PhDs in Press: A plethora of papers!

PhDs in Press: A plethora of papers!

After a bit of a hiatus, PhDs in Press is back! Quite a few (read: 12) of our comrades in the Stanford Neurosciences Program have published in the last 6 months, both as first authors, and nth authors.

Head below the fold for titles and links to papers authored by: Cora AmesMatt Figley, the tag-team of Corbett Bennet and Sergio ArroyoDavid KastnerRyan Squire, Georgia Panagiotakos, George Sebastià Vidal Pérez-Treviño, Matt SacchetWilliam Joo, Yvette Fisher, Gregor Bieri and Kira Mosher.

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PhDs in Press: TRAPing Neurons and Tracking Temporal Lobe Epilepsy

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Part 7 in an occasional feature, highlighting recently published articles featuring an author (or authors) affiliated with the Stanford Neuroscience Ph.D program. This round, we've got two lovely first author papers, by Casey Guenthner and Izumi Toyoda.

Let's begin with my year-mate, Casey Guenthner (Luo Lab), who published his development of a technique, TRAP (Targeted Recombination in Active Populations), that allows genetic targeting of populations of neurons that are defined by whether they were activated in vivo by a set stimulus. For details, check out Casey's abstract, below.

Targeting genetically encoded tools for neural circuit dissection to relevant cellular populations is a major challenge in neurobiology. We developed an approach, targeted recombination in active populations (TRAP), to obtain genetic access to neurons that were activated by defined stimuli. This method utilizes mice in which the tamoxifen-dependent recombinase CreER(T2) is expressed in an activity-dependent manner from the loci of the immediate early genes Arc and Fos. Active cells that express CreER(T2) can only undergo recombination when tamoxifen is present, allowing genetic access to neurons that are active during a time window of less than 12 hr. We show that TRAP can provide selective access to neurons activated by specific somatosensory, visual, and auditory stimuli and by experience in a novel environment. When combined with tools for labeling, tracing, recording, and manipulating neurons, TRAP offers a powerful approach for understanding how the brain processes information and generates behavior.

Guenthner, Miyamichi, Yang, Heller and Luo. Permanent Genetic Access to Transiently Active Neurons via TRAP: Targeted Recombination in Active Populations. Neuron. 2013: 78(5):773-84. doi:10.1016/j.neuron.2013.03.025

I will leave you all with the comment that Casey's cartoon of the mouse whisker pad is glorious in its anatomical accuracy. And it's pretty cute, too. Figure 3b. Check it out below, along with data demonstrating targeting of active neurons in the whisker barrel system.

Figure 3. FosTRAP in the Barrel Cortex of Whisker-Plucked Mice.(A) Experimental scheme: FosTRAP mice had either all whiskers except C2 plucked unilaterally or had only the C2 whisker plucked. After a 2 day recovery period, mice were injected with 150 mg/kg TM, and recombination was examined 7 days later.(B) Tangential views of flattened layer 4 of the primary somatosensory barrel cortex (top) or coronal views through the C2 barrel (bottom). White dots indicate the corners of the C2 barrel on the basis of dense DAPI staining of the barrel walls. Compared with controls (left), removal of only the C2 whisker results in elimination of TRAP signal from the C2 barrel (middle), whereas removal of all whiskers except C2 results in absence of most TRAPed cells in all barrels except C2 (right). The left and middle images are from the same mouse. Images are representative of at least 3–4 mice for each condition. The scale bar represents 250 μm. Guenthner et al 2013.

Just last week, Izumi Toyoda (Buckmaster lab) published her work recording spontaneous seizures in rats with temporal lobe epilepsy. Using 32 recording electrodes per rat, Izumi records from a massive number of brain structures, tracking the spread of seizures within the rodent brain. Her paper compares the propagation of the spontaneous seizures in the rats to known seizure activity in human patients with temporal lobe epilepsy. The results validate the pilocarpine model of temporal lobe epilepsy, showing seizures begin in similar brain locations in human patients and rodent subjects.

Temporal lobe epilepsy is the most common form of epilepsy in adults. The pilocarpine-treated rat model is used frequently to investigate temporal lobe epilepsy. The validity of the pilocarpine model has been challenged based largely on concerns that seizures might initiate in different brain regions in rats than in patients. The present study used 32 recording electrodes per rat to evaluate spontaneous seizures in various brain regions including the septum, dorsomedial thalamus, amygdala, olfactory cortex, dorsal and ventral hippocampus, substantia nigra, entorhinal cortex, and ventral subiculum. Compared with published results from patients, seizures in rats tended to be shorter, spread faster and more extensively, generate behavioral manifestations more quickly, and produce generalized convulsions more frequently. Similarities to patients included electrographic waveform patterns at seizure onset, variability in sites of earliest seizure activity within individuals, and variability in patterns of seizure spread. Like patients, the earliest seizure activity in rats was recorded most frequently within the hippocampal formation. The ventral hippocampus and ventral subiculum displayed the earliest seizure activity. Amygdala, olfactory cortex, and septum occasionally displayed early seizure latencies, but not above chance levels. Substantia nigra and dorsomedial thalamus demonstrated consistently late seizure onsets, suggesting their unlikely involvement in seizure initiation. The results of the present study reveal similarities in onset sites of spontaneous seizures in patients with temporal lobe epilepsy and pilocarpine-treated rats that support the model's validity.

Toyoda, Bower, Leyva, Buckmaster. Early Activation of Ventral Hippocampus and Subiculum during Spontaneous Seizures in a Rat Model of Temporal Lobe Epilepsy. J Neurosci, 3 July 2013, 33(27):11100-11115. doi:10.1523/JNEUROSCI.0472-13.2013

And because I showed a figure from Casey's paper, here is one from Izumi's, highlighting a subset of 16 recording electrodes on which a spontaneous seizure is recorded in an epileptic, pilocarpine-treated rat. Let there be no doubt in your mind - the skill required to implant 32 recording electrodes into a rat is large. I suggest being very impressed with Izumi's surgical skills.

Figure 2. Spontaneous seizures in epileptic pilocarpine-treated rats. A, Seizures spread quickly and extensively. Recordings from a subset of 16/32 electrodes implanted in various brain regions. The approximate seizure offset (arrow) and onset window (bar), bracketed by the latest normal activity and earliest clear seizure activity, are indicated. L indicates left; M, medial; EC, entorhinal cortex; sub, subiculum; R, right; amyg, amygdala; SNpr/c, substantia nigra pars reticulata/compacta; sept, septum; D, dorsal; hipp, hippocampus; olf ctx, olfactory cortex; vdb, ventral diagonal band; dm thal, dorsomedial thalamus; endo n, endopiriform nucleus. B, Precise seizure onsets (arrows) in three regions. C, Seizure durations. Bars represent averages; symbols indicate durations of individual seizures. D, Behavioral seizure onset latencies. Electrographic seizure onset is at 0. Positive (negative) values indicate that behavioral onset followed (preceded) electrographic onset. Bars represent averages; symbols indicate individual seizures. From Toyoda et al, 2013.

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Astra Bryant

Astra Bryant is a graduate of the Stanford Neuroscience PhD program in the labs of Drs. Eric Knudsen and John Huguenard. She used in vitro slice electrophysiology to study the cellular and synaptic mechanisms linking cholinergic signaling and gamma oscillations – two processes critical for the control of gaze and attention, which are disrupted in many psychiatric disorders. She is a senior editor and the webmaster of the NeuWrite West Neuroblog

Ph.D's in Press: anxiety, presynaptic scaffolding, epigenetics and more!

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Part 5 in an occasional feature, highlighting recently published articles featuring an author (or authors) who is a current member of the Stanford Neuroscience Ph.D program. (Part 1, Part 2Part 3, Part 4)* First off, 4th year student Sung-Yon Kim (Deisseroth lab) published his study of distinct subregions of the bed nucelus of the stria terminalis, demonstrating, using optogenetics that BNST neurons that project to distinct brain regions each implement independent features of anxiety. Additional Neuro PhD authors include: Christina Kim, Caitlin Mallory and Joanna Mattis.

