tag:blogger.com,1999:blog-21198061905506863232024-03-20T00:42:57.762-07:00contagious thinkingexploring the postdoctoral interface between virus research, scicomm. and beerConnor Bhttp://www.blogger.com/profile/08132413724023944783noreply@blogger.comBlogger14125tag:blogger.com,1999:blog-2119806190550686323.post-89909831347429768072014-09-14T07:07:00.000-07:002014-09-14T07:07:00.675-07:00cascade SMASH <a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiLusRKcN2lMX7cNCO2YpTIWC9twDA8_QiHwlVgXDV7iVqKN_A19GqSoDxvGZ_1AdvAAbG8rrVsu1yE8vTxdBqhB-wjais9RYEAeeYieQLlXdvY-n10KbyAawv1ohS-vjVAr7wBmQaExh2y/s1600/2014-08-31+19.45.11.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiLusRKcN2lMX7cNCO2YpTIWC9twDA8_QiHwlVgXDV7iVqKN_A19GqSoDxvGZ_1AdvAAbG8rrVsu1yE8vTxdBqhB-wjais9RYEAeeYieQLlXdvY-n10KbyAawv1ohS-vjVAr7wBmQaExh2y/s1600/2014-08-31+19.45.11.jpg" height="320" width="240" /></a>As it was coming to the middle of summer I really wanted to make a summer ale; one similar to American pale ales, which are bitterly hopped with hops like cascade (the floral grapefruit-like ones), light textured and bodied but a bit sweet. For this I followed a standard pale malt + sweet crystal malt + lots of hops at early and late timepoints. No dry hopping was used. A standard ale yeast was used. This ale turned out pretty well and tasted like the usual Brewdog-kind of pale ale. Not the most creative but tastey.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj5EQ94GrfTCtSUkkIzNj1RYeBfVLO8XMKHI2MqFHdTtMPQjGKKHDrTTvConQwGDZlIhHvROx9AYpocvctDY_V9iXmmmZm1qjib9n1s9Q7GB_hjIKpVNsGhWuL0njtwFazmuUoMBwMlNT3p/s1600/2014-08-31+19.47.31.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj5EQ94GrfTCtSUkkIzNj1RYeBfVLO8XMKHI2MqFHdTtMPQjGKKHDrTTvConQwGDZlIhHvROx9AYpocvctDY_V9iXmmmZm1qjib9n1s9Q7GB_hjIKpVNsGhWuL0njtwFazmuUoMBwMlNT3p/s1600/2014-08-31+19.47.31.jpg" height="320" width="240" /></a><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi7wrSnPJiWPfQCFHRRqHfq4bN5s1TvFe42-nL47Qh1AVUaTD05plUugRRLhdQXoKXyxpDFSdjfSgkk_vJOgGt4QUa3uFjW8FWDcI7WMuGkqrt4uxBpipP15gmFeRT5JkyRDx6tgnPTnENj/s1600/2014-07-27+17.07.36.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi7wrSnPJiWPfQCFHRRqHfq4bN5s1TvFe42-nL47Qh1AVUaTD05plUugRRLhdQXoKXyxpDFSdjfSgkk_vJOgGt4QUa3uFjW8FWDcI7WMuGkqrt4uxBpipP15gmFeRT5JkyRDx6tgnPTnENj/s1600/2014-07-27+17.07.36.jpg" height="320" width="240" /></a></div>
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<table style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px; width: 85%px;"><colgroup><col width="25%"></col><col width="85%"></col></colgroup><tbody>
<tr align="left"><th colspan="2"><b><a name='more'></a>Basic Information</b></th></tr>
<tr><td style="margin: 0px;">Batch Name:</td><td style="margin: 0px;">cascade SMASH ale</td></tr>
<tr><td style="margin: 0px;">Brewed By:</td><td style="margin: 0px;">Connor</td></tr>
<tr><td style="margin: 0px;">Style:</td><td style="margin: 0px;">Standard/Ordinary Bitter</td></tr>
<tr><td style="margin: 0px;">Batch Size:</td><td style="margin: 0px;">4.50 L</td></tr>
<tr><td style="margin: 0px;">Boil Time:</td><td style="margin: 0px;">60 min</td></tr>
<tr><td style="margin: 0px;">Initial Boil Volume:</td><td style="margin: 0px;">4.50 L</td></tr>
<tr><td style="margin: 0px;">Mash Method:</td><td style="margin: 0px;">Steeped Grains</td></tr>
<tr><td style="margin: 0px;">Brew Date:</td><td style="margin: 0px;">1/19/14</td></tr>
<tr><td style="margin: 0px;"><br />I was aiming for something greater than this:<br /></td><td style="margin: 0px;"><table style="color: #222222; font-size: 13px; width: 85%px;"><tbody>
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<tr align="left"><th colspan="2"><b>Typical Style Characteristics (google APA for pictures)</b></th></tr>
<tr><td style="margin: 0px;">Style:</td><td style="margin: 0px;">Standard/Ordinary Bitter (closest my program gets to an APA)</td></tr>
<tr><td style="margin: 0px;">O.G.</td><td style="margin: 0px;">1.032 - 1.040</td></tr>
<tr><td style="margin: 0px;">F.G.</td><td style="margin: 0px;">1.007 - 1.011</td></tr>
<tr><td style="margin: 0px;">ABV</td><td style="margin: 0px;">3.2 - 3.8 (could be higher - 5%)</td></tr>
<tr><td style="margin: 0px;">IBU</td><td style="margin: 0px;">25 - 35 (50)</td></tr>
<tr><td style="margin: 0px;">SRM</td><td style="margin: 0px;">4 - 14°L</td></tr>
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<tr align="left"><th colspan="5"><br /><span style="font-weight: normal;">To achieve this I used these:</span><br />Malt Bill</th></tr>
<tr><td style="margin: 0px;">Malt Name</td><td style="margin: 0px;">Weight</td><td style="margin: 0px;">PPG</td><td style="margin: 0px;">SRM</td><td style="margin: 0px;">Type</td></tr>
<tr><td style="margin: 0px;">Light Dry Extract</td><td style="margin: 0px;">0.50 kg</td><td style="margin: 0px;">1.044</td><td style="margin: 0px;">8.00</td><td style="margin: 0px;">Extract/Adjunct</td></tr>
<tr><td style="margin: 0px;">Caramel/Crystal Malt - 60L</td><td style="margin: 0px;">0.10 kg</td><td style="margin: 0px;">1.034</td><td style="margin: 0px;">60.00</td><td style="margin: 0px;">Steeped Grain</td></tr>
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<tr align="left"><th colspan="5"><b>Mash Rest Profile</b></th></tr>
<tr><td style="margin: 0px;">Rest</td><td style="margin: 0px;">Temperature</td><td style="margin: 0px;">Time</td><td style="margin: 0px;">Type</td><td style="margin: 0px;">Details</td></tr>
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<tr align="left"><th colspan="5"><b>Hop Bill</b></th></tr>
<tr><td style="margin: 0px;">Hop Name</td><td style="margin: 0px;">Time Added</td><td style="margin: 0px;">Weight</td><td style="margin: 0px;">AA%</td><td style="margin: 0px;">Type</td></tr>
<tr><td style="margin: 0px;">Cascade (U.S.)</td><td style="margin: 0px;">60 min</td><td style="margin: 0px;">12.00 g</td><td style="margin: 0px;">5.8%</td><td style="margin: 0px;">Leaf Hop</td></tr>
<tr><td style="margin: 0px;">Cascade (U.S.)</td><td style="margin: 0px;">20 min</td><td style="margin: 0px;">9.00 g</td><td style="margin: 0px;">5.8%</td><td style="margin: 0px;">Leaf Hop</td></tr>
<tr><td style="margin: 0px;">Cascade (U.S.)</td><td style="margin: 0px;">5 min</td><td style="margin: 0px;">6.00 g</td><td style="margin: 0px;">5.8%</td><td style="margin: 0px;">Leaf Hop</td></tr>
<tr><td style="margin: 0px;">Cascade (U.S.)</td><td style="margin: 0px;">0 min</td><td style="margin: 0px;">4.00 g</td><td style="margin: 0px;">5.8%</td><td style="margin: 0px;">Leaf Hop</td></tr>
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<tr align="left"><th colspan="5"><b>Yeast Details</b></th></tr>
<tr><td style="margin: 0px;">Yeast Strand</td><td style="margin: 0px;">Quantity</td><td style="margin: 0px;">Attenuation</td><td style="margin: 0px;">Flocculation</td></tr>
<tr><td style="margin: 0px;">Safale S-04 Dry Ale</td><td style="margin: 0px;">7.5g</td><td style="margin: 0px;">60</td><td style="margin: 0px;">High</td></tr>
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<br />And the results were:<br /><br />This is what I got:<br /></td><td style="margin: 0px;"><br /></td></tr>
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<tr align="left"><th colspan="2"><b>Calculated & Measured Statistics</b></th></tr>
<tr><td style="margin: 0px;">Calculated O.G.</td><td style="margin: 0px;">1.044 (72% Efficiency)</td></tr>
<tr><td style="margin: 0px;">Calculated F.G.</td><td style="margin: 0px;">1.020 (60% Yeast Attenuation)</td></tr>
<tr><td style="margin: 0px;">Measured O.G.</td><td style="margin: 0px;">1.050 (inf% Actual Efficiency)</td></tr>
<tr><td style="margin: 0px;">Measured F.G.</td><td style="margin: 0px;">1.010 (80% Actual Attenuation)</td></tr>
<tr><td style="margin: 0px;">ABV</td><td style="margin: 0px;">5.3%</td></tr>
<tr><td style="margin: 0px;">IBU</td><td style="margin: 0px;">55.4</td></tr>
<tr><td style="margin: 0px;">SRM</td><td style="margin: 0px;">5.9°L</td></tr>
<tr><td style="margin: 0px;"><br />comments: from this everything looked nice. The higher than predicted attenuation was worrying but no sign of contamination (might be because of difficulties in measuring the yeast out). I hit the ABV and IBU perfectly. On paper this was pretty good.<br /><br />Two weeks in primary and then two weeks in secondary (lost some in transfer). Used 20g of sugar to prime in bottles.<br /><br /><b>Qualitative:</b><br />Looks:<br />Little sediment (probably because of secondary and no contamination). Maybe a little darker than I would have liked. This comes from the crystal maybe. Reduce it? There was chill haze when served from fridge. Don't do this.<br /><br />Head:<br />Nice head, which dies away quickly. 'Simmer's away lowly during drinking.<br /><br />Aroma:<br />Cascade hops and only cascade hops.<br /><br />Taste:<br />Sweet, bitter, hoppy.<br /><br />Mouthfeel:<br />Light and refreshing.<br /><br />For next time: change crystal? Change hops? Centennial experiment.<br /></td><td style="margin: 0px;"><br /></td></tr>
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Connor Bhttp://www.blogger.com/profile/08132413724023944783noreply@blogger.com0tag:blogger.com,1999:blog-2119806190550686323.post-88923346406489328952014-08-04T03:09:00.000-07:002014-08-04T03:09:17.299-07:00towards a high-resolution understanding of hepatitis C virus<div style="text-align: justify;">
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg1fDkFC_FVyum9nlwoydBV-zXAN4C7HmTaVOsB0652hBXTILn_4_icreHpUfMX9824121sZUEJaTEp7-5vB3iU50_abHNXgMceqcj-Y2PRiFlT3SKm1EAJoKMPKWQa3T51anZ7ldl-cGDu/s1600/C0171720-Hepatitis_C_Virus-SPL.jpg" imageanchor="1" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg1fDkFC_FVyum9nlwoydBV-zXAN4C7HmTaVOsB0652hBXTILn_4_icreHpUfMX9824121sZUEJaTEp7-5vB3iU50_abHNXgMceqcj-Y2PRiFlT3SKm1EAJoKMPKWQa3T51anZ7ldl-cGDu/s1600/C0171720-Hepatitis_C_Virus-SPL.jpg" height="320" width="240" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">HCV virions</td></tr>
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Viruses are sub-microscopic parasites of cells. What this means is that despite our immense interest in them, they are very difficult to observe and study using your eyes or even traditional light microscopy, which is the mainstay of biology over the last few centuries. This is annoying because we are interested in understanding what viruses look like because of what they tells us about their biology as virus particle structure affects many aspects of its lifecycle, such as cell entry, replication and transmission. </div>
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These questions are no more interesting than for HCV, an <a href="http://www.who.int/mediacentre/factsheets/fs164/en/">important human pathogen</a> that has chronically infects between 130 and 150 million people worldwide and leads to between 350,000 and 500,00 deaths a year. Infection often lead on to chronic hepatitis, cirrhosis, fibrosis, hepatocellular carcinoma and eventually liver failure and death. Although there are now effective drugs targeting HCV, HCV and associated diseases are likely to continue to be a public health issue in the future because of their prohibitive cost. We do not yet have an effective vaccine to protect against the virus either. </div>
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One avenue to aid development of antivirals and vaccines is to understand HCV particle (virion) structure and the pathways that promote its assembly and its entry into cells. The catch is that HCV has been extremely challenging to manipulate in the lab under experimental settings. However,<a href="http://www.pnas.org/content/early/2013/05/17/1307527110.short"> a paper published in the journal PNAS</a>, (free here http://www.ncbi.nlm.nih.gov/pubmed/23690609) from the Charles Rice lab in New York (first author: <a href="http://www.kcl.ac.uk/medicine/research/divisions/diiid/departments/infectious/research/catanese/index.aspx">Maria Teresa Catanese</a>) has shown the characterisation of HCV virion structure using a powerful microscopic technique: cryoelectron tomography <a href="http://en.wikipedia.org/wiki/Cryo-electron_microscopy">(cryo-EM</a>), which has improved our understanding of HCV biology. The continuing use of this imaging technology combined with models of HCV entry and assembly may aid in the development of novel HCV drugs and vaccines. </div>
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<b>HCV virion structure</b><br />
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Like many other viruses, HCV virions were initially showed to be composed primarily of a nucleic acid genome (RNA is this case) encased within a protein shell and a lipid 'envelope'. This envelope is covered in glycoproteins, which facilitate binding to host cells and virus entry. This entire structure allows for the efficient protection of the virus genome as well as its assembly, release and subsequent entry.<br />
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An intriguing feature of HCV is its variable buoyant density of infectious particles taken from patient sera and tissue culture supernatant, which is strikingly lower than other RNA viruses. Infectious HCV buoyant density looked more similar to that of human sera lipoproteins that to other viruses. For example, measles virus has a<a href="http://download.springer.com/static/pdf/205/art%253A10.1007%252FBF01250203.pdf?auth66=1406879810_ed3ce39650433259ac749da09ae35a7a&ext=.pdf"> buoyant density of 1.2</a>3 in caesium chloride, which is also similar to <a href="file:///C:/Users/cb270j/Downloads/641-1806-1-PB.pdf">influenza virus</a> in sucrose. Even very closely related viruses to HCV, such as the pestiviruses and the flaviviruses had buoyant densities much higher. Even, liver-tropic viruses such hepatitis B virus <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC304350/">did not have densities this low</a>. This suggested that something else, specific to HCV. Early on in HCV research<a href="http://www.ncbi.nlm.nih.gov/pubmed/8121333"> it was demonstrated</a> that infectious particles associated with human serum lipoproteins. And it is this that might explain some key features of HCV biology and pathogenesis.<br />
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Lipoproteins<a href="http://en.wikipedia.org/wiki/Lipoprotein"> are lipid and protein complexes</a>, mainly synthesized in the liver, which can aid the movement of fats around the cell and body by the proteins emulsifying the fats and hence making them soluble in water. Their structure also aids in the regulated delivery of lipids to cells like liver, muscle and fat cells. The general structure of these particles is that of roughly spherical with the hydrophilic regions aimed outwards while the hydrophobic, fatty parts are buried deep inside. One of the most well-known classes of lipoproteins are the high (good cholestoerol) and low (bad cholesterol)-density lipoproteins (H-/L-DLs). These assemblages are complex and often are composed of many different kinds of proteins and lipids. Of interest to HCV research, lipoproteins such as LDL, intermediate (I) DL and very low (VL) DL have buoyant densities within the same range as the observed infectious HCV particles, suggesting that HCV could be interacting directly with them.<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgrFNHBh0lyjaKuqUz0PC__E18J4xmBB4ezupYJbbY1eebOjk4lR7rQ_D7WPz8UpZXFbYI36kWSJRyhtdTyS9FqY88tS0zyjSvB0OppgNZynB3DHqBJbeN4wM1NNxotxgAT9w09YTyW-pL5/s1600/250px-Chylomicron.svg.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgrFNHBh0lyjaKuqUz0PC__E18J4xmBB4ezupYJbbY1eebOjk4lR7rQ_D7WPz8UpZXFbYI36kWSJRyhtdTyS9FqY88tS0zyjSvB0OppgNZynB3DHqBJbeN4wM1NNxotxgAT9w09YTyW-pL5/s1600/250px-Chylomicron.svg.png" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">a cartoon lipoprotein complex (wikipedia). Cholesterol and triglycerides are found internally to phospholipids and proteins. </td></tr>
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<b>Cryo-EM</b><br />
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What we knew before was that the HCV virion was complicated but very interesting from a scientific point of view and that it had proved to be elusive when trying to study it using the best microscopic techniques we had, for example, cryo-electron micoscopy and tomography. Cryo-EM is a way to study particles, such as viruses, in a their almost-native state following freezing. Frozen suspensions of particles are bombarded with electrons to form an image. Multiple images are interrogated to assemble single particle 3-D reconstructions.<br />
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg2sAfNqKo9GeDZLnQzu8d2h_m7y8IXqy6E7PhqbrUh5zVTvR8mP2_oklBMqSca8GFimQOKVR4Kb7Jx43B9eiKkACO3fqafOfwwXXb40bIzcqGnNeiG_N8V7C6QhoGEL6ioslTcrgiSzuJj/s1600/pnas.1307527110fig01.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg2sAfNqKo9GeDZLnQzu8d2h_m7y8IXqy6E7PhqbrUh5zVTvR8mP2_oklBMqSca8GFimQOKVR4Kb7Jx43B9eiKkACO3fqafOfwwXXb40bIzcqGnNeiG_N8V7C6QhoGEL6ioslTcrgiSzuJj/s1600/pnas.1307527110fig01.jpg" height="400" width="336" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">purification of HCV virions</td></tr>
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The paper of Catanese et al., took advantage of being able to grow HCV in the lab in liver cancer cell lines and modified primary human hepatocytes and were able to infect these cells in the lab and remove the replicated HCV released into the cell supernatant. Once removed, HCV virions were purified using grids, coated with antibodies that specifically recognised and bound to HCV (note that the best way to get purified HCV was to use a genetically engineered HCV that expressed a high-affinity protein tag on its surface). These purified virions were then subjected to cryo-EM to observe exactly what they look liked, in a way that we had never before been able to achieve. The show some very nice pictures of purified HCV and are able to quantify a number of basic biological features of the virus.<br />
