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	<title>Functional Neurogenesis</title>
	
	<link>http://www.functionalneurogenesis.com/blog</link>
	<description>New neurons in the adult brain. How they work and what they're good for.</description>
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		<title>Forming and recalling memories. Artificially.</title>
		<link>http://feedproxy.google.com/~r/FunctionalNeurogenesis/~3/lZcpzIXSnqw/</link>
		<comments>http://www.functionalneurogenesis.com/blog/2012/03/forming-and-recalling-memories-artificially/#comments</comments>
		<pubDate>Fri, 23 Mar 2012 13:29:54 +0000</pubDate>
		<dc:creator>Jason Snyder</dc:creator>
				<category><![CDATA[memory]]></category>
		<category><![CDATA[reviews of papers]]></category>
		<category><![CDATA[Aleena Garner]]></category>
		<category><![CDATA[c-fos]]></category>
		<category><![CDATA[channelrhodopsin]]></category>
		<category><![CDATA[contextual fear conditioning]]></category>
		<category><![CDATA[contextual fear discrimination]]></category>
		<category><![CDATA[DREADD]]></category>
		<category><![CDATA[hM3Dq]]></category>
		<category><![CDATA[Mark Mayford]]></category>
		<category><![CDATA[optogenetics]]></category>
		<category><![CDATA[susumu tonegawa]]></category>
		<category><![CDATA[xu liu]]></category>

		<guid isPermaLink="false">http://www.functionalneurogenesis.com/blog/?p=1444</guid>
		<description><![CDATA[
Memory manipulation has become one of the most hotly pursued topics in neuroscience. After all, much or of who are is based on what we&#8217;ve learned, including memories that we can consciously recall as well as acquired desires and habits that can lead to problems like addiction. In rodents, we&#8217;ve known for decades that damage to [...]]]></description>
			<content:encoded><![CDATA[<p><span style="float: left; padding: 5px;"><a href="http://www.researchblogging.org"><img alt="ResearchBlogging.org" src="http://www.researchblogging.org/public/citation_icons/rb2_large_gray.png" style="border:0;"/></a></span></p>
<p>Memory manipulation has become one of the most hotly pursued topics in neuroscience. After all, much or of who are is based on what we&#8217;ve learned, including memories that we can consciously recall as well as acquired desires and habits that can lead to problems like addiction. In rodents, we&#8217;ve known for decades that damage to the hippocampus can erase recently-formed memories. Studies of reconsolidation have shown us that when a memory is retrieved it becomes labile and allows for new information to be added, thereby creating an updated version. More recently we (humans) have been able to identify the neurons involved in memory formation and show that killing them, and only them, results in memory erasure. Bringing us even closer to the stuff of movies, studies by <a title="synthetic memory" href="http://www.sciencemag.org/content/335/6075/1513.abstract" target="_self">Garner et al. in Science</a> and <a title="optogenetic recall" href="http://www.nature.com/nature/journal/vnfv/ncurrent/full/nature11028.html" target="_self">Liu et al. in Nature</a> have now artificially controlled memory formation and recall. We&#8217;re essentially talking about reactivating memory by pushing a button. Yes &#8211; you can say &#8220;dude, whoah&#8221; now.<span id="more-1444"></span></p>
<h3><span style="color: #2812ec;">Artificially activating neurons</span></h3>
<p>The two studies use contextual fear conditioning as their test of learning and memory. In this test mice freeze in a place where they previously received a footshock. In order to remember the context where they received a footshock certain genes are expressed in the neurons that encode the memory. Both groups hijacked one of these genes, c-fos, using it to drive expression of either a DREADD or channelrhodopsin, for pharmacological or optogenetic control of neural activity, respectively. The DREADD is a receptor for a molecule that doesn&#8217;t exist naturally in rodents, but when the molecule is injected into the mouse by a mad scientist it binds to the DREADD and causes neurons to fire action potentials kind of like would happen when a neuron is involved in forming or retrieving a memory. Channelrhodopsin also allows a neuron to be selectively activated but it is activated by light. In both studies, these tools served somewhat similar roles &#8211; when mice formed a memory the neurons that were involved in encoding that memory (neurons that express c-fos) became labelled in such a way that they could be selectively activated, artificially, by the mad scientist.</p>
<h3><span style="color: #2812ec;">Creating a &#8220;synthetic&#8221; memory</span></h3>
<p>In the Garner et al. study, when a mouse explored a new context (A) the DREADD was expressed presumably only in those neurons that were involved in forming a memory of context A. The next day they put the mice into a different context, B, and delivered footshocks while also activating those neurons previously involved in forming a memory for context A. This is where things get synthetic. Until now, scientists have played with relationships between memories by getting mice to naturally learn or recall two memories at once. But here Garner et al. are teaching the mice one thing naturally (that context B is scary) while simultaneously, artificially, reactivating a neural circuit that represents a previous memory (of context A).</p>
<p>They note that several outcomes could be predicted: 1) By activating context A neurons when the animals form a fearful memory, the mice could form an association such that they freeze whenever those context A neurons are activated in the future. However, this didn&#8217;t happen &#8211; they did several experiments to show that simply activating context A neurons, or even context B neurons, was not sufficient to evoke fear behavior. 2) Maybe the mice would learn to fear context B normally, since the sensory environment would be the same during both memory formation and retrieval. Again, no &#8211; mice were severely impaired at forming fear memories for context B, indicating that activity in context A neurons either interfered with memory formation or&#8230; 3) The artificial activation of context A neurons become a requisite component of the fearful memory for context B. Indeed, only when the mice were put back in context B (where they were shocked) AND those same context A neurons were activated (just as they were during training) the mice showed high levels of freezing.</p>
<h3><span style="color: #2812ec;">Memory recall, push of a button style</span></h3>
<p>The other study, by Liu et al., is a bit more straightforward to understand and the findings are a bit different. Instead of creating a hybrid memory by co-activating a previous memory (artificially) and a new memory (via experience) as in the Garner study, they used light-activation of channelrhodopsin-expressing neurons to reactivate a context fear memory. By doing this they could reliably cause the mice to freeze in a novel context, suggesting that they could artificially induce memory retrieval.</p>
<h3><span style="color: #2812ec;">Differences in artificial memory recall</span></h3>
<p>The Garner study is interesting proof that neuronal populations that are active during learning, even artificially, become essential for memory recall. The fact that only exposure to the shock context or only artificial activation of the context A neurons was insufficient to induce freezing suggests, to me, that these two components of the memory were somewhat distinct. The dogma that &#8220;neurons that fire together wire together&#8221; would lead one to expect that activation of only a subset of the memory trace would lead to more complete reactivation of the full memory. But perhaps the artificially activated neurons did not fire at the right frequencies or intensities to enable them to become completely integrated.</p>
<p>In contrast, with the optogenetic techniques employed by Liu et al., they were able to sufficiently activate neurons to induce memory recall. This was remarkable because, unlike the DREADD approach used by Garner where presumably <em>all</em> the relevant neurons in the brain could be targeted for reactivation, Liu et al. were probably only able to activate tens or hundreds of neurons due to limited expression of channelrhodopsin in the dentate gyrus of the hippocampus and limited ability of light to penetrate brain tissue and activate those neurons. It could be that CA3, which is downstream of the dentate gyrus, did its job and was able to reactivate the full memory trace from only partial inputs.</p>
<h3><span style="color: #2812ec;">Clues about the dentate gyrus</span></h3>
<p>There are a few other things about the Liu et al. study that are particularly noteworthy to me. The first is that they were able to induce recall of a <em>specific</em> experience by activating dentate gyrus neurons. In their control experiments they showed that freezing could only be induced when activating dentate gyrus neurons that were involved in encoding the fear memory but not neurons involved in encoding an unrelated memory. But some of the leading work in the field has shown that the dentate gyrus <a title="what is the dentate gyrus doing?" href="http://www.functionalneurogenesis.com/blog/2010/05/what-is-the-dentate-gyrus-doing-to-ca3/" target="_self">uses the same cells</a> to encode many different types of experiences (via differences in firing rate). So, if it&#8217;s always the same population of active neurons in the dentate gyrus, how could they show this specificity? Wouldn&#8217;t activation of neurons for the unrelated memory be the same as activating neurons encoding the fear memory? Well, their c-fos-driven channelrhodopsin/YFP turned out to be a useful tool because it&#8217;s expressed in neurons for a long time after memory formation, unlike the endogenous c-fos whose expression decays to baseline levels after a couple of hours. They were then able to exploit these differential timecourses to show that two distinct experiences were in fact encoded by two distinct populations of neurons. This was not at all the take home message of the paper but, as an aside, provides some strong evidence that our knowledge about how information is processed by the dentate gyrus incomplete.</p>
<h3><span style="color: #2812ec;">Optogenetic controls. Thank you.</span></h3>