Behavioural states in mammals, such as the anxious state, are characterized by several features that are coordinately regulated by diverse nervous system outputs, ranging from behavioural choice patterns to changes in physiology (in anxiety, exemplified respectively by risk-avoidance and respiratory rate alterations). Here we investigate if and how defined neural projections arising from a single coordinating brain region in mice could mediate diverse features of anxiety. Integrating behavioural assays, in vivo and in vitro electrophysiology, respiratory physiology and optogenetics, we identify a surprising new role for the bed nucleus of the stria terminalis (BNST) in the coordinated modulation of diverse anxiety features. First, two BNST subregions were unexpectedly found to exert opposite effects on the anxious state: oval BNST activity promoted several independent anxious state features, whereas anterodorsal BNST-associated activity exerted anxiolytic influence for the same features. Notably, we found that three distinct anterodorsal BNST efferent projections-to the lateral hypothalamus, parabrachial nucleus and ventral tegmental area-each implemented an independent feature of anxiolysis: reduced risk-avoidance, reduced respiratory rate, and increased positive valence, respectively. Furthermore, selective inhibition of corresponding circuit elements in freely moving mice showed opposing behavioural effects compared with excitation, and in vivo recordings during free behaviour showed native spiking patterns in anterodorsal BNST neurons that differentiated safe and anxiogenic environments. These results demonstrate that distinct BNST subregions exert opposite effects in modulating anxiety, establish separable anxiolytic roles for different anterodorsal BNST projections, and illustrate circuit mechanisms underlying selection of features for the assembly of the anxious state.

Kim et al (2013). Diverging neural pathways assemble a behavioural state from separable features in anxiety. Nature, 496(7444): 219-23.

Poh Hui Chia (Shen lab), who recently defended her thesis research, published her work on intramolecular regulation of presynaptic scaffold protein SYD-2/liprin-a.

SYD-2/liprin-α is a multi-domain protein that associates with and recruits multiple active zone molecules to form presynaptic specializations. Given SYD-2's critical role in synapse formation, its synaptogenic ability is likely tightly regulated. However, mechanisms that regulate SYD-2 function are poorly understood. In this study, we provide evidence that SYD-2's function may be regulated by interactions between its coiled-coil (CC) domains and sterile α-motif (SAM) domains. We show that the N-terminal CC domains are necessary and sufficient to assemble functional synapses while C-terminal SAM domains are not, suggesting that the CC domains are responsible for the synaptogenic activity of SYD-2. Surprisingly, syd-2 alleles with single amino acid mutations in the SAM domain show strong loss of function phenotypes, suggesting that SAM domains also play an important role in SYD-2's function. A previously characterized syd-2 gain-of-function mutation within the CC domains is epistatic to the loss-of-function mutations in the SAM domain. In addition, yeast two-hybrid analysis showed interactions between the CC and SAM domains. Thus, the data is consistent with a model where the SAM domains regulate the CC domain-dependent synaptogenic activity of SYD-2. Taken together, our study provides new mechanistic insights into how SYD-2's activity may be modulated to regulate synapse formation during development.

Chia et al (2013). Intramolecular regulation of presynaptic scaffold portein SYD-2/liprin-a. Molecular and Cellular Neuroscience, 56: 76-84.

In the category of reviews and commentaries, Jana Lim (Brunet lab) co-authored a review on transgenerational epigenetic inheritance.

It is textbook knowledge that inheritance of traits is governed by genetics, and that the epigenetic modifications an organism acquires are largely reset between generations. Recently, however, transgenerational epigenetic inheritance has emerged as a rapidly growing field, providing evidence suggesting that some epigenetic changes result in persistent phenotypes across generations. Here, we survey some of the most recent examples of transgenerational epigenetic inheritance in animals, ranging from Caenorhabditis elegans to humans, and describe approaches and limitations to studying this phenomenon. We also review the current body of evidence implicating chromatin modifications and RNA molecules in mechanisms underlying this unconventional mode of inheritance and discuss its evolutionary implications.

Lim and Brunet (2013). Bridging the transgenerational gap with epigenetic memory. Trends in Genetics, 29(3): 176-186.

Several Neuro PhD students were also second through n-th authors on papers. From the prolific Deisseroth lab, students Aslihan Selimeyoglu and Sung-Yon Kim are coauthors on a paper describing "a prefrontal cortex-brainstem neural projection that controls response to behavioral challenge".

The prefrontal cortex (PFC) is thought to participate in high-level control of the generation of behaviours (including the decision to execute actions1); indeed, imaging and lesion studies in human beings have revealed that PFC dysfunction can lead to either impulsive states with increased tendency to initiate action2, or to amotivational states characterized by symptoms such as reduced activity, hopelessness and depressed mood3. Considering the opposite valence of these two phenotypes as well as the broad complexity of other tasks attributed to PFC, we sought to elucidate the PFC circuitry that favours effortful behavioural responses to challenging situations. Here we develop and use a quantitative method for the continuous assessment and control of active response to a behavioural challenge, synchronized with single-unit electrophysiology and optogenetics in freely moving rats. In recording from the medial PFC (mPFC), we observed that many neurons were not simply movement-related in their spike-firing patterns but instead were selectively modulated from moment to moment, according to the animal’s decision to act in a challenging situation. Surprisingly, we next found that direct activation of principal neurons in the mPFC had no detectable causal effect on this behaviour. We tested whether this behaviour could be causally mediated by only a subclass of mPFC cells defined by specific downstream wiring. Indeed, by leveraging optogenetic projection-targeting to control cells with specific efferent wiring patterns, we found that selective activation of those mPFC cells projecting to the brainstem dorsal raphe nucleus (DRN), a serotonergic nucleus implicated in major depressive disorder4, induced a profound, rapid and reversible effect on selection of the active behavioural state. These results may be of importance in understanding the neural circuitry underlying normal and pathological patterns of action selection and motivation in behaviour.

Warden et al (2013). A prefrontal cortex-brainstem neuronal projection that controls response to behavioural challenge. Nature, 492 (428-432).

Also from the Deisseroth lab, Sung-Yon Kim, Kelly Zalocusky, Joanna Mattis and Logan Grosenick are all authors of the recently published article describing CLARITY, a novel method developed by lead author Kwanghun Chung for producing optically transparent tissue for the purpose of  tissue-intact imaging.

Obtaining high-resolution information from a complex system, while maintaining the global perspective needed to understand system function, represents a key challenge in biology. Here we address this challenge with a method (termed CLARITY) for the transformation of intact tissue into a nanoporous hydrogel-hybridized form (crosslinked to a three-dimensional network of hydrophilic polymers) that is fully assembled but optically transparent and macromolecule-permeable. Using mouse brains, we show intact-tissue imaging of long-range projections, local circuit wiring, cellular relationships, subcellular structures, protein complexes, nucleic acids and neurotransmitters. CLARITY also enables intact-tissue in situ hybridization, immunohistochemistry with multiple rounds of staining and de-staining in non-sectioned tissue, and antibody labelling throughout the intact adult mouse brain. Finally, we show that CLARITY enables fine structural analysis of clinical samples, including non-sectioned human tissue from a neuropsychiatric-disease setting, establishing a path for the transmutation of human tissue into a stable, intact and accessible form suitable for probing structural and molecular underpinnings of physiological function and disease.

Chung (2013). Structural and molecular interrogation of intact biological systems. Nature. doi:10.1038/nature12107

Georgia Panagiotakos is the second author on a paper published in PLOS One, showing the mechanisms underlying the production of the calcium channel associated transcriptional regulator (CCAT), which is encoded by the C-terminus of the voltage-gated calcium channel Cav1.2.

The C-terminus of the voltage-gated calcium channel Cav1.2 encodes a transcription factor, the calcium channel associated transcriptional regulator (CCAT), that regulates neurite extension and inhibits Cav1.2 expression. The mechanisms by which CCAT is generated in neurons and myocytes are poorly understood. Here we show that CCAT is produced by activation of a cryptic promoter in exon 46 of CACNA1C, the gene that encodes CaV1.2. Expression of CCAT is independent of Cav1.2 expression in neuroblastoma cells, in mice, and in human neurons derived from induced pluripotent stem cells (iPSCs), providing strong evidence that CCAT is not generated by cleavage of CaV1.2. Analysis of the transcriptional start sites in CACNA1C and immune-blotting for channel proteins indicate that multiple proteins are generated from the 3′ end of the CACNA1C gene. This study provides new insights into the regulation of CACNA1C, and provides an example of how exonic promoters contribute to the complexity of mammalian genomes.

Gomez-Ospina N, Panagiotakos G, Portmann T, Pasca SP, Rabah D, et al. (2013) A Promoter in the Coding Region of the Calcium Channel Gene CACNA1C Generates the Transcription Factor CCAT. PLoS ONE 8(4): e60526. doi:10.1371/journal.pone.0060526

Matt Figley (Gitler lab) is the third author on a paper in Nature Genetics, discussing the suppression of TDP-43 toxicity in ALS disease models by the inhibition of RNA lariat debranching enzyme.

Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease primarily affecting motor neurons. Mutations in the gene encoding TDP-43 cause some forms of the disease, and cytoplasmic TDP-43 aggregates accumulate in degenerating neurons of most individuals with ALS. Thus, strategies aimed at targeting the toxicity of cytoplasmic TDP-43 aggregates may be effective. Here, we report results from two genome-wide loss-of-function TDP-43 toxicity suppressor screens in yeast. The strongest suppressor of TDP-43 toxicity was deletion of DBR1, which encodes an RNA lariat debranching enzyme. We show that, in the absence of Dbr1 enzymatic activity, intronic lariats accumulate in the cytoplasm and likely act as decoys to sequester TDP-43, preventing it from interfering with essential cellular RNAs and RNA-binding proteins. Knockdown of Dbr1 in a human neuronal cell line or in primary rat neurons is also sufficient to rescue TDP-43 toxicity. Our findings provide insight into TDP-43–mediated cytotoxicity and suggest that decreasing Dbr1 activity could be a potential therapeutic approach for ALS.

Armakola et al (2013). Inhibition of RNA lariat debranching enzyme suppresses TDP-43 toxicity in ALS disease models. Nature Genetics, 44: 1302-1309.

And lastly, Daniel Kimmel, together with first-author Michael Greicius, co-authored a review on neuroimaging insights into network-based neurodegeneration.

Purpose of review: Convergent evidence from a number of neuroscience disciplines supports the hypothesis that Alzheimer's disease and other neurodegenerative disorders progress along brain networks. This review considers the role of neuroimaging in strengthening the case for network-based neurodegeneration and elucidating potential mechanisms.

Recent findings: Advances in functional and structural MRI have recently enabled the delineation of multiple large-scale distributed brain networks. The application of these network-imaging modalities to neurodegenerative disease has shown that specific disorders appear to progress along specific networks. Recent work applying theoretical measures of network efficiency to in-vivo network imaging has allowed for the development and evaluation of models of disease spread along networks. Novel MRI acquisition and analysis methods are paving the way for in-vivo assessment of the layer-specific microcircuits first targeted by neurodegenerative diseases. These methodological advances coupled with large, longitudinal studies of subjects progressing from healthy aging into dementia will enable a detailed understanding of the seeding and spread of these disorders.

Summary: Neuroimaging has provided ample evidence that neurodegenerative disorders progress along brain networks, and is now beginning to elucidate how they do so.

Greicius and Kimmel (2012). Neuroimaging insights into network-based neurodegeneration. Current Opinion in Neurology. 25(6): 727-734.

*Regarding the mechanics of this feature: This is purely through the magic of an ongoing My NCBI search for the names of Neuro PhD students. I wouldn’t be surprised if there were some false negatives in the data set. Neuro students – let me know if I’ve missed your paper, and I’ll gladly add it.

Comment

Astra Bryant

Astra Bryant is a graduate of the Stanford Neuroscience PhD program in the labs of Drs. Eric Knudsen and John Huguenard. She used in vitro slice electrophysiology to study the cellular and synaptic mechanisms linking cholinergic signaling and gamma oscillations – two processes critical for the control of gaze and attention, which are disrupted in many psychiatric disorders. She is a senior editor and the webmaster of the NeuWrite West Neuroblog

Ph.D's in Press (January-February 2013)

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Part 4 in an occasional feature, highlighting recently published articles featuring an author (or authors) who is a current member of the Stanford Neuroscience Ph.D program. (Part 1, Part 2, Part 3)* Starting 2013 on a strong note, we have two papers with first authors from the Stanford Neuro PhD community. First, Logan Grosenick (Suppes and Deisseroth labs) presents new variants of the GraphNet fMRI analysis method.  Second, Jordan Nechvatal (Lyons lab) reviews brain imaging studies on the effect of stress exposure therapy for anxiety disorders (including phobias and PTSD).

Logan Grosenick

Grosenick, Klingenberg, Katovich, Knutson and Taylor. Interpretable whole-brain prediction analysis with GraphNet. Neuroimage, 2013 Jan 5. pii: S1053-8119(12)01248-7. doi: 10.1016/j.neuroimage.2012.12.062. [Epub ahead of print]. (Link)

Abstract: Multivariate machine learning methods are increasingly used to analyze neuroimaging data, often replacing more traditional "mass univariate" techniques that fit data one voxel at a time. In the functional magnetic resonance imaging (fMRI) literature, this has led to broad application of "off-the-shelf" classification and regression methods. These generic approaches allow investigators to use ready-made algorithms to accurately decode perceptual, cognitive, or behavioral states from distributed patterns of neural activity. However, when applied to correlated whole-brain fMRI data these methods suffer from coefficient instability, are sensitive to outliers, and yield dense solutions that are hard to interpret without arbitrary thresholding. Here, we develop variants of the Graph-constrained Elastic Net (GraphNet), a fast, whole-brain regression and classification method developed for spatially and temporally correlated data that automatically yields interpretable coefficient maps (Grosenick et al., 2009b). GraphNet methods yield sparse but structured solutions by combining structured graph constraints (based on knowledge about coefficient smoothness or connectivity) with a global sparsity-inducing prior that automatically selects important variables. Because GraphNet methods can efficiently fit regression or classification models to whole-brain, multiple time-point data sets and enhance classification accuracy relative to volume-of-interest (VOI) approaches, they eliminate the need for inherently biased VOI analyses and allow whole-brain fitting without the multiple comparison problems that plague mass univariate and roaming VOI ("searchlight") methods. As fMRI data are unlikely to be normally distributed, we (1) extend GraphNet to include robust loss functions that confer insensitivity to outliers, (2) equip them with "adaptive" penalties that asymptotically guarantee correct variable selection, and (3) develop a novel sparse structured Support Vector GraphNet classifier (SVGN). When applied to previously published data (Knutson et al., 2007), these efficient whole-brain methods significantly improved classification accuracy over previously reported VOI-based analyses on the same data (Grosenick et al., 2008; Knutson et al., 2007) while discovering task-related regions not documented in the original VOI approach. Critically, GraphNet estimates fit to the Knutson et al. (2007) data generalize well to out-of-sample data collected more than three years later on the same task but with different subjects and stimuli (Karmarkar et al., submitted for publication). By enabling robust and efficient selection of important voxels from whole-brain data taken over multiple time points (>100,000 "features"), these methods enable data-driven selection of brain areas that accurately predict single-trial behavior within and across individuals.

Jordan Nechvatal

Nechvatal and Lyons. Coping changes the brain. Front. Behav. Neurosci., 22 February 2013 | doi: 10.3389/fnbeh.2013.00013. (Link)

Abstract: One of the earliest and most consistent findings in behavioral neuroscience research is that learning changes the brain. Here we consider how learning as an aspect of coping in the context of stress exposure induces neuroadaptations that enhance emotion regulation and resilience. A systematic review of the literature identified 15 brain imaging studies in which humans with specific phobias or post-traumatic stress disorder (PTSD) were randomized to stress exposure therapies that diminished subsequent indications of anxiety. Most of these studies focused on functional changes in the amygdala and anterior corticolimbic brain circuits that control cognitive, motivational, and emotional aspects of physiology and behavior. Corresponding structural brain changes and the timing, frequency, and duration of stress exposure required to modify brain functions remain to be elucidated in future research. These studies will advance our understanding of coping as a learning process and provide mechanistic insights for the development of new interventions that promote stress coping skills.

*Regarding the mechanics of this feature: This is purely through the magic of an ongoing My NCBI search for the names of Neuro PhD students. I wouldn't be surprised if there were some false negatives in the data set. Neuro students - let me know if I've missed your paper, and I'll gladly add it.

Comment

Astra Bryant

Astra Bryant is a graduate of the Stanford Neuroscience PhD program in the labs of Drs. Eric Knudsen and John Huguenard. She used in vitro slice electrophysiology to study the cellular and synaptic mechanisms linking cholinergic signaling and gamma oscillations – two processes critical for the control of gaze and attention, which are disrupted in many psychiatric disorders. She is a senior editor and the webmaster of the NeuWrite West Neuroblog

Ph.Ds in Press

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Part 3 in a semi-annual feature, highlighting recently published articles featuring an author (or authors) who is a current member of the Stanford Neuroscience Ph.D program. (Part 1, Part 2) [Note regarding the mechanics of this feature: This is purely through the magic of an ongoing My NCBI search for the names of Neuro PhD students. I wouldn't be surprised if there were some false negatives in the data set. Neuro students - let me know if I've missed your paper, and I'll gladly add it.]

Without further ado, and with many congratulations to the authors, the papers:

First Author papers:

Magali Arons: Autism-associated mutations in ProSAP2/Shank3 impair synaptic transmission and neurexin-neuroligin-mediated transsynaptic signaling (Arons et al 2012). **Thesis Research**

Corbett Bennett and Sergio Arroyo (co-first authors): Mechanisms generating dual-component nicotinic EPSCs in cortical interneurons (Bennett et al 2012).

Mridu Kapur: Calcium tips the balance: a microtubule plus end to lattice binding switch operates in the carboxyl terminus of BPAG1n4 (Kapur et al 2012)

Kira Mosher: Neural progenitor cells regulate microglia functions and activity (Mosher et al 2012).