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjOk1i1sxpVHgVhGSgHZYWMft6ZnLWT-YPkhmrj-bSdcbpVp8-m3tXMKyE94bzhYjBcCM4GoLGqU8HY-MtGcQ_PcnPFLoLHT4Nt7BOw0JUkMXZ60HhCtJQF4EhYjgEbA6e-DYvwaa0KcoUs/s1600/HCV+EMpnas.1307527110fig07.jpg" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjOk1i1sxpVHgVhGSgHZYWMft6ZnLWT-YPkhmrj-bSdcbpVp8-m3tXMKyE94bzhYjBcCM4GoLGqU8HY-MtGcQ_PcnPFLoLHT4Nt7BOw0JUkMXZ60HhCtJQF4EhYjgEbA6e-DYvwaa0KcoUs/s1600/HCV+EMpnas.1307527110fig07.jpg" height="291" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">HCV single particles by cryo-EM</td></tr>
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Using cryo-EM they were able to show that while HCV particles were generally spherical, their size was quite variable (2.5 fold (40nm to 100nm), which is unlike other related viruses. Catanese et al., were able to visualise HCV interaction with lipoprotein complexes. Like other studies before them they confirmed the presence of certain apolipoproteins and interestingly that these lipoproteins may be preventing binding of antibodies to HCV glycoproteins. This has implications for HCV vaccine design.<br />
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<b>Only the start</b><br />
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I believe that this work (representing a technological advancement) is only the start of improving our understanding of HCV structural biology and how it relates to infection and pathogenesis. Improving upon these data and combining them with crystal structure of <a href="http://www.nature.com/nature/journal/v509/n7500/full/nature13117.html">purified HCV glycoproteins, </a>for example, should provide further knowledge of HCV structural biology. A test of this technology would be to image HCV from clinical material over the course of an infection, but I can see how difficult that may be. However, combining high-resolution imaging (EM and confocal microscopy combined) investigations with hypothesis-driven molecular biology could tease apart the mechanisms of HCV entry, assembly and spread in clinically-relevant model systems (<a href="http://www.sciencedirect.com/science/article/pii/S1046202312001338">humanised mice</a>). Understanding these mechanisms may facilitate targeted therapeutics and vaccine development.<br />
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Connor Bhttp://www.blogger.com/profile/08132413724023944783noreply@blogger.com0tag:blogger.com,1999:blog-2119806190550686323.post-4372601880609581542014-07-27T14:21:00.001-07:002014-07-27T14:21:41.334-07:00wheat beer #1<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: left; margin-right: 1em; text-align: left;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiNI0BcxOVh4xy_Fgx0zDEHkWvhsdvWIhGdHU-0vncsklPZvbdi9aNHawI_mvHw-WfD8ituCJGfF2z9pK6NI_OOdmCB_YXM5pnlWAO9WZT6NY1JrMmf5AfDL1LEt1xP-8ZMqyAJTprplwn5/s1600/2014-07-27+15.22.37.jpg" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiNI0BcxOVh4xy_Fgx0zDEHkWvhsdvWIhGdHU-0vncsklPZvbdi9aNHawI_mvHw-WfD8ituCJGfF2z9pK6NI_OOdmCB_YXM5pnlWAO9WZT6NY1JrMmf5AfDL1LEt1xP-8ZMqyAJTprplwn5/s1600/2014-07-27+15.22.37.jpg" height="320" width="240" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">wheat beer #1</td></tr>
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<span style="font-family: Times, Times New Roman, serif;">One of my next beers I wanted to make was a wheat beer in the style of Hoegarden. I had previously tried out this style earlier this year (see </span><a href="http://homebrewni.blogspot.co.uk/" style="font-family: Times, 'Times New Roman', serif;">here</a><span style="font-family: Times, Times New Roman, serif;">). This beer was nice enough but it was so alcoholic and sugary that it was near-impossible to enjoy drinking it. This next beer was an attempt to rectify this. </span><br />
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<span style="font-family: Times, Times New Roman, serif;">To improve upon the last recipe I made some alterations, namely in reducing the amount of input to bring down the OG. I also simplified it a bit and took out unnecessary carapils and wheat whole grains. The recipe was altered so as to allow 4.5 litre brewing. </span></div>
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<span style="font-family: Times, Times New Roman, serif;"><b>Recipe:</b></span></div>
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEis5R4eDoCkZfhaBhJgMEj44IFBE8sX-SsiTSQ35yyh2gFnBuYLcDu0L88UKS_9G8qSOzQXt9cJrm4Ka7yYVHDQDTtCYHCtz17yky3mZeFf5sUfSVF70Xd4qNmoPIHI2Uw26EZFfVOgKjqe/s1600/2014-06-29+17.10.59.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEis5R4eDoCkZfhaBhJgMEj44IFBE8sX-SsiTSQ35yyh2gFnBuYLcDu0L88UKS_9G8qSOzQXt9cJrm4Ka7yYVHDQDTtCYHCtz17yky3mZeFf5sUfSVF70Xd4qNmoPIHI2Uw26EZFfVOgKjqe/s1600/2014-06-29+17.10.59.jpg" height="320" width="240" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">additions:orange peel and crushed coriander seeds</td></tr>
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<tr align="left"><th colspan="5"><b><span style="font-family: Times, Times New Roman, serif;">Malt Bill</span></b></th></tr>
<tr><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">Malt Name</span></td><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">Weight</span></td><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">PPG</span></td><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">SRM</span></td><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">Type</span></td></tr>
<tr><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">Wheat Dry Extract</span></td><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">0.35 kg</span></td><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">1.044</span></td><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">8.00</span></td><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">Extract/Adjunct</span></td></tr>
<tr><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">Extra Light Dry Extract</span></td><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">0.25 kg</span></td><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">1.044</span></td><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">3.00</span></td><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">Extract/Adjunct<br /></span></td></tr>
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<tr><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">Hop Name</span></td><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">Time Added</span></td><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">Weight</span></td><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">AA%</span></td><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">Type</span></td></tr>
<tr><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">Saaz (Czech)</span></td><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">60 min</span></td><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">5.00 g</span></td><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">3.8%</span></td><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">Pellet Hop</span></td></tr>
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<tr align="left"><th colspan="5"><b><span style="font-family: Times, Times New Roman, serif;">Yeast Details</span></b></th></tr>
<tr><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">Yeast Strand</span></td><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">Quantity</span></td><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">Attenuation</span></td><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">Flocculation</span></td></tr>
<tr><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">Safbrew WB-06 Dry Brewing Yeast</span></td><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">1 pack</span></td><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">76</span></td><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">Low<br /></span></td></tr>
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<tr><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">Measured O.G.</span></td><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">1.055 (inf% Actual Efficiency).</span></td></tr>
<tr><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">Measured F.G.</span></td><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;">1.005 (91% Actual Attenuation)</span></td></tr>
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<tr><td style="margin: 0px;"><span style="font-family: Times, Times New Roman, serif;"><br />The ABV was 6.7% with IBU of 9.3. The colour also looked similar to what a wheat beer would look like.<br /><br />No secondary vessel was used here and then 57g of brewing sugar was added prior to bottling to hit a high level of carbonation.<br /><br /><b>Looks:</b><br />I drank the first bottle after just less than 1 week (because I was brewing another beer at the same time). The look of the beer in the bottle was great, with a slight chlll haze (it was very clear prior to cooling. I kicked up a bit of the dropped out yeast to give it the traditional wheat look. It popped after opening and proceeded to fizz a bit, what I would have expected from the level of carbonation I hit. When poured into the bottle it was evidently very carbonated with a great white head, which would linger, retaining its fluffy cloudiness for 5< minutes. </span></td></tr>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhxCz54yG50D7W37vRiGSyZsnblfkV6Pg9_9wRlHzpk_WpLftxBxv_-Y4Xt_6ZqwWQwcuQwZ2xA5lOwFCykZgoRwkblkJwkuBsOR1DTO-buPDoJQNiKtqJns-14RYcYpDslnDw9HXBW7RoZ/s1600/2014-07-27+15.10.45.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhxCz54yG50D7W37vRiGSyZsnblfkV6Pg9_9wRlHzpk_WpLftxBxv_-Y4Xt_6ZqwWQwcuQwZ2xA5lOwFCykZgoRwkblkJwkuBsOR1DTO-buPDoJQNiKtqJns-14RYcYpDslnDw9HXBW7RoZ/s1600/2014-07-27+15.10.45.jpg" height="320" width="240" /></a><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjhvH9_otgrGK2avf2SMoU8x6gCwf3hTb_RbqIrlZATkZ42XvgFmSReO5eht7icDyB0uWFhXtLBsFxNXssS3rWfKWCpElyFO_mKWDCyYw0zn_FHPvslwpnOUnXNQXwC49sqZ3GxBBOrBrG1/s1600/2014-07-27+15.10.36.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjhvH9_otgrGK2avf2SMoU8x6gCwf3hTb_RbqIrlZATkZ42XvgFmSReO5eht7icDyB0uWFhXtLBsFxNXssS3rWfKWCpElyFO_mKWDCyYw0zn_FHPvslwpnOUnXNQXwC49sqZ3GxBBOrBrG1/s1600/2014-07-27+15.10.36.jpg" height="320" width="240" /></a></div>
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<span style="font-family: Times, Times New Roman, serif;">To make this beer different from standard wheat beers and more like Hoegarden, I added 2.5 grams of each, orange peel and crushed coriander seeds ten minutes before the end of the boil. </span></div>
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<span style="font-family: Times, Times New Roman, serif;">I managed to hit these stats as OG and then after three weeks in the primary, a 91% attenuation, which was particularly high attenuation than I would have predicted. (13.5 and 6 brix at 0 and 3 weeks, respectively). </span></div>
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<span style="font-family: Times, Times New Roman, serif;">It smelt very clean and not hoppy, very like a traditional lager. Hints of fruitiness were picked up but no overriding orange or coriander. </span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiRfsdQ8CfYZwyuwAHC34tRpeJMDnBdMEnm50p3hDBVQE09_YzB3sdS_dyo7VE6CVhR08_zD7rdce3EAvfIkiibB1j6y-Q4l2EsWJm9YuJiXM9nuDx9Ka9b3C959ysLlr_u0NCN3CfaNGDa/s1600/2014-07-27+15.12.33.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiRfsdQ8CfYZwyuwAHC34tRpeJMDnBdMEnm50p3hDBVQE09_YzB3sdS_dyo7VE6CVhR08_zD7rdce3EAvfIkiibB1j6y-Q4l2EsWJm9YuJiXM9nuDx9Ka9b3C959ysLlr_u0NCN3CfaNGDa/s1600/2014-07-27+15.12.33.jpg" height="320" width="240" /></a><span style="font-family: Times, Times New Roman, serif;"><b>Taste:</b></span></div>
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<span style="font-family: Times, Times New Roman, serif;">This beer tasted and felt very crisp and clean (carbonation levels helped! - and the FG?) initially then quite malty like a lager towards the end (predicted given the Saaz hops usage?) but with a hint of fruitiness in there (but just a bit!). However, this beer was way more malty and wheaty than it was fruity and estery. It came across a bit too sugary for my liking, which I guess could be explained by only leaving it 1 week in conditioning. </span></div>
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<span style="font-family: Times, Times New Roman, serif;"><b>General comments:</b></span></div>
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<span style="font-family: Times, Times New Roman, serif;">This was a lovely beer. I have never hit such levels of cleanness and crispness before. It is very similar to a beer like Miller or another dry lager. Compared to the previous wheat effort, it was a lot more enjoyable to drink but essentially tasted very similar (same malts, same hops). In the end it tasted a bit more like erdinger and blue moon rather than hoegarden. </span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg75Aauz_h-oB_UDuvYA0rabjAi476KrwX7OUA-bnYk5zoKc6LU97GOCgtWPuDLxcQD_0PLw_Q3m23xrw7bJk9S2Xq5-fckNGeSdnBJvCVQIlRCz3snkfEwZ_uaALY6I_O4lqJginvCNyUe/s1600/2014-07-27+15.16.09.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg75Aauz_h-oB_UDuvYA0rabjAi476KrwX7OUA-bnYk5zoKc6LU97GOCgtWPuDLxcQD_0PLw_Q3m23xrw7bJk9S2Xq5-fckNGeSdnBJvCVQIlRCz3snkfEwZ_uaALY6I_O4lqJginvCNyUe/s1600/2014-07-27+15.16.09.jpg" height="320" width="240" /></a></div>
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<span style="font-family: Times, Times New Roman, serif;"><b>What would I do differently?</b></span></div>
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<span style="font-family: Times, Times New Roman, serif;">For the next wheat beer attempt I would stick closely to this recipe. I would not leave it for three weeks in primary to decrease the dryness. I would reduce the sugar for carbonation but then would increase the conditioning time. I could also up the herbal content.</span></div>
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<br />Connor Bhttp://www.blogger.com/profile/08132413724023944783noreply@blogger.com0tag:blogger.com,1999:blog-2119806190550686323.post-76831341278344712392014-06-22T09:13:00.001-07:002014-06-22T09:13:13.102-07:00microtwjc analysis 2. unique tweeters<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj3C8rECVZNCfpncAapxIIHfepvs8w8l5EmFseo2d8zc_KgGeQrIDU10xhjpK8o3bYNoq31H2BgqDvowzMgK-Pz0sKH4eU5qlWTgnDvidVKcFJm4ySiMSxmf1UjOWOYLQqBhWhN-beUbWwi/s1600/unique+tweeters.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj3C8rECVZNCfpncAapxIIHfepvs8w8l5EmFseo2d8zc_KgGeQrIDU10xhjpK8o3bYNoq31H2BgqDvowzMgK-Pz0sKH4eU5qlWTgnDvidVKcFJm4ySiMSxmf1UjOWOYLQqBhWhN-beUbWwi/s1600/unique+tweeters.jpg" height="306" width="400" /></a></div>
<span style="font-family: Georgia, Times New Roman, serif;">When considering participants in #microtwjc, we can also measure the number of unique tweeters, tweeters who have not tweeter at a previous session. This allows a measure of growth of #microtwjc to new people. I have plotted unique 'new' tweeters over time for both the total tweeters and the engaged (n<1 tweeters per session) people. Again, both measures are different. But a major finding of this is that #microtwjc has continued to recruit engaged tweeters over the time. This is at a fairly constant rate, except for a couple of spikes. I've shown the cumulative growth of tweeters in the graph below. Total is growing at an average of 1.8 tweeters/session while engaged are growing at an average of 1.3 tweeters per session. Questions arising from this are: are these tweeters staying? What's the loss of engagement like? To do this I could plot tweeters per person per session. Let's try that. </span><br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEizqKIk2vFFv1IQk9ndKAifEbXwEtrITILX1MoodQyEGk1T6D0QcbyXfgBzN2FMLPQL1H3IPH5e4dLxpQO12KmBa3PnMkknS3I6KgZxmF2OblxDO6rd8iI_tc02LglwA1m_2XJjtRTsAwx1/s1600/Copy+of+Data+4.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEizqKIk2vFFv1IQk9ndKAifEbXwEtrITILX1MoodQyEGk1T6D0QcbyXfgBzN2FMLPQL1H3IPH5e4dLxpQO12KmBa3PnMkknS3I6KgZxmF2OblxDO6rd8iI_tc02LglwA1m_2XJjtRTsAwx1/s1600/Copy+of+Data+4.jpg" height="306" width="400" /></a></div>
Connor Bhttp://www.blogger.com/profile/08132413724023944783noreply@blogger.com0tag:blogger.com,1999:blog-2119806190550686323.post-18958616990950454242014-06-22T07:09:00.000-07:002014-06-22T07:09:45.578-07:00dark ale take 2. <div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhzSjtHslcjmmvMv1hxjdP7pHlVR9RnhBnM7gDAoXemGKRM-LX144wGXCc22-VkOEnLUR0JQZ8JHhsfyz7BCLTxEFByd6mKODEAEzXwEAFDOgiD0bx5WtCJdUNoRmhJht3CleYej3IaH_mq/s1600/2014-06-21+20.19.25.jpg" imageanchor="1" style="clear: right; float: right; font-weight: normal; margin-bottom: 1em; margin-left: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhzSjtHslcjmmvMv1hxjdP7pHlVR9RnhBnM7gDAoXemGKRM-LX144wGXCc22-VkOEnLUR0JQZ8JHhsfyz7BCLTxEFByd6mKODEAEzXwEAFDOgiD0bx5WtCJdUNoRmhJht3CleYej3IaH_mq/s1600/2014-06-21+20.19.25.jpg" height="320" width="240" /></a></div>
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<tr align="left"><th colspan="2">Spoiler: it was great.<br />
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<span style="font-weight: normal;">The key to good and science (and good beer) is repetition. The act of doing an experiment again and again allows you to not only find weaknesses in your thinking and doing that you might not have realised but it allows you to act on those weaknesses and improve and rectify them. This is why I tried to make another porter/stout. This was mainly because the last one had some issues (too sugary sweet/ not mellow and not enjoyable to drink). This is a stout after all; it should be relaxing to drink. Guiness anyone?</span><br />