<p>The other aspect of the Liu et al. paper I really liked was the controls. Optogenetics is new, powerful and has already produced many major discoveries. But many are outside of my area of expertise and most have not yet been replicated and so I can&#8217;t help but be a little cautious of the validity of these findings. This was how I felt upon seeing <a title="optogenetic memory recall at sfn / brain windows" href="http://brainwindows.wordpress.com/2009/09/18/optogenetic-induction-of-memory-recall/" target="_self">similar findings</a> presented at SfN way back in 2009 &#8211; cool, but really? The specificity of the induced recall (discussed above), the requisite lack of effect of light in the absence of channelrhodopsin, the fact that activating more neurons with bilateral light delivery enhanced recall, and the fact that activating <em>fewer</em> neurons (but neurons more closely linked to the fear memory) also enhanced artificial recall all bolster the claims and the validity of the method, for me. Cool stuff.</p>
<h3><span style="color: #2812ec;">What&#8217;s next? </span></h3>
<p>Can we implant a memory that doesn&#8217;t exist? Could a population of hippocampal neurons be identified, a priori, that represent a context to be learned in the future? And if you pair activity in those neurons with activity in the amygdala could you elicit fearful behaviour of a context even when nothing dangerous has ever happened there? The answer is probably yes. But it will still be pretty cool (for our grandchildren) to see it demonstrated.</p>
<p style="text-align: center;">&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;</p>
<p><em><strong>Postscript</strong></em> &#8211; be sure to check out <a title="action potential coverage" href="http://blogs.nature.com/actionpotential/2012/03/fear-of-the-light.html" target="_self">coverage</a> of the Liu study over at Nature&#8217;s Action Potential blog. Interesting because of the science but also because it gives a glimpse of the publication process &#8211; what did the reviewers think of the paper? How is it that the Garner and Liu studies were published in Science and Nature on the same day? Do Science and Nature&#8230;.talk to each other?? They have the answer.</p>
<p style="text-align: center;">&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;</p>
<p><span class="Z3988" title="ctx_ver=Z39.88-2004&#038;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&#038;rft.jtitle=Science&#038;rft_id=info%3A%2F10.1126%2Fscience.1214985&#038;rfr_id=info%3Asid%2Fresearchblogging.org&#038;rft.atitle=Generation+of+a+Synthetic+Memory+Trace&#038;rft.issn=&#038;rft.date=2012&#038;rft.volume=&#038;rft.issue=&#038;rft.spage=1513&#038;rft.epage=1516&#038;rft.artnum=http%3A%2F%2Fwww.sciencemag.org%2Fcontent%2F335%2F6075%2F1513.abstract&#038;rft.au=Aleena+R.+Garner&#038;rft.au=David+C.+Rowland&#038;rft.au=Sang+Youl+Hwang&#038;rft.au=Karsten+Baumgaertel&#038;rft.au=Bryan+L.+Roth&#038;rft.au=Cliff+Kentros&#038;rft.au=Mark+Mayford&#038;rfe_dat=bpr3.included=1;bpr3.tags=Neuroscience%2CBehavioral+Neuroscience">Aleena R. Garner, David C. Rowland, Sang Youl Hwang, Karsten Baumgaertel, Bryan L. Roth, Cliff Kentros, &#038; Mark Mayford (2012). Generation of a Synthetic Memory Trace <span style="font-style: italic;">Science</span>, 1513-1516 : <a rev="review" href="10.1126/science.1214985">10.1126/science.1214985</a></span></p>
<p><span class="Z3988" title="ctx_ver=Z39.88-2004&#038;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&#038;rft.jtitle=Nature&#038;rft_id=info%3A%2F10.1038%2Fnature11028&#038;rfr_id=info%3Asid%2Fresearchblogging.org&#038;rft.atitle=Optogenetic+stimulation+of+a+hippocampal+engram+activates+fear+memory+recall&#038;rft.issn=&#038;rft.date=2012&#038;rft.volume=&#038;rft.issue=&#038;rft.spage=&#038;rft.epage=&#038;rft.artnum=&#038;rft.au=Xu+Liu&#038;rft.au=Steve+Ramirez&#038;rft.au=Petti+T.+Pang&#038;rft.au=Corey+B.+Puryear&#038;rft.au=Arvind+Govindarajan&#038;rft.au=Karl+Deisseroth&#038;rft.au=Susumu+Tonegawa&#038;rfe_dat=bpr3.included=1;bpr3.tags=Neuroscience%2CBehavioral+Neuroscience">Xu Liu, Steve Ramirez, Petti T. Pang, Corey B. Puryear, Arvind Govindarajan, Karl Deisseroth, &#038; Susumu Tonegawa (2012). Optogenetic stimulation of a hippocampal engram activates fear memory recall <span style="font-style: italic;">Nature</span> : <a rev="review" href="10.1038/nature11028">10.1038/nature11028</a></span></p>
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		<slash:comments>10</slash:comments>
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		<item>
		<title>Google Scholar vs. Scopus &amp; Web of Science</title>
		<link>http://feedproxy.google.com/~r/FunctionalNeurogenesis/~3/mYJLMhHPzFo/</link>
		<comments>http://www.functionalneurogenesis.com/blog/2012/02/google-scholar-vs-scopus-web-of-science/#comments</comments>
		<pubDate>Thu, 01 Mar 2012 03:36:11 +0000</pubDate>
		<dc:creator>Jason Snyder</dc:creator>
				<category><![CDATA[the act of doing science]]></category>
		<category><![CDATA[citations]]></category>
		<category><![CDATA[google scholar]]></category>
		<category><![CDATA[scopus]]></category>
		<category><![CDATA[web of science]]></category>

		<guid isPermaLink="false">http://www.functionalneurogenesis.com/blog/?p=1423</guid>
		<description><![CDATA[A couple of interesting correspondences (here and here) just appeared in Nature on the legitimacy of Google Scholar for tracking citations. Interesting because I&#8217;ve recently been pondering the same issue but came up with the opposite conclusion, namely that Google Scholar is actually a better tool for tracking citations than either Scopus or Web of [...]]]></description>
			<content:encoded><![CDATA[<p style="text-align: left;"><img class="aligncenter size-full wp-image-1422" title="citation-battle" src="http://www.functionalneurogenesis.com/blog/wp-content/uploads/2012/02/citation-battle.jpg" alt="citation-battle" width="525" height="142" />A couple of interesting correspondences (<a href="http://www.nature.com/nature/journal/v483/n7387/full/483036c.html" target="_self">here</a> and <a href="http://www.nature.com/nature/journal/v483/n7387/full/483036d.html" target="_self">here</a>) just appeared in Nature on the legitimacy of Google Scholar for tracking citations. Interesting because I&#8217;ve recently been pondering the same issue but came up with the opposite conclusion, namely that Google Scholar is actually a better tool for tracking citations than either Scopus or Web of Science (and not only because it&#8217;s a pain to access the latter two).</p>
<p>The main concern by the authors is that citations for a given article are higher in Google Scholar than Scopus or Web of Science (well, one mainly focusses on the fact that they&#8217;re <em>different</em>). Higher because they include theses, patents, websites etc. Maybe also false positives.</p>
<p>I started thinking about this issue when I began applying for jobs. I didn&#8217;t have any fancy papers and so, for people outside of my field, noting the number of citations in my CV seemed like a decent way to make the point that some of these articles have had an impact. As I sent my applications I&#8217;d go back to Web of Science and check for the latest numbers and, this past year, I noticed that citations of some of my articles suddenly increased by up to 20%. Yay! But then I&#8217;d check the next day and they were low again (perhaps relating to <a href="http://wokinfo.com/wok5/faq/" target="_self">changes in how citations were detected</a>). So there was some glitch and I certainly didn&#8217;t want to appear to be inflating the numbers so I turned to Google Scholar. The numbers were higher, but consistent. For the most part the citations seemed completely legitimate as well.</p>
<p>So why were Google Scholar&#8217;s citation counts higher? Looking at my <a title="neurogenesis LTM citations" href="http://scholar.google.ca/scholar?oi=bibs&amp;hl=en&amp;cites=8161534014774224093" target="_self">most cited paper</a>, which has been cited 367 times (Google Scholar) or 267 times (Web of Science) or 287 times (Scopus) I found that Google Scholar included 11 Chinese articles, 10 book chapters, 15 theses, 4 patents, 1 blog (yours truly), 1 grant application, and 6 mysteries. Eliminating these 48 still leaves 319. Quite a bit higher than Web of Science and Scopus, probably because Google counts citations from articles that are still in press (my Neurobiology of Aging paper was published online but &#8220;in press&#8221; for 23 months, during which citations could be tracked in Scholar but not Web of Science). This is probably also why Google Scholar counts 17 citations (16 &#8220;normal&#8221;) of my <a title="neurogenesis stress citations" href="http://scholar.google.ca/scholar?oi=bibs&amp;hl=en&amp;cites=8553431071474251938" target="_self">most recent paper</a> whereas Web of Science only counts 9 &#8211; many of these citing articles were recently published.</p>
<p>So should Chinese articles be excluded? Are book chapters irrelevant? Theses, well, no one reads theses so maybe there&#8217;s a bit of inflation there. I do think it&#8217;s a sign of impact when a blog, grant, or patent refers to your paper and believe that these things <em>should</em> be included in the citation counts (Google still isn&#8217;t great in this regard &#8211; I know of several blog posts on my papers that haven&#8217;t been detected by Google).</p>
<p>These are the reasons I specifically decided to use Google Scholar when adding citation counts to my CV. And so it&#8217;s funny to read about the &#8220;<span style="color: #000000; font-family: arial, helvetica, clean, sans-serif; font-size: 13px; line-height: 19px;">limitations of Google Scholar&#8217;s personalized citation reports&#8221; and how </span>&#8220;I <span style="color: #000000; font-family: arial, helvetica, clean, sans-serif; font-size: 13px; line-height: 19px;">would not recommend using the reports for decisions that could affect careers&#8221;.</span></p>
<p>(for what it&#8217;s worth I did get a job, though clearly it&#8217;s all downhill from here)</p>
<p><span style="color: #000000; font-family: arial, helvetica, clean, sans-serif; font-size: 13px; line-height: 19px;"><br />
</span></p>
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		<slash:comments>6</slash:comments>
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		<item>
		<title>The White House wants your thoughts on open access to scientific publications! Deadline January 12!</title>
		<link>http://feedproxy.google.com/~r/FunctionalNeurogenesis/~3/Fi_YtRJkOGg/</link>
		<comments>http://www.functionalneurogenesis.com/blog/2012/01/the-white-house-wants-your-thoughts-on-open-access-to-scientific-publications-deadline-january-12/#comments</comments>
		<pubDate>Wed, 11 Jan 2012 16:25:45 +0000</pubDate>
		<dc:creator>Jason Snyder</dc:creator>
				<category><![CDATA[open science]]></category>
		<category><![CDATA[open access]]></category>

		<guid isPermaLink="false">http://www.functionalneurogenesis.com/blog/?p=1412</guid>
		<description><![CDATA[Do you live on planet earth? Then you probably pay taxes. And if you pay taxes then you&#8217;re supporting scientific research. Thanks a lot &#8211; that&#8217;s really great. Thanks to you scientists can make discoveries that lead to cures for diseases. And we&#8217;d really love to share these discoveries with you&#8230;but you can&#8217;t afford them.