Suraj Pardhan: Commentary: Progressive inflammation as a contributing factor to early development of Parkinson's disease (Pradhan and Andreasson 2012).

Rohit Prakash: Two-photon optogenetic toolbox for fast inhibition, excitation and bistable modulation. (Prakash et al 2012)

Matthew Sacchet:

Second through n-th Author papers:

Dominic Berns: Mechanisms generating dual-component nicotinic EPSCs in cortical interneurons (Bennett et al 2012).

Michael Betley: Input-specific control of reward and aversion in the ventral tegmental area (Lammel et al 2012).

Gregor Bieri: Neural progenitor cells regulate microglia functions and activity (Mosher et al 2012).

Emily Ferenczi: Dopamine neurons modulation neural encoding and expression of depression-related behaviour (Tye et al 2012).

Matt Figley: Inhibition of RNA lariat debranching enzyme suppresses TDP-43 toxicity in ALS disease models (Armakola et al 2012)

William Joo: The transcriptional regulator lola is required for stem cell maintenance and germ cell differentiation in the Drosophila testis (Davies et al 2012).

Sung-Yon Kim:

  • Dopamine neurons modulation neural encoding and expression of depression-related behaviour (Tye et al 2012).
  • A prefrontal cortex-brainstem neuronal projection that controls response to behavioural challenge (Warden et al 2012).

Ivan Millan:

  • Calcium tips the balance: a microtubule plus end to lattice binding switch operates in the carboxyl terminus of BPAG1n4 (Kapur et al 2012)
  • Parkinson's disease-associated kinase PINK1 regulates Miro protein level and axonal transport of mitochondria (Liu et al 2012)

Matthew Sacchet: Toward an affective neuroscience account of financial risk taking (Wu et al 2012).

 

First Author Papers

Arons, Thynne, Grabrucker, Li, Schoen, Cheyne, Boeckers, Montgomery, Garner (2012). Autism-associated mutations in ProSAP2/Shank3 impair synaptic transmission and neurexin-neuroligin-mediated transsynaptic signaling. J Neurosci 32(43): 14966-78. (Link)

Abstract: Mutations in several postsynaptic proteins have recently been implicated in the molecular pathogenesis of autism and autism spectrum disorders (ASDs), including Neuroligins, Neurexins, and members of the ProSAP/Shank family, thereby suggesting that these genetic forms of autism may share common synaptic mechanisms. Initial studies of ASD-associated mutations in ProSAP2/Shank3 support a role for this protein in glutamate receptor function and spine morphology, but these synaptic phenotypes are not universally penetrant, indicating that other core facets of ProSAP2/Shank3 function must underlie synaptic deficits in patients with ASDs. In the present study, we have examined whether the ability of ProSAP2/Shank3 to interact with the cytoplasmic tail of Neuroligins functions to coordinate pre/postsynaptic signaling through the Neurexin-Neuroligin signaling complex in hippocampal neurons of Rattus norvegicus. Indeed, we find that synaptic levels of ProSAP2/Shank3 regulate AMPA and NMDA receptor-mediated synaptic transmission and induce widespread changes in the levels of presynaptic and postsynaptic proteins via Neurexin-Neuroligin transsynaptic signaling. ASD-associated mutations in ProSAP2/Shank3 disrupt not only postsynaptic AMPA and NMDA receptor signaling but also interfere with the ability of ProSAP2/Shank3 to signal across the synapse to alter presynaptic structure and function. These data indicate that ASD-associated mutations in a subset of synaptic proteins may target core cellular pathways that coordinate the functional matching and maturation of excitatory synapses in the CNS.

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Bennett, Arroyo, Berns, Hestrin (2012). Mechanisms generating dual-component nicotinic EPSCs in cortical interneurons. J Neurosci 32(48): 17287-96. (Link).

Abstract: Activation of cortical nicotinic receptors by cholinergic axons from the basal forebrain (BF) significantly impacts cortical function, and the loss of nicotinic receptors is a hallmark of aging and neurodegenerative disease. We have previously shown that stimulation of BF axons generates a fast α7 and a slow non-α7 receptor-dependent response in cortical interneurons. However, the synaptic mechanisms that underlie this dual-component nicotinic response remain unclear. Here, we report that fast α7 receptor-mediated EPSCs in the mouse cortex are highly variable and insensitive to perturbations of acetylcholinesterase (AChE), while slow non-α7 receptor-mediated EPSCs are reliable and highly sensitive to AChE activity. Based on these data, we propose that the fast and slow nicotinic responses reflect differences in synaptic structure between cholinergic varicosities activating α7 and non-α7 classes of nicotinic receptors.

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Kapur, Wang, Maloney, Millan, Lundin, Tran and Yang (2012). Calcium tips the balance: a microtubule plus end to lattice binding switch operates in the carboxyl terminus of BPAG1n4. EMBO reports 13, 1021-1029. (Link)

Abstract: Microtubules (MTs) are integral to numerous cellular functions, such as cell adhesion, differentiation and intracellular transport. Their dynamics are largely controlled by diverse MT-interacting proteins, but the signalling mechanisms that regulate these interactions remain elusive. In this report, we identify a rapid, calcium-regulated switch between MT plus end interaction and lattice binding within the carboxyl terminus of BPAG1n4. This switch is EF-hand dependent, and mutations of the EF-hands abolish this dynamic behaviour. Our study thus uncovers a new, calcium-dependent regulatory mechanism for a spectraplakin, BPAG1n4, at the MT plus end.

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Mosher, Andres, Fukuhara, Bieri, Hasegawa-Moriyama, He, Guzman, Wyss-Coray (2012). Neural progenitor cells regulate microglia functions and activity. Nat Neurosci 15(11): 1485-7. (Link)

Abstract: We found mouse neural progenitor cells (NPCs) to have a secretory protein profile distinct from other brain cells and to modulate microglial activation, proliferation and phagocytosis. NPC-derived vascular endothelial growth factor was necessary and sufficient to exert at least some of these effects in mice. Thus, neural precursor cells may not only be shaped by microglia, but also regulate microglia functions and activity.

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Pradhan and Andreasson (2012). Commentary: Progressive Inflammation as a contributing factor to early development of Parkinson's disease. Exp Neurol. pii: S0014-4886(12)00456-6. (Link)

Abstract: Parkinson's disease (PD) is a progressive neurodegenerative disorder with three cardinal features of pathology: 1. Aggregation of α-synuclein into intraneuronal structures called Lewy bodies and Lewy neurites. 2. Dysregulated immune activation in the substantia nigra (SN). 3. Degeneration of dopaminergic neurons in the nigrostriatal circuit. The largely correlative nature of evidence in humans has precluded a decisive verdict on the relationship between α-synuclein pathology, inflammation, and neuronal damage. Furthermore, it is unclear whether inflammation plays a role in the early prodromal stages of PD before neuronal damage has occurred and Parkinsonian motor symptoms become apparent. To gain insight into the interaction between the inflammatory response and the development of neuronal pathology in PD, Watson et al. characterized neuroinflammation in a wild-type α-synuclein overexpressing mouse model of prodromal PD. They demonstrate, for the first time, the existence of early and sustained microglial mediated innate inflammation that precedes damage to the nigrostriatal circuit. Additionally they observe the spread of inflammation from the striatum to the SN. This study suggests that early dysregulated inflammation may contribute to progressive nigrostriatal pathology in PD, although the initiating factor that triggers the inflammatory response remains elusive. The novel concept of an early inflammatory response in the development of PD has important implications for preventive and therapeutic strategies for PD.

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Prakash, Yizhar, Grewe, Ramakrishnan, Wang, Goshen, Packer, Peterka, Yuste, Schnitzer, Deisseroth (2012). Two-photon optogenetic toolbox for fast inhibition, excitation and bistable modulation. Nat Methods, doi: 10.1038/nmeth.2215. (Link).

Abstract: 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 TPLSM laboratories. 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 TPLSM technologies across experimental fields and systems.

