tag:blogger.com,1999:blog-36435564950840837432024-03-14T00:43:37.404-07:00Skeptic WonderProtists, memes and random musingsPsi Wavefunctionhttp://www.blogger.com/profile/10829712736757471647noreply@blogger.comBlogger324125tag:blogger.com,1999:blog-3643556495084083743.post-7023936894152010512015-03-04T07:12:00.003-08:002015-03-04T07:12:52.355-08:00Update: Tree of Eukaryotes (parasitology edition)There arose a need for a new tree for a parasitology meeting, so after almost five years, I finally updated the tree of eukaryotes. There are still things that need to be changed, and new orphan lineages that should be added, but here's an updated version showing predominantly parasitic lineages in bold, and lineages known to contain parasites and/or opportunists marked with an asterisk. Since the citations box from the older editions is hard to keep updated, I've removed it, and hope to replace it with references and further reading on this site, where it can be easily modified.<br />
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Once again, note that this tree, which incorporating real data, is an inherently subjective synthesis, and should be used with caution. As always, comments and suggestions welcome.<br />
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References and further reading to be added shortly, once I have more time ;-)<br />
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(The first edition was half a decade ago... time flies!)Psi Wavefunctionhttp://www.blogger.com/profile/10829712736757471647noreply@blogger.com9tag:blogger.com,1999:blog-3643556495084083743.post-2179945901138392132014-12-15T20:17:00.001-08:002014-12-15T20:17:40.380-08:00Return home from SciAm BlogsGreetings and welcome to this particular pond of microbes.<br />
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I'm back! My wonderful time at Scientific American at <a href="http://blogs.scientificamerican.com/ocelloid">The Ocelloid</a> has come to a close, as I am currently not in the right place in life for semi-professional blogging. The pressure of having someone else's brand name associated with the blog actually made it hard for me to write, as all sorts of anxiety issues crawled out of the woodwork at the sight of that. It may take me some time to get back into regular blogging again -- while adjusting to graduate school -- but this is my primary online home again, for now. You know you've been away for a while when Blogger's interface is entirely different.<br />
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Hopefully, the more flexible commenting system here will help re-establish some of the readership and conversation that was lost in transition... well, over two transitions and a very long stagnant period, that is. It may be wishful thinking to expect anyone to remain here, but someone's gotta start sweeping up the dust!<br />
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This is mostly to ensure people coming from my <a href="http://blogs.scientificamerican.com/ocelloid/2014/12/15/extinction-or-lateral-transfer/">last post at SciAm</a> that I do, in fact, still have the keys to this place. Let's ignore that this is the first post of 2014... (whereas that last SciAm post was the... third post of 2014. Sigh.)<br />
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Anyway, I'll lay down this vaguely Christmas-y image of a red alga as a front door mat. Red algae are so vibrant under good optics that all too often the camera doesn't quite do it justice. Charismatic megaflora, if you will.<br />
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To those who have returned with me -- thank you for sticking along this far! And for those who are new -- welcome! Let's see where this particular leg of my blogging adventure heads to. (the leg must be quite confused as to why it suddenly gets a head, but that's besides the point)<br />
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Best wishes,<br />
-Psi-<br />
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<br />Psi Wavefunctionhttp://www.blogger.com/profile/10829712736757471647noreply@blogger.com3tag:blogger.com,1999:blog-3643556495084083743.post-39966516576647625452013-07-27T10:35:00.001-07:002013-07-27T10:35:46.651-07:00Live coverage of Big Protist Conference (ICOP) in Vancouver, 28 Jul -- 02 AugThere's a big protist meeting in Vancouver starting tomorrow, and I've been generously supported by ICOP and ISOP to attend as a reporter. I'd like to invite you all to follow us during and/or peruse the results afterwards -- <a href="http://blogs.scientificamerican.com/ocelloid/2013/07/27/live-coverage-of-protist-bonanza-in-vancouver-icop-2013/"><b>further information is here</b></a>. In summary:<br />
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Twitter: <a href="https://twitter.com/Ocelloid"><b>@ocelloid</b></a><br />
Hashtag: <a href="https://twitter.com/search?q=%23ICOP13&src=typd"><b>#ICOP13</b></a><br />
Blog: <b><a href="http://www.blogger.com/blogs.scientificamerican.com/ocelloid">http:blogs.scientificamerican.com/ocelloid</a></b><br />
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Cheers, and hope to see y'all there, in some form! =)Psi Wavefunctionhttp://www.blogger.com/profile/10829712736757471647noreply@blogger.com0tag:blogger.com,1999:blog-3643556495084083743.post-11805935073392309492013-07-13T12:37:00.002-07:002013-07-13T12:37:41.279-07:00Ongoing page for protistology resources(Yes, I still exist!)<br />
I've been prompted to compile a collection of suggested resources on protist diversity and biology, and quite frankly, I'm getting a bit too lazy to look things up and send the links again and again. So I've made a <a href="http://skepticwonder.fieldofscience.com/p/protistology-resources.html">page on Protistology Resources</a> -- it's still raw, but I hope it can help some people get started. If there's anything you'd like to contribute, including own lab pages, papers, etc -- please feel free to comment or email me!<br />
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If anyone wonders where I hang out these days: I've a blog with Scientific American -- <a href="http://blogs.scientificamerican.com/ocelloid/">The Ocelloid</a>. And yes, I definitely really really need to blog more, both here and there.<br />
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Cheers, and hoping to be around more often.Psi Wavefunctionhttp://www.blogger.com/profile/10829712736757471647noreply@blogger.com0tag:blogger.com,1999:blog-3643556495084083743.post-34951141060541402232011-12-19T02:54:00.001-08:002011-12-19T03:02:42.853-08:00Free ImageJ Macro -- for citing images(of course all IJ macros and IJ itself are free...)<div><br /></div><div>So I got sick of constantly clicking away just to resize an image and add some citation text to the bottom and then name the file that exact thing; in fact, it was a deterrent to blogging -- yes, I am *that* lazy, apparently. At 4 in the morning today, my latent inner yet-unexplored codemonkey decided it needed an ImageJ macro for doing that, and it needed it <i>then</i>, at 4 in the morning, the day before I fly for holidays, and therefore a very busy day. After a couple hours of failed negotiation attempts between brick walls and my head (and much profanity), I finally produced a piece of code that not only does something, but does what I want it to! Being an utter failure at anything technical (engineering aptitude turns out to not be particularly heritable, as my parents' experiment demonstrates), I get soooo excited when something I slap together out of copy+paste and single-finger typing on the keyboard<i> actually works</i>, that I absolutely have to share it with the world. Even if it's pathetically minor and useless. Shhh.</div><div><br /></div><div>World, behold -- an ImageJ macro for adding citations to images!</div><div><blockquote></blockquote><div></div><blockquote><div>// This macro creates citation (or other input) text by adding a 20p strip to the bottom of the image, aligned right</div><div>// Image is saved in Documents as the ref input text</div><div>// WARNING: saving several images with same citation input WILL result in overwrite!</div><div><br /></div><div>ref=getString("Reference", "ref"); </div><div>var width = getWidth();</div><div>var height = getHeight();</div><div>height=height+20;</div><div>run("Canvas Size...","width=&width height=&height position=Top-Center");</div><div><br /></div><div>var textwidth=getStringWidth(ref);</div><div>var textmargin=width-(textwidth+5);</div><div>drawString(ref,textmargin, height-5); </div><div>var path="C:\\";</div><div>var name=path+" "+ref;</div><div>saveAs("Jpeg",name);</div></blockquote><div></div></div><div><blockquote></blockquote>Hopefully this means I'll get back to regular blogging soon, as one more Gate of Laziness has been removed from the path. Now if only IJ could also upload and link those images...</div>Psi Wavefunctionhttp://www.blogger.com/profile/10829712736757471647noreply@blogger.com1tag:blogger.com,1999:blog-3643556495084083743.post-6990222161710933262011-12-14T20:09:00.000-08:002011-12-14T22:36:45.525-08:00Update!Neglect... so much neglect. Been swallowed up by my move to Indiana and settlement attempts. Haven't really been keeping up with my SciAm blogging either, but I do intend to return here and post the occasional snippet of something random and perhaps even technical, that I don't want to bother with in terms of translating to a human language. That was an awful sentence -- see what a lack of writing practice can do?<div><div><br /></div><div>For the few who may care about personal life, well... being a full-time researcher takes up a lot of time, it turns out. Particularly when your experiments aren't really shining in glory or anything like that. And when your gentle introduction to a subject you despised all through undergrad happens to be a grad-level course you absolutely have to do well in. In other words, I've been thrown off into population genetics at the deep end. The course was great, actually, and think I learned *a lot*, but a little bit intensive to someone who merely a year ago defiantly ignored claims that evolution involved 'populations'.</div><div><br /></div><div>In terms of research life, feels like I'm involved tangentially in enough projects to get away with not really doing anything in particular. In addition to maintaining some ciliate and diatom mutation accumulation lines (long, boring and painful multi-year project to ultimately measure the mutation rate and spectrum, which is actually very exciting as a final product!), I'm trying to learn the art of harnessing ciliate growth rates to be able to have them undergo autogamy (recreating their macronuclei, etc etc) at just the right times to gather RNA for sequence data (that is not my project), and figuring out imaging techniques for deciphering the identity of food vacuole bacteria that persist after longterm starvation for some inexplicable reason. In addition, also trying to start up new protist mutation accumulation lines to ultimately get a phylogenetically sounder sense of eukaryotic mutation rates.</div><div><br /></div><div>As you can see, lots of trying and attempting and figuring stuff out, and not a whole lot of results and data, which gets frustrating after some time. But rumour has it that's not unusual when starting in a new lab. </div><div><br /></div><div>Another shift was going from a protistology haven to being some sort of a sole regional expert on protist diversity, entirely for lack of anyone else in the field around here. It's rather alienating, and you can't argue with people about arcane topics in protist phylogeny and taxonomy as they'll just go with whatever you assert. Which renders argumentative assertion a lot less fun. On the other hand, there's an exciting challenge to convert locals to the dark side, and I'm trying to do anything I can in that department, mwahaha! After all, Indiana U used to be quite a bustling centre of protist research, back in the days of Tracy Sonneborn, his deciples and <i>Paramecium</i> genetics. A handful of us in this lab are all that's left of IU's proud protistology tradition...</div><div><br /></div><div>So that's what I've been doing lately, leaving little productive time for blogging (but, of course, plenty of time for <i>unproductive </i>procrastination). Not easy getting started after a long break either...</div></div><div><br /></div><div>Anyway, enough rambling, and onward with moar protists!</div>Psi Wavefunctionhttp://www.blogger.com/profile/10829712736757471647noreply@blogger.com3tag:blogger.com,1999:blog-3643556495084083743.post-12181470595516114482011-07-12T08:41:00.000-07:002011-07-12T08:53:24.053-07:00New paper on Constructive Neutral Evolution<div>Don't have time to blog this right now (off to protistology conference today -- will bring back lots of goodies!), but there's a new review paper about <a href="http://skepticwonder.fieldofscience.com/2010/04/in-defense-of-constructive-neutral.html">CNE</a> out a couple weeks ago. It's paywalled at some rather obscure journal that an institution as big as UBC doesn't have access to, so here's a pdf y'all can [hopefully] access! </div><div><br /></div><div><a href="https://docs.google.com/viewer?a=v&pid=explorer&chrome=true&srcid=1UUzjkp36iaZmQZfPwbmBSsfCzslGNEU4tlFy-WIOMQmHt_reO4xIaEGxQZU6&hl=en_US">Lukes et al. 2011 IUBMB Life</a>: How a Neutral Evolutionary Ratchet Can Build Cellular Complexity</div><div>(<a href="http://onlinelibrary.wiley.com/doi/10.1002/iub.489/abstract">original journal link</a>)</div><div><br /></div>See, if this was published in a proper (ie, open access) journal, I wouldn't have to do this. As taxpayers you all have the right to see this, outdated publishers be damned. <div><br /></div><div>I'm taking off to <a href="http://www.uga.edu/protozoa/meetings/future_meet.html#isop2011">ISoP</a> in Seattle - I might attempt to live tweet parts of it (as <a href="http://twitter.com/Ocelloid">@ocelloid</a>), so do follow us on twitter using the <a href="http://twitter.com/#search?q=%23isop11">#isop11 hashtag</a>! And for those of you who are gonna be there... let's see if you can find me ;-) (spoiler alert: Psi is a pseudonym. Seriously! o.O)</div>Psi Wavefunctionhttp://www.blogger.com/profile/10829712736757471647noreply@blogger.com1tag:blogger.com,1999:blog-3643556495084083743.post-87859277496823296952011-07-05T09:18:00.000-07:002011-07-05T23:30:52.351-07:00Big Announcement: New blog -- The Ocelloid<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjeO_aKGWzM-7XPrPTJjhB9hLeGZKVnDhixSTwSe-p2HbsRdU3uIdbzPmCyc1iWcPBNs9Mu4YFDzf0R_ZaDCRDmKY3tRe4Uj45o0rJFjWkBF_Nf8tR3j-5ZJ7VjmdqMEAZepJ5ADmEAITE1/s1600/Ocelloid2.jpg" onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"><img style="float:left; margin:0 10px 10px 0;cursor:pointer; cursor:hand;width: 200px; height: 200px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjeO_aKGWzM-7XPrPTJjhB9hLeGZKVnDhixSTwSe-p2HbsRdU3uIdbzPmCyc1iWcPBNs9Mu4YFDzf0R_ZaDCRDmKY3tRe4Uj45o0rJFjWkBF_Nf8tR3j-5ZJ7VjmdqMEAZepJ5ADmEAITE1/s400/Ocelloid2.jpg" border="0" alt="" id="BLOGGER_PHOTO_ID_5625719286138941906" /></a>After several months of contained excitement and preparation, the embargo has been lifted and I can finally announce the unveiling of the new <a href="http://blogs.scientificamerican.com/home">Scientific American blog network</a>, of which I am honoured to be a small part at <a href="http://blogs.scientificamerican.com/ocelloid/">The Ocelloid</a>, my new blog -- focusing, like this one, on protists and evolution, although with a stronger attempt at reaching the lay audience. I will continue blogging here at Skeptic Wonder as before, and since I already don't blog as frequently as I should, not much of a difference should be noticed. Basically, my goal is to have The Ocelloid more general audience friendly and introducing people to the protist world from a more superficial 'wow' angle, while Skeptic Wonder will be cater more to the current crowd that seems to consist mostly of people more qualified than I am about this stuff. It has been a bit awkward trying to reach both types of audiences from the same blog so I think this may work out well for everyone. I'll also keep more raw discussions here and The Ocelloid should be more polished up. We'll see where this goes. From time to time I'll cross-post between them but perhaps it's better to keep the recycling to a minimum. <div><div><br /></div><div>Bora has an <a href="http://blogs.scientificamerican.com/network-central/2011/07/05/welcome-the-scientific-american-blog-network/">amazing detailed introduction to the SciAm network</a> which discusses its purpose as well as awesome overviews of the individual blogs. The <a href="http://www.scientificamerican.com/pressroom/pr/release.cfm?site=sciam&date=2011-07-05">official launch press release is here</a>, as well as a <a href="http://blogs.scientificamerican.com/at-scientific-american/2011/07/05/welcome-to-the-scientific-american-blog-network">welcome post from the Editor-in-Chief</a> and a <a href="http://scientificamerican.com/blog/post.cfm?id=new-at-scientific-american-introduc-2011-07-05">post on The Observations</a>. More once I get home, am out of town right now until tmr with crappy internet and no control over own time...</div></div><div><br /></div><div><span class="Apple-style-span" ><b>EDIT 23:30 05.07.11</b>: Just to clarify things: I <i>am </i>keeping Skeptic Wonder and staying here at FoS as well! And there may be another change here coming up, for the better!</span></div>Psi Wavefunctionhttp://www.blogger.com/profile/10829712736757471647noreply@blogger.com4tag:blogger.com,1999:blog-3643556495084083743.post-73044638594441151972011-06-30T21:24:00.000-07:002011-06-30T21:46:09.828-07:00A Tree of Eukaryotes v1.3a<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>Time for a new tree, finally. Some groups have been fixed and the diagram has moved from Powerpoint to a real vector art program (Illustrator), so hopefully it looks a bit nicer now and has slightly fewer glaring errors. Have yet to fix all issues, the biggest (and hardest) being the proportions taken up by the various groups -- the tree appears dominated by Excavates for some reason. Due to lack of convenient taxa for the heteroloboseans and euglenids, I expanded them to the genus level in some cases to attempt to capture some of the diversity better, but that screwed things up for the rest of the tree. Since fixing that would require some hardcore structural changes to the whole tree, I'll do that later, in the next edition (which will not take over a year to come out this time). Given some conferences coming up this summer, and that people have asked, I'll release what I have done now as v1.3a. <div><br /></div><div>Enjoy! (And do complain if you spot anything awry...)<div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjUMQ-vrtrJ5zZqVdKZR07qkMx9Ffs9zp57Oivn_Y_K7ZtO4XU94nSEy6jyxQcz6wXjCEqbqRUNucov1q4m1OChZ70SKb6tSWPO0-freqS4n0t1_s-HZbIsqaU0jY-MJp02WZZ5lHNrEqTl/s1600/ToE+2010+v1-4a+h-res+PsiW.jpg" onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"><img src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjUMQ-vrtrJ5zZqVdKZR07qkMx9Ffs9zp57Oivn_Y_K7ZtO4XU94nSEy6jyxQcz6wXjCEqbqRUNucov1q4m1OChZ70SKb6tSWPO0-freqS4n0t1_s-HZbIsqaU0jY-MJp02WZZ5lHNrEqTl/s400/ToE+2010+v1-4a+h-res+PsiW.jpg" border="0" alt="" id="BLOGGER_PHOTO_ID_5624239506887866786" style="cursor: pointer; width: 309px; height: 400px; " /></a></div><div>Previous versions and discussions, along with trees by other people, <a href="http://skepticwonder.fieldofscience.com/search/label/Tree%20of%20Eukaryotes">can be found here</a>.