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<span style="font-weight: normal;">I had tried a similar recipe before (details </span><a href="http://apostdocinvirology.blogspot.co.uk/2014/04/porter-take-1.html" style="font-weight: normal;">here</a><span style="font-weight: normal;">). The major differences between the two recipes that I planned are: lower original gravity and the addition of flavor elements that would mellow the beer out (oatmeal, coffee, dark chocolate). My thinking was that the worst aspects of the first beer were high OG and lack of complex elements (chocolate etc.). [never though of this but perhaps I shouldn't have used so much crystal].</span><br />
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<span style="font-weight: normal;">Coffee was made in caffetiere, 4 squares of chocolate (Dark, tesco, cheap) were melted in the coffee + boiling water. Oatmeal was steeped. </span><br />
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<span style="font-weight: normal;">This beer brewed well. No complaints. The strangeness happened when I took it to secondary (wanted to experiment with using secondary to get beer clear). After 13 days in primary, the FG was 0.99, which gives an attenuation of 115%. There was also floating white specks across the beer. When I tasted this 'contaminated' batch, it tasted great. Really great. No more strong sweetness. So I took it to secondary and let it go for about 10 days. In the secondary, the white specks gained in number/size during time in secondary. It was more of light smattering of white. This gave me a hint that it was contaminated and not just yeast sediment. This did not happen with my first batch. On both occasions, after primary and secondary, the beer tasted great. So I went ahead and bottled. Was in bottle for around 1 week before I tasted. One bottle was obviously 'overgrown' in that it had large white clumps at the top and lots of gunk at the bottom. Not bottles exploded. So I went ahead and drank it anyway; and it tasted great. Really great again. The beer was also very clear. </span><br />
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<span style="font-weight: normal;">The contamination (lacto?) may have contributed to the low FG and the lack of sweet taste (lactic acid). Either way, it tasted reminiscent of Guinness. It was sweet but dry and ultimately, very drinkable. The contamination could have come from the chocolate or coffee additions or from general beer moving (shaking to oxygenate). I guess I was lucky that this happened in a beer that can handle sour contamination well. Next time I should try and harness the lacto to intentionally modify my dark ale brew. </span><br />
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<br />
Basic Information</th></tr>
<tr><td style="margin: 0px;">Batch Name:</td><td style="margin: 0px;">choc. oatmeal. coffee. stout</td></tr>
<tr><td style="margin: 0px;">Brewed By:</td><td style="margin: 0px;">Connor</td></tr>
<tr><td style="margin: 0px;">Style:</td><td style="margin: 0px;">Oatmeal Stout</td></tr>
<tr><td style="margin: 0px;">Batch Size:</td><td style="margin: 0px;">4.50 L</td></tr>
<tr><td style="margin: 0px;">Boil Time:</td><td style="margin: 0px;">60 min</td></tr>
<tr><td style="margin: 0px;">Initial Boil Volume:</td><td style="margin: 0px;">4.5 L</td></tr>
<tr><td style="margin: 0px;">Mash Method:</td><td style="margin: 0px;">Extract</td></tr>
<tr><td style="margin: 0px;">Brew Date:</td><td style="margin: 0px;">5/17/14</td></tr>
<tr><td style="margin: 0px;">My Rating:</td><td style="margin: 0px;">0/10</td></tr>
</tbody></table>
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<tr align="left"><th colspan="2"><b>Typical Style Characteristics</b></th></tr>
<tr><td style="margin: 0px;">Style:</td><td style="margin: 0px;">Oatmeal Stout</td></tr>
<tr><td style="margin: 0px;">O.G.</td><td style="margin: 0px;">1.048 - 1.065</td></tr>
<tr><td style="margin: 0px;">F.G.</td><td style="margin: 0px;">1.010 - 1.018</td></tr>
<tr><td style="margin: 0px;">ABV</td><td style="margin: 0px;">4.2 - 5.9</td></tr>
<tr><td style="margin: 0px;">IBU</td><td style="margin: 0px;">25 - 40</td></tr>
<tr><td style="margin: 0px;">SRM</td><td style="margin: 0px;">22 - 40°L</td></tr>
<tr><td style="margin: 0px;">Color</td><td style="margin: 0px;"><table style="width: 5%px;"><tbody>
<tr><td style="background-color: #43260c; margin: 0px;" width="10%"></td><td style="background-color: #080302; margin: 0px;" width="10%"></td></tr>
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<tr align="left"><th colspan="2"><b>Calculated & Measured Statistics</b></th></tr>
<tr><td style="margin: 0px;">Calculated O.G.</td><td style="margin: 0px;">1.049 (75% Efficiency)</td></tr>
<tr><td style="margin: 0px;">Calculated F.G.</td><td style="margin: 0px;">1.020 (70% Yeast Attenuation)</td></tr>
<tr><td style="margin: 0px;">Measured O.G.</td><td style="margin: 0px;">1.065 (inf% Actual Efficiency)</td></tr>
<tr><td style="margin: 0px;">Measured F.G.</td><td style="margin: 0px;">0.990 (115% Actual Attenuation)</td></tr>
<tr><td style="margin: 0px;">ABV</td><td style="margin: 0px;">10.0%</td></tr>
<tr><td style="margin: 0px;">IBU</td><td style="margin: 0px;">37.2</td></tr>
<tr><td style="margin: 0px;">SRM</td><td style="margin: 0px;">25.6°L</td></tr>
<tr><td style="margin: 0px;">Color</td><td style="margin: 0px;"><table style="width: 5%px;"><tbody>
<tr><td style="background-color: #211312; margin: 0px;" width="10%"></td></tr>
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</td></tr>
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<table style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px; width: 85%px;"><colgroup><col width="40%"></col><col width="15%"></col><col width="10%"></col><col width="10%"></col><col width="25%"></col></colgroup><tbody>
<tr align="left"><th colspan="5"><b>Malt Bill</b></th></tr>
<tr><td style="margin: 0px;">Malt Name</td><td style="margin: 0px;">Weight</td><td style="margin: 0px;">PPG</td><td style="margin: 0px;">SRM</td><td style="margin: 0px;">Type</td></tr>
<tr><td style="margin: 0px;">Light Dry Extract</td><td style="margin: 0px;">0.50 kg</td><td style="margin: 0px;">1.044</td><td style="margin: 0px;">8.00</td><td style="margin: 0px;">Extract/Adjunct</td></tr>
<tr><td style="margin: 0px;">Oats, Flaked</td><td style="margin: 0px;">0.10 kg</td><td style="margin: 0px;">1.037</td><td style="margin: 0px;">1.00</td><td style="margin: 0px;">Steeped Grain</td></tr>
<tr><td style="margin: 0px;">Chocolate Malt - 350°L</td><td style="margin: 0px;">0.08 kg</td><td style="margin: 0px;">1.028</td><td style="margin: 0px;">350.00</td><td style="margin: 0px;">Steeped Grain</td></tr>
<tr><td style="margin: 0px;">Barley, Flaked</td><td style="margin: 0px;">0.06 kg</td><td style="margin: 0px;">1.032</td><td style="margin: 0px;">2.00</td><td style="margin: 0px;">Steeped Grain</td></tr>
<tr><td style="margin: 0px;">Caramel/Crystal Malt - 60L</td><td style="margin: 0px;">0.03 kg</td><td style="margin: 0px;">1.034</td><td style="margin: 0px;">60.00</td><td style="margin: 0px;">Steeped Grain</td></tr>
</tbody></table>
<br style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;" />
<table style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px; width: 85%px;"><colgroup><col width="25%"></col><col width="10%"></col><col width="10%"></col><col width="10%"></col><col width="35%"></col></colgroup><tbody>
<tr align="left"><th colspan="5"><b>Mash Rest Profile</b></th></tr>
<tr><td style="margin: 0px;">Rest</td><td style="margin: 0px;">Temperature</td><td style="margin: 0px;">Time</td><td style="margin: 0px;">Type</td><td style="margin: 0px;">Details</td></tr>
</tbody></table>
<br style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;" />
<table style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px; width: 85%px;"><colgroup><col width="40%"></col><col width="15%"></col><col width="15%"></col><col width="10%"></col><col width="20%"></col></colgroup><tbody>
<tr align="left"><th colspan="5"><b>Hop Bill</b></th></tr>
<tr><td style="margin: 0px;">Hop Name</td><td style="margin: 0px;">Time Added</td><td style="margin: 0px;">Weight</td><td style="margin: 0px;">AA%</td><td style="margin: 0px;">Type</td></tr>
<tr><td style="margin: 0px;">Northern Brewer (U.K.)</td><td style="margin: 0px;">30 min</td><td style="margin: 0px;">12.00 g</td><td style="margin: 0px;">9.0%</td><td style="margin: 0px;">Leaf Hop</td></tr>
</tbody></table>
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<table style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px; width: 85%px;"><colgroup><col width="40%"></col><col width="25%"></col><col width="15%"></col><col width="35%"></col></colgroup><tbody>
<tr align="left"><th colspan="5"><b>Yeast Details</b></th></tr>
<tr><td style="margin: 0px;">Yeast Strand</td><td style="margin: 0px;">Quantity</td><td style="margin: 0px;">Attenuation</td><td style="margin: 0px;">Flocculation</td></tr>
<tr><td style="margin: 0px;">WY1098 Wyeast British Ale</td><td style="margin: 0px;">3</td><td style="margin: 0px;">74</td><td style="margin: 0px;">Medium</td></tr>
</tbody></table>
<br style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;" />
<table style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px; width: 85%px;"><colgroup><col width="25%"></col><col width="20%"></col><col width="55%"></col></colgroup><tbody>
<tr align="left"><th colspan="3"><b>Dates</b></th></tr>
<tr><td style="margin: 0px;">5/17/14</td><td style="margin: 0px;">Brew Date</td><td style="margin: 0px;"></td></tr>
<tr><td style="margin: 0px;">5/17/14</td><td style="margin: 0px;">Cooking</td><td style="margin: 0px;"></td></tr>
<tr><td style="margin: 0px;">5/31/14</td><td style="margin: 0px;">Secondary</td><td style="margin: 0px;"></td></tr>
<tr><td style="margin: 0px;">6/9/14</td><td style="margin: 0px;">Bottle</td><td style="margin: 0px;"></td></tr>
</tbody></table>
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<table style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px; width: 85%px;"><tbody>
<tr align="left"><td style="margin: 0px;"><b>Notes</b></td></tr>
<tr><td style="margin: 0px;">Brix 16.5 means 1.065 OG.<br />
13 days in secondary<br />
6 brix at secondary.9%?Something is off with numbers.<br />
<br />
<br />
Tastes dry but pleasant. Not very alcoholic. nice to drink.<br />
<br />
White scum on top. No smell and tasted nice! Lactobaccilus contamination?<br />
<br />
for bottling I added 20g sugar. This was calculated for 1 gallon but I had lost some in transfer to secondary.<br />
<br />
1.5 weeks in bottles before tasting.<br />
<br />
Lost one bottle (had off-colour sediment and lots of white floating clumps). discarded.<br />
<br />
<br /></td></tr>
</tbody></table>
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<span style="font-family: Georgia, Times New Roman, serif;"><br /></span>
<span style="font-family: Georgia, Times New Roman, serif;">This arrangement has been going on for about two years now and we have not had a chance to evaluate what we have done. In essence, we have conducted a two year experiment into using science communication. By doing a brief eye-balling online it looks like #microtwjc is longest running, functional twitter journal club. The original twitter journal (http://www.twitjc.com/) ran for 2.5 years (June 2011 - December 2013), with a half-year break between June 2013 and December 2013 (other breaks were taken). This means that #microtwjc affords an optimal chance of getting something useful out of its study. </span><br />
<span style="font-family: Georgia, Times New Roman, serif;"><br /></span>
<span style="font-family: Georgia, Times New Roman, serif;">For the last few months we have been trying to gather as much data about #microtwjc as we can. This covers number of tweeters over time at each session, number of tweets per tweeter per session, papers discussed, journals most chosen etc., etc. These data can be used to assess the worth and potential for #microtwjc to be better in the future. It also serves as a model to understand the use of twitter and social media for science communication and public engagement with science in the future. </span><br />
<span style="font-family: Georgia, Times New Roman, serif;"><br /></span>
<span style="font-family: Georgia, Times New Roman, serif;">In a series of posts I will try and analyse these data with a hope of finding some useful knowledge and wisdom about #microtwjc. You can view the data <a href="https://docs.google.com/spreadsheet/ccc?key=0AkndkyADVTYVdHJuN3VaaEllSkNoeEstZm02OHVWWEE&usp=sharing">here</a>.</span><br />
<span style="font-family: Georgia, Times New Roman, serif;"><br /></span>
<span style="font-family: Georgia, Times New Roman, serif;">A brief description of the methods to get the numbers discussed in this post. 1) each session was logged in storify or topsy format. 2) logged on to each site and searched for each session by date, name etc. 3) went through and counted number of tweeters and number of tweets they made. *this data collection was carried out by a number of the moderators of #microtwjc* . You know who you are. If any of you want to explore these data further, go do it. It's all open. </span><br />
<span style="font-family: Georgia, Times New Roman, serif;"><br /></span>
<span style="font-family: Georgia, Times New Roman, serif;">Firstly, I took the numbers and divided them per session (fig 1. ). What I quickly realised is that many tweeters tweeted only once, advertising the session, apologising for not being there. I felt these people were not 'engaged' with the session and as we are primarily interested in 'engagement' I decided to clean up the data and remove them from later analysis (posts to come). The engaged tweeters are shown in magenta (fig. 1.). The average tweeters per session was higher in the non-engaged group (As expected) with an average of ~8 compared to ~6. The spread of tweeters was also greater, mostly accounted for by session 1 (fig. 2 green). </span><br />
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgpkCbxoMsTNpiIDyVjG5n4sQgRlLCgNrJ6kJdlPdOLsOjFG0oKkwUt0I6RWaQYeg5ia51MU98OtKcrArKv57RVNaheuOn_R4WPsLZVhfZmnGFQcIs1o7pm1AYEddZ7fuiA1oICw731tfxe/s1600/Slide1.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><span style="font-family: Georgia, Times New Roman, serif;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgpkCbxoMsTNpiIDyVjG5n4sQgRlLCgNrJ6kJdlPdOLsOjFG0oKkwUt0I6RWaQYeg5ia51MU98OtKcrArKv57RVNaheuOn_R4WPsLZVhfZmnGFQcIs1o7pm1AYEddZ7fuiA1oICw731tfxe/s1600/Slide1.jpg" height="300" width="400" /></span></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-family: Georgia, Times New Roman, serif;">fig 1. number of tweeters: total (green); tweeters tweeting more than once 'engaged' (magenta).</span></td></tr>
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<span style="font-family: Georgia, Times New Roman, serif;"> Fig. 2. shows the data from fig. 1. shown over time for each session. This allows us to pick up peaks of troughs of activity and 'engagement'. </span><br />
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi7jVsMzta99qQYaBwqzuG8TenTda4IzbE3PuUF18Dco-1AueroH46UHUnBXEIQ_x2tyeWfoXjIQmGFzuV9JmkjoVA1xUVbHyW9QpPFLDN0XjW7bcZcOi_mDBiUdO94Oa-Bo-fZ07mJTrM6/s1600/Slide3.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><span style="font-family: Georgia, Times New Roman, serif; font-size: x-small;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi7jVsMzta99qQYaBwqzuG8TenTda4IzbE3PuUF18Dco-1AueroH46UHUnBXEIQ_x2tyeWfoXjIQmGFzuV9JmkjoVA1xUVbHyW9QpPFLDN0XjW7bcZcOi_mDBiUdO94Oa-Bo-fZ07mJTrM6/s1600/Slide3.jpg" height="300" width="400" /></span></a></td></tr>
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<tr><td class="tr-caption" style="font-size: 13.333333969116211px;"><span style="font-family: Georgia, Times New Roman, serif;">fig 2. number of tweeters taking part in each session: total (green); tweeters tweeting more than once 'engaged' (magenta).</span></td></tr>
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<span style="font-family: Georgia, Times New Roman, serif;"><span style="font-size: x-small;"><br /></span><span style="font-size: 13.333333969116211px;"> Comparing the number of 'engaged' tweeters with total tweeters for each session we can come up with a map of engagement over each session (fig. 3.). This largely parallels fig. 2. but shows it better. </span></span><div>
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEit6-9XpxqHzfs6-5tLUxFa1LnsP35zkfwlE5bFNeZhv3R3i4dUaOtFnSpalJtKEwp3GyGODHQnYuu-i9E-eQPzRZvFoUqBJtevLY5rToXZtKar32g37OV9C9xaRyd02WAymtOO2EwFNUYQ/s1600/Slide4.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><span style="font-family: Georgia, Times New Roman, serif;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEit6-9XpxqHzfs6-5tLUxFa1LnsP35zkfwlE5bFNeZhv3R3i4dUaOtFnSpalJtKEwp3GyGODHQnYuu-i9E-eQPzRZvFoUqBJtevLY5rToXZtKar32g37OV9C9xaRyd02WAymtOO2EwFNUYQ/s1600/Slide4.jpg" height="300" width="400" /></span></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-family: Georgia, Times New Roman, serif;">fig. 3. percentage of tweeters who tweeted more than once per session (engaged) (orange).</span></td></tr>
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<span style="font-family: Georgia, Times New Roman, serif;">I think two conclusions can be gleamed from this small analysis of #microtwjc tweets. 1) There is a more active 'engaged' community of tweeters and 2) tweeters and engaged tweeters changes over time. The reasons why are unknown. There looks to be a difference between years 1 and 2 (session 1 - 26). Your comments are welcome below. </span><br />