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Sacchet and Knutson (2012). Spatial smoothing systematically biases the localization of reward-related brain activity. Neuroimage 66C:270-277. (Link)

Abstract: Neuroimaging methods with enhanced spatial resolution such as functional magnetic resonance imaging (FMRI) suggest that the subcortical striatum plays a critical role in human reward processing. Analysis of FMRI data requires several preprocessing steps, some of which entail tradeoffs. For instance, while spatial smoothing can enhance statistical power, it may also bias localization towards regions that contain more gray than white matter. In a meta-analysis and reanalysis of an existing dataset, we sought to determine whether spatial smoothing could systematically bias the spatial localization of foci related to reward anticipation in the nucleus accumbens (NAcc). An activation likelihood estimate (ALE) meta-analysis revealed that peak ventral striatal ALE foci for studies that used smaller spatial smoothing kernels (i.e. <6mm FWHM) were more anterior than those identified for studies that used larger kernels (i.e. >7mm FWHM). Additionally, subtraction analysis of findings for studies that used smaller versus larger smoothing kernels revealed a significant cluster of differential activity in the left relatively anterior NAcc (Talairach coordinates: -10, 9, -1). A second meta-analysis revealed that larger smoothing kernels were correlated with more posterior localizations of NAcc activation foci (p<0.015), but revealed no significant associations with other potentially relevant parameters (including voxel volume, magnet strength, and publication date). Finally, repeated analysis of a representative dataset processed at different smoothing kernels (i.e., 0-12mm) also indicated that smoothing systematically yielded more posterior activation foci in the NAcc (p<0.005). Taken together, these findings indicate that spatial smoothing can systematically bias the spatial localization of striatal activity. These findings have implications both for historical interpretation of past findings related to reward processing and for the analysis of future studies.

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Sacchet, Mellinger, Sitaram, Braun, Birbaumer, Fetz (2012). Volitional control of neuromagnetic coherence. Front Neurosci. 6: 189. (Link)

Abstract: Coherence of neural activity between circumscribed brain regions has been implicated as an indicator of intracerebral communication in various cognitive processes. While neural activity can be volitionally controlled with neurofeedback, the volitional control of coherence has not yet been explored. Learned volitional control of coherence could elucidate mechanisms of associations between cortical areas and its cognitive correlates and may have clinical implications. Neural coherence may also provide a signal for brain-computer interfaces (BCI). In the present study we used the Weighted Overlapping Segment Averaging method to assess coherence between bilateral magnetoencephalograph sensors during voluntary digit movement as a basis for BCI control. Participants controlled an onscreen cursor, with a success rate of 124 of 180 (68.9%, sign-test p < 0.001) and 84 out of 100 (84%, sign-test p < 0.001). The present findings suggest that neural coherence may be volitionally controlled and may have specific behavioral correlates.

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Second through n-th Author Papers

Armakola, Higgins, Figley, Barmada, Scarborough, Diaz, Fang, Shorter, Krogan, Finkbeiner, Farese, Gitler (2012). Inhibition of RNA lariat debranching enzyme suppresses TDP-43 toxicity in ALS disease models. Nat Genet. 44(12): 1302-9. (Link)

Abstract: Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease primarily affecting motor neurons. Mutations in the gene encoding TDP-43 cause some forms of the disease, and cytoplasmic TDP-43 aggregates accumulate in degenerating neurons of most individuals with ALS. Thus, strategies aimed at targeting the toxicity of cytoplasmic TDP-43 aggregates may be effective. Here, we report results from two genome-wide loss-of-function TDP-43 toxicity suppressor screens in yeast. The strongest suppressor of TDP-43 toxicity was deletion of DBR1, which encodes an RNA lariat debranching enzyme. We show that, in the absence of Dbr1 enzymatic activity, intronic lariats accumulate in the cytoplasm and likely act as decoys to sequester TDP-43, preventing it from interfering with essential cellular RNAs and RNA-binding proteins. Knockdown of Dbr1 in a human neuronal cell line or in primary rat neurons is also sufficient to rescue TDP-43 toxicity. Our findings provide insight into TDP-43-mediated cytotoxicity and suggest that decreasing Dbr1 activity could be a potential therapeutic approach for ALS.

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Davies, Lim, Joo, Tam, Fuller (2012). The transcriptional regulator lola is required for stem cell maintenance and germ cell differentiation in the Drosophila testis. Dev Bio 373(2): 310-21. (Link)

Abstract: Stem cell behavior is regulated by extrinsic signals from specialized microenvironments, or niches, and intrinsic factors required for execution of context-appropriate responses to niche signals. Here we show that function of the transcriptional regulator longitudinals lacking (lola) is required cell autonomously for germline stem cell and somatic cyst stem cell maintenance in the Drosophila testis. In addition, lola is also required for proper execution of key developmental transitions during male germ cell differentiation, including the switch from transit amplifying progenitor to spermatocyte growth and differentiation, as well as meiotic cell cycle progression and spermiogenesis. Different lola isoforms, each having unique C-termini and zinc finger domains, may control different aspects of proliferation and differentiation in the male germline and somatic cyst stem cell lineages.

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Lammel, Lim, Ran, Huang, Betley, Tye, Deisseroth, Malenka (2012). Input-specific control of reward and aversion in the ventral tegmental area. Nature 491(7423):212-7. (Link)

Abstract: Ventral tegmental area (VTA) dopamine neurons have important roles in adaptive and pathological brain functions related to reward and motivation. However, it is unknown whether subpopulations of VTA dopamine neurons participate in distinct circuits that encode different motivational signatures, and whether inputs to the VTA differentially modulate such circuits. Here we show that, because of differences in synaptic connectivity, activation of inputs to the VTA from the laterodorsal tegmentum and the lateral habenula elicit reward and aversion in mice, respectively. Laterodorsal tegmentum neurons preferentially synapse on dopamine neurons projecting to the nucleus accumbens lateral shell, whereas lateral habenula neurons synapse primarily on dopamine neurons projecting to the medial prefrontal cortex as well as on GABAergic (γ-aminobutyric-acid-containing) neurons in the rostromedial tegmental nucleus. These results establish that distinct VTA circuits generate reward and aversion, and thereby provide a new framework for understanding the circuit basis of adaptive and pathological motivated behaviours.

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Liu, Sawada, Lee, Yu, Silverio, Alapatt, Millan, Shen, Saxton, Kanao, Takahashi, Hattori, Imai, Lu (2012). Parkinson's disease-associated kinase PINK1 regulates Miro protein level and axonal transport of mitochondria. PLoS Genet. 8(3): e1002537. (Link)

Abstract: Mutations in Pten-induced kinase 1 (PINK1) are linked to early-onset familial Parkinson's disease (FPD). PINK1 has previously been implicated in mitochondrial fission/fusion dynamics, quality control, and electron transport chain function. However, it is not clear how these processes are interconnected and whether they are sufficient to explain all aspects of PINK1 pathogenesis. Here we show that PINK1 also controls mitochondrial motility. InDrosophila, downregulation of dMiro or other components of the mitochondrial transport machinery rescued dPINK1 mutant phenotypes in the muscle and dopaminergic (DA) neurons, whereas dMiro overexpression alone caused DA neuron loss. dMiro protein level was increased in dPINK1 mutant but decreased in dPINK1 or dParkin overexpression conditions. In Drosophila larval motor neurons, overexpression of dPINK1 inhibited axonal mitochondria transport in both anterograde and retrograde directions, whereas dPINK1 knockdown promoted anterograde transport. In HeLa cells, overexpressed hPINK1 worked together with hParkin, another FPD gene, to regulate the ubiquitination and degradation of hMiro1 and hMiro2, apparently in a Ser-156 phosphorylation-independent manner. Also in HeLa cells, loss of hMiro promoted the perinuclear clustering of mitochondria and facilitated autophagy of damaged mitochondria, effects previously associated with activation of the PINK1/Parkin pathway. These newly identified functions of PINK1/Parkin and Miro in mitochondrial transport and mitophagy contribute to our understanding of the complex interplays in mitochondrial quality control that are critically involved in PD pathogenesis, and they may explain the peripheral neuropathy symptoms seen in some PD patients carrying particular PINK1 or Parkinmutations. Moreover, the different effects of loss of PINK1 function on Miro protein level inDrosophila and mouse cells may offer one explanation of the distinct phenotypic manifestations of PINK1 mutants in these two species.

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Tye, Mirzabekov, Warden, Ferenczi, Tsai, Finkelstein, Kim, Adhikari, Thompson, Andalman, Gunaydin, Witten, Deisseroth (2012). Dopamine neurons modulate neural encoding and expression of depression-related behaviour. Nature. doi: 10.1038/nature11740. (Link)

Abstract: Major depression is characterized by diverse debilitating symptoms that include hopelessness and anhedonia. Dopamine neurons involved in reward and motivation are among many neural populations that have been hypothesized to be relevant, and certain antidepressant treatments, including medications and brain stimulation therapies, can influence the complex dopamine system. Until now it has not been possible to test this hypothesis directly, even in animal models, as existing therapeutic interventions are unable to specifically target dopamine neurons. Here we investigated directly the causal contributions of defined dopamine neurons to multidimensional depression-like phenotypes induced by chronic mild stress, by integrating behavioural, pharmacological, optogenetic and electrophysiological methods in freely moving rodents. We found that bidirectional control (inhibition or excitation) of specified midbrain dopamine neurons immediately and bidirectionally modulates (induces or relieves) multiple independent depression symptoms caused by chronic stress. By probing the circuit implementation of these effects, we observed that optogenetic recruitment of these dopamine neurons potently alters the neural encoding of depression-related behaviours in the downstream nucleus accumbens of freely moving rodents, suggesting that processes affecting depression symptoms may involve alterations in the neural encoding of action in limbic circuitry.

