Friday Paper List January 25th

I am definitely very behind in my reading list ūüôā

1. Recurrent inhibitory circuitry as a mechanism for grid formation Jonathan J Couey, Aree Witoelar, Sheng-Jia Zhang, Kang Zheng, Jing Ye, Benjamin Dunn, Rafal Czajkowski, May-Britt Moser, Edvard I Moser, Yasser Roudi & Menno P Witter ; Nature Neuroscience 2013 (link)

2. Grid cells require excitatory drive from the hippocampus Tora Bonnevie, Benjamin Dunn, Marianne Fyhn, Torkel Hafting, Dori Derdikman, John L Kubie, Yasser Roudi, Edvard I Moser & May-Britt Moser ; Nature Neuroscience 2013 (link)

One thing that I have been told about as I slowly catch up on hippocampal literature is that Edvard and May-Britt Moser are a bit of a dynamic duo/powerhouse in the field. So it is supposedly common for them to publish multiple high impact articles. There is a short blurb here about the two papers on the website for the Kavli Institute for Systems Neuroscience/Center for the Biology of Memory which they are directors for.

3. Gating of Sensory Input by Spontaneous Cortical Activity Artur Luczak, Peter Bartho, and Kenneth D. Harris ; J. Neuroscience 2013 (link)

4. Spatiotemporal Dynamics of Functional Clusters of Neurons in the Mouse Motor Cortex during a Voluntary Movement Riichiro Hira, Fuki Ohkubo, Katsuya Ozawa, Yoshikazu Isomura, Kazuo Kitamura, Masanobu Kano, Haruo Kasai, and Masanori Matsuzaki ; J. Neuroscience 2013 (link)

5. New Modules Are Added to Vibrissal Premotor Circuitry with the Emergence of Exploratory Whisking Jun Takatoh, Anders Nelson, Xiang Zhou, M. McLean Bolton, Michael D. Ehlers, Benjamin R. Arenkiel, Richard Mooney, and Fan Wang ; Neuron 2013 (link)

6.  Inducing Gamma Oscillations and Precise Spike Synchrony by Operant Conditioning via Brain-Machine Interface Ben Engelhard, Nofar Ozeri, Zvi Israel, Hagai Bergman, and Eilon Vaadia ;  Neuron 2013 (link)

7. Concurrent activation of striatal direct and indirect pathways during action initiation Guohong Cui, Sang Beom Jun, Xin Jin, Michael D. Pham, Steven S. Vogel, David M. Lovinger & Rui M. Costa ; Nature 2013 (link)

Nice commentary on this paper here.

8. LTP requires a reserve pool of glutamate receptors independent of subunit type Adam J. Granger, Yun Shi, Wei Lu, Manuel Cerpas, & Roger A. Nicoll ; Nature 2013 (link)

Nice commentary on this paper here.

9. On-demand optogenetic control of spontaneous seizures in temporal lobe epilepsy Esther Krook-Magnuson, Caren Armstrong, Mikko Oijala & Ivan Soltesz ; Nature Communications 2013 (link)

One can’t help but think about the potential for something like this in medicine, but of course gene therapy is still a work in progress.¬†Then of course there is greater hope that by the time gene therapy is more common in humans we would be able to simply fix the fundamental mechanism responsible for the pathology instead of creating ways to treat the symptoms.

These last two are not “hot off the presses”. They were published in December and just now caught my attention…my selective attention…¬†retrospectively¬†that is… ūüėõ

10. Selective Attention in an Insect Visual Neuron Steven D. Wiederman, and David C. O’Carroll ; Current Biology 2012 (link)

Commentary on this paper here.

11. Cueing Attention after the Stimulus Is Gone Can Retrospectively Trigger Conscious Perception Claire Sergent, Valentin Wyart, Mariana Babo-Rebelo, Laurent Cohen, Lionel Naccache, and Catherine Tallon-Baudry ; Current Biology 2012 (link)

Commentary on this paper here.

