Friday Paper List – posted Sunday July 21st

Sorry for the late post. I’ve been in a bit of a slump.

To the papers!

1) Ultrasensitive fluorescent proteins for imaging neuronal activity Tsai-Wen Chen, Trevor J. Wardill, Yi Sun, Stefan R. Pulver, Sabine L. Renninger, Amy Baohan, Eric R. Schreiter, Rex A. Kerr, Michael B. Orger, Vivek Jayaraman, Loren L. Looger, Karel Svoboda & Douglas S. Kim ; Nature 2013 (link)

  • This beautiful panel from figure 2 pretty much summarizes how transformative the new GCaMP6 is 🙂
  • gcamp6example

2)  Bidirectional NMDA receptor plasticity controls CA3 output and heterosynaptic metaplasticity David L Hunt, Nagore Puente, Pedro Grandes & Pablo E Castillo ; Nature Neuroscience 2013 (link)

3) Impaired hippocampal rate coding after lesions of the lateral entorhinal cortex Li Lu, Jill K Leutgeb, Albert Tsao, Espen J Henriksen, Stefan Leutgeb, Carol A Barnes, Menno P Witter, May-Britt Moser & Edvard I Moser ; Nature Neuroscience 2013 (link)

4) Specific evidence of low-dimensional continuous attractor dynamics in grid cells KiJung Yoon, Michael A Buice, Caswell Barry, Robin Hayman, Neil Burgess & Ila R Fiete ; Nature Neuroscience 2013 (link)

5) Attention-dependent reductions in burstiness and action-potential height in macaque area V4 Emily B Anderson, Jude F Mitchell & John H Reynolds ; Nature Neuroscience 2013 (link)

6) Functional labeling of neurons and their projections using the synthetic activity–dependent promoter E-SARE Takashi Kawashima, Kazuo Kitamura, Kanzo Suzuki, Mio Nonaka, Satoshi Kamijo, Sayaka Takemoto-Kimura, Masanobu Kano, Hiroyuki Okuno, Kenichi Ohki & Haruhiko Bito ; Nature Methods 2013 (link)

7) Cellular and Synaptic Architecture of Multisensory Integration in the Mouse Neocortex Umberto Olcese, Giuliano Iurilli, and Paolo Medini ; Neuron 2013 (link)

8) Motor Cortex Feedback Influences Sensory Processing by Modulating Network State Edward Zagha, Amanda E. Casale, Robert N.S. Sachdev, Matthew J. McGinley, and David A. McCormick  ; Neuron 2013 (link)

9) Shared Representations for Working Memory and Mental Imagery in Early Visual Cortex Anke Marit Albers, Peter Kok, Ivan Toni, H. Chris Dijkerman, and Floris P. de Lange ; Current Biology 2013 (link)

10) Memory for Distant Past Events in Chimpanzees and Orangutans Gema Martin-Ordas, Dorthe Berntsen, and Josep Call ; Current Biology 2013 (link)

11) Statistical Analysis of Molecular Signal Recording Joshua I. Glaser, Bradley M. Zamft, Adam H. Marblestone, Jeffrey R. Moffitt, Keith Tyo, Edward S. Boyden, George Church, Konrad P. Kording ; PLoS Computational Biology 2013 (link)

  • New details exploring the molecular ticker-tape recording of neural activity.

12) Light Scattering Properties Vary across Different Regions of the Adult Mouse Brain Saif I. Al-Juboori, Anna Dondzillo., Elizabeth A. Stubblefield, Gidon Felsen, Tim C. Lei, Achim Klug ; PLoS One 2013 (link)

13) Low-Dimensional Sensory Feature Representation by Trigeminal Primary Afferents Michael R. Bale, Kyle Davies, Oliver J. Freeman, Robin A. A. Ince, and Rasmus S. Petersen ; J Neuroscience 2013 (link)

Friday Paper List – July 12th

This week’s post starts off heavy on the technology side of things. As I have mentioned before I am a big fan of methods in neuroscience. In particular I’m a huge sucker for all things optogenetics related…

Optogenetics gives us the ability to control behavior in animals using lasers!! See below for two examples.

Optogenetics turned the cat above into spiderman and gave the one below some new dance moves.

Of course talking about cool neurotechnology inevitably leads to Ed Boyden; the two go together like peanut butter and jelly. These first couple of papers were brought to my attention via links shared from Dr. Boyden’s tweets.