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<span style="font-family: Georgia, Times New Roman, serif;">The hope is that these data can be compiled, analysed, uploaded onto a data repository (figshare) and then use this to publish (PLoS, for example). This process will be completely open and collaborative. </span></div>
Connor Bhttp://www.blogger.com/profile/08132413724023944783noreply@blogger.com0tag:blogger.com,1999:blog-2119806190550686323.post-68871608163503271282014-06-17T07:19:00.001-07:002014-06-17T07:19:38.299-07:00basic liver biology - why things go wrong when it's infected<div style="text-align: justify;">
<span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;"><i><b>Being a virologist is hard. Not only do you have to know molecular biology but you also have to know cell biology and if you are interested in how viruses cause disease, you have to know anatomy and physiology. As you can imagine, while being extremely interesting, it is very time consuming This is why I have spent the last few days (weeks now) trying to come to terms with my liver. </b></i></span><br />
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<span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;"><i><b>Your liver is pretty amazing. Chances are you take it's special role for granted but you really shouldn't. This is something that I have been thinking about over the last few months after starting a postdoc into hepatitis C virus (HCV) biology, while I pondered on what it must feel like to lose the function of your liver. To appreciate what is happening during a disease like viral hepatitis, you have to understand how the liver does it job when it's not sick. This post will hopefully be the beginning of a series of blog posts aimed at trying to understand HCV infection and pathogenesis and how my research fits into it. FYI - I have not included any references in this post because what I am writing is established understanding in basic textbooks. This post will act as background as I continue my exploration of the liver and HCV.</b></i></span><br />
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<span style="font-family: 'Helvetica Neue', Arial, Helvetica, sans-serif;">You probably won't have seen your liver and your only experience of its metabolic work will have been after you've had a few drinks and you don't remain inebriated for too long. But it also does much, much more. </span><span style="font-family: 'Helvetica Neue', Arial, Helvetica, sans-serif;">Your liver carries out a complex array of functions, very difficult to summarise in a post like this (but I'll give it a go). Your liver operates a central role in keeping you alive by carrying out a 'biotransformative' role, lying between absorption (your intestines do this) and excretion (your kidneys do this). Biotransformation exists as two major metabolic functions: altering and breaking down molecules (catabolism) and synthesising them and releasing them into your blood stream to feed the rest of your body (anabolism). Another variation in this role is to break down toxins that can damage your body and it can even release hormones and bile, allowing it to function as a gland (again, variations of catabolism and anabolism). It can also store glycogen, an important carbohydrate storage vessel. What did I say, it is a complicated organ, so no wonder things go bad when it gets infected. The most important feature of your liver that allows it to function as a biotransformative organ is its close association with your blood stream and to do this, your liver employs some interesting physiological tricks. But it is these tricks that open it up to infections and disease</span></div>
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgF7a866iIFSu3lq7VUzDoFUe2pPBS2FskUR8HqVX_4dVBQtvkcxF5eMYfxS0xSW16ZtZEHYiehZ4Bxk3DxxfdXRlfjbGEz9bnsL63kHKEFxLx9jcD9gKC9_gntNJXgHkZqiWghaUpOH-Av/s1600/liver+intergate.ca.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgF7a866iIFSu3lq7VUzDoFUe2pPBS2FskUR8HqVX_4dVBQtvkcxF5eMYfxS0xSW16ZtZEHYiehZ4Bxk3DxxfdXRlfjbGEz9bnsL63kHKEFxLx9jcD9gKC9_gntNJXgHkZqiWghaUpOH-Av/s1600/liver+intergate.ca.jpg" height="270" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">your liver, in relation to stomach and pancreas. Note the lobes and blood supply. (integrated.ca.com) </td></tr>
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<span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;">Anatomically, your liver is a large (1.5 kg), triangular organ in the top right hand side of your chest, beside your stomach and your intestines. It is divided into four sections, referred to as lobes. Allowing it to carry the job of breaking down and releasing important molecules into your bloodstream, is it's intimate relationship with your circulatory system, which is composed of blood and lymph fluids. Testament to this relationship is its reported blood flow of 1.5 litres per minute. Unlike other organs it has a dual blood supply made up of two major blood vessels run through your liver, the hepatic artery, which brings in oxygen-rich blood, and the the hepatic portal vein that brings in absorbed nutrients and toxins from your small intestine and allows the blood to flow back into circulation. What makes this dual supply even more impressive is the</span><span style="font-family: 'Helvetica Neue', Arial, Helvetica, sans-serif;"> dense network of smaller blood-circulating</span><span style="font-family: 'Helvetica Neue', Arial, Helvetica, sans-serif;"> endothelial cells that are in near-direct contact with your liver cells throughout your liver tissue. This anatomic arrangement allows maximisation of the surface area to volume ratio of you liver for optimal biotransformation.</span></div>
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjfE5IKKbCxzXoqLXsGuKcSijT5N8lp9w5KWMwn4_BXxozlslBsI7ctozbXaNu6Ovb23o7LDdW9gv8ot39WtOc5BpCPan3PrPmvBvqu7Er2t3acrNjANCHMnuQmhzCs1bolQe78DpJycc-Y/s1600/Liver-lobule+dnwalker.com.jpg" imageanchor="1" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjfE5IKKbCxzXoqLXsGuKcSijT5N8lp9w5KWMwn4_BXxozlslBsI7ctozbXaNu6Ovb23o7LDdW9gv8ot39WtOc5BpCPan3PrPmvBvqu7Er2t3acrNjANCHMnuQmhzCs1bolQe78DpJycc-Y/s1600/Liver-lobule+dnwalker.com.jpg" height="311" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">hepatic lobules centred around a central vein (dnwalker.com)</td></tr>
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<span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;">The liver is a honeycomb mesh of four major cell types, which for ease of understanding are referred to either as parenchymal (hepatocytes) or non-parenchymal (endothelial, macrophage and fibroblast). </span><span style="font-family: 'Helvetica Neue', Arial, Helvetica, sans-serif;">Your liver parenchymal cells are largely made up of a single cell type, the hepatocyte, which are arranged into single-cell thick epithelial sheets. These cells are the business end of the liver and the one that is responsible for the majority of its metabolic activity (and mass). The main aim of the liver is to maximise the interaction between the hepatocyte and the blood. To do this, your liver employs endothelial cells to form the aforementioned dense network of blood supply between hepatocytes. These endothelial cells form hollow tracts, known as sinusoids, which line sheets of hepatocytes. Two other cell types, the macrophage-like 'kupfer' cells and the fibroblastic 'stellate' cells sit in close proximity to the liver sinusoids and serve immunological, filtering and healing roles, which I won't discuss here. But have covered <a href="http://ruleof6ix.fieldofscience.com/2011/09/your-liver-as-viral-filter-who-what.html">elsewhere </a>before. </span><br />
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<span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;">If you threw these four cell types into a pile together, very little would happen, but when arranged in the way that they are in your liver, they can efficiently interact with your blood. </span><span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;">The patterns that these cell types are arranged in come in three flavours: classical hepatitic lobules, portal lobules and acini. Each pattern describes a different spatial interaction of hepatocytes with endothelial cells. </span><span style="font-family: 'Helvetica Neue', Arial, Helvetica, sans-serif;">The major structural unit of the liver is the classical hepatitic lobule. Within a single lobe of your liver there are many classical hepatitic lobules, each lobule is composed of a hexagonal arrangement of hepatocytes and endothelial cells. Both the hepatoyctes and endothelial cells are organised around a central vein with five-fold symmetry</span><span style="font-family: 'Helvetica Neue', Arial, Helvetica, sans-serif;">. At each point of the hexagon lies a 'portal triad' of hepatic arterioles, venules and bile ducts. The oxygen-rich blood coming from the hepatic artery and then moving through the liver lobules into the hepatic portal vein. Other patterns can be observed in your liver, and the lobules can also be divided into acini (with two-fold symmetry between portal triads and the other is the portal lobules, which is relevant for bile drainage. <table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgO6CqpOmlouDDpsUXYE8y5-BhCwaNwTZ9X5iqKwFbMnwHOqezYn1zOp4g57592TG0ZdYDOftsBurSLXHVKaNGiTmaSWlWybFvdIHunntdu7Z5sdnmC8oEWckmjsgI5KHjb2w2hRC0j1SGx/s1600/liver+histology.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgO6CqpOmlouDDpsUXYE8y5-BhCwaNwTZ9X5iqKwFbMnwHOqezYn1zOp4g57592TG0ZdYDOftsBurSLXHVKaNGiTmaSWlWybFvdIHunntdu7Z5sdnmC8oEWckmjsgI5KHjb2w2hRC0j1SGx/s1600/liver+histology.jpg" height="251" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">cells in the hepatic lobules: not hepatocytes, sinosoidal endothelial cell and kupfer cells</td></tr>
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<span style="font-family: 'Helvetica Neue', Arial, Helvetica, sans-serif;"><br /></span><span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;">And so we come to the business end of the liver. Each cell has it's own role but it is the interactions between each of them allow the liver to carry out its important job. Importantly, the hepatocytes are the metabolic workhorses of the liver, and rightly, they make up the vast majority of the liver's mass. But in order to absorb and secrete, they must be in close contact with the blood supply and it is this interaction that is facilitated by the non-parenchymal cells, which essentially bridge the liver and the circulation. Most importantly, the endothelial cells form what are known as 'sinusoids', single-cell thick vessels with 'leaky' (fenestrated with no basement membrane) walls allowing extremely easy transport of blood fluid over the hepatocytes. But what happens inside the hepatocytes? I will explore this cell type in more detail in the next post.</span></div>
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhlbiAnwA5cjCHDDjdoRbHKzC6Kh0NhNzRNRCjo0O_8kBIaPiiiZI-YTrC5YFbL7YZ4edUAe_L5mOQnMpxM3kJhPF7HJM46Of5DGS3vI_WSSV6_ptPM-eVVgLuO2y7W8swpVy-Lq1ZB3_of/s1600/Liver4+hakeem-sy.gif" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhlbiAnwA5cjCHDDjdoRbHKzC6Kh0NhNzRNRCjo0O_8kBIaPiiiZI-YTrC5YFbL7YZ4edUAe_L5mOQnMpxM3kJhPF7HJM46Of5DGS3vI_WSSV6_ptPM-eVVgLuO2y7W8swpVy-Lq1ZB3_of/s1600/Liver4+hakeem-sy.gif" height="373" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">the hepatocyte in relation to endothelial cells (hakeem-sy.com)</td></tr>
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Connor Bhttp://www.blogger.com/profile/08132413724023944783noreply@blogger.com1tag:blogger.com,1999:blog-2119806190550686323.post-78477943884216945012014-05-18T07:47:00.001-07:002014-05-18T07:47:56.107-07:00my weeks picks (18th May 2014)<b><span style="font-family: Arial, Helvetica, sans-serif;">virology</span></b><br />
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<span style="font-family: Arial, Helvetica, sans-serif;">my PhD supervisor,Paul Duprex,will be on TWiV today at ASM (2 p.m Eastern Time) <span style="background-color: white; line-height: 34px; white-space: pre-wrap;">Paul Duprex </span><a class="twitter-atreply pretty-link" dir="ltr" href="https://twitter.com/10queues" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;">@10queues</a><span style="background-color: white; line-height: 34px; white-space: pre-wrap;"> and Julie Pfeiffer speaking about their work on </span><a class="twitter-hashtag pretty-link js-nav" data-query-source="hashtag_click" dir="ltr" href="https://twitter.com/search?q=%23TWiV&src=hash" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;">#TWiV</a><span style="background-color: white; line-height: 34px; white-space: pre-wrap;"> 18th May!" Livestream link here: </span><span style="line-height: 34px; white-space: pre-wrap;">https://www.facebook.com/thisweekinvirology/app_142371818162</span></span><br />
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<span style="font-family: Arial, Helvetica, sans-serif;"><span style="line-height: 34px; white-space: pre-wrap;">Two new anti Hepatitis C virus drugs reach the market this year sparking any to question if HCV will be completely controllable. Here's a nice rundown on the drugs and their costs: http://www.theglobeandmail.com/life/health-and-fitness/health/the-cure-for-hepatitis-c-is-upon-us-but-at-a-costly-penny/article18224668/</span></span><br />
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<span style="font-family: Arial, Helvetica, sans-serif;"><span style="line-height: 34px; white-space: pre-wrap;">The first case of MERS in the US was spotted in the last two weeks </span><span style="background-color: white; line-height: 34px; white-space: pre-wrap;">First </span><a class="twitter-hashtag pretty-link js-nav" data-query-source="hashtag_click" dir="ltr" href="https://twitter.com/search?q=%23MERS&src=hash" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;">#MERS</a><span style="background-color: white; line-height: 34px; white-space: pre-wrap;"> case in the U.S.: Patient traveled from KSA to Chicago, then took a bus to Indiana </span><span class="tco-ellipsis" style="background-color: white; line-height: 34px; white-space: pre-wrap;"></span><a class="twitter-timeline-link" data-expanded-url="http://www.cdc.gov/media/releases/2014/p0502-US-MERS.html" dir="ltr" href="http://t.co/O61xlvIGsS" rel="nofollow" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;" target="_blank" title="http://www.cdc.gov/media/releases/2014/p0502-US-MERS.html"><span class="invisible" style="background-color: white; line-height: 0; text-decoration: none; white-space: pre-wrap;">http://www.</span><span class="js-display-url" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;">cdc.gov/media/releases</span><span class="invisible" style="background-color: white; line-height: 0; text-decoration: none; white-space: pre-wrap;">/2014/p0502-US-MERS.html</span><span class="tco-ellipsis" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;"><span class="invisible" style="line-height: 0;"> </span>…</span></a> expect this kind of story to continue to appear. Looks like no real evidence of spread of disease but have to wait until incubation period has ran its course. </span><br />
<span style="font-family: Arial, Helvetica, sans-serif;">science. For more info on MERS, specifically testing and the apparent increase in cases, read this interview with Christian Drosten, virologist-extraordinaire. <span style="background-color: white; line-height: 34px; white-space: pre-wrap;">MT </span><a class="twitter-atreply pretty-link" dir="ltr" href="https://twitter.com/profvrr" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;">@profvrr</a><span style="background-color: white; line-height: 34px; white-space: pre-wrap;">: Great interview with Christian Drosten on </span><a class="twitter-hashtag pretty-link js-nav" data-query-source="hashtag_click" dir="ltr" href="https://twitter.com/search?q=%23MERS&src=hash" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;">#MERS</a><span style="background-color: white; line-height: 34px; white-space: pre-wrap;"> </span><a class="twitter-timeline-link" data-expanded-url="http://bit.ly/1hvGQs6" dir="ltr" href="http://t.co/WDVu2jTARh" rel="nofollow" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;" target="_blank" title="http://bit.ly/1hvGQs6"><span class="tco-ellipsis"></span><span class="invisible" style="line-height: 0;">http://</span><span class="js-display-url">bit.ly/1hvGQs6</span></a></span><br />
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<span style="font-family: Arial, Helvetica, sans-serif;">Another coronavirus that hasn't had as much interest in comparison to MERS but should: <span style="background-color: white; line-height: 34px; white-space: pre-wrap;">Concerns grow over deadly pig virus. Would be great if coronaviruses would just stop... </span><span class="tco-ellipsis" style="background-color: white; line-height: 34px; white-space: pre-wrap;"></span><a class="twitter-timeline-link" data-expanded-url="http://www.bbc.co.uk/news/science-environment-27256466" dir="ltr" href="http://t.co/8qor5B0zjq" rel="nofollow" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;" target="_blank" title="http://www.bbc.co.uk/news/science-environment-27256466"><span class="invisible" style="background-color: white; line-height: 0; text-decoration: none; white-space: pre-wrap;">http://www.</span><span class="js-display-url" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;">bbc.co.uk/news/science-e</span><span class="invisible" style="background-color: white; line-height: 0; text-decoration: none; white-space: pre-wrap;">nvironment-27256466</span><span class="tco-ellipsis" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;"><span class="invisible" style="line-height: 0;"> </span>…</span></a> devastating to pigs and the economy. No risk to humans though.</span><br />