I wanted to link a post here from Labrigger, one of my favorite blogs. ¬†The post is about how Henry Markram was just awarded 500,000,000 euros for his Human Brain Project where he is going to simulate a human brain with a giant supercomputer….. yeah….

I think the gif below pretty much sums up how the majority of the neuroscience community feels when asked if

a) this is a good idea

b) this is a smart way to spend the money


c) this will work…

Friday Papers Post: January 18th (posted on Saturday the 19th..sorry)

Busier than I expected this weekend so the post is a little late!

So I guess three weeks in and I already missed my friday deadline… posting at 1am on saturday.. so close..

Anyway enjoy the papers.

1.¬†A polymer-based neural microimplant for optogenetic applications: design and first in vivo study Birthe Rubehn, Steffen B. E. Wolff, Philip Tovote, Andreas Lu Őąthi and Thomas Stieglitz ;¬†Lab on a Chip 2013¬†(link)

I am a sucker for all toys and this one promises to let you do it all. It slices, it dices, it shines light, it delivers drugs, it records neurons, and keeps vegetables fresh for months!

2. Spectral analysis of whisking output via optogenetic modulation of vibrissa cortex in rat R. Pashaie and R. Falk ; Biomedical Optics Express 2013 (link)

Barrel Cortex and Optogenetics – that’s all it takes for me. But seriously this looks interesting.

3.¬†Mice Create What‚ÄďWhere‚ÄďWhen Hippocampus-Dependent Memories of Unique Experiences Laetitia Fellini and Fabio Morellini ;¬†Journal of Neuroscience 2013 (link)

4. Distinct Pathways for Rule-Based Retrieval and Spatial Mapping of Memory Representations in Hippocampal Neurons Rapeechai Navawongse and Howard Eichenbaum ; Journal of Neuroscience 2013 (link)

5. An optimized fluorescent probe for visualizing glutamate neurotransmission Jonathan S Marvin, Bart G Borghuis, Lin Tian, Joseph Cichon, Mark T Harnett, Jasper Akerboom, Andrew Gordus, Sabine L Renninger, Tsai-Wen Chen, Cornelia I Bargmann, Michael B Orger, Eric R Schreiter, Jonathan B Demb, Wen-Biao Gan, S Andrew Hires & Loren L Looger ; Nature Methods 2013 (link)

It’s kind of exciting to imagine a future where we can image everything. Some kind of ideal setup where you are doing high speed imaging capturing the membrane potentials of each cell (voltage sensitive imaging – so a voltage indicator) with indicators for action potentials (calcium imaging/ calcium indicators) and indicators for all of the different neurotransmitters being released. Basically a real time cartoon where you can visualize every single process going on while the brain is functioning. A cool dream for now.

6. Behavioral tagging of extinction learning Jociane de Carvalho Myskiw, Fernando Benetti, and Iván Izquierdo ; PNAS 2013 (link)

7. Layer-specific excitatory circuits differentially control recurrent network dynamics in the neocortex Riccardo Beltramo, Giulia D’Urso, Marco Dal Maschio, Pasqualina Farisello, Serena Bovetti, Yoanne Clovis, Glenda Lassi, Valter Tucci, Davide De Pietri Tonelli & Tommaso Fellin ; Nature Neuroscience 2013 (link)

This paper looks extremely interesting! I can’t wait to read it!

8. The organization of two new cortical interneuronal circuits Xiaolong Jiang, Guangfu Wang, Alice J Lee, Ruth L Stornetta & J Julius Zhu ; Nature Neuroscience 2013 (link)

This paper also not only looks to be extremely interesting but also appears to be a tour de force of patch clamp recording! Really impressive work!

The next three papers are not “hot off the presses” like the others, but rather papers that came up for one reason or another this week and I wanted to share.

9. Automated whole-cell patch-clamp electrophysiology of neurons in vivo Suhasa B Kodandaramaiah, Giovanni Talei Franzesi, Brian Y Chow, Edward S Boyden & Craig R Forest ; Nature Methods 2012 (link)

This paper is a shout out to someone who means a whole lot to me. You know who you are. I’m very proud of you buddy and can’t wait to hear about the amazing things you are doing!