1) Physical Principles for Scalable Neural Recording Adam H. Marblestone, Bradley M. Zamft, Yael G. Maguire, Mikhail G. Shapiro, Thaddeus R. Cybulski, Joshua I. Glaser, P. Benjamin Stranges, Reza Kalhor, David A. Dalrymple, Dongjin Seo, Elad Alon, Michel M. Maharbiz, Jose M. Carmena, Jan M. Rabaey, Edward S. Boyden, George M. Church,and Konrad P. Kording (link)

  • This paper has already been posted, but this is supposedly a new draft. Plus as I said the first time I think this is a really neat paper!

2) On the Technology Prospects and Investment Opportunities for Scalable Neuroscience Thomas Dean, Biafra Ahanonu, Mainak Chowdhury, Anjali Datta, Andre Esteva, Daniel Eth, Nobie Redmon, Oleg Rumyantsev, and Ysis Tarter (link)

3) Neural Dust: An Ultrasonic, Low Power Solution for Chronic Brain-Machine Interfaces Dongjin Seo , Jose M. Carmena , Jan M. Rabaey  , Elad Alon , and Michel M. Maharbiz ; arXiv 2013 (link)

  • Just have to insert another quick comment here… this is awesome!

4) In vivo robotics: the automation of neuroscience and other intact-system biological fields Suhasa B. Kodandaramaiah, Edward S. Boyden, and Craig R. Forest ; Annals of the New York Academy of Sciences 2013 (link)

5) All-Optical Switch and Transistor Gated by One Stored Photon Wenlan Chen, Kristin M. Beck, Robert Bücker, Michael Gullans, Mikhail D. Lukin, Haruka Tanji-Suzuki, Vladan Vuletić ; Science 2013 (link)

  • This isn’t directly tied to neuroscience, but I get really excited about the future of technology when it comes to everything involving computing with light; from silicon photonics to the recent buzz about 5-d Superman memory crystals.. so awesome!

6) Very long-term memories may be stored in the pattern of holes in the perineuronal net Roger Y. Tsien ; PNAS 2013 (link)

  • What better way to dive back into things more brain related than with some wild speculation?! Dr. Tsien is a nobel laureate so I think that means he gets to write papers like this 🙂 Anyway I have heard of different theories about PNN before and this paper seems to add to the mystique surrounding them.

7) Axon position within the corpus callosum determines contralateral cortical projection Jing Zhou, Yunqing Wen, Liang She, Ya-nan Sui, Lu Liu, Linda J. Richards, and Mu-ming Poo ; PNAS 2013 (link)

8) Water diffusion in brain cortex closely tracks underlying neuronal activity Tomokazu Tsurugizawa, Luisa Ciobanu, and Denis Le Bihan ; PNAS 2013 (link)

  • This is really interesting!

9) Correlations in ion channel expression emerge from homeostatic tuning rules Timothy O’Leary, Alex H. Williams, Jonathan S. Caplan, and Eve Marder ; PNAS 2013 (link)

10) Optogenetic dissection reveals multiple rhythmogenic modules underlying locomotion Martin Hägglunda, Kimberly J. Doughertya, Lotta Borgiusa, Shigeyoshi Itoharab, Takuji Iwasatoc, and Ole Kiehna ; PNAS 2013 (link)

11) Transformation of odor selectivity from projection neurons to single mushroom body neurons mapped with dual-color calcium imaging Hao Li, Yiming Li, Zhengchang Lei, Kaiyu Wang, and Aike Guo ; PNAS 2013 (link)

12) The Thalamostriatal Pathway and Cholinergic Control of Goal-Directed Action: Interlacing New with Existing Learning in the Striatum Laura A. Bradfield, Jesus Bertran-Gonzalez, Billy Chieng, and Bernard W. Balleine ; Neuron 2013 (link)

  • How Did the Chicken Cross the Road? With Her Striatal Cholinergic Interneurons, Of Course Geoffrey Schoenbaum, Thomas A. Stalnaker, and Yael Niv ; Neuron 2013 (link)

13) Modular Use of Peripheral Input Channels Tunes Motion-Detecting Circuitry Marion Silies, Daryl M. Gohl, Yvette E. Fisher, Limor Freifeld, Damon A. Clark, and Thomas R. Clandinin ; Neuron 2013 (link)

14) Sparse and Background-Invariant Coding of Vocalizations in Auditory Scenes David M. Schneider and Sarah M.N. Woolley ; Neuron 2013 (link)

15) Contributions of the 12 Neuron Classes in the Fly Lamina to Motion Vision John C. Tuthill, Aljoscha Nern, Stephen L. Holtz, Gerald M. Rubin, and Michael B. Reiser ; Neuron 2013 (link)

16) Sensory Population Decoding for Visually Guided Movements Sonja S. Hohl, Kris S. Chaisanguanthum, and Stephen G. Lisberger ; Neuron 2013 (link)

