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	<title>Byte Size Biology &#187; microbiology</title>
	<atom:link href="http://bytesizebio.net/index.php/tag/microbiology/feed/" rel="self" type="application/rss+xml" />
	<link>http://bytesizebio.net</link>
	<description>The musings and ravings of a computational biologist about science, computers, music and, you know, stuff</description>
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		<title>Microbial Pancakes</title>
		<link>http://bytesizebio.net/index.php/2012/01/15/microbial-breakfast/</link>
		<comments>http://bytesizebio.net/index.php/2012/01/15/microbial-breakfast/#comments</comments>
		<pubDate>Sun, 15 Jan 2012 23:50:03 +0000</pubDate>
		<dc:creator>Iddo</dc:creator>
				<category><![CDATA[Funny]]></category>
		<category><![CDATA[Microbiology]]></category>
		<category><![CDATA[food]]></category>
		<category><![CDATA[microbiology]]></category>

		<guid isPermaLink="false">http://bytesizebio.net/?p=5813</guid>
		<description><![CDATA[&#160; Prepared by daughter. Not to scale. Species not yet identified. Delicious. &#160;]]></description>
			<content:encoded><![CDATA[<p>&nbsp;</p>
<p>Prepared by daughter. Not to scale. Species not yet identified. Delicious.</p>
<p>&nbsp;</p>
<p><a href="http://bytesizebio.net/wp-content/uploads/2012/01/microbe-breakfast.png"><img class="alignnone  wp-image-5814" title="microbe-breakfast" src="http://bytesizebio.net/wp-content/uploads/2012/01/microbe-breakfast.png" alt="" width="527" height="397" /></a></p>
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		<title>Gut microbes and diabetes</title>
		<link>http://bytesizebio.net/index.php/2012/01/08/gut-microbes-and-diabetes/</link>
		<comments>http://bytesizebio.net/index.php/2012/01/08/gut-microbes-and-diabetes/#comments</comments>
		<pubDate>Mon, 09 Jan 2012 04:07:43 +0000</pubDate>
		<dc:creator>Iddo</dc:creator>
				<category><![CDATA[metabolic syndrome]]></category>
		<category><![CDATA[Microbiology]]></category>
		<category><![CDATA[microbiology]]></category>

		<guid isPermaLink="false">http://bytesizebio.net/?p=5757</guid>
		<description><![CDATA[It seems that every day we are discovering more about the role of microbes to our health. We really have to revise our definition of what a human (or any other animal or plant) is: we are not just a creatures of 10,000,000,000,000 cells containing the DNA we got from mother and father. We have [...]]]></description>
			<content:encoded><![CDATA[<p>It seems that every day we are discovering more about the role of microbes to our health. We really have to revise our definition of what a human (or any other animal or plant) is: we are not just a creatures of 10,000,000,000,000 cells containing the DNA we got from mother and father. We have 10 times that many cells which are microbial, and we are only now beginning to understand how profoundly they affect us.</p>
<p>Together with obesity, insulin resistance is the harbringer of <a href="http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0004546/" target="_blank">metabolic syndrome</a>. Insulin resistance is when the body cannot use insulin effectively. Insulin is needed to help control the amount of sugar in the body. As a result, blood sugar and fat levels rise.  Therein lies the path to morbid obesity, diabetes, stroke, and heart problems.</p>
<p><span style="float: left; padding: 5px;"><a href="http://www.researchblogging.org"><img style="border: 0;" src="http://www.researchblogging.org/public/citation_icons/rb2_large_gray.png" alt="ResearchBlogging.org" /></a></span></p>
<p><span style="float: left; padding: 5px;"><a href="http://researchblogging.org/news/?p=3176"><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></p>
<p>So what&#8217;s the connection of metabolic disease to bacteria? Well, for one thing, we know that in obese people the bacterial population in the gut is different, and the different population of bacteria may lead to a vicious cycle contributing to obesity.</p>
<p>Another possible connection has to do with an  important group of molecules in our body called <a href="http://en.wikipedia.org/wiki/Toll-like_receptor" target="_blank">Toll-like receptors</a>, or  TLRs. TLRs are a family of  membrane proteins that sense a wide variety of bacterial populations and activate our innate immune system. TLRs are like a first-defense warning station: they sense the bacterial enemy first, and, if needed, activate the proper defense mechanisms. Researchers studying TLR-2 have created knockout mice lacking TLR-2, and they discovered is that many of TLR-2 knockout mice do not develop insulin resistance when fed with a high-fat diet. Think about it: all the McCrap you can eat, yet your blood sugar level remains normal (although you still grow fat).  So why does that happen? How come these mice lacking a bacterial sensor also seem immune to insulin resistance?</p>
<p>&nbsp;</p>
<p><a href="http://bytesizebio.net/wp-content/uploads/2012/01/Fat-mouse-drinking-diet-coke.gif"><img class="alignnone  wp-image-5801" title="Fat-mouse-drinking-diet-coke" src="http://bytesizebio.net/wp-content/uploads/2012/01/Fat-mouse-drinking-diet-coke.gif" alt="" width="480" height="360" /></a></p>
<p>To answer this, we must understand that TLR receptors (quite a few are known so far) are known to serve as a bridge (or &#8220;mediate crosstalk&#8221;) between the immune system and the body&#8217;s metabolism.  Mice without TLR-5 develop eating disorder known as <a href="http://en.wikipedia.org/wiki/Polyphagia" target="_blank">hyperphagia</a> which is characterized by an increased appetite; they also show other pre-diabetic  symptoms: hypertension, high lipids, and insulin resistance. I have <a href="http://bytesizebio.net/index.php/2010/04/25/obesity-the-role-of-the-immune-system/" target="_blank">posted before</a> about how TLR-5 may control the type of gut bacteria mice have and, in turn, control their propensity for obesity.</p>
<p>TLR-4 deficient mice, on the other hand, seem to be protected from insulin resistance, just like TLR-2 deficient mice. So a connection between these front-line sensors of the immune system and whole body metabolism is well-known.</p>
<p>A group of researchers from Brazil have decided to look further into these &#8220;diabetes resistant&#8221; mice. The thing about mutant TLR deficient mice, is that they are normally grown in sterile conditions because possible infections and because the uncontrollable gut microbes add uncontrolled variables to any experiment. When scientists cannot precisely control for experimental conditions, they face two choices: One, they can deviate from the model to emulate &#8220;real world&#8221; better, but sacrifice control of one or more of the variables in an experiment. Or, maintain full control of the experiment and sacrifice a simulation whatever they are trying to model. Most scientists go with the second option: they would prefer to have a well-controlled model, even if it supposedly detracts from its supposed practicality and application to &#8220;real life&#8221;. That is because a model (in our case, mutant TLR mice), is somewhat removed from the real thing anyway: mutant TLR-deficient are basically a  an artificial construct used to investigate the effect of knocking out a TLR from the mouse, so hopefully we can draw conclusions about humans. So the second type of possible error is the one scientists generally prefer to make.</p>
<p>&nbsp;</p>
<div id="attachment_5807" class="wp-caption alignnone" style="width: 529px"><a href="http://bytesizebio.net/wp-content/uploads/2012/01/Toll-Like-Receptors-Pathway.jpg"><img class=" wp-image-5807 " title="Toll-Like Receptors Pathway" src="http://bytesizebio.net/wp-content/uploads/2012/01/Toll-Like-Receptors-Pathway-742x1024.jpg" alt="" width="519" height="717" /></a><p class="wp-caption-text">Toll-like receptors: it&#39;s complicated.</p></div>
<p>But Andrea Caricilli and colleagues have decided to look at TLR-2 knockout mice in non-sterile conditions. Rememebr: TLR-2 knockouts seem to have protection from insulin resistance. What Caricilli and her colleagues discovered was quite the opposite of what was known so far: TLR-2 knockout mice were not protected from insulin resistance. Quite the opposite: the mutant mice developed metabolic syndrome. But did  the gut bacteria do it? To check that, the researchers treated the mice with broad-spectrum antibiotics for 20 days. After that, the bacterial species that re-colonized the mice&#8217;s guts were quite different in their composition from the bacterial species that originally inhabited them. And they did not have meteabolic disease, or the symptoms were much less severe.</p>