10. Neural signals of extinction in the inhibitory microcircuit of the ventral midbrain Wei-Xing Pan, Jennifer Brown, & Joshua Tate Dudman ; Nature Neuroscience 2013 (link)

I just briefly heard about this paper in a talk. Looks very good and I especially appreciate the clever use of optogenetics to identify cell type specificity in extracellular recordings.

11. An overview of the tasks used to test working memory in rodents. Dudchenko PA; Neuroscience & Biobehavioral Reviews 2004 (link)

I have been meaning to compile a list of all the different memory tasks and what types of memory they aim to test for a while now. It looks like this paper is going to be perfect!

Hopefully next post will be on time.

Friday Paper List: January 10th

Lots of exciting papers below!

1. Cell Type-Specific Inhibitory Inputs to Dendritic and Somatic Compartments of Parvalbumin-Expressing Neocortical Interneuron Hiroyuki Hioki, Shinichiro Okamoto, Michiteru Konno, Hiroshi Kameda, Jaerin Sohn, Eriko Kuramoto, Fumino Fujiyama, and Takeshi Kaneko ; J Neuroscience 2013 (link)

The quest towards cell type specific circuits continues!

2. Neocortical Somatostatin-Expressing GABAergic Interneurons Disinhibit the Thalamorecipient Layer 4 Han Xu, Hyo-Young Jeong, Robin Tremblay, and Bernardo Rudy ; Neuron 2013 (link)

More cell type specificity!

3. Parallel Processing of Environmental Recognition and Locomotion in the Mouse Striatum Hagar G. Yamin, Edward A. Stern, and Dana Cohen ; J Neuro 2013 (link)

Parallel processing streams are exciting. The striatum occupies a bit of a blind spot in my neuro-knowledge so I wanted to add this to my list.

4. Cortico-cortical projections in mouse visual cortex are functionally target specific Lindsey L Glickfeld, Mark L Andermann, Vincent Bonin & R Clay Reid ; Nature Neuroscience 2013 (link)

This is an exciting paper that adds to the exceptional work from Clay Reid using calcium imaging to ask some important basic questions about cortical processing.

This paper asks if the projections to the higher visual areas from V1 are functionally specific or not. They frame the question as having two possibilities (excerpts from the paper and figure below):

1. “One possibility is that the net input from V1 to each target area reflects the diverse visual response tuning of all V1 neurons (Fig. 1a, top). In this model each higher visual area receives the same input, and its functional properties may be determined through local computations. “

2. “Alternatively, V1 may provide functionally distinct input to each downstream area (Fig. 1a, bottom). In this model, these target-specific projections could account for the specialization found in the higher visual areas.”

figure 1A

This paper is a good example of the increase in work being published on the mouse visual system There is a big movement headed up by Dr. Reid and Christof Koch at the Allen Brain Institute called Mindscope. It will be interesting to see how it works out. You can read about Mindscope in a Nature commentary here. Also Dr. Reid and Dr. Kock have been presenting a really great lecture series called, “Coding & Vision 101” ¬†you can check out here!¬†I highly recommend it if you are interested in the visual system and interested in a good general overview.

Speaking of the mouse visual system, there was a great bundle of papers published last year on some functional mapping from the Reid and Callaway labs. It’s kind of funny that the two papers have almost identical titles ūüôā

The editorial, Exploring the Next Frontier of Mouse Vision is here.

Reid lab: Functional Specialization of Mouse Higher Visual Cortical Areas (link)

Callaway lab: Functional Specialization of Seven Mouse Visual Cortical Areas (link)

Anyway, looking forward to reading this paper.