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<span style="font-family: Arial, Helvetica, sans-serif;">This week, Boston City council announced their backing for the opening of the category 4 National Emerging infectious disease laboratory (NEIDL). <a class="twitter-hashtag pretty-link js-nav" data-query-source="hashtag_click" dir="ltr" href="https://twitter.com/search?q=%23NEIDL&src=hash" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;">#NEIDL</a><span style="background-color: white; line-height: 34px; white-space: pre-wrap;"> update: ordnance defeated, vote was 5 for ban, 8 against </span></span><br />
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<span style="font-family: Arial, Helvetica, sans-serif;"><span style="background-color: white; line-height: 34px; white-space: pre-wrap;">Some lovely imaging work on Nipah virus transport of structural glycoproteins within neurons: </span><span style="background-color: white; line-height: 34px; white-space: pre-wrap;">live cell imaging of nipah virus glycoprotein transport in neuronal cells </span><a class="twitter-timeline-link" data-expanded-url="http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1004107" dir="ltr" href="http://t.co/WiLUhi9T5E" rel="nofollow" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;" target="_blank" title="http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1004107"><span class="tco-ellipsis"></span><span class="invisible" style="line-height: 0;">http://www.</span><span class="js-display-url">plospathogens.org/article/info%3</span><span class="invisible" style="line-height: 0;">Adoi%2F10.1371%2Fjournal.ppat.1004107</span><span class="tco-ellipsis"><span class="invisible" style="line-height: 0;"> </span>…</span></a><span style="background-color: white; line-height: 34px; white-space: pre-wrap;"> fascinating</span></span><br />
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<b><span style="font-family: Arial, Helvetica, sans-serif;">Science</span></b><br />
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<span style="font-family: Arial, Helvetica, sans-serif;">Pfizer/Astrazeneca deal breaking continues to go on but what effect will it have on UK R&D? <span style="line-height: 34px; white-space: pre-wrap;">Pfizer and AstraZeneca "The Wyeth deal alone saw Pfizer scrap 19,000 staffers". </span><a class="twitter-timeline-link" data-expanded-url="http://www.theguardian.com/business/2014/apr/28/pfizer-astrazeneca-takeover-bad-news-uk-research?CMP=twt_fd" dir="ltr" href="http://t.co/jxrd5oMdqo" rel="nofollow" style="line-height: 34px; text-decoration: none; white-space: pre-wrap;" target="_blank" title="http://www.theguardian.com/business/2014/apr/28/pfizer-astrazeneca-takeover-bad-news-uk-research?CMP=twt_fd"><span class="tco-ellipsis"></span><span class="invisible" style="line-height: 0;">http://www.</span><span class="js-display-url">theguardian.com/business/2014/</span><span class="invisible" style="line-height: 0;">apr/28/pfizer-astrazeneca-takeover-bad-news-uk-research?CMP=twt_fd</span><span class="tco-ellipsis"><span class="invisible" style="line-height: 0;"> </span>…</span></a><span style="line-height: 34px; white-space: pre-wrap;"> </span></span><br />
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<span style="font-family: Arial, Helvetica, sans-serif;"><br /><ul class="tweet-actions js-actions" style="display: inline-block; list-style: none; margin: 9px 0px 0px; padding: 0px;">and an ex UK soldier sues the Ministry of Defense over vaccine-induced disease </ul>
<br /><span style="background-color: white; line-height: 34px; white-space: pre-wrap;">Ex-soldier takes on MoD over vaccine. Gulf war syndrome </span><a class="twitter-timeline-link" data-expanded-url="http://www.bbc.co.uk/news/uk-27259202" dir="ltr" href="http://t.co/U5gYLx4B2t" rel="nofollow" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;" target="_blank" title="http://www.bbc.co.uk/news/uk-27259202"><span class="tco-ellipsis"></span><span class="invisible" style="line-height: 0;">http://www.</span><span class="js-display-url">bbc.co.uk/news/uk-272592</span><span class="invisible" style="line-height: 0;">02</span><span class="tco-ellipsis"><span class="invisible" style="line-height: 0;"> </span>…</span></a></span><div class="stream-item-footer" style="line-height: 18px; padding-top: 3px;">
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<span style="font-family: Arial, Helvetica, sans-serif;">Two vaccine stories this week: Do newer vaccine overwhelm the developing immune system? <span style="line-height: 34px; white-space: pre-wrap;">Debunking an anti-vaccine claim: Giving so many vaccines overwhelms a child's immune system </span><a class="twitter-timeline-link" data-expanded-url="http://bit.ly/Q0c3fq" dir="ltr" href="http://t.co/56D0tbdkso" rel="nofollow" style="line-height: 34px; text-decoration: none; white-space: pre-wrap;" target="_blank" title="http://bit.ly/Q0c3fq"><span class="tco-ellipsis"></span><span class="invisible" style="line-height: 0;">http://</span><span class="js-display-url">bit.ly/Q0c3fq</span><span class="invisible" style="line-height: 0;"></span><span class="tco-ellipsis"><span class="invisible" style="line-height: 0;"> </span></span></a><span style="line-height: 34px; white-space: pre-wrap;"> </span><a class="twitter-timeline-link" data-pre-embedded="true" dir="ltr" href="http://t.co/kXsHjRe304" style="line-height: 34px; text-decoration: none; white-space: pre-wrap;">pic.twitter.com/kXsHjRe304</a></span><br />
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<span style="font-family: Arial, Helvetica, sans-serif;">The Glasgow Science Festival is coming up, check out here for information http://glasgowsciencefestival.org.uk/ . come and see me there!</span><br />
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<span style="font-family: Arial, Helvetica, sans-serif;">Sleep deprivation for personal/work gain. Where did it come from? <span style="background-color: white; line-height: 34px; white-space: pre-wrap;">Thomas Edison and the Cult of Sleep Deprivation </span><a class="twitter-timeline-link" data-expanded-url="http://pocket.co/sHnm5" dir="ltr" href="http://t.co/zkeNIZJSMM" rel="nofollow" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;" target="_blank" title="http://pocket.co/sHnm5"><span class="tco-ellipsis"></span><span class="invisible" style="line-height: 0;">http://</span><span class="js-display-url">pocket.co/sHnm5</span><span class="invisible" style="line-height: 0;"></span><span class="tco-ellipsis"><span class="invisible" style="line-height: 0;"> </span></span></a></span><br />
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<b><span style="font-family: Arial, Helvetica, sans-serif;">homebrew</span></b><br />
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<span style="font-family: Arial, Helvetica, sans-serif;">here's where I tried to make a porter/stout homebrew. It turned out OK.<a class="twitter-timeline-link" data-expanded-url="http://apostdocinvirology.blogspot.co.uk/2014/04/porter-take-1.html" dir="ltr" href="http://t.co/3rAzjVvsJ8" rel="nofollow" style="text-decoration: none;" target="_blank" title="http://apostdocinvirology.blogspot.co.uk/2014/04/porter-take-1.html"><span class="invisible" style="line-height: 0;">http://</span><span class="js-display-url">apostdocinvirology.blogspot.co.uk/2014/04/porter</span><span class="invisible" style="line-height: 0;">-take-1.html</span><span class="tco-ellipsis"><span class="invisible" style="line-height: 0;"> </span>…</span></a></span></div>
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<b><span style="font-family: Arial, Helvetica, sans-serif;">life</span></b><br />
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<span style="font-family: Arial, Helvetica, sans-serif;">One week ago I passed my Ph.D. viva, ending 3.5 years of supervision from Paul Duprex and Bert Rima. Thanks guys!</span>Connor Bhttp://www.blogger.com/profile/08132413724023944783noreply@blogger.com0tag:blogger.com,1999:blog-2119806190550686323.post-21441183988972397242014-04-27T10:04:00.001-07:002014-04-27T10:04:22.567-07:00porter take 1<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj29Aw1QVyXVqqlGfj4zuRuzRjXor2qhNrzHBlEnTyytJ98gOCincY6Am42ctWHtnKYNpjeAQ-YhF5bylaUnZf0pLHYZRDGTmBGqUIaNCnra5hE38Y5r4a0IOSjoIRXsYnXWjNMA3CRwYr3/s1600/2014-04-19+21.05.42.jpg" imageanchor="1" style="clear: right; float: right; margin-bottom: 1em; margin-left: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj29Aw1QVyXVqqlGfj4zuRuzRjXor2qhNrzHBlEnTyytJ98gOCincY6Am42ctWHtnKYNpjeAQ-YhF5bylaUnZf0pLHYZRDGTmBGqUIaNCnra5hE38Y5r4a0IOSjoIRXsYnXWjNMA3CRwYr3/s1600/2014-04-19+21.05.42.jpg" height="320" width="240" /></a>Doing science all day and talking about science in this blog can get a bit repetitive. But luckily I have a hobby to rest my mind, which takes the form of homebrewing beer (only on extract at the minute). I dabbled a bit before and am now continuing to dabble after my move to Glasgow. My first 'new' homebrew experience is making a porter-like beer (maybe on the 'robust' side), which in my head was a 'less-smooth' stout. You can read the exact description <a href="http://www.bjcp.org/2008styles/style12.php">here</a>. This was actually brewed for a friend of mine's birthday in April..<br />
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Below is the recipe I followed: and results.<br />
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<table style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px; width: 85%px;"><tbody>
<tr align="left"><th colspan="2"><b>Basic Information</b></th></tr>
<tr><td style="margin: 0px;">Batch Name:</td><td style="margin: 0px;">porter1</td></tr>
<tr><td style="margin: 0px;">Brewed By:</td><td style="margin: 0px;">Connor</td></tr>
<tr><td style="margin: 0px;">Style:</td><td style="margin: 0px;">Robust Porter</td></tr>
<tr><td style="margin: 0px;">Batch Size:</td><td style="margin: 0px;">4.50 L</td></tr>
<tr><td style="margin: 0px;">Boil Time:</td><td style="margin: 0px;">45 min</td></tr>
<tr><td style="margin: 0px;">Initial Boil Volume:</td><td style="margin: 0px;">4.5 L</td></tr>
<tr><td style="margin: 0px;">Mash Method:</td><td style="margin: 0px;">Steeped Grains and extract</td></tr>
<tr><td style="margin: 0px;">Brew Date:</td><td style="margin: 0px;">1/22/14</td></tr>
<tr><td style="margin: 0px;">My Rating:</td><td style="margin: 0px;">5/10 (being harsh)</td></tr>
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<tr align="left"><th colspan="2"><b>Typical Style Characteristics</b></th></tr>
<tr><td style="margin: 0px;">Style:</td><td style="margin: 0px;">'Robust Porter'</td></tr>
<tr><td style="margin: 0px;">O.G.</td><td style="margin: 0px;">1.048 - 1.065</td></tr>
<tr><td style="margin: 0px;">F.G.</td><td style="margin: 0px;">1.012 - 1.016</td></tr>
<tr><td style="margin: 0px;">ABV</td><td style="margin: 0px;">4.8 - 6.5</td></tr>
<tr><td style="margin: 0px;">IBU</td><td style="margin: 0px;">25 - 50</td></tr>
<tr><td style="margin: 0px;">SRM</td><td style="margin: 0px;">22 - 35°L</td></tr>
<tr><td style="margin: 0px;">Color dark black/ruby?</td><td style="margin: 0px;"><table style="width: 5%px;"><tbody>
<tr><td style="background-color: #43260c; margin: 0px;" width="10%"></td><td style="background-color: #080302; margin: 0px;" width="10%"></td></tr>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiXVPUu4cVAZE-pc66B1088MGP9idjZjU6t2R2fk67oImBk-POeOoU4VOhoaq7-S_bpZXlZ09CNT5uFCUOOYAIwCQ_ApCr9L8IoSHm3FLl2YlqVPo22hVTFWM9Vqjwf6O4y-nRdD83PeiA-/s1600/2014-03-23+20.55.10.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiXVPUu4cVAZE-pc66B1088MGP9idjZjU6t2R2fk67oImBk-POeOoU4VOhoaq7-S_bpZXlZ09CNT5uFCUOOYAIwCQ_ApCr9L8IoSHm3FLl2YlqVPo22hVTFWM9Vqjwf6O4y-nRdD83PeiA-/s1600/2014-03-23+20.55.10.jpg" height="320" width="240" /></a><br style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;" /><table style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px; width: 85%px;"><colgroup><col width="25%"></col><col width="85%"></col></colgroup><tbody>
<tr align="left"><th colspan="2"><b>Calculated & Measured Statistics</b></th></tr>
<tr><td style="margin: 0px;">Calculated O.G.</td><td style="margin: 0px;">1.067 (75% Efficiency)</td></tr>
<tr><td style="margin: 0px;">Calculated F.G.</td><td style="margin: 0px;">1.026 (65% Yeast Attenuation)</td></tr>
<tr><td style="margin: 0px;">Measured O.G.</td><td style="margin: 0px;">1.074 (inf% Actual Efficiency)</td></tr>
<tr><td style="margin: 0px;">Measured F.G.</td><td style="margin: 0px;">1.020 (73% Actual Attenuation)</td></tr>
<tr><td style="margin: 0px;">ABV</td><td style="margin: 0px;">7.5%</td></tr>
<tr><td style="margin: 0px;">IBU</td><td style="margin: 0px;">57.2</td></tr>
<tr><td style="margin: 0px;">SRM</td><td style="margin: 0px;">29.3°L</td></tr>
<tr><td style="margin: 0px;">Color - dark, can see ruby when light shone through it. But pretty opaque. </td><td style="margin: 0px;"><table style="width: 5%px;"><tbody>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhsst0dHc_0CvbO2CO1iercYjg6D5hlgHrInBZZC35AmQYrScmfx0363FV6xvVQyCOyRoT4Quv_3gz_Aj6uA4Ik9_azRlxGsRVBMhzwlqGvfVJeJsw1MrHb5_mKf0__btppeGIunnAzpO9L/s1600/2014-03-24+20.34.49.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhsst0dHc_0CvbO2CO1iercYjg6D5hlgHrInBZZC35AmQYrScmfx0363FV6xvVQyCOyRoT4Quv_3gz_Aj6uA4Ik9_azRlxGsRVBMhzwlqGvfVJeJsw1MrHb5_mKf0__btppeGIunnAzpO9L/s1600/2014-03-24+20.34.49.jpg" height="320" width="240" /></a><br style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;" /><table style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px; width: 85%px;"><colgroup><col width="40%"></col><col width="15%"></col><col width="10%"></col><col width="10%"></col><col width="25%"></col></colgroup><tbody>
<tr align="left"><th colspan="5"><b>Malt Bill</b></th></tr>
<tr><td style="margin: 0px;">Malt Name</td><td style="margin: 0px;">Weight</td><td style="margin: 0px;">PPG</td><td style="margin: 0px;">SRM</td><td style="margin: 0px;">Type</td></tr>
<tr><td style="margin: 0px;">Light Dry Extract</td><td style="margin: 0px;">0.75 kg</td><td style="margin: 0px;">1.044</td><td style="margin: 0px;">8.00</td><td style="margin: 0px;">Extract/Adjunct</td></tr>
<tr><td style="margin: 0px;">Chocolate Malt - 350°L</td><td style="margin: 0px;">0.10 kg</td><td style="margin: 0px;">1.028</td><td style="margin: 0px;">350.00</td><td style="margin: 0px;">Steeped Grain</td></tr>
<tr><td style="margin: 0px;">Barley, Flaked</td><td style="margin: 0px;">0.06 kg</td><td style="margin: 0px;">1.032</td><td style="margin: 0px;">2.00</td><td style="margin: 0px;">Steeped Grain</td></tr>
<tr><td style="margin: 0px;">Caramel/Crystal Malt - 10L</td><td style="margin: 0px;">0.03 kg</td><td style="margin: 0px;">1.035</td><td style="margin: 0px;">10.00</td><td style="margin: 0px;">Steeped Grain</td></tr>
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<tr align="left"><th colspan="5"><b>Mash Rest Profile</b></th></tr>
<tr><td style="margin: 0px;">Rest</td><td style="margin: 0px;">Temperature</td><td style="margin: 0px;">Time</td><td style="margin: 0px;">Type</td><td style="margin: 0px;">Details</td></tr>
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<tr align="left"><th colspan="5"><b>Hop Bill</b></th></tr>
<tr><td style="margin: 0px;">Hop Name</td><td style="margin: 0px;">Time Added</td><td style="margin: 0px;">Weight</td><td style="margin: 0px;">AA%</td><td style="margin: 0px;">Type</td></tr>
<tr><td style="margin: 0px;">Northern Brewer (U.K.)</td><td style="margin: 0px;">30 min</td><td style="margin: 0px;">20.00 g</td><td style="margin: 0px;">9.0%</td><td style="margin: 0px;">Leaf Hop</td></tr>
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<tr align="left"><th colspan="5"><b>Yeast Details</b></th></tr>
<tr><td style="margin: 0px;">Yeast Strand</td><td style="margin: 0px;">Quantity</td><td style="margin: 0px;">Attenuation</td><td style="margin: 0px;">Flocculation</td></tr>
<tr><td style="margin: 0px;">Safale British ale yeast. </td><td style="margin: 0px;">3x10_9</td><td style="margin: 0px;">75</td><td style="margin: 0px;">High</td></tr>
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<br style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px;" /><table style="background-color: white; color: #222222; font-family: arial, sans-serif; font-size: 13px; width: 85%px;"><colgroup><col width="25%"></col><col width="20%"></col><col width="55%"></col></colgroup><tbody>
<tr align="left"><th colspan="3"><b>Dates</b></th></tr>
<tr><td style="margin: 0px;"></td><td style="margin: 0px;">Cooking</td><td style="margin: 0px;"></td></tr>
<tr><td style="margin: 0px;">1/22/14</td><td style="margin: 0px;">Brew Date</td><td style="margin: 0px;"></td></tr>
<tr><td style="margin: 0px;">3/30/14</td><td style="margin: 0px;">Bottle</td><td style="margin: 0px;"></td></tr>
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<tr align="left"><td style="margin: 0px;"><b>Notes</b><br />I measured the OG with a refractometer, which gave a reading of 18 brix making it an OG of 1.074. Not far off what was expected but (stupidly) over what is recommended by the 'regulations' on a porter. This might explain some of the 'sweeter' characteristics I get when tasted (see below). </td></tr>