There [...]]]></description>
			<content:encoded><![CDATA[<p>Do you live on planet earth? Then you probably pay taxes. And if you pay taxes then you&#8217;re supporting scientific research. Thanks a lot &#8211; that&#8217;s really great. Thanks to you scientists can make discoveries that lead to cures for diseases. And we&#8217;d really love to share these discoveries with you&#8230;but you can&#8217;t afford them.</p>
<p>There are lots of problems with the way scientific findings are communicated but this is perhaps the saddest one. The public pays for scientific research and then is charged again to read the results. People who do not have access to massive library holdings simply cannot access scholarly publications. Many scientists themselves cannot even access the papers they need because their institution cannot afford the subscriptions.</p>
<p>Fortunately, things are changing. For example, the National Institutes of Health requires that all federally-funded research be deposited into <a title="Pubmed Central overview" href="http://www.ncbi.nlm.nih.gov/pmc/about/intro/" target="_self">Pubmed Central</a> where it is freely available to the public within 12 months of publication (this allows publishers to still make money off the article for a while, which is very kind of the US government). Another example is the new publishing model put forth by PLoS One and other journals, where the authors pay a fee that covers the costs of publication, archiving etc. Then the articles are made freely available to all because subscriptions are not needed to cover costs.</p>
<p>The way things are going, it is only a matter of time before scholarly publications and scientific information becomes freely communicated to those that paid for it. How long this transformation will take is the big question and there are two big movements in the US government that will play a big role. Two big movements that need your input.</p>
<p>First, there&#8217;s the <strong><a href="Research Works Act" target="_self"><strong style="font-weight: bold;">The Research Works Act</strong></a></strong>, a bill that, if turned into law, would prevent the open dissemination of scholarly articles. It would be a major step backwards. The Research Works Act would end Pubmed Central. It would dramatically slow down the pace and effectiveness of science. It&#8217;s put forth by members of congress who receive donations from publishers (e.g. Elsevier) that make massive profits off of taxpayer-funded scientific publications. Essentially, it wants to protect an outdated business model at the expense of education, scientific progress, human health, the environment, the economy, or anything else that benefits from the results of scientific research. See below for more information on the Research Works Act and, if you think it needs to be stopped, contact your representatives asap. If you&#8217;re not American you can still contact Representatives Issa and Maloney, who are sponsoring it. Many are also pushing scientists to contact their professional societies and university presses which are often in favor of preventing open access, for example through their membership with the American Association of Publishers (see <a href="http://www.michaeleisen.org/blog/?p=837" target="_self">here</a> and <a href="http://cameronneylon.net/blog/update-on-publishers-and-sopa-time-for-scholarly-publishers-to-disavow-the-aap/" target="_self">here</a>).</p>
<p>The second big thing, which must be related, is that the White House has put out a <a style="font-weight: bold;" href="http://www.federalregister.gov/articles/2011/11/04/2011-28623/request-for-information-public-access-to-peer-reviewed-scholarly-publications-resulting-from" target="_self">Request for Information</a>, seeking input on how to promote open access to scholarly publications. Do you think it&#8217;s important for scientific information to be easily and freely available to all? If so, you now have a chance to offer feedback that could directly impact legislation on the topic. But you have to respond by Jan. 12. Apparently this Request for Information was extended an additional 10 days because the only input received was from for-profit publishers with no input coming from scientists themselves.</p>
<p style="text-align: center;">&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;-</p>
<p>Below is a list of links to the official US government sites for the Research Works Act and the open access RFI, people&#8217;s answers to the request for information, and sample letters to the representatives sponsoring the Research Works Act. Check them out:</p>
<p><a href="Research Works Act" target="_self"><strong>The Research Works Act</strong></a> proposed by Representatives Issa and Maloney.</p>
<p><strong>The White House <a href="http://www.federalregister.gov/articles/2011/11/04/2011-28623/request-for-information-public-access-to-peer-reviewed-scholarly-publications-resulting-from" target="_self">Request for Information</a></strong> on public access to scientific publications (and <a href="http://www.whitehouse.gov/blog/2011/12/21/extended-deadline-public-access-and-digital-data-rfis" target="_self">update</a> on the deadline extension plus link to related RFI on the management of digital data)</p>
<p>Kevin Zelnio&#8217;s <a href="http://blogs.scientificamerican.com/evo-eco-lab/2012/01/06/scientists-fight-for-access/" target="_self">passionate post</a> urging scientists to get off their butts and do something about this. This is the first I read on the topic and what got me motivated to actually do something.</p>
<p>Michael Eisen&#8217;s <a href="http://www.michaeleisen.org/blog/?p=807" target="_self">post</a> on Elsevier&#8217;s financial contributions to Rep. Maloney, who is putting forth the Research Works Act. His follow-up <a href="http://www.michaeleisen.org/blog/?p=807#comment-52065" target="_self">comment</a> comparing publishers to obstetricians is great.</p>
<p>Heather Piwowar&#8217;s <a href="http://researchremix.wordpress.com/2012/01/07/rwa-job-losses/" target="_self">analysis</a> of whether the Research Works Act protects jobs or is just fear mongering.</p>
<p>Cameron Neylon&#8217;s <a href="http://cameronneylon.net/blog/ip-contributions-to-scientific-papers-by-publishers-an-open-letter-to-rep-maloney-and-issa/" target="_self">open letter</a> to Representatives Issa and Maloney on the misguided idea that journals add value to articles which then needs to be protected as intellectual property, his <a href="https://plus.google.com/109191289222453878220/posts/YcCfzguqGA2" target="_self">note</a> that the public pays for science not 2 but 3 or 4 no wait 5 times over, and <a href="https://docs.google.com/document/d/1SfwUrb5vK2o4IWfVMbMP79nM-mpIVh7oZ1_H4jKkHz8/edit" target="_self">his response</a> to the RFI on public access to scientific publications.</p>
<p>Bjorn Brembs&#8217; <a href="http://bjoern.brembs.net/news.php?extend.818" target="_self">response</a> to the RFI on public access to scientific publications.</p>
<p>John Dupuis&#8217; very thorough list of <a href="http://scienceblogs.com/confessions/2012/01/around_the_web_some_posts_on_t_1.php" target="_self">links</a> on the Research Works Act.</p>
<p>A thorough list of links and thoughts in Peter Suber&#8217;s <a href="https://plus.google.com/109377556796183035206/posts/QYAH1jSJG6L" target="_self">Google+ post</a>.</p>
<img src="http://feeds.feedburner.com/~r/FunctionalNeurogenesis/~4/Fi_YtRJkOGg" height="1" width="1"/>]]></content:encoded>
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		<item>
		<title>Astrocytes: a story in pictures. Ok, just a bunch of pictures.</title>
		<link>http://feedproxy.google.com/~r/FunctionalNeurogenesis/~3/7dV2H6AuTps/</link>
		<comments>http://www.functionalneurogenesis.com/blog/2011/12/astrocytes-a-story-in-pictures-ok-just-a-bunch-of-pictures/#comments</comments>
		<pubDate>Tue, 13 Dec 2011 15:07:05 +0000</pubDate>
		<dc:creator>Jason Snyder</dc:creator>
				<category><![CDATA[pretty photos]]></category>
		<category><![CDATA[blood vessels]]></category>
		<category><![CDATA[fluorescent images]]></category>
		<category><![CDATA[GFAP]]></category>
		<category><![CDATA[histology]]></category>
		<category><![CDATA[immunohistochemistry]]></category>
		<category><![CDATA[thymidine kinase]]></category>

		<guid isPermaLink="false">http://www.functionalneurogenesis.com/blog/?p=1402</guid>
		<description><![CDATA[
One trick on the confocal microscope is to use a larger pinhole so that a greater thickness of the section is captured in the image. Images acquired this way are comparable to a bunch of thin sections that are then merged into a &#8220;z-stack&#8221; except that some of the tissue is out of focus, giving [...]]]></description>
			<content:encoded><![CDATA[<p><a href="http://www.flickr.com/photos/functionalneurogenesis/6485389563/sizes/l/in/photostream/"><img class="aligncenter" title="Flowing GFAP" src="http://farm8.staticflickr.com/7002/6485389563_90257b17db.jpg" alt="" width="500" height="500" /><br />
</a>One trick on the confocal microscope is to use a larger pinhole so that a greater thickness of the section is captured in the image. Images acquired this way are comparable to a bunch of thin sections that are then merged into a &#8220;z-stack&#8221; except that some of the tissue is out of focus, giving rise to the blurry &#8220;rushing water&#8221; look that you see here.<br />