5. Neuronal correlates of visual time perception at brief timescales J. Patrick Mayo, and Marc A. Sommer ; PNAS 2013 (link)

6. Biased Associative Representations in Parietal Cortex Jamie K. Fitzgerald, David J. Freedman, Alessandra Fanini, Sharath Bennur, Joshua I. Gold, and John A. Assad ; Neuron 2013 (link)

John Assad presented a lot of this work and similar studies carried out by David Freedman at last years COSYNE meeting. I think it is really good work and very interesting.

7. Distinct Roles of Medial and Lateral Entorhinal Cortex in Spatial Cognition Tiffany Van Cauter, Jeremy Camon, Alice Alvernhe, Coralie Elduayen, Francesca Sargolini and Etienne Save ; Cerebral Cortex 2013 (link)

8. Functional Microcircuit Recruited during Retrieval of Object Association Memory in Monkey Perirhinal Cortex Toshiyuki Hirabayashi, Daigo Takeuchi, Keita Tamura, and Yasushi Miyashita ; Neuron 2013 (link)

9. Organization of Cortical and Thalamic Input to Pyramidal Neurons in Mouse Motor Cortex Bryan M. Hooks, Tianyi Mao, Diego A. Gutnisky, Naoki Yamawaki, Karel Svoboda, and Gordon M. G. Shepherd ; J Neuro 2013 (link)

Really detailed beautiful exploration of functional connectivity using the channelrhodopsin-2-assisted circuit mapping technique. If you aren’t familiar with this technique it is based on the beautiful caged glutamate mapping that Gordon Shepherd (Jr.) and Karel Svoboda refined, but in many ways even better ūüôā You can read about it from two early papers using the powerful technique here and here.

10. Deconstructing Complexity: Serial Block-Face Electron Microscopic Analysis of the Hippocampal Mossy Fiber Synapse Scott A. Wilke, Joseph K. Antonios, Eric A. Bushong, Ali Badkoobehi, Elmar Malek, Minju Hwang, Masako Terada, Mark H. Ellisman, and Anirvan Ghosh ; J Neuro 2013 (link)

I think this is just an amazing demonstration of some of the future of neuroscience!

11. Feedback Inhibition Enables Theta-Nested Gamma Oscillations and Grid Firing Fields Hugh Pastoll, Lukas Solanka, Mark C.W. van Rossum, and Matthew F. Nolan; Neuron 2013 (link)

This looks very interesting!

12. Brain Reactivity Differentiates Subjects with High and Low Dream Recall Frequencies during Both Sleep and Wakefulness Jean-Baptiste Eichenlaub, Olivier Bertrand, Dominique Morlet and Perrine Ruby ; Cerebral Cortex 2013 (link)

I just thought this sounded neat because dreaming is one of those neat things on the fringe of neuroscience research.

13. In vivo reprogramming of circuit connectivity in postmitotic neocortical neurons¬†Andres De la Rossa, Camilla Bellone, Bruno Golding, Ilaria Vitali, Jonathan Moss, Nicolas Toni, Christian L√ľscher¬†& Denis Jabaudon¬†; Nature Neuroscience 2013¬†(link)

This final paper just looks amazing! I mean WOW! Can we all just step back for a few seconds and look at what this paper actually does?!

The progress being made in genetics from induced pluripotent stem cells to stuff like this just blows my mind. It is an exciting time to be in neuroscience and biological sciences in general!

First Friday Paper List Post

So the tentative plan for the meat of this blog is to have at the least a post every Friday containing a list of papers from the week that caught my attention. Important disclaimer:¬†every week I comb through publications and save the papers that I find interesting and want to read at some point. I have not read all of these papers! (I’m not superhuman). I try my best to read most of the papers¬†eventually, but I usually have a large backlog of unread papers (like the guy in the picture up top). Without further ado, ladies and gentlemen I give you the first¬†Friday Paper List post!