<p>So here it is: changing the mice&#8217;s gut microbiota changed them from mice with insulin resistance to mice without insulin resistance. Yes, there are mutant mice, but still: insulin resistance was turned off  by changing the types of microbes in the gut.</p>
<p>They then transplanted the microbiota from TLR-2 mutants which had insulin resistance to regular mice. And what do you know: the regular mice then showed symptoms of insulin resistance and metabolic disease.</p>
<p>There is a lot more to this paper than these two experiments: they have also investigated many other parameters, trying to come up with the chain of events that bacteria trigger when causing metabolic disease. I won&#8217;t get into that, the paper is quite long with some 20(!)  figures. A lot of work went into this. But the bottom line again supports what has been shown in other studies: the bacteria that live in our gut are responsible for our metabolism, and it is the interaction between the bacteria and our immune system that not only protects us from pathogens, but also protects us (or not) from metabolic disease.</p>
<p>&nbsp;</p>
<p><a href="http://science.slashdot.org/story/12/01/10/1649204/gut-bacteria-can-control-diabetes"><img class="alignnone  wp-image-1743" title="SlashdotLogo" src="http://bytesizebio.net/wp-content/uploads/2009/07/SlashdotLogo.gif" alt="" width="75" height="83" /></a> <strong>Update:</strong> this post has been <a href="http://science.slashdot.org/story/12/01/10/1649204/gut-bacteria-can-control-diabetes" target="_blank">slashdotted</a>. Exercise extreme caution.</p>
<hr />
<p><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.jtitle=PLoS+Biology&amp;rft_id=info%3Adoi%2F10.1371%2Fjournal.pbio.1001212&amp;rfr_id=info%3Asid%2Fresearchblogging.org&amp;rft.atitle=Gut+Microbiota+Is+a+Key+Modulator+of+Insulin+Resistance+in+TLR+2+Knockout+Mice&amp;rft.issn=1545-7885&amp;rft.date=2011&amp;rft.volume=9&amp;rft.issue=12&amp;rft.spage=0&amp;rft.epage=&amp;rft.artnum=http%3A%2F%2Fdx.plos.org%2F10.1371%2Fjournal.pbio.1001212&amp;rft.au=Caricilli%2C+A.&amp;rft.au=Picardi%2C+P.&amp;rft.au=de+Abreu%2C+L.&amp;rft.au=Ueno%2C+M.&amp;rft.au=Prada%2C+P.&amp;rft.au=Ropelle%2C+E.&amp;rft.au=Hirabara%2C+S.&amp;rft.au=Castoldi%2C+%EF%BF%BD.&amp;rft.au=Vieira%2C+P.&amp;rft.au=Camara%2C+N.&amp;rft.au=Curi%2C+R.&amp;rft.au=Carvalheira%2C+J.&amp;rft.au=Saad%2C+M.&amp;rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CMedicine%2CHealth%2CMicrobiology+%2C+Metabolism%2C+Immunology%2C+Systems+Biology%2C+Gastroenterology">Caricilli, A., Picardi, P., de Abreu, L., Ueno, M., Prada, P., Ropelle, E., Hirabara, S., Castoldi, A., Vieira, P., Camara, N., Curi, R., Carvalheira, J., &amp; Saad, M. (2011). Gut Microbiota Is a Key Modulator of Insulin Resistance in TLR 2 Knockout Mice <span style="font-style: italic;">PLoS Biology, 9</span> (12) DOI: <a href="http://dx.doi.org/10.1371/journal.pbio.1001212" rev="review">10.1371/journal.pbio.1001212</a></span></p>
<p>&nbsp;</p>
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		</item>
		<item>
		<title>Not dead yet</title>
		<link>http://bytesizebio.net/index.php/2011/10/19/not-dead-yet/</link>
		<comments>http://bytesizebio.net/index.php/2011/10/19/not-dead-yet/#comments</comments>
		<pubDate>Wed, 19 Oct 2011 14:50:26 +0000</pubDate>
		<dc:creator>Iddo</dc:creator>
				<category><![CDATA[Microbiology]]></category>
		<category><![CDATA[Dead Sea]]></category>
		<category><![CDATA[environmental microbiology]]></category>
		<category><![CDATA[microbial ecology]]></category>
		<category><![CDATA[microbiology]]></category>

		<guid isPermaLink="false">http://bytesizebio.net/?p=5544</guid>
		<description><![CDATA[&#160; The Dead Body That Claims It Isn&#8217;t: I&#8217;m not dead. The Dead Collector: What? Large Man with Dead Body: Nothing. There&#8217;s your ninepence. The Dead Body That Claims It Isn&#8217;t: I&#8217;m not dead. The Dead Collector: &#8216;Ere, he says he&#8217;s not dead. Large Man with Dead Body: Yes he is. The Dead Body That [...]]]></description>
			<content:encoded><![CDATA[<p><a href="http://bytesizebio.net/wp-content/uploads/2011/10/monty-python-bring-out-your-dead.jpg"><img class="alignnone size-full wp-image-5553" title="monty python bring out your dead" src="http://bytesizebio.net/wp-content/uploads/2011/10/monty-python-bring-out-your-dead.jpg" alt="" width="400" height="222" /></a></p>
<blockquote><p>&nbsp;</p>
<p><em>The Dead Body That Claims It Isn&#8217;t: I&#8217;m not dead.<br />
The Dead Collector: What?<br />
Large Man with Dead Body: Nothing. There&#8217;s your ninepence.<br />
The Dead Body That Claims It Isn&#8217;t: I&#8217;m not dead.<br />
The Dead Collector: &#8216;Ere, he says he&#8217;s not dead.<br />
Large Man with Dead Body: Yes he is.<br />
The Dead Body That Claims It Isn&#8217;t: I&#8217;m not.<br />
The Dead Collector: He isn&#8217;t.<br />
Large Man with Dead Body: Well, he will be soon, he&#8217;s very ill.<br />
The Dead Body That Claims It Isn&#8217;t: I&#8217;m getting better.<br />
Large Man with Dead Body: No you&#8217;re not, you&#8217;ll be stone dead in a moment.</em></p></blockquote>
<p>&#8211; <a href="http://youtu.be/Sh8mNjeuyV4" target="_blank">Monty Python and the Holy Grail</a></p>
<p>So it goes between John Cleese, Eric Idle and John Young.</p>
<p>But there is a sea, or rather lake, that is not dead yet either, feels happy, and is going for a walk on Thursday. The <a href="http://g.co/maps/b9xsk" target="_blank">Dead Sea</a>, located in the Judean Desert, roughly divided between Jordan and Israel, has a salinity of 33% &#8211; more than eight times that of seawater (3.5%). No animals or plants can survive these conditions, and the lake does look dead to the casual observer. But in the late 1930s Benjamin Elazari Volcani discovered that the Dead Sea does, in fact, <a href="http://www.nature.com/nature/journal/v152/n3853/abs/152274c0.html" target="_blank">support several types of microorganisms</a>. A bit of history: Volcani&#8217;s research into microbial life in the Dead Sea led to him being awarded the the first doctoral degree in microbiology by the Hebrew University of Jerusalem, 1943. In 1975, Mullakhanbhai and Larsen <a href="http://www.springerlink.com/content/pj34101u862u6014/">named</a> <em>Halobacterium volcanii</em>, a halophilic isolate, after B.E. Volcani. It is now know as the archaean, not bacterium, <em>Haloferax volcanii</em>.</p>
<div id="attachment_5557" class="wp-caption alignnone" style="width: 410px"><a href="http://bytesizebio.net/wp-content/uploads/2011/10/dead_sea.jpg"><img class="size-full wp-image-5557" title="OLYMPUS DIGITAL CAMERA" src="http://bytesizebio.net/wp-content/uploads/2011/10/dead_sea.jpg" alt="" width="400" height="320" /></a><p class="wp-caption-text">At 33% salinity we all float. When you&#39;re down here with us, you&#39;ll float too.</p></div>
<p><span style="float: left; padding: 5px;"><a href="http://www.researchblogging.org"><img style="border: 0;" src="http://www.researchblogging.org/public/citation_icons/rb2_large_gray.png" alt="ResearchBlogging.org" /></a></span><br />
Several other archeael isolates were found, noting that the Dead Sea is not quite dead yet. In fact, the lake sports what might be an underreported biodiversity. In addition to archaea it also has <a href="http://rspb.royalsocietypublishing.org/content/265/1404/1461.short" target="_blank">fungi</a>, <a href="http://gbe.oxfordjournals.org/content/3/1039.full" target="_blank">bacteria,</a> <a href="http://gbe.oxfordjournals.org/content/3/1039.full" target="_blank">protozoa</a> and mermaids. OK, maybe not mermaids.</p>
<p>Now the Dead Sea has been found to be more alive than ever. A groups of Israeli and German divers have found freshwater springs deep in the Dead Sea. The springs are about 30m deep, and lie in of large craters 30meters in diameter. Look at the video below, taken by the divers. Between 1:54 and 2:10 you can see the freshwater mixing with the saltwater. The stark differences in salinity makes for a surreal underwater smoke effect. And, the real kicker, at 2:26 you can see a thick microbial mat, like gunk all over the rocks near the spring.</p>
<p><iframe src="http://www.youtube.com/embed/MHLiobkTUd0?rel=0" frameborder="0" width="560" height="315"></iframe></p>