<tr><td style="margin: 0px;"><br />I actually did a 45 minute boil, adding the hops at 30 minutes.<br /><br />I used half the yeast pack with no reconstitution. (should have made a starter). After three weeks in primary at 18-20 degrees C (room measured at 18 but fermenter likely higher?). The brx value was 11, meaning an FG of 1.020 (attenuation of 73%). This level of attenuation is on target of this yeast strain. However, this probably resulted in the inherent 'sweetness' of the beer. This also left the ABV at about 7% (it tastes like it too). To give a low level of carbonation I added 18g dextran to it prior to bottling. Bottles were left for at least 1 - 2 weeks. Many more being left longer.<br /><br />At Week 1. Flat. No head. Little yeast at bottom.<br />Caramel aroma.<br /><br />Taste. Initial. Flat. Mild sweet. Malty.<br /><br />Residual. Bitter chocolate. Hoppy.<br /><br />Mouthfeel. Medium dry. Low in body.<br /><br />Alcohol. Can tell it.<br /><br />Best to gulp.<br /><br />At week 2. Much the same, sweetness appears more and obviously more carbonated but no head still.<br /><br />For next time I would make it less sweet and carbonate it more but would like more body and head. How is this possible? Could incorporate bitter flavors: coffee? cocoa powder to round off the flavour. I also think a better yeast start wouldn't go amiss to bring the FG down. </td></tr>
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Connor Bhttp://www.blogger.com/profile/08132413724023944783noreply@blogger.com0tag:blogger.com,1999:blog-2119806190550686323.post-49135522641974146012014-04-27T08:58:00.001-07:002014-04-27T08:58:35.692-07:00Virology, science, scicomm and life <span style="color: #444444; font-family: Arial, Helvetica, sans-serif;"><b>Virology</b></span><br />
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<span style="color: #444444; font-family: Arial, Helvetica, sans-serif;">Vincent Racaniello posts an intrigueing question over at Virology blog and debate ensures. What are your thoughts? <span style="background-color: white; line-height: 34px; white-space: pre-wrap;">why do some viruses have a segmented genome? </span><a class="twitter-timeline-link" data-expanded-url="http://www.virology.ws/2014/04/22/virology-question-of-the-week-why-a-segmented-viral-genome/" dir="ltr" href="http://t.co/x6uOV8biZd" rel="nofollow" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;" target="_blank" title="http://www.virology.ws/2014/04/22/virology-question-of-the-week-why-a-segmented-viral-genome/"><span class="tco-ellipsis"></span><span class="invisible" style="line-height: 0;">http://www.</span><span class="js-display-url">virology.ws/2014/04/22/vir</span><span class="invisible" style="line-height: 0;">ology-question-of-the-week-why-a-segmented-viral-genome/</span><span class="tco-ellipsis"><span class="invisible" style="line-height: 0;"> </span>…</span></a><span style="background-color: white; line-height: 34px; white-space: pre-wrap;"> measles versus influenza</span></span><br />
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<span style="color: #444444; font-family: Arial, Helvetica, sans-serif;"><span style="background-color: white; line-height: 34px; white-space: pre-wrap;">A recent study published in the lancet looked at what viruses might be causing CNS disease in African malaria-endemic regions </span><a class="twitter-timeline-link" data-expanded-url="http://www.thelancet.com/pdfs/journals/langlo/PIIS2214109X13700603.pdf" dir="ltr" href="http://t.co/D5bJu5M1WV" rel="nofollow" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;" target="_blank" title="http://www.thelancet.com/pdfs/journals/langlo/PIIS2214109X13700603.pdf"><span class="invisible" style="line-height: 0;">http://www.</span><span class="js-display-url">thelancet.com/pdfs/journals/</span><span class="invisible" style="line-height: 0;">langlo/PIIS2214109X13700603.pdf</span><span class="tco-ellipsis"><span class="invisible" style="line-height: 0;"> </span>…</span></a><span style="background-color: white; line-height: 34px; white-space: pre-wrap;"> not big surprise that mumps virus appeared to be a big cause (also lethal) - no mumps vaccination there. But </span><span style="background-color: white; line-height: 34px; white-space: pre-wrap;">major result of this paper </span><span style="background-color: white; line-height: 34px; white-space: pre-wrap;">is that in >2/3s patients we have no idea what caused disease. Unkn</span><span style="background-color: white; line-height: 34px; white-space: pre-wrap;">own viruses anyone?</span></span><br />
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<span style="color: #444444; font-family: Arial, Helvetica, sans-serif;"><span style="background-color: white; line-height: 34px; white-space: pre-wrap;">"</span><a class="twitter-atreply pretty-link" dir="ltr" href="https://twitter.com/hannanorsted" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;">@hannanorsted</a><span style="background-color: white; line-height: 34px; white-space: pre-wrap;">: For those interested in innate immunity, read this article: </span><a class="twitter-timeline-link" data-expanded-url="http://bit.ly/1ro0jl0" dir="ltr" href="http://t.co/URQ1KdlYhk" rel="nofollow" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;" target="_blank" title="http://bit.ly/1ro0jl0"><span class="tco-ellipsis"></span><span class="invisible" style="line-height: 0;">http://</span><span class="js-display-url">bit.ly/1ro0jl0</span><span class="invisible" style="line-height: 0;"></span><span class="tco-ellipsis"><span class="invisible" style="line-height: 0;"> </span></span></a><span style="background-color: white; line-height: 34px; white-space: pre-wrap;"> </span><a class="twitter-atreply pretty-link" dir="ltr" href="https://twitter.com/PLOSPathogens" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;">@PLOSPathogens</a><span style="background-color: white; line-height: 34px; white-space: pre-wrap;">" and </span><a class="twitter-hashtag pretty-link js-nav" data-query-source="hashtag_click" dir="ltr" href="https://twitter.com/search?q=%23measles&src=hash" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;">#measles</a><span style="background-color: white; line-height: 34px; white-space: pre-wrap;"> virus! This paper looked at what RNA sequences were being recognised in measles virus-infected cells. Showed bias towards A/U-rich regions of the L gene mRNA. </span></span><br />
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<span style="color: #444444; font-family: Arial, Helvetica, sans-serif;"><span style="background-color: white; line-height: 34px; white-space: pre-wrap;">PLoS published a </span><span style="line-height: 34px; white-space: pre-wrap;">nice short look at RSV pathogenesis and potential for vaccine design </span><a class="twitter-timeline-link" data-expanded-url="http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1004016" dir="ltr" href="http://t.co/ELeslr53s7" rel="nofollow" style="line-height: 34px; text-decoration: none; white-space: pre-wrap;" target="_blank" title="http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1004016"><span class="tco-ellipsis"></span><span class="invisible" style="line-height: 0;">http://www.</span><span class="js-display-url">plospathogens.org/article/info%3</span><span class="invisible" style="line-height: 0;">Adoi%2F10.1371%2Fjournal.ppat.1004016</span><span class="tco-ellipsis"><span class="invisible" style="line-height: 0;"> </span>…</span></a><span style="line-height: 34px; white-space: pre-wrap;"> highlighting many of the issues with RSV regions but also showed where research could lead to, including new vaccines.</span></span><br />
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<span style="color: #444444; font-family: Arial, Helvetica, sans-serif;"><span style="line-height: 34px; white-space: pre-wrap;">GAVI outlined </span><span style="background-color: white; line-height: 34px; white-space: pre-wrap;">their plans to expand impact of vaccines by 2020 </span><span class="tco-ellipsis" style="background-color: white; line-height: 34px; white-space: pre-wrap;"></span><a class="twitter-timeline-link" data-expanded-url="http://pocket.co/sVDgY" dir="ltr" href="http://t.co/2Ouginb9d3" rel="nofollow" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;" target="_blank" title="http://pocket.co/sVDgY"><span class="invisible" style="background-color: white; line-height: 0; text-decoration: none; white-space: pre-wrap;">http://</span><span class="js-display-url" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;">pocket.co/sVDgY</span><span class="invisible" style="background-color: white; line-height: 0; white-space: pre-wrap;"></span><span class="tco-ellipsis" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;"><span class="invisible" style="line-height: 0;"> </span></span></a></span><br />
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<span style="color: #444444; font-family: Arial, Helvetica, sans-serif;">More infographics. <span style="background-color: white; line-height: 34px; white-space: pre-wrap;">Measles infographics. I like these but think asymptomatic cases change it </span><span class="tco-ellipsis" style="background-color: white; line-height: 34px; white-space: pre-wrap;"></span><a class="twitter-timeline-link" data-expanded-url="http://pocket.co/sVDgi" dir="ltr" href="http://t.co/xtJV2w636J" rel="nofollow" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;" target="_blank" title="http://pocket.co/sVDgi"><span class="invisible" style="background-color: white; line-height: 0; text-decoration: none; white-space: pre-wrap;">http://</span><span class="js-display-url" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;">pocket.co/sVDgi</span><span class="invisible" style="background-color: white; line-height: 0; white-space: pre-wrap;"></span><span class="tco-ellipsis" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;"><span class="invisible" style="line-height: 0;"> </span></span></a> I wouldlike more complicated infographics..</span><br />
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<span style="color: #444444; font-family: Arial, Helvetica, sans-serif;"><span style="background-color: white; line-height: 34px; white-space: pre-wrap;">China and the SARS Epidemic, what was learned in ten years? Applicable to SA and MERS situation </span><span class="tco-ellipsis" style="background-color: white; line-height: 34px; white-space: pre-wrap;"></span><a class="twitter-timeline-link" data-expanded-url="http://pocket.co/sVD5l" dir="ltr" href="http://t.co/uLaW0P7sLl" rel="nofollow" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;" target="_blank" title="http://pocket.co/sVD5l"><span class="invisible" style="background-color: white; line-height: 0; text-decoration: none; white-space: pre-wrap;">http://</span><span class="js-display-url" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;">pocket.co/sVD5l</span><span class="invisible" style="background-color: white; line-height: 0; white-space: pre-wrap;"></span><span class="tco-ellipsis" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;"><span class="invisible" style="line-height: 0;"> </span></span></a> An important history lesson if the Saudi Health Ministry are reading. But then there are also science issues: <span style="line-height: 34px; white-space: pre-wrap;">Why can't we predict evolution of MERS? Poor understanding of virus fitness. What constraints are acting? </span><span class="tco-ellipsis" style="line-height: 34px; white-space: pre-wrap;"></span><a class="twitter-timeline-link" data-expanded-url="http://www.winnipegfreepress.com/world/mers-virus-hasnt-changed-not-reason-for-surge-in-saudi-cases-expert-256852541.html?device=mobile" dir="ltr" href="http://t.co/vCSvV7tfhK" rel="nofollow" style="line-height: 34px; text-decoration: none; white-space: pre-wrap;" target="_blank" title="http://www.winnipegfreepress.com/world/mers-virus-hasnt-changed-not-reason-for-surge-in-saudi-cases-expert-256852541.html?device=mobile"><span class="invisible" style="line-height: 0; text-decoration: none; white-space: pre-wrap;">http://www.</span><span class="js-display-url" style="line-height: 34px; text-decoration: none; white-space: pre-wrap;">winnipegfreepress.com/world/mers-vir</span><span class="invisible" style="line-height: 0; text-decoration: none; white-space: pre-wrap;">us-hasnt-changed-not-reason-for-surge-in-saudi-cases-expert-256852541.html?device=mobile</span><span class="tco-ellipsis" style="line-height: 34px; text-decoration: none; white-space: pre-wrap;"><span class="invisible" style="line-height: 0;"> </span>…</span></a></span><br />
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<span style="color: #444444; font-family: Arial, Helvetica, sans-serif;"><span style="background-color: white;"><span style="line-height: 34px; white-space: pre-wrap;">'Don’t worry, I’m not contagious' – and other microbiological delusions are discussed in this insightful piece</span> </span><span class="tco-ellipsis" style="background-color: white; line-height: 34px; white-space: pre-wrap;"></span><a class="twitter-timeline-link" data-expanded-url="http://pocket.co/sVDV5" dir="ltr" href="http://t.co/6kXfx8oy4i" rel="nofollow" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;" target="_blank" title="http://pocket.co/sVDV5"><span class="invisible" style="background-color: white; line-height: 0; text-decoration: none; white-space: pre-wrap;">http://</span><span class="js-display-url" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;">pocket.co/sVDV5</span><span class="invisible" style="background-color: white; line-height: 0; white-space: pre-wrap;"></span><span class="tco-ellipsis" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;"><span class="invisible" style="line-height: 0;"> </span></span></a></span><br />
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<span style="color: #444444; font-family: Arial, Helvetica, sans-serif;"><span style="background-color: white; line-height: 34px; white-space: pre-wrap;">it's about the little things - new virology blog. I follow the author but can't remember who... Help? </span><span class="tco-ellipsis" style="background-color: white; line-height: 34px; white-space: pre-wrap;"></span><a class="twitter-timeline-link" data-expanded-url="http://pocket.co/sVDcJ" dir="ltr" href="http://t.co/pzYxVHPFah" rel="nofollow" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;" target="_blank" title="http://pocket.co/sVDcJ"><span class="invisible" style="background-color: white; line-height: 0; text-decoration: none; white-space: pre-wrap;">http://</span><span class="js-display-url" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;">pocket.co/sVDcJ</span><span class="invisible" style="background-color: white; line-height: 0; white-space: pre-wrap;"></span><span class="tco-ellipsis" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;"><span class="invisible" style="line-height: 0;"> </span></span></a> Turns out it was Mike Nicholl. Go read it. It's very good. </span><br />
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<span style="color: #444444; font-family: Arial, Helvetica, sans-serif;">For some reason I got interested n fruit bats and the Niger river in west Africa... <span style="background-color: white; line-height: 34px; white-space: pre-wrap;">Fruit bat annual migrations in west Africa re seasons </span><span class="tco-ellipsis" style="background-color: white; line-height: 34px; white-space: pre-wrap;"></span><a class="twitter-timeline-link" data-expanded-url="http://www.nrcresearchpress.com/doi/abs/10.1139/z83-299" dir="ltr" href="http://t.co/ciJYh54ao7" rel="nofollow" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;" target="_blank" title="http://www.nrcresearchpress.com/doi/abs/10.1139/z83-299"><span class="invisible" style="background-color: white; line-height: 0; text-decoration: none; white-space: pre-wrap;">http://www.</span><span class="js-display-url" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;">nrcresearchpress.com/doi/abs/10.113</span><span class="invisible" style="background-color: white; line-height: 0; text-decoration: none; white-space: pre-wrap;">9/z83-299</span><span class="tco-ellipsis" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;"><span class="invisible" style="line-height: 0;"> </span>…</span></a> <span style="background-color: white; line-height: 34px; white-space: pre-wrap;">What links west Africa? The Niger River of course. </span><a class="twitter-timeline-link" data-expanded-url="http://geography.howstuffworks.com/africa/the-niger-river.htm" dir="ltr" href="http://t.co/gdKGYK83LX" rel="nofollow" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;" target="_blank" title="http://geography.howstuffworks.com/africa/the-niger-river.htm"><span class="tco-ellipsis"></span><span class="invisible" style="line-height: 0;">http://</span><span class="js-display-url">geography.howstuffworks.com/africa/the-nig</span><span class="invisible" style="line-height: 0;">er-river.htm</span><span class="tco-ellipsis"><span class="invisible" style="line-height: 0;"> </span>…</span></a></span><br />
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<span style="color: #444444; font-family: Arial, Helvetica, sans-serif;"><b>Other science</b></span><br />
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<span style="color: #444444; font-family: Arial, Helvetica, sans-serif;">The Independant reported </span><span style="background-color: white; color: #444444; font-family: Arial, Helvetica, sans-serif; line-height: 34px; white-space: pre-wrap;">How a genetic disease was cured in an adult for the first time </span><a class="twitter-timeline-link" data-expanded-url="http://ind.pn/1iEBJtk" dir="ltr" href="http://t.co/HtCjHElkWz" rel="nofollow" style="background-color: white; font-family: Arial, Helvetica, sans-serif; line-height: 34px; text-decoration: none; white-space: pre-wrap;" target="_blank" title="http://ind.pn/1iEBJtk"><span class="tco-ellipsis"></span><span class="invisible" style="line-height: 0;">http://</span><span class="js-display-url">ind.pn/1iEBJtk</span><span class="invisible" style="line-height: 0;"></span><span class="tco-ellipsis"><span class="invisible" style="line-height: 0;"> </span></span></a><span style="background-color: white; color: #444444; font-family: Arial, Helvetica, sans-serif; line-height: 34px; white-space: pre-wrap;"> thi was using CRISPR/Cas9 technology. This was also done using adult MICE and high-powered injections.</span><br />
