large-scale optogenetic mapping in the mouse cortex (2015)

One of the major goals in neuroscience is to understand and map the connectivity of the brain. While this is no small undertaking, recent technological advances have allowed brain mapping to reach unprecedented levels. Optogenetic tools have been developed that permit selective manipulation and investigation of neural systems. Here, we have mapped in vivo intracortical activity in the mouse by combining arbitrary point optogenetic stimulation and regional voltage-sensitive dye (VSD) imaging. We first show that optogenetic photostimulation using channelrhodopsin-2 (ChR2) led to cortical maps that were similar to the maps generated with sensory stimulation. ChR2-evoked maps confirmed known intrahemispheric relationships (such as between barrel cortex and motor cortex) and known interhemispheric relationships (such as between homotopic areas). We used ChR2 point stimulation to map a number of cortical areas and used network analysis to examine relationships between cortical areas. We found asymmetrical connections between primary and secondary sensory cortex and defined the parietal association cortex as a hub node. We then applied this mapping method to map altered cortical connectivity in the early and late stages after a targeted cortical stroke (1 week post-stroke and 8 weeks post-stroke, respectively). Network analysis based on ChR2-evoked responses revealed a symmetrical bilateral sham network that was disrupted after stroke. At 1 week post-stroke, we observed wide-spread depression of ChR2-evoked activity that extended to the contralesional hemisphere. By 8 weeks post-stroke significant recovery was observed. When we considered the network as a whole, we found that scaling the ChR2-evoked activity from the stroke groups to match the sham group mean resulted in a relative distribution of responses that was indistinguishable from the sham group, suggesting network-wide down-scaling and connectional diaschisis after stroke. When connections within the peri-infarct were isolated, we did not observe equal down-scaling of responses after stroke. Our findings suggest that during recovery, most cortical areas undergo homeostatic upscaling, resulting in a relative distribution of responses that is similar to the pre-stroke (sham) network, albeit still depressed. However, recovery within the peri-infarct zone is heterogeneous and these cortical points do not follow the recovery scaling factor expected for the entire network.

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Spatial and temporal details of spontaneous cortical activity provide insights into functions in the adult and developing brain (2014)

While the body rests, the mind remains active. In fact, the brain exhibits a rich pattern of structured activity despite having few immediate sensory or motor tasks. During infancy, this brain activity appears tailored to assist in the maturation of neural systems. In the adult, it influences memory consolidation and maintenance of synaptic connections. In this thesis, I address these differences by using voltage-sensitive dye imaging to record spontaneous cortical activity in rodents during development and adulthood.In the adult, I examine slow-wave activity, a key form of spontaneous activity. I show that functionally related regions of the cortex activate synchronously, forming a core set of structures that underlie spontaneous activation. I also show that sensory connections shape the patterns of this activity. These effects hold true in the quietly awake mouse, to a lesser extent. These findings are consistent with an active role for slow-wave activity in the maintenance of cortical connections. In the infant, I examine a dominant form of brain activity, the spindle burst. This pattern of activity follows spontaneous sensory inputs generated by the developing sensory systems, including small twitches in the limbs and tail. It is generally thought to remain localized with the appropriate cortical sensory system, but using wide-field imaging, I show it spreads medially across the cortex. This suggests a potential role in the maturation of connections between sensory and motor regions. I explored this possibility more closely by recording activity in early life from the whisker system of the rat. In the adult, connections exist between the sensory and motor regions of the whisker system. To gain insight into whether the spontaneous activation of these systems contributed to their development, I compared the activity evoked by stimulation to the spontaneous activation of these systems. I found synchronized spontaneous activation of motor and sensory areas that were not yet functionally connected. This suggests that other structures synchronize these areas to promote the maturation of connections between them. Overall, this work reveals details about spontaneous activity that provide clues to why the brain devotes time and energy to activity disconnected from the outside world.

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Light-based mapping of sensorimotor cortex in mice (2013)

No abstract available.

The role of filopodia in the formation of spine synapses (2011)