<p>It would be very interesting to find out who, exactly, comprises this mat. As far as I know, this analysis has not been published yet. But the initial results are <a href="http://news.nationalgeographic.com/news/2011/09/110928-new-life-dead-sea-bacteria-underwater-craters-science/">reported in National Geographic</a>:</p>
<blockquote><p>Preliminary analyses of samples collected in the craters suggest that the springs&#8217; bacterial communities are very diverse—akin to what you&#8217;d find living on rocks in a regular saltwater sea, he added.</p>
<p>The top of the springs&#8217; rocks are covered with green biofilms, which use both sunlight and sulfide—naturally occurring chemicals from the springs—to survive. Exclusively sulfide-eating bacteria coat the bottoms of the rocks in a white biofilm.</p>
<p>Not only have the organisms evolved in such a harsh environment, Ionescu speculates that the bacteria can somehow cope with sudden fluxes in fresh water and saltwater that naturally occur as water currents shift around the springs.</p></blockquote>
<p>&nbsp;</p>
<p>All I can say is: wow. Microbial mats in the Dead Sea, which we only find about now. The  Dead Sea thriving with whole carpets of life. Who&#8217;d've thunk?</p>
<hr />
<p><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.jtitle=Nature&amp;rft_id=info%3Adoi%2F10.1038%2F152274c0&amp;rfr_id=info%3Asid%2Fresearchblogging.org&amp;rft.atitle=Bacteria+in+the+Bottom+Sediments+of+the+Dead+Sea&amp;rft.issn=0028-0836&amp;rft.date=1943&amp;rft.volume=152&amp;rft.issue=3853&amp;rft.spage=274&amp;rft.epage=275&amp;rft.artnum=http%3A%2F%2Fwww.nature.com%2Fdoifinder%2F10.1038%2F152274c0&amp;rft.au=ELAZARI-VOLCANI%2C+B.&amp;rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CMicrobiology+%2C+Limnology">ELAZARI-VOLCANI, B. (1943). Bacteria in the Bottom Sediments of the Dead Sea <span style="font-style: italic;">Nature, 152</span> (3853), 274-275 DOI: <a href="http://dx.doi.org/10.1038/152274c0" rev="review">10.1038/152274c0</a></span></p>
<p><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.jtitle=Archives+of+Microbiology&amp;rft_id=info%3Adoi%2F10.1007%2FBF00447326&amp;rfr_id=info%3Asid%2Fresearchblogging.org&amp;rft.atitle=Halobacterium+volcanii+spec.+nov.%2C+a+Dead+Sea+halobacterium+with+a+moderate+salt+requirement&amp;rft.issn=0302-8933&amp;rft.date=1975&amp;rft.volume=104&amp;rft.issue=1&amp;rft.spage=207&amp;rft.epage=214&amp;rft.artnum=http%3A%2F%2Fwww.springerlink.com%2Findex%2F10.1007%2FBF00447326&amp;rft.au=Mullakhanbhai%2C+M.&amp;rft.au=Larsen%2C+H.&amp;rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CMicrobiology">Mullakhanbhai, M., &amp; Larsen, H. (1975). Halobacterium volcanii spec. nov., a Dead Sea halobacterium with a moderate salt requirement <span style="font-style: italic;">Archives of Microbiology, 104</span> (1), 207-214 DOI: <a href="http://dx.doi.org/10.1007/BF00447326" rev="review">10.1007/BF00447326</a></span></p>
<p><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.jtitle=Proceedings+of+the+Royal+Society+B%3A+Biological+Sciences&amp;rft_id=info%3Adoi%2F10.1098%2Frspb.1998.0458&amp;rfr_id=info%3Asid%2Fresearchblogging.org&amp;rft.atitle=Fungal+life+in+the+extremely+hypersaline+water+of+the+Dead+Sea%3A+first+records&amp;rft.issn=0962-8452&amp;rft.date=1998&amp;rft.volume=265&amp;rft.issue=1404&amp;rft.spage=1461&amp;rft.epage=1465&amp;rft.artnum=http%3A%2F%2Frspb.royalsocietypublishing.org%2Fcgi%2Fdoi%2F10.1098%2Frspb.1998.0458&amp;rft.au=Buchalo%2C+A.&amp;rft.au=Nevo%2C+E.&amp;rft.au=Wasser%2C+S.&amp;rft.au=Oren%2C+A.&amp;rft.au=Molitoris%2C+H.&amp;rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CEcology+%2F+Conservation%2CMicrobiology">Buchalo, A., Nevo, E., Wasser, S., Oren, A., &amp; Molitoris, H. (1998). Fungal life in the extremely hypersaline water of the Dead Sea: first records <span style="font-style: italic;">Proceedings of the Royal Society B: Biological Sciences, 265</span> (1404), 1461-1465 DOI: <a href="http://dx.doi.org/10.1098/rspb.1998.0458" rev="review">10.1098/rspb.1998.0458</a></span></p>
]]></content:encoded>
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		<slash:comments>1</slash:comments>
		</item>
		<item>
		<title>Using phylogenetics to reconstruct a 59 million year old drug</title>
		<link>http://bytesizebio.net/index.php/2011/10/03/using-phylogenetics-to-reconstruct-a-59-million-year-old-drug/</link>
		<comments>http://bytesizebio.net/index.php/2011/10/03/using-phylogenetics-to-reconstruct-a-59-million-year-old-drug/#comments</comments>
		<pubDate>Mon, 03 Oct 2011 19:59:33 +0000</pubDate>
		<dc:creator>Iddo</dc:creator>
				<category><![CDATA[bioengineering]]></category>
		<category><![CDATA[Microbiology]]></category>
		<category><![CDATA[Bioinformatics]]></category>
		<category><![CDATA[immunology]]></category>
		<category><![CDATA[microbiology]]></category>
		<category><![CDATA[phylogenetics]]></category>

		<guid isPermaLink="false">http://bytesizebio.net/?p=5443</guid>
		<description><![CDATA[Good news: Press Release 2011-10-03 The Nobel Assembly at Karolinska Institutet has today decided that The Nobel Prize in Physiology or Medicine 2011 shall be divided, with one half jointly to Bruce A. Beutler and Jules A. Hoffmann for their discoveries concerning the activation of innate immunity and the other half to Ralph M. Steinman [...]]]></description>
			<content:encoded><![CDATA[<p>Good news:</p>
<blockquote>
<p style="text-align: center;"><strong>Press Release</strong><br />
<strong> 2011-10-03</strong><br />
<strong> The Nobel Assembly at Karolinska Institutet has today decided that</strong><br />
<strong> The Nobel Prize in Physiology or Medicine 2011</strong><br />
<strong> shall be divided, with one half jointly to</strong><br />
<strong> Bruce A. Beutler and Jules A. Hoffmann</strong><br />
<strong> for their discoveries concerning the activation of innate immunity</strong><br />
<strong> and the other half to</strong><br />
<strong> Ralph M. Steinman</strong><br />
<strong> for his discovery of the dendritic cell and its role in adaptive immunity</strong></p>
</blockquote>
<p>&nbsp;</p>
<p>(Unfortunately, Steinman died between the committee&#8217;s decision and the announcement. He still received the Prize, though.)</p>
<p>However, it is <em>not</em> news (and not good)  that we are losing the arms race against bacteria. We are overusing antibiotics in medicine and in agriculture, virtually nurturing today&#8217;s and tomorrow&#8217;s killers. A <a href="http://www.wired.com/wiredscience/2011/02/not-many-antibiotics/" target="_blank">report</a>  in Wired earlier this year paints a bleak picture:</p>
<blockquote><p>Truly new antibiotics are critically needed because bacteria, having no experience of them, cannot immediately mount resistance to them — something that does happen with me-too compounds featuring some slight molecular change. But they’re rare. As this chart from the research group Extending the Cure shows, antibiotic development has slowed dramatically over the past 30 years, and among the few drugs being brought forth, most share the mechanisms of already-existing classes.</p>
<p><a href="http://bytesizebio.net/wp-content/uploads/2011/10/ExTheCure.jpg"><img class="alignnone size-full wp-image-5461" title="ExTheCure" src="http://bytesizebio.net/wp-content/uploads/2011/10/ExTheCure.jpg" alt="" width="640" height="367" /></a></p></blockquote>
<p>To understand the extent of the crisis, we have to remember that antibiotics are the foundation of a huge number of  medical procedures, from cancer treatment to dentistry. Taking away this foundation would cripple modern medicine. Together with vaccines and public hygiene, antibiotics are the reason that many of us live longer &#8212; and better &#8212; than our grandparents&#8217; generation and before that.</p>
<p>So lacking drug company motivation (more on that in McKenna&#8217;s <a href="http://www.wired.com/wiredscience/2011/02/not-many-antibiotics/" target="_blank">report</a>) and facing a dwindling supply of effective antibiotics, what are we to do?</p>
<p>A good start is to take a second look at nature. For example, here is a Kangaroo being born:</p>
<p><object width="640" height="360" classid="clsid:d27cdb6e-ae6d-11cf-96b8-444553540000" codebase="http://download.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=6,0,40,0"><param name="allowFullScreen" value="true" /><param name="allowscriptaccess" value="always" /><param name="src" value="http://www.youtube.com/v/2lCKc8tURtc?version=3&amp;hl=en_US&amp;rel=0" /><param name="allowfullscreen" value="true" /><embed width="640" height="360" type="application/x-shockwave-flash" src="http://www.youtube.com/v/2lCKc8tURtc?version=3&amp;hl=en_US&amp;rel=0" allowFullScreen="true" allowscriptaccess="always" allowfullscreen="true" /></object></p>
