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  • Neurobiology | The University of Chicago
    the genome the team generated transcriptome sequence data which can be used to measure gene expression based on RNA levels in 12 different tissues types Short range brain The team estimates the O bimaculoides genome is 2 7 billion base pairs in size with numerous long stretches of repeated sequences They identified more than 33 000 protein coding genes placing the octopus genome at slightly smaller in size but with more genes than a human genome The large size of the octopus genome was initially attributed to whole genome duplication events during evolution which can lead to increased genomic diversity and complexity This phenomenon has occurred twice in ancestral vertebrates for example However Ragsdale and his colleagues found no evidence of duplications Instead the evolution of the octopus genome was likely driven by the expansion of a few specific gene families widespread genome shuffling and the appearance of novel genes The most notable expansion was in the protocadherins a family of genes that regulate neuronal development and short range interactions between neurons The octopus genome contains 168 protocadherin genes 10 times more than other invertebrates and more than twice as many as mammals It was previously thought that only vertebrates possessed numerous and diverse protocadherin genes The research team hypothesized that because cephalopod neurons lack myelin and function poorly over long distances protocadherins were central to the evolution of a nervous system whose complexity depends on short range interactions Other gene families that were dramatically expanded in the octopus include zinc finger transcription factors which are mainly expressed in embryonic and nervous tissues and are thought to play roles in development The octopus genome contains around 1 800 C2H2 zinc finger transcription factors the second largest gene family so far discovered in animals olfactory receptor genes in elephants are the largest at around 2 000 Overall however gene family sizes in octopuses are largely similar to those found in other invertebrates A Cuisinart genome A unique feature of the octopus genome appears to be widespread genomic rearrangements In most species specific cohorts of genes tend to be close together on the chromosome However most octopus genes show no such connections Hox genes for example control body plan development and cluster together in almost all animals Octopus Hox genes are scattered throughout the genome with no apparent linkages The octopus genome is enriched in transposons also known as jumping genes which can rearrange themselves on the genome While their role in octopuses is unclear the team found elevated transposon expression in neural tissues Transposons are known to affect the regulation of gene expression and play major roles in shaping genome structure With a few notable exceptions the octopus basically has a normal invertebrate genome that s just been completely rearranged like it s been put into a blender and mixed said Caroline Albertin co lead author and graduate student in the Department of Organismal Biology and Anatomy at the University of Chicago This leads to genes being placed in new genomic

    Original URL path: http://neurobiology.uchicago.edu/ (2015-10-09)
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  • A note from the Chair, Dr. S. Murray Sherman | Neurobiology | The University of Chicago
    uses cutting edge two photon imaging techniques to uncover the circuit mechanisms of cortical function David Freedman joined the Department of Neurobiology as an Assistant Professor in 2008 following postdoctoral fellowships at M I T and Harvard Medical School His laboratory is focused on the neuronal mechanisms of visual learning memory and recognition Christian Hansel Professor in the Department of Neurobiology was also hired in 2008 and is focused on understanding the cellular mechanisms of plasticity in the cerebellum Christian was a postdoctoral fellow at Johns Hopkins University and most recently was a faculty member in the Department of Neuroscience at Erasmus University in Rotterdam Netherlands Leslie Osborne previously a postdoctoral fellow at the University of California in San Francisco joined the department in 2009 She is an Assistant Professor and her laboratory combines experimental and theoretical approaches to understand the mechanisms of sensory motor processing for controlling eye movements Wei Wei is the newest addition to the department She was previously a postdoctoral fellow at the University of California at Berkley investigating the strategies for circuit assembly and development in the visual system On the macro level these new faculty members have joined and are collaborating with a growing

    Original URL path: http://neurobiology.uchicago.edu/page/note-chair-dr-s-murray-sherman (2015-10-09)
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  • News and Research Highlights | Neurobiology | The University of Chicago
    understanding overall brain function Ragsdale lab comfirms 50 year old hypothesis that neocortex cell types are found in bird brain nuclei Hansel Lab illustrates dendrites on cells in the cerebellum are more than mere bystanders Grove Lab explores secret origins of the vertebrate brain see full article David Freedman Lab gains insight into brain circuits for visual categorization see full article Peggy Mason lab uncovers empathy driven helping behavior in