<span id="more-1402"></span></p>
<p><a href="http://www.flickr.com/photos/functionalneurogenesis/6485419029/sizes/l/in/photostream/"><img class="aligncenter" title="third ventricle" src="http://farm8.staticflickr.com/7145/6485419029_32b8cdaa6d.jpg" alt="" width="500" height="500" /></a></p>
<p>The third ventricle. Serious stuff.</p>
<p><a href="http://www.flickr.com/photos/functionalneurogenesis/6472541823/sizes/l/in/photostream/"><img class="aligncenter" title="at the hippocampal fissue" src="http://farm8.staticflickr.com/7013/6472541823_7a14b81119.jpg" alt="" width="500" height="500" /></a></p>
<p>An ultrasaturated look at the hippocampal fissure. Usually I&#8217;m not a fan of oversaturated neuro pix because strong signal is blown out and detail is lost. The converse, however, is that the faint signal become more visible and detail is gained. Need to work on some <a title="hdr" href="http://en.wikipedia.org/wiki/High_dynamic_range_imaging" target="_self">high dynamic range</a> solution which would give the best of both worlds.</p>
<p style="text-align: center;"><a href="http://www.flickr.com/photos/functionalneurogenesis/6467436623/sizes/l/in/photostream/"><img class=" aligncenter" title="clutching" src="http://farm8.staticflickr.com/7157/6467436623_ed93c59658.jpg" alt="clutching" width="500" height="481" /></a></p>
<p style="text-align: center;">If GFAP was a catcher&#8217;s mitt then, uhh, cell nuclei would be&#8230;</p>
<p><a href="http://www.flickr.com/photos/functionalneurogenesis/6485416041/sizes/l/in/photostream/"><img class="aligncenter" title="third ventricle pt2" src="http://farm8.staticflickr.com/7009/6485416041_5f291975a4.jpg" alt="" width="500" height="500" /></a></p>
<p>Dorsal third ventricle. Seriousness continues. This thing could eat you.</p>
<p style="text-align: center;"><a href="http://www.flickr.com/photos/functionalneurogenesis/6463677657/sizes/l/in/photostream/"><img class="aligncenter" title="intense detail" src="http://farm8.staticflickr.com/7002/6463677657_ea7a50aff4.jpg" alt="" width="500" height="500" /></a></p>
<p style="text-align: center;">Check out the <a href="http://www.flickr.com/photos/functionalneurogenesis/6463677657/sizes/o/in/photostream/" target="_self">highest resolution version</a> of this and imagine falling in. You&#8217;re dead.</p>
<p><a href="http://www.flickr.com/photos/functionalneurogenesis/6485377151/sizes/l/in/photostream/"><img class="aligncenter" title="with ectopic young neurons" src="http://farm8.staticflickr.com/7169/6485377151_c5d71368ab.jpg" alt="" width="500" height="500" /></a></p>
<p>Not quite as impressive but illustrates something I&#8217;ve observed periodically in mice but never in rats: newborn neurons (in red) in the molecular layer.</p>
<p style="text-align: center;"><a href="http://www.flickr.com/photos/functionalneurogenesis/6328239006/sizes/l/in/photostream/"><img class="aligncenter" title="with red granule cells" src="http://farm7.staticflickr.com/6240/6328239006_6ab9612351.jpg" alt="" width="500" height="500" /></a></p>
<p style="text-align: center;">An argument against the conventional red, green and blue color scheme of histological imagery.</p>
<p><a href="http://www.flickr.com/photos/functionalneurogenesis/5928301834/sizes/l/in/photostream/"><img class="aligncenter" title="dentate gyrus, with blood vessel" src="http://farm7.staticflickr.com/6018/5928301834_63c08c85c8.jpg" alt="" width="500" height="500" /></a></p>
<p>An argument for the conventional red, green and blue color scheme of histological imagery. (Check out all the radial cell processes extending through the lower blade of the dentate gyrus. Red = thymidine kinase)</p>
<p style="text-align: center;"><a href="http://www.flickr.com/photos/functionalneurogenesis/5934613930/sizes/l/in/photostream/"><img class="aligncenter" title="blood vessel" src="http://farm7.staticflickr.com/6134/5934613930_448fb06ed9.jpg" alt="" width="500" height="500" /></a></p>
<p style="text-align: center;">The blood vessel from the above image, bigger.</p>
<p><a href="http://www.flickr.com/photos/functionalneurogenesis/6463700285/sizes/l/in/photostream/"><img class="aligncenter" title="more blood vessels" src="http://farm8.staticflickr.com/7175/6463700285_d6c17f1c2f.jpg" alt="" width="500" height="500" /></a></p>
<p>A transverse cut through two blood vessels (in contrast to the parallel cut, above). Where&#8217;s Waldo fans: find the catcher&#8217;s mitt cell in this picture.</p>
<p>More images on <a title="functional neurogenesis on Flickr" href="http://www.flickr.com/photos/functionalneurogenesis/" target="_self">Flickr</a>.</p>
<img src="http://feeds.feedburner.com/~r/FunctionalNeurogenesis/~4/7dV2H6AuTps" height="1" width="1"/>]]></content:encoded>
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		<title>Can you enjoy a good cup of coffee in the thick of experimenting?</title>
		<link>http://feedproxy.google.com/~r/FunctionalNeurogenesis/~3/GSlxXTkmrJY/</link>
		<comments>http://www.functionalneurogenesis.com/blog/2011/11/can-you-enjoy-a-good-cup-of-coffee-in-the-thick-of-experimenting/#comments</comments>
		<pubDate>Sat, 26 Nov 2011 15:40:33 +0000</pubDate>
		<dc:creator>Jason Snyder</dc:creator>
				<category><![CDATA[the act of doing science]]></category>

		<guid isPermaLink="false">http://www.functionalneurogenesis.com/blog/?p=1395</guid>
		<description><![CDATA[More specifically,
Can you enjoy a good cup of coffee when you have 8 straight hours of experimenting with maximum 10 minute breaks here and there but it takes you 5 minutes just to get to the lab kitchen from the behavior space let alone make a coffee and get back in time and you can&#8217;t make a [...]]]></description>
			<content:encoded><![CDATA[<p>More specifically,</p>
<p>Can you enjoy a good cup of coffee when you have 8 straight hours of experimenting with maximum 10 minute breaks here and there but it takes you 5 minutes just to get to the lab kitchen from the behavior space let alone make a coffee and get back in time and you can&#8217;t make a coffee at home and bring it in a thermos or travel mug (which would be room temperature (the worst temperature for enjoying coffee) by the time you wanted it nay NEEDED it) because those items have already been moved to Canada where you&#8217;ll also soon be moving which explains why you couldn&#8217;t do these experiments according to a more relaxed schedule but instead have to get as much done as is humanly possible in the few weeks that remain?</p>
<p>SO? CAN YOU?</p>
<p>Yes:<img class="aligncenter size-full wp-image-1396" title="ultrapure vacuum filtered coffee" src="http://www.functionalneurogenesis.com/blog/wp-content/uploads/2011/11/iced-coffee.jpg" alt="ultrapure vacuum filtered coffee" width="500" height="375" /></p>
<p>*<span style="font-size:x-small;">Stay tuned for &#8220;Can you enjoy a good meal when you have 8 straight hours of experimenting with maximum 10 minute breaks here and there but it takes you 5 minutes just to get to the lab kitchen from the behavior space let alone make a meal and get back in time and you can&#8217;t make a meal at home and bring it in a thermos or travel mug because it would lose its form upon being stuffed into a drinking vessel but then why are you so hung up on appearances stop being so superficial and just stuff it in a thermos.&#8221;</span></p>
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		<item>
		<title>Saving the best for last: neurogenesis, plasticity and memory. #SFN11</title>
		<link>http://feedproxy.google.com/~r/FunctionalNeurogenesis/~3/6zaj4Jjy0ss/</link>
		<comments>http://www.functionalneurogenesis.com/blog/2011/11/saving-the-best-for-the-end-neurogenesis-plasticity-and-memory-sfn11/#comments</comments>
		<pubDate>Thu, 17 Nov 2011 05:19:46 +0000</pubDate>
		<dc:creator>Jason Snyder</dc:creator>
				<category><![CDATA[memory]]></category>
		<category><![CDATA[plasticity]]></category>
		<category><![CDATA[acsf-ltp]]></category>
		<category><![CDATA[circuits]]></category>
		<category><![CDATA[frankland]]></category>
		<category><![CDATA[gaba]]></category>
		<category><![CDATA[ge]]></category>
		<category><![CDATA[gu]]></category>
		<category><![CDATA[Hen]]></category>
		<category><![CDATA[kheirback]]></category>
		<category><![CDATA[mossy fiber]]></category>
		<category><![CDATA[niibori]]></category>
		<category><![CDATA[nmda]]></category>
		<category><![CDATA[nr2b]]></category>
		<category><![CDATA[optogenetics]]></category>
		<category><![CDATA[SFN]]></category>
		<category><![CDATA[synaptic plasticity]]></category>

		<guid isPermaLink="false">http://www.functionalneurogenesis.com/blog/?p=1375</guid>
		<description><![CDATA[
Previously, I wrote about new SFN data on the role for newborn neurons in regulating emotion. The second half of the SFN meeting rounded out the story because the bulk of the functional presentations focussed on the role of new neurons in that other, classic function of the hippocampus: memory. Spanning synaptic plasticity, circuit function, [...]]]></description>
			<content:encoded><![CDATA[<p><img class="aligncenter size-full wp-image-1376" title="blue dcx" src="http://www.functionalneurogenesis.com/blog/wp-content/uploads/2011/11/blue-dcx.jpg" alt="blue dcx" width="500" height="171" /></p>