<p>Awww&#8230;</p>
<p>The interesting thing about Kangaroos and other marsupials is that their young are being exposed at a very precarious stage to the outside world. Roo is born in a fetal state: underdeveloped, blind, barely moving and has little to no body temperature regulation. All of these problems are taken care of by Kanga&#8217;s protecting Roo&#8217;s six minute trip to her pouch where things are warm and cozy, and maternal milk flows in abundance. All except one: pathogens. During his trip, Roo can acquire a whole bunch of nasty bugs from Kanga&#8217;s fur and the air. Also, the pouch is not exactly a sterile environment and there is a possibility of infection there. So how is little Roo to survive the trip to the pouch and subsequent stay?</p>
<div id="attachment_5463" class="wp-caption alignnone" style="width: 408px"><a href="http://bytesizebio.net/wp-content/uploads/2011/10/711px-Joey_in_pouch.jpg"><img class="size-full wp-image-5463  " title="711px-Joey_in_pouch" src="http://bytesizebio.net/wp-content/uploads/2011/10/711px-Joey_in_pouch.jpg" alt="" width="398" height="335" /></a><p class="wp-caption-text">Joey in pouch. Photograph by Geoff Shaw (Zoology, University of Melbourne, Australia). From Wikimedia Commons.</p></div>
<p>The answer is <a href="http://en.wikipedia.org/wiki/Innate_immune_system">innate immunity</a>, that collection of mechanisms which protect the host in a non-specific manner. While his <a href="http://en.wikipedia.org/wiki/Adaptive_immune_system">adaptive immunity</a> is quite undeveloped, Roo does produce some killer all-purpose peptides he can use against microbes. The same class of peptides are produced in Kanga&#8217;s milk. Collectively they are known as cathelicidins. Only about 30 amino acids long, these highly charged molecules kill both gram-positive and gram-negative bacteria.</p>
<p>&nbsp;</p>
<p>Since the tammar wallaby genome has <a href="http://genomebiology.com/2011/12/8/R81" target="_blank">recently been sequenced</a>,  a group of Australian scientists has decided to <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0024030" target="_blank">hunt for cathelicidins in the tammar&#8217;s genome</a>. They also looked for cathelicidins in the genomes of the duck-billed platypus (a monotreme) in the opossum (an American marsupial), in human, mouse, cow &amp; sheep (all placentals).  Here is what they found. Each leaf on the tree represents a cathelicidin gene. The leaf colors and shapes are for different species of origin.</p>
<div id="attachment_5472" class="wp-caption alignnone" style="width: 610px"><a href="http://bytesizebio.net/wp-content/uploads/2011/10/cathelicidin-tree.png"><img class="size-full wp-image-5472 " style="border-width: 1px; border-color: black; border-style: solid;" title="cathelicidin-tree" src="http://bytesizebio.net/wp-content/uploads/2011/10/cathelicidin-tree.png" alt="From Wang J,  et al. 2011 PLoS ONE 6(8): e24030. doi:10.1371/journal.pone.0024030" width="600" height="439" /></a><p class="wp-caption-text">From Wang J, et al. 2011 PLoS ONE 6(8): e24030. doi:10.1371/journal.pone.0024030 Reproduced under CC license.</p></div>
<p>The marsupials and monotremes have a much higher diversity of cathelicidin genes than the placental mammals. Note that there are many duplicates of the cathelicidin gene in Pig and Cow, but these duplications are very recent as we can tell by the highly similar sequences of the genes. These duplications are probably because herd animals are more susceptible to pathogens.  In any case,  pig and cow have higher copy number of cathelicidin genes, and thus perhaps a large number of proteins, but not many different ones as in marsupials and monotremes. Diverse cathelicidin genes in the genome can offer a wider protective umbrella against many different types of pathogens.</p>
<p>Back to the antibiotic crisis: can we use marsupial cathelicidins as an antibiotic in humans? Do cathelicidins kill human pathogens? Are they toxic to humans? The authors checked the first two. They used cathelicidins from wallaby and platypus to kill human pathogens: <em>P. aeruginosa, K. pneumoniae</em> and <em>A. baumanii</em>, including antibiotic resistant strains. Cathelicidins were much more effective than, well, antibiotics against those bacteria. Also, cathelicidins did not kill human red blood cells, which makes them a potential drug. Of course,  immune reaction against cathelicidins as a foreign  still needs to be checked, among many, many other things, but the whole idea of looking at marsupials is that, as mamals, they may be able to supply us with clues on how to synthesize a cathelicidin to be used as a drug in humans.<br />
<span style="float: left; padding: 5px;"><a href="http://www.researchblogging.org"><img style="border: 0;" src="http://www.researchblogging.org/public/citation_icons/rb2_large_gray.png" alt="ResearchBlogging.org" /></a></span><br />
The really cool thing about this study is that the authors used phylogenetics to design an ancestral wallaby cathelicidin. They aligned all the wallaby cathelicidin protein sequences, which were conserved in 40 of the 46 amino-acid positions. They used PAML, GASP and <a href="http://toolkit.tuebingen.mpg.de/ancescon" target="_blank">Ancescon</a> to reconstruct an ancestral wallaby sequence, estimated to be 59 million years old, marked by an asterisk (*) in the above gene tree.  They then synthesized the ancestral WAM (Wallaby Anti Microbial) peptide and used it to kill bacteria. Guess what: the ancestral WAM was even better than the existing WAMs, as even a lower concentration was needed to kill bacteria. They <a href="http://www.plosone.org/annotation/listThread.action?inReplyTo=info%3Adoi%2F10.1371%2Fannotation%2F64f893f5-aaf7-4d04-8a17-edaa3ec3cfeb&amp;root=info%3Adoi%2F10.1371%2Fannotation%2F64f893f5-aaf7-4d04-8a17-edaa3ec3cfeb" target="_blank">are still working on red blood cell toxicity</a> (yay for PLoS-enabled comments!)</p>
<p>So maybe the answer to  the increase in bacterial resistance to antibiotics lies in Kanga&#8217;s pouch. After all, she was very protective of Roo.</p>
<p><strong>EDIT</strong>: clarified that the part about synthesizing and testing ancestral-WAM to kill bacteria.</p>
<p>&nbsp;</p>
<p><a href="http://bytesizebio.net/wp-content/uploads/2011/10/kangaroo.gif"><img class="alignnone size-full wp-image-5480" title="kangaroo" src="http://bytesizebio.net/wp-content/uploads/2011/10/kangaroo.gif" alt="" width="181" height="156" /></a></p>
<hr />
<p><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.jtitle=PLoS+ONE&amp;rft_id=info%3Adoi%2F10.1371%2Fjournal.pone.0024030&amp;rfr_id=info%3Asid%2Fresearchblogging.org&amp;rft.atitle=Ancient+Antimicrobial+Peptides+Kill+Antibiotic-Resistant+Pathogens%3A+Australian+Mammals+Provide+New+Options&amp;rft.issn=1932-6203&amp;rft.date=2011&amp;rft.volume=6&amp;rft.issue=8&amp;rft.spage=0&amp;rft.epage=&amp;rft.artnum=http%3A%2F%2Fdx.plos.org%2F10.1371%2Fjournal.pone.0024030&amp;rft.au=Wang%2C+J.&amp;rft.au=Wong%2C+E.&amp;rft.au=Whitley%2C+J.&amp;rft.au=Li%2C+J.&amp;rft.au=Stringer%2C+J.&amp;rft.au=Short%2C+K.&amp;rft.au=Renfree%2C+M.&amp;rft.au=Belov%2C+K.&amp;rft.au=Cocks%2C+B.&amp;rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CHealth%2CBioinformatics%2C+%2C+Biotechnology%2C+Bioinformatics%2C+Biomedical+Engineering%2C+Evolutionary+Biology%2C+Immunology%2C+Microbiology+%2C+Molecular+Biology">Wang, J., Wong, E., Whitley, J., Li, J., Stringer, J., Short, K., Renfree, M., Belov, K., &amp; Cocks, B. (2011). Ancient Antimicrobial Peptides Kill Antibiotic-Resistant Pathogens: Australian Mammals Provide New Options <span style="font-style: italic;">PLoS ONE, 6</span> (8) DOI: <a href="http://dx.doi.org/10.1371/journal.pone.0024030" rev="review">10.1371/journal.pone.0024030</a></span></p>
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		<title>Microbial marketing</title>
		<link>http://bytesizebio.net/index.php/2011/09/13/5419/</link>
		<comments>http://bytesizebio.net/index.php/2011/09/13/5419/#comments</comments>
		<pubDate>Tue, 13 Sep 2011 17:06:00 +0000</pubDate>
		<dc:creator>Iddo</dc:creator>
				<category><![CDATA[Art]]></category>
		<category><![CDATA[Film]]></category>
		<category><![CDATA[Microbiology]]></category>
		<category><![CDATA[advertising]]></category>
		<category><![CDATA[marketing]]></category>
		<category><![CDATA[microbiology]]></category>

		<guid isPermaLink="false">http://bytesizebio.net/?p=5419</guid>