1. PKM-ő∂ is not required for hippocampal synaptic plasticity, learning and memory¬†Lenora J. Volk, Julia L. Bachman, Richard Johnson, Yilin Yu & Richard L. Huganir ;¬†Nature 2013¬†(link)

2. Prkcz null mice show normal learning and memory Anna M. Lee, Benjamin R. Kanter, Dan Wang, Jana P. Lim, Mimi E. Zou, Chichen Qiu, Thomas McMahon, Jahan Dadgar, Sarah C. Fischbach-Weiss & Robert O. Messing ; Nature 2013 (link)

I wanted to start with a brief highlight of the first big neuroscience news story that brought in the new year; which was the “dethroning” of PKM-ő∂ as the “memory molecule”. I was particularly intrigued by these findings because of the connection with my advisor and her work on the subject. Her paper wasn’t as much about asking if PKM-ő∂ was necessary and sufficient for LTP maintenance (this was already published), but instead I think the¬†take-home message from her paper was providing a clear demonstration that LTP was important for storing memories in a behaving animal, or as the paper puts it testing the “maintenance hypothesis”. I think the News and Views article about these two papers does the best job of giving an overview on what these papers do and don’t say, as well as the important new questions they raise. I had a bit more to say about this myself, but I decided to move those ramblings to a separate post.

3. Orienting Towards Ensembles: From Single Cells to Neural Populations Christopher M. Lewis and Andreea E. Lazar ; Journal of Neuroscience 2013 (link)

I like these Journal Club reviews written by graduate students.

4. No Consistent Relationship between Gamma Power and Peak Frequency in Macaque Primary Visual Cortex Xiaoxuan Jia, Dajun Xing, and Adam Kohn ; Journal of Neuroscience 2013 (link)

5. Transsynaptic Tracing with Vesicular Stomatitis Virus Reveals Novel Retinal Circuitry Kevin T. Beier, Bart G. Borghuis, Rana N. El-Danaf, Andrew D. Huberman, Jonathan B. Demb, and Constance L. Cepko ; Journal of Neuroscience 2013 (link)

I think any paper that discovers novel connections is very exciting!

6. Alert Response to Motion Onset in the Retina Eric Y. Chen, Olivier Marre, Clark Fisher, Greg Schwartz, Joshua Levy, Rava Azeredo da Silviera, and Michael J. Berry II ; Journal of Neuroscience 2013 (link)

I think it is pretty amazing that there is so much processing in the retina, so early on in the visual system. Also it would be interesting to see how this might tie in with responses in the superior colliculus.

7. Different Orientation Tuning of Near- and Far-Surround Suppression in Macaque Primary Visual Cortex Mirrors Their Tuning in Human Perception S. Shushruth, Lauri Nurminen, Maryam Bijanzadeh, Jennifer M. Ichida, Simo Vanni, and Alessandra Angelucci ; Journal of Neuroscience 2013 (link)

8. Synchronous and Asynchronous Theta and Gamma Activity during Episodic Memory Formation John F. Burke, Kareem A. Zaghloul, Joshua Jacobs, Ryan B. Williams, Michael R. Sperling, Ashwini D. Sharan, and Michael J. Kahana ; Journal of Neuroscience 2013 (link)

9. What are the mechanisms for analogue and digital signalling in the brain? Dominique Debanne, Andrzej Bialowas & Sylvain Rama ; Nature Reviews Neuroscience 2013 (link)

10. Gating of attentional effort through the central thalamus Nicholas D Schiff, Sudhin A Shah, Andrew E Hudson, Tanya Nauvel, Steven F Kalik, and Keith P Purpura ; Journal of Neurophysiology 2013 (link)

11. High-performance execution of psychophysical tasks with complex visual stimuli in MATLAB Wael F. Asaad, Navaneethan Santhanam, Steven McClellan, and David J. Freedman ; Journal of Neurophysiology 2013 (link)

12. Novel two-alternative forced choice paradigm for bilateral vibrotactile whisker frequency discrimination in head-fixed mice and rats Johannes M. Mayrhofer, Vida Skreb, Wolfger von der Behrens, Simon Musall, Bruno Weber, and Florent Haiss ; Journal of Neurophysiology 2013 (link)