</div></div><div><br /></div><div><b>References</b></div><div>A shit ton (see image). But ResearchBlogging.org doesn't allow indexing 'shit ton', so I'm gonna be pathetically lazy and just cite this:</div><div><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Trends+in+Ecology+%26+Evolution&rft_id=info%3Adoi%2F10.1016%2Fj.tree.2005.09.005&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=The+tree+of+eukaryotes&rft.issn=01695347&rft.date=2005&rft.volume=20&rft.issue=12&rft.spage=670&rft.epage=676&rft.artnum=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0169534705003046&rft.au=Keeling%2C+P.&rft.au=Burger%2C+G.&rft.au=Durnford%2C+D.&rft.au=Lang%2C+B.&rft.au=Lee%2C+R.&rft.au=Pearlman%2C+R.&rft.au=Roger%2C+A.&rft.au=Gray%2C+M.&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CProtistology%2C+Evolutionary+Biology">Keeling, P., Burger, G., Durnford, D., Lang, B., Lee, R., Pearlman, R., Roger, A., & Gray, M. (2005). The tree of eukaryotes <span style="font-style: italic;">Trends in Ecology & Evolution, 20</span> (12), 670-676 DOI: <a rev="review" href="http://dx.doi.org/10.1016/j.tree.2005.09.005">10.1016/j.tree.2005.09.005</a></span></div>Psi Wavefunctionhttp://www.blogger.com/profile/10829712736757471647noreply@blogger.com10tag:blogger.com,1999:blog-3643556495084083743.post-55477380663361981312011-06-21T15:10:00.000-07:002011-06-21T16:17:57.846-07:00An update!<p> </p><p>No, not the annoying kind that secretly restarts your computer in the background because you just bought it and haven't gotten around to deactivating auto-update yet and told it to fuck off the last few times so it didn't pop up the window anymore because it was sad. Or the kind that Adobe's PDF reader mysteriously wants about four times a day. Just a very late bloggy kind.<br /></p><p>Apologies for disappearing for a while there. Personal issues came up and didn't really feel like writing about science (or reading much about it for a while). Long story short, I'm may well be a failed scientist at this point (no grad school for me, yay), and the academic career is one of the few where once you fall off the track, it's practically impossible to get back on. And unlike in most other careers, the skills you acquire by that point are nontransferable anywhere else, meaning you're screwed, period. Add to that the worst economy since the Great Depression, and the party starts off with a bang. That said, I'll continue with my attempts to sneak past academia's fortifications under the cover of night, if no other reason than that banging my head against brick walls fucking arouses me.</p><p>Anyway, I'm getting back to blogging now. Should at least take advantage of the fact I still have a computer and internet; might be a bit harder to blog when unemployed and homeless ;-)</p><p><b>News</b><br />There are some exciting developments next month: one I can't tell you about yet as it's part of bigger news; the other is that I'll be going to a phycology-protistology meeting (PSA-ISoP) mid-July and will be officially blogging it! There's lots of awesome research going on in the area and I'm happy I'll be able to share some of it with you.</p><p><strong>Microscopy Reddit Community</strong><strong> - <a href="http://www.reddit.com/r/microscopy/">/r/microscopy</a></strong><br />Every once in a while a stack of undeciphered micrographs appears before someone's conscience, and every once in a while a resolution of this issue is attempted by approaching yours truly. I'm still a novice to the realm of the small, and usually fail to identify creatures (or artefacts) in question, leaving behind a trail of disappointment and pristine befuddlement. Forwarding those images to friends and colleagues would be awkward, since those people have enough on their plate to begin with. In short, would be nice to have a centralised place where people could share images and others could voluntarily look them over and comment on them. Micro*scope/EOL is a nice image repository, but generally the images there are of good quality and are finished products; furthermore, I still don't know how to work the interface there despite having access privileges. What would be great is if people could host images wherever they like, and then link to them in a centralised place for discussion where anyone could participate. In other words, <a href="http://www.reddit.com/">Reddit</a>. </p><p>There already was a microscopy subreddit (a Reddit community), but it was largely inactive and abandoned. Anyway, I'm now a moderator there, and would like to develop it into a community where micrographs of all sorts can be shared and discussed, with emphasis on microbial organisms (but sliced up macrobes welcome too). Creating an account is really easy, as is submitting a link (just make sure it goes to /r/microscopy and not some other area of reddit). We need participants though, so if you have any neglected mystery images, please post them, and if you're in the mood to browse micrographs from time to time, feel free to stop by! Just keep in mind anyone can see the subreddit including the images, so careful with potentially publication-worthy data...</p><p>Hope to see you there!</p><p><b>Random link</b><br />There's a <a href="http://shilovpope.livejournal.com/"><b>really awesome Russian underwater macrophotography blog</b></a> I came across a while ago that you should all know about. The photos are stunning, mainly of pretty tiny inverts in the White Sea in northern Russia (and plenty of shots of Northern Lights and white nights and all that).</p>Psi Wavefunctionhttp://www.blogger.com/profile/10829712736757471647noreply@blogger.com8tag:blogger.com,1999:blog-3643556495084083743.post-52714527305827944862011-05-21T08:03:00.000-07:002011-05-21T08:47:04.895-07:00Sticky proteins, complexity drama and selection's blind eye<span style="color: rgb(0, 0, 153);">*For your entertainment, rejected titles:</span><br /><span style="color: rgb(0, 0, 153);">[Sticky proteins and complex relationships]</span><br /><span style="color: rgb(0, 0, 153);">[(protein) Relationship drama: promiscuous proteins in small populations]</span><br /><span style="color: rgb(0, 0, 153);">[Not all is good that sticks: non-adaptive complexity gain through compensatory protein adhesion]</span><br /><span style="color: rgb(0, 0, 153);">[Man, I suck at titles]</span><br /><br />NB: This post can be considered as part 2.5 of my <a href="http://skepticwonder.fieldofscience.com/2010/04/in-defense-of-constructive-neutral.html">In defense of constructive neutral evolution series</a>; also recommended for some background are <a href="http://skepticwonder.blogspot.com/2010/03/in-defense-of-constructive-neutral.html">part 1, discussing selection, drift and Neutral Theory</a>, and<a href="http://skepticwonder.fieldofscience.com/2010/04/in-defense-of-constructive-neutral.html"> part 2, discussing Constructive Neutral Evolution</a>; to answer a popular question, part 3 *will* materialise <s>eventually</s> once I get off my ass and write it.<br /><br /><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: 0pt none;" /></a></span>Constructive neutral evolution is one mechanism of complexity increase without any associated increase in fitness – or, in other words, non-adaptive complexity gain. Basically, a random interaction between two proteins can lead to a fixed dependency if this interaction compensates for a mutation that was otherwise lethal – termed 'pressuppression'. In this way, previously unnecessary dependencies accumulate to make a very bulky, bureaucratic system that essentially does the same thing. We've all seen it in our institutions, and evolution is about as efficient.<br /><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj0g_i6c2ye6kYtc-V2yPEYbfvJn3kAkLLu4kUb33pAWqplsVqQ4K0g8T1NYjorYR40dalbRhR7Tmon0KSwnzSDQWICJGn3gkVYjS-Yw4aIWugXTlWR3swF3_cF90oYa8vooaydH4SxmOf3/s1600/CNE+overview"><img style="cursor: pointer; width: 400px; height: 274px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj0g_i6c2ye6kYtc-V2yPEYbfvJn3kAkLLu4kUb33pAWqplsVqQ4K0g8T1NYjorYR40dalbRhR7Tmon0KSwnzSDQWICJGn3gkVYjS-Yw4aIWugXTlWR3swF3_cF90oYa8vooaydH4SxmOf3/s400/CNE+overview" alt="" id="BLOGGER_PHOTO_ID_5457685210013458626" border="0" /></a><br /></div>Now, one bottleneck in this model is waiting for proteins to actually interact. Proteins are quite sticky and non-specific by nature, but usually not too much as that can be quite deleterious. Piling up a bunch of proteins on each other has a non-negligible chance of interfering with their function, and one would expect for chance interactions to not be excessively promiscuous, although those who have done regulatory genetics and protein work are probably aware just how annoyingly non-specific some of the protein binding can get. Luckily, there is now a possibly mechanism boosting these chance interactions, and thus alleviating that particular bottleneck in the Constructive Neutral Evolution process, rapidly accelerating complexification and protein network obfuscation to the extent where the interaction map looks like a web; not a finely organised web of an orb-weaver but rather one of those clumpy webs that are a clusterfuck of stickiness and silk. Enter this week's <a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09992.html">Fernández and Lynch 2011 <span style="font-style: italic;">Nature</span></a> paper, from here onwards referred to as "the paper".<br /><br />Protein 'stickiness' can be enhanced by biochemical means. Proteins vary in stability, and themselves come in populations – generally, most are in the optimal conformation that is presumably functional, but some individuals are messed up. This happens well past the sequence and folding errors, and some perfectly 'normal' proteins can be in a suboptimal state at any given time. Clearly, this affects the overall efficiency of the protein – even if it's enzymatically awesome, the overall 'protein' as we biologists understand it (<span style="font-style: italic;">sans</span> population aspect) would decline in efficiency if a large chunk of its population is in a misfolded state.<br /><br />One aspect that pushes around the proportion of the protein in the 'right' conformation is how well it plays with water. It shouldn't be too surprising that hydrophobic regions induce instability. What was new to me, but perhaps old news to those who actually <span style="font-style: italic;">understood</span> chemistry, is that the exposure of the polar(hydrophilic) protein backbone to water also has a destabilising effect – and not only that, but often more significant than that of exposed hydrophobic regions! This may seem counterintuitive – doesn't water <span style="font-style: italic;">like</span> hydrophilic regions? And there lies our problem.<br /><br />Water molecules are attracted to polar groups, and the amino acid backbone is quite polar. This means little water molecules wander in towards the backbone and form hydrogen bonds with it. The problem is twofold: first of all, the protein, like all molecules, likes to 'jiggle'. The more it can jiggle in its given conformation, the more favourable that conformation is thermodynamically since its satisfied by more states. Entropy, etc. (now we're *really* entering territory I know nothing about, since my phys chem experience is locked away by PTSD...). Hooking up this backbone with water molecules reduces its 'jiggle' room, and makes it less thermodynamically stable – making change to other conformations more probable, therefore possibly leading to more errors in the protein population.<br /><br />Secondly, as detailed further in the paper, water likes to hang out with more of itself. Water molecules are happiest in foursomes, sharing four hydrogen bonds with their neighbours. When a creepy protein backbone emerges and lures an unsuspecting water molecule away into the protein's murky depths, the water molecule cannot form as many bonds with its fellows (or as many hydrogen bonds, period), and is really sad and lonely. Or, in proper terms, the system becomes less stable, since thermodynamics will favour an arrangement where these water molecules are all happily coordinated with each other, and not being molested in a corner by an amino acid polar group. In other words, exposing the polar backbone (Solvent-Accessible Backbone Hydrogen Bonds, SABHBs in the paper) to water induces what is called Protein-Water Interfacial Tension (PWIT).<br /><br />One way this tension can be released and the backbone exposure ('coded for' by genes, by the way) can be compensated for is if a random other protein (or more of its own kind) are recruited to cover that exposed backbone. This would help stabilise the protein conformation, and allow this potentially deleterious drawback to be tolerated (and get fixed in the population). Ultimately, the second (and third, etc) protein can become exapted for something useful, although just an eventual dependency is good enough to make sure these proteins stick together permanently. The crazy web of interactions gets crazier.<br /><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiUlaeB9Fqh5fzV3j0A8ovOC1nauvLQbsF0RggfX5Y4LToZTiiiFPfUwmULBD-SIoHsWOurmPZ-tGAxB0n0wFTAvDlIuUTBasLCvkxVZEtHVvg1wpd9vrr0vFT4lYmJOaqjs6HG1OwOkXOv/s1600/PWIT+based+on+FernandezLynch2011N.jpg"><img style="cursor: pointer; width: 271px; height: 400px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiUlaeB9Fqh5fzV3j0A8ovOC1nauvLQbsF0RggfX5Y4LToZTiiiFPfUwmULBD-SIoHsWOurmPZ-tGAxB0n0wFTAvDlIuUTBasLCvkxVZEtHVvg1wpd9vrr0vFT4lYmJOaqjs6HG1OwOkXOv/s400/PWIT+based+on+FernandezLynch2011N.jpg" alt="" id="BLOGGER_PHOTO_ID_5609161102458889202" border="0" /></a><br /><span style="font-size:85%;">Fernández & Lynch's fig1a suffices perfectly but I like making diagrams, so I made one anyway. See text.</span><br /></div><span style="color: rgb(153, 0, 0);">(Disclaimer: I'm horrible at chemistry, this may all have been thoroughly wrong...read the paper.)</span><br /><br />Now I'm about the last person to willingly blog about biochemistry, and this seems to have little only a distant relevance to evolution, particularly the non-adaptive kind that fascinates yours truly. It will make sense in a bit. Recall from a few seconds ago (hey, already difficult for some of us) that protein instability leads to reduced protein efficiency. This reduction is generally tolerated, however, until it's bad enough to have a higher chance of being removed. Recall from [what should be] introductory population genetics that selection acts probabilistically, with true slightly deleterious mutations have a lesser, but still significant, chance of fixation than strongly deleterious mutations, which selection has a higher chance of taking care of before drift quietly fixes it. (<a href="http://skepticwonder.blogspot.com/2010/03/in-defense-of-constructive-neutral.html">more detail in older post here</a>) Since proteins are, quite unsurprisingly, also governed by fundamental principles of population genetics, drift becomes involved there too.<br /><br />As populations get smaller, drift becomes a more dominant force relative to selection, and the window of 'effectively neutral' mutations – slightly beneficial and slightly deleterious, but unlikely to be dealt with by selection – <span style="font-style: italic;">increases</span>. More mess is tolerated. This means more protein inefficiencies are allowed to fix in the population, those induced by backbone exposure among them. Since there are now more proteins that are no longer happy with themselves (or, rather, have an increased Protein-Water Interfacial Tension), they are more likely to stick together for biochemical stability. And here Constructive Neutral Evolution can come in too, allowing further deleterious mutations that are now presuppressed by the recruited proteins. In a way, this greases the presuppression process, rather than competing with it as this <a href="http://www.bbc.co.uk/news/science-environment-13445951">BBC news piece </a>made Ford Doolittle appear to suggest.<br /><br />Now, this is all great in theory, but is there any real data in support of this? For one thing, there is a clear increase of interactome (set of all interactions in an organism) complexity correlating with decrease in effective population size, suggesting a link between lax selection and accumulating complexity. Furthermore, the proteins in organisms of these smaller populations have more blistering backbone exposures to water. Supporting the relationship with population size further yet with the advantage of more phylogenetically independent events (but less interactome data), bacterial intracellular endosymbionts <span style="font-style: italic;">consistently</span> exhibit higher protein backbone exposure (hydration) than their free-living counterparts. Selection appears to disfavour not only polar backbone exposure (also described as 'poorly wrapped proteins' in the paper), but once again, the rise of interaction complexity as a whole. (<a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09992.html">Fernández and Lynch 2011 <span style="font-style: italic;">Nature</span></a>, in case you somehow managed to miss that)<br /><br />Obviously I like this paper because it adds another mechanism to the arsenal of evolutionary processes happening independently of adaptation. But moreover, I don't think one can find too many examples of biochemistry mixed with population genetics. You hardly find cell and developmental biologists thinking about population genetics, and perhaps many biochemists have never even been exposed to such a subject. When fields that should never come that close together do, some really nice explosions of insight can occur (my sad attempt at chemical metaphors). We really need to talk to other more, and maybe even wander over to other departments from time to time. It's sometimes (often) frustrating to communicate with those strange ones from afar, but just like ethnic xenophobia, its interdisciplinary counterpart must also be overcome.