		<description><![CDATA[An original viral (or rather, fungal and bacterial) marketing campaign for the movie Contagion. Although the film tells the story of a fictional viral outbreak, the marketers of Warner Brothers Canada kept it in the realm of microbiology by teaming up with 25 microbiologists and creating what is probably the first agar-plated billboard, which they [...]]]></description>
			<content:encoded><![CDATA[<p>An original viral (or rather, fungal and bacterial) marketing campaign for the movie <a href="http://www.imdb.com/title/tt1598778/" target="_blank">Contagion</a>. Although the film tells the story of a fictional viral outbreak, the marketers of Warner Brothers Canada kept it in the realm of microbiology by teaming up with 25 microbiologists and creating what is probably the first agar-plated billboard, which they placed in a storefront in Toronto. The bacteria and mold were plated and grew in the letters, but it looks like contaminants formed their own random colonies, purposefully creating a rather eerie effect. Thanks to Zack Moss, a student in my lab, for pointing me to this. More details in the <a href="http://www.vancouversun.com/technology/Bacterial+billboard+brings+culture+Hollywood+marketing/5390504/story.html" target="_blank">Vancouver Sun</a>. </p>
<p><iframe width="640" height="390" src="http://www.youtube.com/embed/LppK4ZtsDdM?rel=0" frameborder="0" allowfullscreen></iframe></p>
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		<title>Shavuot is a microbial holiday</title>
		<link>http://bytesizebio.net/index.php/2011/06/07/shavuot-is-a-microbial-holiday/</link>
		<comments>http://bytesizebio.net/index.php/2011/06/07/shavuot-is-a-microbial-holiday/#comments</comments>
		<pubDate>Tue, 07 Jun 2011 19:41:37 +0000</pubDate>
		<dc:creator>Iddo</dc:creator>
				<category><![CDATA[Biotechnology]]></category>
		<category><![CDATA[Microbiology]]></category>
		<category><![CDATA[culture]]></category>
		<category><![CDATA[food]]></category>
		<category><![CDATA[microbiology]]></category>

		<guid isPermaLink="false">http://bytesizebio.net/?p=5025</guid>
		<description><![CDATA[&#160; Tonight is Shavuot. That wonderful holiday which includes midnight studies, water-bombing and dairy products. Mmmmm&#8230;. cheese. A food product heavily embedded in the science of microbiology. Cheese is the founding product of the biotech industry (along with beer and bread). So here&#8217;s to Lactobacilli and Lactococci which are at the center of the production [...]]]></description>
			<content:encoded><![CDATA[<p>&nbsp;</p>
<p>Tonight is Shavuot. That wonderful holiday which includes midnight studies, water-bombing and dairy products. Mmmmm&#8230;. cheese. A food product heavily embedded in the science of microbiology. Cheese is the founding product of the biotech industry (along with beer and bread).</p>
<div id="attachment_5031" class="wp-caption alignnone" style="width: 384px"><a href="http://bytesizebio.net/wp-content/uploads/2011/06/Julius_Schnorr_von_Carolsfeld-_Ruth_im_Feld_des_Boaz.jpg"><img class="size-full wp-image-5031 " title="Julius_Schnorr_von_Carolsfeld-_Ruth_im_Feld_des_Boaz" src="http://bytesizebio.net/wp-content/uploads/2011/06/Julius_Schnorr_von_Carolsfeld-_Ruth_im_Feld_des_Boaz.jpg" alt="" width="374" height="320" /></a><p class="wp-caption-text">Boaz asking Ruth on a date to the cheese and wine festival.</p></div>
<p>So here&#8217;s to <em>Lactobacilli</em> and <em>Lactococci</em> which are at the center of the production of dairy products. Breaking down milk sugar (lactose) into lactic acid, which curdles the milk protein casein.   Left to its own devices, this process generally produces rotten milk, since other bacteria may join the fray. Cheesemaking starts the process by  adding some rennet first. Rennet was originally and still being produced from cows&#8217; upper stomachs. The active ingredient in rennet is chymosin, used to curdle milk drunk by calfs.  But 90% of  cheeses produced in the US and the UK now are made using recombinant chymosin,  produced in the fungus <em>Aspergillus niger.</em></p>
<p><em> </em></p>
<p><em> </em></p>
<p><em> </em></p>
<p><em> </em></p>
<p><em> </em></p>
<p><em></p>
<div id="attachment_5028" class="wp-caption alignnone" style="width: 370px"><a href="http://bytesizebio.net/wp-content/uploads/2011/06/Lactobacillus_sp_01.png"><img class="size-full wp-image-5028   " title="Lactobacillus_sp_01" src="http://bytesizebio.net/wp-content/uploads/2011/06/Lactobacillus_sp_01.png" alt="" width="360" height="286" /></a><p class="wp-caption-text">Lactobacillus sp. Source: wikipedia</p></div>
<p></em></p>
<p><em> </em></p>
<p><em> </em></p>
<p><em> </em></p>
<p><em> </em></p>
<p><em> </em></p>
<p>Cheese also needs to ripen. <em>Propionibacterium freudenreichii</em> ferments lactate in the cheese to produce, among other things, carbon dioxide. This produces the holes we see in Swiss cheese. But it&#8217;s a finicky bug, and needs its faithful symbiotic companion <em>Lactobacillus helveticus</em> (&#8220;Swiss <em>Lactobacillus</em>&#8220;) to provide it with essential amino acids necessary for its growth.  <em>P. freudenreichii</em> is named after Eduardo von Freudenreich, a 19th century microbiologist who, among other things, wrote a seminal book on dairy microbiology.</p>
<div id="attachment_5030" class="wp-caption alignnone" style="width: 314px"><a href="http://bytesizebio.net/wp-content/uploads/2011/06/Asterix_Corse_02.png"><img class="size-full wp-image-5030" title="Asterix_Corse_02" src="http://bytesizebio.net/wp-content/uploads/2011/06/Asterix_Corse_02.png" alt="" width="304" height="287" /></a><p class="wp-caption-text">Some cheeses are somewhat riper than others, as Asterix, Obelix and Dogmatix discover.</p></div>
<p>By the way, <em>Propionibacterium acne</em> a relative of <em>Propionibacterium freudenreichii</em> is a bacteria found on our skin which at times causes&#8230; yes, acne. But don&#8217;t think about acne when you eat Swiss cheese. (Now I put some people off Swiss for quite a while).</p>
<div id="attachment_5037" class="wp-caption alignnone" style="width: 501px"><a href="http://bytesizebio.net/wp-content/uploads/2011/06/Masherbrum_Peak_Baltoro_Trek_Pakistan.jpg"><img class="size-full wp-image-5037  " title="Masherbrum_Peak,_Baltoro_Trek,_Pakistan" src="http://bytesizebio.net/wp-content/uploads/2011/06/Masherbrum_Peak_Baltoro_Trek_Pakistan.jpg" alt="" width="491" height="369" /></a><p class="wp-caption-text">&quot;Acne&quot; comes from &quot;acme&quot; which means point, edge or peak. Here is an acme, but not acne.</p></div>
<p>Finally, mold. <em>Penicillinum roqufortii </em> provides those beautiful blue streaks in the sheep-milk cheese Roquefort&#8230; and the taste. Only cheeses aged in the natural Combalou caves of Roquefort-sur-Soulzon may bear the name Roquefort. Which is why it is so damn expensive.</p>
<p>&nbsp;</p>
<p>And I haven&#8217;t even started upon Camembert (the real one is made from unpasteurized milk) ripened by  <em>Penicillium candidum</em> and <em>Penicillium camemberti. </em>Or kefir, made from the eternal Kefir grains, a matrix of bacteria and polysaccharides  that can be reused forever&#8230;. but I&#8217;m too hungry for cheesecake to continue this.</p>
<p>&nbsp;</p>
<p>EDIT: typos. Thanks <a href="http://martin.jambon.free.fr/">Martin</a>!</p>
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		<title>In defense of &#8216;prokaryotes&#8217;</title>
		<link>http://bytesizebio.net/index.php/2011/06/02/in-defense-of-prokaryotes/</link>
		<comments>http://bytesizebio.net/index.php/2011/06/02/in-defense-of-prokaryotes/#comments</comments>
		<pubDate>Thu, 02 Jun 2011 14:51:01 +0000</pubDate>
		<dc:creator>Iddo</dc:creator>
				<category><![CDATA[Microbiology]]></category>
		<category><![CDATA[Taxonomy]]></category>
		<category><![CDATA[archaea]]></category>
		<category><![CDATA[bacteria]]></category>
		<category><![CDATA[evolution]]></category>
		<category><![CDATA[microbiology]]></category>
		<category><![CDATA[semantics]]></category>
		<category><![CDATA[taxonomy]]></category>
		<category><![CDATA[vocabulary]]></category>

		<guid isPermaLink="false">http://bytesizebio.net/?p=4991</guid>
		<description><![CDATA[Fine, I get it. &#8220;Prokaryotes&#8221; is a wrong taxonomic term. It&#8217;s wrong to lump bacteria and archaea together. That would be like saying &#8220;eutoichic&#8221; to lump all bacteria, archaea, plants and fungi together because they have cell walls. (&#8220;τοίχος&#8221; =wall in Greek. My Google Translate-foo is STRONG!)  Still, there are so many things in common among [...]]]></description>