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Warden, Selimbeyoglu, Mirzabekov, Lo, Thompson, Kim, Adhikari, Tye, Frank, Deisseroth (2012). A prefrontal cortex-brainstem neuronal projection that controls response to behavioural challenge. Nature 492(7429):428-32. (Link).

Abstract: The prefrontal cortex (PFC) is thought to participate in high-level control of the generation of behaviours (including the decision to execute actions); indeed, imaging and lesion studies in human beings have revealed that PFC dysfunction can lead to either impulsive states with increased tendency to initiate action, or to amotivational states characterized by symptoms such as reduced activity, hopelessness and depressed mood. Considering the opposite valence of these two phenotypes as well as the broad complexity of other tasks attributed to PFC, we sought to elucidate the PFC circuitry that favours effortful behavioural responses to challenging situations. Here we develop and use a quantitative method for the continuous assessment and control of active response to a behavioural challenge, synchronized with single-unit electrophysiology and optogenetics in freely moving rats. In recording from the medial PFC (mPFC), we observed that many neurons were not simply movement-related in their spike-firing patterns but instead were selectively modulated from moment to moment, according to the animal's decision to act in a challenging situation. Surprisingly, we next found that direct activation of principal neurons in the mPFC had no detectable causal effect on this behaviour. We tested whether this behaviour could be causally mediated by only a subclass of mPFC cells defined by specific downstream wiring. Indeed, by leveraging optogenetic projection-targeting to control cells with specific efferent wiring patterns, we found that selective activation of those mPFC cells projecting to the brainstem dorsal raphe nucleus (DRN), a serotonergic nucleus implicated in major depressive disorder, induced a profound, rapid and reversible effect on selection of the active behavioural state. These results may be of importance in understanding the neural circuitry underlying normal and pathological patterns of action selection and motivation in behaviour.

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Wu, Sacchet, Knuston (2012). Toward an affective neuroscience account of financial risk taking. Front Neurosci 6: 159. (

Ph.Ds in press #2

#2 in a semi-annual feature, highlighting recently published articles featuring an author (or authors) who is a current member of the Stanford Neuroscience Ph.D program. (For part 1, go here) [Note regarding the mechanics of this feature: This is purely through the magic of an ongoing My NCBI search for the names of Neuro PhD students. I wouldn't be surprised if there were some false negatives in the data set. Neuro students - let me know if I've missed your paper, and I'll gladly add it.]

[Additional Note: Links in the list below access anchor links within the main body of the post (which contains full titles, abstracts, and additional links to the article themselves). To allow link functionality, please continue reading this post below the fold.]

Without further ado, and with many congratulations to the authors, the papers:

First Author papers:
  • Kelsey Clark *Thesis Research!*

Persistent Spatial Information in the Frontal Eye Field during Object-Based Short-Term Memory. (Clark et al 2012)

  • Jacqueline Grant *Thesis Research!*

Reversal of Paralysis and Reduced Inflammation from Peripheral Administration of B-Amyloid in TH1 and TH17 Versions of Experimental Autoimmune Encephalomyelitis. (Grant et al 2012)

  • Emily Ferenczi

When the electricity (and the lights) go out: transient changes in excitability. (Nat. Neuro preview, Ferenczi and Deisseroth 2012)

  • Jack Wang

Axon degeneration: where the Wlds things are. (review, Wang and Barres 2012).

Second through n-th Author papers:
  • Astra Bryant

Thalamic Excitation and Network Oscillations in Stargazer Mice. (Lacey et al 2012)

  • Egle Cekanaviciute

Delayed administration of a small molecule tropomyosin-related kinase B ligand promotes recovery after hypoxic-ischemic stroke. (Han et al 2012)

  • Matt Kaufman

Neural population dynamics during reaching. (Churchland et al 2012)

  • Joline Fan* and Sergey Stavisky

A recurrent neural network for closed-loop intracortical brain-machine interface decoders. (Sussillo et al 2012) *technically Bioengineering PhD

  • Ivan Millan

Nemitin, a novel Map8/Map1s interacting protein with Wd40 repeats. (Wang et al 2012)

  • Rohit Prakash

Multiscale computational models for optogenetic control of cardiac function. (Abilez et al 2011)

  • Forea Wang

Division and subtraction by distinct cortical inhibitory networks in vivo (Wilson et al 2012)

  • Nicholas Weiler

Deep molecular diversity of mammalian synapses: why it matters and how to measure it. (O'Rourke et al 2012)

[Continue reading below the fold to allow link functionality above]

First Author Papers

Clark, Noudoost, Moore (2012). Persistent Spatial Information in the Frontal Eye Field during Object-Based Short-Term Memory. J. Neurosci 32(32):10907-10914. (Link)

Abstract: Spatial attention is known to gate entry into visual short-term memory, and some evidence suggests that spatial signals may also play a role in binding features or protecting object representations during memory maintenance. To examine the persistence of spatial signals during object short-term memory, the activity of neurons in the frontal eye field (FEF) of macaque monkeys was recorded during an object-based delayed match-to-sample task. In this task, monkeys were trained to remember an object image over a brief delay, regardless of the locations of the sample or target presentation. FEF neurons exhibited visual, delay, and target period activity, including selectivity for sample location and target location. Delay period activity represented the sample location throughout the delay, despite the irrelevance of spatial information for successful task completion. Furthermore, neurons continued to encode sample position in a variant of the task in which the matching stimulus never appeared in their response field, confirming that FEF maintains sample location independent of subsequent behavioral relevance. FEF neurons also exhibited target-position-dependent anticipatory activity immediately before target onset, suggesting that monkeys predicted target position within blocks. These results show that FEF neurons maintain spatial information during short-term memory, even when that information is irrelevant for task performance.

Grant, Ghosn, Axtell, Herges, Kuipers, Woodling, Andreasson, Herzenberg, Herzenberg, Steinman (2012). Reversal of Paralysis and Reduced Inflammation from Peripheral Administration of B-Amyloid in TH1 and TH17 Versions of Experimental Autoimmune Encephalomyelitis. Sci Transl Med. 4(145):145ra105. (Link)

Abstract: β-Amyloid 42 (Aβ42) and β-amyloid 40 (Aβ40), major components of senile plaque deposits in Alzheimer's disease, are considered neurotoxic and proinflammatory. In multiple sclerosis, Aβ42 is up-regulated in brain lesions and damaged axons. We found, unexpectedly, that treatment with either Aβ42 or Aβ40 peptides reduced motor paralysis and brain inflammation in four different models of experimental autoimmune encephalomyelitis (EAE) with attenuation of motor paralysis, reduction of inflammatory lesions in the central nervous system (CNS), and suppression of lymphocyte activation. Aβ42 and Aβ40 treatments were effective in reducing ongoing paralysis induced with adoptive transfer of either autoreactive T helper 1 (T(H)1) or T(H)17 cells. High-dimensional 14-parameter flow cytometry of peripheral immune cell populations after in vivo Aβ42 and Aβ40 treatment revealed substantial modulations in the percentage of lymphoid and myeloid subsets during EAE. Major proinflammatory cytokines and chemokines were reduced in the blood after Aβ peptide treatment. Protection conferred by Aβ treatment did not require its delivery to the brain: Adoptive transfer with lymphocytes from donors treated with Aβ42 attenuated EAE in wild-type recipient mice, and Aβ deposition in the brain was not detected in treated EAE mice by immunohistochemical analysis. In contrast to the improvement in EAE with Aβ treatment, EAE was worse in mice with genetic deletion of the amyloid precursor protein. Therefore, in the absence of Aβ, there is exacerbated clinical EAE disease progression. Because Aβ42 and Aβ40 ameliorate experimental autoimmune inflammation targeting the CNS, we might now consider its potential anti-inflammatory role in other neuropathological conditions.

Ferenczi and Deisseroth (2012). When the electricity (and the lights) go out: transient changes in excitability. Nat. Neurosci. 15(8):1058-60. (Link)

Abstract: News and Views regarding Raimondo, J.V., Kay, L., Ellender, T.J. & Akerman, C.J. Nat. Neurosci. 15, 1102–1104 (2012).

Wang and Barres (2012). Axon degeneration: where the Wlds things are. Curr Biol 22(7):R221-3. (Link)

Abstract: Expression of the Wld(s) protein significantly delays axon degeneration in injuries and diseases, but the mechanism for this protection is unknown. Two recent reports present evidence that axonal mitochondria are required for Wld(S)-mediated axon protection.