In the mammalian brain, excitatory (glutamatergic) synapses are mainly located on dendritic spines; bulbous protrusions enriched with F-actin. Dendritic filopodia are thin protrusions thought to be involved in the development of spines. However, limited evidence illustrating the emergence of spines from filopodia has been found. In addition, the molecular machinery required for filopodia induction and transformation to spines is not well understood. Paralemmin-1 has been shown to induce cell expansion and process formation and is concentrated at the plasma membrane, in part through a lipid modification known as palmitoylation. Palmitoylation of paralemmin-1 may also serve as a signal for its delivery to subcellular lipid microdomains to induce changes in cell morphology and membrane dynamics making it a candidate synapse-inducing molecule. Using live imaging as well as loss and gain-of-function approaches, our analysis identifies paralemmin-1 as a regulator of filopodia induction, synapse formation, and spine maturation. We show neuronal activity-driven translocation of paralemmin-1 to membranes induces rapid protrusion expansion, emphasizing the importance of paralemmin-1 in paradigms that control structural changes associated with synaptic plasticity and learning. Finally, we show that knockdown of paralemmin-1 results in loss of filopodia and compromises spine maturation induced by Shank1b, a protein that facilitates rapid transformation of newly formed filopodia to spines. To investigate the role of filopodia in synapse formation, we contrasted the roles of molecules that affect filopodia elaboration and motility, versus those that impact synapse induction and maturation. Expression of the palmitoylated protein motifs found in growth associated protein 43kDa, enhanced filopodia number and motility, but reduced the probability of forming a stable axon-dendrite contact. Conversely, expression of neuroligin-1 (NLG-1), a synapse inducing cell adhesion molecule, resulted in a decrease in filopodia motility, but an increase in the number of stable axonal contacts. Moreover, siRNA knockdown of NLG-1, reduced the number of presynaptic contacts formed. Postsynaptic scaffolding proteins such as Shank1b, a protein that induces the maturation of spine synapses, reduced filopodia number, but increased the stabilization of the initial contact with axons. These results suggest that increased filopodia stability and not density may be the rate-limiting step for synapse formation.

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Unconventional Forms of Synaptic Plasticity of the Hippocampus and the Striatum (2008)

No abstract available.

Master's Student Supervision (2010 - 2018)
Mesoscale Brain Explorer, a flexible Python-based image analysis and visualization tool (2017)

Imaging of mesoscale brain activity is used to map interactions between brain regions. This work has benefited from the pioneering studies of Grinvald et al., who employed optical methods to image brain function by exploiting the properties of intrinsic optical signals and small molecule voltage-sensitive dyes. Mesoscale interareal brain imaging techniques have been advanced by cell targeted and selective recombinant indicators of neuronal activity. Spontaneous resting state activity is often collected during mesoscale imaging to provide the basis for mapping of connectivity relationships using correlation. However, the information content of mesoscale datasets is vast and is only superficially presented in manuscripts given the need to constrain measurements to a fixed set of frequencies, regions of interest, and other parameters. We describe a new open source tool written in python, termed mesoscale brain explorer (MBE), which provides an interface to process and explore these large datasets. The platform supports automated image processing pipelines with the ability to assess multiple trials and combine data from different animals. The tool provides functions for temporal filtering, averaging, and visualization of functional connectivity relations using time-dependent correlation. Here, we describe the tool and show applications, where previously published datasets were reanalyzed using MBE.

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Spatially resolving acute functional changes in descending cortical motor output after targeted stroke (2015)

We evaluated the effects of mini-strokes targeted to individual pial arterioles on motor and cortical function within the first hours after ischemia. This was done in Thy-1 line 18 channelrhodopsin-2 (ChR2) transgenic mice. Using optogenetics, we directly assessed both the excitability and motor output of cortical neurons in a rapid, repeated, and relatively non-invasive manner independent of behavioral state or training. Occlusion of individual arterioles within the motor cortex led to a ministroke that was verified using laser speckle contrast imaging. Surprisingly, ministrokes targeted to a relatively small region of the forelimb motor map, with an ischemic core of 0.07 ± 0.03 mm², impaired motor responses evoked from points across widespread areas of motor cortex even 1.5 mm away. Contrasting averaged ChR2-evoked electroencephalographic, spinal (ChR2 evoked potential), and electromyographic responses revealed a mismatch between measures of cortical excitability and motor output within 60 min after stroke. This mismatch suggests that apparently excitable cortical neurons (even >1 mm into peri-infarct areas, away from the infarct core) were impaired in their capacity to generate spinal potentials leading to even more severe deficits in motor output at muscles. We suggest that ischemia, targeted to a subset of motor cortex, leads to relatively small reductions in excitability within motor cortex, and cumulative depression of both descending spinal circuits and motor output in response to the activation of widespread cortical territories even outside of the area directly affected by the ischemia.