			<content:encoded><![CDATA[<p>Fine, I get it. &#8220;Prokaryotes&#8221; is a wrong taxonomic term. It&#8217;s wrong to lump bacteria and archaea together. That would be like saying &#8220;eutoichic&#8221; to lump all bacteria, archaea, plants and fungi together because they have cell walls. (&#8220;τοίχος&#8221; =wall in Greek. My Google Translate-foo is STRONG!)  Still, there are so many things in common among bacteria and archaea: small, unicellular, cell wall (<a href="http://en.wikipedia.org/wiki/Mycoplasma" target="_blank">most</a>), no well-defined organelles (<a href="http://en.wikipedia.org/wiki/Bacterial_microcompartment" target="_blank">but see this</a>), fission (most), compact genomes, <a href="http://www.nature.com/nature/journal/v357/n6374/abs/357173a0.html" target="_blank">few introns</a>, prophages, genomic islands&#8230; and the list goes on.</p>
<div id="attachment_4993" class="wp-caption alignnone" style="width: 490px"><a href="http://bytesizebio.net/wp-content/uploads/2011/06/great-wall-of-china.jpg"><img class="size-full wp-image-4993 " title="great-wall-of-china" src="http://bytesizebio.net/wp-content/uploads/2011/06/great-wall-of-china.jpg" alt="" width="480" height="360" /></a><p class="wp-caption-text">Not a cell wall</p></div>
<p>So, for example, when I am developing computational metagenomics analysis tools, they invariably tend to target both bacteria and archaea. However, these tools are usually not good for microbial eukaryotes, due to different rRNA size, the larger genomes with more non-coding regions, lack of operons, organelles genomes, introns, etc. So for this utilitarian purpose, &#8220;prokaryotes&#8221; would be a good verbal shortcut to the cumbersome &#8220;bacteria and archaea&#8221; when describing or documenting the software. So can we all agree on &#8220;prokaryotes&#8221; as a verbal shortcut of necessity but not as a taxonomic definition? Or am I missing something substantial here?</p>
<p>An illustrative example of the rational, cool-headed debate that may ensue:</p>
<div class="wp-caption alignnone" style="width: 750px"><img title="Herpetology" src="http://imgs.xkcd.com/comics/herpetology.png" alt="" width="740" height="325" /><p class="wp-caption-text">Herpetology Credit: xkcd.com</p></div>
<p>&nbsp;</p>
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		<title>Crowdsourcing genomics</title>
		<link>http://bytesizebio.net/index.php/2011/05/19/crowdsourcing-genomics/</link>
		<comments>http://bytesizebio.net/index.php/2011/05/19/crowdsourcing-genomics/#comments</comments>
		<pubDate>Thu, 19 May 2011 18:59:28 +0000</pubDate>
		<dc:creator>Iddo</dc:creator>
				<category><![CDATA[Bioinformatics]]></category>
		<category><![CDATA[Education]]></category>
		<category><![CDATA[Genomics]]></category>
		<category><![CDATA[Microbiology]]></category>
		<category><![CDATA[bacteriophages]]></category>
		<category><![CDATA[HHMI]]></category>
		<category><![CDATA[microbiology]]></category>
		<category><![CDATA[teaching]]></category>
		<category><![CDATA[viruses]]></category>

		<guid isPermaLink="false">http://bytesizebio.net/?p=4937</guid>
		<description><![CDATA[&#160; Miami University has  joined the National Genomics Research Initiative (NGRI) offered by HHMI Science Education Alliance (SEA) in their Phage Genomics course. The students go directly into the lab, participating in an authentic research experience. In a full-year academic course they: isolate and characterize bacterial viruses from their local soil prepare the viral DNA [...]]]></description>
			<content:encoded><![CDATA[<p>&nbsp;</p>
<p>Miami University has  joined the National Genomics Research Initiative (NGRI) offered by HHMI Science Education Alliance (SEA) in their <a href="http://www.hhmi.org/grants/sea/initiative.html" target="_blank">Phage Genomics course</a>. The students go directly into the lab, participating in an authentic research experience. In a full-year academic course they:</p>
<ul>
<li>isolate and characterize bacterial viruses from their local soil</li>
<li>prepare the viral DNA for sequencing</li>
<li>annotate and compare the sequenced genome</li>
</ul>
<p><span style="float: left; padding: 5px;"><a href="http://www.researchblogging.org"><img class="alignnone" style="border: 0;" src="http://www.researchblogging.org/public/citation_icons/rb2_large_gray.png" alt="ResearchBlogging.org" width="70" height="85" /></a></span></p>
<p>The <a href="http://microbiology.muohio.edu/" target="_blank">Department of Microbiology at Miami University</a> is offering this course in the upcoming year: four of our faculty will be teaching it. Phage isolation, electron microscopy, DNA sequencing in the first semester, annotation and comparative genomics in the second. And <em>I </em>get to teach the bioinformatics bit: annotation and comparative genomics. Woo-hoo! The great thing about this course, is that unlike most lab courses, the students (and faculty) will be setting up experiments intended not only to teach, but also to discover something new.  Also, the results of the research are meaningful. Genomics data generated by student participants will be used by other researchers to answer medical, ecological, and evolutionary scientific questions. Bacteriophages (viruses that infect bacteria) affect the biopsphere so profoundly, it is almost impossible to imagine. Their sheer biomass is equal to that of <a href="http://bytesizebio.net/index.php/2011/04/14/book-review-small-and-packs-a-punch/" target="_blank">75 million blue whales</a>, and marine bacteriophages  kill about half of marine microbes <em>every day</em>. Bacteriophages have a huge host range, mind-boggling number of particles in the biosphere (10<sup>30</sup>) and, above all, the genetic diversity is unmatched by all other life combined. Participating students will see how their data may be used by other researchers in the SEA network &#8212; truly collaborative, crowdsourced science. Here are the<a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=nuccore&amp;cmd=search&amp;term=%28Science%20Education%20Alliance%29%20AND%20%22genbank%22[Filter]" target="_blank"> genomic sequences</a> of SEA-sequenced bacteriophages already in GenBank.</p>
<p>If you are an incoming Miami freshman, and want to jump in and do some real science, it doesn&#8217;t get much better than this. Check out our course page, and ask about the <a href="http://microbiology.muohio.edu/undergrad/advanced.html#223" target="_blank">Bacteriophage Biology</a> course in your orientation. You may even get your name on a paper like these students from other participating universities.</p>
<p><a href="http://www.hhmi.org/grants/sea/media/slideshows/ngri_students/student_pop.html"><img class="alignnone size-full wp-image-4942" title="ngri_students_th" src="http://bytesizebio.net/wp-content/uploads/2011/05/ngri_students_th.jpg" alt="" width="354" height="240" /></a></p>
<p><span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.jtitle=PLoS+ONE&amp;rft_id=info%3Adoi%2F10.1371%2Fjournal.pone.0016329&amp;rfr_id=info%3Asid%2Fresearchblogging.org&amp;rft.atitle=Expanding+the+Diversity+of+Mycobacteriophages%3A+Insights+into+Genome+Architecture+and+Evolution&amp;rft.issn=1932-6203&amp;rft.date=2011&amp;rft.volume=6&amp;rft.issue=1&amp;rft.spage=0&amp;rft.epage=&amp;rft.artnum=http%3A%2F%2Fdx.plos.org%2F10.1371%2Fjournal.pone.0016329&amp;rft.au=Pope%2C+W.&amp;rft.au=Jacobs-Sera%2C+D.&amp;rft.au=Russell%2C+D.&amp;rft.au=Peebles%2C+C.&amp;rft.au=Al-Atrache%2C+Z.&amp;rft.au=Alcoser%2C+T.&amp;rft.au=Alexander%2C+L.&amp;rft.au=Alfano%2C+M.&amp;rft.au=Alford%2C+S.&amp;rft.au=Amy%2C+N.&amp;rft.au=Anderson%2C+M.&amp;rft.au=Anderson%2C+A.&amp;rft.au=Ang%2C+A.&amp;rft.au=Ares%2C+M.&amp;rft.au=Barber%2C+A.&amp;rft.au=Barker%2C+L.&amp;rft.au=Barrett%2C+J.&amp;rft.au=Barshop%2C+W.&amp;rft.au=Bauerle%2C+C.&amp;rft.au=Bayles%2C+I.&amp;rft.au=Belfield%2C+K.&amp;rft.au=Best%2C+A.&amp;rft.au=Borjon%2C+A.&amp;rft.au=Bowman%2C+C.&amp;rft.au=Boyer%2C+C.&amp;rft.au=Bradley%2C+K.&amp;rft.au=Bradley%2C+V.&amp;rft.au=Broadway%2C+L.&amp;rft.au=Budwal%2C+K.&amp;rft.au=Busby%2C+K.&amp;rft.au=Campbell%2C+I.&amp;rft.au=Campbell%2C+A.&amp;rft.au=Carey%2C+A.&amp;rft.au=Caruso%2C+S.&amp;rft.au=Chew%2C+R.&amp;rft.au=Cockburn%2C+C.&amp;rft.au=Cohen%2C+L.&amp;rft.au=Corajod%2C+J.&amp;rft.au=Cresawn%2C+S.&amp;rft.au=Davis%2C+K.&amp;rft.au=Deng%2C+L.&amp;rft.au=Denver%2C+D.&amp;rft.au=Dixon%2C+B.&amp;rft.au=Ekram%2C+S.&amp;rft.au=Elgin%2C+S.&amp;rft.au=Engelsen%2C+A.&amp;rft.au=English%2C+B.&amp;rft.au=Erb%2C+M.&amp;rft.au=Estrada%2C+C.