Second through n-th author papers

Abilez, Wong, Prakash, Deisseroth, Zarins, Kuhl (2011). Multiscale computational models for optogenetic control of cardiac function. Biophys J, 101(6):1326-34. (Link)

Abstract: The ability to stimulate mammalian cells with light has significantly changed our understanding of electrically excitable tissues in health and disease, paving the way toward various novel therapeutic applications. Here, we demonstrate the potential of optogenetic control in cardiac cells using a hybrid experimental/computational technique. Experimentally, we introduced channelrhodopsin-2 into undifferentiated human embryonic stem cells via a lentiviral vector, and sorted and expanded the genetically engineered cells. Via directed differentiation, we created channelrhodopsin-expressing cardiomyocytes, which we subjected to optical stimulation. To quantify the impact of photostimulation, we assessed electrical, biochemical, and mechanical signals using patch-clamping, multielectrode array recordings, and video microscopy. Computationally, we introduced channelrhodopsin-2 into a classic autorhythmic cardiac cell model via an additional photocurrent governed by a light-sensitive gating variable. Upon optical stimulation, the channel opens and allows sodium ions to enter the cell, inducing a fast upstroke of the transmembrane potential. We calibrated the channelrhodopsin-expressing cell model using single action potential readings for different photostimulation amplitudes, pulse widths, and frequencies. To illustrate the potential of the proposed approach, we virtually injected channelrhodopsin-expressing cells into different locations of a human heart, and explored its activation sequences upon optical stimulation. Our experimentally calibrated computational toolbox allows us to virtually probe landscapes of process parameters, and identify optimal photostimulation sequences toward pacing hearts with light.

Churchland, Cunningham, Kaufman, Foster, Nuyujukian, Ryu, Shenoy (2012). Neural population dynamics during reaching. Nature, 487(7405):51-6. (Link).

Abstract: Most theories of motor cortex have assumed that neural activity represents movement parameters. This view derives from what is known about primary visual cortex, where neural activity represents patterns of light. Yet it is unclear how well the analogy between motor and visual cortex holds. Single-neuron responses in motor cortex are complex, and there is marked disagreement regarding which movement parameters are represented. A better analogy might be with other motor systems, where a common principle is rhythmic neural activity. Here we find that motor cortex responses during reaching contain a brief but strong oscillatory component, something quite unexpected for a non-periodic behaviour. Oscillation amplitude and phase followed naturally from the preparatory state, suggesting a mechanistic role for preparatory neural activity. These results demonstrate an unexpected yet surprisingly simple structure in the population response. This underlying structure explains many of the confusing features of individual neural responses.

Han, Pollak, Yang, Siddiqui, Doyle, Taravosh-Lahn, Cekanaviciute, Han, Goodman, Jones, Jing, Massa, Longo, Buckwalter (2012). Delayed administration of a small molecule tropomyosin-related kinase B ligand promotes recovery after hypoxic-ischemic stroke. Stroke 43(7):1918-24. (Link)

Abstract: Stroke is the leading cause of long-term disability in the United States, yet no drugs are available that are proven to improve recovery. Brain-derived neurotrophic factor stimulates neurogenesis and plasticity, processes that are implicated in stroke recovery. It binds to both the tropomyosin-related kinase B and p75 neurotrophin receptors. However, brain-derived neurotrophic factor is not a feasible therapeutic agent, and no small molecule exists that can reproduce its binding to both receptors. We tested the hypothesis that a small molecule (LM22A-4) that selectively targets tropomyosin-related kinase B would promote neurogenesis and functional recovery after stroke.

Lacey, Bryant, Brill, Huguenard (2012). Thalamic Excitation and Network Oscillations in Stargazer Mice. J Neurosci 32(32): 11067-11081. (Link)

Abstract: Disturbances in corticothalamic circuitry can lead to absence epilepsy. The reticular thalamic nucleus (RTN) plays a pivotal role in that it receives excitation from cortex and thalamus and, when strongly activated, can generate excessive inhibitory output and epileptic thalamocortical oscillations that depend on postinhibitory rebound. Stargazer (stg) mice have prominent absence seizures resulting from a mutant form of the AMPAR auxiliary protein stargazin. Reduced AMPAR excitation in RTN has been demonstrated previously in stg, yet the mechanisms leading from RTN hypoexcitation to epilepsy are unknown and unexpected because thalamic epileptiform oscillatory activity requires AMPARs. We demonstrate hyperexcitability in stg thalamic slices and further characterize the various excitatory inputs to RTN using electrical stimulation and laser scanning photostimulation. Patch-clamp recordings of spontaneous and evoked EPSCs in RTN neurons demonstrate reduced amplitude and increased duration of the AMPAR component with an increased amplitude NMDAR component. Short 200 Hz stimulus trains evoked a gradual approximately threefold increase in NMDAR EPSCs compared with single stimuli in wild-type (WT), indicating progressive NMDAR recruitment, whereas in stg cells, NMDAR responses were nearly maximal with single stimuli. Array tomography revealed lower synaptic, but higher perisynaptic, AMPAR density in stg RTN. Increasing NMDAR activity via reduced [Mg2+]o in WT phenocopied the thalamic hyperexcitability observed in stg, whereas changing [Mg2+]o had no effect on stg slices. These findings suggest that, in stg, a trafficking defect in synaptic AMPARs in RTN cells leads to a compensatory increase in synaptic NMDARs and enhanced thalamic excitability.

O'Rourke, Weiler, Micheva, Smith (2012). Deep molecular diversity of mammalian synapses: why it matters and how to measure it. Nat. Rev. Neurosci. 13(6):365-79. (Link)

Abstract: Pioneering studies in the middle of the twentieth century revealed substantial diversity among mammalian chemical synapses and led to a widely accepted classification of synapse type on the basis of neurotransmitter molecule identity. Subsequently, powerful new physiological, genetic and structural methods have enabled the discovery of much deeper functional and molecular diversity within each traditional neurotransmitter type. Today, this deep diversity continues to pose both daunting challenges and exciting new opportunities for neuroscience. Our growing understanding of deep synapse diversity may transform how we think about and study neural circuit development, structure and function.

Sussillo, Nuyujukian, Fan, Kao, Stavisky, Ryu, Shenoy (2012). A recurrent neural network for closed-loop intracortical brain-machine interface decoders. J. Neural Eng. 9(2):026027. (Link)

Abstract: Recurrent neural networks (RNNs) are useful tools for learning nonlinear relationships in time series data with complex temporal dependences. In this paper, we explore the ability of a simplified type of RNN, one with limited modifications to the internal weights called an echostate network (ESN), to effectively and continuously decode monkey reaches during a standard center-out reach task using a cortical brain-machine interface (BMI) in a closed loop. We demonstrate that the RNN, an ESN implementation termed a FORCE decoder (from first order reduced and controlled error learning), learns the task quickly and significantly outperforms the current state-of-the-art method, the velocity Kalman filter (VKF), using the measure of target acquire time. We also demonstrate that the FORCE decoder generalizes to a more difficult task by successfully operating the BMI in a randomized point-to-point task. The FORCE decoder is also robust as measured by the success rate over extended sessions. Finally, we show that decoded cursor dynamics are more like naturalistic hand movements than those of the VKF. Taken together, these results suggest that RNNs in general, and the FORCE decoder in particular, are powerful tools for BMI decoder applications.

Wang, Lundin, Millan, Zeng, Chen, Yang, Allen, Chen, Bach, Hsu, Maloney, Kapur, Yang (2012). Nemitin, a novel Map8/Map1s interacting protein with Wd40 repeats. PLoS One. 7(4):e33094. (Link)

Abstract: In neurons, a highly regulated microtubule cytoskeleton is essential for many cellular functions. These include axonal transport, regional specialization and synaptic function. Given the critical roles of microtubule-associated proteins (MAPs) in maintaining and regulating microtubule stability and dynamics, we sought to understand how this regulation is achieved. Here, we identify a novel LisH/WD40 repeat protein, tentatively named nemitin (neuronal enriched MAP interacting protein), as a potential regulator of MAP8-associated microtubule function. Based on expression at both the mRNA and protein levels, nemitin is enriched in the nervous system. Its protein expression is detected as early as embryonic day 11 and continues through adulthood. Interestingly, when expressed in non-neuronal cells, nemitin displays a diffuse pattern with puncta, although at the ultrastructural level it localizes along the microtubule network in vivo in sciatic nerves. These results suggest that the association of nemitin to microtubules may require an intermediary protein. Indeed, co-expression of nemitin with microtubule-associated protein 8 (MAP8) results in nemitin losing its diffuse pattern, instead decorating microtubules uniformly along with MAP8. Together, these results imply that nemitin may play an important role in regulating the neuronal cytoskeleton through an interaction with MAP8.