The two papers above are both innovative methodology papers. I get a lot of flack from my peers for being too much of a methods geek. I stand by my belief that methods are extremely important (maybe down the road I’ll make a post where I get on my soapbox about methods) and I’ll certainly be posting more methods papers down the road. Whether or not I post¬†too many is of course up for debate ūüôā

Finally I wanted to post a few more papers that are not exactly “hot off the presses” from this week, but they were very recent and caught my attention. The first is:

13. Visual Stimulation Reverses the Directional Preference of Direction-Selective Retinal Ganglion Cells Michal Rivlin-Etzion, Wei Wei, Marla B. Feller ; Neuron 2012 (link)

I think this is an extremely interesting paper and I’ll quote the paper’s discussion for one reason why, “The signiÔ¨Ācance of these Ô¨Āndings comes in the observation¬†that dynamic circuit interactions can overcome an anatomical¬†bias and change the ultimate computation performed by a¬†neuronal circuit. Indeed, although modern ultrastructural tools¬†provide a wealth of anatomical knowledge of the location of¬†synaptic connections within a circuit, functional connectivity is¬†subject to neuromodulators that control synaptic efÔ¨Ācacy,¬†neuronal dynamics, and excitability (Harris-Warrick and Marder,1991; Bargmann, 2012). Hence, a wiring diagram does not¬†predict the function of a circuit but rather provides a substrate¬†that constrains the possible computations.”¬†

Besides being a clear statement from the authors on the connectome debate , I think this is relevant when considering the results I mentioned earlier from the Lee lab showing how depolarization could create a place cell. It’s interesting to think about how much of a cell’s function is shaped by connectivity versus other properties, and how these are changed and implemented in the brain.

These next few papers all relate to the continued exploration of the different layers of cortex.

14. High-Resolution fMRI Reveals Laminar Differences in Neurovascular Coupling between Positive and Negative BOLD Responses Jozien Goense, Hellmut Merkle, Nikos K. Logothetis ; Neuron 2012 (link)

I was not going to mention the above paper without giving a shout out to the amazing work of Gang Chen a postdoc I had the honor of working with at Vanderbilt. I think he does fantastic work. When I was looking for his paper on the subject, I found out that despite my memory of it being accepted ages ago last year, it officially just came out this month! So here it is below:

15. Layer-specific BOLD activation in awake monkey V1 revealed by ultra-high spatial resolution functional magnetic resonance imaging Gang Chen , Feng Wang, John C. Gore, Anna W. Roe ; NeuroImage 2013 (link)

16. Laminar dependence of neuronal correlations in visual cortex Matthew A Smith, Xiaoxuan Jia, Amin Zandvakili, and Adam Kohn ; Journal of Neurophysiology 2012 (link)

17. Correlated Variability in Laminar Cortical Circuits Bryan J. Hansen, Mircea I. Chelaru, Valentin Dragoi ; Neuron 2012 (link)

As a quick and final aside I recently read and enjoyed:

18. Image sequence reactivation in awake V4 networks Sarah L. Eagleman and Valentin Dragoi PNAS 2012 (link)

but I was under the impression that this Dragoi cited above¬†was the same as the Dragoi who has great work on sequences in hippocampus with Buzsaki…. but now I realize I was completely wrong. The latter is George Dragoi. I was so excited that someone was working across hippocampus and cortex! Too bad it was a mistake ūüôā

Alright first Friday Paper List post is done! 18 papers mentioned (not counting randomly linked ones). Not too shabby. This definitely took a bit longer than I expected, but I think it’s an alright start. I promise things won’t be so lengthy once classes start back up.

As always please please please make comments in the reply thing below! I would really love to get any feedback or thoughts on any of the papers. Plus if there are any papers I missed that just came out and you think are worth mentioning please share!

Highlights of 2012

Everyone and their mom makes one of these Best of The Year lists or something related, so here is my version. Join me in looking back at what I consider some of the highlights from 2012 in neuroscience. As always I will present a numbered list. This is not supposed to be a ranking; I just like lists.