&amp;rft.au=Filliger%2C+L.&amp;rft.au=Findley%2C+A.&amp;rft.au=Forbes%2C+L.&amp;rft.au=Forsyth%2C+M.&amp;rft.au=Fox%2C+T.&amp;rft.au=Fritz%2C+M.&amp;rft.au=Garcia%2C+R.&amp;rft.au=George%2C+Z.&amp;rft.au=Georges%2C+A.&amp;rft.au=Gissendanner%2C+C.&amp;rft.au=Goff%2C+S.&amp;rft.au=Goldstein%2C+R.&amp;rft.au=Gordon%2C+K.&amp;rft.au=Green%2C+R.&amp;rft.au=Guerra%2C+S.&amp;rft.au=Guiney-Olsen%2C+K.&amp;rft.au=Guiza%2C+B.&amp;rft.au=Haghighat%2C+L.&amp;rft.au=Hagopian%2C+G.&amp;rft.au=Harmon%2C+C.&amp;rft.au=Harmson%2C+J.&amp;rft.au=Hartzog%2C+G.&amp;rft.au=Harvey%2C+S.&amp;rft.au=He%2C+S.&amp;rft.au=He%2C+K.&amp;rft.au=Healy%2C+K.&amp;rft.au=Higinbotham%2C+E.&amp;rft.au=Hildebrandt%2C+E.&amp;rft.au=Ho%2C+J.&amp;rft.au=Hogan%2C+G.&amp;rft.au=Hohenstein%2C+V.&amp;rft.au=Holz%2C+N.&amp;rft.au=Huang%2C+V.&amp;rft.au=Hufford%2C+E.&amp;rft.au=Hynes%2C+P.&amp;rft.au=Jackson%2C+A.&amp;rft.au=Jansen%2C+E.&amp;rft.au=Jarvik%2C+J.&amp;rft.au=Jasinto%2C+P.&amp;rft.au=Jordan%2C+T.&amp;rft.au=Kasza%2C+T.&amp;rft.au=Katelyn%2C+M.&amp;rft.au=Kelsey%2C+J.&amp;rft.au=Kerrigan%2C+L.&amp;rft.au=Khaw%2C+D.&amp;rft.au=Kim%2C+J.&amp;rft.au=Knutter%2C+J.&amp;rft.au=Ko%2C+C.&amp;rft.au=Larkin%2C+G.&amp;rft.au=Laroche%2C+J.&amp;rft.au=Latif%2C+A.&amp;rft.au=Leuba%2C+K.&amp;rft.au=Leuba%2C+S.&amp;rft.au=Lewis%2C+L.&amp;rft.au=Loesser-Casey%2C+K.&amp;rft.au=Long%2C+C.&amp;rft.au=Lopez%2C+A.&amp;rft.au=Lowery%2C+N.&amp;rft.au=Lu%2C+T.&amp;rft.au=Mac%2C+V.&amp;rft.au=Masters%2C+I.&amp;rft.au=McCloud%2C+J.&amp;rft.au=McDonough%2C+M.&amp;rft.au=Medenbach%2C+A.&amp;rft.au=Menon%2C+A.&amp;rft.au=Miller%2C+R.&amp;rft.au=Morgan%2C+B.&amp;rft.au=Ng%2C+P.&amp;rft.au=Nguyen%2C+E.&amp;rft.au=Nguyen%2C+K.&amp;rft.au=Nguyen%2C+E.&amp;rft.au=Nicholson%2C+K.&amp;rft.au=Parnell%2C+L.&amp;rft.au=Peirce%2C+C.&amp;rft.au=Perz%2C+A.&amp;rft.au=Peterson%2C+L.&amp;rft.au=Pferdehirt%2C+R.&amp;rft.au=Philip%2C+S.&amp;rft.au=Pogliano%2C+K.&amp;rft.au=Pogliano%2C+J.&amp;rft.au=Polley%2C+T.&amp;rft.au=Puopolo%2C+E.&amp;rft.au=Rabinowitz%2C+H.&amp;rft.au=Resiss%2C+M.&amp;rft.au=Rhyan%2C+C.&amp;rft.au=Robinson%2C+Y.&amp;rft.au=Rodriguez%2C+L.&amp;rft.au=Rose%2C+A.&amp;rft.au=Rubin%2C+J.&amp;rft.au=Ruby%2C+J.&amp;rft.au=Saha%2C+M.&amp;rft.au=Sandoz%2C+J.&amp;rft.au=Savitskaya%2C+J.&amp;rft.au=Schipper%2C+D.&amp;rft.au=Schnitzler%2C+C.&amp;rft.au=Schott%2C+A.&amp;rft.au=Segal%2C+J.&amp;rft.au=Shaffer%2C+C.&amp;rft.au=Sheldon%2C+K.&amp;rft.au=Shepard%2C+E.&amp;rft.au=Shepardson%2C+J.&amp;rft.au=Shroff%2C+M.&amp;rft.au=Simmons%2C+J.&amp;rft.au=Simms%2C+E.&amp;rft.au=Simpson%2C+B.&amp;rft.au=Sinclair%2C+K.&amp;rft.au=Sjoholm%2C+R.&amp;rft.au=Slette%2C+I.&amp;rft.au=Spaulding%2C+B.&amp;rft.au=Straub%2C+C.&amp;rft.au=Stukey%2C+J.&amp;rft.au=Sughrue%2C+T.&amp;rft.au=Tang%2C+T.&amp;rft.au=Tatyana%2C+L.&amp;rft.au=Taylor%2C+S.&amp;rft.au=Taylor%2C+B.&amp;rft.au=Temple%2C+L.&amp;rft.au=Thompson%2C+J.&amp;rft.au=Tokarz%2C+M.&amp;rft.au=Trapani%2C+S.&amp;rft.au=Troum%2C+A.&amp;rft.au=Tsay%2C+J.&amp;rft.au=Tubbs%2C+A.&amp;rft.au=Walton%2C+J.&amp;rft.au=Wang%2C+D.&amp;rft.au=Wang%2C+H.&amp;rft.au=Warner%2C+J.&amp;rft.au=Weisser%2C+E.&amp;rft.au=Wendler%2C+S.&amp;rft.au=Weston-Hafer%2C+K.&amp;rft.au=Whelan%2C+H.&amp;rft.au=Williamson%2C+K.&amp;rft.au=Willis%2C+A.&amp;rft.au=Wirtshafter%2C+H.&amp;rft.au=Wong%2C+T.&amp;rft.au=Wu%2C+P.&amp;rft.au=Yang%2C+Y.&amp;rft.au=Yee%2C+B.&amp;rft.au=Zaidins%2C+D.&amp;rft.au=Zhang%2C+B.&amp;rft.au=Z%C3%BAniga%2C+M.&amp;rft.au=Hendrix%2C+R.&amp;rft.au=Hatfull%2C+G.&amp;rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CBioinformatics%2C+Molecular+Biology%2C+Microbiology%2C%2C+Virology">Pope, W., Jacobs-Sera, D., Russell, D., Peebles, C., Al-Atrache, Z., Alcoser, T., Alexander, L., Alfano, M., Alford, S., Amy, N., Anderson, M., Anderson, A., Ang, A., Ares, M., Barber, A., Barker, L., Barrett, J., Barshop, W., Bauerle, C., Bayles, I., Belfield, K., Best, A., Borjon, A., Bowman, C., Boyer, C., Bradley, K., Bradley, V., Broadway, L., Budwal, K., Busby, K., Campbell, I., Campbell, A., Carey, A., Caruso, S., Chew, R., Cockburn, C., Cohen, L., Corajod, J., Cresawn, S., Davis, K., Deng, L., Denver, D., Dixon, B., Ekram, S., Elgin, S., Engelsen, A., English, B., Erb, M., Estrada, C., Filliger, L., Findley, A., Forbes, L., Forsyth, M., Fox, T., Fritz, M., Garcia, R., George, Z., Georges, A., Gissendanner, C., Goff, S., Goldstein, R., Gordon, K., Green, R., Guerra, S., Guiney-Olsen, K., Guiza, B., Haghighat, L., Hagopian, G., Harmon, C., Harmson, J., Hartzog, G., Harvey, S., He, S., He, K., Healy, K., Higinbotham, E., Hildebrandt, E., Ho, J., Hogan, G., Hohenstein, V., Holz, N., Huang, V., Hufford, E., Hynes, P., Jackson, A., Jansen, E., Jarvik, J., Jasinto, P., Jordan, T., Kasza, T., Katelyn, M., Kelsey, J., Kerrigan, L., Khaw, D., Kim, J., Knutter, J., Ko, C., Larkin, G., Laroche, J., Latif, A., Leuba, K., Leuba, S., Lewis, L., Loesser-Casey, K., Long, C., Lopez, A., Lowery, N., Lu, T., Mac, V., Masters, I., McCloud, J., McDonough, M., Medenbach, A., Menon, A., Miller, R., Morgan, B., Ng, P., Nguyen, E., Nguyen, K., Nguyen, E., Nicholson, K., Parnell, L., Peirce, C., Perz, A., Peterson, L., Pferdehirt, R., Philip, S., Pogliano, K., Pogliano, J., Polley, T., Puopolo, E., Rabinowitz, H., Resiss, M., Rhyan, C., Robinson, Y., Rodriguez, L., Rose, A., Rubin, J., Ruby, J., Saha, M., Sandoz, J., Savitskaya, J., Schipper, D., Schnitzler, C., Schott, A., Segal, J., Shaffer, C., Sheldon, K., Shepard, E., Shepardson, J., Shroff, M., Simmons, J., Simms, E., Simpson, B., Sinclair, K., Sjoholm, R., Slette, I., Spaulding, B., Straub, C., Stukey, J., Sughrue, T., Tang, T., Tatyana, L., Taylor, S., Taylor, B., Temple, L., Thompson, J., Tokarz, M., Trapani, S., Troum, A., Tsay, J., Tubbs, A., Walton, J., Wang, D., Wang, H., Warner, J., Weisser, E., Wendler, S., Weston-Hafer, K., Whelan, H., Williamson, K., Willis, A., Wirtshafter, H., Wong, T., Wu, P., Yang, Y., Yee, B., Zaidins, D., Zhang, B., Zúniga, M., Hendrix, R., &amp; Hatfull, G. (2011). Expanding the Diversity of Mycobacteriophages: Insights into Genome Architecture and Evolution <span style="font-style: italic;">PLoS ONE, 6</span> (1) DOI: <a rev="review" href="http://dx.doi.org/10.1371/journal.pone.0016329">10.1371/journal.pone.0016329</a></span></p>
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		<title>Social media used to track disease outbreak</title>
		<link>http://bytesizebio.net/index.php/2011/04/25/social-media-used-to-track-disease-outbreak/</link>
		<comments>http://bytesizebio.net/index.php/2011/04/25/social-media-used-to-track-disease-outbreak/#comments</comments>
		<pubDate>Mon, 25 Apr 2011 21:13:59 +0000</pubDate>
		<dc:creator>Iddo</dc:creator>
				<category><![CDATA[blogging]]></category>
		<category><![CDATA[Microbiology]]></category>
		<category><![CDATA[Social media]]></category>
		<category><![CDATA[epidemiology]]></category>
		<category><![CDATA[facebook]]></category>
		<category><![CDATA[legionella]]></category>
		<category><![CDATA[legionelliosis]]></category>
		<category><![CDATA[microbiology]]></category>
		<category><![CDATA[twitter]]></category>

		<guid isPermaLink="false">http://bytesizebio.net/?p=4887</guid>
		<description><![CDATA[&#160; There are some interesting developments regarding the February outbreak of Legionelliosis which was traced to the Playboy mansion. Reminder: over 120 delegates of the DOMAINFest in Santa Monica, California came down with symptoms of a respiratory illness. The convention included a trip to the Playboy mansion, which later was suspected as the outbreak source. [...]]]></description>
			<content:encoded><![CDATA[<p>&nbsp;</p>
<p>There are some interesting developments regarding the <a href="http://bytesizebio.net/index.php/2011/02/14/playboy-pleasure-palace-provides-pneumophila/" target="_blank">February outbreak of Legionelliosis</a> which was traced to the Playboy mansion. Reminder: over 120 delegates of the DOMAINFest in Santa Monica, California came down with symptoms of a respiratory illness. The convention included a trip to the Playboy mansion, which later was suspected as the outbreak source. The convention was held Feb 1-4, 2011. The first inquiry to the  LA County Department of Health (LAC DPH) of a suspected legionellesis outbreak was made by the media on February 11. When tracing the outbreak, LAC DPH and CDC scientists discovered a trail of reports preceding February 11 in social media,  including Facebook and Twitter. The <a href="http://en.wikipedia.org/wiki/Legionellosis#Los_Angeles.2C_United_States.2C_2011" target="_blank">Wikipedia entry</a> was updated almost <a href="http://en.wikipedia.org/w/index.php?title=Legionellosis&amp;diff=prev&amp;oldid=413324117" target="_blank">at the same time when the LAC DPH inquiry was made</a>.</p>