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<span style="color: #444444; font-family: Arial, Helvetica, sans-serif;"><b>scicomm</b></span><br />
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<span style="color: #444444; font-family: Arial, Helvetica, sans-serif;"><span style="background-color: white; line-height: 34px; white-space: pre-wrap;">The varieties of peer review: </span><a class="twitter-timeline-link" data-expanded-url="http://neurodojo.blogspot.co.uk/2014/04/the-varieties-of-peer-review.html" dir="ltr" href="http://t.co/fmm4KgBv9h" rel="nofollow" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;" target="_blank" title="http://neurodojo.blogspot.co.uk/2014/04/the-varieties-of-peer-review.html"><span class="tco-ellipsis"></span><span class="invisible" style="line-height: 0;">http://</span><span class="js-display-url">neurodojo.blogspot.co.uk/2014/04/the-va</span><span class="invisible" style="line-height: 0;">rieties-of-peer-review.html</span><span class="tco-ellipsis"><span class="invisible" style="line-height: 0;"> </span>…</span></a><span style="background-color: white; line-height: 34px; white-space: pre-wrap;"> by </span><a class="twitter-atreply pretty-link" dir="ltr" href="https://twitter.com/DoctorZen" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;">@DoctorZen</a><span style="background-color: white; line-height: 34px; white-space: pre-wrap;"> via </span><a class="twitter-atreply pretty-link" dir="ltr" href="https://twitter.com/jasonpriem" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;">@jasonpriem</a><span style="background-color: white; line-height: 34px; white-space: pre-wrap;"> </span><a class="twitter-hashtag pretty-link js-nav" data-query-source="hashtag_click" dir="ltr" href="https://twitter.com/search?q=%23peerreview&src=hash" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;">#peerreview</a><span style="background-color: white; line-height: 34px; white-space: pre-wrap;"> </span><a class="twitter-timeline-link" data-pre-embedded="true" dir="ltr" href="http://t.co/7bdA66COKH" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;">pic.twitter.com/7bdA66COKH</a> . Where do you want to fit in?</span><br />
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<span style="color: #444444; font-family: Arial, Helvetica, sans-serif;">Defectivebrayne <span style="line-height: 34px; white-space: pre-wrap;">did a video summary of the last </span><a class="twitter-hashtag pretty-link js-nav" data-query-source="hashtag_click" dir="ltr" href="https://twitter.com/search?q=%23microtwjc&src=hash" style="line-height: 34px; text-decoration: none; white-space: pre-wrap;">#microtwjc</a><span style="line-height: 34px; white-space: pre-wrap;"> paper about the designer synthetic yeast chromosome:</span><span class="tco-ellipsis" style="line-height: 34px; white-space: pre-wrap;"></span><a class="twitter-timeline-link" data-expanded-url="http://youtu.be/60rcoVfKh10" dir="ltr" href="http://t.co/I9WwdR3kSQ" rel="nofollow" style="line-height: 34px; text-decoration: none; white-space: pre-wrap;" target="_blank" title="http://youtu.be/60rcoVfKh10"><span class="invisible" style="line-height: 0; text-decoration: none; white-space: pre-wrap;">http://</span><span class="js-display-url" style="line-height: 34px; text-decoration: none; white-space: pre-wrap;">youtu.be/60rcoVfKh10</span><span class="invisible" style="line-height: 0; white-space: pre-wrap;"></span><span class="tco-ellipsis" style="line-height: 34px; text-decoration: none; white-space: pre-wrap;"><span class="invisible" style="line-height: 0;"> </span></span></a> . This is very good and informative and capturesmany of the points that were discussed at that session. </span><br />
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<span style="color: #444444; font-family: Arial, Helvetica, sans-serif;"><b>life in general</b></span><br />
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<span style="color: #444444; font-family: Arial, Helvetica, sans-serif;"><span style="background-color: white; line-height: 34px; white-space: pre-wrap;">Finally made it to Glasgow brewdog. Working my way down the list </span><a class="twitter-timeline-link" data-pre-embedded="true" dir="ltr" href="http://t.co/0Efsnxhxxg" style="background-color: white; line-height: 34px; text-decoration: none; white-space: pre-wrap;">pic.twitter.com/0Efsnxhxxg</a> - and then went again that week. Some great beers on showcase there.</span>Connor Bhttp://www.blogger.com/profile/08132413724023944783noreply@blogger.com0tag:blogger.com,1999:blog-2119806190550686323.post-82512117099152022222014-04-16T13:05:00.000-07:002014-04-16T13:05:17.816-07:00Negatively regulating cell tropism modulates viral pathogenesis<div style="text-align: justify;">
<span style="color: #444444; font-family: Helvetica Neue, Arial, Helvetica, sans-serif;"><a href="http://ruleof6ix.fieldofscience.com/">I seem to keep saying this</a> but it's good to have in mind: viruses are obligate intracellular parasites. They infect cells and this is what allows them to replicate and persist (and evolve) in the environment. What cells these viruses infect helps dictate <i>how</i> they infect and importantly, how they cause disease. The process of causing disease is known as pathogenesis and is the subject of this post. Knowing what cells a virus infects - and how they infect the cells - provides an understanding of basic virus biology and may influence the development of new antiviral treatments and vaccine design and implementation. Of course this isn't the only factor influencing viral infection, pathogenesis and transmission but it's a pretty major one and it's one factor that I have articulated interest in during and after my formative PhD years. </span></div>
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<tr><td class="tr-caption" style="text-align: center;">a reconstruction of prototypical alphavirus particle (Sindbis virus)</td></tr>
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<span style="color: #444444; font-family: Helvetica Neue, Arial, Helvetica, sans-serif;">I have always felt (probably simplistically) that a virus actively <i>chooses</i> what cells to infect. Viruses evolve and adapt to particular host factors that allow it to enter, replicate in and assemble new infectious particles, which carry on the infectious cycle. On the scale of a human body, a virus might have adapted to infect epithelial cells lining your respiratory tract to allow initial infection, it might infect lymphocytes allowing modulation of systemic immunity, which may also provide the virus with access to tissues around the body that can lead to a large boost in replication facilitating virus excretion and transmission. Each one of these steps,in my head, the virus has chosen to infect. But what if a virus chooses not to infect a certain cell type, or at least limit replication. This is something I have not considered before. That was until I read this paper out recently. Not open access sadly:</span></div>
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<span style="color: #444444; font-family: Helvetica Neue, Arial, Helvetica, sans-serif;"><a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12869.html?WT.ec_id=NATURE-20131219"><br /></a></span></div>
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<a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12869.html?WT.ec_id=NATURE-20131219"><span style="color: #444444;">RNA viruses can hijack vertebrate microRNAs to suppress innate immunity</span></a></h1>
<ul class="authors citation-authors" style="background-color: white; font-family: arial, helvetica, 'MS Pゴシック', 'MS ゴシック', Osaka, 'MS PGothic', sans-serif; font-size: 14px; font-weight: bold; line-height: 23.916749954223633px; margin: 0px 0px 10px; padding: 0px;"><a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12869.html?WT.ec_id=NATURE-20131219"><span style="color: #444444;">
<li class="vcard" style="display: inline; list-style: none; margin: 0px; padding: 0px;"><span class="fn" style="text-decoration: none;">Derek W. Trobaugh</span><span class="comma" style="text-decoration: none;">,</span> </li>
<li class="vcard" style="display: inline; list-style: none; margin: 0px; padding: 0px;"><span class="fn" style="text-decoration: none;">Christina L. Gardner</span><span class="comma" style="text-decoration: none;">,</span> </li>
<li class="vcard" style="display: inline; list-style: none; margin: 0px; padding: 0px;"><span class="fn" style="text-decoration: none;">Chengqun Sun</span><span class="comma" style="text-decoration: none;">,</span> </li>
<li class="vcard" style="display: inline; list-style: none; margin: 0px; padding: 0px;"><span class="fn" style="text-decoration: none;">Andrew D. Haddow</span><span class="comma" style="text-decoration: none;">,</span> </li>
<li class="vcard" style="display: inline; list-style: none; margin: 0px; padding: 0px;"><span class="fn" style="text-decoration: none;">Eryu Wang</span><span class="comma" style="text-decoration: none;">,</span></li>
<li class="vcard" style="display: inline; list-style: none; margin: 0px; padding: 0px;"><span class="fn" style="text-decoration: none;">Elik Chapnik</span><span class="comma" style="text-decoration: none;">,</span> </li>
<li class="vcard" style="display: inline; list-style: none; margin: 0px; padding: 0px;"><span class="fn" style="text-decoration: none;">Alexander Mildner</span><span class="comma" style="text-decoration: none;">,</span> </li>
<li class="vcard" style="display: inline; list-style: none; margin: 0px; padding: 0px;"><span class="fn" style="text-decoration: none;">Scott C. Weaver</span><span class="comma" style="text-decoration: none;">,</span> </li>
<li class="vcard no-comma" style="display: inline; list-style: none; margin: 0px; padding: 0px;"><span class="fn" style="text-decoration: none;">Kate D. Ryman</span> </li>
<li class="vcard last-author c1 no-comma" style="display: inline; list-style: none; margin: 0px; padding: 0px;">& <span class="fn" style="text-decoration: none;">William B. Klimstra</span></li>
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<li class="first" style="background-attachment: scroll; background-image: none; background-position: 0px 0.6ex; background-repeat: no-repeat no-repeat; float: left; list-style: none; margin: 0px; padding: 0px 0.5em 0px 0px;"><a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12869.html?WT.ec_id=NATURE-20131219" style="font-size: 14px;"><span style="color: #444444;"><dd class="journal-title" style="display: inline; font-style: italic; margin: 0px; padding: 0px 3px 0px 0px; text-transform: capitalize;">Nature</dd> <dd style="display: inline; margin: 0px; padding: 0px 3px 0px 0px;"><time datetime="2013-12-18">(2013)</time></dd> <dd class="doi" style="background-image: url(http://www.nature.com/view/images/bg_pipe.gif); background-position: 0px 0.4ex; background-repeat: no-repeat no-repeat; display: inline; margin: 0px 0px 0px 4px; padding: 0px 3px 0px 10px;">doi:10.1038/nature12869</dd></span></a></li>
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<span style="color: #444444;"><span style="font-family: Helvetica Neue, Arial, Helvetica, sans-serif;">To recap the paper, which has a particular pop. Sci title, (which I don't particularly like) but it's an interesting enough paper anyway. This group was interested in what stopped their favourite positive-sense RNA virus <a href="http://en.wikipedia.org/wiki/Eastern_equine_encephalitis_virus">(North American eastern equine encephalitis virus, or EEEV, an rare infection limited to North America)</a> from replicating in one certain cell type, myeloid dendritic cells. These cells are very important for antiviral immunity and act to coordinate our antiviral response to pathogens. Thus <a href="http://en.wikipedia.org/wiki/Dendritic_cell">their biology</a> affects protection from infection, disease progression and ultimately survival. They do this by sensing components of viruses or their replication and signalling to other cells that they have found an intruder. This signalling takes the form of an increase in interferon production and likely secretion of pro inflammatory proteins, designed to promote anti pathogen responses following infection. As myeloid dendritic cells pose a significant barrier to infection viruses have evolved multiple strategies to interact with and manipulate this cell type. </span><span style="font-family: 'Helvetica Neue', Arial, Helvetica, sans-serif;">Many viruses infect this cell type (for one example see <a href="http://ruleof6ix.fieldofscience.com/2011/12/influenza-putting-trojan-into-horse-but.html">this</a>) and from within the cell influence it's behaviour b</span><span style="font-family: 'Helvetica Neue', Arial, Helvetica, sans-serif;">ut what EEEV does is a bit different. It simply avoids ever entering these cell types. And how it achieves this was the aim of this paper. </span></span></div>
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<tr><td class="tr-caption" style="text-align: center;">electron micrograph of EEEV virus particles (red) inside host cells </td></tr>
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<span style="font-family: 'Helvetica Neue', Arial, Helvetica, sans-serif;"><span style="color: #444444;">What they found was that EEEV harbours sequences that are recognised by myeloid specific miRNAs, in particular <a href="http://mir-142-3p./">miR-142-3p.</a> This miRNA bound to viral genomes and prevented critical translation and subsequent replication and infection. Deletion of the region within the viral genome alleviated this restriction in replication in culture and addition of the region to other RNAs restricted their expression. There is also a mouse model for EEEV pathogenesis and when mice were infected with wild type or miR-142-3p binding region-deleted viruses they noticed a striking difference on infection and pathogenesis. Deletion of miR binding led to a decrease in virulence associated with increased replication in lymph nodes (as you might expect from a virus with little myeloid restriction) and secretion if interferons. </span></span></div>
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<span style="font-family: 'Helvetica Neue', Arial, Helvetica, sans-serif;"><span style="color: #444444;">Now this is cool but it's not all simple. This region is also required for replication in mosquitoes (the vector species for EEEV). This is not thought to be mediated by a miR-142-3p interaction, presumably because it is not present in the insect genome. What is also difficult about this work is that they base their conclusions on whole-sale deletion of the miR-binding region and not targeted nucleotide substitutions, which could rule out any other functions this region might have, for example in RNA secondary structure or protein-RNA interactions. Until these experiments are done I think that the complete role of this region in the EEEV genome will not be cleared up. However, the interaction of miR-142-3p and the virus genome appears solid and with some interesting consequences.</span></span></div>
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<span style="color: #444444; font-family: Helvetica Neue, Arial, Helvetica, sans-serif;">These data show that EEEV contains an RNA sequence within its genome that directly limits its replication in these important cells in order to influence pathogenesis by physically interacting with host miRNAs. And, importantly, the virus doesn't really care - it actually likes it that way. It actively uses this 'negative tropism' to modulate the hosts immune response towards it, favouring its own replication and immune subversion. Uncovering secrets of viruses like this is fascinating and can have an impact on human health. Importantly it may lead to engineered vaccines for viruses, especially EEEV. Imagine an EEEV that replicated in myeloid cells, triggering an antiviral response in infected hosts that would limit disease but produce long-term protection? This work is put in context when you consider than influenza viruses that cannot express their genes in myeloid cells (antigen presenting cells specifically) by engineering of miR-142 into its genome (in the tenOever lab) <a href="http://www.ncbi.nlm.nih.gov/pubmed/22778433">do not stimulate an antiviral IFN response. </a> Taken together with this work on EEEV, the myeloid cell/miR-142/pathogen axis looks like an interesting target when considering the link between infection, disease and rational vaccine design. But like any gene product that is involved in lots of aspects of host biology <a href="http://dev.biologists.org/content/early/2014/02/19/dev.105908">like miR-142</a> be wary when extrapolating from cell cultures and mice. </span></div>
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Connor Bhttp://www.blogger.com/profile/08132413724023944783noreply@blogger.com0tag:blogger.com,1999:blog-2119806190550686323.post-22707375051437284572014-03-30T06:56:00.001-07:002014-03-30T06:56:28.939-07:00parasitesStarting to write again, take 1:<br />