  • Pursuing the Link between Neurons and Behavior Douglas A. Ruff and Marlene R. Cohen ; Neuron 2013 (link)

17) GluN2B in corticostriatal circuits governs choice learning and choice shifting Jonathan L Brigman, Rachel A Daut, Tara Wright, Ozge Gunduz-Cinar, Carolyn Graybeal, Margaret I Davis, Zhihong Jiang, Lisa M Saksida, Seiichiro Jinde, Matthew Pease, Timothy J Bussey, David M Lovinger, Kazu Nakazawa & Andrew Holmes ; Nature Neuroscience 2013 (link)

18) Sensory cortex limits cortical maps and drives top-down plasticity in thalamocortical circuits Andreas Zembrzycki, Shen-Ju Chou, Ruth Ashery-Padan, Anastassia Stoykova & Dennis D M O’Leary ; Nature Neuroscience 2013 (link)

19) Complementary Roles of the Hippocampus and the Dorsomedial Striatum during Spatial and Sequence- Based Navigation Behavior Ce ́line Fouquet, Be ́ne ́dicte M. Babayan, Aure ́lie Watilliaux, Bruno Bontempi, Christine Tobin, Laure Rondi-Reig ; PLoS ONE 2013 (link)

20) Convergence of Cortical and Sensory Driver Inputs on Single Thalamocortical Cells Alexander Groh, Hajnalka Bokor, Rebecca A. Mease, Viktor M. Plattner, Balázs Hangya, Albrecht Stroh, Martin Deschenes and László Acsády ; Cerebral Cortex 2013 (link)

21) Seamless Reconstruction of Intact Adult-Born Neurons by Serial End-Block Imaging Reveals Complex Axonal Guidance and Development in the Adult Hippocampus Gerald J. Sun, Kurt A. Sailor, Qasim A. Mahmood, Nikhil Chavali, Kimberly M. Christian, Hongjun Song, and Guo-li Ming ; J Neuroscience 2013  (link)

22) Input-Output Features of Anatomically Identified CA3 Neurons during Hippocampal Sharp Wave/Ripple Oscillation In Vitro Norbert Ha ́jos, Ma ́ria R. Karlo ́cai, Bea ́ta Ne ́meth, Istva ́n Ulbert, Hannah Monyer, Ga ́bor Szabo ́, Ferenc Erde ́lyi, Tama ́s F. Freund, and Attila I. Gulya ́s ; J Neuroscience 2013  (link)

23) Layer 4 in Primary Visual Cortex of the Awake Rabbit: Contrasting Properties of Simple Cells and Putative Feedforward Inhibitory Interneurons Jun Zhuang, Carl R. Stoelzel, Yulia Bereshpolova, Joseph M. Huff, Xiaojuan Hei , Jose-Manuel Alonso, and Harvey A. Swadlow ; J Neuroscience 2013  (link)

24) Direct-Pathway Striatal Neurons Regulate the Retention of Decision-Making Strategies Susan M. Ferguson, Paul E. M. Phillips, Bryan L. Roth, Ju ̈rgen Wess, and John F. Neumaier ; J Neuroscience 2013  (link)

25) In Vivo Two-Photon Ca2􏰇 Imaging Reveals Selective Reward Effects on Stimulus-Specific Assemblies in Mouse Visual Cortex Pieter M. Goltstein, Emily B. J. Coffey, Pieter R. Roelfsema, and Cyriel M. A. Pennartz ; J Neuroscience 2013  (link)

26) Proximodistal Segregation of Nonspatial Information in CA3: Preferential Recruitment of a Proximal CA3-Distal CA1 Network in Nonspatial Recognition Memory Nozomu H. Nakamura, Vera Flasbeck, Nicolas Maingret, Takashi Kitsukawa, and Magdalena M. Sauvage ; J Neuroscience 2013  (link)

27) Response Selectivity Is Correlated to Dendritic Structure in Parvalbumin-Expressing Inhibitory Neurons in Visual Cortex Caroline A. Runyan and Mriganka Sur ; J Neuroscience 2013  (link)

28) Two Projection Streams from Macaque V1 to the Pale Cytochrome Oxidase Stripes of V2 Frederick Federer, Delaney Williams, Jennifer M. Ichida, Sam Merlin, and Alessandra Angelucci ; J Neuroscience 2013  (link)

29) Transformation of Receptive Field Properties from Lateral Geniculate Nucleus to Superficial V1 in the Tree Shrew Stephen D. Van Hooser, Arani Roy, Heather J. Rhodes, Julie H. Culp, and David Fitzpatrick ; J Neuroscience 2013  (link)

30) Reevaluation of the Beam and Radial Hypotheses of Parallel Fiber Action in the Cerebellar Cortex Samuel W. Cramer, Wangcai Gao, Gang Chen, and Timothy J. Ebner ; J Neuroscience 2013  (link)

31) Closed-loop optogenetic intervention in mice Caren Armstrong, Esther Krook-Magnuson, Mikko Oijala & Ivan Soltesz ; Nature Protocols 2013 (link)

  • I think this is a valuable paper if not just for the supplementary table that lists all the equipment and vendors for different things important for optogenetics. I highly approve.