1. The Great Debate

The Great Brain Mapping Debate (Brain Brawl): Tony Movshon versus Sebastian Seung (link)

This was just fantastic. I highly recommend watching the video of this great debate. I had a wonderful time watching this live from my hotel room when I was in Chicago for grad school interviews. You can read some of the articles about this here, here, and here.

2.  Optogenetic activation of an engram!?

Optogenetic stimulation of a hippocampal engram activates fear memory recall Xu Liu, Steve Ramirez, Petti T. Pang, Corey B. Puryear, Arvind Govindarajan, Karl Deisseroth & Susumu Tonegawa ; Nature 2012 (link)


Generation of a Synthetic Memory Trace Aleena R. Garner, David C. Rowland, Sang Youl Hwang, Karsten Baumgaertel, Bryan L. Roth, Cliff Kentros, Mark Mayford ; Science 2012 (link)

 Ok that is certainly a bold description, but I think it is fairly appropriate for both. When these two papers came out I was extremely excited. I think what these papers accomplish represents a pretty big milestone for neuroscience. Of course I favor the Tonegawa manuscript because I have a known weakness for a certain scientific method. You can read about the two papers and how a similar accomplishment was shown in a previous SFN poster in 2009 here (I recommend reading the comments as well).

3. ¬†Zebrafish in the matrix (sort of.. ok not really.. but it’s so cool)

Brain-wide neuronal dynamics during motor adaptation in zebrafish Misha B. Ahrens, Jennifer M. Li, Michael B. Orger, Drew N. Robson, Alexander F. Schier, Florian Engert & Ruben Portugues ; Nature 2012 (link)

My list is dangerously close to becoming a highlight reel from the Nature Action Potential blog and you can certainly read an interesting commentary about this paper from them here. But let me just say I think this might be my favorite paper of the year. What really made this paper special for me was watching the first supplementary movie showing real time motor adaptation as they switch the gain for neural activity controlling the perceived motion. Seeing and hearing the neurons fire while the fish tries to “swim against the current” in order to stay still is really awesome.

4. PV+ neurons and their effect on visual cortex

Activation of specific interneurons improves V1 feature selectivity and visual perception Seung-Hee Lee, Alex C. Kwan, Siyu Zhang, Victoria Phoumthipphavong, John G. Flannery, Sotiris C. Masmanidis, Hiroki Taniguchi, Z. Josh Huang, Feng Zhang, Edward S. Boyden, Karl Deisseroth & Yang Dan ; Nature 2012 (link)


Division and subtraction by distinct cortical inhibitory networks in vivo Nathan R. Wilson, Caroline A. Runyan, Forea L. Wang & Mriganka Sur ; Nature 2012 (link)

even though it didn’t make the 2012 cut these should¬†be considered along with..

Parvalbumin-Expressing Interneurons Linearly Transform Cortical Responses to Visual Stimuli Bassam V. Atallah, William Bruns, Matteo Carandini, and Massimo Scanziani ; Neuron 2011 (link)

How specific subtypes of interneurons are involved in neural function is a question that is going to be asked for a long time. The battle to classify neurons into subtypes is itself an ongoing process (popular 2004 Markram review here). I constantly wonder if the subtypes we can target in optogenetics right now are even all that relevant or specific enough. It seems to be a case of the tail wagging the dog with so many papers looking at specific roles of what has become the holy trinity of genetically targetable subsets: PV+, SOM, and VIP interneurons. But I should save a discussion on neural subtypes for another time. Let me tell you what I liked about these papers. I enjoyed them because they are a perfect example of multiple papers asking almost the exact same questions, using almost the exact same methods getting published at almost the exact same time (sometimes this happens in different journals as you can see above for the engram papers or sometimes in the same journal with a nice little editorial to compare the two). When this happens it creates a wonderful opportunity for comparison. It is especially great when the papers come up with drastically different conclusions! I find it to be a sobering reminder that we are all doing science and sometimes just because results are published in¬†Nature or Science¬†it doesn’t mean the findings are ready to be engraved in stone. Of course there are interesting methodological differences between these three papers – awake verses anesthetized for example; however they still come up with fundamentally different results that anesthesia alone might not explain. ¬†So I think it is fun to question whether the differences are due to preparations and methods or our lack of understanding on another level. Only time will tell.