<br /><br />-----<br />Figure 2a annoyed me a little as it ignored phylogenetic relationships, which is a big no-no when comparing properties of taxa. The figure is technically fine, especially since there aren't any correlation analyses there, but it's hard to discount phylogenetic history as being the cause behind the correlation of the traits without actually the characters on a tree. Anyway, since I like playing with data and running statistical analyses on things, especially when I didn't actually have to go through the pain of obtaining the data myself, I mapped some characters (interactome complexity from fig2a) on a phylogeny:<br /><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhyqGcMEYKbYq83LKl5qon96Dp2tYG3vZD0V2jt3fWmGuTYJEe7NPu8OD_TfnOgXQScrSBDCLDrWuDs-cYhrxsncBYpkV5z1X1STOwfC2RU4B_Uo_Z4ACfl7c9j6C9vuFJRpcCOh8Z1xqap/s1600/Interactome-charstate-PsiW.jpg"><img style="cursor: pointer; width: 400px; height: 265px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhyqGcMEYKbYq83LKl5qon96Dp2tYG3vZD0V2jt3fWmGuTYJEe7NPu8OD_TfnOgXQScrSBDCLDrWuDs-cYhrxsncBYpkV5z1X1STOwfC2RU4B_Uo_Z4ACfl7c9j6C9vuFJRpcCOh8Z1xqap/s400/Interactome-charstate-PsiW.jpg" alt="" id="BLOGGER_PHOTO_ID_5609142973815972210" border="0" /></a><br /></div><br /><br />Unfortunately, even the most basic statistical operations become an epic headache when trees are involved, and very quickly things become painfully complicated, for the human as well as the computer. Especially when you're handed a dataset of mixed categorical and continuous characters, as I learned the hard way last night. After fighting Mesquite for a good many hours, I finally had to resort to extracting the Ne*µ (effective pop size * mutation rate; roughly put, both lead to increased selection efficiency) estimates from Lynch & Conery 2003 – relying on an intersection of two datasets meant that our taxon sampling was quite sad by the end of this enterprise. Anyway, I ran a pairwise comparison test (<a href="http://www.ncbi.nlm.nih.gov/pubmed/10660474">Maddison 1999 <span style="font-style: italic;">J Theor Biol</span></a>) on the data, which probably isn't the best thing ever, but I got something resembling significance: p = 0.019. Depending on how statistically noisy your field is, you may even deem this acceptable. In any case, not too bad given my crude (and somewhat clueless) analysis and limited taxon sampling:<br /><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiMqdNVwjAdEAdqOEKLgMzEbN0LeIlsb9GXQ-qwGnHVlL0gV8qCNPVQ75leFsJwRCu_A_NdZOU3xil9vexS2k1MGiXhrxPcEKIfp0aUMNDUuD2nRyAzzTdxKeXpg7VcTvMWyr0FfpPbmN6F/s1600/Pairwise-Interactome-PsiW.jpg"><img style="cursor: pointer; width: 400px; height: 201px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiMqdNVwjAdEAdqOEKLgMzEbN0LeIlsb9GXQ-qwGnHVlL0gV8qCNPVQ75leFsJwRCu_A_NdZOU3xil9vexS2k1MGiXhrxPcEKIfp0aUMNDUuD2nRyAzzTdxKeXpg7VcTvMWyr0FfpPbmN6F/s400/Pairwise-Interactome-PsiW.jpg" alt="" id="BLOGGER_PHOTO_ID_5609162049032415890" border="0" /></a><br /></div>Moral of the story: the inverse correlation between interactome complexity and effective population size is unlikely to be a mere artefact of shared phylogenetic history. In other words, Fernández & Lynch's hypothesis stands strong.<br /><br />I mostly did this because I thought it'd take a couple hours max. If hours meant days, that wasn't too far off... but hey, I learned something!<br /><br />Acknowledgments: thanks to Lucas Brouwers for helping me wade through the heavy biochemical stuff, and to Mike Lynch for explaining the key idea of the paper a while earlier. Otherwise I would've probably been too daunted to even read it, let alone blog about it...<br />Oh, and my Twitter people for random phylogenetics advice ;-)<br /><br /><span style="font-weight: bold;">Reference</span><br /><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Nature&rft_id=info%3Adoi%2F10.1038%2Fnature09992&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Non-adaptive+origins+of+interactome+complexity&rft.issn=0028-0836&rft.date=2011&rft.volume=&rft.issue=&rft.spage=&rft.epage=&rft.artnum=http%3A%2F%2Fwww.nature.com%2Fdoifinder%2F10.1038%2Fnature09992&rft.au=Fern%C3%A1ndez%2C+A.&rft.au=Lynch%2C+M.&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CCell+Biology%2C+Biochemistry%2C+Molecular+Biology%2C+Evolutionary+Biology">Fernández, A., & Lynch, M. (2011). Non-adaptive origins of interactome complexity <span style="font-style: italic;">Nature</span> DOI: <a rev="review" href="http://dx.doi.org/10.1038/nature09992">10.1038/nature09992</a></span><br /><br /><span style="color: rgb(0, 0, 153);">[will add some supplementary refs once I return to internet on Monday...]</span>Psi Wavefunctionhttp://www.blogger.com/profile/10829712736757471647noreply@blogger.com3tag:blogger.com,1999:blog-3643556495084083743.post-54226375370514863072011-05-17T05:08:00.000-07:002011-05-17T07:05:53.678-07:00Ratcheting up some splice leaders: a note on directionality<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: 0pt none;" /></a></span>In the sea of eukaryotic genetic diversity also lurk different manners of doing day-to-day genome work itself. Ciliates run two nuclear genomes, trypanosome kinetoplasts contain a chainmail suit of RNA editing circles and dinoflagellates are just weird in every genome compartment they have. Their plastids contain tiny minicircles often containing but a single gene, capable of "rolling" transcription where the minicircle is much like a Mesopotamian cylindrical seal, leaving a concatenated repeated string of genes on the transcript. The mitochondria have linear genomes with short fragmented repeated chunks of important genes all over them. But the nuclear genome is the most fucked up: for one thing, dinoflagellates lack a few histones, and have enormous genomes stored in absolutely bizarre chromosomes. More importantly for our story: every single gene must be trans-spliced with a 'splice leader', a short sequence that attaches at the beginning of the mRNA transcript and brings to it the 3' cap necessary for transcription to work. Oddly enough, Euglenozoans like the trypanosomes and euglenids seem to have a very similar system, evolved entirely by chance* convergence (Lukes et al. 2009 <span style="font-style: italic;">PNAS</span> goes over this remarkable convergence in more detail).<br /><br />*Or perhaps something happened to both that made them prone to evolve this bizarre system.<br /><br />Genomic quirks are not just interesting in their own right as some arcane oddities, but can reveal a great deal about the dynamics of genomes in general. The dinoflagellate splice leader system turns out to yield a very crisp illustration of the power of ratchets and the toll of reverse transcription on genomes.<br /><br />To reiterate, every single nuclear gene transcript in a dinoflagellate must be spliced with the 3'cap-bearing 'splice leader', or else it simply won't work. This means that the dino is full of mature transcripts with splice leaders attached to the transcribed genes. Enter reverse transcriptases, which are prevalent in probably most, if not all, eukaryotic genomes, thanks to viruses and their partners in genomic parasitism crimes, transposons. When they're not busy moving transposons around and helping viruses move in, they reverse transcribe random gene transcripts for fun, that may then, on occasion, be successfully recombined back into the genome. This process probably doesn't happen [successfully] every day, but over thousands or millions of years (and countless individuals) is rampant enough to leave a noticeable trace in the genome.<br /><br />So we have a load of transcripts floating around with an extra sequence stitched onto them from the splice leader. Do the reverse transcriptases care in the slightest? Of course not: to them, a ribonucleotide is a ribonucleotide, give or take some trace biophysical stuff that <span style="font-style: italic;">might</span> make a couple people cringe at what I just said. (meaning, I wouldn't be surprised if there could be some slight but ultimately detectable biases there too) This means that splice leader, on occasion, actually makes its way back into the nuclear genome attached to the beginning of the gene.<br /><div style="text-align: center;"><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjzmhuVo9UAglNYT4QnERgi3iGma4bIKPhB-LapKiX8FUDntVgKo7OzNn5zJzaXLkkVqqngtx3LwuIaX7d_lHzwiZP11sLlix8oqqKDR2MxiD-B5OCQojUz1jGAwGLajWEViGVGlYeNQMgG/s1600/Dino+SL+evol+ref+Slamo+Keeling+2008.jpg"><img style="cursor: pointer; width: 400px; height: 332px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjzmhuVo9UAglNYT4QnERgi3iGma4bIKPhB-LapKiX8FUDntVgKo7OzNn5zJzaXLkkVqqngtx3LwuIaX7d_lHzwiZP11sLlix8oqqKDR2MxiD-B5OCQojUz1jGAwGLajWEViGVGlYeNQMgG/s400/Dino+SL+evol+ref+Slamo+Keeling+2008.jpg" alt="" id="BLOGGER_PHOTO_ID_5590219218708898130" border="0" /></a><br /><div style="text-align: left;">However, this splice leader does not substitute for the usual splice leader trans-splicing, since the 3' cap must be added again, or else the transcript will not be translated. That now-nuclear gene-attached splice leader ends up being <span style="font-style: italic;">completely useless</span>, and is able to gradually degrade into benign junk, provided it doesn't mess with the translation of the gene. What is really cool is that one can actually see this gradual degradation, as shown in Slamovits and Keeling 2008 <span style="font-style: italic;">Current Biol</span>:<br /></div><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiyhLjkdu35IWeVjqNOT2y13x38A5l_n-SzjrffvBV9nMqRodWxa2bULPrxvkn7VCNnTsvCSR7QHekqsZBHWEP8ZN60yFJkMPFZjMr0hBl5cXXA5sQcDMOUrBdKhyphenhyphen4vgBvvZgeCJCCQb-0O/s1600/Slamovits+Keeling+2008+Curr+Biol+Dino+SL+evol.jpg"><img style="cursor: pointer; width: 400px; height: 227px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiyhLjkdu35IWeVjqNOT2y13x38A5l_n-SzjrffvBV9nMqRodWxa2bULPrxvkn7VCNnTsvCSR7QHekqsZBHWEP8ZN60yFJkMPFZjMr0hBl5cXXA5sQcDMOUrBdKhyphenhyphen4vgBvvZgeCJCCQb-0O/s400/Slamovits+Keeling+2008+Curr+Biol+Dino+SL+evol.jpg" alt="" id="BLOGGER_PHOTO_ID_5590223702110684754" border="0" /></a><br /><span style="font-size:85%;">Mmmm, actual data! Note how the oldest SL piece closest to the gene (on the right) is the most degraded. (<a href="http://dx.doi.org/10.1016/j.cub.2008.04.054">Slamovits & Keeling 2008 Curr Biol</a>)<br /></span><br /><div style="text-align: left;">Once the unnecessary splice leader chunk becomes part of the gene, the gene gets transcribed and trans-spliced like any other – meaning it is once again susceptible to replaying that same process of reverse transcription, except this time it already has a relict sequence. It can acquire a second one on top of that. This explains how there can be several concatenated splice leader relics tagging along, like in the above figure.<br /><br />Splice leader trans-splicing not necessarily promoting reverse transcription – only makes it easier to detect. In other words, it inadvertently makes for a wonderfully convenient system where you can actually track what happens to a gene after it gets reverse transcribed. Once the gene makes its new home, the old gene copy is still present and they generally would be functionally redundant, so the dual-copy state is extremely unstable as ultimately the loss of one of the copies will be tolerated. If the newly transcribed copy is lost, we never see it and thus don't talk about it in the first place. However, once the clean original is lost, only the gene with the crap from the splice leader remains, and reversal to the original state is so improbable it's practically impossible. In other words, this process is a wonderful example of an evolutionary ratchet.<br /></div><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjvCQs3ot-o7VW7dMgit-HmW3cf8cljz7prAY13Qq_GCyNL3yaHbJw-baNzpMDxE5L2Ddgio8dwdAqCPAKYIraasz_uKiGGmBioXmG0OUZ-h_mfYfYpIasBFPY56zoEWWg8MaRbbAEasjXC/s1600/Dino+SL+evol+ratchet+ref+Slamo+Keeling+2008.jpg"><img style="cursor: pointer; width: 400px; height: 314px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjvCQs3ot-o7VW7dMgit-HmW3cf8cljz7prAY13Qq_GCyNL3yaHbJw-baNzpMDxE5L2Ddgio8dwdAqCPAKYIraasz_uKiGGmBioXmG0OUZ-h_mfYfYpIasBFPY56zoEWWg8MaRbbAEasjXC/s400/Dino+SL+evol+ratchet+ref+Slamo+Keeling+2008.jpg" alt="" id="BLOGGER_PHOTO_ID_5590234644895902706" border="0" /></a><br /></div>Ratchets are interesting because they confer intrinsic directionality to a system, even in the absense of external pressures (like selection). The accumulation of splice leader junk in the dinoflagellate's genes isn't particularly healthy, nor is it particularly deleterious – it's effectively neutral. However, one can argue that we do have an example of bloated complexity here. Since you can't go back and lose chunks of splice leaders, this ratchet essentially ensures that left to its own devices, this aspect of genome complexity will increase on its own. At a certain point, there will probably be ever-increasing selection against accumulating further splice leaders, and those lineages that go too far will simply die off – the central tendency doesn't care, and the ratchet will keep on going regardless of what selection 'wants'.<br /><br />This ratchet example is therefore an elegant case of evolutionary direction that's not particularly well explained by the central dogmas of Modern Synthesis or (neo)Darwinism, where selection is the force that crafts order and directionality, with mutation a mere passive provider of material to be molded. I will go into a deeper discussion of this in another post (there's a cool paper coming out soon), but I think it's worth briefly mentioning here too while we're at it. The "mutation" step (to which, I guess, this trans-splicing and reverse-transcription process can be awkwardly attached) here is what provides a drive, a push in a certain direction, and towards increasing complexity, no less (although that last detail is irrelevant). While selection is present and provides constraints (if both genes are lost, for example, the organism dies), it does not do the 'driving' or 'forcing' in this system. Very crudely put, selection here is<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjQgYGXmjrzc4lA1YMyzKpf4uQIm4e2l0nGcRg0suRxbSM4K8NuWsUvxi40RFwoIHeBXOy-lS8FUcf7s93GtOXC2MmSudRaM3aBDh4M5q28_nOkHESDOTwMpq7u35GK8jXEBK98U6sFi1ft/s1600/Neutral_Directionality.jpg"><img style="float: right; margin: 0pt 0pt 10px 10px; cursor: pointer; width: 242px; height: 335px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjQgYGXmjrzc4lA1YMyzKpf4uQIm4e2l0nGcRg0suRxbSM4K8NuWsUvxi40RFwoIHeBXOy-lS8FUcf7s93GtOXC2MmSudRaM3aBDh4M5q28_nOkHESDOTwMpq7u35GK8jXEBK98U6sFi1ft/s400/Neutral_Directionality.jpg" alt="" id="BLOGGER_PHOTO_ID_5593192480221838530" border="0" /></a> the passive phenomenon, and mutation is at the wheel.<br /><br />Another case of intrinsic directionality, but where reversal is allowed, is your garden variety directional bias – where proceeding in one direction is more probable than going backwards. A very basic example of that is if the replication machinery favours a certain type of nucleic acid – left to its own devices, the genome base composition would be skewed in that direction. Boundaries can also induce an apparent directionality, but in this case it's no longer intrinsic... that's, again, a topic for another day.<br /><br />This idea was a part of the Mutationism theories in the early 20th century, which were a little extreme and perhaps premature, since mutation was far from being even marginally understood at the time. In the usual melodramatic manner characteristic of academia and the scientific community, the pendulum swung far to the opposite extreme, and Modern Synthesis was born. It became heresy to think that mutation itself can actively contribute to direction and order. The field became engulfed in a false dichotomy, where either selection or mutation can actively provide direction, with the modern folk siding with the former. That is a serious mistake and an unnecessary waste of great explanatory potential – you can go so much farther with selection, drift, mutation and recombination all at the wheel, each pulling with different magnitudes in various directions. Well, technically, you wouldn't if you were the thing being pulled – which resonates so well with the absense of 'ascension' or general active directionality in the evolutionary system as a whole. Evolution is a slow, painful, inefficient and rather stochastic process, partly because the cart is being pulled in so many ways.<br /><br />(The latter part, concerning directional biases and Mutationism, is based on various publications and conversations with Arlin Stoltzfus and Dan McShea, whom I gratefully acknowledge. =D)<br /><br /><span style="font-weight: bold;">References:</span><br /><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Current+Biology&rft_id=info%3Adoi%2F10.1016%2Fj.cub.2008.04.054&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Widespread+recycling+of+processed+cDNAs+in+dinoflagellates&rft.issn=09609822&rft.date=2008&rft.volume=18&rft.issue=13&rft.spage=0&rft.epage=0&rft.artnum=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0960982208005769&rft.au=Slamovits%2C+C.&rft.au=Keeling%2C+P.&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CProtistology%2C+Molecular+Biology%2C+Evolutionary+Biology"><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Journal+of+Evolutionary+Biology&rft_id=info%3Adoi%2F10.1046%2Fj.1420-9101.2001.00283.x&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=The+minor+transitions+in+hierarchical+evolution+and+the+question+of+a+directional+bias&rft.issn=1010-061X&rft.date=2001&rft.volume=14&rft.issue=3&rft.spage=502&rft.epage=518&rft.artnum=http%3A%2F%2Fdoi.wiley.com%2F10.1046%2Fj.1420-9101.2001.00283.x&rft.au=McShea%2C+D.&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CEvolutionary+Biology">McShea, D. (2001). The minor transitions in hierarchical evolution and the question of a directional bias <span style="font-style: italic;">Journal of Evolutionary Biology, 14</span> (3), 502-518 DOI: <a rev="review" href="http://dx.doi.org/10.1046/j.1420-9101.2001.00283.x">10.1046/j.1420-9101.2001.00283.x</a></span><br /><br />Slamovits, C., & Keeling, P. (2008). Widespread recycling of processed cDNAs in dinoflagellates <span style="font-style: italic;">Current Biology, 18</span> (13) DOI: <a rev="review" href="http://dx.doi.org/10.1016/j.cub.2008.04.054">10.1016/j.cub.2008.04.054</a></span><br /><br /><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Evolution+%26+development&rft_id=info%3Apmid%2F16686641&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Mutationism+and+the+dual+causation+of+evolutionary+change.&rft.issn=1520-541X&rft.date=2006&rft.volume=8&rft.issue=3&rft.spage=304&rft.epage=17&rft.artnum=&rft.au=Stoltzfus+A&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CEvolutionary+Biology">Stoltzfus A (2006). Mutationism and the dual causation of evolutionary change. <span style="font-style: italic;">Evolution & development, 8</span> (3), 304-17 PMID: <a rev="review" href="http://www.ncbi.nlm.nih.gov/pubmed/16686641">16686641</a></span>Psi Wavefunctionhttp://www.blogger.com/profile/10829712736757471647noreply@blogger.com2tag:blogger.com,1999:blog-3643556495084083743.post-46504177011271519342011-05-09T03:17:00.000-07:002011-05-09T03:31:52.274-07:00Protistology Q&A on Reddit + gratuitous ciliate videoEarlier today I felt like procrastinating a little and posted a protistology IAmA thread on Reddit (basically threads where the opening poster answers questions, titles formatted like this: I Am A XYZ, Ask Me Anything). I expected a couple questions before the thread disappears forever into the obscurity of the great internet graveyard. Shockingly enough, apparently people actually care about science or something because I was typing away non-stop at a blizzard of questions for a few hours, until now. It was quite inspiring to see the type of questions people can come up with (even the basic badly-worded ones show that at least people care enough to ask), and learned a few things along the way too. Anyway, I'll come back to answer more stuff tomorrow, but here's the thread for the curious. Feel free to stop by and ask stuff! I find that sometimes the blog comment area can be a bit intimidating if you feel you have a dumb question, so you don't ask anything. Reddit dilutes that effect, and is quite a bit more anonymous.<br /><br /><a href="http://www.reddit.com/r/IAmA/comments/h6wq3/iama_protistologist_i_study_the_99_of_eukaryotes/"><span style="font-weight: bold;">Protistology Q&A on Reddit</span></a><br /><br />And now to randomly show off a random Haptorian ciliate – meet <span style="font-style: italic;">Litonotus</span>, a vicious predator armed with terrifying toxicysts, which you can see as long narrow things in its cytoplasm. Also note the two prominent macronuclei visible as clear-ish round areas in the cell. <span style="font-style: italic;">Litonotus</span> is cool and all, but the bastard preys on creatures like <span style="font-style: italic;">Euplotes</span>, which are kind of adorable (imagine <span style="font-style: italic;">Litonotus</span> eats kittens...that's how bad it is). Nature is red in <s>tooth</s> cytostome and <s>claw</s> cilium indeed...