<div id="attachment_4888" class="wp-caption alignnone" style="width: 583px"><a href="http://bytesizebio.net/wp-content/uploads/2011/04/playboy-timeline.png"><img class="size-full wp-image-4888" title="playboy-timeline" src="http://bytesizebio.net/wp-content/uploads/2011/04/playboy-timeline.png" alt="" width="573" height="433" /></a><p class="wp-caption-text">Source: LA Times. From a presentation by Dr. Caitlin Reed </p></div>
<p>&nbsp;</p>
<p><a href="http://bytesizebio.net/wp-content/uploads/2011/04/wikipedia-leg1.png"><img class="alignnone size-large wp-image-4893" style="border: 1px solid black;" title="wikipedia-leg" src="http://bytesizebio.net/wp-content/uploads/2011/04/wikipedia-leg1-1024x691.png" alt="" width="717" height="484" /></a></p>
<p><a href="http://bytesizebio.net/wp-content/uploads/2011/04/wikipedia-leg.png"></a></p>
<p>Note that there is quite a bit of information in this entry already!</p>
<p>The scientists identified several risk factors: staying at either one of the hotels, and two parties. They assessed the exposure risk based on the fraction of people who were in those venues and who became sick. To do so, they circulated questionnaires, via email and a Facebook list. They came up with this:</p>
<p>&nbsp;</p>
<div id="attachment_4889" class="wp-caption alignnone" style="width: 575px"><a href="http://bytesizebio.net/wp-content/uploads/2011/04/risk-illness.png"><img class="size-full wp-image-4889" title="risk-illness" src="http://bytesizebio.net/wp-content/uploads/2011/04/risk-illness.png" alt="" width="565" height="426" /></a><p class="wp-caption-text">Source: LA Times. From a presentation by Dr. Caitlin Reed </p></div>
<p>&nbsp;</p>
<p>The February 3 &#8220;Venue A&#8221; party seemed to hold the largest <a href="http://en.wikipedia.org/wiki/Relative_risk" target="_blank">relative risk</a> (RR), by far.  That was the Playboy mansion. Indeed, checking the water at the grotto where the party was held:</p>
<div id="attachment_4890" class="wp-caption alignnone" style="width: 575px"><a href="http://bytesizebio.net/wp-content/uploads/2011/04/leg-isolation.png"><img class="size-full wp-image-4890" title="leg-isolation" src="http://bytesizebio.net/wp-content/uploads/2011/04/leg-isolation.png" alt="" width="565" height="424" /></a><p class="wp-caption-text">Source: LA Times. From a presentation by Dr. Caitlin Reed</p></div>
<p>&nbsp;</p>
<p>The scientists concluded that use of social media to trace outbreaks has its pros and cons. The biggest pro was the ability to contact all conference attendees quickly, even though they are geographically dispersed. Also, the Facebook list, tweets and email encouraged a fast response to the survey. They did have some red herrings, and had to put effort into rumor control. I am not sure how much the last two were amplified by the social media effect.</p>
<p>&nbsp;</p>
<p>The <a href="http://documents.latimes.com/social-media-playboy/" target="_blank">full slide presentation</a>, and <a href="http://latimesblogs.latimes.com/lanow/2011/04/playboy-mansion-outbreak-investigators-use-facebook-twitter-social-media-to-track-mystery-illness.html" target="_blank">more information</a> are at the <em>Los Angeles Times</em>.</p>
<p>&nbsp;</p>
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		<title>Thursday Odds and Ends</title>
		<link>http://bytesizebio.net/index.php/2011/04/07/thursday-odds-and-ends/</link>
		<comments>http://bytesizebio.net/index.php/2011/04/07/thursday-odds-and-ends/#comments</comments>
		<pubDate>Thu, 07 Apr 2011 16:22:49 +0000</pubDate>
		<dc:creator>Iddo</dc:creator>
				<category><![CDATA[Science]]></category>
		<category><![CDATA[computers]]></category>
		<category><![CDATA[microbiology]]></category>
		<category><![CDATA[miscellania]]></category>
		<category><![CDATA[MRSA]]></category>
		<category><![CDATA[Paleontology]]></category>

		<guid isPermaLink="false">http://bytesizebio.net/?p=4808</guid>
		<description><![CDATA[&#160; A woman in Chesterfield, Ohio robbed a convenience store using her MRSA-infected arm as a weapon.  Warning: graphic picture of MRSA infected arm. Or a zombie limb. You can never know in northwestern Ohio. A US vector biologist got infected with Zika virus which is  a mosquito-borne pathogen causing joint pain and fatigue. He [...]]]></description>
			<content:encoded><![CDATA[<p>&nbsp;</p>
<p>A woman in Chesterfield, Ohio robbed a convenience store using her <a href="http://en.wikipedia.org/wiki/Methicillin-resistant_Staphylococcus_aureus" target="_blank">MRSA</a>-infected <a href="http://www.woio.com/Global/story.asp?S=13264250" target="_blank">arm as a weapon</a>.  Warning: graphic picture of MRSA infected arm. Or a zombie limb. You can never know in northwestern Ohio.</p>
<div id="attachment_4811" class="wp-caption alignnone" style="width: 310px"><a href="http://bytesizebio.net/wp-content/uploads/2011/04/MRSA_SEM_9994_lores.jpg"><img class="size-medium wp-image-4811" title="MRSA_SEM_9994_lores" src="http://bytesizebio.net/wp-content/uploads/2011/04/MRSA_SEM_9994_lores-300x214.jpg" alt="" width="300" height="214" /></a><p class="wp-caption-text">Scanning Electron Microscope image of Methicillin-Resistant Staphylococcus aureus or MRSA. Credit: Janice Carr. Source: wikipedia</p></div>
<p>A US vector biologist got infected with Zika virus which is  a mosquito-borne pathogen causing joint pain and fatigue. He then <a href="http://news.sciencemag.org/sciencenow/2011/04/sex-after-a-field-trip-yields-sc.html" target="_blank">passed in on to his wife during sexual intercourse</a>. This would be the first documented case of sexual transmission of an insect-borne pathogen. Also, &#8220;Honey, I<em>swear</em>, I got it from a mosquito bite&#8221; is the new excuse for two-timing spouses everywhere.</p>
<p><a href="http://bytesizebio.net/wp-content/uploads/2011/04/Mosquito_cartoon.gif"><img class="alignnone size-full wp-image-4812" title="Mosquito_cartoon" src="http://bytesizebio.net/wp-content/uploads/2011/04/Mosquito_cartoon.gif" alt="" width="208" height="288" /></a></p>
<p>April&#8217;s fool came and went on the intertubes.  My favorite was the <a href="http://www.thinkgeek.com/interests/looflirpa/e8b9/" target="_blank">arsenic based sea-monkeys</a>.</p>
<p>&nbsp;</p>
<p>Great news for geeky kids of the 1980&#8242;s: the Commodore 64 is back!  Same nice bulky keyboard-in computer, with just a little bit more than 64K of RAM underneath:</p>
<p>&nbsp;</p>
<p><a href="http://bytesizebio.net/wp-content/uploads/2011/04/C64_startup_animiert.gif"><img class="alignnone size-full wp-image-4810" title="C64_startup_animiert" src="http://bytesizebio.net/wp-content/uploads/2011/04/C64_startup_animiert.gif" alt="" width="360" height="248" /></a></p>
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<blockquote><p>&#8220;The upcoming Commodore 64 looks exactly like the ancient model which reshaped the home computer sector decades ago, though underneath the bonnet things have been brought well into the 21st century.</p>
<p>&#8220;Even though the computer refrains from relinquishing its old charm, it will come packed with modern computer hardware. The new Commodore 64 model will contain a mini-ITC motherboard, a dual core Intel 525 Atom processor, DDR3 RAM between 2GB and 4GB and Nvidia Ion2 graphics unit.</p>
<p>&#8220;Commodore says that the device will run on the Ubuntu 10.04 LTS OS and will come with a DVD drive, with support for Blu-Ray, a multi-format memory card reader and five USB slots. The new Commodore 64 will also come with Wi-Fi support and will come pre-loaded with 3D games and other applications including a Microsoft Office compatible productivity suite.<br />
Read more: <a href="http://www.itproportal.com/2011/04/06/iconic-commodore-64-all-set-comeback/#ixzz1IqxQ1LXX">http://www.itproportal.com/2011/04/06/iconic-commodore-64-all-set-comeback/#ixzz1IqxQ1LXX</a></p>
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<p>Finally, remember the name: <em><a href="http://palaeoblog.blogspot.com/2011/04/zhuchengtyrannus-magnus-new-tyrannosaur.html">Zhuchengtyrannus magnus</a></em> (zoo-CHENG TEER-ah-nus MAG-nus) or Z. magnus. A new dinosaur discovered in Zucheng, China. Related to <em>Tyrannosaurus rex</em> it is 4m tall, 11m long, 6 tons of carnivorous mass. The <a href=" http://dx.doi.org/10.1016/j.cretres.2011.03.005">original paper</a>.</p>
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