    Original URL path: http://neurobiology.uchicago.edu/DeptNews.shtml (2015-10-09)
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  • Jason MacLean | Neurobiology | The University of Chicago
    techniques are limited to the examination of either large brain regions missing the resolution needed to analyze the underlying mechanisms or to single neurons missing the activity of the circuit in which the neurons are embedded Experiments at the circuit level are essential to answering these questions because studies in which single or even a few cells are monitored fundamentally miss the emergent properties of these circuits Select Publications Gururangan S S Sadovsky A J MacLean J N 2014 Analysis of Graph Invariants in Functional Neocortical Circuitry Reveals Generalized Features Common to Three Areas of Sensory Cortex PLoS computational biology 10 7 e1003710 Runfeldt M J Sadovsky A J MacLean J N 2014 Acetylcholine Functionally Reorganizes Neocortical Microcircuits Journal of neurophysiology jn 00071 Sadovsky A J and MacLean J N 2014 Mouse Visual Neocortex Supports Multiple Stereotyped Patterns of Microcircuit Activity The Journal of Neuroscience 34 23 7769 7777 Sadovsky A and Jason N MacLean J 2013 Scaling of Topologically Similar Functional Modules Defines Mouse Primary Auditory and Somatosensory Microcircuitry J Neuroscience August 28 2013 33 35 14048 14060 Kruskal PB Li L and MacLean JN 2013 Circuit reactivation dynamically regulates synaptic plasticity in neocortex Nat Commun 4 2574 Sadovsky AJ Kruskal PB Kimmel JM Ostmeyer J Neubauer FB and MacLean JN 2011 Heuristically optimal path scanning for high speed multiphoton circuit imaging J Neurophysiol 106 1591 1598 Hoffman KL Battaglia FP Harris K MacLean JN Marshall L Mehta MR 2007 The upshot of up states in the neocortex from slow oscillations to memory formation J Neurosci 27 11838 41 MacLean J N Watson B O Aaron G B and Yuste R 2005 Internal dynamics determine the cortical response to thalamic stimulation Neuron 48 811 823 Yuste R MacLean J N Smith J and Lanser A 2005 Perspective Opinion Can

    Original URL path: https://neurobiology.uchicago.edu/page/maclean (2015-10-09)
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  • David Freedman | Neurobiology | The University of Chicago
    visual stimuli as a result of experience This contrasted sharply with the response patterns in brain areas considered to be more involved in sensory processing such as the middle temporal and inferior temporal cortices which seemed more involved in visual feature encoding and did not reflect more abstract or meaningful information about stimuli Understanding how feature based sensory encoding in visual cortex is transformed into more abstract and meaningful representations in subsequent neuronal processing stages is the central goal of our research Our hope is that a greater understanding of the brain mechanisms of visual learning memory and recognition in healthy subjects will provide a step toward addressing a number of neurological diseases and conditions such as Alzheimer s disease schizophrenia stroke and attention deficit disorder that can leave patients impaired in tasks that require visual learning recognition and or evaluating and responding appropriately to sensory information Select Publications Ibos G and Freedman D J Dynamic integration of task relevant visual features in posterior parietal cortex Neuron 83 1 13 2014 Swaminathan S K Masse N Y and Freedman D J A comparison of lateral and medial intraparietal areas during a visual categorization task Journal of Neuroscience 33 13157 13170 2013 Rishel C A Huang G and Freedman D J Independent category and spatial encoding in parietal cortex Neuron 77 969 979 2013 Fitzgerald J K Freedman D J Fanini A Bennur S Gold J I and Assad J A Biased associative representations in parietal cortex Neuron 77 180 191 2013 Swaminathan S K and Freedman D J Preferential encoding of visual categories in parietal cortex compared to prefrontal cortex Nature Neuroscience 15 315 320 2012 Fitzgerald J K Freedman D J and Assad J A Generalized Associative Representations in Parietal Cortex Nature Neuroscience 14 1075 1079 2011 Freedman D

    Original URL path: https://neurobiology.uchicago.edu/page/freedman (2015-10-09)
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  • Christian Hansel | Neurobiology | The University of Chicago
    plasticity motif in the brain In addition to LTD and LTP we also examine intrinsic plasticity in Purkinje cells We have shown that the intrinsic excitability of Purkinje cells can be amplified by a downregulation of calcium dependent SK2 type potassium channels and that this form of plasticity complements LTD and LTP in information storage In the lab we use patch clamp recording techniques incl patch clamp recordings from Purkinje cell dendrites as well as confocal calcium imaging to study the cellular and molecular mechanisms underlying learning and memory These studies are complemented by the use of additional techniques such as immunohistochemistry and behavioral testing More recently we also study the effects of alcohol on cerebellar function and motor adaptation and the role of deficits in cerebellar associative learning in autism spectrum disorder ASD The Hansel lab Christian Hansel Principal Investigator Giorgio Grasselli Postdoc Claire Piochon Postdoc Dana Simmons PhD Student Heather Titley Postdoc Gabrielle Watkins PhD Student Select Publications Kloth AD et al 2015 Cerebellar associative sensory learning defects in five mouse autism models eLife 4 e06085 Piochon C et al 2014 Cerebellar plasticity and motor learning deficits in a copy number variation mouse model of autism Nat Commun 5 5586 Van Beugen BJ Qiao X Simmons DH De Zeeuw CI and Hansel C 2014 Enhanced AMPA receptor function promotes cerebellar long term depression rather than potentiation Learn Mem 21 662 667 Rinaldo L and Hansel C 2013 Muscarinic acetylcholine receptor activation blocks long term potentiation at cerebellar parallel fiber Purkinje cell synapses via cannabinoid signaling Proc Natl Acad Sci USA 110 11181 11186 Du X et al 2013 Second cistron in CACNA1A gene encodes a transcription factor mediating cerebellar development and SCA6 Cell 154 118 133 He Q Titley H Grasselli G Piochon C and Hansel C 2013