<br /><div style="text-align: center;"><iframe src="http://www.youtube.com/embed/OSnMgtFDpzQ" allowfullscreen="" frameborder="0" height="390" width="640"></iframe><br /></div>Psi Wavefunctionhttp://www.blogger.com/profile/10829712736757471647noreply@blogger.com2tag:blogger.com,1999:blog-3643556495084083743.post-77686436509060959702011-05-07T21:57:00.000-07:002011-05-07T22:04:41.925-07:00MolBiol Carnival #10: Assays, cyanobacteria and metabolism regulation<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://molbiocarnival.blogspot.com/"><img style="float: left; margin: 0pt 10px 10px 0pt; cursor: pointer; width: 239px; height: 239px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg_RhxuX8CLBjWS2lUFPTXGEnFJ4EHwxCRUpznO94jB8k8trlG8PE6onfT84Xe7OkO8pniS6tsLBRTuV1eyPWZfPPOyWPlFbhA2_FYrL5nLYGOP3nwoGCKeVf1Jd5jwg8Cj5WJX84yb0yTv/s400/MolBiolCarn.png" alt="" id="BLOGGER_PHOTO_ID_5603118879082527682" border="0" /></a>Welcome to the 10th edition of the MolBiol Carnival!<br /><br />Apologies for the delay – am behind on pretty much everything and frantically trying to tie up loose ends of my degree, fun times. Also, it's kinda awkward to write up a carnival post with only THREE submissions – you guys really need to submit more and/or write more MolBiol posts!<br /><br />It seems molecular biology doesn't get blogged about specifically as much as evolution and diversity – perhaps because molecular biologists are usually busy troubleshooting their PCRs and RNA work for weeks on end, and have little time left over to write. In fact, judging from recent woes experienced by some of my lab buddies, I'm beginning to doubt the existence of RNA and believe it may all be a giant elaborate hoax invented to enslave more grad students. Have any of you ever *seen* RNA? That's what I thought...<br /><br />This month we have a very biochemical (post-translational, if you will) MolBiol Carnival featuring enzyme spec, cyanobacterial biofuel precursors and some sweet diastereomer metabolism regulation.<br /><br /><a href="http://bitesizebio.com/articles/working-with-enzymes-part-i-the-simple-kinetic-spectrophotometric-assay/"><span style="font-weight: bold;">Enzyme Assay</span></a><br />Christopher Dieni at <a href="http://bitesizebio.com/">BitesizeBio</a> has a nice write-up on measuring enzyme kinetics using UV spectrophotometry, complete with procedure, tips and troubleshooting – the kind of thing you wish accompanied <span style="font-style: italic;">every</span> assay you've been assaulted by. Not being anything close to a biochemist, I had no idea you could actually observe enzyme action using something as simple as a spec, so this is quite cool!<br /><br /><a href="http://www.nasw.org/users/mslong/2011/2011_04/Biofuels.htm"><span style="font-weight: bold;">Cyanobacteria and biofuel production</span></a><br />With growing concerns with using land plants for biofuels (for one thing, kind of odd to use food to power cars when not everyone has enough of it...), increasing attention has been turned towards algae eukaryotic and not. For one thing, algae are already quite good at photosynthesising and are vastly more abundant than plants, and arguably have the largest contribution to global photosynthesis – not surprising given the earth's surface is 70% ocean. <a href="http://www.nasw.org/users/mslong/">Michael Scott Long</a> at a NASW.org blog explains recent developments in genetic engineering and domestication of cyanobacteria for fatty acid production.<br /><br /><a href="http://ittakes30.wordpress.com/2011/04/19/think-you-know-metabolism-think-again/"><span style="font-weight: bold;">Diastereomers and regulation of metabolism</span></a><br />Stereoisomers are the beginning chemistry student's worst nightmare – they're so similar and easy to mix up, particularly if you're like me and can't tell left from right to begin with. However, a bacterium (rather, its enzymes) would have little trouble with the stereochemistry portion of a intro biochem class – to them, stereoisomers are day and night (and other things). Glucose and galactose are 'close enough' to each other for a biochem student, but a flipped arrangement at just a single stereocentre is enough to require a whole new set of enzymes and drastic changes in the pathway. E.coli prefers glucose, but can also process galactose (compromising its growth rate) by embellishing its metabolic pathways a little – the products of galactose digestion are sent to the tricarboxylic acid cycle via the glycoxylate shunt. Becky Ward at <a href="http://ittakes30.wordpress.com/">It Takes 30</a> discusses how sugar type availability affects the transcriptional regulation of this glycoxylate shunt, among other things, featuring a galactose-loving mutant.<br /><br />---<br />This was fun. Wish there were more submissions – having to write up random blog posts forces me to revisit forgotten subjects and explore new ones: I'd never brave a post on metabolic regulation on my own! By not submitting, y'all are having a deleterious effect on my education... ;-)<br /><br />The next edition will be hosted by our resident microbiologist <a href="http://twitter.com/labratting">@labratting</a> at <a href="http://labrat.fieldofscience.com/">Lab Rat</a>, and she better get more than three submissions... come on, we do so much molecular biology in almost every field of biology! Write 'er up, dammit!Psi Wavefunctionhttp://www.blogger.com/profile/10829712736757471647noreply@blogger.com1tag:blogger.com,1999:blog-3643556495084083743.post-42646911101189358302011-05-02T01:07:00.000-07:002011-05-02T01:23:18.592-07:00Protists gone motile! (and a Euglenid metaboly video)So I caved and got me a Youtube account, partly inspired by a comment in the previous post. Accumulated half a metric shit ton of random protist videos by now, and compressing them for Bloggers crappy video sharing system would take way too much time, and I barely have the time to grab stills and post them here. So finally there's a suitable outlet for my raw video data – maybe someday when I'm not going completely insane and falling behind on a million things I didn't really have time for in the first place, I may put together a properly edited video. But don't hold your breath for it...<br /><br />We have some pretty awesome microscopy and video equipment in the lab, and I'm lucky to have a PI nice enough not to mind some of us using it to fuck around with random samples in the middle of the night. I hope it may help bring the microbial world a little closer to you, and add a whole new dimension of <span style="font-style: italic;">time</span> to our protists.<br /><br />Let's start off with some euglenid metaboly, since it's quite hard to talk about without seeing it. Actually, the true reason is that it's about the first thing my cursor landed on when I opened my pile of videos for file conversion. But just as we ascribe purpose to evolutionary happenings, we can likewise ascribe purpose to my selection here ;-)<br /><br />Since I'm lazy and behind on about a million things (to the point where I must mention it twice), just gonna copy the short description I wrote for this bug on the YouTube page. Enjoy!<br /><div style="text-align: center;"><iframe src="http://www.youtube.com/embed/IjiJJgT61mk" allowfullscreen="" frameborder="0" height="390" width="640"></iframe><br /><div style="text-align: left;"><blockquote>This is a heterotrophic euglenid, perhaps a Peranema sp., exhibiting metaboly in all its splendour. The cell might be slightly squashed or otherwise damaged, keeping the flagellate conveniently in one place. The clear vesicle near the base of the flagellum that grows and shrinks is the contractile vacuole, the flagellate's analogue of the animal secretory system. At the tail end are refractile starch granules used to store energy.<br /><br />Metaboly is a form of cell movement that is most famously exemplified by ciliates, but also known in some other flagellates. It appears to be caused by the specific arrangement of microtubule (cell skeleton) bundles at the cell periphery, and greatly enhanced by the 'armour plates' of the euglenid surface, which is lined with long pellicle strips going from the flagellar insertion all the way to the tip of the 'tail' -- as the cell twists about, the strips slide against each other and result in this movement. Euglenids with fused pellicle strips, like Phacus, are incapable of metaboly. The function of this movement is unknown, and there may not be any in particular.<br /><br />The hairy thing next to the euglenid is a badly mangled ciliate.<br /><br />Freshwater, Apr 2011, Vancouver<br /></blockquote></div></div>And please let me know if you have any requests, comments or suggestions for these videos. I'm new to the world of moving pictures (instead I see videos as image sequences, like any proper cell biologist ought to...), so I'm in an even greater state than usual in not knowing what the hell I'm doing.Psi Wavefunctionhttp://www.blogger.com/profile/10829712736757471647noreply@blogger.com2tag:blogger.com,1999:blog-3643556495084083743.post-1239401290786708012011-04-27T03:09:00.000-07:002011-04-27T03:42:16.622-07:00Marine Microforay – foram and a thecofilosean partyApologies for disappearing for a while – had an interview, finals and then my arm decided to temporarily rediscover RSI-like symptoms just when I had a term paper to write, so I had to lay off extraneous typing for a while. Then I realised just how much of my life depends on typing, and losing that ability would not only make me worthless and unemployable, but also unable to communicate with many of my friends who happen to be inconveniently dispersed around the globe. So yeah, I should probably stop casually dismissing ergonomics about now...as should you, if you haven't already!<br /><br />I've accumulated another batch of microscopic findings, this time from marine samples. By the looks of it, I might be moving to the Midwest soon, and thus be deprived of my ocean (and mountains *sob*), so I figured that focusing on marine protists while I have the chance would be a good idea. Swampy pondwater is available pretty much anywhere anyway.<br /><br />From time to time, you can be lucky enough to find a foram shell in the sediments around here. Live forams can be found too, but much more rarely – I have a couple, but still need to process the videos. This is not a snail:<br /><div style="text-align: center;"><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiKMlIIOijBS9SWUJHi7XYTGCM7RpJVdqfiagfmlu5O6sgcQ-5FLIZ3V3BjPWFbK_-I9NK92EZcI9nqq9cK5OQK9aMT5bpNsXroS-PzNa7tlhGrGSuijq3U2n8HRdC4BMJmTRpnkIhS2_AJ/s1600/Foram-80086.jpg"><img style="cursor: pointer; width: 400px; height: 249px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiKMlIIOijBS9SWUJHi7XYTGCM7RpJVdqfiagfmlu5O6sgcQ-5FLIZ3V3BjPWFbK_-I9NK92EZcI9nqq9cK5OQK9aMT5bpNsXroS-PzNa7tlhGrGSuijq3U2n8HRdC4BMJmTRpnkIhS2_AJ/s400/Foram-80086.jpg" alt="" id="BLOGGER_PHOTO_ID_5592052298196558066" border="0" /></a><br /><span style="font-size:85%;">Foram. Wreck Beach. 20x obj, DIC except for last image, which is in phase.</span><br /></div><br />To save loading time, the rest are below the fold.<br /><a name='more'></a><br /><br />A pennate diatom of some sort, on its side. The girdle, where the two valves ('shells') meet, can be seen along the middle.<br /><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiy3jiiP6OI66T9nO-0KXlk8sDx9qoZmb7HFzRrlmf_obxcY5h_zbUdqpga30lWauseg5S5gkQczvUF_Eb-aIoBx26mIPrmIP4ZZV5axBKkEaHqt_ifuTLdJ9Fw3zgkgO3UarsPI2ykdwlF/s1600/Diatom-1080054-s.jpg"><img style="cursor: pointer; width: 351px; height: 400px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiy3jiiP6OI66T9nO-0KXlk8sDx9qoZmb7HFzRrlmf_obxcY5h_zbUdqpga30lWauseg5S5gkQczvUF_Eb-aIoBx26mIPrmIP4ZZV5axBKkEaHqt_ifuTLdJ9Fw3zgkgO3UarsPI2ykdwlF/s400/Diatom-1080054-s.jpg" alt="" id="BLOGGER_PHOTO_ID_5592053361766269650" border="0" /></a><br />40x obj, DIC<br /></div><br />A flagellate of some sort. Has a strange groove from which flagella appear to emerge (see bottom second from left). Looks like some sort of <a href="http://tolweb.org/images/Thecofilosea/124280">thecofilosean</a>/cryomonad like <span style="font-style: italic;">Protaspis</span>, but might be some heterotrophic euglenid for all I know.<br /><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjHprTzP8IJwl8T9FUPd-MG5-hGv4vFcQpCMi31v7I-8c7-PHxvh1i357jnak2ML2oSA70l0ya-RV_zyAEvsFbzZPLQqVjO2FdscWWaWz-6SbhRVF-6xTWeo2By3BYA-ezmlzwQ0ONpi40e/s1600/Flagellate-1080073-e.jpg"><img style="cursor: pointer; width: 400px; height: 140px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjHprTzP8IJwl8T9FUPd-MG5-hGv4vFcQpCMi31v7I-8c7-PHxvh1i357jnak2ML2oSA70l0ya-RV_zyAEvsFbzZPLQqVjO2FdscWWaWz-6SbhRVF-6xTWeo2By3BYA-ezmlzwQ0ONpi40e/s400/Flagellate-1080073-e.jpg" alt="" id="BLOGGER_PHOTO_ID_5592055467038892418" border="0" /></a><br /></div><br />A marine <span style="font-style: italic;">Thecamoeba</span>-like thing: (as suggested by ridges on the surface)<br /><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhZoxxY4S7h679HWVT_xOtOl3crTw4UO2FuKsnkG7XGJe5FoVO0ielpfafUflsOGYBT6GyOqi4PK-VFJnk5Lu0UAkmkdFsv7PGi1qAlyhoP8ofdqyWF4QYzKLwFxuC0hrrMKrUMZp-0zBGJ/s1600/Thecamoeba-like-1080058.jpg"><img style="cursor: pointer; width: 386px; height: 400px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhZoxxY4S7h679HWVT_xOtOl3crTw4UO2FuKsnkG7XGJe5FoVO0ielpfafUflsOGYBT6GyOqi4PK-VFJnk5Lu0UAkmkdFsv7PGi1qAlyhoP8ofdqyWF4QYzKLwFxuC0hrrMKrUMZp-0zBGJ/s400/Thecamoeba-like-1080058.jpg" alt="" id="BLOGGER_PHOTO_ID_5592055469319988002" border="0" /></a><br /></div><br />The partial collar and flagellar pocket suggest euglenidness. <a href="http://www.plingfactory.de/Science/Atlas/Kennkarten%20Algen/Euglenophycea/source/Entosiphon%20sulcatum.html"><span style="font-style: italic;">Entosiphon</span> sp</a>, perhaps? Eats diatoms. Short flagella perplex me though; I vaguely recall having searched long and hard for their continuation, but they appeared truly short despite that.<br /><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh6hjD9Ld923VXXDtK6lekIaS4uQuegxwygjvgYq7gtvOIfGS8dj1ZDQxE69MPLlpOJ5ab9HC0qpcsGFEjXXCQyMTtzUku1vUww7Fy3I1T-ftu7P1m8kT0JqnXqIPI2J_hw582NX6Wwu6i9/s1600/Flagellate2-1080089.jpg"><img style="cursor: pointer; width: 400px; height: 246px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh6hjD9Ld923VXXDtK6lekIaS4uQuegxwygjvgYq7gtvOIfGS8dj1ZDQxE69MPLlpOJ5ab9HC0qpcsGFEjXXCQyMTtzUku1vUww7Fy3I1T-ftu7P1m8kT0JqnXqIPI2J_hw582NX6Wwu6i9/s400/Flagellate2-1080089.jpg" alt="" id="BLOGGER_PHOTO_ID_5592074332314726418" border="0" /></a><br /><div style="text-align: left;"><br />And another individual, presumably of the same species or closely related.<br /></div><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjTdTuapbM4aqKw2l5MKy0T9XeIn7dvMmB6tambuBJwBwcq7ku7EChBbNnG61rIP8nZE6FiGMczZ-iwOiMqnEwkP0R1MNZpNHV4N6ZkBu6tY7grHz7ZzHMQt0eb1RRe2LUujkrqIKwuSEdu/s1600/Flagellate-1080135.jpg"><img style="cursor: pointer; width: 400px; height: 132px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjTdTuapbM4aqKw2l5MKy0T9XeIn7dvMmB6tambuBJwBwcq7ku7EChBbNnG61rIP8nZE6FiGMczZ-iwOiMqnEwkP0R1MNZpNHV4N6ZkBu6tY7grHz7ZzHMQt0eb1RRe2LUujkrqIKwuSEdu/s400/Flagellate-1080135.jpg" alt="" id="BLOGGER_PHOTO_ID_5592074323199885938" border="0" /></a><br /></div><br />This might be a cercomonad that ate something colourful and refractile. I recall it moved in a rather cercomonad-y fashion. Glides like hell.<br /><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg3dO6BiHVokWG63Dm1TmpBZe1im4nwpPkIECILVd2KH0Nz-5mnGUX-ZsqLz1PV7ryiGax9ZZt5t3Uq4MGu7-8dKALw5xJ_HGEChMwbf0_5pmbF7kutwJie0znTV8SNYyrUnW6vu1w4RkbW/s1600/Flagellate-1080124.jpg"><img style="cursor: pointer; width: 400px; height: 262px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg3dO6BiHVokWG63Dm1TmpBZe1im4nwpPkIECILVd2KH0Nz-5mnGUX-ZsqLz1PV7ryiGax9ZZt5t3Uq4MGu7-8dKALw5xJ_HGEChMwbf0_5pmbF7kutwJie0znTV8SNYyrUnW6vu1w4RkbW/s400/Flagellate-1080124.jpg" alt="" id="BLOGGER_PHOTO_ID_5592074318998004370" border="0" /></a><br /></div><br />An obvious thecofilosean. <span style="font-style: italic;">Verrucomonas</span> or <span style="font-style: italic;">Protaspis</span>; leaning towards <span style="font-style: italic;">Verrucomonas</span> based on position of the massive nucleus (see top right) and how intensely the ventral groove bisects the cell; not sure how reliable those characters are. Looks like fig 1n in <a href="http://dx.doi.org/10.1016/j.ympev.2010.07.007">Chantangsi et al. 2010 <span style="font-style: italic;">Mol Phyl Evol</span></a>, which is <span style="font-style: italic;">Verrucomonas longifila</span> (also fig 1h and 3h in <a href="http://ijsb.sgmjournals.org/cgi/content/full/60/8/1962">Chantangsi & Leander 2010 IJSEM</a>). Can't say much else except that it's a gliding flagellate with a tendency to protrude fine pseudopodia from the groove along its bottom. Thecofiloseans aren't particularly overstudied or anything...<br /><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjhVBJNarIJxZrEIH4XMr8bxyRT-12p3QLztOAb_lRrOA1ZfPrPXAxgSHcGajHzinFvENdvg4jUa2py8UJbzf_IekfNtYVZelGU9n41Xfi3yyfgASukGwOCwIBHaqWKLAfN0mHCocqnMMxI/s1600/Flagellate-1080109.jpg"><img style="cursor: pointer; width: 400px; height: 121px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjhVBJNarIJxZrEIH4XMr8bxyRT-12p3QLztOAb_lRrOA1ZfPrPXAxgSHcGajHzinFvENdvg4jUa2py8UJbzf_IekfNtYVZelGU9n41Xfi3yyfgASukGwOCwIBHaqWKLAfN0mHCocqnMMxI/s400/Flagellate-1080109.jpg" alt="" id="BLOGGER_PHOTO_ID_5592074312456411346" border="0" /></a><br /><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhBxThU0U6bPlLk6D5_wK8USJWGkc0x459SuULLZDsHIoM4KGZ__nIwmRoRf-iU6Xhc0RvJwVMrRlUhEsJFV9Sr-ap-EOshhCEIjG1qQ1qKMKoMGmnKRvP_1ah9wRZ6KluqjdJDJ0nCZqHX/s1600/Flagellate-1080117.jpg"><img style="cursor: pointer; width: 400px; height: 262px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhBxThU0U6bPlLk6D5_wK8USJWGkc0x459SuULLZDsHIoM4KGZ__nIwmRoRf-iU6Xhc0RvJwVMrRlUhEsJFV9Sr-ap-EOshhCEIjG1qQ1qKMKoMGmnKRvP_1ah9wRZ6KluqjdJDJ0nCZqHX/s400/Flagellate-1080117.jpg" alt="" id="BLOGGER_PHOTO_ID_5592074319377334578" border="0" /></a><br /></div><br />Another thecofilosean with colourful refractile inclusions – probably food-related (characteristic groove evident in rightmost image).<br /><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjKKHetA5N3ft1yS2GWtV5TOqsn_-2rgmD5v0zKnQRDlyM9CmVjRFkGJT2vv60MHX2aC2M6s9QhoRIGdLE3ud7cxIND_NIfIv61rVFVkr2AvaDztJmaeZUBbCiOT3wK9F4PRtZtBqFcFTwF/s1600/Flagellate-1080171.jpg"><img style="cursor: pointer; width: 400px; height: 86px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjKKHetA5N3ft1yS2GWtV5TOqsn_-2rgmD5v0zKnQRDlyM9CmVjRFkGJT2vv60MHX2aC2M6s9QhoRIGdLE3ud7cxIND_NIfIv61rVFVkr2AvaDztJmaeZUBbCiOT3wK9F4PRtZtBqFcFTwF/s400/Flagellate-1080171.jpg" alt="" id="BLOGGER_PHOTO_ID_5592078849291023810" border="0" /></a><br /></div><br />A <span style="font-style: italic;">Lecythium</span>-like creature. <span style="font-style: italic;">Lecythium</span> is a cercozoan organic-test-bearing amoeba with thin filose pseudopods. Plenty found in freshwater too.