<p>Previously, I wrote about new SFN data on the role for newborn neurons in regulating emotion. The second half of the SFN meeting rounded out the story because the bulk of the functional presentations focussed on the role of new neurons in that other, classic function of the hippocampus: memory. Spanning synaptic plasticity, circuit function, and then linking it all to behavior, we have quite a complete story here.</p>
<p><span style="color: #ff0000;"><em><strong>SYNAPTIC PLASTICITY IN YOUNG NEURONS</strong></em></span></p>
<p>Every time I get worked up about all various neurogenesis findings I think about one acronym that returns me to a state of inner peace: ACSF-LTP. Yes, I plagiarized that last line from my <a title="Neurogenesis and the septotemporal axis at #SFN11" href="http://www.functionalneurogenesis.com/blog/2011/11/neurogenesis-and-the-septotemporal-axis-at-sfn11/" target="_self">previous post</a>. We all know about LTP right? The ability of synapses to strengthen their connections in response to activity? It has been used for decades as a physiological model of memory formation. It&#8217;s pretty well accepted that newborn neuron ACSF-LTP is a unique form of LTP &#8211; one that is insensitive to GABAergic inhibition (hence &#8220;Artificial Cerebro Spinal Fluid&#8221; LTP, in contrast to LTP that also requires inhibition of GABA neurotransmission), one that requires a the NR2B subunit of the NMDA receptor, and one that is induced more easily than that of mature neurons. ACSF-LTP has quite a history:</p>
<ol>
<li>It was first <a title="Heterogenous properties of dentate granule neurons in the adult rat" href="http://www.newneuron.com/uploads/publications/article2.pdf" target="_self">shown</a> by Sabrina Wang in Martin Wojtowicz&#8217;s lab back in 2000. The first demonstration of a unique functional role for new neurons. That work was done in single neurons from rat, by patch clamping.</li>
<li>I <a title="Effects of Adult Neurogenesis on Synaptic Plasticity in the Rat Dentate Gyrus" href="http://jn.physiology.org/content/85/6/2423.full" target="_self">followed up</a> on that work in the Wojtowicz lab and found that this LTP could be observed in field recordings, i.e. this LTP stood out amongst the background of activity from all granule neurons when you stimulated their synaptic inputs. In fact, it was the <em>only</em> type of LTP observed in the absence of GABA blockers (making it pretty easy to identify and measure, even by novice electrophysiologists such as myself).</li>
<li><a title="A Critical Period for Enhanced Synaptic Plasticity in Newly Generated Neurons of the Adult Brain" href="http://www.cell.com/neuron/fulltext/S0896-6273(07)00334-0" target="_self">Ge et al</a> (2007) confirmed these findings in single neurons in mice and characterized the &#8220;critical period&#8221;, showing that only immature neurons displayed this plasticity, and not older adult-born neurons.</li>
<li><a title="Chronic Fluoxetine Stimulates Maturation and Synaptic Plasticity of Adult-Born Hippocampal Granule Cells" href="http://www.jneurosci.org/content/28/6/1374.long" target="_self">Wang et. al</a> (2008) did a nice trick and increased neurogenesis with fluoxetine and in turn increased ACSF-LTP. Irradiation abolished both.</li>
<li><a title="Adult-Generated Hippocampal Neurons Allow the Flexible Use of Spatially Precise Learning Strategies" href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0005464" target="_self">Garthe et al</a> (2009) used a chemical method for stopping neurogenesis. ACSF-LTP was gone.</li>
<li><a title="Increasing adult hippocampal neurogenesis is sufficient to improve pattern separation" href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3084370/?tool=pubmed" target="_self">Sahay et al</a> (2011) also increased neurogenesis and therefore ACSF-LTP, via a novel transgenic method.</li>
</ol>
<p><em><strong>AND NOW</strong></em>, I saw a poster by <a title="Modulating behavior and plasticity in the dentate gyrus by targeting NR2B-containing NMDA receptors on adult-born granule cells" href="http://www.abstractsonline.com/Plan/ViewAbstract.aspx?sKey=5b66d19a-55f7-4dae-9f0a-2353b5b669a2&amp;cKey=3ff53c6e-e4f4-4734-afb3-bc294acceb54&amp;mKey=%7b8334BE29-8911-4991-8C31-32B32DD5E6C8%7d" target="_self">Kheirback et. al</a>, who now used a completely novel method to confirm the existence of this special form of plasticity in new neurons. They used Nestin CreER and a floxed NR2B to delete the NR2B subunit specifically from young neurons. This didn&#8217;t kill neurons, it didn&#8217;t affect plasticity in mature neurons, but it wiped out ACSF-LTP. This is not entirely surprising because the NR2B subunit is known to endow new neuron with their enhanced plasticity. It just was a novel, elegant and specific way to demonstrate it.</p>
<p>Whereas the behavioral data on new neurons is less advanced and more variable, the fact that ACSF-LTP has been demonstrated in different species (mouse and rat), is absent after using different methods to reduce neurogenesis (irradiation, chemical, transgenic), is enhanced after using different methods for increasing neurogenesis (fluoxetine, transgenic) arguably makes it the strongest support for a real, significant function for hippocampal neurogenesis.</p>
<p>Going back to these NR2B-deficient new neurons, these mice also had behavioral effects: they had impaired ability to behaviorally distinguish contexts during fear conditioning, reduced object exploration, and no preference for a novel object over a familiar object. There was also a tendency, albeit less robust, for these mice to be more innately anxious and fearful.</p>
<p><span style="color: #ff0000;"><em><strong>OPTOGENETICS</strong></em></span></p>
<p>ACSF-LTP is so well documented because the anatomy and physiology of the inputs to granule neurons is not super complex. In contrast, if there&#8217;s one brain region that could really benefit from optogenetics, it&#8217;s the dentate gyrus output onto CA3. The connectivity is such that it is practically impossible to stimulate only new neurons with conventional techniques and record from their postsynaptic targets. At least the ones that are further away, like pyramidal neurons. This can be overcome by shining light on the dentate gyrus and ensuring that only new neurons are activated, through selective expression of channelrhodopsin or its variants. This is exactly what <a title="Recently generated neurons in the adult brain are critical for memory retrieval" href="http://www.abstractsonline.com/Plan/ViewAbstract.aspx?sKey=09544396-f5eb-4e70-a9ef-941086004e7d&amp;cKey=71ef1b8b-fd3e-40b2-bdb5-b48a9dc16652&amp;mKey=%7b8334BE29-8911-4991-8C31-32B32DD5E6C8%7d" target="_self">Gu et al</a> did. They characterized, for the first time, mossy fiber LTP in new neurons and found that 4-week-old neurons have greater LTP than either 3 or 8-week-old cells. Using archaerhodopsin to inhibit new neurons they also found that these 4-week-old cells are especially important for memory retrieval in fear conditioning and water maze paradigms. The deficits were not huge, but they were consistent. Considering that they used viral methods to express archaerhodopsin, which probably only infects a small proportion of the total new neuron population, the effect these new neurons are having on behavior is quite remarkable.</p>
<p><strong><span style="color: #ff0000;"><em>SO WE HAVE SYNAPSES AND BEHAVIOR, BUT WHAT&#8217;S IN THE MIDDLE? </em></span></strong></p>
<p>The most commonly-proposed, but least understood, cognitive function for new neurons is pattern separation. Originally a computational term, it refers to the process by which neurons take similar inputs (spatiotemporal patterns of incoming synaptic activity) and maximize their differences. When brains do this well we are able to distinguish very similar experiences in our memory. When it fails you spend 30 minutes looking for your car before you remember that you parked in a different lot. The discrimination of safe from dangerous contexts during fear conditioning is used more and more as a behavioral test of pattern separation. While it <em>may</em> depend on pattern separation by new neurons, this has never been shown. To get at this, <a title="The role of hippocampal adult neurogenesis in context discrimination" href="http://www.abstractsonline.com/Plan/ViewAbstract.aspx?sKey=19cacc88-faab-469f-a013-34f7592d3b43&amp;cKey=1cfee4ef-a30d-402b-8012-6fee78a34272&amp;mKey=%7b8334BE29-8911-4991-8C31-32B32DD5E6C8%7d" target="_self">Niibori et al</a>. used the catFISH method to see what is happening in CA3 neuronal ensembles when mice don&#8217;t have neurogenesis. catFISH uses the spatiotemporal patterns of activity-dependent gene expression to identify neuronal populations that were activated by different experiences. It&#8217;s been shown that when rodents are put into 2 different contexts, distinct ensembles of CA3 neurons are activated by the 2 experiences. The memory traces are kept distinct in order to not confuse the experiences. If new neurons are indeed performing a pattern separation function then you&#8217;d predict that, in their absence, the same population of CA3 neurons is activated by the 2 experiences. And this is exactly what Niibori et al found. Furthermore, confirming that new neurons are not just performing this separation function, but are actually required to behaviorally distinguish the 2 environments, mice lacking neurogenesis showed similar levels of fear behavior in both a context that was paired with shock as well as a context that had never been paired with shock. And so the hypothesized role for new neurons in pattern separation just got a whole lot stronger.</p>