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Moderate or deep local hypothermia does not prevent the onset of ischemia-induced dendritic damage (2011)

Apical dendrites of layer 5 pyramidal neurons can rapidly undergo a structural perturbation within minutes of ischemia onset. This “blebbing” is a morphological phenomenon in which dendrites display regions of spherical and/or ellipsoid swellings, resembling a “beads-on-a-string” appearance. We investigated the acute (up to 2 hours after reperfusion) effects of localised cortical hypothermia, a well-recognised neuroprotective strategy, on ischemia-induced dendritic structural damage. Using in vivo two-photon imaging combined with a global ischemia model of occluding the common carotid arteries in C57Bl/6 mice, we monitored in real time these dynamic structural alterations during ischemia and reperfusion. We show that moderate (31°C) and deep hypothermia (22°C) delays but does not block the onset of dendritic blebbing during global ischemia. Deep hypothermic treatment also tended to promote more consistent recovery of dendritic structure during reperfusion. These results suggest that those employing therapeutic hypothermia will need to consider that it does not spare neurons from structural changes that are the result of ischemia, but may interact with mechanisms that control the onset of damage and recovery during reperfusion.

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Novel methodology to map the motor cortex (2011)

It is very well established that the motor cortex has a distinct cortical location that can be mapped in a variety of species from mice to humans. Traditionally, mapping the motor cortex requires electrodes to stimulate the brain and define motor output pathways. Although effective, electrode-based methods are labor-intensive, potentially damaging to the cortex, can have off-target effects, and are not well suited to long-term application in the same brain due to its invasive nature. As an alternative method to traditional motor mapping, transgenic mice expressing the light-sensitive ion channel channelrhodopsin-2 in predominantly layer-5 output cortical neurons were photostimulated. Implanted electromyogram electrodes or a noninvasive motion sensor were used as a readout of motor cortex output. In addition, electroencephalogram electrodes were used to directly monitor the activity of the motor cortex during periods of optical stimulation. Optical stimulation with a 473 nm laser was delivered to hundreds of cortical locations, in vivo, using a stage scanning laser system. Electrophysiological signals from the muscles and the cortex were used to create highly reproducible automated maps of the mouse forelimb and hindlimb motor cortex much faster than with previous methods. This method was well suited to mapping the same brain over a period of weeks using an implanted cranial window. It is anticipated that this novel methods will facilitate the study of changes in the location and properties of motor maps after skilled training or damage to the nervous system.

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Optical probing of hemodynamic responses in vivo with channelrhodopsin-2 (2011)

Maintenance of neuronal function depends on the timely delivery of oxygen and glucose through changes in blood flow that are linked to the level of ongoing neuronal and glial activity, yet the mechanisms underlying this stimulus-dependent control of blood flow remain unclear. Here, using transgenic mice expressing channelrhodopsin-2 in a subset of layer 5b pyramidal neurons, we report that changes in intrinsic optical signals and blood flow can be evoked by activation of channelrhodopsin-2 neurons without direct involvement of other cell types. We have used a combination of imaging and pharmacology to examine the importance of glutamatergic synaptic signaling in neurovascular coupling. In contrast to sensory-evoked responses, we observed that glutamate-dependent neuronal signalling is not essential for the production of channelrhodopsin-evoked hemodynamic responses. Our results rather suggest that ChR2-activated neurons are coupled to the surrounding vasculature through a glutamate-dependent astrocytic pathway mediated by the Group I metabotropic glutamate receptor mGluR5.

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Uncrossed cortical and thalamic circuits to mediate sensory processing weeks after stroke (2011)

One of the enduring principles in neurobiology is that most sensory activity is processed in the hemisphere opposite (contralateral) to the sensation. After a relatively small stroke, function can re-map to related peri-infarct cortical areas. However, after a large stroke, areas with spared and related function may only be present within the “unaffected” hemisphere leading to ipsilateral (un-crossed) sensory processing. We investigated the mechanism of the ipsilateral cortical representation of tactile information before, and 1 and 8-10 weeks after stroke using voltage sensitive dye imaging of forelimb-evoked sensory responses in mice. In control animals before stroke, we observed bilateral cortical activation in response to unilateral stimulation. Ipsilateral forelimb responses before stroke were dependent on the contralateral cortex and presumably mediated through transcallosal fibers that homotopically connect the somatosensory cortices. Large strokes that affected both sensory and motor cortices led to a shift in processing of forelimb sensory stimuli to predominantly the unaffected hemisphere. Pharmacological silencing of the peri-infarct cortex or thalamus within the stroke-affected hemisphere failed to affect prominent non-crossed responses in animals 8-10 weeks after stroke, yet these treatments blocked ipsilateral responses in control animals. Ipsilateral forelimb responses after 8-10 weeks of recovery from a large stroke were attributed to non-crossed ascending circuits that were dependent on the ipsilateral thalamus and apparently substitute for damaged transcallosal cortico-cortical connections. These results indicate that ipsilateral sensory responses present in animals after 8-10 weeks of recovery from stroke are through a fundamentally different mechanism that involves circuits well upstream of the peri-infarct tissue with little dependence on the thalamus or cortex within the stroke-affected hemisphere.

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