<br /><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgVOuEoM5sWxrsmYA1g1VI2zo0flCjifnsvYKYAoKYJF-Q0Mcke0vxU5hklc9R9MA72eacneEeOOk9E4EIWKsyQ1HjKkoJrULE-7c150Q_ZhqaWTwJPrY2EBbxOQF54cNtFdLcrt8iWruVD/s1600/Lecythium-like-1080176.jpg"><img style="cursor: pointer; width: 400px; height: 96px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgVOuEoM5sWxrsmYA1g1VI2zo0flCjifnsvYKYAoKYJF-Q0Mcke0vxU5hklc9R9MA72eacneEeOOk9E4EIWKsyQ1HjKkoJrULE-7c150Q_ZhqaWTwJPrY2EBbxOQF54cNtFdLcrt8iWruVD/s400/Lecythium-like-1080176.jpg" alt="" id="BLOGGER_PHOTO_ID_5592078852388461682" border="0" /></a><br /></div><br />A...thing. Appears to have colourful food vacuoles or something. In the top right image there's a barely visible groove edge of some sort along the right edge, with a kink too. Anyone offended if I write this off as a marine cercozoan, eg. cryomonad of some sort?<br /><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgFS-s3LyTxHeW6Bs-6viEH0ohm4lOmscT3KWeVGc1QANd7R_3UoEXg6mTLFoQ2ZF2tkqwvZ-UbdZ2cVbbSrIEpkB7WfvajrkbYFODGAeY2Ooqcw766AY2t_YvPrn0hoKOeHVgJCr1pMKcp/s1600/Unknown-1080061.jpg"><img style="cursor: pointer; width: 357px; height: 400px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgFS-s3LyTxHeW6Bs-6viEH0ohm4lOmscT3KWeVGc1QANd7R_3UoEXg6mTLFoQ2ZF2tkqwvZ-UbdZ2cVbbSrIEpkB7WfvajrkbYFODGAeY2Ooqcw766AY2t_YvPrn0hoKOeHVgJCr1pMKcp/s400/Unknown-1080061.jpg" alt="" id="BLOGGER_PHOTO_ID_5592055472192765010" border="0" /></a><br /></div><br /><span style="font-style: italic;">Metromonas simplex</span>. It anchors to the substrate with the curly end of its flagellum and sways back and forth rhythmically, for hours on end. Back and forth, back and forth. Like a metronome, hence its name. Apparently it's got nothing better to do. Intend to upload some videos eventually... it's really cool! Uncertain affinity at this point, despite how quickly these guys are found <span style="font-style: italic;">everywhere</span> after leaving some benthic seawater in a dish. Thinking I could quickly yoink a couple off the dish and PCR them to resolve the issue with little effort, I very quickly found out <span style="font-style: italic;">why</span> no one's ever bothered and succeeded: these things are practically impossibly to pry off the surface! I think they've invented superglue or something...<br /><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiaoXjqNE-9XWVsU1EXqUeOJnz3LOJ3DPm-eUrNSJ8O6A2djznTlBr-4UFNmBwKY9Vq2nQjI_pL7SH9Eg-0Odol9MW73gQMpOHE4fKZ_vETqk8kN0qUqolSPjqNNk99aYll4I_9cxcESF8p/s1600/Metromonas-1080131.jpg"><img style="cursor: pointer; width: 400px; height: 90px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiaoXjqNE-9XWVsU1EXqUeOJnz3LOJ3DPm-eUrNSJ8O6A2djznTlBr-4UFNmBwKY9Vq2nQjI_pL7SH9Eg-0Odol9MW73gQMpOHE4fKZ_vETqk8kN0qUqolSPjqNNk99aYll4I_9cxcESF8p/s400/Metromonas-1080131.jpg" alt="" id="BLOGGER_PHOTO_ID_5592078852627901938" border="0" /></a><br /></div><br />Part of a decaying arthropod. Spherical things might be parasites/cysts, or some animal cell type I'm totally oblivious too. Wish there was an easy way to learn what the various cell types look like in arthropods – most introductory literature is tissue-oriented. I'm perplexed by the surface of the spherical things visible in the top right and bottom left images.<br /><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjsGN_RTmIufWGYPIJq8ci-ImmAsOyWagMWqPSvpyTR6zIz7y9v8q8G1yGKABJiuUmaMVEMdjwjn-uBSxd2789Gj1Qt79zdVSKG29Pp6Bf_wdzuiV6DZzznckoOX-YjFNdnSnqQAdPRLqKq/s1600/Unknown-1080104.jpg"><img style="cursor: pointer; width: 400px; height: 396px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjsGN_RTmIufWGYPIJq8ci-ImmAsOyWagMWqPSvpyTR6zIz7y9v8q8G1yGKABJiuUmaMVEMdjwjn-uBSxd2789Gj1Qt79zdVSKG29Pp6Bf_wdzuiV6DZzznckoOX-YjFNdnSnqQAdPRLqKq/s400/Unknown-1080104.jpg" alt="" id="BLOGGER_PHOTO_ID_5592078860127896578" border="0" /></a><br />20x obj, DIC<br /></div><br />The rest are from a different marine sample, captured by video camera.<br /><br />This ciliate appears to be related to <span style="font-style: italic;">Paramecium</span> based on the shape of its oral region, as well as the rectangular grid-like arrangement of the cortex. In the bottom middle image, the macronucleus is apparent as a clear-ish area in the cytoplasm. I think the top right features a contractile vacuole with its channel towards the left end.<br /><div style="text-align: center;"><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiN9dvNjeTr9a6maQfat16xkGPkdKFpA-gUGWQqk8AtOHcRsn5Qa5psIvyYug3SQwljmAu3rgZBZdSnjcOE2fZ3Ow-nclyHT4S0KufFgr6s__HGT1YC_igxjwIk4ciILE_5Jbs81gDddZhG/s1600/Tape3-Mar2011-111-2-1.jpg"><img style="cursor: pointer; width: 286px; height: 152px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiN9dvNjeTr9a6maQfat16xkGPkdKFpA-gUGWQqk8AtOHcRsn5Qa5psIvyYug3SQwljmAu3rgZBZdSnjcOE2fZ3Ow-nclyHT4S0KufFgr6s__HGT1YC_igxjwIk4ciILE_5Jbs81gDddZhG/s400/Tape3-Mar2011-111-2-1.jpg" alt="" id="BLOGGER_PHOTO_ID_5592049902130982658" border="0" /></a><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjLFQnkyvVrnSBzdWw_-P7Q09JfP6B2JTtLafEoZJ4fdC9nEM2NIAc7bHsCGJiSELS_IFbXdxPIQJ3ucwthEmDhZjy_CAN23ZlzWSFC6bl20SrT808ABkAAKQGICBGDatC7sDHz8UXdGGnY/s1600/Tape3-Mar2011-111-1-1.jpg"><img style="cursor: pointer; width: 287px; height: 151px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjLFQnkyvVrnSBzdWw_-P7Q09JfP6B2JTtLafEoZJ4fdC9nEM2NIAc7bHsCGJiSELS_IFbXdxPIQJ3ucwthEmDhZjy_CAN23ZlzWSFC6bl20SrT808ABkAAKQGICBGDatC7sDHz8UXdGGnY/s400/Tape3-Mar2011-111-1-1.jpg" alt="" id="BLOGGER_PHOTO_ID_5592049900675392658" border="0" /></a></div><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg1RiYiq7dkm0_hhsPakCj3N4hih7KvYBmyQXiemAUjP85gHySHPhGS0sfwTVWmRk6n6eQKM6_cvMhzkbjs5hWN-cwF6yCO1RaJ_NPycvIRSc3wPkQgMw30q2X6OXybdTl7r-C4ayiBYdqd/s1600/Tape3-Mar2011-110-2-1.jpg"><img style="cursor: pointer; width: 177px; height: 145px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg1RiYiq7dkm0_hhsPakCj3N4hih7KvYBmyQXiemAUjP85gHySHPhGS0sfwTVWmRk6n6eQKM6_cvMhzkbjs5hWN-cwF6yCO1RaJ_NPycvIRSc3wPkQgMw30q2X6OXybdTl7r-C4ayiBYdqd/s400/Tape3-Mar2011-110-2-1.jpg" alt="" id="BLOGGER_PHOTO_ID_5589101986984586674" border="0" /></a><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEju5iPF75kOWZHosJz5JL4L6iMDjdghoMPZ708CJcncjF0g04ro0RZ9fdlCNsIOeF2yTOvlFEthwuvggWk6LpeuzoyVNO5IMWyKU2RHLprSpAiMT1V31wHwlRbeU5WruO_KlySOWDy74b5z/s1600/Tape3-Mar2011-110-4.jpg"><img style="cursor: pointer; width: 178px; height: 145px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEju5iPF75kOWZHosJz5JL4L6iMDjdghoMPZ708CJcncjF0g04ro0RZ9fdlCNsIOeF2yTOvlFEthwuvggWk6LpeuzoyVNO5IMWyKU2RHLprSpAiMT1V31wHwlRbeU5WruO_KlySOWDy74b5z/s400/Tape3-Mar2011-110-4.jpg" alt="" id="BLOGGER_PHOTO_ID_5592049889068822082" border="0" /></a><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgoCF8_PrXBDRnT_U3QA8ttCVT9rti2Mo4UMzHK8Nij9vNI3RMoRCJeVcLu_dN63WUKIvwp171yVc5NtrZm1bYPHPbg5An0Ureca_WqoEphjUL9MBUTZPBxMfOpCFEyYkKDoukkufJypqXV/s1600/Tape3-Mar2011-110-3.jpg"><img style="cursor: pointer; width: 216px; height: 144px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgoCF8_PrXBDRnT_U3QA8ttCVT9rti2Mo4UMzHK8Nij9vNI3RMoRCJeVcLu_dN63WUKIvwp171yVc5NtrZm1bYPHPbg5An0Ureca_WqoEphjUL9MBUTZPBxMfOpCFEyYkKDoukkufJypqXV/s400/Tape3-Mar2011-110-3.jpg" alt="" id="BLOGGER_PHOTO_ID_5592049886603605362" border="0" /></a><br />Top two: 20x obj; bottom: 40x. DIC<br /></div><br />Heterotrophic euglenid, or a cercozoan of some sort. Probably the former as there seem to be visible edges of pellicle strips in the top right image. The flagellar pocket also points towards a euglenid identity, though the flagella are a bit short and on the thin side. Could be out of focus though.<br /><div style="text-align: center;"><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgh2vXjbVBkqSUGp71N0_8kJr5i6tS9PCpaUgXOX8-ZiIveanzWNRbHXbv54cbDU8sGWXXBRAkKBcfo8nVcAe9VHlfuEz_feepe7QQCaOn64GNgCrGI_A5VWQLJTmhjrtiSWj0AXqfl9kur/s1600/Thecofilosean_cnd.jpg"><img style="cursor: pointer; width: 400px; height: 257px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgh2vXjbVBkqSUGp71N0_8kJr5i6tS9PCpaUgXOX8-ZiIveanzWNRbHXbv54cbDU8sGWXXBRAkKBcfo8nVcAe9VHlfuEz_feepe7QQCaOn64GNgCrGI_A5VWQLJTmhjrtiSWj0AXqfl9kur/s400/Thecofilosean_cnd.jpg" alt="" id="BLOGGER_PHOTO_ID_5589102908104184738" border="0" /></a><br /></div><br /><span style="font-style: italic;">Discocelis saleuta</span>, a common marine flagellate of uncertain affinity. The disc shape is very characteristic and cool, would probably make an interesting SEM subject. Apparently the cell edge can be lined with extrusomes (Vørs 1988 ref'd in <a href="http://dx.doi.org/10.1017/S0031182010001708">Walker et al. 2011 <span style="font-style: italic;">Parasitol</span></a> <a href="http://journals.cambridge.org/downloadsup.php?file=/S0031182010001708sup001.pdf&code=b225e8ea09e83d0c67d2aaa56a4c8e16&mime=application/pdf">S1:88</a>); given the flagellate is a mere 5µm, it's hard to imagine how those could even fit in there.<br /><div style="text-align: center;"><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiSwU_5-kpqAK9FF0B84OedZzZzh0SfLsZPGAryRucwx330JUL-AJn92XxwW3PCgUJP5Q2GuifNrJhRYLlFvlq0IjXVPZqX_SVEHY7lWC2NK0TDixEwZ7V-MY7fhjn2KfvKcP_SSAyZ8RwX/s1600/Discocelis.jpg"><img style="cursor: pointer; width: 400px; height: 276px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiSwU_5-kpqAK9FF0B84OedZzZzh0SfLsZPGAryRucwx330JUL-AJn92XxwW3PCgUJP5Q2GuifNrJhRYLlFvlq0IjXVPZqX_SVEHY7lWC2NK0TDixEwZ7V-MY7fhjn2KfvKcP_SSAyZ8RwX/s400/Discocelis.jpg" alt="" id="BLOGGER_PHOTO_ID_5589101974938153794" border="0" /></a><br /></div><br />That was probably way too many images...Psi Wavefunctionhttp://www.blogger.com/profile/10829712736757471647noreply@blogger.com2tag:blogger.com,1999:blog-3643556495084083743.post-74276355577456197062011-04-12T06:41:00.000-07:002011-04-12T07:00:35.925-07:00Adorable velvet worm compositeToo busy to write a proper post these days, but just happened across a cool <span style="font-style: italic;">Current Biology </span><a href="http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRT-52KNP7V-6&_user=1022551&_coverDate=04%2F12%2F2011&_rdoc=1&_fmt=high&_orig=gateway&_origin=gateway&_sort=d&_docanchor=&view=c&_acct=C000050484&_version=1&_urlVersion=0&_userid=1022551&md5=d449413704ab4a28429431f92af895f7&searchtype=a">quick guide to onychophorans</a>(=velvet worms), with a pretty picture showing their diversity (and really pretty textile-like patterns):<br /><div style="text-align: center;"><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiJoufPAMEeDDrXxgZh-0fPPn6_vMzq_yXg_0QjpdMmEK4CCNm6m_HKtLrTr_KF9NBj_ZACqQituJowy25qS-7RAccge_TJa_7oXIjWZiKKKBFNgneuHiCMHo_MNI_I3KXVWJHg5YK2zvV_/s1600/Blaxter+Sunnucks+2011+Curr+Biol+Onychophorans.jpg"><img style="display: block; margin: 0px auto 10px; text-align: center; cursor: pointer; width: 240px; height: 400px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiJoufPAMEeDDrXxgZh-0fPPn6_vMzq_yXg_0QjpdMmEK4CCNm6m_HKtLrTr_KF9NBj_ZACqQituJowy25qS-7RAccge_TJa_7oXIjWZiKKKBFNgneuHiCMHo_MNI_I3KXVWJHg5YK2zvV_/s400/Blaxter+Sunnucks+2011+Curr+Biol+Onychophorans.jpg" alt="" id="BLOGGER_PHOTO_ID_5594692905753249346" border="0" /></a><span style="font-size:85%;">Australian onychophorans (<a href="http://dx.doi.org/10.1016/j.cub.2011.02.017"><span style="font-style: italic;">Blaxter & Sunnucks 2011 Curr Biol</span></a>)</span></div><br />The guide itself is quite interesting, recommend reading it if you have time. To entice you, they talk about the diversity of breeding behaviours found in onychophorans:<br /><blockquote>"<span style="color: rgb(0, 0, 153);">Some are fully live-bearing (viviparous), with well-developed placenta-like, extra-embryonic structures that attach to the mother's uterine wall and nourishes growing embryos until the birth of sequences of self-reliant, mini velvet worms.</span>"<br /></blockquote>Onychophorans are way cooler than arthropods ;p<br /><br />And they can be social with dominant/submissive behaviours, which I talked about in an <a href="http://skepticwonder.fieldofscience.com/2010/04/social-onychophorans.html">earlier post</a> (which happens to be one of my most visited, probably because it's not about protists =( ).<br /><br />And with that, there may or may not be a surprise while I'm away, so stay tuned. In any case, I should engage in some form of proper blogging sometime after the 20th... (finals, shoot me)Psi Wavefunctionhttp://www.blogger.com/profile/10829712736757471647noreply@blogger.com1tag:blogger.com,1999:blog-3643556495084083743.post-88928939674956862232011-04-08T05:46:00.000-07:002011-04-08T06:00:12.115-07:00Personal army of diplomonads (doodle)Accidentally discovered the Symbols tool in Illustrator, and had a little too much fun creating a personal army of swirling multi-coloured diplomonads:<br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjYRI1VoXLg67g8yjQtQ1NZRplbOX94xHUZVw9I8mbhz4ei5Hu9o7RnJ7ANZdFxJr7t5LeoGd0zsAwGeSvujjz-fkAJ3Sqdczef-I-gCiltD3F-J0ainTj_TgM5Klwz35-cNTRW17GvnTxi/s1600/Diplo_Swarm.jpg"><img style="display: block; margin: 0px auto 10px; text-align: center; cursor: pointer; width: 400px; height: 360px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjYRI1VoXLg67g8yjQtQ1NZRplbOX94xHUZVw9I8mbhz4ei5Hu9o7RnJ7ANZdFxJr7t5LeoGd0zsAwGeSvujjz-fkAJ3Sqdczef-I-gCiltD3F-J0ainTj_TgM5Klwz35-cNTRW17GvnTxi/s400/Diplo_Swarm.jpg" alt="" id="BLOGGER_PHOTO_ID_5593193341113165074" border="0" /></a>They really remind me of diodes. Incidentally, they can also invade diagrams and make them barely legible:<br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEis93FqdwWkYcbjqiSCzssLIOeOmD45TWb2k-rQ2jTS1-1s3_b8MQOZdlKhNgqLzF9Jx7whMHteE-LddIhm13xZvq3Xipa5h5ydtjqdEmxNAiCY0tdTW1QxQorD_wubDtdX4oo0gyvi58bH/s1600/Diplo_Swarm_invasion.jpg"><img style="display: block; margin: 0px auto 10px; text-align: center; cursor: pointer; width: 400px; height: 378px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEis93FqdwWkYcbjqiSCzssLIOeOmD45TWb2k-rQ2jTS1-1s3_b8MQOZdlKhNgqLzF9Jx7whMHteE-LddIhm13xZvq3Xipa5h5ydtjqdEmxNAiCY0tdTW1QxQorD_wubDtdX4oo0gyvi58bH/s400/Diplo_Swarm_invasion.jpg" alt="" id="BLOGGER_PHOTO_ID_5593193335341089122" border="0" /></a>Aren't you glad I haven't gotten around to making cartoon-y spiders and cockroaches yet?<br /><br />In other news, I'm rather swamped for the next week and a half (as if I wasn't before), as laws of the universe mandate that right between classes and finals not only do you end up with a [potentially awesome] trip across the continent but a particular obscure somewhat rare flagellate you've been searching for throughout the past 5 months or so randomly decides to announce itself unexpectedly. Not only are protists sentient and exceptionally intelligent, the sly little bastards are also evil as fuck.<br /><br />I do have a couple posts in the making, but don't guarantee anything until after the 20th (this includes replying to comments and emails too)...<br /><br />May this round of finals be my last...! For <span style="font-style: italic;">this</span> degree anyway...Psi Wavefunctionhttp://www.blogger.com/profile/10829712736757471647noreply@blogger.com0tag:blogger.com,1999:blog-3643556495084083743.post-39112992377124387282011-04-06T02:02:00.000-07:002011-04-07T11:09:53.131-07:00RQ#03 Is there really a non-natural selection?I haven't done a <a href="http://skepticwonder.fieldofscience.com/search/label/random%20question">random question</a> in a while. This is the third one, apparently.<br />
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<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: right; margin-left: 1em; text-align: right;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhcfjnUqeCMCsXWx-yRM9vyDJ2H8qYC7uW4Kp81k8VIQPJprOPmwoCnuDI_LJ7jjNrr_K4nhbJV-AL0N1NbWypBWsg794WBmPBkvrRgVBVsKXzPFjD-w3fmL01gDDi82NtZqSakP8AgPFw/s1600/grocery_still_life.jpg" imageanchor="1" style="clear: right; cssfloat: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" height="224" r6="true" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhcfjnUqeCMCsXWx-yRM9vyDJ2H8qYC7uW4Kp81k8VIQPJprOPmwoCnuDI_LJ7jjNrr_K4nhbJV-AL0N1NbWypBWsg794WBmPBkvrRgVBVsKXzPFjD-w3fmL01gDDi82NtZqSakP8AgPFw/s320/grocery_still_life.jpg" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">A grocery store still life, primarily <em><a href="http://serc.carleton.edu/genomics/units/brassica_photos.html">Brassica oleracae</a></em></td></tr>
</tbody></table>Lately I've been involved in some fairly theoretically discussions about evolution, which tend to push one to pay more attention to terminological precision. <s>Or get very confused</s> And get very confused regardless. Additionally, I hang around some biologists with minority opinions on certain aspects of evolution, and ultimately end up talking about evolution differently, to the point of using different words or same words differently. The usual side effects of specialisation. This becomes particularly evident in heated argument with someone outside your tribe – you start speaking slightly different dialects, if you will. Of course, where there's variation, there's opportunity to pick the variant that suits you better. Ideally, that has something to do with accuracy, since we are, hopefully, still attempting to do science and what-not.<br />
<br />
Let's start with the easier of the usage and terminology discrepancies – the term 'natural selection'. Is it useful or does the simpler 'selection' make it redundant? I tend to drop the 'natural' part; laziness and word limits may help, but I think there may be valid theoretical or philosophical merit in doing so:<br />
<br />
1. 'Natural selection' was initially proposed in contrast to 'artificial selection', which was used as an effective pedagogical/explanatory move. It got the point across, particularly in an age when humans were unquestionably special and distinct from the natural world. Nowadays, few scientists would seriously make a distinction between human and non-human nature in the context of biology, and thus there really is no artificial selection<span style="font-style: italic;"> per se</span>. 'Artificial selection' is 'natural selection' performed by humans to pressure their organisms towards traits the humans find favourable. In this case, the humans are part of the environment, playing a similar role to predators, except they breed the variants they like instead of instantly culling them. With no need for an 'artificial selection', is there still a need for 'natural selection', since there no longer is a valid contrast?<br />
<br />
2. 'Natural selection' is often equated with adaptation. This isn't to say 'selection' by itself isn't, but 'natural selection' is the variant used most often in popular writing, some of which can be careless and inconsistent with its terminology. While presumably many of the authors do truly understand that selection and adaptation are different things, adaptationism has led some to consider the difference irrelevant. If adaptation is the sole phenomenon responsible for all the observable or cool things in biology, does it really matter if it's used interchangeably with natural selection? When a term is learned and frequently used incorrectly, it is extremely difficult to fix even in an individual, let alone a population. While 'natural selection' is not meant to be conflated with adaptation, it is, and has thus been tainted.<br />
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<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh3X70TS9r5-YF3ITlGUxvzAZavI8MDClFqR-RcKDcg2DYIP4j0R4tv0ucsf2IPRxH8Falgi8LC_4ME-_oHNzUQpG1CkdLhLysdP8hVGzRD0xjSfi-ih5vxLRpnhZ_1tbumCc8n5JrkgLM/s1600/mix.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><br />