<p><span style="color: #ff0000;"><em><strong>WHERE ARE WE AT?</strong></em></span></p>
<p>There&#8217;s only so much functional work going on out there. Some behavior, less electrophysiology, a new method for measuring circuit properties. Your study of a phenomenon feels complete when you&#8217;ve seen presentations that cover function at these different levels of analysis. When they replicate and then build upon previous findings it&#8217;s even more of a confirmation that progress is being made. I have to say I think it was a pretty good meeting for adult neurogenesis.</p>
<img src="http://feeds.feedburner.com/~r/FunctionalNeurogenesis/~4/6zaj4Jjy0ss" height="1" width="1"/>]]></content:encoded>
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		<item>
		<title>Enhanced integrative properties of immature neurons #sfn11</title>
		<link>http://feedproxy.google.com/~r/FunctionalNeurogenesis/~3/w3VBKsJ6dx4/</link>
		<comments>http://www.functionalneurogenesis.com/blog/2011/11/enhanced-integrative-properties-of-immature-neurons-sfn11/#comments</comments>
		<pubDate>Wed, 16 Nov 2011 05:49:52 +0000</pubDate>
		<dc:creator>Jason Snyder</dc:creator>
				<category><![CDATA[uncategorized]]></category>
		<category><![CDATA[calcium imaging]]></category>
		<category><![CDATA[electrophysiology]]></category>
		<category><![CDATA[mongiat]]></category>
		<category><![CDATA[schinder]]></category>
		<category><![CDATA[SFN]]></category>
		<category><![CDATA[spiking]]></category>

		<guid isPermaLink="false">http://www.functionalneurogenesis.com/blog/?p=1368</guid>
		<description><![CDATA[How do the physiological properties of new neurons translate to a behavioral role? Are they just like mature neurons or are they unique? One idea that&#8217;s been thrown around is that their plastic period, their critical period, might endow them with an enhanced ability to associate information and contribute to memory formation. While we know [...]]]></description>
			<content:encoded><![CDATA[<p>How do the physiological properties of new neurons translate to a behavioral role? Are they just like mature neurons or are they unique? One idea that&#8217;s been thrown around is that their plastic period, their critical period, might endow them with an enhanced ability to associate information and contribute to memory formation. While we know that hippocampal neurons are already plastic and very capable of physiologically linking together different stimuli the big hope seems to be that maybe immature neurons are <em>even better </em>at this.</p>
<p><img class="aligncenter size-full wp-image-1369" title="spiking" src="http://www.functionalneurogenesis.com/blog/wp-content/uploads/2011/11/spiking.jpg" alt="spiking" width="500" height="163" /></p>
<p>A related question is how fewer synapses and unique inhibitory connectivity affects their information processing capabilities. The verdict is out on whether new neurons are more or less involved in information processing than their mature counterparts. Currently, the best information we have is from studies looking at activity, measured by immediate early gene expression, in response to behavioral stimulation. The <em>true</em> measure of whether a neuron is involved in information processing / representation is if it spikes, i.e. fires action potentials, in response to a specific stimulus. Since new neurons have fewer synapses it&#8217;s very possible that they aren&#8217;t able to represent many different types of information, and therefore aren&#8217;t capable of associating information during memory formation. On the other hand, new neurons synapses are more plastic, perhaps making them better able to associate information even if they have fewer synapses.<span id="more-1368"></span></p>
<p>And so I wasn&#8217;t surprised that the Schinder lab was the one to answer these questions at SFN. They were the ones who finally definitively <a title="Reliable activation of immature neurons in the adult hippocampus" href="http://www.functionalneurogenesis.com/blog/2011/02/are-new-neurons-really-more-excitable-yes/" target="_self">showed</a> that immature neurons are indeed more excitable than mature neurons. And on Saturday, Lucas Mongiat presented right next to me during the poster session and was kind enough, once 5 o&#8217;clock rolled around, to take a few extra minutes to tell me their <a title="SFN abstract" href="http://www.abstractsonline.com/Plan/ViewAbstract.aspx?sKey=045dc723-9746-4379-89ea-5a976a7484bb&amp;cKey=a309d6c9-f1d5-4421-8f7d-214b965f4441&amp;mKey=%7b8334BE29-8911-4991-8C31-32B32DD5E6C8%7d" target="_self">new story</a> (after traveling all night from Argentina and coming straight to his poster board from the airport!).</p>
<p>They first addressed the question of whether or not immature neurons are more likely to be &#8220;activated&#8221; than mature neurons. Activation was measured in retrovirally-labeled neurons in hippocampal slices by two methods: calcium imaging and spiking in response to perforant path stimulation. Input-output curves showed that immature neurons were more likely to be activated than mature neurons, regardless of the stimulus strength. Mature neurons could be made to behave like immature neurons if picrotoxin was added to the bath, blocking inhibitory connections.</p>
<p>So what&#8217;s going on with inhibition? At the time of spiking, inhibition and excitation were equivalent in the mature neurons, making it hard to become excited and fire an action potential. In contrast, inhibition occurred later in immature neurons, making it easier to fire in response to perforant path activity. Their next question was whether or not new neurons are more likely to associate inputs at a physiological level.</p>
<p>To answer this, they used two stimulating electrodes to activate different perforant path inputs onto granule neurons. Calcium responses were measured to identify activated neurons. The idea is that the two inputs will activate populations of neurons. Some neurons will be activated only by input 1 and others only by input 2. However, another population will be activated by both inputs and those neurons are the ones that are best suited for associating information as would happen during memory formation. Comparing immature (4w old) and mature (8w) adult-born cells as well as the overall population (which would be a mixed age, though mostly older than the adult-born cells) it was only the immature adult-born cells that were more likely to respond to both inputs. That the mature adult-born cells were similar to the general population suggests that adult-born cells eventually mature to become similar to perinatal-born cells.</p>
<p>While I&#8217;m no expert electrophysiologist, these data are exciting because they show for the first time that new neurons have the physiological potential to associate inputs better than mature neurons. Computational models and behavioral predictions needed this!</p>
<p>The different timecourse of inhibition makes me wonder how immature neurons handle timing of activity. For example, if input 1 is strongly activated and a subthreshold input 2 follows shortly thereafter, is input 2 potentiated and better able to activate the postsynaptic cell in the future? Does the delayed inhibition make them better at temporal summation? Does it alter the recruitment of immature neurons into cell assemblies, since this is dictated by the precise timing of neuronal firing?</p>
<p>DATA? MORE DATA? PLEASE?!?!</p>
<img src="http://feeds.feedburner.com/~r/FunctionalNeurogenesis/~4/w3VBKsJ6dx4" height="1" width="1"/>]]></content:encoded>
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		<item>
		<title>Neurogenesis and the septotemporal axis at #SFN11</title>
		<link>http://feedproxy.google.com/~r/FunctionalNeurogenesis/~3/tDqOCvJtmjE/</link>
		<comments>http://www.functionalneurogenesis.com/blog/2011/11/neurogenesis-and-the-septotemporal-axis-at-sfn11/#comments</comments>
		<pubDate>Mon, 14 Nov 2011 08:03:57 +0000</pubDate>
		<dc:creator>Jason Snyder</dc:creator>
				<category><![CDATA[anxiety / depression]]></category>
		<category><![CDATA[reviews of the field]]></category>
		<category><![CDATA[Belzung]]></category>
		<category><![CDATA[environmental enrichment]]></category>
		<category><![CDATA[fluoxetine]]></category>
		<category><![CDATA[Herkenham]]></category>
		<category><![CDATA[Lehmann]]></category>
		<category><![CDATA[septal]]></category>
		<category><![CDATA[stress]]></category>
		<category><![CDATA[Tanti]]></category>
		<category><![CDATA[temporal]]></category>

		<guid isPermaLink="false">http://www.functionalneurogenesis.com/blog/?p=1348</guid>