Friday Paper List – July 5th

Another summer friday paper list. Hopefully you have been able to get out and enjoy the warm weather even though work might be trying to pull you back in.

Papers below!

1) Deep Cortical Layers Are Activated Directly by Thalamus Christine M. Constantinople and Randy M. Bruno ; Science 2013 (link)

2) Attention enhances synaptic efficacy and the signal-to-noise ratio in neural circuits Farran Briggs, George R. Mangun & W. Martin Usrey ; Nature 2013 (link)

3) Dual-mode operation of neuronal networks involved in left–right alternation Adolfo E. Talpalar, Julien Bouvier, Lotta Borgius, Gilles Fortin, Alessandra Pierani & Ole Kiehn ; Nature 2013 (link)

4) In-vivo single neuron axotomy triggers axon regeneration to restore synaptic density in specific cortical circuits A. J. Canty, L. Huang, J. S. Jackson, G. E. Little, G. Knott, B. Maco & V. De Paola ; Nature Communications 2013 (link)

5) Inhibition of inhibition in visual cortex: the logic of connections between molecularly distinct interneurons Carsten K Pfeffer, Mingshan Xue, Miao He, Z Josh Huang & Massimo Scanziani ; Nature Neuroscience 2013 (link)

6) Optimal control of reaching includes kinematic constraints Michael Mistry, Evangelos Theodorou, Stefan Schaal, and Mitsuo Kawato ; J Neurophysiology 2013 (link)

7) Two-Photon Processor and SeNeCA: a freely available software package to process data from two-photon calcium imaging at speeds down to several milliseconds per frame Jakub Tomek, Ondrej Novak, and Josef Syka ; J Neurophysiology 2013 (link)

8) Contrast Dependence and Differential Contributions from Somatostatin- and Parvalbumin-Expressing Neurons to Spatial Integration in Mouse V1 Hendrikje Nienborg, Andrea Hasenstaub, Ian Nauhaus, Hiroki Taniguchi, Z. Josh Huang, and Edward M. Callaway ; J Neuroscience 2013 (link)

9) Two-Photon Imaging of Nonlinear Glutamate Release Dynamics at Bipolar Cell Synapses in the Mouse Retina Bart G. Borghuis, Jonathan S. Marvin, Loren L. Looger, and Jonathan B. Demb ; J Neuroscience 2013 (link)

10) Mechanisms for Extracting a Signal from Noise as Revealed through the Specificity and Generality of Task Training Dorita H. F. Chang, Zoe Kourtzi, and Andrew E. Welchman ; J Neuroscience 2013 (link)

11) Neural Correlates of Short-Term Memory Reorganization in Humans with Hippocampal Damage Carsten Finke, Hannah Bruehl, Emrah Du ̈zel, Hauke R. Heekeren, and Christoph J. Ploner ; J Neuroscience 2013 (link)

12) Transcranial Alternating Current Stimulation Modulates Large-Scale Cortical Network Activity by Network Resonance Mohsin M. Ali, Kristin K. Sellers, and Flavio Fröhlich ; J Neuroscience 2013 (link)

13) Spatial Stream Segregation by Auditory Cortical Neurons John C. Middlebrooks and Peter Bremen ; J Neuroscience 2013 (link)

14) A Mechanism for Frequency Modulation in Songbirds Shared with Humans Ana Amador and Daniel Margoliash ; J Neuroscience 2013 (link)

15) Heterogeneous Attractor Cell Assemblies for Motor Planning in Premotor Cortex Maurizio Mattia, Pierpaolo Pani, Giovanni Mirabella, Stefania Costa, Paolo Del Giudice, and Stefano Ferraina ; J Neuroscience 2013 (link)

16) Theoretical principles underlying optical stimulation of myelinated axons expressing channelrhodopsin-2 Richard L. Arlowa, Thomas J. Foutza, Cameron C. McIntyrea ; Neuroscience 2013 (link)

Remember it’s important to take a break from reading papers every now and then. So if you can, try to get out and have fun with friends!