</a></div>3. Use of 'natural selection' implies that phenomena like sexual selection and kin selection are somehow distinct, or special. These are secondary phenomena, special cases or manifestations of selection. That is, sex and kin selection are subtypes of 'natural selection' and do not lie on equal hierarchical level as it may first seem. While most of the scientific community has no problems understanding this, it is perhaps not the clearest delineation of the terms for the general public or students. This way, we can also keep 'artificial selection' to refer to domestication (although I don't see the necessity in doing so) without it contrasting with the 'natural' kind.<br />
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4. This is the least important point, but rather a more personal one. I dislike Darwin-worship; I'm not a 'Darwinian' (nor a "Neo-Darwinian), don't know what that means and frankly don't consider this question relevant now, over a century after Darwin's death. While history of science is indeed fascinating and undeniably worthwhile to learn about, we shouldn't trap ourselves in our history. In fact, I think equating evolution with Darwinism is a bit offensive to all the hard work and frustration of subsequent researchers that have contributed to the field – do they not matter? They work for evolution, not Darwin. 'Natural selection' has been too often tightly associated with 'Darwinism', and often plays a part in Darwin-worship. In other words, the term has acquired some baggage; mind you, not through Darwin but rather through his fervent supporters afterwards.<br />
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5. Population geneticists seem perfectly happy with just 'selection'. They're the ones who actually study the mechanisms of this stuff, so if it works for them, perhaps it should be adequate for the rest of us?<br />
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<br />
I don't mean to nitpick on words and 'mere semantics', but given the difficulty of conveying ideas to those outside your field and the general public, any site of potential confusion is worth trimming if we can. Those on the writing end are also prone to sloppiness and mistakes, so we too are susceptible to the confusion potential. That said, 'natural selection' has stuck around for this long – perhaps there is a beneficial reason I missed out on? This is an honest question – I've never really been formally trained in evolutionary biology save for a basic first year level, and may thus miss large chunks of theory. As I mentioned before, I'm being 'brought up' in some minority circles of evolutionary thought.<br />
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<span style="font-weight: bold;">Why should we still use 'natural selection'? </span><br />
Your turn. Just be gentle with the philosophy – I'm rather slow at following complicated abstract theoretical discussions, which is why I do experimental science ;-)Psi Wavefunctionhttp://www.blogger.com/profile/10829712736757471647noreply@blogger.com15tag:blogger.com,1999:blog-3643556495084083743.post-57890757299635760792011-04-04T04:20:00.000-07:002011-04-04T06:54:10.228-07:00"Just another ciliate" – importance of sexy descriptions<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: 0pt none;" /></a></span>There are species descriptions, and then there are species descriptions. All too often, you come across a mention of some obscure but ridiculously cool-looking organism, with only a very scant description of what it looks like and what it does. Much less often, you can come across yet-another-new-species (usually of a ciliate), but a particularly nicely described one. Again, those super nice descriptions tend to be of ciliates, largely due to the likes of <a href="http://scholar.google.ca/scholar?hl=en&q=wilhelm+foissner&btnG=Search&as_sdt=0%2C5&as_ylo=&as_vis=0">Wilhelm Foissner</a> and his academic offspring. Descriptive detail can only make species more interesting, and eventually of great potential to be useful for science. (Conversely, many a taxon has been rendered invalid due to poor description)<br /><br />A sexy description is also a great way to lure readers into noticing your otherwise garden variety new species. Case in point – I see this <a href="http://ijsb.sgmjournals.org/cgi/content/abstract/ijs.0.024794-0v1">random <span style="font-style: italic;">IJSEM</span> paper</a> on a couple new marine ciliate <span style="font-style: italic;">Frontonia</span> species – nothing too earth shattering. Being rather compulsive about skimming over any mention of a protist I see in the literature, I click. Being rather lazy and a shallow-minded picture-loving type, I head straight for the figures. Unexpectedly, they dazzle me with sexiness. Desperate for something easy to blog about for the next little while (impending interview, exams, end-of-term chaos, etc), I suddenly find your otherwise-routine new species description quite exciting and blog about it. Here, <span style="font-style: italic;">Frontonia mengi </span>and<span style="font-style: italic;"> F.magna</span> get screentime largely thanks to their authors.<br /><br />Some of us in science are <span style="font-style: italic;">that</span> simple minded. If more people realised that and preyed upon our ilk with shiny pictures, think how much more presentable science as a whole would be!<br /><br />(That said, no amount of gloss and shine can make your data more or less wrong. But it can, and does, dazzle some of us into overlooking a flaw or three...)<br /><br />Actually, the above was just a long-winded elaborate excuse to post ciliate porn. Ah, check out the kineties on that ass!<br /><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhrxALlLTXmc-kdiD2-GEFJUhw696oGsIQbt_73KKsBorcJsVLncShaL5H6_pzL0pw6-aIcFmqFHYQWwohS6fEbrUa6hnEBUAo3S99mDPRpTsfhBWTLAMpiBWwh6V___60M6q7x-7Lrus5m/s1600/Fan+et+al+2010+IJSEM+Frontonia+f3.jpg"><img style="cursor: pointer; width: 400px; height: 334px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhrxALlLTXmc-kdiD2-GEFJUhw696oGsIQbt_73KKsBorcJsVLncShaL5H6_pzL0pw6-aIcFmqFHYQWwohS6fEbrUa6hnEBUAo3S99mDPRpTsfhBWTLAMpiBWwh6V___60M6q7x-7Lrus5m/s400/Fan+et+al+2010+IJSEM+Frontonia+f3.jpg" alt="" id="BLOGGER_PHOTO_ID_5591697365160907906" border="0" /></a><br /><span style="font-size:85%;"><span style="font-style: italic;">Frontonia mengi</span>. See text. (<a href="http://ijsb.sgmjournals.org/cgi/content/abstract/ijs.0.024794-0v1">Fan et al. 2010 <span style="font-style: italic;">IJSEM</span></a>)</span><br /><br /><div style="text-align: left;">Well, those were mostly just shots of its oral ciliature, but close enough. The root structures of the cilia are highlighted with silver nitrate and carbonate staining, yielding the pretty staining effect. a-c section through the 'mouth'; d shows the "membranelle" around the 'mouth'. e shows the area behind the mouth; arrowhead points to the cytopyge. 'Cytopyge'? Well, a cell's gotta get rid of its waste somehow, and ciliates actually have the cellular analogue of an asshole. Not the socially dysfunctional kind. So yeah, look at that ass. g shows detail of the cortex, h is the overall view of the ventral ciliature. At i, the rows of cilia "stitch together" at the 'anterior suture'. k shows the germline micronucleus (Mi) and somatic macronucleus (Ma).<br /><br />Now for some delicious DIC:<br /><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjjQzQiy4lbk_djIz25Q13FWYorpKqL1Xo90RzgOPW2WAfhswBGCpGKVheYFwir2FEmeuPouDBKsxlVlS4C3EsBsLuR9CqhD3igc_3MijkirpPZnAgaQxz5mS36yymwC99SJ3lKghufshKl/s1600/Fan+et+al+2010+IJSEM+Frontonia+f1.jpg"><img style="cursor: pointer; width: 400px; height: 341px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjjQzQiy4lbk_djIz25Q13FWYorpKqL1Xo90RzgOPW2WAfhswBGCpGKVheYFwir2FEmeuPouDBKsxlVlS4C3EsBsLuR9CqhD3igc_3MijkirpPZnAgaQxz5mS36yymwC99SJ3lKghufshKl/s400/Fan+et+al+2010+IJSEM+Frontonia+f1.jpg" alt="" id="BLOGGER_PHOTO_ID_5591702291615317698" border="0" /></a><br /><span style="font-size:85%;"><span style="font-style: italic;">Frontonia mengi.</span> See text. (<a href="http://ijsb.sgmjournals.org/cgi/content/abstract/ijs.0.024794-0v1">Fan et al. 2010 <span style="font-style: italic;">IJSEM</span></a>)</span><br /></div><br />Crisp DIC intoxicates me. The seductive allure of polarisation-derived faux-3D relief is nearly impossible to resist, especially when you have the fine complex cell of a ciliate. In fact, good DIC is often better than staining, since you don't have to fix (kill) anything. Unfortunately in the case of some larger ciliates, some degree of squishing must be done otherwise the sample is too damn thick for crisp DIC. I think the gist of microscopy can be summarised as the never-ending compromise between care of specimen and care of the optical setup. The most powerful microscopy generally requires total destruction of the specimen, whereas the most natural and undisturbed data can only be attained with simple techniques and weak optics. It's like the Heisenberg principle of microscopy: the more accurately you determine the state of your specimen, the more mangled your specimen gets.<br /><br />I digress. In the above plate, a-e show general views of several individuals of <span style="font-style: italic;">F.mengi</span>. Remember my rant <a href="http://skepticwonder.fieldofscience.com/2011/03/reticulose-amoeba-cells-can-be-fine.html">a couple posts ago</a> about the usefulness of depicting morphotypical (shape type) variation? I hope it is evident here how that can be useful. For example, if only figure a was published, one could be mislead to consider that large vacuole a characteristic feature of this particular ciliate species. The other four images, however, show that to be a feature of just that specimen instead (non-contractile vacuoles, in this case). Furthermore, the authors even invluded a table of morphometric data, measuring the body dimensions and some visible subcellular details (like numbers of kineties and nuclear size) of 23 individuals.<br /><br />The arrow in 1b points to a contractile vacuole – one could just make out the channel leading to the cell's exterior for expelling its contents. f-g show sections of the mouth, live. h shows detail of the cell surface, the oral apparatus quite visible (as is the cytopyge). i details the cytopharyngeal rods, which are specialised structures this genus of ciliates employs to devour long strands of algae. The characteristically massive ciliate nuclei are visible in j – the arrow points to the macronucleus while the arrow<span style="font-style: italic;">head</span> points to the micronucleus. No staining necessary, fuck yah.<br /><br />Frontonia, like many ciliates, is also armed and dangerous. The surface is loaded with extrusomes (k), which can fire leaving a trail, much like the cryptomonad <a href="http://skepticwonder.fieldofscience.com/2011/03/cryptomonads-solar-powered-armoured.html">ejectisomes</a> (l). m and n show the contractile vacuole and its exit pore, respectively. The contractile vacuole is necessary for osmotic regulation, especially in freshwater species, and is somewhat analogous in function to our kidneys.<br /><br />The second species, Frontonia magna, is also well-described. In these specimens, one can make out the algal filament and its constituents – particularly in b, e and f. Like F.menga, it's also loaded with extrusomes (h). I particularly like i, which shows the ciliature of the anterior suture. It's quite hawt.<br /><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiNefd-whVeY5LVdBOhB7W4Iuyb0lCUO0lkejXUSO_bEdqlCcsoL_od1j2zNUjrlEaS8irajY0tYKNIY_OGUT76WfkOY4015i0271VyPBzVA0qbUICTqW1L_BKEUk6Ns5jSRfvzoiiPaf7X/s1600/Fan+et+al+2010+IJSEM+Frontonia+f5.jpg"><img style="cursor: pointer; width: 400px; height: 347px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiNefd-whVeY5LVdBOhB7W4Iuyb0lCUO0lkejXUSO_bEdqlCcsoL_od1j2zNUjrlEaS8irajY0tYKNIY_OGUT76WfkOY4015i0271VyPBzVA0qbUICTqW1L_BKEUk6Ns5jSRfvzoiiPaf7X/s400/Fan+et+al+2010+IJSEM+Frontonia+f5.jpg" alt="" id="BLOGGER_PHOTO_ID_5591700965522868546" border="0" /></a><br /><span style="font-style: italic;font-size:85%;" >Frontonia magna</span><span style="font-size:85%;">. </span><span style="font-size:85%;">See text. (<a href="http://ijsb.sgmjournals.org/cgi/content/abstract/ijs.0.024794-0v1">Fan et al. 2010 <span style="font-style: italic;">IJSEM</span></a>)</span><br /><div style="text-align: left;"><br />Of course, no description is properly complete (in my opinion) without drawings to accompany the micrographs. Drawings highlight the important features observed by the authors, and are useful in combining information gathered from multiple sections and imaging techniques in a convenient summary. Making an accessible visual summary of a huge pile of microscopy data is no easy task, and is very much an art.<br /><br />Continuing with <span style="font-style: italic;">F.magna</span>, a summarises the ventral view of a typical individual. b provides a sketch of the sutures, without the distracting detail. c shows the side view, along with the contractile vacuole. d shows the relative sizes and positions of the nuclei. e, again, emphasises variation – it shows the various ways a cell appears after overeating with algal filaments protruding all over the place. It's amazing how hard prey can try to make their predator look like an entirely new freaking domain of life, by stretching it out and colouring it in all sorts of funny ways. A similar phenomenon has been responsible for an entire mistaken genus, <span style="font-style: italic;">Ouramoeba</span>, in the otherwise totally awesome Leidy 1874 work on amoebae. The algal prey is detailed in g, while h details the cilia around the oral apparatus.<br /><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiFGFhHqjj231wGxpVHGzOEWYQj2-qtJ4g7APE_XDhx4jPvtaa6JX209R2CGFuiDFtE23HwRmbNYTItXPjeGU7nNsLtUevOvKCyzf2lw0_ZA8ej1hlDL0p_hOpyceaKiHkeC1JK5rW7qMRg/s1600/Fan+et+al+2010+IJSEM+Frontonia+f4.jpg"><img style="cursor: pointer; width: 400px; height: 268px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiFGFhHqjj231wGxpVHGzOEWYQj2-qtJ4g7APE_XDhx4jPvtaa6JX209R2CGFuiDFtE23HwRmbNYTItXPjeGU7nNsLtUevOvKCyzf2lw0_ZA8ej1hlDL0p_hOpyceaKiHkeC1JK5rW7qMRg/s400/Fan+et+al+2010+IJSEM+Frontonia+f4.jpg" alt="" id="BLOGGER_PHOTO_ID_5591710807064607234" border="0" /></a><br /><span style="font-style: italic;font-size:85%;" >Frontonia magna </span><span style="font-size:85%;">See text. (<a href="http://ijsb.sgmjournals.org/cgi/content/abstract/ijs.0.024794-0v1">Fan et al. 2010 <span style="font-style: italic;">IJSEM</span></a>)</span><br /></div><br />Of course, no species description these days is complete without a healthy phylogeny, and Fan et al. got that covered too. I feel I've stolen more than enough figures already, so I'll just say their <span style="font-style: italic;">Frontonia</span> spp. fit snugly within Peniculia, a group including the famous <span style="font-style: italic;">Paramecium</span>, and the two species are sister to each other. There's also a composition of drawings from multiple sources for other members of this genus, so this paper is a nice current reference for <span style="font-style: italic;">Frontonia</span>, if you ever wake up one morning needing one. Believe me, these cravings may strike at the oddest hour.<br /><br />Anyway, I just thought these figures really deserve to see the light of day, and not just remain buried away in what will very soon be just the back issues of a microbial systematics journal. While some may look down on routine-seeming research like basic species descriptions for they do not provide a fancy high-level synthesis or anything, but ultimately, these fancy high-level syntheses are built on lower-ranking papers like these, and cannot exceed the quality of their constituents. It is primary 'basic' literature like this that forms the foundation of science; without species descriptions, without "yet another gene/genome/tree/whatever", there will be nothing to base the more glamorous studies on. This is why impact factor is a load of bullshit, and anyone whose hands itch to oppress "low impact" science should be kept the hell away from research funding strategies, for they obviously have no fucking clue how research works in the first place. Grrr. How can anyone vote against a species description as awesome as <a href="See%20text.%20%28Fan%20et%20al.%202010%20IJSEM%29">Fan et al. 2010</a> above?<br /><br /><span style="font-weight: bold;">Reference</span><br /><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=INTERNATIONAL+JOURNAL+OF+SYSTEMATIC+AND+EVOLUTIONARY+MICROBIOLOGY&rft_id=info%3Adoi%2F10.1099%2Fijs.0.024794-0&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Two+new+marine+Frontonia+species%2C+F.+mengi+spec.+nov.+and+F.+magna+spec.+nov.+%28Protozoa%3B+Ciliophora%29%2C+with+notes+on+their+phylogeny+based+on+SSU+rRNA+gene+sequence+data&rft.issn=1466-5026&rft.date=2010&rft.volume=&rft.issue=&rft.spage=&rft.epage=&rft.artnum=http%3A%2F%2Fijs.sgmjournals.org%2Fcgi%2Fdoi%2F10.1099%2Fijs.0.024794-0&rft.au=Fan%2C+X.&rft.au=Chen%2C+X.&rft.au=Song%2C+W.&rft.au=Al-Rasheid%2C+K.&rft.au=Warren%2C+A.&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CProtistology%2C+Taxonomy">Fan, X., Chen, X., Song, W., Al-Rasheid, K., & Warren, A. (2010). Two new marine Frontonia species, F. mengi spec. nov. and F. magna spec. nov. (Protozoa; Ciliophora), with notes on their phylogeny based on SSU rRNA gene sequence data <span style="font-style: italic;">INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY</span> DOI: <a rev="review" href="http://dx.doi.org/10.1099/ijs.0.024794-0">10.1099/ijs.0.024794-0</a></span><br /></div></div></div></div>Psi Wavefunctionhttp://www.blogger.com/profile/10829712736757471647noreply@blogger.com2tag:blogger.com,1999:blog-3643556495084083743.post-75744504515545793602011-03-28T03:27:00.000-07:002011-04-06T04:43:12.089-07:00Dermamoeba – Having your coat and eating it too<span style="float: left; padding: 5px;"><a href="http://researchblogging.org/news/?p=2521"><img alt="This post was chosen as an Editor's Selection for ResearchBlogging.org" src="http://www.researchblogging.org/public/citation_icons/rb_editors-selection.png" style="border:0;"/></a></span>We've been neglecting the micro-squishies lately (filose amoebae ain't proper squishies – too many fine protrusions in the way). Amoebozoa is a eukaryotic supergroup comprised of predominantly lobose amoebae, meaning their pseudopods are rounded and not fine and pointy (like those in the preceding post's organism – <span style="font-style: italic;">Filoreta</span>). Aside from the test-bearing Arcellinids, amoebozoans tend to be naked amoebae ('gymnamoebae'), like the well-known <span style="font-style: italic;">Amoeba proteus</span>, often erroneously referred to as a 'primitive', 'simple' or 'ancient' organism. "Naked amoeba" is a bit of a misnomer – while they don't lug rocks and heavy dishware around like testate amoebae, they generally carry some sort of cover, as most cells do. Gymnamoebae just pack light. Some, like <span style="font-style: italic;">Cochliopodium</span>, dress themselves in intricate scales, while others, like many Vannellids, are covered in thin, pointy glycostyles. <span style="font-style: italic;">Dermamoeba</span>, in turn, wears a thick, heavy coat.