		<description><![CDATA[As I&#8217;ve alluded, science, and therefore the SFN meeting where much science is unveiled, is a cycle of confusion and clarification. Currently, confusion may be prevailing in the adult hippocampal neurogenesis field since new neurons have been implicated in everything mammals do &#8211; spatial and nonspatial memory, anxiety, depression, addiction, social behavior, stress regulation, blinking [...]]]></description>
			<content:encoded><![CDATA[<p>As I&#8217;ve alluded, science, and therefore the SFN meeting where much science is unveiled, is a cycle of confusion and clarification. Currently, confusion may be prevailing in the adult hippocampal neurogenesis field since new neurons have been implicated in everything mammals do &#8211; spatial and nonspatial memory, anxiety, depression, addiction, social behavior, stress regulation, blinking etc. This should not be entirely surprising since the hippocampus itself, where these young neurons reside, has many different functions. But how can we reconcile these seemingly disparate functions?</p>
<p>Every time I get worked up about all these neurogenesis findings I think about two words that return me to a state of inner peace, calmness, and&#8230;.mental turmoil that all of my experiments will have to be performed twice: Septal and Temporal. Neurogenesis aside, the septal and temporal ends of the hippocampus are connected to different brain structures that cause the septal hippocampus to be more involved in spatial processing/cognition and the temporal hippocampus to be more involved in regulating stress and emotion. Which has the potential to explain everything.<span id="more-1348"></span></p>
<p><em><strong><span style="color: #ff0000;">Two posters today did a great job of analyzing neurogenesis in these different parts of the hippocampus and relating these findings to function.</span></strong></em> First, <a href="http://www.abstractsonline.com/Plan/ViewAbstract.aspx?sKey=e5cd926f-5220-4cbd-9031-50765643851b&amp;cKey=375684f7-1321-43ab-9975-4da27fe43157&amp;mKey=%7b8334BE29-8911-4991-8C31-32B32DD5E6C8%7d" target="_self">Tanti et al.</a> showed that while a chronic stress model of depression reduced neurogenesis along the entire septotemporal axis, the antidepressant fluoxetine (aka Prozac) rescues this deficit <em>specifically</em> in the temporal hippocampus. In contrast, environmental enrichment, which may be viewed as more of a spatial and cognitive stimulus, selectively (and massively!) increased neurogenesis in the septal hippocampus with no effect in the temporal hippocampus. A nice dissociation where different classes of stimuli (drugs that regulate emotion vs. knowledge about objects and environments) regulate plasticity in different parts of the hippocampus.</p>
<p>This was complemented by a thorough study by <a href="http://www.abstractsonline.com/Plan/ViewAbstract.aspx?sKey=73c05bd0-0c26-42fc-96a8-f179cb902b2e&amp;cKey=0790e356-c995-4180-8678-f76c2b96903f&amp;mKey=%7b8334BE29-8911-4991-8C31-32B32DD5E6C8%7d" target="_self">Lehman et al.</a>, who recently <a href="http://www.ncbi.nlm.nih.gov/pubmed/20308988" target="_self">showed</a> that new neurons aid in the recovery from psychosocial stress, they asked whether &#8220;depressed&#8221; mice that suffered social defeat showed regional differences in neurogenesis. The prediction would be that neurogenesis should be specifically reduced in the temporal hippocampus, since this is the region that regulates the stress and emotional responses. They too were curious about the effects of environmental enrichment, since they&#8217;ve previously found that enrichment can rescue mice from a depressed state, but only if neurogenesis was present. The story sounds complicated when I tell you that they did all these experiments in normal mice and mice that had their adrenal glands removed, and had low levels if stress hormones (glucocorticoids). But a surprisingly clear picture emerged:</p>
<p>Social defeat (getting beaten up by a big bully mouse and then having to constantly live next to him) increased glucocorticoids and led to anxiety/depressive behaviors. Furthermore, social defeat specifically reduced neurogenesis in the temporal (i.e. &#8220;emotional&#8221;) hippocampus. The culprit was glucocorticoids - by removing glucocorticoids both the &#8220;depression&#8221; and neurogenesis impairments could be reversed. In a complementary experiment, they found that environmental enrichment is also a stressor, but a good stressor. Environmental enrichment increased glucocorticoids yet its other effects were beneficial &#8211; the mice were less anxious, less depressed, and they had increased neurogenesis. And just as with social defeat, the effects of environmental enrichment were also dependent on glucocorticoids: when glucocorticoids were removed, environmental enrichment did not reduce anxiety/depression and it did not increase neurogenesis.</p>
<p><span style="color: #ff0000;"><em><strong>The take home message is that stress hormones have bad effects on behavior and neurogenesis in the context of social stress, but they have good effects on behavior and neurogenesis in the context of environmental enrichment.</strong></em></span> And while we don&#8217;t yet know if septal neurogenesis is more important for spatial/cognitive behaviors and temporal hippocampus for emotional regulation, both of these posters did a great job of convincing me that this is a direction we need to pursue if we are to understand the many functions of new neurons. They also made it clear that there are complex interactions between stress, neurogenesis and behavior. To the point that I can live (for a little bit) with not knowing exactly <em>how</em> these neurons are working, but knowing that these diverse functions are clearly possible.</p>
<img src="http://feeds.feedburner.com/~r/FunctionalNeurogenesis/~4/tDqOCvJtmjE" height="1" width="1"/>]]></content:encoded>
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		<item>
		<title>What I learned while presenting at #SFN11</title>
		<link>http://feedproxy.google.com/~r/FunctionalNeurogenesis/~3/pnOLQ2yszMY/</link>
		<comments>http://www.functionalneurogenesis.com/blog/2011/11/what-i-learned-at-while-presenting-at-sfn11/#comments</comments>
		<pubDate>Sun, 13 Nov 2011 06:09:48 +0000</pubDate>
		<dc:creator>Jason Snyder</dc:creator>
				<category><![CDATA[reviews of the field]]></category>
		<category><![CDATA[SFN]]></category>

		<guid isPermaLink="false">http://www.functionalneurogenesis.com/blog/?p=1331</guid>
		<description><![CDATA[It&#8217;s hard to explore SFN when you&#8217;ve got your own poster to tend to. I thought I could hop around the development section before things got busy but there was no &#8220;before things got busy.&#8221; The design of the conference also can work against presenters because the presentations you&#8217;d like to see the most are [...]]]></description>
			<content:encoded><![CDATA[<p>It&#8217;s hard to explore SFN when you&#8217;ve got your own poster to tend to. I thought I could hop around the development section before things got busy but there was no &#8220;before things got busy.&#8221; The design of the conference also can work against presenters because the presentations you&#8217;d like to see the most are being displayed simultaneously with your own. So next year I vow to present something really boring.</p>
<p>Of course, much can be learned while pinned down at your own poster. When you work in one lab, or one institution, your thoughts about the brain tend to have a specific focus based on the ideas of the people around you. Of course, new papers come out that challenge those thoughts but, man, papers move slooooowly. Scientists have not done a stellar job of using the internet to quickly communicate ideas. However, once a year at SFN a whole bunch of people come to your poster and give you their thoughts on the brain. Sometimes their thoughts are only presented in the language of distorted eyebrows and raised inflections but this is way better than typical social interactions with strangers, which usually go something like &#8220;You study brain cells/memory? Dude, I sure could use some more of those/that!&#8221;</p>
<h3><strong><span style="color: #333399;">So, what did my visitors think?</span></strong></h3>
<p><strong><span style="color: #333399;"><br />
</span></strong></p>
<p><span style="color: #ff0000;"><em><strong>I had several visitors who specifically came by because they knew about me through the blog and through Twitter.</strong></em></span> Thank you for stopping by! You often never know if your online thoughts are useful, but I was happy to hear that several of you have used the blog as a teaching tool and a way to keep up with the field. I wish I could have these interactions with my readers more often than once a year at SFN. Then again I&#8217;d probably never be able to keep up with the comments so&#8230;no I didn&#8217;t say that &#8211; get engaged! I also heard one person, who does in vivo electrophysiology on my favorite brain regions, tell me that they&#8217;d tweet about neuroscience but they have nothing interesting to add to the conversation! Bollocks! Do you know how many in vivo electrophysiologists are on Twitter? Like, <a href="https://twitter.com/#!/MillerLabMIT" target="_self">one</a>? And how many experts are reviewing the literature on <a href="http://researchblogging.org/" target="_self">Research Blogging</a>? Your knowledge is valuable. I would follow you in an instant.</p>