Wilson, Runyan, Wang, Sur (2012). Division and subtraction by distinct cortical inhibitory networks in vivo. Nature. 488(7410) (Link)

Abstract: Brain circuits process information through specialized neuronal subclasses interacting within a network. Revealing their interplay requires activating specific cells while monitoring others in a functioning circuit. Here we use a new platform for two-way light-based circuit interrogation in visual cortex in vivo to show the computational implications of modulating different subclasses of inhibitory neurons during sensory processing. We find that soma-targeting, parvalbumin-expressing (PV) neurons principally divide responses but preserve stimulus selectivity, whereas dendrite-targeting, somatostatin-expressing (SOM) neurons principally subtract from excitatory responses and sharpen selectivity. Visualized in vivo cell-attached recordings show that division by PV neurons alters response gain, whereas subtraction by SOM neurons shifts response levels. Finally, stimulating identified neurons while scanning many target cells reveals that single PV and SOM neurons functionally impact only specific subsets of neurons in their projection fields. These findings provide direct evidence that inhibitory neuronal subclasses have distinct and complementary roles in cortical computations.

PhDs in Press

While scouring Pubmed for published articles featuring Stanford Neuro-student authors for a recent post, I had two thoughts. 1) Students in the Stanford Neuro program were on a hell of a lot of papers

2) There was definitely a better way to highlight those papers than a retrospective every 6-months that took forever to type up and even longer to actually read (see thought 1).

Thus was born a new semi-regular feature for the neuroblog: PhDs in Press - of which this post is the first example.

Part shameless publicity, part proud bragging, part intra-program PSA, this feature will highlight recently published articles featuring an author (or authors) who is a current member of the Stanford Neuroscience Ph.D program.

[Note regarding the mechanics of this feature: This is purely through the magic of an ongoing My NCBI search for the names of Neuro PhD students. I wouldn't be surprised if there were some false negatives in the data set. Neuro students - let me know if I've missed your paper, and I'll gladly add it.]

[Additional Note: Links in the list below access anchor links within the main body of the post (which contains full titles, abstracts, and additional links to the article themselves). To allow link functionality, please continue reading this post below the fold.]

Without further ado, and with many congratulations to the authors, the papers:

First Author papers:
Second through n-th Author papers:

[Continue reading below the fold to allow link functionality above]

First Author Papers

Adelson et al 2012. Neuroprotection from Stroke in the Absence of MHCI or PirB. Neuron. 2012 Mar 22;73(6):1100-7. Epub 2012 Mar 21.

Abstract: Recovery from stroke engages mechanisms of neural plasticity. Here we examine a role for MHC class I (MHCI) H2-Kb and H2-Db, as well as PirB receptor. These molecules restrict synaptic plasticity and motor learning in the healthy brain. Stroke elevates neuronal expression not only of H2-Kb and H2-Db, but also of PirB and downstream signaling. KbDb knockout (KO) or PirB KO mice have smaller infarcts and enhanced motor recovery. KO hippocampal organotypic slices, which lack an intact peripheral immune response, have less cell death after in vitro ischemia. In PirB KO mice, corticospinal projections from the motor cortex are enhanced, and the reactive astrocytic response is dampened after MCAO. Thus, molecules that function in the immune system act not only to limit synaptic plasticity in healthy neurons, but also to exacerbate brain injury after ischemia. These results suggest therapies for stroke by targeting MHCI and PirB.

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Maheswaranathan et al 2012. Emergent bursting and synchrony in computer simulations of neuronal cultures. Front. Comput. Neurosci6:15. doi: 10.3389/fncom.2012.00015

Abstract: Experimental studies of neuronal cultures have revealed a wide variety of spiking network activity ranging from sparse, asynchronous firing to distinct, network-wide synchronous bursting. However, the functional mechanisms driving these observed firing patterns are not well understood. In this work, we develop an in silico network of cortical neurons based on known features of similar in vitro networks. The activity from these simulations is found to closely mimic experimental data. Furthermore, the strength or degree of network bursting is found to depend on a few parameters: the density of the culture, the type of synaptic connections, and the ratio of excitatory to inhibitory connections. Network bursting gradually becomes more prominent as either the density, the fraction of long range connections, or the fraction of excitatory neurons is increased. Interestingly, biologically prevalent values of parameters result in networks that are at the transition between strong bursting and sparse firing. Using principal components analysis, we show that a large fraction of the variance in firing rates is captured by the first component for bursting networks. These results have implications for understanding how information is encoded at the population level as well as for why certain network parameters are ubiquitous in cortical tissue.

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Wang et al 2012. Axon degeneration: molecular mechanisms of a self-destruction pathway. J Cell Biol. 2012 Jan 9;196(1):7-18. Review.

Abstract: Axon degeneration is a characteristic event in many neurodegenerative conditions including stroke, glaucoma, and motor neuropathies. However, the molecular pathways that regulate this process remain unclear. Axon loss in chronic neurodegenerative diseases share many morphological features with those in acute injuries, and expression of the Wallerian degeneration slow (WldS) transgene delays nerve degeneration in both events, indicating a common mechanism of axonal self-destruction in traumatic injuries and degenerative diseases. A proposed model of axon degeneration is that nerve insults lead to impaired delivery or expression of a local axonal survival factor, which results in increased intra-axonal calcium levels and calcium-dependent cytoskeletal breakdown.

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Second through Nth-Author Papers

Byers et al 2012. SNCA triplication Parkinson's patient's iPSC-derived DA neurons accumulate α-synuclein and are susceptible to oxidative stress. PLoS One. 2011;6(11):e26159. Epub 2011 Nov 16.

Abstract: Parkinson's disease (PD) is an incurable age-related neurodegenerative disorder affecting both the central and peripheral nervous systems. Although common, the etiology of PD remains poorly understood. Genetic studies infer that the disease results from a complex interaction between genetics and environment and there is growing evidence that PD may represent a constellation of diseases with overlapping yet distinct underlying mechanisms. Novel clinical approaches will require a better understanding of the mechanisms at work within an individual as well as methods to identify the specific array of mechanisms that have contributed to the disease. Induced pluripotent stem cell (iPSC) strategies provide an opportunity to directly study the affected neuronal subtypes in a given patient. Here we report the generation of iPSC-derived midbrain dopaminergic neurons from a patient with a triplication in the α-synuclein gene (SNCA). We observed that the iPSCs readily differentiated into functional neurons. Importantly, the PD-affected line exhibited disease-related phenotypes in culture: accumulation of α-synuclein, inherent overexpression of markers of oxidative stress, and sensitivity to peroxide induced oxidative stress. These findings show that the dominantly-acting PD mutation is intrinsically capable of perturbing normal cell function in culture and confirm that these features reflect, at least in part, a cell autonomous disease process that is independent of exposure to the entire complexity of the diseased brain.

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Akam et al 2012. Oscillatory dynamics in the hippocampus support dentate gyrus-CA3 coupling. Nat Neurosci. 2012 Apr 1. doi: 10.1038/nn.3081.

Abstract: Gamma oscillations in the dentate gyrus and hippocampal CA3 show variable coherence in vivo, but the mechanisms and relevance for information flow are unknown. We found that carbachol-induced oscillations in rat CA3 have biphasic phase-response curves, consistent with the ability to couple with oscillations in afferent projections. Differences in response to stimulation of either the intrinsic feedback circuit or the dentate gyrus were well described by varying an impulse vector in a two-dimensional dynamical system, representing the relative input to excitatory and inhibitory neurons. Responses to sinusoidally modulated optogenetic stimulation confirmed that the CA3 network oscillation can entrain to periodic inputs, with a steep dependence of entrainment phase on input frequency. CA3 oscillations are therefore suited to coupling with oscillations in the dentate gyrus over a broad range of frequencies.

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Tasic et al 2012. Extensions of MADM (Mosaic Analysis with Double Markers) in Mice. PLoS One. 2012;7(3):e33332. Epub 2012 Mar 27.

Abstract: Mosaic Analysis with Double Markers (MADM) is a method for generating genetically mosaic mice, in which sibling mutant and wild-type cells are labeled with different fluorescent markers. It is a powerful tool that enables analysis of gene function at the single cell level in vivo. It requires transgenic cassettes to be located between the centromere and the mutation in the gene of interest on the same chromosome. Here we compare procedures for introduction of MADM cassettes into new loci in the mouse genome, and describe new approaches for expanding the utility of MADM. We show that: 1) Targeted homologous recombination outperforms random transgenesis in generation of reliably expressed MADM cassettes, 2) MADM cassettes in new genomic loci need to be validated for biallelic and ubiquitous expression, 3) Recombination between MADM cassettes on different chromosomes can be used to study reciprocal chromosomal deletions/duplications, and 4) MADM can be modified to permit transgene expression by combining it with a binary expression system. The advances described in this study expand current, and enable new and more versatile applications of MADM

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