<br /><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj7QuH2rK-R8Opi5ScHE4lfg3aAxcr1GcHPo1I85QIemudHSbHR-gfjmrkoGLC3-Mlh78qKqFUiVZKXF1oIs0RQMoUyLEoyiMjZ92N_sCDfQ2OOnvWPvYNCrId1DjytMCOhpjogoxss7oO1/s1600/Smirnov+et+al+2011+EJP+Dermamoeba+01.jpg"><img style="cursor: pointer; width: 400px; height: 120px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj7QuH2rK-R8Opi5ScHE4lfg3aAxcr1GcHPo1I85QIemudHSbHR-gfjmrkoGLC3-Mlh78qKqFUiVZKXF1oIs0RQMoUyLEoyiMjZ92N_sCDfQ2OOnvWPvYNCrId1DjytMCOhpjogoxss7oO1/s400/Smirnov+et+al+2011+EJP+Dermamoeba+01.jpg" alt="" id="BLOGGER_PHOTO_ID_5588749229454055570" border="0" /></a><br /><span style="font-size:85%;">5-8 <span style="font-style: italic;">Dermamoeba</span> going about its business (n – nucleus, cv – contractile vacuole). 9 – <span style="font-style: italic;">Dermamoeba</span> lounging about in cysts (c) upon devouring some algae (chain-forming diatom or some <span style="font-style: italic;">Trebonema</span>-like thing). Nom nom nom. (<a href="http://dx.doi.org/10.1016/j.ejop.2010.12.002">Smirnov et al. 2011 <span style="font-style: italic;">EJP</span></a>)</span><br /></div><br /><span style="font-style: italic;">Dermamoeba</span>'s fine coat consists of thick bi-layered glycocalyx (a covering of fluffy sugar-proteins), sometimes with additional 'dense matter' lining the cell membrane. Upon encystation, an extra layer, the cell wall, is formed, but the contraption is thick enough without it already, at about half a micron.<br /><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgLBX-OnHNufObYOb-x_CegnGA6UT_8uGfmHBwgIrBfsMFrPhUMqhJlRC-TK3oBBbH3IG2vf4pQyneCq_JSlZiGkxBqN6k14YkgFjAD28wGpoOr_ncH-Orp0jH5KemQzZkM0HOmE4UA1TsF/s1600/Smirnov+et+al+2011+EJP+Dermamoeba+03.jpg"><img style="cursor: pointer; width: 400px; height: 154px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgLBX-OnHNufObYOb-x_CegnGA6UT_8uGfmHBwgIrBfsMFrPhUMqhJlRC-TK3oBBbH3IG2vf4pQyneCq_JSlZiGkxBqN6k14YkgFjAD28wGpoOr_ncH-Orp0jH5KemQzZkM0HOmE4UA1TsF/s400/Smirnov+et+al+2011+EJP+Dermamoeba+03.jpg" alt="" id="BLOGGER_PHOTO_ID_5588749239829213714" border="0" /></a><br /><span style="font-size:85%;">EM sections through the intense <span style="font-style: italic;">Dermamoeba</span> cell coat. m – cell membrane, gl – glycocalyx, adm – 'arrangement of dense material' (ie, "we don't know"). The glycocalyx often forms pretty patterns when sectioned. (15 is part of a Golgi body) </span><span style="font-size:85%;">(<a href="http://dx.doi.org/10.1016/j.ejop.2010.12.002">Smirnov et al. 2011 <span style="font-style: italic;">EJP</span></a>)</span><br /><br /></div>This thick coat poses some problems of its own. Amoebae eat by engulfing prey with their pseudopods – and this involves some degree of nudity and cell membrane exposure. Half a micron of glycocalyx wouldn't be particularly flexible, and and not much fun to digest. <span style="font-style: italic;">Dermamoeba</span> has to nibble on its coat before the meal. Upon contacting prey (typically algae), the amoeba forms a concave food cup around it, from the centre of which the cell coat gradually disappears. As the food cup deepens, the prey is pulled in to meet its doom via thick bundles of actin microfilaments spanning much of the cell – another unusual feature of this process. The prey is consequently engulfed for eventual digestion. As a result, the prey-containing vacuole has no glycocalyx for the amoeba to choke on (or rather, presumably, waste energy digesting).<br /><div style="text-align: center;"><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEghGCOu2-fA1X5LIED8uB2wQ2v8yyWZU3i-7R2L9yH85XWHESfPa6PNMAeSoDKtVPTwYDvNN1hiYa1nsyUyQ32ck4AoC9Jtm9HT2OFnsFDy290QcUlp1VSN22tPOeRPPaRwjr9XDytEYK01/s1600/Smirnov+et+al+2011+EJP+Dermamoeba+feeding.jpg"><img style="cursor: pointer; width: 270px; height: 400px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEghGCOu2-fA1X5LIED8uB2wQ2v8yyWZU3i-7R2L9yH85XWHESfPa6PNMAeSoDKtVPTwYDvNN1hiYa1nsyUyQ32ck4AoC9Jtm9HT2OFnsFDy290QcUlp1VSN22tPOeRPPaRwjr9XDytEYK01/s400/Smirnov+et+al+2011+EJP+Dermamoeba+feeding.jpg" alt="" id="BLOGGER_PHOTO_ID_5587267267693746610" border="0" /></a><br /><span style="font-size:85%;">Diagram of <span style="font-style: italic;">Dermamoeba</span>'s unusual feeding procedure. After the algal prey (al) is contacted by the amoeba (am), the glycocalyx (gl) is digested and the prey is drawn in by thick actin microfilament bundles (mf). The resulting food vacuole (fv) is conveniently devoid of coat material. </span><span style="font-size:85%;">(<a href="http://dx.doi.org/10.1016/j.ejop.2010.12.002">Smirnov et al. 2011 <span style="font-style: italic;">EJP</span></a>)</span></div><br />And here the food cup is 'live', or was before some electron microscopist brutally murdered it in osmic acid and sliced it up:<br /><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjISrfwDhsZX2WJB5v5cd8yX8dVSOoeBU4T9Zlu8hB3bhm-DBgC6MEWMvFRDMb8cXwviOtq2CITD29Q-dPdsrW_34CGWAgRkYX9Kj5ETXrZBmk1fMQpAn9hYFNiuyxFM14ECd6ZL9ehuohJ/s1600/Smirnov+et+al+2011+EJP+Dermamoeba+02.jpg"><img style="cursor: pointer; width: 400px; height: 177px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjISrfwDhsZX2WJB5v5cd8yX8dVSOoeBU4T9Zlu8hB3bhm-DBgC6MEWMvFRDMb8cXwviOtq2CITD29Q-dPdsrW_34CGWAgRkYX9Kj5ETXrZBmk1fMQpAn9hYFNiuyxFM14ECd6ZL9ehuohJ/s400/Smirnov+et+al+2011+EJP+Dermamoeba+02.jpg" alt="" id="BLOGGER_PHOTO_ID_5588749233360115922" border="0" /></a><br /><span style="font-size:85%;">EM sections through prey (al) being engulfed by the amoeba (am). Note the disappearance of the glycocalyx (gl) at the centre of the invagination. (<a href="http://dx.doi.org/10.1016/j.ejop.2010.12.002">Smirnov et al. 2011 <span style="font-style: italic;">EJP</span></a>)</span></div><br />How do some of the other coat-bearing amoebae get around their irremovable clothing? Without going into much detail (amoebozoan surface coverings are <span style="font-style: italic;">really</span> cool...), the glycostyle-bearing <span style="font-style: italic;">Pellita</span> simple sticks small 'subpseudopodia' through it for both moving about and feeding. In fact, some propose that the glycostyles may help it move by reducing the surface area in contact with the substrate – keeping the sticky cell membrane away on stilts.<br /><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhcq-MM-9K-BPpF0rqnwnMfZF95ulLNTWjX3KtQrhY9hP1LgLJyVPwRLz7qTvqzZe3ptOr-jbmlSxgo2hxSUD4ASHuqxAvKPazwZ8UzLDlrE6MF-DbHC_xa5630Feu9YVwvV-9ekmO51QQG/s1600/Smirnov+Kudryavtsev+2005+EJP+Pellita.jpg"><img style="cursor: pointer; width: 380px; height: 318px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhcq-MM-9K-BPpF0rqnwnMfZF95ulLNTWjX3KtQrhY9hP1LgLJyVPwRLz7qTvqzZe3ptOr-jbmlSxgo2hxSUD4ASHuqxAvKPazwZ8UzLDlrE6MF-DbHC_xa5630Feu9YVwvV-9ekmO51QQG/s400/Smirnov+Kudryavtsev+2005+EJP+Pellita.jpg" alt="" id="BLOGGER_PHOTO_ID_5588794791696494450" border="0" /></a><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj1Hk5S3wFlQrlfAwZIhwFd9jXzWmicqtW0TnJGlh1r8aNrzA6rlggOpKJfXfO_IamE-R69qA4BjWfJ6jA3zhe36e3BS7Ct-VRhmfUJH4MFLwCW8iYHSdKkySn26lMhezvw4YAHgaYXxSHr/s1600/Smirnov+Kudryavtsev+2005+EJP+Pellita+glycostyle.jpg"><img style="cursor: pointer; width: 57px; height: 342px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj1Hk5S3wFlQrlfAwZIhwFd9jXzWmicqtW0TnJGlh1r8aNrzA6rlggOpKJfXfO_IamE-R69qA4BjWfJ6jA3zhe36e3BS7Ct-VRhmfUJH4MFLwCW8iYHSdKkySn26lMhezvw4YAHgaYXxSHr/s400/Smirnov+Kudryavtsev+2005+EJP+Pellita+glycostyle.jpg" alt="" id="BLOGGER_PHOTO_ID_5588794783837610850" border="0" /></a><br /><span style="font-size:85%;">Top left: <span style="font-style: italic;">Pellita</span> walking on stilts of glycostyles (depicted at the right). Bottom: extruding sub-feet across stilts for feeding. (<a href="http://dx.doi.org/10.1016/j.ejop.2005.05.002">Smirnov & Kudryavtsev 2005 <span style="font-style: italic;">EJP</span></a>)</span><br /><br /><div style="text-align: left;">I'm decidedly avoiding amoebozoan systematics here. <a href="http://coo.fieldofscience.com/search/label/Amoebozoa">Christopher Taylor did a nice overview of it</a> at the Catalogue of Organisms a while back, but keep in mind that some of the groups did jump around since then, and the phylogenies are in the works. Maybe if more people cared, the taxonomy could be resolved sooner...<br /><br /><span style="font-size:85%;">PS: My committee* has voted to remove "Sunday Protist" from Sunday Protist titles, since:<br />a) They seldom come out on Sundays anyway (lulz); and<br />b) Takes up too much valuable headline real estate. Since we bloggers are supposedly playing pseudo-journalists or something, might as well play it right... ;-)<br />(and c) Structure and I aren't the best of friends.)<br /><br />* Given how inefficient my brain is at accomplishing anything, I've concluded it can only be composed of a close neural approximation of a committee. Explains the indecisiveness as well. Probably requires a double majority to pass any major decisions, and hence is about as effective as the Californian government. Without the sovereign debt crisis, fortunately.</span><br /><br /><span style="font-weight: bold;">References</span><br /><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=European+Journal+of+Protistology&rft_id=info%3Adoi%2F10.1016%2Fj.ejop.2005.05.002&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Pellitidae+n.+fam.+%28Lobosea%2C+Gymnamoebia%29+%E2%80%93+a+new+family%2C+accommodating+two+amoebae+with+an+unusual+cell+coat+and+an+original+mode+of+locomotion%2C++n.g.%2C+n.sp.+and++comb.+nov&rft.issn=09324739&rft.date=2005&rft.volume=41&rft.issue=4&rft.spage=257&rft.epage=267&rft.artnum=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0932473905000271&rft.au=SMIRNOV%2C+A.&rft.au=KUDRYAVTSEV%2C+A.&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CCell+Biology%2C+Protistology">SMIRNOV, A., & KUDRYAVTSEV, A. (2005). Pellitidae n. fam. (Lobosea, Gymnamoebia) – a new family, accommodating two amoebae with an unusual cell coat and an original mode of locomotion, n.g., n.sp. and comb. nov <span style="font-style: italic;">European Journal of Protistology, 41</span> (4), 257-267 DOI: <a rev="review" href="http://dx.doi.org/10.1016/j.ejop.2005.05.002">10.1016/j.ejop.2005.05.002</a></span><br /><br /><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=European+Journal+of+Protistology&rft_id=info%3A%2F10.1016%2Fj.ejop.2010.12.002&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Dermamoeba+algensis+n.+sp.+%28Amoebozoa%2C+Dermamoebidae%29+%E2%80%93+An+algivorous+lobose+amoeba+with+complex+cell+coat+and+unusual+feeding+mode&rft.issn=&rft.date=2011&rft.volume=&rft.issue=&rft.spage=&rft.epage=&rft.artnum=http%3A%2F%2Fdx.doi.org%2F10.1016%2Fj.ejop.2010.12.002&rft.au=Smirnov+AV&rft.au=Bedjagina+OM&rft.au=Goodkov+AV&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CCell+Biology%2C+Protistology">Smirnov AV, Bedjagina OM, & Goodkov AV (2011). Dermamoeba algensis n. sp. (Amoebozoa, Dermamoebidae) – An algivorous lobose amoeba with complex cell coat and unusual feeding mode <span style="font-style: italic;">European Journal of Protistology</span> : <a rev="review" href="http://www.blogger.com/10.1016/j.ejop.2010.12.002">10.1016/j.ejop.2010.12.002</a></span><br /></div></div>Psi Wavefunctionhttp://www.blogger.com/profile/10829712736757471647noreply@blogger.com0tag:blogger.com,1999:blog-3643556495084083743.post-77413460293538240512011-03-24T03:39:00.000-07:002011-03-24T04:58:47.945-07:00Reticulose amoeba: cells can be fine nets tooAgain, the protist kingdom is a special paradise for a cell biologist: as soon as one steps outside the plant and animal kingdoms (and yeast), diversity of cellular forms and structures explodes beyond reason. Cells can also take the shape of a fine net with no obvious cell body proper:<br /><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjQColPx7JzSQFNKTX-LXBwd3NtQw1IbM3XKhkvahXmz-vpHBHMfdijxGmaeUN-zS1q3JLClaxnvrf-4XnG1pxLnnnczTxVb0vK1MgW_fdN3Kl_VxU-fWEUXKI9AN_FVj7x_l3M_UJyCfv2/s1600/Reticulose+amoeba+02.jpg"><img style="cursor: pointer; width: 400px; height: 338px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjQColPx7JzSQFNKTX-LXBwd3NtQw1IbM3XKhkvahXmz-vpHBHMfdijxGmaeUN-zS1q3JLClaxnvrf-4XnG1pxLnnnczTxVb0vK1MgW_fdN3Kl_VxU-fWEUXKI9AN_FVj7x_l3M_UJyCfv2/s400/Reticulose+amoeba+02.jpg" alt="" id="BLOGGER_PHOTO_ID_5587593940552586706" border="0" /></a><br /><span style="font-size:85%;">Cover slip floated ~ 1wk on marine sample from intertidal silt at Stanley Park. (40x obj, DIC and phase, resp.)</span><br /><span style="color: rgb(255, 0, 0);font-size:85%;" >EDIT: Confirmed <span style="font-style: italic;">Filoreta</span>. </span><br /></div><br />Almost overlooked it thinking it was just slide gunk. Amoebae suffer all too often from that fate – apparently <span style="font-style: italic;">Parvamoeba</span>, one of the most common and ubiquitous amoebae, was only described in the early 90's (<a href="http://cat.inist.fr/?aModele=afficheN&cpsidt=3803586">Rogerson 1993 <span style="font-style: italic;">EJP</span></a>) because it was tiny and no one noticed.<br /><br />Could be something like <a href="http://tolweb.org/onlinecontributors/app?page=ViewImageData&service=external&sp=36046"><span style="font-style: italic;">Filoreta</span></a> sp. (Rhizarian), but something feels off about it. <span style="font-style: italic;">Filoreta</span> doesn't seem to stretch cytoplasm between filopodia like this specimen does. Maybe it's more like the amoebozoan <a href="http://starcentral.mbl.edu/microscope/portal.php?pagetitle=classification&BLOCKID=9&CHILDID=13507"><span style="font-style: italic;">Corallomyxa</span></a> and <a href="http://starcentral.mbl.edu/microscope/portal.php?pagetitle=classification&BLOCKID=9&CHILDID=13506&namebankID=1688865"><span style="font-style: italic;">Stereomyxa</span></a>, or <a href="http://dx.doi.org/10.1016/j.protis.2009.01.001">stramenopile</a> <a href="http://www.eol.org/pages/2911795"><span style="font-style: italic;">Leukarachnion</span></a>. Then again, amoebae are notoriously dynamic in their morphology. Something that's a far bigger issue in the microbial world is the necessity of getting a sense of the morphotype range of a species; one specimen doesn't quite cut it as it does for animal taxonomy.<br /><br />In fact, perhaps instead of the ridiculious (for us) ICZN and ICBN requirements for submission of material for curation (many species neither like being cultured nor preserve all that well on a slide), for microbial species there should be a requirement for additional images of different specimens, if possible, to try to capture some of the morphological range. But then again, I'm not a taxonomist, so what do I know.<br /><br />Right, midterm... (hey, at least I procrastinate productively!)Psi Wavefunctionhttp://www.blogger.com/profile/10829712736757471647noreply@blogger.com2tag:blogger.com,1999:blog-3643556495084083743.post-44590918125113588922011-03-23T04:27:00.000-07:002011-03-23T06:24:23.314-07:00Mystery Micrograph #27<div style="text-align: center;"><div style="text-align: left;">Busy week here, so have a mystery micrograph:<br /></div><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgViN1a-BYJ4NgI4hGf5SPU9X4VZqHF2wcrp3opaYhBk12fGIrDltN8i2ahjYEh_c3XiwhJIFPjq874IXMl5Hymu9i2FULtXovQQ_Y51xXnmuTHhPn_QO193Ws1OTj2kjbn5euMZdU6S-Tb/s1600/MM27.jpg"><img style="cursor: pointer; width: 400px; height: 255px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgViN1a-BYJ4NgI4hGf5SPU9X4VZqHF2wcrp3opaYhBk12fGIrDltN8i2ahjYEh_c3XiwhJIFPjq874IXMl5Hymu9i2FULtXovQQ_Y51xXnmuTHhPn_QO193Ws1OTj2kjbn5euMZdU6S-Tb/s400/MM27.jpg" alt="" id="BLOGGER_PHOTO_ID_5584978139855455698" border="0" /></a><br />To be referenced later. Won't reveal the scale yet. </div><br />Kekeke. *evil grin*<br /><span style="font-size:85%;">Anyway, I have a "mid"term, almost two weeks before the term ends. Took the art of neglecting coursework to a whole new dimension this term – incredibly difficult to give a fuck in term 2 of year 5. Lots of catching up to do...</span>Psi Wavefunctionhttp://www.blogger.com/profile/10829712736757471647noreply@blogger.com1tag:blogger.com,1999:blog-3643556495084083743.post-81914891644284017302011-03-17T00:58:00.000-07:002011-03-17T01:35:28.342-07:00Trypanosomatid plastids and uninentional scientific comedyOne need not read past the abstract:<br /><blockquote><span style="color: rgb(0, 0, 153);">"It is usually assumed that the trypanosomatid plastid shared a common origin with that of euglenids, but Δ4 desaturase phylogenies suggest that it could have originated via an independent, tertiary endosymbiosis involving a haptophyte alga. It is also possible that ancestors of the Trypanosomatidae initially possessed a primary plastid that later was replaced by a secondary or tertiary plastid."</span> –<a href="http://www.journalofparasitology.org/doi/abs/10.1645/GE-1810.1"> Bodyl et al 2010 <span style="font-style: italic;">J Parasitol</span> </a>(<a href="http://www.smorfland.uni.wroc.pl/uploads/Main/GE-1810.pdf">pdf</a>)</blockquote>I could go on for many, many pages about the implausibility of most entirely unnecessary serial plastid symbiosis theories; I could go on for pages yet on how little a single gene phylogeny means these days; I could go over the typical first few lectures on phylogenetic reconstruction and the fundamental principle of parsimony. But instead, I've quickly thrown together a diagram highlighting the KEY problem with Bodyl et al.'s hypothesis:<br /><div style="text-align: center;"><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhSGtZH6LrdJhxgAlcuFByPqYr-jBEpvlba1G3BiN0KOJSUALdY1oI5tGqKqLzH9zx5anaRA0koNQ76mNhju36KINLRa3XQP3meACtioFDxksxHr9Qchm8tWsxXjjAloW7JSEQsSJXBhbhc/s1600/Plastid+symbiosis+rocket+science.png"><img style="cursor: pointer; width: 400px; height: 237px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhSGtZH6LrdJhxgAlcuFByPqYr-jBEpvlba1G3BiN0KOJSUALdY1oI5tGqKqLzH9zx5anaRA0koNQ76mNhju36KINLRa3XQP3meACtioFDxksxHr9Qchm8tWsxXjjAloW7JSEQsSJXBhbhc/s400/Plastid+symbiosis+rocket+science.png" alt="" id="BLOGGER_PHOTO_ID_5584955300454613346" border="0" /></a><br /><span style="font-size:85%;">Taxa in black – non-photosynthetic and non-plastid-bearing.</span><br /><br /></div><span style="font-weight: bold;">Trypanosomes don't have plastids. </span><br /><br />Or any reason to suspect they might.<br /><br />*to be fair, they are (I hope) talking about a plastid in their ancestry, but those things are seldom lost completely due to inevitable strong dependencies.<br /><br />In fact, unlike apicomplexans, trypanosomes are nested firmly within a completely non-photosynthetic phylum in a predominantly non-photosynthetic subgroup of an almost-exclusively non-photosynthetic supergroup. Furthermore, the many possible phylogenies of euglenid evolution overwhelmingly support a single symbiotic event; character evolution supports this further, in one of the few cases where there's actually little room for dispute. Endosymbiosis may not be excessively rare, but it ain't common either, particularly in a full-fledged form involving vast transfer of plastid genes to the nucleus AND mechanisms of plastid targeting of the synthesised proteins. Too many an ambitious biologist completely forget about targeting, or that there's actual cell biology happening around their beloved gene sequences.<br /><br />For a properly scientific and civil demolition of an earlier iteration of this ridiculous idea, see <a href="http://dx.doi.org/10.1016/j.tim.2004.04.001">Leander 2004 <span style="font-style: italic;">Tr Microbiol</span></a> (<a href="http://www.botany.ubc.ca/bleander/images/TiMEugs.pdf">pdf</a>). That smell of something burning? No need to worry – probably just coming from the link.