<p><strong><span style="color: #ff0000;"><em>&#8220;At first there was agreement on the behavioral function of neurogenesis but now everything is going in different directions.&#8221;</em></span></strong> Yes! Adult neurogenesis is a great example of the more you learn the more confused you get! Things may have seemed congruent 5 years ago but that was when there was only half a dozen studies that had examined the problems that arise when new neurons are ablated. Since then people have gone on to study more types of behavior and, as is also the case with the hippocampus, new neurons have been found to contribute to more and more types of behaviors. This has also given us additional opportunities for failed replication, and therefore doubt and confusion. One visitor commented on the <a href="http://www.ncbi.nlm.nih.gov/pubmed/22016545" target="_self">recent paper</a> that found memory impairments only if you kill new neurons <em>after</em> learning and we agreed that killing new neurons before behavioral testing could allow for other neurons to compensate, and make it appear that these new neurons are not doing anything significant. Of course, we have <a href="http://www.ncbi.nlm.nih.gov/pubmed/21814201" target="_self">shown</a> that often (e.g. at &#8220;baseline&#8221;) new neurons may be dispensable but that when an animal is stressed they are critical. And so explanations <em>are</em> emerging as to why some observe a behavioral function for new neurons and others do not, it&#8217;s just that it seems to be unbearably slow or remarkably fast depending on your mood.</p>
<p><span style="color: #ff0000;"><strong><em>I learned that there&#8217;s someone out there studying neurogenesis as related to maternal behavior&#8230;.IN SHEEP! </em></strong></span>And they find that these neurons mature very slowly, like, <a href="http://www.functionalneurogenesis.com/blog/2011/06/new-neurons-mature-very-slowly-in-monkeys/" target="_self">primate slow</a>. I love it when we think we have things completely figured out and then the data goes a totally different direction when you throw wool into the equation. Like, if we put cute little wool sweaters on our mice, would that make new neurons mature slower? One of the next big questions. Testable. Do it.</p>
<p>For those that missed my poster, fear not, for I have submitted it to <a href="http://precedings.nature.com/" target="_self">Nature Precedings</a> and will notify you here when they&#8217;ve posted it (couple days). For those that came to my poster today, sorry, you didn&#8217;t have to come to my poster.</p>
<p>Jason</p>
<img src="http://feeds.feedburner.com/~r/FunctionalNeurogenesis/~4/pnOLQ2yszMY" height="1" width="1"/>]]></content:encoded>
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		<title>Saturday Nov 12, #SFN11, poster A27 = me</title>
		<link>http://feedproxy.google.com/~r/FunctionalNeurogenesis/~3/KxqvXsyrN5s/</link>
		<comments>http://www.functionalneurogenesis.com/blog/2011/11/saturday-nov-12-sfn11-poster-a27-me/#comments</comments>
		<pubDate>Wed, 09 Nov 2011 06:23:06 +0000</pubDate>
		<dc:creator>Jason Snyder</dc:creator>
				<category><![CDATA[pretty photos]]></category>
		<category><![CDATA[#SFN11]]></category>
		<category><![CDATA[GFAP]]></category>
		<category><![CDATA[SFN]]></category>
		<category><![CDATA[thymidine kinase]]></category>
		<category><![CDATA[TK]]></category>
		<category><![CDATA[transgenic rat]]></category>

		<guid isPermaLink="false">http://www.functionalneurogenesis.com/blog/?p=1323</guid>
		<description><![CDATA[Update: The poster is now available at Nature Precedings.
Still acquiring histological images for my SfN poster. My recurring problem is that I end up taking pictures of things because they&#8217;re pretty and not because they have anything to do with the task at hand. Today&#8217;s case in point:
Well, this does relate to my SfN poster [...]]]></description>
			<content:encoded><![CDATA[<p><em><span style="color: #000000;"><strong>Update: The poster is now available at <a href="http://precedings.nature.com/documents/6592/version/1" target="_self">Nature Precedings</a>.</strong></span></em></p>
<p>Still acquiring histological images for my SfN poster. My recurring problem is that I end up taking pictures of things because they&#8217;re pretty and not because they have anything to do with the task at hand. Today&#8217;s case in point:</p>
<p><a href="http://www.flickr.com/photos/functionalneurogenesis/6328239006/sizes/l/in/photostream/"><img class="aligncenter" title="astrocytes and radial glia" src="http://farm7.static.flickr.com/6240/6328239006_6ab9612351.jpg" alt="" width="500" height="500" /></a>Well, this does relate to my SfN poster a little bit. Red shows cell nuclei, most of which are dentate gyrus granule neurons. And white is GFAP immunostaining, which largely labels astrocytes but in this part of the brain also labels radial glia, the stem cells (or to be less controversial, &#8220;precursor&#8221; cells) of the hippocampus. Radial glia can be identified by the long process (almost like a dendrite) that they extend through the granule cell layer. There are a few in the above picture.<span id="more-1323"></span></p>
<p>What I was really looking for was a photo more along the lines of this, which may appear on my poster if I cannot find a better (prettier) example in the next few days:</p>
<p><a href="http://www.flickr.com/photos/functionalneurogenesis/6327521793/sizes/l/in/photostream/"><img class="aligncenter" title="thymidine kinase-positive radial cell" src="http://farm7.static.flickr.com/6240/6327521793_89d0df4b91.jpg" alt="" width="500" height="500" /></a>Here, dead center, is an example of a radial glial cell with a green GFAP process and a little bifurcating hat that sits on the cell body at the base of the granule cell layer. What&#8217;s special in this case is the fact that these are transgenic rats in which thymidine kinase is also expressed in the GFAP+ cells. By giving the rats &#8220;treats&#8221; laced with valganciclovir we can then specifically kill the radial cells, and prevent adult neurogenesis. This is the same strategy used to inhibit adult neurogenesis in several lines of mice. Now we can do it in rats too (which is great because rats have a bigger brain making them more amenable for some kinds of experiments, and they&#8217;re also smarter).</p>
<p>To hear the full story stop by the <a title="jason snyder's #sfn11 poster" href="http://www.abstractsonline.com/Plan/ViewAbstract.aspx?sKey=045dc723-9746-4379-89ea-5a976a7484bb&amp;cKey=a5fafc55-c417-4ae7-8c53-49206a800e8b&amp;mKey=%7b8334BE29-8911-4991-8C31-32B32DD5E6C8%7d" target="_self">poster</a> on Saturday. Actually, stop by regardless of whether you want to see the poster. Isn&#8217;t that how SfN works?</p>
<p>Here is the abstract:</p>
<blockquote><p>A transgenic rat model for reducing adult neurogenesis. Saturday, Nov 12, 2011, 1:00 PM &#8211; 2:00 PM. 30.05/A27</p>
<p><strong>JS Snyder</strong>, L Grigereit, M Brewer, J Pickel, HA Cameron. NIH/NIMH, Bethesda, MD, USA</p>
<p>Our understanding of the function of adult neurogenesis is largely founded on animal models. Models of reduced neurogenesis, in particular, suggest new neurons contribute to various aspects of learning, memory and emotional behavior. While many different methods for reducing adult neurogenesis exist in the mouse, fewer tools are available in the rat. Additional means for reducing neurogenesis in the rat would be useful if they offer additional specificity over existing methods (e.g. irradiation or chemical) and do not require special equipment (e.g. irradiator). Since the rat offers certain advantages for behavioral neuroscience studies (complexity of behavior, brain size, extensive literature) we sought to develop a genetic method for reducing neurogenesis in this species. Specifically, we created transgenic rats expressing herpes simplex virus thymidine kinase (TK), which renders mitotic cells sensitive to the antiviral drug ganciclovir. TK was expressed under control of the GFAP promoter, thereby allowing for the selective killing of GFAP+ radial precursors in the adult brain. Wild-type and GFAP-TK rats were treated with 7.5mg of orally-available valganciclovir daily for 5 days each week and injected with the cell division marker BrdU after 1, 2, 3, or 4 weeks of treatment. GFAP-TK rats gained weight normally and appeared healthy throughout treatment. Four weeks after the last group received BrdU all rats were perfused. Consistent with a role for GFAP+ radial precursors in generating new dentate granule neurons in the rat, BrdU+ granule cells were reduced by 78% after 1 week of valganciclovir treatment and ~85% thereafter in GFAP-TK rats compared to wild types. Current experiments are exploring neurogenesis reduction in the subventricular zone-olfactory bulb of GFAP-TK rats, another brain region known to give rise to adult-born neurons via GFAP+ precursors. Given the extent of adult neurogenesis reduction in the dentate gyrus, we expect that these rats will be a valuable tool for investigating functions of neurons born in the adult brain.</p></blockquote>
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