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Viruses are parasites. Specifically, they are obligate intracellular parasites. I end up thinking about these kinds of parasites everyday in work and in my personal life. While they replicate inside all kinds of cells, can cause disease and may actually manipulate your behaviour, they are only one often-devastating example of the parasite world all around us. And, as sad it is to admit it (as a card-carrying 'virologist'), other kinds of parasites might actually be just as interesting as they are. What kinds of parasites, I hear you ask? Well, watch this<a href="https://www.ted.com/talks/ed_yong_suicidal_wasps_zombie_roaches_and_other_tales_of_parasites"> amazing TED talk of Ed Yong</a> or, if you prefer paper, read this recent book on the topic by Dickson Despommier:<a href="https://cup.columbia.edu/book/978-0-231-16194-7/people-parasites-and-plowshares"> 'People, parasites, and plowshares'. </a><br />
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<br />Connor Bhttp://www.blogger.com/profile/08132413724023944783noreply@blogger.com1tag:blogger.com,1999:blog-2119806190550686323.post-16960287829214738262014-02-16T09:42:00.000-08:002014-02-16T09:42:12.560-08:00Interferons - they're a cGAS (i)<div style="text-align: justify;">
<span style="font-family: Times, 'Times New Roman', serif;">I'm a typical virologist, I am always talking about interferons. A while ago, </span><a href="http://ruleof6ix.fieldofscience.com/2011/05/interferons-interferons-interferons.html" style="font-family: Times, 'Times New Roman', serif;">under a slightly different guise</a><span style="font-family: Times, 'Times New Roman', serif;">, I wrote about the biological function of interferon proteins in stimulating the expression of myriad genes, many of which have proven antiviral activity. The fact that these genes and their protein products have antiviral functions makes them extremely interesting to researchers, like me, looking for new ways to treat human and animal infections with these viruses. Or even to anyone really who is interested in viral disease, evolution and medicine. These interferon stimulated proteins are especially interesting for studying viruses for which no vaccine exists. I'm thinking HIV, hepatitis C virus and even emerging infections like Ebola and rabies viruses. And until we develop good vaccines against these agents we're probably going to need antivirals. Note that even if we did have vaccines for these viruses they might not be economically viable to use and so we're back to making antivirals. Either that or we just screw those affected by the viruses. That's not going to happen.</span></div>
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<span style="font-family: Times, Times New Roman, serif;">Here's the issue though. Problem is, it takes years and years (major understatement) of research for humans to generate new antiviral drugs. So what if evolution has done the hard work for us? This is where the interferon proteins and their antiviral effectors come in. Turns out, evolution has done the hardwork for us. And this is where this paper, first author <a href="http://www.utsouthwestern.edu/labs/schoggins/">John Schoggins</a>, with a host of other authors (many of which also carried out the experimental work) who worked in many labs, mainly across the US. Have a look at the paper for a list. These guys, along with an early paper featuring Sam Wilson and others (see my blog post linked to above), are pioneering the exploration of the - brace yourselves - the 'interferome' with a hope of generating novel antiviral drugs. My words not theirs. </span></div>
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<span style="font-family: Times, Times New Roman, serif;"><br /></span><span style="font-family: Times, Times New Roman, serif;">Schoggins et al. 2013</span></blockquote>
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<span style="font-family: Times, Times New Roman, serif;"><br /></span><span style="font-family: Times, Times New Roman, serif;"><span style="background-color: white; color: #333333; font-size: 14px; font-weight: bold; line-height: 23.916749954223633px;">The type I interferon (IFN) response protects cells from viral infection by inducing hundreds of interferon-stimulated genes (ISGs), some of which encode direct antiviral effectors</span><sup style="background-color: white; color: #333333; font-size: 12px; font-weight: bold; line-height: 0;"><a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12862.html#ref1" id="ref-link-1" style="clear: both; color: #5c7996; text-decoration: none;" title="Der, S. D., Zhou, A., Williams, B. R. & Silverman, R. H. Identification of genes differentially regulated by interferon [agr], [bgr], or [ggr] using oligonucleotide arrays. Proc. Natl Acad. Sci. USA 95, 15623-15628 (1998)">1</a>, <a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12862.html#ref2" id="ref-link-2" style="clear: both; color: #5c7996; text-decoration: none;" title="de Veer, M. J. et al. Functional classification of interferon-stimulated genes identified using microarrays. J. Leukoc. Biol. 69, 912-920 (2001)">2</a>, <a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12862.html#ref3" id="ref-link-3" style="clear: both; color: #5c7996; text-decoration: none;" title="Schoggins, J. W. & Rice, C. M. Interferon-stimulated genes and their antiviral effector functions. Curr. Opin. Virol. 1, 519-525 (2011)">3</a></sup><span style="background-color: white; color: #333333; font-size: 14px; font-weight: bold; line-height: 23.916749954223633px;">. Recent screening studies have begun to catalogue ISGs with antiviral activity against several RNA and DNA viruses</span><sup style="background-color: white; color: #333333; font-size: 12px; font-weight: bold; line-height: 0;"><a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12862.html#ref4" id="ref-link-4" style="clear: both; color: #5c7996; text-decoration: none;" title="Schoggins, J. W. et al. A diverse range of gene products are effectors of the type I interferon antiviral response. Nature 472, 481-485 (2011)">4</a>, <a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12862.html#ref5" id="ref-link-5" style="clear: both; color: #5c7996; text-decoration: none;" title="Liu, S. Y., Sanchez, D. J., Aliyari, R., Lu, S. & Cheng, G. Systematic identification of type I and type II interferon-induced antiviral factors. Proc. Natl Acad. Sci. USA 109, 4239-4244 (2012)">5</a>, <a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12862.html#ref6" id="ref-link-6" style="clear: both; color: #5c7996; text-decoration: none;" title="Metz, P. et al. Identification of type I and type II interferon-induced effectors controlling hepatitis C virus replication. Hepatology 56, 2082-2093 (2012)">6</a>, <a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12862.html#ref7" id="ref-link-7" style="clear: both; color: #5c7996; text-decoration: none;" title="Fusco, D. N. et al. A genetic screen identifies interferon-[agr] effector genes required to suppress hepatitis C virus replication. Gastroenterology 144, 1438-1449 (2013)">7</a>, <a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12862.html#ref8" id="ref-link-8" style="clear: both; color: #5c7996; text-decoration: none;" title="Zhao, H. et al. A functional genomic screen reveals novel host genes that mediate interferon-alpha/'s effects against hepatitis C virus. J. Hepatol. 56, 326-333 (2012)">8</a>, <a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12862.html#ref9" id="ref-link-9" style="clear: both; color: #5c7996; text-decoration: none;" title="Zhang, Y., Burke, C. W., Ryman, K. D. & Klimstra, W. B. Identification and characterization of interferon-induced proteins that inhibit alphavirus replication. J. Virol. 81, 11246-11255 (2007)">9</a>, <a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12862.html#ref10" id="ref-link-10" style="clear: both; color: #5c7996; text-decoration: none;" title="Wilson, S. J. et al. Inhibition of HIV-1 particle assembly by 2[prime],3[prime]-cyclic-nucleotide 3[prime]-phosphodiesterase. Cell Host Microbe 12, 585-597 (2012)">10</a>, <a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12862.html#ref11" id="ref-link-11" style="clear: both; color: #5c7996; text-decoration: none;" title="Schoggins, J. W. et al. Dengue reporter viruses reveal viral dynamics in interferon receptor-deficient mice and sensitivity to interferon effectors in vitro. Proc. Natl Acad. Sci. USA 109, 14610-14615 (2012)">11</a>, <a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12862.html#ref12" id="ref-link-12" style="clear: both; color: #5c7996; text-decoration: none;" title="Karki, S. et al. Multiple interferon stimulated genes synergize with the zinc finger antiviral protein to mediate anti-alphavirus activity. PLoS ONE 7, e37398 (2012)">12</a>, <a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12862.html#ref13" id="ref-link-13" style="clear: both; color: #5c7996; text-decoration: none;" title="Meng, X. et al. C7L family of poxvirus host range genes inhibits antiviral activities induced by type I interferons and interferon regulatory factor 1. J. Virol. 86, 4538-4547 (2012)">13</a></sup><span style="background-color: white; color: #333333; font-size: 14px; font-weight: bold; line-height: 23.916749954223633px;">. However, antiviral ISG specificity across multiple distinct classes of viruses remains largely unexplored. Here we used an ectopic expression assay to screen a library of more than 350 human ISGs for effects on 14 viruses representing 7 families and 11 genera. We show that 47 genes inhibit one or more viruses, and 25 genes enhance virus infectivity. Comparative analysis reveals that the screened ISGs target positive-sense single-stranded RNA viruses more effectively than negative-sense single-stranded RNA viruses. Gene clustering highlights the cytosolic DNA sensor cyclic GMP-AMP synthase (</span><i style="background-color: white; color: #333333; font-size: 14px; font-weight: bold; line-height: 23.916749954223633px;">cGAS</i><span style="background-color: white; color: #333333; font-size: 14px; font-weight: bold; line-height: 23.916749954223633px;">, also known as </span><i style="background-color: white; color: #333333; font-size: 14px; font-weight: bold; line-height: 23.916749954223633px;">MB21D1</i><span style="background-color: white; color: #333333; font-size: 14px; font-weight: bold; line-height: 23.916749954223633px;">) as a gene whose expression also broadly inhibits several RNA viruses. </span><i style="background-color: white; color: #333333; font-size: 14px; font-weight: bold; line-height: 23.916749954223633px;">In vitro</i><span style="background-color: white; color: #333333; font-size: 14px; font-weight: bold; line-height: 23.916749954223633px;">, lentiviral delivery of enzymatically active cGAS triggers a STING-dependent, IRF3-mediated antiviral program that functions independently of canonical IFN/STAT1 signalling. </span><i style="background-color: white; color: #333333; font-size: 14px; font-weight: bold; line-height: 23.916749954223633px;">In vivo</i><span style="background-color: white; color: #333333; font-size: 14px; font-weight: bold; line-height: 23.916749954223633px;">, genetic ablation of murine cGAS reveals its requirement in the antiviral response to two DNA viruses, and an unappreciated contribution to the innate control of an RNA virus. These studies uncover new paradigms for the preferential specificity of IFN-mediated antiviral pathways spanning several virus families.</span></span></blockquote>
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<span style="font-family: Times, Times New Roman, serif;">Now I have to come clean. This is now the area of science in which I find myself now operating so I might be a tad biased - or over zealous - about it's benefits. But the use interferon proteins as antiviral and immuno modulating drugs supports my claim. Although I cannot currently think of any drugs that have come from studying interferon induced proteins (apart from interferons themselves). But this is probably because our knowledge of them is currently so limited. Hence the current research focus. </span></div>
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<span style="font-family: Times, Times New Roman, serif;">So now for the science (see the paper abstract above). <a href="http://ruleof6ix.fieldofscience.com/2011/05/interferons-interferons-interferons.html">You can read all about interferon proteins (IFNs) here as well as IFN stimulated genes (ISGs).</a> Trust me, they are fascinating. Earlier work showed that IFNs, which themselves are induced by infection, induce the expression of hundreds of ISGs inside a cell. Each one of these ISGs work in concert and induce an antiviral state within the cell and surrounding cells in a given tissue, which functions to prevent or slow down the infection. And perhaps counter intuitively some event promoted infection when looked at independently of the other ISGs (hence probably an artefact). Each one of these genes might represent a novel target to tackle infectious diseases. For example: Maybe we could synthesise a recombinant protein version of these ISGs? or we could find a way to upregulate the expression of the ISG? or we could use it as a intellectual and physical scaffold to develop novel, next generation drugs based on ISGs? The list is endless. But now I'm getting a head of myself. </span></div>
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<span style="font-family: Times, Times New Roman, serif;">To determine if a gene or protein has antiviral or pro viral activity (which as I've explained above, is important for developing new drugs), these guys over expressed each ISG inside mammalian cells them infected a range of recombinant viruses expressing reporter genes, like GFP. Now two things make this particularly artificial: 1) the majority of cells used were deficient in STAT1 (an important IFN signalling molecule). This was probably done to limit the activity of each ISG to its direct antiviral effects and exclude any feedback loops operating. 2) the screen was carried using retroviral introduction and over-expression the genes. The fact that you are using viral infection to test antiviral function might screw with your results, whereby the very act of infecting could stimulate an IFN response. When you read the paper this was actually the case but all in all, this method of screening appears to work well, but of course requires much downstream work validating and characterising any 'hits'.</span></div>
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<span style="font-family: Times, Times New Roman, serif;">This screen allowed them to 'easily' prefer on a screen for good candidate ISGs for further characterisation. This screen importantly by using a range of biologically diverse viruses allowed them to find an ISG that inhibited a broad range of viruses. I say easily because on paper it might seem easy but I really don't think it is. It is a lot of work and each virus used comes with its own idiosyncrasies (e.g. cytopathic effects), which can be difficult to control for. But trying to find a broad antiviral is a bit like finding the holy grail of ISG (and indeed antiviral) research. Finding a broad spectrum antiviral (or antibiotic) is important not just on an economical basis but on a basis of rapidly developing new treatment for pathogens for which we have no information on. And as the paper describes, Schoggins and colleagues claim to have found just that.</span></div>
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<span style="font-family: Times, Times New Roman, serif;">After screening hundreds of these ISGs against a panel of viruses, Schoggins et al. focussed on only one, <a href="http://www.invivogen.com/review-cgamp">which is called cGAS.</a> The reason why they picked this one is that through bioinformatic analsysis it appeared to have the same effect when over-expressed as IRF1. IRF1 is a very important molecule in the IFN pathway acting as a transcription factor up-regulating the expression of the ISGs and if cGAS clustered with IRF1, then maybe cGAS also had a very important role in antiviral immunity. At the time, cGAS was poorly characterised, thus the group focussed on cGAS as a broad spectrum antiviral. However, note that although they refer to cGAS as 'pan-viral', cGAS appears to predominantly inhibit positive sense RNA viruses as opposed to negative sense RNA viruses. The screened viruses also mainly included enveloped viruses, rather than non-enveloped viruses, which again might skew the results. For a mechanistic understanding of cGAS and antiviral immunity keep posted. Part (ii) will be up soon. But for now, be content that a 'broad spectrum' antiviral was discovered.</span></div>
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Connor Bhttp://www.blogger.com/profile/08132413724023944783noreply@blogger.com0tag:blogger.com,1999:blog-2119806190550686323.post-82203813988442377242014-02-10T11:59:00.001-08:002014-02-10T11:59:03.188-08:00first dayOK so I started my new position today as a postdoc at the <a href="http://www.gla.ac.uk/researchinstitutes/iii/cvr/">Medical Research Centre (MRC) Centre for Virus Research (CVR) in Glasgow, Scotland</a>. This is a position in the lab of <a href="http://www.gla.ac.uk/researchinstitutes/iii/staff/johnmclauchlan/">Dr John McLauchlan</a> who works on Hepatitis C virus. I have moved here following my Ph.D in Queen's University, Belfast. The project sounds very interesting as does the lab and associated staff and students. I got sorted out with HR and am now trying to get to grips with the reading around the subject and will be getting into the lab this week. Hopefully I will be able to discuss more about the project, hepatitis C and postdoctoral life in this blog. Keep an eye out for more updates as time goes by!Connor Bhttp://www.blogger.com/profile/08132413724023944783noreply@blogger.com0