<br /><br />Lastly, as ridiculous as this hypothesis is and as amusing as it is that this actually survived peer review (no offense to <span style="font-style: italic;">J Parasitol</span>, but phylogenies and evolution do not seem to be their strong point based on some other cases...), I fully support it being published. It is the excessive censorship of atypical theories rather than sketchy papers that "stiffles [scientific] thought"...<br /><br />(Note: I would've submitted this to the high IF <a href="http://www.thejayfk.com/"><span style="font-style: italic;">Journal of Are You Fucking Kidding</span></a>, but I'm out of hard liquor and would thereby fail the <a href="http://www.thejayfk.com/?page_id=32">author instructions</a>...)<br /><br /><span style="font-weight: bold;">References</span><br /><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Journal+of+Parasitology&rft_id=info%3Adoi%2F10.1645%2FGE-1810.1&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Did+Trypanosomatid+Parasites+Contain+a+Eukaryotic+Alga%E2%80%93Derived+Plastid+in+Their+Evolutionary+Past%3F&rft.issn=0022-3395&rft.date=2010&rft.volume=96&rft.issue=2&rft.spage=465&rft.epage=475&rft.artnum=http%3A%2F%2Fwww.bioone.org%2Fdoi%2Fabs%2F10.1645%2FGE-1810.1&rft.au=Body%C5%82%2C+A.&rft.au=Mackiewicz%2C+P.&rft.au=Milanowski%2C+R.&rfe_dat=bpr3.included=1;bpr3.tags=Biology">Bodył, A., Mackiewicz, P., & Milanowski, R. (2010). Did Trypanosomatid Parasites Contain a Eukaryotic Alga–Derived Plastid in Their Evolutionary Past? <span style="font-style: italic;">Journal of Parasitology, 96</span> (2), 465-475 DOI: <a rev="review" href="http://dx.doi.org/10.1645/GE-1810.1">10.1645/GE-1810.1</a></span><br /><br /><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Trends+in+Microbiology&rft_id=info%3Adoi%2F10.1016%2Fj.tim.2004.04.001&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Did+trypanosomatid+parasites+have+photosynthetic+ancestors%3F&rft.issn=0966842X&rft.date=2004&rft.volume=12&rft.issue=6&rft.spage=251&rft.epage=258&rft.artnum=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0966842X04000927&rft.au=LEANDER%2C+B.&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CProtistology%2C+Evolutionary+Biology">LEANDER, B. (2004). Did trypanosomatid parasites have photosynthetic ancestors? <span style="font-style: italic;">Trends in Microbiology, 12</span> (6), 251-258 DOI: <a rev="review" href="http://dx.doi.org/10.1016/j.tim.2004.04.001">10.1016/j.tim.2004.04.001</a></span>Psi Wavefunctionhttp://www.blogger.com/profile/10829712736757471647noreply@blogger.com2tag:blogger.com,1999:blog-3643556495084083743.post-47636962090264346112011-03-16T15:50:00.000-07:002011-03-16T15:57:48.874-07:00Out in the field: freshwater microforay picture dump<div>I've probably accumulated about 10-20GB of protist pics by now. And a couple DV tapes' worth of video. Still got some work to do before I can catch up with my 80GB of Arabidopsis epidermis pictures (mostly of all sorts of mutilated stomata), but this is for fun rather than data, and thus accumulates much slower. Most of them are crap or uninteresting by now, but the others might as well get dumped here as raw data from 'field work'. The wonderful thing about microscopy is that the more you know, the more new things you observe, and the more interesting it gets. Eg. once you're no longer distracted by trying to identify unknown things, you pay more attention to behaviour. Anyway, I'll dump the photos in random installments here and there, hope there's at least something interesting for you from time to time.</div><br />To begin, a fuzzy ciliate of sorts. Prominent contractile vacuole, and I think in the left image I think you can make out its macronucleus or two. Can't see the mouth so IDing it is a bit difficult.<br /><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiq30JUWWbj_OKwS6rU7PIiwWfzxLurGQ81yiCOloaw8JQFNUBfwVXkVf_S3jTT2FHcZ4pLKgZ8VQm9fPzk5HfISdZCFNnoqxJalke-3oCAQJaArMRk3BpzYUAaGgtQzXPS9z4vCo7dsx80/s1600/P1070611-1.jpg"><img style="cursor: pointer; width: 268px; height: 252px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiq30JUWWbj_OKwS6rU7PIiwWfzxLurGQ81yiCOloaw8JQFNUBfwVXkVf_S3jTT2FHcZ4pLKgZ8VQm9fPzk5HfISdZCFNnoqxJalke-3oCAQJaArMRk3BpzYUAaGgtQzXPS9z4vCo7dsx80/s400/P1070611-1.jpg" alt="" id="BLOGGER_PHOTO_ID_5579825495983404626" border="0" /></a><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhxZbctbo7e2xyZW5MTBdHiGvJx7SyS0px9B8NlBQhZnRmX0644nfPYTn0-PYlY9Fpb1h1AEAsTwe0r8iL72g1HU39oQsEvfNE4pZqyJQAbaT1L0Ovfx4AkDgVQZ2J1JPXHUWmwrF5bjbIn/s1600/P1070612-1.jpg"><img style="cursor: pointer; width: 263px; height: 251px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhxZbctbo7e2xyZW5MTBdHiGvJx7SyS0px9B8NlBQhZnRmX0644nfPYTn0-PYlY9Fpb1h1AEAsTwe0r8iL72g1HU39oQsEvfNE4pZqyJQAbaT1L0Ovfx4AkDgVQZ2J1JPXHUWmwrF5bjbIn/s400/P1070612-1.jpg" alt="" id="BLOGGER_PHOTO_ID_5579825497505497666" border="0" /></a><br /></div><br />[to shave off some page loading time, the rest is below the jump (if it works)]<br /><a name='more'></a><br /><br />This one's got a big mouth. Seems to be <i><a href="http://starcentral.mbl.edu/microscope/portal.php?pagetitle=assetfactsheet&imageid=9693">Lembadion</a></i><a href="http://starcentral.mbl.edu/microscope/portal.php?pagetitle=assetfactsheet&imageid=9693"> sp</a>., an oligohymenophoran ciliate. Guessing the yellowish particles are prey or food storage of some sort.<br /><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgbnSGWZMPOY15OvVGyo3UtjfrC-fJa-R7l9eujTs8qU_5vPBVEy11vKJf0rlI2YEGANjf73kRFhE2necWUgG953yNuZ2S7FjxPAgT5oYhoV-9O4_khj3hORL1mKalAs0PNfbNPMyhTWbPU/s1600/P1070614-1.jpg"><img style="cursor: pointer; width: 271px; height: 300px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgbnSGWZMPOY15OvVGyo3UtjfrC-fJa-R7l9eujTs8qU_5vPBVEy11vKJf0rlI2YEGANjf73kRFhE2necWUgG953yNuZ2S7FjxPAgT5oYhoV-9O4_khj3hORL1mKalAs0PNfbNPMyhTWbPU/s400/P1070614-1.jpg" alt="" id="BLOGGER_PHOTO_ID_5579826194514827938" border="0" /></a><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgvi1-_Qg2Nm-mo8dU8dJBZjcA0-oa4hSG_xLBi-TuQCRwHEWwBcP6DJ_twEB8Mfc5gIyFvFeA9GDlA3ig-LJvilb6fksN1ggsRNjhSm2dBfL1o-WELwg9Va4BgaY5TEOtvt0UHwtmLngis/s1600/P1070613-2.jpg"><img style="cursor: pointer; width: 271px; height: 299px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgvi1-_Qg2Nm-mo8dU8dJBZjcA0-oa4hSG_xLBi-TuQCRwHEWwBcP6DJ_twEB8Mfc5gIyFvFeA9GDlA3ig-LJvilb6fksN1ggsRNjhSm2dBfL1o-WELwg9Va4BgaY5TEOtvt0UHwtmLngis/s400/P1070613-2.jpg" alt="" id="BLOGGER_PHOTO_ID_5579825501568595266" border="0" /></a><br /><br /></div>Epalxellid of sorts, perhaps of the genus <i><a href="http://starcentral.mbl.edu/microscope/portal.php?pagetitle=classification&BLOCKID=9&CHILDID=1691&namebankID=489668">Epalxella</a></i> itself:<br /><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgXKRibcKkU-1RSws4QcR_6CGRUmTZfuUZH-Nc_0H85VPYhWzUlZoJCMI93ZSsfsO9A3L7jmyqBBR3S6tAIeR6_qptnlByTZqbCXoah3ik1X5K4SMJ0S7OzWTi65qDhArB8F1EoRtxZtwa2/s1600/P1070616-1.jpg"><img style="cursor: pointer; width: 267px; height: 302px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgXKRibcKkU-1RSws4QcR_6CGRUmTZfuUZH-Nc_0H85VPYhWzUlZoJCMI93ZSsfsO9A3L7jmyqBBR3S6tAIeR6_qptnlByTZqbCXoah3ik1X5K4SMJ0S7OzWTi65qDhArB8F1EoRtxZtwa2/s400/P1070616-1.jpg" alt="" id="BLOGGER_PHOTO_ID_5579826201410460850" border="0" /></a><br /></div><br />What appeared to be a developmentally-'unique' double stentor; or one in the process of division that remained attached. Actually, may well be division, didn't think they'd keep filtering away in the midst of cytokinesis:<br /><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgJGycbnaB-m4QaK32JrDzFb1CH_Nu9cunUshEvOPD3h0LBDapuHSYQTZuvI7mbBj0VPRyo7qT7DhSmj1BNR9twnf15yZXe4cX_s7FKDVmyL0GMnmwxqSZD-1MlIx-d7Z8H9G_iAa_1FsnG/s1600/P1070720-1.jpg"><img style="cursor: pointer; width: 400px; height: 164px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgJGycbnaB-m4QaK32JrDzFb1CH_Nu9cunUshEvOPD3h0LBDapuHSYQTZuvI7mbBj0VPRyo7qT7DhSmj1BNR9twnf15yZXe4cX_s7FKDVmyL0GMnmwxqSZD-1MlIx-d7Z8H9G_iAa_1FsnG/s400/P1070720-1.jpg" alt="" id="BLOGGER_PHOTO_ID_5579826203983598658" border="0" /></a><br /></div><br /><div style="text-align: center;"><div style="text-align: left;">Goniomonas, the non-photosynthetic sister group to plastid-bearing cryptomonads:<br /></div><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhcFkyB4bhYKoxEtMqHE32_dkVb0v464nlFcbojdHgA8hYsnScwJDPkIoAS-U_7XWypCzJYJEaa-M1AHU0eZSwCMGKy2zQmOzrCw63NoPlLNy3HLe1IduwaCVzW8UrJH64lfiZP4ZQEo9ED/s1600/P1070641-1.jpg"><img style="cursor: pointer; width: 204px; height: 230px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhcFkyB4bhYKoxEtMqHE32_dkVb0v464nlFcbojdHgA8hYsnScwJDPkIoAS-U_7XWypCzJYJEaa-M1AHU0eZSwCMGKy2zQmOzrCw63NoPlLNy3HLe1IduwaCVzW8UrJH64lfiZP4ZQEo9ED/s400/P1070641-1.jpg" alt="" id="BLOGGER_PHOTO_ID_5579776577154433154" border="0" /></a><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjDA8IItmlsePpRyX0d9pxGgJFF2xK1ixIh1a-gI2nVuzJVClkegd6GJJNpAwflCanzHqao9SdkF6KoXrG_B0tmvD3H9JkQr8nEX2-iJeFNk4DCeENWuyyXc-x6gzfGJwPsVeJuCaxCkS50/s1600/P1070642-1.jpg"><img style="cursor: pointer; width: 204px; height: 230px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjDA8IItmlsePpRyX0d9pxGgJFF2xK1ixIh1a-gI2nVuzJVClkegd6GJJNpAwflCanzHqao9SdkF6KoXrG_B0tmvD3H9JkQr8nEX2-iJeFNk4DCeENWuyyXc-x6gzfGJwPsVeJuCaxCkS50/s400/P1070642-1.jpg" alt="" id="BLOGGER_PHOTO_ID_5579776578591898354" border="0" /></a><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEittaaGdJ8m4Laydr-ARPbMhJd2xzTMBMyhvnHGYmud3GBWLkv_T2CuZyhV1d6qtFU7ER7ifyypg4snZb0fspIJSn2wZzoaqogCxQ0SPjgTg02l1zOmeZ3Anrq6KZp2PjVQRgxz5GsdkWwD/s1600/P1070640-1.jpg"><img style="cursor: pointer; width: 204px; height: 230px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEittaaGdJ8m4Laydr-ARPbMhJd2xzTMBMyhvnHGYmud3GBWLkv_T2CuZyhV1d6qtFU7ER7ifyypg4snZb0fspIJSn2wZzoaqogCxQ0SPjgTg02l1zOmeZ3Anrq6KZp2PjVQRgxz5GsdkWwD/s400/P1070640-1.jpg" alt="" id="BLOGGER_PHOTO_ID_5579752768136940258" border="0" /></a><br /><br /></div><span style="font-style: italic;">Diplophrys</span>, a stramenopile with a conspicuous lipid(?) droplet and very fine filopodia.<br /><div style="text-align: center;"><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiovknOtewXzIYB4tYYhxru7jPSfRdQke_ekAd8zAo6s-tH48G5XmSCA1FOQjSpCgGTgxQRxA3M5q_oDhonLRp0NYuI65bbBH3AT0_beebJ185aAay6MwN1O0xEiSGxbzueBuXQU8x3Eftd/s1600/P1070651-1.jpg"><img style="cursor: pointer; width: 259px; height: 269px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiovknOtewXzIYB4tYYhxru7jPSfRdQke_ekAd8zAo6s-tH48G5XmSCA1FOQjSpCgGTgxQRxA3M5q_oDhonLRp0NYuI65bbBH3AT0_beebJ185aAay6MwN1O0xEiSGxbzueBuXQU8x3Eftd/s400/P1070651-1.jpg" alt="" id="BLOGGER_PHOTO_ID_5579776592079087586" border="0" /></a><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEii628C4IQCIbNspzYwVMV5-NV3OBGmdkbJbDe3xITW9BHqfVl39NoEx45pcdSxh7yLDVj3eEP9G0vOzxtNxdkCzw5GWoEt2UCfxM0uMUV5nXQcnFFn89H4owGOlflPsE0dRnhn8DZNwUDI/s1600/P1070652-1.jpg"><img style="cursor: pointer; width: 258px; height: 268px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEii628C4IQCIbNspzYwVMV5-NV3OBGmdkbJbDe3xITW9BHqfVl39NoEx45pcdSxh7yLDVj3eEP9G0vOzxtNxdkCzw5GWoEt2UCfxM0uMUV5nXQcnFFn89H4owGOlflPsE0dRnhn8DZNwUDI/s400/P1070652-1.jpg" alt="" id="BLOGGER_PHOTO_ID_5579823226632071826" border="0" /></a><br /></div><br />View of surface pellicle strips on some photosynthetic euglenid:<br /><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEicmMn5ZH5sY4pCG5B2kApBaOEkOsl49UWLqLKst1VJfHDEQHgmqeh8TqecUx4mfB5-Gm6Ht0KcMK3r9xOLu5K6evgj77_JcA_CMRN9LiWLc4orH_aB8KNCv_nPnqcgtTnmY8apXMkf4BaT/s1600/P1070509-1.jpg"><img style="cursor: pointer; width: 400px; height: 214px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEicmMn5ZH5sY4pCG5B2kApBaOEkOsl49UWLqLKst1VJfHDEQHgmqeh8TqecUx4mfB5-Gm6Ht0KcMK3r9xOLu5K6evgj77_JcA_CMRN9LiWLc4orH_aB8KNCv_nPnqcgtTnmY8apXMkf4BaT/s400/P1070509-1.jpg" alt="" id="BLOGGER_PHOTO_ID_5579826204960325986" border="0" /></a><br /></div><br />Some sort of glissomonad, I think. Looks hatchet/pike-like, would totally name it something silly like <span style="font-style: italic;">Hatchetomonas</span> were it undescribed...<br /><div style="text-align: center;"><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiDmwiUsIgCNgOfUO3_FojHt5MLooD4KbBFZx93bueD9A0dklFb-Nxo1w3bBGRkKQpZIDHzNeyFvRwffS0FN2MSSUOan5hJNoICB8ig2Ixv-9fFrn7bLgQ1cEBznPrCZSshskIYjC9Gg10v/s1600/P1070527-stack.jpg"><img style="cursor: pointer; width: 400px; height: 165px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiDmwiUsIgCNgOfUO3_FojHt5MLooD4KbBFZx93bueD9A0dklFb-Nxo1w3bBGRkKQpZIDHzNeyFvRwffS0FN2MSSUOan5hJNoICB8ig2Ixv-9fFrn7bLgQ1cEBznPrCZSshskIYjC9Gg10v/s400/P1070527-stack.jpg" alt="" id="BLOGGER_PHOTO_ID_5579752764323530034" border="0" /></a><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjE4tYH5kJqMvdhUU5UOnwpwYBeupb64uZSifRGlgdod0YRuEU-gCmrhkBGznoqPAomY3WxbLTq9zXN9TmRqpssFtG2lk80-_LAi6RJ-S31MTOc_1rNLxoe5NtAMFGuPRv0ztR0kLrFYlio/s1600/P1070526-stack.jpg"><img style="cursor: pointer; width: 400px; height: 145px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjE4tYH5kJqMvdhUU5UOnwpwYBeupb64uZSifRGlgdod0YRuEU-gCmrhkBGznoqPAomY3WxbLTq9zXN9TmRqpssFtG2lk80-_LAi6RJ-S31MTOc_1rNLxoe5NtAMFGuPRv0ztR0kLrFYlio/s400/P1070526-stack.jpg" alt="" id="BLOGGER_PHOTO_ID_5579752760855958610" border="0" /></a><br /></div><br /><br />Some filose amoeba with seemingly eruptive lobopodia in addition to thin filopodia. Can <a href="http://skepticwonder.fieldofscience.com/2009/10/sunday-protist-nucleariids.html">nucleariids</a> (amoeboid sister group to fungi) do this? Though the prominent nucleus at its centre points towards nucleariidness:<br /><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi40QxVXyZMDNYXvhloz58wHzMMnLSA6uZ0otiiL6WwyCotGtm6768Fsi6f8Nv0Zb25qwS-Bw4ssgKrmxYfpA_0LqfNp0QWFS_vUzMr7oHSa_WzoLKHEAT6ZuE-nhrHeCt8r1MQtBe8vlG3/s1600/P1070692-1.jpg"><img style="cursor: pointer; width: 266px; height: 305px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi40QxVXyZMDNYXvhloz58wHzMMnLSA6uZ0otiiL6WwyCotGtm6768Fsi6f8Nv0Zb25qwS-Bw4ssgKrmxYfpA_0LqfNp0QWFS_vUzMr7oHSa_WzoLKHEAT6ZuE-nhrHeCt8r1MQtBe8vlG3/s400/P1070692-1.jpg" alt="" id="BLOGGER_PHOTO_ID_5579823244902075650" border="0" /></a><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi149ykgHSSd3ZKKpOCOEWKjl_hMnNRrOZab8kTD96iw-_kXzJR8JocNucD39cTKKIEveksvcdiwvV3IkB9fPBfn7WgRI-5Zr6heYeL9f_dGwZLJH98lt-JsgUh3-kxeeVa9JpXCf61DvH-/s1600/P1070690-1.jpg"><img style="cursor: pointer; width: 271px; height: 305px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi149ykgHSSd3ZKKpOCOEWKjl_hMnNRrOZab8kTD96iw-_kXzJR8JocNucD39cTKKIEveksvcdiwvV3IkB9fPBfn7WgRI-5Zr6heYeL9f_dGwZLJH98lt-JsgUh3-kxeeVa9JpXCf61DvH-/s400/P1070690-1.jpg" alt="" id="BLOGGER_PHOTO_ID_5579823237170554210" border="0" /></a><br /></div><br />An amoeba with branching filopodia. Quite vacuolated. Fucked if I know what it is. Some sort of <a href="http://protist.i.hosei.ac.jp/PDB/Images/sarcodina/Vampyrella/index.html">vampyrellid</a>? (eg vaguely like <a href="http://protist.i.hosei.ac.jp/PDB4/PCD2855/htmls/42.html">this</a>)<br /><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiNk92WoUT5OlNBdDolj23V2w4r9Y0YigIBV_MNMY32UaPb1s84OJNjtNZAzQVFpUPYjGJHFy19A_scZ67CbbP6k_-UyqQBb4VvrjnkEd5qZ65FlgeJ8-qTR2kzbHhX-ysE9EsRXiQhOMla/s1600/P1070655-1.jpg"><img style="cursor: pointer; width: 384px; height: 400px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiNk92WoUT5OlNBdDolj23V2w4r9Y0YigIBV_MNMY32UaPb1s84OJNjtNZAzQVFpUPYjGJHFy19A_scZ67CbbP6k_-UyqQBb4VvrjnkEd5qZ65FlgeJ8-qTR2kzbHhX-ysE9EsRXiQhOMla/s400/P1070655-1.jpg" alt="" id="BLOGGER_PHOTO_ID_5579823235116572610" border="0" /></a><br /></div><br />Nucleariid like the previously mentioned <a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhdpgTtVLgeCIE84RurF1xDH3SZ5SP_rIGwG8GX33dcQgEOvFO2YD7A_GuELOAke0ru5LsqB1QttaRrcODM4eSc3FGC4TUkNkXlZpJTDc9_9CjLC50uzi7qyCeu5QGbzZAwmOp2isBgT6kW/s1600-h/Rabdiophrys.jpg"><span style="font-style: italic;">Rhabdiophrys</span></a>? Or vampyrellid? Damn, identifying amoebae was way easier when I knew less of them...<br /><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh-j6KQAC__vvb5rJcEdZ8fdYoe7aO0a3zDi0sWzQq1e5bkrc-nK7x1inu0WPN1QwELtKDMPgnox2KSGB9N1h5kQ2CwMy426hsxgW7KJwUKLIsvMZvK6uqPnEwk3e4I0VwJQ_u8g5xE4NfA/s1600/P1070697-1.jpg"><img style="cursor: pointer; width: 400px; height: 384px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh-j6KQAC__vvb5rJcEdZ8fdYoe7aO0a3zDi0sWzQq1e5bkrc-nK7x1inu0WPN1QwELtKDMPgnox2KSGB9N1h5kQ2CwMy426hsxgW7KJwUKLIsvMZvK6uqPnEwk3e4I0VwJQ_u8g5xE4NfA/s400/P1070697-1.jpg" alt="" id="BLOGGER_PHOTO_ID_5579825490234578434" border="0" /></a><br /></div><br />Some small round thing that liked to wrap its [attached-to-substrate] flagellum around itself. Ummm, that sort of made sense, right? Don't think I'm allowed to ever write species descriptions for some reason...<br /><div style="text-align: center;"><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjazeGDhzX4Wx9NL0rmtgocKS6iZzRkfM1oFmoi6D-FKUmzb9xpA6jPqLc2j9L_K47ppbVqZ9isnRkR5bOKQiljF1kn7TF7Efn_Ee5m3m1Ip047h78OSZqHi3RRI8hWUvP1CvEkR_P-bnm3/s1600/P1070501-stack.jpg"><img style="cursor: pointer; width: 400px; height: 299px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjazeGDhzX4Wx9NL0rmtgocKS6iZzRkfM1oFmoi6D-FKUmzb9xpA6jPqLc2j9L_K47ppbVqZ9isnRkR5bOKQiljF1kn7TF7Efn_Ee5m3m1Ip047h78OSZqHi3RRI8hWUvP1CvEkR_P-bnm3/s400/P1070501-stack.jpg" alt="" id="BLOGGER_PHOTO_ID_5579752754227855714" border="0" /></a><br /></div><br />"You really like amoebae" I was told the other week. Yes I do, and FYI, <span style="font-style: italic;">someone</span>'s chlorarachniophytes are amoebae too. All that said, I remain abysmal at identifying the buggers; this, my friends, is some filosey amoeba of sorts. Yup.<br /><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi6AztVHxzlLInapYJfvjNL5LUqjl5dsKcCvJBao_xQB7QoXZaBGH5VWFN9Y6ddJknoRDBOd-uWVFt9xNarBW4f1AWIHDlFQxzoFNH0xoWlh3Ig93349_ylwiAmTWWTLfULtUFuzOotUzug/s1600/P1070505-stack.jpg"><img style="cursor: pointer; width: 475px; height: 77px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi6AztVHxzlLInapYJfvjNL5LUqjl5dsKcCvJBao_xQB7QoXZaBGH5VWFN9Y6ddJknoRDBOd-uWVFt9xNarBW4f1AWIHDlFQxzoFNH0xoWlh3Ig93349_ylwiAmTWWTLfULtUFuzOotUzug/s400/P1070505-stack.jpg" alt="" id="BLOGGER_PHOTO_ID_5579776592628140082" border="0" /></a><br /></div><br />The following is from an anoxic rotting leaf sample (same as in the previous <i>Trimastix</i> post) – a very long and narrow cell, appears to be a euglenid based on how it moves the free flagellum (tip-heavy action); it's attached to the glass with the other flagellum. Guessing it's a <i>Heteronema</i> sp.; appears similar to <i><a href="http://starcentral.mbl.edu/microscope/portal.php?pagetitle=assetfactsheet&imageid=4700">H.acutissimum</a></i>, but the latter is marine and for euglenids, the marine vs. freshwater distinction is generally considered sufficient to be a different species.<br /><div style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgsxVBZul7O6tH45xx8iaaiG5PYjn1c92ZotKVTJFtoeNDOprsuukcGzpjAbLpZc_vVhgmZYRqLejguWMM770_aT7YV0oSmAwC9onCypYR09TfIMn1lls1zDwuuiZrrh8tFPY4gfkNUUq5R/s1600/P1070491_stills_WLT.jpg"><img style="cursor: pointer; width: 400px; height: 105px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgsxVBZul7O6tH45xx8iaaiG5PYjn1c92ZotKVTJFtoeNDOprsuukcGzpjAbLpZc_vVhgmZYRqLejguWMM770_aT7YV0oSmAwC9onCypYR09TfIMn1lls1zDwuuiZrrh8tFPY4gfkNUUq5R/s400/P1070491_stills_WLT.jpg" alt="" id="BLOGGER_PHOTO_ID_5579752755290735794" border="0" /></a><br /></div><br /><div>And now I'm off too look at more samples. Will take a while to go through my stockpile of protist pics already, but must still get more...</div>Psi Wavefunctionhttp://www.blogger.com/profile/10829712736757471647noreply@blogger.com0