And again I can’t shake the pesky problem of questioning how specific our subgroups are to begin with. Sorry to beat the dead horse but just keep in mind this question, what does it mean to target PV+ neurons in the first place? How arbitrary are our classifications? Papers such as this one certainly have to be considered when reading these papers.

Ok I tried my best to avoid the subtype classification conundrum… oh well. I promise I’ll try and touch on it again in more detail another time.

5. Primate Optogenetics continues to mature

Saccadic eye movements evoked by optogenetic activation of primate V1 Mehrdad Jazayeri, Zachary Lindbloom-Brown & Gregory D Horwitz ; Nature Neuroscience 2012 (link)

This paper was¬†particularly¬†important to me this year because it was very relevant to some of my own work (shameless plug here). I have several thoughts on this paper as well as the recent influx of primate optogenetic publications that came out this year. I’m going to save that rant for a later post. Below are the other papers that came out involving primate optogenetics. Again, I will write a whole post about these later because I have a pretty long winded rant about the Jazayeri et al. and Cavenaugh et al. papers in particular.

Optogenetically Induced Behavioral and Functional Network Changes in Primates Annelies Gerits, Reza Farivar, Bruce R. Rosen, Lawrence L. Wald, Edward S. Boyden, Wim Vanduffel ; Current Biology 2012 (link)

Optogenetic Inactivation Modifies Monkey Visuomotor Behavior James Cavanaugh, Ilya E. Monosov, Kerry McAlonan, Rebecca Berman, Mitchell K. Smith, Vania Cao, Kuan H. Wang, Edward S. Boyden and Robert H. Wurtz ; Neuron 2012 (link)

In Vivo Optogenetic Control of Striatal and Thalamic Neurons in Non-Human Primates Adriana Galvan, Xing Hu, Yoland Smith,Thomas Wichmann ; PLoS One 2012 (link)

6. Wait.. what makes a Place Cell?

Hippocampal Place Fields Emerge upon Single-Cell Manipulation of Excitability During Behavior Doyun Lee, Bei-Jung Lin, Albert K. Lee ; Science 2012 (link)

So this year also marked the beginning of my diving into the world of hippocampus literature.. just picture that scene where¬†Alice falls down the rabbit hole. The world of place cells, grid cells, head direction cells, episode cells, and phase precession continues to blow my mind with every new paper I read.¬†One of the small joys of playing catch-up in a new field of research literature is starting with the early stuff and moving in chronological order. It’s always great when you read an old paper and think, “Woah that’s amazing! ….but I wonder what would happen if they looked at _______” and then finding a paper a couple years later that asks and answers your exact question!

But back to this paper. Place cells and place fields are a staple of hippocampal literature and I think their discovery is one of the more amazing phenomena in neuroscience research. This paper from the Lee lab¬†(had to have a shameless plug for my friends at the farm) is great because it takes the standard model of what makes a place cell a place cell and completely flips it upside down! In fact the implications and questions this paper raises kind of scares me! I mean.. I can barely wrap my head around what the paper might mean. If all it takes to make a pyramidal cell a “place cell” is to depolarize it a little… then what does that mean about the wiring of the neurons themselves? Do the anatomical connections not matter? Of course they matter, but I just love the questions this paper raises. Definitely an exciting step forward in our attempt to understand the brain.

So this post turned out much longer than I anticipated. I can promise if you think they will all be this long then you should definitely lower your expectations

but hopefully as (and if) I continue to do this blog, posts will improve and become more concise; because the last thing anyone needs is to waste all of their time reading my rants when there are so many papers to catch up on!


What papers did you enjoy this year? What were some of the neuroscience reports that you thought where most interesting? Please please please share at least one of them in the comments!