    Original URL path: https://neurobiology.uchicago.edu/page/hansel (2015-10-09)
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  • Leslie Osborne | Neurobiology | The University of Chicago
    analyzing variability in both neural responses and behavior Variation in how our brains record what we see and program how we act creates variability in our behavior It is difficult if not impossible to swing a golf club the same way every stroke or to hit a baseball on every swing An analysis of such variation can reveal more than the overall level of precision in the system it can tell us about the brain s underlying computational processing as well Because neural responses are probabilistic fluctuations in responses to repeated stimuli allow us to describe the input output function Quantitative analysis of fluctuations in behavior shows us how the underlying neural signals were read out to produce movement Understanding where noise arises in the brain has implications for advancing research in neuromotor control and in developing therapies for disorders where control is impaired like Parkinson s disease In my lab we focus on an eye movement behavior known as smooth pursuit that allows our eyes to track moving targets Precision is at a premium in pursuit since failure to exactly match a target s motion causes its image to blur as it slides across the retina We find that pursuit can be a reliable read out of the target motion the brain perceives giving us a means to infer the visual activity that gave rise to the behavioral response Through simultaneous multi electrode recording of neural activity in extrastriate cortex and high resolution recordings of eye movement we are working to uncover the mechanisms by which visual information is represented in the activity of cortical populations translated into motor commands and how the whole system learns and adapts in order to maintain precise behavior Select Publications L C Osborne and S G Lisberger 2009 Spatial and temporal integration of

    Original URL path: https://neurobiology.uchicago.edu/page/osbourne (2015-10-09)
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  • Wei Wei | Neurobiology | The University of Chicago
    mechanisms of visual processing in the retina and also have broader implications in the fundamental questions of synapse development and organization in the central nervous system Select Publications Zhe Pei Qiang Chen David Koren Benno Giammarinaro Hector Acaron Ledesma and Wei Wei 2015 Conditional Knock Out of Vesicular GABA Transporter Gene from Starburst Amacrine Cells Reveals the Contributions of Multiple Synaptic Mechanisms Underlying Direction Selectivity in the Retina J Neurosci 23 September 2015 35 38 13219 13232 Jason W Triplett Wei Wei Cristina Gonzalez Neal T Sweeney Andrew D Huberman Marla B Feller and David A Feldheim 2014 Dendritic and Axonal Targeting Patterns of a Genetically Specified Class of Retinal Ganglion Cells that Participate in Image Forming Circuits Neural Development 2014 Feb 5 9 2 doi 10 1186 1749 8104 9 2 Michal Rivlin Etzion Wei Wei and Marla Feller 2012 Visual stimulation reverses the directional preference of direction selective retinal ganglion cells Neuron 76 518 525 Wei Wei and Marla B Feller 2011 Organization and development of direction selective circuits in the retina Review Trends in Neurosciences Dec 34 12 638 45 Epub 2011 Aug 26 Michal Rivlin Etzion Kaili Zhou Wei Wei Justin Elstrott Phong Nguyen Ben Barres Andrew Huberman and Marla Feller 2011 Transgenic mice reveal unexpected diversity of On Off direction selective retinal ganglion cell subtypes and brain structures involved in motion processing J Neurosci Jun 15 31 24 8760 9 Wei Wei Aaron M Hamby Kaili Zhou Marla B Feller 2011 Development of asymmetric inhibition underlying retinal direction selectivity in the retina Nature 469 7330 402 6 Wei Wei Justin Elstrott Marla B Feller 2010 Two photon targeted recording of GFP expressing neurons for light responses and live cell imaging in the mouse retina Nature Protocols 5 1347 1352 Peter G Fuerst Freyja Bruce Miao

    Original URL path: https://neurobiology.uchicago.edu/page/wei-wei (2015-10-09)
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